Musings of the Mad Biologist

My Blog Has Moved!

2010-12-04T14:56:00.003-05:00

For anyone who's still showing up around these parts, I wanted to let you know that, as I said I would, I've begun blogging regularly again... Just not here. For a variety of reasons, some explained here, I've decided to start up a new blog on a completely new hosting service. So point your browsers to carloartieri.com if you're inclined to keep following my musings!

Which Doctors?

2010-10-13T16:16:00.004-04:00

Sorry for the lack of posts lately, but I've been oscillating between busy and sick - sometimes lurking in the quantum paradox of both. Case in point: I've been quite ill for the past week, suffering from sinus pain, congestion, the sniffles, and horrible phlegmy sneezes. It didn't seem like I was going to recover on my own, so I decided to set up an appointment with my doctor.

Now I'm a bit cautious regarding my doctor. She seems like a nice elderly woman, but there's a disturbing amount of woo being peddled in her waiting room. For instance, she's an advocate of laser acupuncture, which, umm... seems like some sort of Austin Powers-style combination of technology and Traditional Chinese Medicine. (Traditional Chinese Laser Acupuncture is both anachronistic AND oxymoronic). However, she's never actually pushed any of this woo on me until now.

During my latest appointment, she diagnosed me as having an ear infection, and proceeded to prescribe an antibiotic and a decongestant. All well and good, I thought. Unfortunately, before she could write out those prescriptions and send me on my way, I foolishly decided to inquire about some pain I've been having in my wrists. I spent almost the entire summer working on a computational study, you see, and thus I probably over-worked my poor hands typing. She told me that there were drugs that could help me with this, but that she thought that we should try something that she'd recently learned about - something that could cure all¹ of my problems.

My doctor told me that she'd learned of an energy technique that would allow her to determine what combination of medication would best help me. She then called in her secretary and they both huddled over me making pseudo-mystical movements. The doctor then touched my watch and ring in turn with one hand, while the other hand was held in the air with thumb and forefinger clenched. She proceeded to mumble some words while her secretary repeatedly attempted to pry her fingers apart. After a minute or so of this, she proceeded to tell me that neither my watch, nor my ring were 'negative', and thus they were not impeding my body's healing energies. "Umm... good?" I replied.

She then proceeded in the same manner, this time touching various herbal remedies against my body while chanting various doses, and frequencies: touching one bottle to my arm followed by "Mmmmm... One tablet before meals. no Mmmmm... One tablet after meals. Aha!", for example. All the while, her secretary was prying her fingers apart over and over.

Finally, it was determined(?) that I should take one pill each of StemEnhance and StemFlo, which, according to their producer's website:

StemEnhance is the very first product on the market from the product category called "stem cell enhancers" - products that support your natural stem cell physiology. It consists of a patented natural concentrate of an edible aquatic botanical known as Aphanizomenon flos-aquae (AFA) that includes Mobilin™.

Right. But is any of this scientifically studied?

Yes. Several clinical studies have been conducted on the product, in addition to several in-vitro trials.

Ah, well good to know. Actually, my doctor gave me several photocopied pages about the stuff that claim that proof of its efficacy was published in the New England Journal of Medicine. Unfortunately I guess I'll have to sift through its entire archives to find out WHICH article demonstrates this. Oh, also my doctor gave me a trial sample of the pills as well as a card indicating that she is Executive Director of STEMTech, the company that makes both of the amazing natural products she prescribed. I'm not sure if that's relevant to this story.

Ungh, I think I need to find another doctor²...

¹Well according to the information sheet I received, I'd estimate that this thing can cure pretty much any problem you can name. Wait... Irritable Bowel Syndrome isn't on the list, but Autism is. Great, now the kooks don't have to worry about vaccines anymore.

² Unfortunately, this isn't a trivial task. It means that I have to look for another doctor who is on my insurance program who is accepting patients and is in close vicinity to my home or work. Guess I'd better get looking...

Book Club: The Structure of Scientific Revolutions...

2010-09-12T13:00:00.000-04:00

I've always been under the impression that Thomas Khun's The Structure of Scientific Revolutions (TSSR; 1962; University of Chicago Press) was a controversial book. For those unaware, this is the book wherein the author argued that science 'progressed' through 'paradigm shifts' - that is to say that most legitimate science takes place within a given accepted paradigm (e.g., the Earth is the center of the universe), until the weight of observations leads to a crisis (e.g., astronomical observations disagree with expectations), which results in a series of alternative paradigms being proposed until one is eventually accepted (e.g., heliocentrism). The cycle then begins anew.

Using this paraphrased formulation of Kuhn's model, I don't think anyone would have a problem with it, and for the first 120 pages of a ~200 page book, neither did I. It's what happens towards the end of the book that I think many people have taken issue with, including myself.

To begin with the author has a very nebulous application of his concept of paradigms¹. Paradigms are defined at least 22 different ways within the book (I didn't count, it's discussed in the postscript), which makes it difficult to nail down what a paradigm shift actually is. A paradigm isn't strictly the current framework of our understanding of a topic (models, laws, constants, forlmulae, etc.), it also has a behavioral component. Scientists raised within a given paradigm do not switch to a new one easily - if ever - and thus a current false paradigm will accrue large numbers of ad hoc/post hoc elements to explain away all of its inconsistencies.

Kuhn essentially argues that paradigm shifts do not equal progress. Towards the end, the book falls over the edge of relativism, where it becomes clear that since there will inevitably be a paradigm shift again, there's no way to know that this paradigm will be better than the last. The only way that TSSR is able to get away with such an argument is by very cursorily panning Popper's doctrine of falsifiability - something that I must admit did not sit right with me. I need to elaborate on this point in order to make this clear:

According to Popper, no scientific theory is ever 'proven', rather the strength of a theory relies on its ability to resist falsification. Every time a prediction made by the theory is verified, we become a bit more confident in its validity - though it could ultimately turn out to be false in the end. Thus the relative 'value' of a scientific theory lies in its ability to make predictions. A theory that makes no predictions is unfalsifiable, and thus useless. Theories that make more predictions, if those are then verified, are more valuable than those that make fewer predictions, because they necessarily explain more about the nature of reality.

Now, there's a cagey aspect to Popper's doctrine that has to do with what happens to a scientific theory when its predictions are falsified. The theory is supposed to be rejected, but in practice it's often not necessary to reject the entire theory, but rather re-evaluate the components that fail to agree with observation. This is where Kuhn dismisses Popper's doctrine because, according to him, one can always propose ad hoc adjustments to a theory until it falls in line with observation. Thus paradigms cannot truly be evaluated on their ability to make predictions.

If we could interpret Kuhn's paradigms in a Popperian framework, we could argue that the progress of science generally leads to theories that explain more of the universe and thus make more predictions. Thus, any new paradigm would have many more observations to account for, and thus the likelihood of new major paradigm shifts decreases with time, which can be interpreted as 'progress'. Kuhn however, argues (if I understand correctly) that because any theory can be made to fit observations with sufficient ad and post hoc tweaking, we cannot really be sure that there's actually any progress being made.

It's actually quite difficult to read a book with this sort of defeatist(?), relativistic philosophy because it seems to ignore the practical observation that what we think we know about the universe in modern times actually allows us to do more things than we could in the past. It's sometimes frustrating to see Kuhn pick particular examples to bolster his points. Lack of progress, for instance is illustrated by explaining that Pliny's epicycles and Copernicus' heliocentrism made the same predictions. Is this really the norm?

Overall, I think that Kuhn's concept (vague as it is) of paradigms is incredibly useful in understanding the history of science. However, I think that he goes quite far in interpreting the consequences of his paradigms when it comes to the progress of science. Taken at face value, we're told a lot of odd things such as people operating within a given paradigm cannot communicate with those operating within another, that new paradigms aren't necessarily based on evidence, or that progress is illusory, etc. TSSR is an immensely interesting book, but it veers into very controversial lines of reasoning when it reaches its more 'psychological' claims.

I don't know if anyone's doing this, but I think it would be very useful to get the perspective of scientists who lived through paradigm changes, in order to see if some of Kuhn's behavioral hypotheses are valid. Thinking about past paradigm shifts is interesting, but understanding more current ones, if they're occurring, may be more informative.

¹This is something that Kuhn himself admits in the postscript to the book, published 7 years after the 1st edition. He doesn't think it changes the veracity of his model, however.

Bikin' Hardcore!

2010-09-06T20:45:00.003-04:00

I've discovered a new love: that of cycling. I'd actually been planning to buy a bike for the past six years or so, and now that I've gone out and done it, I'm chiding myself for not having 'pulled the trigger' sooner. Biking is awesome. The reason for my reluctance was, of course, financial: Biking for 'realz' requires the initial investment in a bike, plus several necessary accessories that quickly add up. It's more than worth it.

I now bike 11.5 km (~7.5 mi) to work every day using a local commuter trail. Amazingly, it takes me about 40 mins, which is often faster than taking public transit (and is always faster than taking public transit on weekends due to all of the track maintenance work). Also, biking > 20 km per day has really gone a long way to assisting 'Operation Iron-Carlo', or my attempt to be in the best shape I've ever been in by the time I'm 30. I'm actually making better-than-expected progress on this front, so I have no doubt that I will succeed.

To that end, today a friend and I went on an epic almost 50K bike ride all the way from Rockville MD to Capitol Hill in DC.

Here's a rough sketch of the route we took. There are more efficient routes to get from Rockville to DC, but they're not as nice and scenic.

The commuter trails for this trip are beautiful and a great ride. All told, it took about 3.5 hours - mostly because we weren't speeding along at breakneck pace. Instead we took it easy, and chatted about science-fiction novels most of the way. Who would've thought that you could mix geekyness and exercise? I'm sure that I'll have the chance to check out many more of the excellent bike trails they've got in this area... As long as I don't get anymore flat tires.

Feeling the Burn...

2010-08-29T17:45:00.004-04:00

This was a pretty rough summer for me on many fronts: some personal, some professional. The latter had a lot to do with my effort to juggle a fairly time-consuming research project, while trying to manage an ever-shifting 'side-project' that lacked a clear objective and continued to metamorphose as the weeks went by. Sadly, I ended up writing 25 pages of a manuscript that will not see the light of publication in its current form¹.

I worked really hard on that side-project, so much so that I essentially abandoned my 'main' research for ~2 months. That's really not a lot of wasted time in the grand scheme of things. I suppose I've wasted more time in the past, but that was 4 years ago now and I've become quite used to being extremely organized about effort.

This brings us to the title of my post - I feel like I experienced a minor burn-out. I can tell that my general love of science, which is to say the amount of time I spend actively immersing myself in scientific culture outside of the work I'm required to do, dropped a bit during this season. I stopped reading science books, stopped following science blogs, stopped talking about science outside the lab, etc. As I'm sure I've said many times on the blog, this isn't very conducive to being in the sciences: research is a difficult job to pursue if you're not regularly thinking about possible ways to expand your work. It's also a heck of a lot of work to not enjoy, if you catch my drift.

I can feel some of my enthusiasm returning though. This is partially seasonal: Autumn is by far my favorite time of the year, and I'm looking forward to such niceties as colorful leaves, pumpkin pies, and not sweating to death every single day (the ice-water that flows through my Canadian veins isn't built for the heat here). However, the major part of my changing attitude is probably getting back to my main project. This is what I came here to do, and what I what I wrote-up for my funding proposal: It's what I actually wanted to work on. Oh, it's also helping that I'm reading science books again - Thomas Kuhn's The Structure of Scientific Revolutions will be a book club post soon!

Hopefully I'll come around soon. Hey, if everything becomes rosy again and I get a few hours of free time, maybe I'll continue blogging about that crazy alien book again. Who knows?

¹All is not lost, however, as I learned a lot of useful information/techniques in preparing said manuscript, and large sections of it will be cannibalized for a forthcoming study.

The Bleeding Edge...

2010-08-25T08:00:00.001-04:00

Prior to my postdoc, I've never done research using 'bleeding edge' technology, which the Wikipedia defined as:

Bleeding edge technology refers to technology that is so new that the user is required to risk unreliability, and possibly greater expense, in order to use it.

While every project requires some degree of methods development, pretty much everything I've done before used well established protocols and procedures. This is no longer the case.

One of the techniques of which I've been making extensive use is RNA-seq, or short-read sequencing of RNA. The gist of this technique is that you extract RNA from a cell fragment it into small pieces and then convert it to DNA. You then generate millions of short reads (~75-100 bp nowadays) off of this DNA using flow-cell based sequencers (see the link I provided to RNA-seq for details) and map (align) these reads to the genome of the organism with which you're working. The read 'density' (or number of reads mapping to any given region of the genome) is correlated with abundance of the RNA in the original pool, and thus you get a digital read out of the abundance of all of the transcripts in the cell. In principle this technology has many benefits over traditional methods of transcriptome profiling, such as allowing isoform detection, and is widely expected to eventually replace microarrays.

While this is all fine and dandy, the more I use RNA-seq, the more concerned I become about it. A lot of people have jumped on this bandwagon and there hasn't been a lot of work done to investigate potential biases and caveats associated with the instruments required to generate these data. Here's a couple of examples: The relationship between number of reads mapping to a given gene/exon and its expression level only holds if reads are randomly distributed with respect to what's being sequenced - there shouldn't be sequences that are preferentially sequenced or underrepresented. Unfortunately, this does seem to be the case - either during fragmentation or sequencing library preparation, biases are introduced making certain sequences more or less common than would be expected by chance. It appears that this does not have a large effect on expression estimates of highly expressed genes, but genes with low expression, or short coding sequences show more variability than they should.

A much more significant problem is that many papers seem to have assumed that RNA-seq is somehow beyond the need to 'normalize' data (that is control for systematic biases). It isn't (see Srivastava and Chen 2010, for example). A slew of recent papers have shown that there are biases associated with short read data, especially when the cells/tissues/organisms being compared have radically different expression profiles. Normalization is required, but rarely applied. Oh, and I haven't even gotten into the serious problem of lack of replicates in many of these studies.

These are just some of the issues RNA-seq users face. Now, you may be asking yourself why I'm telling you this; I assure you it's not a rant. My bigger point is this: Our lab has been spending an inordinate amount of time investigating the very real biases that these issues may be creating in our data. However, at the same time, other groups are using the tools available, limited as some may be, and publishing work under the assumption that such biases are not 'show stoppers'. Whether they are or not is difficult to say at this point, but we're pretty much at the mercy of labs with a much better grasp of statistics to come up with solutions as to how to properly normalize and handle these data.

To what extent is it reasonable to use the tools available and assume that they're 'good enough'? Science is always progressing/refining its products, so is it okay to use particular methods, even if you suspect that they're producing uncontrolled biases? I think that the vast majority of what's being done in the field is quality (as far as we know what quality is) but the use of such new technology is somewhat worrisome.

Thoughts?

Paying the Piper...

2010-08-22T20:00:00.000-04:00

It's an interesting fact that when you're young, you really tend to think about the consequences of all of the loans you end up taking out in order to pay for post-secondary education (at least if you're growing up in North America, that is). Once the student loans get up into the 5 digits, what's another ten grand here or there? This is further compounded because the loans sit completely in the back of your mind for years and years, providing much needed cash seemingly without consequence.

Unfortunately school ends, and everyone must eventually 'pay the piper'.

In the folk legend, the Pied Piper of Hamelin takes care of the city's rat problem by playing his magic flute and causing the vermin to jump into the nearby river. When the city refuses to pay him for his deed, he retaliates by using his magic flute to ensorcel the city's children and march them out of town, after which they are never seen again. Thus the origin of the idiom, 'Time to pay the Piper'. Image cred.

All told, I'm roughly $25,000 in debt - not that bad if you consider that I spent 10 years in University. Now that I'm a postdoc, I've begun having to pay it back - as expected, I should add. This is the point where one realizes that say, $1,000 is actually a lot of money. Put into more concrete terms, if I wanted to pay back $1000 in one year, that would be ~$83.34 per month, a not insubstantial amount of dough, when one considers that that's essentially an extra cell phone bill.

I know what you're thinking: This is all obvious. Unfortunately, I don't really think that it is, at least to many people. Paying ~$300/month for 5 years is fairly typical of someone coming out of university in North America. That's a pretty big chunk of change when you're living on a postdoc's salary. Many Europeans, for example, come out of post-secondary education without any tuition-based debt, which is pretty amazing.

As scientists, not only do we experience arrested development by spending a decade (or more in school), but we're further cramped by living in relative squalor for the first few years in the work-force (assuming that most people consider a postdoc being actually in the work-force...)! Oh well, them's the breaks, I guess. Someday I'll have the dough to do all of those wonderful things I've always wanted to do. Bah, who am I kidding?!?

Belated Monday Rant: American Banking...

2010-08-17T21:49:00.003-04:00

Because some people may be unfamiliar with the rants on my blog, I'll say at the outset that I'm quite enjoying my experience living in America. Just because I take issue with a few differences between the States and Canada (e.g., public transit here) doesn't mean I'm a hater. Don't get any crazy ideas. That being said, I'm somewhat annoyed by the American banking system. On the outside banks appear to be very similar to the way they work in Canada; however, when you have to deal with tellers face-to-face, you begin to notice differences... aggravating differences.

I use two banks and both of them require that I fill out paper forms in order to carry out any transactions. Wanna make a deposit? Fill out a form helpfully titled 'Out of State Banking Form' (despite my not banking out of state) wherein you're required to itemize all deposits, write out your name and address, include your account number, etc. WTF? Isn't this what computers are for??? Here's how it works in Canada:

TELLER: How may I help you?

ME: I'd like to deposit [INSERT CHECKS/MONEY ORDERS/CASH/FOREIGN CURRENCY].

TELLER: Please swipe your client card and key in your PIN.

ME: *does as requested* *hands teller deposits*

TELLER: Is there anything else I can help you with?

Am I crazy for not having memorized my bank account numbers? I have a client card, why should I carry around more stuff? I got a card from one of my banks that just has my bank account # printed on it for cripes' sake! Whether you want to deposit or withdraw funds, it's all about filling out paper forms here.

Also, it's incredibly difficult to handle foreign currency in the States. Some banks won't deal with it at all, and others have specific people who handle these things. If you want to drive yourself crazy, go look up the process of cashing foreign checks in the US: it's a nightmare. Banks will take your check and send it to 'clearance', which apparently involves them contacting the issuer of the check and asking them to send the money in US funds. You're required to pay all applicable fees associated with clearing a check, which I've read can cost over $100. I've actually been on forums where people have said that some banks won't bother clearing CDN checks < $50 because they know that the fees will be more than the check is worth!

I've never had any problem dealing with foreign currency in Canada, checks or otherwise. There may be a ~$5 exchange fee associated with depositing a US check, but I've never been told that I couldn't do it. I actually got a check in USD from a Canadian bank (which also happened to be underwritten by the Bank of America) and I had to wait at my local branch of The Bank of America for about an hour as the teller had to make phone calls and faxes in order to 'validate' the check.

I'm fully aware that there are specific reasons for why things are the way that they are here. In fact, when I was having difficulty resolving how NSERC was going to pay out the Post-Doctoral Fellowship I scored this year, I did a bunch of reading about it. Banks in the States are much more fragmented than in most other countries because of various systems of regulation that have changed with the ebb and flow of the political climate in the past. Thus it's not trivial for them to institute the same level of standardization/integration that is seen in other countries (see Canada's Interac system, for example). While I get all that, this knowledge is of no use to me: I swear that I forget to fill out all the little paperwork every single time I go to the bank. Oh well, when in Rome...

Book Club: The Lying Stones of Marrakech...

2010-08-15T19:02:00.004-04:00

I had to go back a read my book club about Leonardo's Mountain of Clams and the Diet of Worms to refresh my memory as to how I felt about Stephen Jay Gould's last collection of essays. As I thought, apparently I felt much the same about those than I did about his penultimate book collecting his essays from Natural History Magazine. The Lying Stones of Marrakech (LSoM; 2000; Harmony Books), like the previous 8 books in the series, features around 30 essays dealing with a variety of topics ostensibly within the overall umbrella concept of 'natural history'. I say 'ostensibly' however, because even more so than in the previous book, the essays contained herein begin to 'lose the plot'.

There are certainly interesting discoveries and concepts to be found in LSoM, but they tend to be presented in essays that are long-winded, rambling, and lacking in focus in comparison to the excellence that was Gould's earlier work. Almost every essay begins on a tangent so removed from the actual topic being discussed that I was left wondering how in the hell the author would bring the two together. Gould was certainly a talented writer that I admire very much, but he is no James Burke (at least not in field of story telling) and I often found the unification of the disparate threads of the narrative unsatisfying.

I read a rather mean spirited obituary for Gould a few years back in which the author accused him of quotational sophism - that is to say that Gould would quote classics for the sole purpose of sounding as 'high-falutin'' as possible. I have to admit that if the writer of said obituary was only familiar with the author's later works, I could see how he'd reached this conclusion. Gould ends pretty much every essay with a quote of dubious relevance - to the point where I'm not even sure what he was trying to say. I assume that his intent was to bring up random works of classic literature in order to bring them back into the limelight, perhaps intriguing a few people to go out and read them for themselves¹.

I just really don't know what to make of this collection. What I've appreciated about Gould's writing in the past was his ability to present complex topics in an interesting and enjoyable way. At this point in his career, it seems as though he shifted away from talking about the 'hard science' and became far more interested in science history, hermeneutics, and a mushy form of political advocacy that assumed that most people were firmly in the middle ground between extremes (Gould always maintained that the number of Americans that didn't believe in the theory of evolution was a small but vocal minority of the population - despite what some polls have suggested). Because of the frankly, unnecessary length of the essays, you kind-of have to work to get to the interesting bits, which is a shame, I think. There's only one last collection - the 10th volume - in the series that I've yet to read. I suppose that I will do so, even though my enthusiasm has been dampened. If the reviews on Amazon.com are any indication, Gould's verbose direction in essay writing continued right through to the end.

¹Although not really answering my question, in a previous book Gould did say that he liked to illustrate concepts using quotations from classic sources so that they would be timeless. The problem here is that the quotations often do a poor job of illustrating the points he's trying to make.

New York, New York...

2010-08-12T17:00:00.001-04:00

I often feel that there are two 'Americas'. On the one hand, you have the fairytale America, depicted in countless films, TV series, books, and songs. On the other, the 'real' America, where the 'rubber meets the road' and the fantasy gives way to the visible. It's arguable that perhaps nowhere is this more evident than New York City, a place that positively breathes with its own mythology. There's nothing here that you haven't heard mentioned, at least in passing, by countless celebrities (both major and minor) or talking heads on TV: Times Square, Soho, Wall St., Greenwich Village (which I had to explain to the folks how to pronounce), Carnegie Hall, The Empire State Building... the list goes on. In fact, it's difficult not to be impressed by the spectacle of it all.

Times Square at night is kind of insane. I've heard that New Yorkers avoid it like the plague. It's so busy and so bright that it doesn't feel like night time at all. I want a taxidermist to display Dick Clarke's remains here permanently. It's not the same without him.

I think that my father was a bit disappointed that Little Italy is only a single street (Mulberry). Apparently it was previously larger. Chinatown, which lies immediately south, has exploded in the past few decades, and has encroached on most of Little Italy's territory.

In the brief time that I was here, I tried to experience at least a little bit of what 'The Big Apple' has to offer. For instance, I finally got to try cannoli, which are Sicilian pastries that are quite popular among Italian-American communities. Despite having grown up in an Italian household, I'd never tried them before (neither had my dad, actually). They're delicious - Fat-Carlo approves! In terms of edibles, I don't think that we were staying in the best part of Manhattan (Midtown, Clinton). None of the delis in our vicinitywere actual delicatessens - instead they sold pre-prepared Middle-Eastern food; thus my father was cheated out of the authentic salami he was expecting...

The 'villages' (Greenwich, East, and West) are very nice, and apparently, very, very, expensive. Listening to the tour drivers describe the cost of rent here made us wonder how anybody can afford to live on the island.

My father really wanted to take a walk down and see where the World Trade Center attacks occurred. Here's a picture and, as you can see, nine years after the fact the area still hasn't recovered. They're building a memorial tower that will be completed in 2012.

This narrow little street happens to be the very famous and very influential Wall St. Immediately to the right of where I took this photo is the New York Stock Exchange, where a bunch of folks toss around imaginary numbers and get rich, apparently.

While I doubt I could afford to live anywhere near the areas that we visited, I think that I would enjoy living in NYC. Despite my rather humble beginnings, I have become quite the 'city boy'. I think that I would appreciate the amenities that a big, bustling place like this has to offer. That being said, my one (and likely not only) problem with the place is that people seem to be rather superficial. There's a pretty hefty amount of 'fashion' running around, and anyone who knows anything about me knows that when it comes to trends, I couldn't care less¹.

The Manhattan skyline as seen from Brooklyn at night.

What series of photos of NYC would be complete without at least a single shot of Lady Liberty herself, as seen from the ferry heading to Liberty Island? Pro tip, it takes quite a while of waiting in line to get to the island and there isn't any opportunity to use the restroom until you get on the boat. I'd skip coffee or beverages in the morning...

Given that I visited New York with my parents, this trip was probably more 'touristy' than one I would've planned myself (I'd much rather read about the sites in a Lonely Planet and then go see them on foot, rather than booking a tour bus, for instance). Some of the 'main attractions' are rather busy, and there's more than enough to see without really ever having to stand in lines. There are quite a few areas of the city that I don't feel that I explored enough (if at all) and I'd certainly like to return here one day in the future - time and finances permitting!

¹Though I feel the need to begin caring at least somewhat about fashion. Being single does have its disadvantages!

Truly Becoming a 'Mad Biologist'...

2010-08-09T11:23:00.007-04:00

So I'm sitting on a bus, having temporarily left the Washington, DC area to spend a few days in New York City. In front of me is the book I've been reading on this trip: a collection of Kafka's works called 'The Metamorphosis and Other Stories'. This gets me to thinking: What is the point of reading Kafka (and trust me, some effort is involved in its reading) if I'm not really going to have anyone to talk to about it?

In the past couple of months, I've had multiple people talk to me about my blog, including friends, family, colleagues, acquaintances met at scientific meetings, and even one visiting professor. Who knew that so many people were taking the time to read what I was writing here? Anyways, the majority of them have made comments about how unfortunate it is that I essentially stopped blogging (in fact I'm not sure that anyone's going to be reading this, given that I've been 'off the grid' for so long that I doubt anyone comes here anymore). Truth is, every time someone brings up the blog, it wounds me a little bit; there are lots of memories invested in this small corner of cyberspace, and my decision to cut down on blogging was not made lightly.

The past - what has it been now? - 5 months have been rather tumultuous for me. As always, my work has been taking up the lion's share of my time, and I diverted all of my efforts into working on a side-project with a highly uncertain future. If it comes together perhaps I'll be able to talk about it some day. On a more personal note, I have recently found myself a bachelor after many, many years of having been off of the 'market'. This really isn't necessarily a 'bad' thing, however; a career in the sciences is a harsh mistress and sometimes neither person is willing to sacrifice their goals in order to accommodate a relationship. It's not like I'm worried, many opportunities for such things lie ahead.

Anyways, in the tradition of past blog posts here is a map of my current journey:

I think I want to start blogging regularly again...

GSA Drosophila Conference 2010...

2010-04-11T02:57:00.002-04:00

Spent the past 4 days at the 2010 Drosophila conference here in Washington DC. I neither presented a talk nor a poster (I'm a new postdoc sans results yet). While there was lots of cool stuff to see, I still feel rather awkward about going to any conference wherein I'm not presenting anything. Having something to talk about gets your face 'out there' in the community, whereas someone like me really has to make an effort to talk to important people. I think I did an ok job, but need to improve my 'schmoozing' skills. By next year, I'll have something worth talking about.

Switching to Micro Blog...

2010-04-09T13:37:00.000-04:00

Hmm... people's comments (as well as the stunning realization that I will fall out of contact with everyone unless this site remains up) has made me think of re-inventing Musings of the Mad Biologist as a 'micro-blog', where I'll post short (say 1 paragraph) updates pertaining to myself on a regular basis. Stay tuned (that is assuming everyone hasn't left all ready).

So long, thanks for all the fish...

2010-03-30T23:04:00.001-04:00

A few mornings ago, I was exposed to an unexpected bout of 'inside baseball' regarding landing a job in academia. Turns out that faculty hiring committees are pretty ruthless, and the interview process is quite rough (perhaps even more so than I assumed). Candidates are expected to have a very broad range of knowledge, extending far beyond their own field. This requires a lot of reading and a lot of thinking. Some day, perhaps sooner than I expect, I will be applying for such jobs, and if I'm to land one, I'm going to have to put yet more work into honing my skills as a scientist.

I'm certain that I'm not the first person to realize that a postdoc is very different from a Ph.D. For one, I put in far more hours here than I did before. Also, none of these hours involve doing things like perusing blogs or reading interesting science news. I have way too much responsibility to my lab mates and work that needs doing to be able to do any of that. And it's not getting any better: in fact, as my time here progresses, I'm gaining more responsibility and more projects to look into. I've actually changed my lifestyle such that I go to the gym early every single morning, then stay at the lab until 7:30 - 8:00 pm every night before a 1 hour commute home. To be honest, the last thing I want to do is sit down and blog about science.

I've come to a crossroads that I'm sure that every aspiring scientist must come to at some point during their life. It's a very competitive field, and many people aren't willing to make the necessary sacrifices required to eventually get their own lab. I think I'm doing pretty good so far: last week I hit the double-digits in terms of Pubmed citations - and I've got another paper recently accepted. Yesterday I found out that my application for the coveted NSERC Postdoctoral Fellowship award was accepted. This is very, very good, and puts me on track to get a good job out out all of this 'science' stuff. A Nature paper would be really nice at this point, and I think that I really need to focus on building my 'portfolio'.

My time would be much better spent writing research proposals, manuscripts, and review papers than it would contributing to a blog. I've really had to admit to myself that I just don't have time to run this thing. Actually, it's worse than that - I really don't have time to participate much in the blogosphere.

So, though it be bittersweet, I feel that I must shut down this adventure that I've been pursuing for the past few years. Thanks to all the folks who commented and participated in the discussions we had here - I've learned a lot and had a good time in the process. I wish that I could have written more, and perhaps had a more fond farewell over a series of posts, but it's probably better that I just get a post up here letting people know that the hammer has come down.

Things are looking good, I'm excited about what I'm doing, and I'm really enjoying living here in the States. I'm going to try to put together some sort of profile on one of the social media sites or something so that people will always have a place to contact me. If that happens, I'll let you know.

I wish you all well in your endeavors, thanks for making this a lot of fun!

Carlo

Grey Aliens: Part 2...

2010-03-10T21:48:00.004-05:00

I continue to flagellate myself with the brain melting inanity that is Nigel Kerner's Grey Aliens and the Harvesting of Souls (GAHS; 2010; Bear & Co.). Having made my way roughly 1/4 of the way into the book, I have no idea what to think anymore. In fact, I have NO idea what this book it about, or what any of this stuff has to do with aliens.

I can't even begin to adequately describe the odd directions that this book takes. We began with a brief discussion of how governments have the power to cover up the vast conspiracy that is the Grey aliens' attempt to use Earth's life as their genetic experiment. Subsequently, we rapidly changed gears into a discussion about the nature of mind/body duality and the true nature of God that has something to do with quantum mechanics and the only way to overcome the horror that is the second law of thermodynamics. Allow me to make the barest attempt to explain:

Like all good people who reject the scientific method, the author of GAHS rests a couple of chapters worth of discussion on a harshly debatable premise: The very fact that we seek 'meaning' in our lives somehow proves that pure materialism is false. I didn't really get this argument because it basically boils down to the author pointing out the science doesn't know everything (true) and thus arguing that in order to understand the 'big' questions in life, we need to turn away from science (false). I wish that people didn't completely misinterpret the whole scientific method thing. Saying that we only accept that which can be demonstrated empirically or for which there is abundant, positive evidence does not mean that science cannot 'explain' love, or art, or poetry. Subjectivity can be explained by science, but that doesn't diminish the value that subjective emotions and feelings have in our everyday lives. Oh, and as a side note, no amount of 'thought experiment' can prove that the brain is not the seat of consciousness. Phineas Gage says 'hi'.

Ok, so now that we're unconvinced that there has to be a 'deeper meaning' to everything - and that's 'deeper' in the Deepak Chopra sense - the author proceeds to take us on a journey through a fantastical cosmology that unites the most random Eastern philosophy with Physics buzz-words that is completely bereft of explanation, evidence, or sanity. Well, I suppose that there's some sense. I said in the previous post on this topic that according to the author's false assumptions about the second law of thermodynamics, nothing ordered in the universe could exist. Apparently the author realizes this as well, because he claims that there are two universes: ours controlled by 'forces' that cause everything to break apart (except of course for the nuclear forces that hold atomic nuclei together, oh and the electromagnetic forces that hold electrons in orbit, and... well, we'll get there) and another universe called the 'Godverse' that is defined as (and I quote):

A universe that is eternal and thus timeless, where all extremes of values that are perfect are inherent and free; a universal field of abstract reality, as real and abiding in its own scale of reference as the physical material reality of this universe.

ACK!!!!! What does that even mean?!?!? Unfortunately (or fortunately?), it's not explained. Anyways, the Godverse is a place of perfect attraction, and thus only via the Godverse's effect on this reality is the second law of thermodynamics kept at bay. The Godverse, is where gravity comes from, for example, which means that gravity is not a force, but rather an un-force, as forces always repel - except of course for those that don't. The perfect points of singularity in the Godverse, called Godheads, come into contact with the evil universe, or whatever, and create big bangs, which is why we're here. Oh, I should also mention that the author manages to do something that previous theologists have been loath to do. He defines God: "That in which all absolutes are confined." Am I ever glad that that conundrum's been solved.

I've watched Unsolved Mysteries. UFO people always try to convince you that there's evidence to support their claims. In this case, the author begins the book by talking about how he's approaching the question as a scientist, then calls scientists fools, then tells us that we have have to resist explanations of the truth in terms of the scientific method alone (P. 46). He then proceeds to lay out a cosmology on par with anything out of the dark ages without evidence or explanation. What's it gonna be? Why don't people understand that without setting standards of evidence (which may be wrong and subject to revision as required) we quickly reach a point of Nietzschian nihilism where we cannot actually know anything.

I though I was reading a book about aliens?!?!?!?

Grey Aliens: Part 1...

2010-03-08T23:30:00.003-05:00

I finally picked up Nigel Kerner's Grey Aliens and the Harvesting of Souls (GAHS; 2010; Bear & Co.), and have resolved to write several blog posts about it, somewhat in the same style as I did for The Case for a Creator before. Unfortunately, I think that this one is going to be a more difficult read than the aforementioned title, and that's saying a lot.

I've only gotten through the first few chapters of GAHS, and I'm already fairly upset. Despite the following quotation appearing on page 4:

"The book takes a serious look at the [alien] situation in terms of the sociological consequences of this profound threat to our humanity, with strict recourse to purely scientific rather than mystical paradigms."

the book is written in a way that is very, very unscientific. That is to say that the author flows from one vague concept to the next without ever really explaining anything. For instance, we move from a brief statement about how aliens contacted Hitler in order to make sure that he eliminated dark-skinned people because the melanin in their skin acts as a protective coat against alien genetic manipulation, to how the author suggested that the bloodline of Jesus Christ has been preserved throughout the ages before the Davinci Code came out.

We're tritely told that anyone who believes in evolution is a 'fool', because the Second Law of Thermodynamics (SLOT) applies to everything at all times - which is strange because I was always under the impression that the 'SLOT' (the author obviously likes acronyms) applied only to closed systems. In fact, if everything tended towards chaos all the time, then life itself would be impossible, which it plainly is not. Perhaps this is part of the alien conspiracy as well...

The book then quickly treads the familiar ground of 'How can aliens not be real given that there are so many UFO reports?'. All possible criticisms are quickly dismissed. Why are UFO stories never verified? Because aliens control all of the world's governments and are covering it up. How come alien sightings only come for industrialized, Northern Hemisphere nations? Because the aliens avoid the darker skinned people of Earth because of their natural melanin resistance. And so on...

Sometimes I feel that the author is so unfamiliar with Occam's razor that if he ever tried to apply it he may accidentally cut himself. If the aliens are so damned omnipotent and intelligent, then why aren't they stopping thousands of books and TV shows exposing their nefarious actions from being produced each year? Wait, I get it. Nothing has done a better job of convincing me that the whole alien invasion thing is bunk than these sorts of books. That was a close call; the aliens almost won right then and there!

My eyes are now open. Damn you Greys!!!

Board Games!

2010-03-07T14:13:00.005-05:00

Life continues to be perpetually hectic, however, I have resolved to take one day off per week (Sunday). Working 7 days a week for over a month was pretty darned tiring, and I while I think that I accomplished a lot, I don't think that anyone would disagree with the idea that it's not worth giving up your entire life, no matter how much you enjoy your job.

I got a nice piece of news a few days ago: The final paper based on my Ph.D. research has been accepted for publication into BMC Biology! This was the one detailing the work I did on my 'major' project, i.e., the one that took me 2.5 years of work. I want to blog about it, but given how infrequent my posts have been of late, we'll see if I actually get around to it. Acceptance of this paper is really nice, because it means that I can focus 100% of my effort on my postdoctoral work - it's very typical for people starting up postdocs to be finishing up Ph.D. stuff on the side for a year or more. I still have one review paper regarding my Ph.D. that I'm in the midst of writing, but unfortunately, that's not a huge priority at the moment.

As my previous blog post alluded to, I've been 'going out' a lot lately. Aside from all of the sleep and hang-over related issues, such behavior is also quite expensive, and I've been looking for alternative, cheaper ways to spend time with friends. Hence, we're trying to get a board gaming group together!

I received a copy of the German game Settlers of Catan for Chimmz. Catan is really popular and well-known with the board game crowd, but if you're not familiar with the game, it's a pretty relaxed and easy-to-learn game involving the colonization of a small island. Each player takes control of a different colony, placing settlements at the intersections of different land tiles that randomly produce resources as gameplay progresses. Players then use the resources in order to expand their colonies and interfere with those of their opponents.

Part of Catan's extreme popularity has to do with its relative simplicity (it can easily be learned in an evening) and its quick play (games last around an hour - depending on the number of players, 3-4, though there's a $20 expansion set that increases the number of players to 6). Some board games can get far more complicated than Catan, but those are only for the extreme hardcore crowd. Catan's really something that anyone can enjoy, and I've been surprised by how many people I've met who play it.

One of our rounds of Catan in progress.

After getting my ass whupped in three rounds of Settlers (I hadn't played in a while and my strategy was abysmal...), our host pulled out a French game called Caylus, which was considerably more advanced, but also very, very cool.

In Caylus, players take the role of nobles tasked with building a castle city for a medieval French Monarch. Each player controls a pool of workers who must be distributed among a series of tasks such as trading in the market, laboring for money, building additional structures in the castle/city, or petitioning the local provost to allow/disallow building of certain structures among many others. As players complete tasks in the game, they're awarded victory points - determining the ultimate victor - or royal favors, which boost the player's ability to more efficiently distribute his/her resources.

There's a lot to think about during each round of play, and there are a few aspects to Caylus that make the game stand out. For one, there's no 'randomness' to the game: every aspect of the game is determined by how players choose to distribute their resources - there are no dice rolls. Each location on the board can only serve one player per round, and thus players have to take turns competing for limited spots. Players even invest resources in order to determine the order of play, so it really is a fine balancing game.

Caylus's playing field. Although it looks pretty crazy complicated, it doesn't take that long to get the hang of it.

I have to admit that it was all quite overwhelming at first, however, it really didn't take that long to get the hang of it. Again I got my ass beat, though.

You'd assume that people in science are generally all quite nerdy; but such is not the case. I've had surprisingly little opportunity to play such games, even though I really do enjoy them. Good board games tend to be rather expensive (> $40 and sometimes much higher), which is fine as long as you play them a lot. Despite the fact that I suck at them, I hoping that we'll have a lot more chances to play these games while I'm here!

Alcohol, Alternative to Feeling like Yourself...

2010-03-04T01:03:00.003-05:00

Tonight I poured about $40 worth of booze down my kitchen drain. That's not a lot by Canadian standards, but here in America, $40 bucks will net you a decent amount of sauce.

Here's the deal: without exaggeration, I've drank more during the 5 months that I've been a postdoc than during my entire 4 years of being a Ph.D. student. This is partially due to having lived with a significant other during my Ph.D., thus not having the need to 'go out' very much, but that's not all of it.

It shouldn't be a secret to anyone reading this blog that postdoc-ing is a crazy amount of work. This is entirely why I'm not able to update my blog even half as often as I'd like. Crazy work means crazy stress, and frequent stress makes 'getting out of the house' - which typically involves going to a local pub - all the more appealing. I think that a lot of people here, myself included, really enjoy any opportunity they can get to go out and 'relax'.

Alcohol consumption has not affected my work, and hopefully it hasn't affected my interpersonal relationships either. But over the past couple of weeks, I've noticed a disturbing trend towards increased social drinking. There have actually been weeks where I've gone out and drank significantly 4 out of 7 evenings, which is pretty unreasonable. Not to mention expensive.

This isn't the first time I've wanted to stop drinking, or at least cut down significantly. In fact, I've probably seriously considered this 3 or 4 times before. While some people may look at not drinking as 'no big deal', it kind of is. Alcohol's a huge part of North American culture, and it's difficult to refuse a glass of wine at a formal event, for example. It's also surprisingly difficult to attend parties hosted by friends if you're the only sober person - the sober guest outstays his welcome, after all.

Oh well, is it possible to enjoy one's self without drinking? Or is the solution to drink moderately? The latter seems like the obvious choice, but then what's the point of drinking if you're not at least trying to get a 'buzz'? I tend to be really good about not drinking to excess, but, all of this drinking seems like a bad idea. Being in a high stress situation, it's easy to see how someone would begin drinking all the time - not just socially. Oh well, we'll see how this goes.

Don't Go Into Science for the Money...

2010-02-24T23:16:00.003-05:00

I have received no less than 4 phone calls from the Canadian National Student Loans Service Centre in the past 3 days informing me that I have to begin paying back my government student loan by the end of March. I'm not talking about pre-recorded messages - I mean actual people calling me to remind me that I need to start paying¹. I'm also paying back a bank loan I took out to pay for my ludicrously expensive undergraduate degree at Dalhousie.

It's nice that postdocs make considerably more money than graduate students, but I'm not really seeing any of that extra dough. Did I mention that the Washington, D.C. area is ridiculously expensive to live in? I don't know anyone who pays less than $1000 USD per month on a single bedroom apartment, and that's assuming that you live a ways out of the city proper. By the time you pay your rent, bills, and debts each month, there's very little money left.

Some people have told me that they find that groceries are much cheaper in the States, but I don't see it. About the only thing that's much more economical here is liquor, and now I think I know why...

P.S. This post is way more morose than I intended it to be. I'm tired and feeling broke. Sorry!

¹Incidentally, I called the NSLSC when I first began my postdoc in order to set up a payment plan and they told me that I wasn't allowed to. I had to wait for the 6 month 'grace' period to be over. I still have to pay the capitilized interest on those 6 months, however. Thanks for nothing.

Bad Biology: District 9...

2010-02-22T21:26:00.005-05:00

Don't worry, I'm not breaking with my plan of ranting on Mondays. I assure you that this post has all of the trappings of a rant. However, the post does contain 'spoilars' so if you haven't seen District 9, you may want to pass on this one.

I've been a pretty big movie buff for years now, and yet I haven't been watching a lot films since moving to the United States. One reason for this is simply time constraints, but a second is perhaps more practical: I have no idea where to rent movies anywhere near where I live. Thus, I've decided to remedy this situation by getting a Netflix account. That's besides the point though.

I have been watching some movies - basically anything interesting that I've found on blu-ray for cheap. One film that I picked up a few weeks ago, based on the recommendations of various people and web sites, was District 9. I know I'm late to the party, but I had to discuss this one.

Now, I could talk about the rather preposterous notion that various, powerful world governments would let South Africa commit apartheid against the most significant discovery in the history of human civilization¹. However, as you've probably figured out from the title of the post, that's not what bothered me the most. Rather, it's the simple fact that there is SO much wrong with the idea that some alien sludge could transform a human into one of said aliens that I don't even know where to begin.

Ok, first off, based on casual inspection of said aliens, we have to assume that their biology is fairly significantly different from our own:

The aliens kinda look like crustaceans. Aside from the lack of inventive exobiology, I doubt that their cellular biology is near-identical to ours. Image cred here.

In order for such a mutagenic cocktail to work, it needs to supply the cellular machinery required to effect the transformation: people don't possess genes 'for' turning into aliens. Nor - considering a more basic level - do we possess genes for making chitin exoskeletons, for instance. Even assuming that the cocktail contains all such proteins (as well as an appropriate vector for delivery, and the proper regulatory machinery to activate them at the appropriate times, etc.) there's still the fundamental problem that such molecules would have to be able to 'work' with the molecules that humans already do possess.

This is non-trivial. I did a Ph.D. in speciation biology and it's easy to observe that proteins derived from different species that share a common ancestor only ~2.5 million years ago cannot properly work together. And this results only from passive evolutionary forces. How in the hell are we supposed to believe that species that evolved independently on different planets have compatible molecular machinery??? Do they even use DNA? How about proteins containing the exact same 20 amino acids that terrestrial life does?

Giving the sci-fi nerd the benefit of the doubt, let's assume that the aliens studied humans and developed this cocktail with their sophisticated technology. Why would they ALSO use it to power their ships?!?!? That's like a motor oil company telling their chemists that they want the Valvoline to ALSO cure cancer. WTF?

I have to cut District 9 a bit of slack simply because it never claimed to be a 'hard' sci-fi story - as alluded to above, it's not like the rest of the film's elements were believable. Regardless, as I've brought up before, I think that the popular conception of aliens is somewhat marred by our inability to contemplate the implications of species adapted to worlds that are likely to be different from our own. There's no guarantee that such aliens would be bipedal, or be able to breathe our atmosphere, or be able to eat our food - cripes, we get sick eating species that yet other species have no problem consuming.

I'm not exactly sure what I'm looking for when it comes to sci-fi aliens, but I am certain that I haven't found it yet. Aliens are either so familiar as to be completely boring (such as the races in Star Trek that didn't even have weird stuff glued to their foreheads to distinguish them from humans), or so different as to be completely terrifying. What about the non-familiar, yet not hostile? Oh right, because that would be awkward, uncomfortable, and slightly frightening, which is pretty much exactly what I'd imagine any plausible alien encounter would be like. District 9, on the other hand, is mostly devoid of such feelings, and rather shares some parallels with 80s movies and old SNL skits: humanity's immediate reaction to the discovery that we're not alone in the cosmos is annoyance.

¹Now don't get me wrong, I am familiar with the concept of a literary device, and it's evident that the entire premise of the alien presence is meant to convey a more fundamental message. However, such devices work best when they're set within the context of a believable narrative. If the story is so jarringly ridiculous that we cannot suspend our disbelief enough to empathize with the characters, the device fails.

Book Club: Evidence as to Man's Place in Nature...

2010-02-18T19:00:00.001-05:00

I've been meaning to read Thomas Henry Huxley's Evidence as To Man's Place in Nature (EMPN; 1863) for a long time now. I saw an online lecture given by Sean B. Carroll, the famous evo-devo guru, who said that the book was both still relevant and much easier to read than say, The Origin of Species. I agree.

The history of EMPN is quite interesting. Huxley (a.k.a. 'Darwin's Bulldog') was a firm evolutionist and supporter of Darwin's theory from its inception and, following the publication of Darwin's book (1859), had discussed the idea of publishing his own book about the subject with his friends. Even those that supported the idea of evolution cautioned him that given the controversial nature of the subject, publishing such a book could sink his career.

Huxley specifically wanted to write a book about the relationship between humans and apes, and became embroiled in a controversy while researching the material for such an undertaking. Richard Owen, a very famous 18th century British biologist/paleontologist (the man who coined the term 'dinosaur'), published a paper in 1860 arguing that humans could be considered apart from the apes because only their brains possessed a posterior lobe, a posterior cornu, and the hippocampus minor. Curiously however, previous anatomical treatises had indicated that these structures were shared among all apes.

Huxley confronted Owen about his erroneous assertions first privately, then publicly, even going so far as to contact other experts in order to get them to plead with Owen to change his tune. All the while, Owen refused to admit that he was wrong, despite numerous publications and mounds of evidence indicating that these structures were not unique to humans. In the end Huxley ended up writing and publishing EMPN as a series of essays, spured primarily by a desire to prove Owen wrong. By the time of the book's publication, the evidence against Owen was overwhelming, and people began questioning why Britain's premier biologist seemed to be fabricating data in order to undermine the hypothesis that humans were related to apes. Huxley's book was so carefully written and detailed that it came off as eminently reasonable as compared to Owen's controversy, and thus it was both well-respected and extremely popular.

The book itself is divided into 3 parts, the first of which is a long and quite tedious summary of everything we know about the history, anatomy, and behavior of apes. While dry and technical, it's still quite interesting to learn about how Europeans first encountered their nearest relatives, and the lengths that Victorian-era folk had to go to to study them. In short, people during Huxley's time knew very little about ape behavior and life-history, and only had a limited number of skeletons available for comparative anatomy.

The second part is much more interesting. Huxley begins by arguing that a proper taxonomy (classification) of living organisms is based upon similarity among species. Members of a genus, for example, should be more similar to one another than any is to members of a separate genus¹. After establishing this, Huxley goes on to point out that no one argues that animal species cannot be classified into a Linnean taxonomy based on such criteria. Therefore, he points out, if it can be 'shewn' that humans are more similar to apes than any other species AND that humans possess no anatomical features that are so radically different from those of apes that they obviously call for Homo sapiens to be classified outside of the animal kingdom, then logically, humans are apes. It's at this point that Huxley goes into a long anatomical treatise, specifically intended to shoot down the claims of people like Richard Owen, or that humans possess unique structures that apes do not (note here that there's no doubt that there are differences, among great apes, but these are quantitative, not qualitative).

Finally, after establishing that humans should be classified as primates, Huxley broaches the obvious, post-Darwinian notion that humans probably evolved from ape-like ancestors. This section is particularly interesting, because it played a large part in making the author's career. Though he spends a decent number of pages on the subject of human evolution, Huxley never speculates beyond what the extremely limited (at the time) evidence suggests. He's incredibly cautious, throwing out caveats when appropriate, which solidified his reputation as a 'man of science'. In fact, even fellow scientists who strongly disagreed with Huxley's views respected him, because his arguments were sound and logical, rather than pleas to passion.

All in all, EMPN is a short, eminently quotable book that, despite being 'Victorianly wordy', is still completely readable. I'm trying to get involved in teaching a graduate-level course in evolutionary biology (specifically targeted towards human evolution) , and if I don't assign the book as required reading, I'd certainly draw a lot of good information from it.

¹An interesting aside here is that modern anatomical taxonomy recognizes that a blanket statement such as 'is more similar to' can often be misleading, especially in very complex, speciose groups such as insects. Modern taxonomy (or at least one branch of it) focuses on shared derived characteristics, or 'synapomorphies'. For instance, all apes lost the tail that their ancestors possessed. Shared inherited characters are passive, whereas newly derived characters are far more informative.

Monday Rant: Methods...

2010-02-15T23:14:00.003-05:00

A couple of years ago, I blogged about the problem with the materials and methods sections of scientific publications - then specifically in the context of microarrays. However, I feel the need to extend this rant far beyond the bounds of any particular technique/discipline. My rant today can be summed up in a single sentence: If I cannot reproduce the work that you're presenting in this paper, it's not science.

For all of the non-scientists out there, here's how a scientific publication (typically) works. Essentially, every time you want to write up the results of your work, you prepare it in a manuscript with five basic sections: An abstract summarizing the entire manuscript, an introduction giving background and context, and stating the objectives of the study, a methods sections explaining how things were done, a section passively detailing the results of the work, and a final discussion section interpreting the results in the context of the introduction (what have we learned?).

Modern publications have become ridiculously bloated, partially because the level of technical detail in any given field is ever-increasing, but also because in fields like mine - speciation genomics - any given study is going to generate a huge amount of data to present. If you disagree with the 'bloated' comment, then go back and look at Watson and Crick's 1 page Nobel Prize winning paper from 1953. Publishing is expensive, and Journals are always looking for ways to keep the published page-count to a minimum. Thus we end up in a situation where many a methods section ends up as a supplementary section that's online available online, where, frankly, it's likely that it was never properly peer-reviewed.

Even considering the fact that many scientific journals are moving online (i.e., that is no longer publishing expensive print versions), it's still questionable how much of the original data submitted for any given publication actually gets reviewed. Many genome-scale datasets are immense, and 20+ megabyte Excel spreadsheets are rather daunting. Thus the responsibility for making sure that your work is adequately documented and described really does ultimately rest in your own hands.

And this is why it's so unfortunate that I so frequently hear people complain about the quality of methods sections. It's absolutely typical to see people say things like "RNA was extracted according to standard protocols," or "X was performed as per Smith et al. 2002." That last one is particularly annoying when you go back to the paper they reference and find that it says that the technique was performed according to 'standard' protocols.

I know it's annoying and that everyone's busy, but if I had things my way I'd like it if everything was described in detail in every publication. I'm not opposed to having individual protocols made available as supplementary material online, but I should be able to understand the entirety of what was done by reading a paper's methods section, without having to refer back to another slew of texts or attempt to interpret what 'standard' methods were used. This is such a huge problem that I'm surprised that it's not being discussed more among the scientific community - perhaps I'm just out of the loop?

Snowmaggedon and the Fever of Cabins...

2010-02-10T18:30:00.005-05:00

I'm really beginning to know what 'cabin fever' is. I spent almost all of Friday, Saturday, and Sunday indoors because of the heavy snowfall the D.C. region's received over the weekend. Unfortunately, another blizzard started up last night, shutting down the entire bus and above ground Metro rail system meaning that I couldn't even make it into the lab today if I wanted to (which I did want to).

Snow's a really big deal here. The city doesn't typically get much of it, and thus unlike where I grew up in Eastern Canada, they're not really prepared for it. Main roads aren't very well plowed and side streets are lucky if they get plowed at all. Sidewalks, for the most part, aren't cleared at all, and thus for several days after the snowfall, it's impossible to go anywhere by foot.

To give you an idea of how much people panicked when they heard about this second wave of snow, here's a photo I snapped yesterday of the entire meat aisle in my local Safeway. Pretty crazy hunh?

The snow is creating a huge problem for us. Our lab orders fresh fly food weekly from Tennessee, but the NIH has been closed since Friday last week and since roads and airports are going to be closed for a bit, it's highly unlikely that we're going to be able to get our order in this week. That means emergency transfers only and halted experiments: never a good thing.

I realize that only a crazy postdoc complains about not being able to go into work, but I'm acutely aware that I have a ton of work to do. Until I solve the difficulties I've been having with my flies, I'm not going to be able to relax and get into a 'work grove'. Also, it's now been a whole week since I've been to the gym, and I'm getting soft.

P.S. By commenter demand, I've decided to order that crazy alien conspiracy book from Amazon next time that I make a purchase. I can't even claim that I'll read it with an 'open mind' while keeping a straight face: let's face it, there's a 99.999999999999999% that I'm going to take it apart chapter-by-chapter on the blog. It's gonna be fun!

Priorities...

2010-02-08T21:38:00.004-05:00

Last month was a tough one, as should clearly have been evident from my low blogging output. Our entire lab was burning the midnight oil on a big collaborative data analysis project, and the shear amount of time I was spending on work was basically making my brain mush. Thus my normal diet of perusing geeky websites and blogs has suffered, along with my reading of science-related books. Most of my free time has instead been directed towards pursuits of a more escapism bent (e.g., escaping into the fuzzy haze of alcohol, or escape into the wonderful world of blasting evil aliens¹).

These all feed into one another, you know. Reading science books gives me ideas for blog posts, as does reading and commenting on other blogs. Sure, I could talk about some of the awful fantasy novels I've read in the past few weeks, but who'd want to hear about that?

Actually, given my normal blog readership, I doubt that fantasy would be too low brow (don't take offense, I'm the one reading the books!). Also, given that it's technically Monday, allow me to spew forth a micro-rant. Is there anyone who actually likes to read fantasy novels in which the characters are constantly saved from impossible situations via crappy Deus Ex Machina tropes? Have you ever reached the end of a book and realized that the main characters didn't actually accomplish anything, but were rather miraculously saved from every situation by [INSERT DRAGON/MAGIC/LEGENDARY TOILET SEAT/NATURAL DISASTER/ETC. HERE]? Also, doesn't it bother anyone that the Evil Dark Lord™ who managed to conquer and subjugate all but a plucky young band of mismatched heroes + Love Interest™, is otherwise completely incapable of doing anything right?

Ok, I'm done. I promised myself I wouldn't read any of those books anymore, but I've been trying to save on expenditures this month and have been going back to the 'To read' pile - most of which is made up of fantasy novels I'd purchased years ago.

Anyways... sorry, back to the topic. So yeah, gotta get back into reality and immerse myself in science reading again. In order to facilitate this, I finally picked up a copy of Thomas Henry Huxley's Evidence as to Man's Place in Nature (1863). This is a book I've been wanting to read for a while, and given that it's quite brief, I hope to be able to have a book club post about it soon.

Also, I've mostly run out of aliens to shoot.

¹As a good friend of mine says to me at least once a week: "I can't believe you're a doctor."

P.S. Also, like TheBrummell, I've unfortunately been forced to turn on comment word verification due to the mysterious rise in the amount of crazy comment spam.

Pure Insanity...

2010-02-08T08:18:00.003-05:00

Having survived the 'snowpocalypse', I emerged from my apartment yesterday with the intent of making my way to the Barnes and Noble down the street. The going was tough, but I eventually made it, only to be greeted by the craziest book I've ever seen! Please, please read the synopsis if it's the only thing you do today:

Grey Aliens and the Harvesting of Souls: The Conspiracy to Genetically Tamper with Humanity

Nigel Kerner, Bear & Company, 2010

In 1997 Nigel Kerner first introduced the notion of aliens known as Greys coming to Earth, explaining that Greys are sophisticated biological robots created by an extraterrestrial civilization they have long since outlived. In this new book Kerner reveals that the Greys are seeking to master death by obtaining something humans possess that they do not: souls. Through the manipulation of human DNA, these aliens hope to create their own souls and, thereby, escape the entropic grip of the material universe in favor of the timeless realm of spirit.

Kerner explains that genetic manipulation by the Greys has occurred since biblical times and has led to numerous negative qualities that plague humanity, such as violence, greed, and maliciousness. Racism, he contends, was developed by the aliens to prevent their genetic experiments from being compromised by breeding with others outside their influence. Examining historical records, Kerner shows that Jesus, who represented an uncorrupted genetic line, warned his disciples about the threat posed by these alien interlopers, while Hitler, a pure product of this alien intelligence, waged genocide in an attempt to rid Earth of all those untouched by this genetic tampering. Despite the powerful grip the Greys have on humanity, Kerner says that all hope is not lost. Greys exist wholly in the material world, so if we follow the spiritual laws of reincarnation and karma, aiming for enlightenment and rising above the material--a state the Greys are unable to reach--we can free ourselves from their grasp.

THIS is why I hate conspiracy theories...

Not-so-Monday Rant: Genre Adulation...

2010-02-07T13:04:00.003-05:00

Work continues to be a massive time-sink. Not only am I heavily involved in helping out our lab in a large collaborative project, but I also seem to be hitting some road bumps in terms of getting my own project off of the ground. Hopefully I'll get this stuff cleared up real soon. I missed last week's 'Monday Rant', but given that something's been bothering me a bit for the past couple of weeks, I figured I'd write up a Sunday rant instead.

I have a rather cynical personal philosophy about entertainment 'media'. It goes something like this: 90 - 95% of everything is crap. This goes for movies, books, games, music, etc... you name it. Now a movie or music critic may take offense at this and argue that actually, if we assume that the quality of any product lies along a normal distribution, then it could be argued that most products are of 'average' quality, while only some are 'great' or otherwise the aforementioned 'crap'.

Obviously I'd disagree. Allow me to use an analogy to illustrate my view. Have you ever heard the joke about the two people who are running away from a bear? The first turns to the second and says, "I don't think we can outrun this bear!" The second then replies, "I don't have to outrun the bear. I only have to outrun you." Similarly, if I have a limited amount of funds, why in the hell would I ever choose to spend my money on anything but the best quality products I can afford? Of course, we don't always know what the 'best' quality products are - we don't have perfect information - but that's where the 5-10% not crap thing comes in: there may be a range of 'bests' but you're generally pretty sure of what doesn't fall into that category.

Back to entertainment. Most entertainment media are not a huge investment. Buying a CD or going to see a movie are typically activities in which you can afford to waste money (by trying out an untested band/film). However, as the investment increases, I generally become more discerning.

That was a very long-winded introduction to the topic of today's rant: genre adulation. Genre adulation is what happens when a person loves a category of film/music/etc. so much that they fail to recognize that 90% of it is crap (this applies to everything, remember?) Having grown up involved in geeky subculture, I've had the opportunity to witness a lot of this first hand. I myself used to read any fantasy novel no matter how dreadful. And some of them were positively AWFUL. In addition, there are always the anime nerds, the Japanese videogame nerds, the sci-fi nerds, the sports nerds, etc.

All of this being said, this doesn't really affect others, does it? I mean, who cares if an overweight, pasty, white kid flunks out of university because his stint as president of the anime society took up too much of his time and money¹? If their obsessions were completely internalized and never leaked out to their public personas, then people who loved all six Star Wars movies (and the books - even The Truce at Bakura and the abysmal Courtship of Princess Leia *shiver*) wouldn't get on anyone's nerves. However, some people who demonstrate such 'fandom' generally let that sort of stuff seep into every aspect of their lives.

This is compounded with the fact that genre adulation completely breaks down the marketplace of ideas. If a company knows that it will sell tons of fantasy novels, no matter how awfully written they are, then there's no incentive to spend money on hiring talented authors. As mentioned above, I was certainly guilty of this sort of obsession in my youth; until I begin noticing novels with frequent grammatical/spelling errors. How much effort are you really putting into publishing if you're putting out books where the names/genders of major characters keep switching around because of typos?

While the market angle is certainly a bother, another fundamentally messed up aspect to unbridled adoration of certain genres is that it can be really creepy. The prime example of this is Japanese Animation. 'Anime' as it is known by its fans, gets a really bum rap, which, unfortunately, it often deserves. I know I'm sticking my head out here, but there are some really, really good animated films to have come out of Japan. Hayao Miyazaki is one of the greatest film makers of all time, and his work rivals anything that Disney has to offer. Going a bit 'lower brow', some of the anime 'classics' like Ghost in the Shell and Akira, are pretty amazingly imaginative pieces of work. On the flipside, there's a world of difference between Princess Mononoke or Spirited Away and Sailor Moon. If a 30 year-old guy had 100s of tapes full of Rainbow Brite and My Little Pony, saying that he was really into 'the culture of animated films' wouldn't make you feel any better².

Any genre, series, band, etc. that has never released anything sub-par is either a) very special, or b) very young. I love Martin Scorcese's films, but I still think that his remake of Cape Fear was pretty crap. I've heard it said that being overly critical of a series/genre may cause it to disappear, thus if you like most of it, it makes sense to support all of it. I suppose that if you enjoy spending your money on mediocrity, that makes sense. However, I've got a sneaking suspicion that neither science-fiction, anime, country music, nor Joss Whedon are suddenly going to go away because the fans decided to 'vote with their dollars' and not buy some particular underwhelming piece of dross being foisted upon them. To each their own I suppose, but remember, if you keep buying the crap, they'll keep shoveling it down your throat.

¹Back in the day it would have been money spent on VHS tapes and material for cataloging their impressive collection of umpteen thousand hours of Sailor Moon fansubs. Nowadays it would probably more likely be money spend on external hard drives to store all of those stories about pre-pubescent girls riding giant mechanized robots.

²On a side note, this actually drives me nuts about anime fans. I've heard so many times that fans of the genre want it to be respected in the mainstream. They want North Americans and Europeans to understand that in Japan, there are cartoons made for adults. Fair enough, but people aren't going to begin accepting grown men watching foreign cartoons about half-naked 15 year old girls when they don't accept grown men watching ANY domestic cartoons about young girls. There's an argument to made about anime as an art form and its general acceptability to Western tastes, but pick your 'effing battles for Darwin's sake!

Monday Rant: Pseudointellectualism...

2010-01-25T22:15:00.003-05:00

For much of my Ph.D. I worked at the bench, often listening to podcasts for up to 6 hours a day. Towards the end of my work, however, I became entirely focused on computational data analysis and thesis writing, and thus my podcast listening dropped precipitously. Now that I'm back on the bench in my new lab, I've got more opportunity to listen to my iPod than ever before, and I've been trying out quite a few new shows.

I've come to realize something about my preferences though: they're rather black-and-white. I really only like shows that a) discuss serious topics and feature interviews with actual 'experts', or b) don't take themselves seriously at all but rather seek to entertain. The shows in the middle, e.g., non-experts trying to have serious discussions about particular topics, tend to irritate me. This is mostly due to pseudointellectualism.

There are 2 types of pseudointellectuals that I find particularly aggravating. The first is obvious: It's absolutely annoying to listen to people try to sound intelligent about topics they really know nothing about. I tend to listen to a lot of podcasts about 'nerdy' stuff like videogames, science, geek culture, technology, etc. and unfortunately some of these geeks really seem to think they're authorities on everything¹. It's not particularly interesting to listen to a bunch of former English/Journalism majors have a 1-hour round table discussion about how they'd improve the fiscal strategies of major electronics firms. Having listened to these types of podcasts for a good ~4 years now, I can confidently say that most of these folks have no idea what they're talking about, and furthermore, couldn't predict the future of technology 6 months out let alone long-term trends. I don't understand why so many shows about 'nerddom' feel like they need to go 'off the rails' and talk about subjects far outside their ken. If you're a podcast about comic books, talk about frickin' comic books and leave discussions about Marvel's corporate strategy to Disney.

The second, and personally more aggravating version of pseudointellectualism - and the one that happens to be far more prevalent among the podcasts that I listen to - is the attempt to somehow objectively quantify personal opinion. I sorry to hear that you didn't like Avatar, but no matter how many polysyllabic words you manage to produce, or random references to classical literature you can come up with, you're never going to be able to convince others that your opinion is somehow an objective evaluation of reality. This is because preferences are not objective.

Not everyone likes him, but I've always enjoyed reading Roger Ebert's writing, for example. I don't agree with every one of his reviews, but at least I know where he's coming from. I respect his opinions, and I understand his preferences; I don't read his work because I think that he has some kind of ability to objectively score a film the precise number of stars it 'scientifically' deserves. Furthermore, Ebert acknowledges the non-objectivity of personal opinion all the time; the point of a review is to inform the public opinion, not to reflect it.

The 'Overthinking it' Podcast, which unfortunately suffers from a bit of both of my lamentations of today, made an interesting point during an episode to the effect that the internet is really just a bunch of people (i.e., 15 year olds) who think they know everything, arguing all the time. Allow me to indicate at this moment that the irony of this statement in the context of my blog is not lost upon me. Be that as it may, I'd like to think that the ultimate mark of the pseudointellectual is the belief that there are simple solutions to complex issues that much better-trained, more highly educated people have spent a lot of time thinking about without clear resolutions. This is really why I'd much rather hear either discussions about the issues retaining all of their complexity, or shows that avoid serious discussion of the issues in favor of levity.

It's really ok to admit that you're not an expert on everything.

¹For more detail, go see a previous rant of mine regarding 'sci-fi power', or the fact that many sci-fi nerds seem to think that reading science fiction suddenly makes them geniuses.

And we Walked off to look for America...

2010-01-21T22:27:00.005-05:00

Let us be lovers we'll marry our fortunes together
I've got some real estate here in my bag
So we bought a pack of cigarettes and Mrs. Wagner pies
And we walked off to look for America

-Simon And Garfunkel, America (1968)

I had an eye opening conversation with an American friend of mine about the social atmosphere among postdocs at the US National Institutes of Health. During the talk, he made a point about the fact that he doesn't always feel that foreign postdocs are interested in meeting or talking to Americans. Rather, foreigners tend to hang out with one another. At face value this appears to be easily explained; however, consider the following: 1) foreigners don't necessarily hang out with people from their own countries, and tend to speak English with one another anyways, 2) there are very, very few people who are postdoc-ing at this institution who are from the Washington area. Even Americans here are likely far away from home.

It's interesting to think about the fact that most postdocs at the NIH are foreigners (they quoted a value of 65% during my orientation). It's a strange twist of irony that Americans can feel like strangers on their own soil.

We proceeded to talk about why foreigners may naturally congregate with other foreigners - presumably any foreigners. When you think about it, it's kind of a weird thing: we've come to the United States for employment and training purposes, and we're also granted an opportunity to learn more about another culture. Could you imagine postdoc-ing in Europe (assuming you're from America) and being completely uninterested in learning anything about the local culture?

I think that this is a multi-layered, complex issue that certainly involves elements of feeling more comfortable with people sharing your experience of moving to a new country. However, I also think that this very point about culture plays a significant role as well.

I honestly have to agree with my American friend in his assessment that most foreigners' general impression of American culture skews towards the negative. I've actually met more than one person whose sole reason for postdoc-ing in the States is because of the career opportunities it will open up; otherwise they'd never have dreamed of living here.

Sometimes I'm shocked by how Americans can be surprised by the stereotypes they get labeled with. A recent NPR 'Planet Money' podcast featured the host saying that he couldn't understand why all foreigners think that all Americans are completely obsessed with making the most money that they possibly can. Obviously not everyone fits this stereotype, but if you think of the American media that makes it out into other countries, it's not surprising that it exists. Think of the lengths that people will go to to prositute themselves on 'reality TV' for a chance at fame. Or furthermore, as many commentators have remarked, many foreigners are baffled by the tone of the discussion regarding American healthcare reform in terms of dollars and cents.

It's unfortunate that in many ways, America is an easy country to 'hate'. For instance, you can tune into the powerful conservative media here and hear them regularly say rather offensive things about other nations. America is also rather well known for its pride, and it's not shocking that some people interpret this fierce pride as snobbery.

However, it's much more unfortunate that a country of ~300 million people has such a vocal minority of people in the media as ambassadors. Ann Coulter, Rush Limbaugh, Bill O'Reilly, and Glenn Beck actually do not represent the opinions of the majority of Americans. And say what you will about American media, but not everyone is chomping at the bit to embarrass themselves for 15 minutes of fame.

The outside world's view of America was substantially tarnished by 8 years of an unpopular presidency coupled to a perhaps even more unpopular war. I hate to think that this kind of stigma is often applied to individual American's themselves.

I'd venture that most foreigners here actually do not actively avoid hanging out with Americans. I've met quite a few people here who, like myself, very much enjoy the atmosphere of the area, and are quite interested in experiencing more of American culture (see the Turduckening, for example). But, there are certainly those who aren't afraid to let people around them know that they're only here for the postdoc.

I know from my own experience in Canada that there's a lot of ill-will among non-Americans about the US. Before now, I'd never thought about how that it would feel to bear the brunt of that negativity, especially on American soil.

I'm hoping that the phenomenon of foreigners hanging out with other foreigners is mostly due to our interest in learning about different cultures from people who are sharing our experiences, and not because of a dislike of the locals. All of the Americans that I've met since coming here have been awesome, and I think that they deserve better than that.

Monday Rant: Fat...

2010-01-19T21:06:00.004-05:00

It's been a while since I've had a good rant¹, thus I'm bringing back the tradition of ranting every Monday. Today's rant: my unhealthy obsession with fatness.

I was a fat kid. Tales of Fat-Carlo and his mean-spirited bastardliness abound, and the world is a better place without him. This may sound weirdly harsh, but I assure you, dropping a little over 3 stone in one summer was the best thing I ever did.

Seriously, how many people who complain about their weight constantly do you know? I know a lot, and you probably do too. I'd venture that there are very few people who are overweight who are perfectly happy with their own perception of their bodies. I wasn't - in fact it bothered me constantly. Here's a secret: people actually treat you differently when you're fat. Trust me, I've seen both sides.

It may very well have to do with the fact that being obese is a surefire sign that you don't have a lot of discipline. This probably looks like a controversial statement, especially in an age where everyone is looking for so called 'fat genes'. This also happens to be an age where everyone's worried about the adverse psychological effects of negative self-image (it's ok to be overweight), while every single piece of media is presenting ideal body types that scream that it is not, in fact, ok to be overweight. Was I overweight because I was genetically predisposed to be so, or because my parents didn't enroll me in sports? No. Actually, I was overweight because I ate too damned much and sat on my ass playing videogames all the time.

So here's the deal: I got fit, which improved my self-confidence as well as my interpersonal relationships, presumably including my attractiveness to the opposite sex². This in turn led to me being a happier, generally less morose individual, thus improving my overall quality of life.

The only downside: I am now completely obsessed with fat. My girlfriend complains about it all the time - I always think I'm fat. However, I'd argue that I'm not entirely wrong on that count: I did put on quite a bit of weight in the last 2 years of my Ph.D., but I'm already about 1/2 way to having lost it all again.

It's not only my girlfriend though, my new friends here in the States, specifically those of the female persuasion, have begun remarking about how I act like a girl when it comes to eating at restaurants or bars. I should note that they're the ones applying the gender stereotypes, not I! So what if I never buy anything at the grocery store without checking the nutritional information? And what's the big deal if I generally avoid beer, or desert? I've stared down the gullet of the beast, and that, my friends, is a long, dark, and greasy road.

There is such a thing as eating disorders, and there's also such a thing as being too thin. I suffered from the latter at the beginning of my M.Sc.:

It's absolutely weird to look at pictures of myself with hair...

However, nowadays I have fallen prey to neither. I eat healthily, and I'm certainly bigger than I was back then. Sometimes I wonder if people aren't really upset with the fact that I'm being so nitpicky about calories and fat, but that rather, by choosing to eat the healthy alternatives, I'm pointing out their own personal lack of discipline?

Oh well, I'm not going to change. I may stress out a bit now and again about my ever fluctuating weight (welcome to adutlhood?), but at least I'm happy.

¹To be honest, there hasn't been very much that's been ticking me off - imagine that!

²I haven't tested this in a controlled environment, but I now have abundant data supporting this conjecture...

That was quite a nerdy joke.

We Work Hard, We Play Hard...

2010-01-17T23:20:00.004-05:00

As a follow up post to my previous lament, 'The Scientific Life', I'd like to talk about another more positively social aspect of my time since coming to the NIH. Through conversations with people who'd spent time at the National Institutes of Health, I'd gotten the impression that the place wasn't very 'social'. In a way, this is somewhat true: unlike a university, there isn't a meaningful 'student life' atmosphere to the place. Furthermore, since it's primarily made up of postdocs, most people tend to be workaholics (e.g., there are very few 1 hour group lunches).

However, that's not to say that there's nothing going on. There is an organization of postdoctoral fellows that put together regular parties and happy hours. It was at one such party that I met many of the friends that I hang around with regularly nowadays. Interestingly, though perhaps not surprisingly, our little group is almost entirely made up of internationals - I suppose that there's something about moving to another country that ups your gregariousness so that you'll make some friends. So far so good.

So good in fact that I've been doing a hell of a lot more 'social activities' (i.e., drinking) in the first 3 months of my postdoc than I did during my entire Ph.D. (that may be a bit of an exaggeration, but it sure feels like it). Last night, a gang of us hit The Reef, a small night club in Adams Morgan that happens to be filled with aquariums containing tropical fish. I haven't been to a nightclub in at least 4 years, but one nice thing about hitting the dance floor here is that it's not packed with awkward 19 year olds (though awkward 21 year olds aren't really much better...).

It's nice to be socializing with fellow committed scientists¹. This is because it usually results in the nerd quotient being turned up to 11. We've begun this weird tradition of drawing out strange schematics on the tables of bars or restaurants, assuming that they're covered in paper. For instance:

The above insanity resulted from an attempt to understand the chronological relationship between a couple of movies. In order to calibrate our scale, we had to throw on a couple of known movies, of course. Thus was born the standard Ben-Hur to Star Trek IV: The Voyage Home scale of chronology. A physicist in our group also suggested that we add a perpendicular line to the standard timeline in order to add on films that existed in universes completely different from our own, such as The Lord of the Rings. This of course made Star Wars difficult to classify, because technically it should be in the same universe... never mind.

So yeah, part of the reason that it's difficult to find time to blog, read books, or play videogames is because of work. But that's only part of it. As mentioned above, I'm also very busy going out there and doing stuff. A cold beer (or 5) after a hard day's work is a treat indeed. I guess the motto of the postdocs that I've met is: We Work Hard, We Play Hard.

¹I've ranted before about how many graduate students aren't 'committed'. I also didn't consider myself a scientist as a graduate student; more of a scientist-in-training.

P.S. Thankfully the C&C Music Factory was able to remain solvent due to the generous support of TARP funds...

The Scientific Life...

2010-01-14T22:42:00.004-05:00

It was at the end of my M.Sc. that I decided that I wanted to spend my life doing science. I'm sure that some people were able to make such a decision at a much younger age (Stephen Jay Gould famously claimed that he'd known that he wanted to be a paleontologist since visiting the Natural History Museum in New York as a 5 year old) however, I was not in that position. For one thing, after having spent two years in the lab, I'd had the opportunity to meet a few postdocs and for the most part, they tended to be rather bitter, joyless people¹.

Given the number of hours that postdocs put into their work, it's perhaps not surprising that they can occasionally be negative. A topic that's already come up a few times even in my short experience as a postdoc has been whether having your own lab is worth the insane amount of effort it takes to obtain it. Competition is fierce, and while it's certainly doable with sufficient effort and determination, it's a rather daunting process to attempt to crack academia when you know that there are people willing to sacrifice EVERYTHING for their work. Everyone I know works hard, but I think that most scientists enjoy having some life outside of the lab!

I have to admit that the whole 'science is horrible' lament feels a lot worse when you lay it out on the table like that: it's easy for a group of grad students or postdocs to get all morose and whiny when sitting around a table over beer. However, the same people typically don't seem to have the same problems when sitting in the lab doing actual work. This could mean one of two things: either it's not so bad when you're in the midst of doing the kinds of things you love, or you only realize how crazy hard you've been working when you sit down to reflect on the last time you actually took a day off. Perhaps it's a bit of both, though I'd obviously prefer to think it is the former.

I'd like to think that there's more to having a successful life in the sciences than pure research output. There's also the ability to communicate one's work and convince others that you're valuable enough to hire. These things take 'people' skills - something you won't learn by burying yourself in your work. Hopefully I'm not being naive, but even if this is nothing but a fiction, it's a pleasant one that helps keep me sane. I've been working quite hard so far, but I've also been enjoying myself very much, so there's no sign of a grizzled old bitter version of myself popping up anytime soon.

¹I've met quite a range of differently tempered postdocs at this point. Many (most?) are quite well-balanced.

The Biology of Avatar...

2010-01-11T22:36:00.000-05:00

The following discussion is pretty much spoiler-free...

I know that some people get annoyed when 'smart-asses' try to dissect films that are supposed to be consumed as 'entertainment'. Of course the lightsaber is ridiculous, and many aspects of Star Trek are unrealistic, but I find it interesting to discuss the themes of science-fiction films from a critical perspective. If 'unrealistic' was a legitimate criticism against a film's value as entertainment or art, we'd surely have to admit that this would delegitimize > 95% of films, irrespective of genre.

With this out of the way, I can now get to my discussion of the biology of James Cameron's most recent blockbuster, Avatar. I really liked Avatar; probably more than most snobby film aficionados did. Yes, it is Dances with Wolves crossed with Ferngully: The Last Rainforest and Aliens - no one is denying that the theme of the 'noble savage' has been done countless times before (even more recently, e.g., The Last Samurai). However, there's a classical school of thought that would argue that, when it comes to these timeless quasi-mythological archetypes, it's not so much that the story itself should be original, but rather that our interest be piqued by how it's told¹.

From the perspective of someone interested in nature, Avatar's imaginative scenery was wonderful. Some of its ideas were legitimately quite cool, like those thorny lizards that glided by using pink bio luminescent helicopter blade-like appendages. It was also quite neat that the character creators did a good job of making the world of Pandora's fauna seem like it was all interrelated: all creatures, with one notable exception discussed below, seemed to be built on a hexpodal body plan, with two sets of eyes on either side of the head. Furthermore, the creatures all seemed to have a similar breathing system on their 'chests' that was independent of their feeding mouths. It's rather refreshing to see such wild imagination bounded in a sense of the 'possible' - the concept of evolutionary descent between these organisms is clear...

Which makes the primary focus of the film, the blue skinned humanoid Navi, somewhat puzzling. Don't get me wrong, I understand exactly why the Navi don't have 4 eyes and breathe out of their chests: it would be difficult for the audience to relate to such obviously alien entities. For the purposes of (arguably) compelling storytelling, Cameron probably made the right choice (this probably also helps him sell the dubious concept that Navi and human 'DNA' can be mixed...). However, I'm not the only one of my friends who noted how out of place the humanoid aliens felt when compared to the rest of the creatures on their world. Perhaps they're evolved from an offshoot lineage whose other extant members - if there are any - just didn't get any screen time?

And how about the whole 'everything in the forest can communicate with everything else by jacking-in with their crazy brain-stem tentacle things' aspect? On the one hand it seems evolutionarily questionable - for such a symbiotic relationship to develop, all participants must benefit. Here we're talking about planet-wide group selection, which would obviously present innumerable opportunities for exploitation. If the group includes everything, it's difficult to envision where significant selection is going to come from (you could probably play Avatar over John Maynard Smith's grave in order to dig for oil...).

On the other hand, this entire concept of biological interconnectedness provides a biological rationality for the concept of God. As people's memories and emotions are electrochemically transferred to other organisms, some aspect of their personalities can live on beyond their death. It may be conservatively unrealistic based on our modern understanding of evolution, it is thought provoking in its implications (remember though that xenobiology is the only science that is allowed to extrapolate from a datum).

While I could sit here and tear apart many aspects of Avatar's science, such as how someone should have taught Sigourney Weaver how to use a micropipette, I have to admit that I'm not inclined to. My real gripe is with the fact that so many science-fiction tales cast aliens in a universe devoid of context. For example, Star Wars is more fantasy than science, but even as a kid that that giant worm thing that lived all alone on the asteroid in The Empire Strikes Back always bugged me. What in the hell does it eat?!?!? The occasional tiny ship that lands in its mouth? The point is that exciting aliens are usually thought up in the same way that mythical creatures are - from out of nowhere.

Cameron actually tried to give his alien world a sense of place and an underlying logic that may not necessarily be 100% plausible (if not impossible). At least it demonstrates some thought with respect to how an alien world may have evolved. Regardless of its entertainment value, I'm willing to forgive its fluffy inaccuracies on account it being a huge step in the right direction for incorporating biology into mainstream science fiction.

¹Think of how Indiana Jones and his famous leitmotif evokes all of the best elements of classical swashbuckling action heroes. The themes are not original, but the way that they were cast for a new audience is what was appealing.

Testing Pluralism...

2010-01-06T23:00:00.000-05:00

Y'all may have figured it out by now, but postdoc-ing is not conducive to blogging... at all. I'm out of the house by 7:30 am in the morning and rarely home before 8:30 pm. Unfortunately dear readers, blogging has to take a back seat to such things as cleaning the apartment, cooking food, and calling loved ones. Sadly, I don't even read books anymore; there's just not enough time. We'll see how things go, but I feel that if I can't get at least 3 posts a week up here (I haven't even been putting up that many lately), it's not really worth it. I will set 3 updates per week as my goal, and we'll see how I do.

Science is often associated with a strong emphasis on reductionism, or the notion that complex systems can be understood by dissecting them and studying their parts in isolation. Though overly reductive approaches can be misleading, there's no denying that reductionism has been a great boon to our understanding of the universe.

There's one aspect to reductionism that always irked me a little: the idea that when we're evaluating multiple competing hypotheses formulated to explain some phenomenon, we need to discover the one hypothesis that is primarily responsible for our observation. This sort of thing is extremely common in the evolution/ecology literature. Take, for example, the long standing debate over the selective forces responsible for the origin(s) and maintenance of sexual reproduction. There are several theories (more like a dozen), and many reviews of the subject speak as though we're trying to determine the single most universally important explanation for the origins and maintenance of sex.

An alternative possibility to the aforementioned conundrum, especially when there's good evidence supporting multiple hypotheses is pluralism: perhaps some or many hypotheses interact synergistically in order to produce the observed phenomenon. Obviously in some cases, one hypothesis only exists to the exclusion of some other. However, in many cases it is at least theoretically possible that many factors are combining to produce a net total effect. Think for example of all of the debate regarding whether certain human behavioral factors (say homosexuality) are environmental or genetic.

Unfortunately, that last example, human behavior, also acts as an example of a situation where a form of extreme reductionism is applied to a plurality. People will accept that both factors - genes and environment - play a role, but they're interested in which of the two factors plays the dominant role. In some cases this is justified, such as when a particular environmental factor increases your risk of getting a particular disease by X fold. However, such considerations often ignore the entire concept of gene-by-environment interactions (G×E). For example, you may have a situation where a particular genotype is only deleterious in a given environment. Evolutionary biology studies would seem to suggest that G×E situations are extremely common even though their potential effects are often ignored.

All of this would seem to suggest that pluralist approaches should be the norm. At least I thought so for a time. But I read a recent paper (Meirmans and Neiman 2006) that pointed out something that I realized should have been rather obvious: it's much more difficult to devise methods through which to test pluralist hypotheses.

Think of it this way: the scientific method is all about testing hypotheses. You set up an experiment - the scope of 'experiment' can vary immensely - which seeks to reject a 'null' hypothesis in favor of a preferred explanation for a phenomenon. The more specific your proposed explanation (hypothesis), the easier it should be to reject if it is false (this follows directly from Popper's classical doctrine of falsifiability). It's rather easy to envision a situation wherein you create a hypothesis that is so 'plural' that it's extremely difficult to falsify, thus eliminating its explanatory utility.

While Meirmans and Neiman (2006) still advocate embracing pluralism - their paper is specifically in the context of the work surrounding the evolutionary origins of sex - they caution that plurality should still remain conservative. That is to say that we should still stick with the minimum number of separate mechnisms required to explain the data. Furthermore, the experiments should be designed to rigorously rule out the possibility that either of the independent hypotheses could explain the data on their own.

Essentially, what this all boils down to is the idea that Occam's Razor would demand that pluralism only be invoked when we've ruled out the possibility that any of our individual hypotheses could explain the data on their own. Furthermore, when pluralism is invoked, it should be done in such a way that it is still testable/falsifiable. It would be nice if we could all just respect each other's opinions. Unfortunately we'll have to hold back on doing so until we can show that we're all actually correct!

Meirmans, S. and M. Neiman. 2006. Methodologies for testing a pluralist idea for the maintenance of sex. Biological Journal of the Linnean Society 89: 605-613.

Happy Arbitrary Beginning of the Interval it Takes for the Earth to Complete a Rotation Around the Sun!

2010-01-03T12:53:00.003-05:00

Dear Darwin, life has been intense lately. I have been so much more busy so far during my postdoc than I ever was during my Ph.D. - both work-wise and socially. I haven't arrived home at my apartment any earlier than 2 a.m. in the past three days, and when I get home from the lab today, I think I'm in for a nice relaxing 'veg' session on the couch (I've got season 2 and 3 of Dexter to watch on Blu-ray).

Last night I went to my first music show here in D.C. Long time readers of the blog may remember that during my Ph.D. I was introduced to the genre of music known as 'metal', and had the opportunity to attend many live, very, very loud shows. It seems that my postdoc will likely introduce me to many American 'punk' acts - a genre of music in which I was once pretty interested, but stopped listening to the better part of a decade ago.

Anyways, the 9:30 club in D.C. featured The Extraordinaires, a Philadelphia-based indie folk-rock (?) band opening for Gogol Bordello. Gogol Bordello's self-described genre is 'gypsy-punk', blending Eastern European Polka instrumentation with ska and punk style music. They've got a pretty amazing stage presence, and their music is all over the place with English, Russian, Spanish (and perhaps other) vocals jumping in and out of single songs. They're really something that has to be seen live.

The lead singer, Eugene Hütz Nikolaev, hails from the Ukraine and really plays up that whole Eastern European Gypsy angle. Image cred here.

It was great fun and a great end to three straight nights of New Year celebrations in America.

The Post-ChimmZ Update at 14,000 Feet…

2009-12-30T22:15:00.007-05:00

Well, I didn’t see a lot of activity on many of the blogs I frequented during the past week. I assume that, like me, many people took a short holiday to spend ChimmZ with their families or significant others (though I assume that most of them prefer to think of it as Xmas or ‘Super-Kwanza’). I’ve spent the last few days busily running around, visiting family and a few friends in Moncton, New-Brunswick, Canada.¹.

While always enjoyable, my trips home typically follow one of two paths: either I end up doing very-little (e.g., my friends and family are working) and getting a lot of reading/gaming in. Otherwise, they tend to be extremely busy, with every evening planned and accounted for – father’s mother one night, mother’s mom the next, etc. – and the pile of books, games, and graphic novels that I lugged with me remains untouched. Both provide a nice break from the daily grind at the lab, but my plans to get through the reviewer’s comments on my latest submitted manuscript went up in smoke.

I got to do all of the things that I traditionally associate with coming home for ChimmZ, such as eating lots of seafood (including two fresh lobsters² and my parent’s delicious bouillabaisse) and my grandmother’s traditional French Acadian foods (see pics below). I’m pretty happy about my portion sizes whilst I was home: in 5 days I really only ate too much during two meals, and even then I was 'reasonable'. Strangely, the whole lactose-intolerant thing is giving me a valid reason to *only* eat a normal amount of my Italian grandmother’s cooking. The specter of Fat-Carlo hovers above me still, you see, and I must remain vigilant.

Meat pie has always been one of my favorite holiday delicacies. Come on, it's meat in a pie!

When most people think of 'poutine', they imagine fries topped with gravy and cheese. However, French Acadians have a dish known as poutine râpée, which consists of a boiled potato dumpling with a pork filling.

Many consider the dish to be extremely visually unappealing, but I've always found it to be delicious. It's typically served with a generous heaping of sugar or salt.

Among the usual questions from family members regarding such things as how I’m enjoying living in the States and what I think about the Washington area (answer to both: enjoying it a lot), I received a few requests to describe exactly what I’m working on. Since moving initially into the speciation then developmental biology arenas, I’ve found that this is a really difficult question to answer. It’s surprisingly easy to offend people by saying that it's really complicated and technical, but it ACTUALLY IS really complicated and technical. I routinely have trouble explaining my work to 4th year biology majors (or ‘seniors’ as they’re referred to here in the States). Some cursory overview of trying to use interspecific hybrids in order to understand how development diverges between species is as far as I typically get³. Oh well, I suppose that there are better things to complain about.

While fairly busy and not entirely relaxing per se, my trip home was a nice getaway from all of the work I've got to do. I suppose that I'm now ready to get my nose back to the ol' grindstone. However, before I end this blog post, my folks gave me a bunch of pictures that they took at my recent Ph.D. graduation ceremony, so I'm going to throw a couple of them up here.

Here's me being 'hooded' on stage. I had the honor of being hooded by one of my supervisory committee members, Dr. Brian Golding.

Here's a pic of me and the folks. Gotta love those school colors and that mortarboard.

All those years of work for a piece of paper. Well, it IS a nice piece of paper...

¹A.k.a. ‘The middle of nowhere’ as far as a woman at the Continental Airlines booth at Dulles, Int’l in D.C. was concerned.

²The whole point of ChimmZ is to begin a new holiday with the ‘stupid’ traditions removed – I’m sure that these would vary from person to person, but I’d include seasonal depression, useless gift-buying, eating far past being full, etc. I realize that this would be difficult to pull off as a global tradition, but I’d vote to have the meal of lobsters being ChimmZ’s version of the Thanksgiving turkey.

³When bringing up interspecific hybrids, I’ve often found that ‘Ligers’ form a good point of reference. They’re basically my favorite animal... and most people have seen Napoleon Dynamite.

Where's George?

2009-12-21T22:35:00.009-05:00

While at a local Starbucks today, I received a curious $1 bill as part of my change:

As you can see, the bill is marked up with a series of colorful stamps asking such things as 'How far does your $$ go?'.

The bill directed me to a website: www.wheresgeorge.com to see where the bill had come from, and find out where it is going next. Dutifully, I did so, only to find that the bill had traveled only from Walkertown, North Carolina to Rockville, Maryland - a measly 260 miles in the past 198 days.

Not very far at all...

I was hoping for a buck that had criss-crossed the country, but I guess not. I've registered the thing, so if it moves on to sunnier climes or something, I'll find out about it.

On another note, I've been inspired by the very nice postings of microscopy pictures by Psi Wavefunction to post a very nice microscopy picture of my own:

During the earliest stage of Drosophila development, before the activation of the zygotic genome, the embryo goes through 14 cycles of nuclear division before cellularization, called the syncitial divisions (this means that the entire embryo is one big fluid filled sack with multiple nuclei in it). What you're looking at is a DAPI stained late syncitial stage embryo. Each of the separate specks is a nucleus containing one full genomic complement. If you look at the full-sized image, you'll be able to see that the nuclei in the middle of the embryo are in the process of dividing. Thus the nuclear divisions were occurring at the time when this embryo was fixed. I think that's pretty darned cool!

Epic Snowstorm!

2009-12-20T10:52:00.006-05:00

Having grown up in the Great Northern Frozen Wastes of Canada, I'm usually pretty dismissive about people's complaints regarding the weather here in the greater Washington area. While it does rain a lot, it's certainly a noticeably milder clime than the Atlantic Canada of my birth, or Ontario for that matter (British Columbia, on the other hand, is milder than here). Despite being informed that it 'rarely snows here' upon my arrival, yesterday we had an epic snowstorm, the like of which would rival anything from back home:

This is the view of the parking lot from my apartment, which now sits under 60 cm (24 inches) of snow!

Yesterday totally sucked. The buses were still operating in the morning, so I decided to go into work. I worked for two hours, setting up experiments and collections when I saw an alert that all above ground subway stations (including those within 3 miles of my place) were being shut down at 1 pm. I packed away my stuff and rushed to the station only to find that they'd decided to shut down 45 minutes early.

These icicles have formed from the snow melt off in the past 24 hours.

I tried to walk home, but they hadn't cleared all of the sidewalks. Returning to an underground subway station an hour-and-a-half later with the intention of going into town to get some food, I found out that they were going to try to send a single train up to Rockville in order to get all of the stranded people home. Thankfully this train was successful, and I was able to get home, soggy and cold but really only slightly worse for wear.

Another view from my balcony, this time of the road behind the building.

Unfortunately, the metro remains closed today (Sunday) and thus my entire weekend of lab-work is completely shot. Oh well, I guess I have paper revisions and reading to do...

Book Club: Scroogenomics...

2009-12-19T19:00:00.000-05:00

Economics are endlessly fascinating and frustrating in equal measure. They're fascinating because they often quantify the subtle quirks underlying the behaviors of free actors. They're also frustrating because they often model these behaviors in ways that disagree with the simple observation that people do not behave in a perfectly self-interested manner. In the past, I've often found myself to be somewhat dismissive of human behavioral studies¹, and thus I haven't made a serious effort to understand the field of economics. Hopefully, I'll be able to change that over time.

Recently I've begun listening to NPR's Planet Money podcast. A few weeks ago, they interviewed University of Pennsylvania economist Joel Waldfogel about his new book, Scroogenomics: Why you Shouldn't Buy Gifts for Christmas (2009; Princeton University Press) and, based on the conversation of that interview, I decided to pick it up (along with Waldfogel's previous book The Tyranny of the Market²). Scroogenomics makes a lot of very interesting points, but I think that a few of its conclusions may be slightly misguided - more on that in a moment.

Essentially, Waldfogel is concerned with customer satisfaction; this is to say, how much is a product that you've spent money to buy actually worth to you? When you're buying for yourself, you'd expect that most things you purchase are worth their actual sale value to you. It would be pretty strange for someone to consistent buy things that they personally felt were over-priced. Now, it's important to realize that different people value different things. Thus, in the case of someone buying you a gift, they have to use their knowledge of your behavior to determine what you'd want (something that's not always easy to do, and gets more difficult with decreasing frequency of contact/degree of relatedness). Thus, with a few exceptions³, the best you can hope for from a gift in terms of satisfaction, is for it to be as good as you could have done buying it for yourself. However, on average you will be less satisfied per dollar spent on gifts rather than on products/services you purchase for yourself.

Thus, during the holidays a large amount of money is essentially wasted on things that people would never have bought for themselves (or more specifically things that people value at less than their actual cost). Furthermore, there's an entire market for products that no one wants, e.g., Xmas novelties and clothing. By extrapolating from the results of surveys given to undergraduates, Waldfogel estimates the global waste to be roughly 25 billion USD annually.

The principle opposition to his logic that Waldfogel has received is the following: by giving you a gift, the giver is deriving personal satisfaction, thus there may be a net gain in satisfaction overall. However, Waldfogel objects to this in terms of opportunity costs: if the giver derived the same satisfaction by giving you a gift you actually wanted, the overall satisfaction would be improved. Thus there remains an average net loss in satisfaction no matter what (but see below).

There's certainly validity to the author's overarching argument: There is a ton of waste occurring during the holidays. However, I do have a few minor objections to some of the finer points of his analysis.

All of the concrete estimates of waste that Waldfogel generates are, like far too many aspects of behavioral studies, based on surveys administered to undergraduates. Ignoring the details about survey quality and potential biases, it seems to me a that we've invested many years and a fair amount of effort into understanding the undergrad psyche. But is this really a representative sample from which to extrapolate to a global scale (I should note that the surveys have been repeated on undergraduates in non-US countries as well)? I'm sure that there's a lot of waste occurring, but 25 billion seems like it should have some fairly large error bars attached.

Secondly, I know that I'm not the only person who grew up in a family where everyone generally asks everyone else what they'd like for Xmas. I don't remember a lot of random gift buying, and especially not on large-ticket items (this last point is discussed a bit in the book - the more expensive the item, the less likely that it's 'randomly' chosen). Thus our gift buying is far more 'optimal' - often I even received cash, which is the most 'optimal' because then I can choose to buy what I'd like. However, there's also a sort of twist to this issue that may mitigate some of the author's argument: if you grew up in a family where the gifts had to be surprises, then it's likely that the gifter's satisfaction is predicated on 1) not having asked what they should buy you and 2) not having given you cash. Thus, when we calculate the net satisfaction (i.e., the satisfaction granted to the giver plus the receiver minus the gift's cost) we cannot assume the existence of an optimal situation in terms of recipient satisfaction (i.e., that you got exactly what you wanted and the giver received maximum satisfaction). Thus, it is possible that while net satisfaction is lower than a theoretical maximum, it is nevertheless at a practical maximum. Wow, that was a bit heavy.

Anyways, these nit-picky concerns don't undermine the book's message that the holidays are wasteful, and even more so because some people consider it taboo to ask the recipient of a gift what they actually want while refusing to give cash. Thus I declare that such things are not taboo in the tradition of ChimmZ - problem solved.

¹I don't have a general problem with behavioral work, rather I think it should be evaluated on a case-by-case basis. However, somewhat by default, it's impossible to control human behavioral studies to the same degree of rigor that is demanded of say, animal behavioral studies. I've read quite a few papers involving tiny sample sizes, shoddy statistics, lack of proper controls, and interpretation involving the author's 'pet theory', to the exclusion of alternative possibilities.

²I'd planned to blog about both books in a single post, however, The Tyranny of the Market is quite a bit more 'academic' and would certainly warrant a separate post all to itself.

³There are situations wherein a gift can satisfy you more than you could yourself, such as when someone has access to a good/service that you do not, or if someone finds a rare good that they know you were looking for and were unable to find yourself. However, in both these cases, the increased satisfaction is predicated on the buyer knowing you very well.

New Toys and the Holiday Rush...

2009-12-16T22:49:00.007-05:00

Sorry for the lack of meaningful posts this week dear readers, but I've been busy. As I've mentioned before, being an atheist and not particularly attached to any specific tradition, I've been celebrating my own yearly end-of-year holiday known as 'ChimmZ'. I like it because it rolls off of the tongue: 'Merry ChimmZ to everyone!'. I'm having a bunch of my new NIH friends over for a holiday Turkey, which has become a de facto ChimmZ tradition for me during these past few years. Thus I've had to spend evenings preparing my apartment, and purchasing food.

Something I didn't realize during all of this, is that getting a turkey at this time of year in the US is rather difficult-ish (it's the turkey 'off-season' as one of my buddies put it). Apparently, the majority of turkeys are mercilessly slaughtered during the Thanksgiving rush - we consumed no less than 3 birds - leaving very few bird for the ChimmZ season. Though Xmas turkey was pretty common during my childhood, my American friends inform me that such is not the case here. It was tough, but I've found one.

My own ChimmZ tradition also involves making my mother's signature potato-based turkey stuffing; I am not a big fan of bread-based stuffings at all. However, this is again going to pose somewhat of a problem this year because the 'secret' ingredient in my mother's stuffing, summer savoury, is nigh impossible to get in these parts. A quick perusal of the Wikipedia page on the spice indicated that it is apparently a very 'Atlantic Canada thing' (perhaps even a French Atlantic Canada thing), and while I'm pretty sure it's readily available in the parts of Canada wherein I've lived, I didn't see it at the grocery store here. I will try to substitute sage instead. We'll see how it turns out...

On the flipside, I got an early ChimmZ gift that may help in the blogging dept: A 10" Dell netbook!

I've been watching the prices on netbooks pretty carefully for a while now. Although I love my Macbook, I've been looking for something a bit more portable (writing screenplays at Starbucks is exhausting and carrying a heavy laptop doesn't help). When the prices dropped below $300 for something decent, I dove in.

Here at the NIH, we're not allowed to use our home computers at work, so my Macbook basically sits at home. I'm rarely near my place, and furthermore, I've been doing quite a bit of traveling lately, so a computer that I can tote along with me that easily fits in the bottom of a backpack or murse is quite appealing.

Also, speaking of computers at work, I finally received my new work 'rig': A 27" loaded iMac!

This thing has the single, sweetest display I have ever seen in my life: 27 giant inches of crystal clear OS X Snow Leopard computational biology goodness.

You may also notice that it came with Apple's new 'Magic Mouse', which is the coolest. thing. evar! It has the Mac multi-touch controls on its surface. After I pay off my current litany of bills, I'm totally going to get one for home.

Ok, sorry about that, I've always been a bit of a computer nerd, which is probably a good thing, since I tend to sit in front of them for much of my day. I'll try to throw up something more substantial soon.

Statistics are a One Way Street...

2009-12-10T21:36:00.003-05:00

This is the second of my two posts intended to discuss some basic statistical concepts as they pertain to my experiences in academia (I'm sure that I'll talk about other statistically related concepts in the future, but two topics were on my mind at this time). The previous post is here.

Of the many things that I learned during the course of my Doctoral studies, perhaps the one that was most drilled into my psyche was the appreciation for the importance applying statistics to complex biological inferences. I knew nothing about stats as I exited my Master's degree (ask TheBrummell about how incredulous everyone was that I didn't know what a χ² test was), and it took a solid 3 years for me to build up a competent understanding of the complexities of applied stats.

I'd like to point out a typical example of a statistical issue pertaining to large modern datasets. Imagine that we want to test some characteristic, say evidence of positive selection, having acted upon all of the genes in the genome of the fruit fly, Drosophila melanogaster (as compared to some other species). Let's say that we'll consider evidence of positive selection, any gene that has a less than 1/20 chance of having evolved under neutral of negative selective regimes (properly, we're saying that we're confident that there's only a 5% chance that we incorrectly rejected the null hypothesis that positive selection did not occur, which can also be represented by saying we've chosen α = 0.05). We run our test, calculate our stats and find that, out of 15,000 genes in the Drosophila genome, 900 of them show evidence of having undergone recent positive selection, or adaptive evolution (900 gene have a p value of less than 0.05).

However, anyone doing work in evolutionary genomics will realize that we've left out a critical step in the analysis here. Remember that our statistical test was based on the understanding that we'd expect our chance of being incorrect about our inference to be 1/20. Thus, in a large number of tests, we'd expect 15,000 * 1/20 = 750 false positives due entirely to chance. We have to be a lot more stringent about our analysis, and one way to do this is to apply the method developed by Carlo Emilio Bonferroni¹ and divide our α value by the number of tests: α_corrected = 0.05 / 15,000 = 3.33 x 10^-6. In order to be highly stringent, we should only consider genes significant if their p values are less than 3.33 x 10^-6.

This entire little exercise seems rather obvious and uninstructive. The diminished power to reliably detect statistical significance with increasing number of tests is called 'the cost of multiplicity', and it warns us that large-scale experimental designs need to have strong power to detect minute differences, or else we'll expect to see a huge number of false positives in our data. But this also poses a somewhat more interesting corollary, which is kind of the very long winded point of this post: experiments that are impossible to control statistically aren't worth doing in the first place.

When I say that stats are a one-way street, I mean that once you begin applying statistical methodology to your analyses, and more importantly, you begin to understand the caveats and issues associated with the analysis of various types of data, you really can't turn that statistical switch off.

Sometimes it feels like folks such as myself are perpetually raining on other people's parades. I see graphs plotting curves showing only the averages, without any type of indication of the error or distribution surrounding these estimates, and yet I'm told that these curves are 'different' (how do we know that?). Or how about parametric tests being applied without consideration to non-parametric data? Situations such as these are very common, especially in particular disciplines.

There's a saying from the field of biochemistry: if you need statistics to tell you that there's a significant difference between experimental and control samples, the difference is probably insignificant. This logic, and the laissez-faire attitude that many people take with regards to statistical application has to do with the classical approach of working with specific proteins/loci and conducting experiments of large effect. It's certainly true that you probably do not need a statistical test in order to to verify that two bands on a Western blot are at different positions, or different intensities (in such studies the experimental 'signal' is typically much stronger than the technical noise). However, such logic is applied to genome-level datasets only at extreme peril.

The issue here is really that applied statistics are often complicated, they involve difficult to interpret numbers, and the software required to pull off complex statistical tests isn't always easily accessible or user-friendly (it's actually typically one or the other on the latter point). Not everyone is familiar with the technologies and applications required to analyze large, complex datasets and sometimes this may lead to people ignoring important analyses and controls.

More than ever before, science has become an extremely collaborative endeavor - different labs have different specialties, and projects have become so far reaching and broad in scope that it's rare that a single group will contain all of the people required to properly carry out an analysis of some of the data generated by some of the most 'cutting edge' techniques. More and more people are coming around to the idea that the only way to reliably analyze such data is through the help of competent statisticians, but this is often applied post hoc - or after the data have been generated in the first place. I've heard a few stories of people being approached with something along the line of, 'Here, I've got this huge dataset. Can you find anything significant in it?'.

Experiments are about explicitly testing hypotheses. These hypotheses can be general, and they can be vague (depending on the situation); but when we try to extract meaning out of an experiment after the fact, there's no guarantee that the experiment will have been properly designed in the first place. That's the danger of ignoring statistical principles, and a challenge faced by modern high-throughput science. I've met a few people who share my views about the importance of cross-disciplinary collaboration, but I still feel that this isn't the general rule, which is unfortunate.

¹I need to point out that I've glossed over some really important technical stuff here. Bonferroni correction assumes some details about the dataset that don't typically apply to genome level studies: namely that all tests are perfectly independent. Genes co-evolve, are co-regulated, are involved in complexes, etc. and thus cannot be said to be meaningfully doing anything completely independently. For a much more detailed description regarding the limitations and alternatives to Bonferroni correction, consult the seminal paper Benjamini and Hochberg 1995.

Also, I blogged some time before about a short review that I'd written for Fly. The article is now freely available here. If you're interested in the technical stuff I've been up to, take a look.

The False Confidence of Replicability...

2009-12-08T22:41:00.003-05:00

This is the first in a couple of brief posts I've had on my mind about the subject of statistics-as-applied-to-research. I could have combined them into a single post, but having spent a few years in the blog-o-sphere, I've come to realize that most people don't have time to read long posts. Better to cut them up into easily digested chunks.

One of the first principles taught in science is the importance of having replicates in experiments. That is to say that you should do experiments more than once (and certainly more than twice) in order to make sure that the observed result wasn't simply a 'fluke' or the manifestation of some introduced error - usually human. This is all well and good, however, what's often glossed over is the fact that there are multiple kinds of replicates. Allow me to illustrate by example.

Imagine that you want to compare two populations of humans, say Norwegians and Japanese, in order to determine whether there are significant differences in average height between them. Let's also imagine that the instrument you have on hand to measure these differences is a piece of string, which you know from previous experience to be 1 meter long. One replicate you could perform would be to measure one randomly selected person from each population, over and over. This is called a technical replicate, and while this may seem rather pointless, it actually gives you an idea of the measurement error, or the variability among different measurements made with your instrument (remember, we're using a piece of string to estimate people's height, which may not be very precise).

While useful, doing such a thing would not give you much power to determine whether there are significant height differences between these two populations - our Norwegian may be unusually short, for instance. In order to obviate such a problem, and get a better estimate of average population parameters, you'd want to measure multiple people from each population (and probably sort them by biological sex). These are called biological replicates, and are generally considered to be the most important kind of replicates. They tell you something about the variability within species; something critically important in evolutionary studies¹. Many rejected manuscripts are soundly thrashed for assuming that their particular sample is 'typical' of a larger species without having demonstrated that this is the case empirically.

Now imagine that you complete this experiment, and find that Japanese are consistently taller (on average) than Norwegians. This result continues to hold as you increase your sample size, and thus your confidence in your findings increases.

Hold on a second! In turns out that some time after publishing your study, you find out that there's something funny about your rope. Though you didn't notice it at first, it appears that the rope tends to stretch out when it gets wet, thus whenever you measured Norwegians in the wet rainy weather that characterizes their country, your definition of a meter changed, biasing your measurements towards smaller numbers. On the other hand, the dryness of the same string in Japan had no such effect. Thus, while the experiments were highly replicable, they may have no biological meaning and instead result from systematic biases in the procedure.

I wrote this post because of an annoying sentence I read in an otherwise interesting book, Scroogenomics² (2009; Princeton University Press), by Joel Waldfogel. Basically, Waldfogel, an economist, implied that because the results of surveys administered to undergraduate students gave consistent results over multiple years, this means that the information obtained from these surveys is economically meaningful. Now without going into details (I'm planning a book club post about two of Waldfogel's books), or harping on the logic of inferring trends about US population level spending preferences from such a small, biased sample of people, I'll note that the results you obtain from surveys depends strongly on the questions you ask. Poor questions can give consistent-yet-meaningless (in terms of what you're interested in) results.

I'm not saying that the data presented in the book are wrong, but rather that we often have a tendency to become overconfident about results simply because some particular technique is highly reproducible. Unfortunately, it's only by studying the same phenomenon using different techniques (e.g., in situs coupled to Westerns) that we can reliably rule out systematic biases in a particular protocol - though this doesn't rule out the possibility of systematic biases having been introduced into the sample prior to the measurement. While this may all seem rather academic and tedious, both happen to be the province of science, and it's only by constant questioning of results that such biases are expunged.

¹Traits that are highly variable withing species often make poor candidates regarding inferences about directional selection - if the trait is so important, why is it so variable? It's not so simple however, when we realize that processes such as balancing selection may specifically put pressure on a population to maintain variability. The immune system is a classical example of a system that is under continuous selection and yet maintains high variability.

²The title of this book seems to have two readings. I believe it's intended to be read 'Scrooge-e-nomics' and not 'Screw-genomics'.

Rant: Platitudes...

2009-12-07T19:09:00.004-05:00

With the exception of the weekend involving an awesome midnight movie and some indoor rock-climbing with friends, last week was pretty shite. We discovered mites in one of our lab fly incubators, which threw the lab into automatic 'code red' lock-down mode, suspending all of our work for a couple of days. I actually spent one day, Wednesday, at work from 8:30 am until 11:40 pm - not fun at all. Different labs handle mites in different ways: Population geneticists and evolutionists are sometimes relatively lax about them (while certain species of mites prey on eggs, others simply eat the fungus off in the food), but classical geneticists tend to abhor them. Regardless, it pays to have clean stocks.

A dreaded mite. This isn't the exact same kind as that which infests Drosophila stocks, however, they look relatively similar. Mite are part of subphylum Chelicerata, which includes spiders, scorpions, and horseshoe crabs. Image cred here.

Such work time disruptions are both bad for blogging, and sanity, and thus I shall now rant.

Some people seem to find almost perverse pleasure in the saying, and/or reading of meaningless little catch-phrases. Often, such statements are presented in the form of timeless wisdom that, as far as I can tell, despite its supposed antiquity, serves absolutely no purpose whatever.

Consider the following: Imagine that while traveling, you asked a pedestrian for directions to a famous monument, say the Lincoln Memorial, to which he replied: "The destination is unimportant, it's the journey that matters. Take care friend," and then walked on his way. Would you find that satisfying? Would you suddenly brighten up and forget about what you were planning to do that day? Probably not (I'd say definitely not, but you meet the occasional oddball).

And yet time and time again, I've seen meaningless statements like these in framed pictures on people's walls. I've never understood these things, even when I was a little kid. Furthermore, I've come to believe that they exist solely to console people who are unable to deal with the reality of their lives. Unfortunately, I don't think anybody actually believes that they work.

This may sound harsh, but you need only think about it for a few seconds. Feeling lonely because you've moved away from friends or loved ones? Well, 'Home is where the heart is' after all. Try using that to console a homeless person. They'll probably reply that their heart is freezing under a torn blanket while they're begging for change on the corner Yonge and Bloor. Similarly, beauty may be in the eye of the beholder, but it would do you more good if it was in your face. And what in the hell does 'a penny saved is a penny earned' mean? I know what the idiom is supposed to mean, but seriously!

I have this dream of buying up insipid little frames from gift stores and filling them with memorable-yet-vacuous quotations from 80s movies. A frame containing the words 'Get to tha' choppa'', or 'It's game over man', or even 'Goonies never say die!' in flowing script would be just about as meaningful as any clichéd aphorism out there. And while it would be unlikely that I'd derive 'personal inspiration' (or whatever) from looking at these frames, at least I could obtain mirth, which would be far more useful in dealing with my problems than coming to the stunning realization that you get what you pay for or some similar platitude.

Book Club: The Republican Noise Machine...

2009-12-01T07:30:00.000-05:00

I've claimed a couple of times on this blog that I don't understand a lot of the media here in the States. I guess that's only partially true. I understand the 'logic' behind the talking heads and opinion-based 'news' - that is to say, the value in packaging news in such a way that it fits neatly into the pre-conceived biases of those you'd like to sell it to. I guess that what I'd really like to know is why this type of media seems to be so overwhelming in the USA.

David Brock's The Republican Noise Machine (RNM; 2004; Three Rivers Press) is a book that sets out to answer this question; and, as far as I can tell, does a pretty good job of it. Before discussing the book, I should say a few words about its controversial author. Brock is a former conservative columnist and author who was responsible for a somewhat famously relentless series of smear attacks on former President Bill Clinton during the 90s. However, towards the end of that decade, Brock claims to have had a change of heart, based partially on his own re-evaluation of the excesses of the charges laid against the Clintons¹, but perhaps more significantly because he decided to come out the closet and admit that he was gay. Brock began by writing a famous Esquire magazine article in 1997 titled 'Confessions of a Right-Wing Hit Man', which cost him his job at the conservative American Spectator, and followed this up with a full-length memoir, Blinded by the Right, which, while a bestseller, did not sit well with some members of the left. According to some reviews, it's difficult to trust a book whose purpose is to expose how much of a liar the author is.

The Republican Noise Machine, on the other hand, is not a memoir, but rather a well-written history of the economic and political pressures that shaped the media from the time of the Nixon administration to the present, and how those pressures led to the the he said/she said style of journalism that predominates the present discourse.

At the risk of oversimplification, the book lays out the following thesis. The controversial Republican nomination of Barry Goldwater for President in 1964, foreshadowed the birth of the modern American conservative movement. This is to say, the unification of traditional Republican values (small government, free-market economics, etc.) with moderate to extreme social conservatism. In the case of Goldwater, this social conservatism manifested itself as opposition to the civil rights act of 1964, but in the 70s and 80s, this would move more strongly in the direction of the so-called 'Religious Right'.

In the 1970s, several proponents of the new conservatism wrote extensively about how the media painted white conservatives in a negative light and were obviously 'liberally biased' - thus originating this common canard. These books, particularly Edith Efron's The News Twisters (1971), became quite influential among conservative circles during the Nixon administration, given how that President had a notorious, and some would argue deserved, dislike of the media. Then Vice-President Spiro Agnew's attacks on the 'liberal media' are legendary, spawning such well-remembered phrases as "pusillanimous pussyfooters", "nattering nabobs of negativism", and "hopeless, hysterical hypochondriacs of history".

The Nixon administration was responsible for initiating the long road towards modern deregulation of American media. In time, this changed the media-scape in at least 2 significant ways: 1) it removed provisions that prevented the media from informing the public only of news that supported a particular ideological agenda, and probably more importantly, 2) it removed anti-monopoly restrictions on media ownership, such that by the end of the 90s, almost all 'news' was owned by a handful of major networks. The consolidation of media power into the hands of a few individuals shifted the news towards being more about profits than integrity, but also, in the case of a few media barons such as Rupert Murdoch and Sun Myung Moon, allowed them to set up right-wind propaganda machines.

Now this is where it gets a bit complicated: Brock argues that conservatives are in some ways easier to market to than liberals. Modern conservatives have cultivated a 'package deal' of talking points and interests that reaches a large segment of their base. Liberals, on the other hand, are characterized by their diversity of viewpoints and lack of organization - Dawkins often refers to mobilizing atheists as 'herding cats'. Thus while conservatives do not make up an overwhelming majority of the population in the US, programming targeted at them tends to reach far higher proportion of their population than liberal shows would among liberals.

Thus, over time, a non-serendipitous combination of factors - politcal, economic, and social - pushed the center of the public discourse further and further towards the right, and this despite the actual center of the public opinion not having followed suit. Although RNM doesn't paint this shift out to be part of a grand 'conspiracy theory', it sometimes almost seems like one. Based on fairly extensively referenced quotations and documents, it's made very clear that some people have worked behind the scenes - sometimes in and around the government, but more often within the upper echelons of the media - to bring about a movement towards 'fairness' (i.e., always presenting both sides to every story, no matter how lopsided), and 'opinion journalism' or the process of conveniently editorializing all news such that it fits a particular agenda. This probably shouldn't be surprising given the extreme amount of money spent on right-wing 'think-tanks' and lobbying organizations when compared to any similar efforts from the left.

Anyways, the Republican Noise Machine is a really dense read that presents far too much information to summarize effectively in one blog post. It's well referenced, makes use of extensive quotations, and seems to have been generally much more well-received than Brock's controversial confessional memoir. I have to say that the book is also very well-written. It's obvious that the author isn't pandering to the 'lowest common denominator' and makes elegant use of sentence structure and flow that's absent from most books I read (which probably shouldn't be surprising since I read a lot of science books specifically targeted at the general public).

Regardless of the validity of the overall thesis (though in my limited experience in reading about the history of American politics, I'm inclined to trust that it's largely accurate), the book was quite illuminating in terms of it's exposition of a part of American culture with which I have no experience and very little, if any, contact. Brock's ultimate 'point' in writing the book is to argue that all competitive populist movements, free markets or democracy itself, require information symmetry. If one side of the debate controls the flow of information - either corporations or one political party - then citizens cannot make informed decisions. Despite their constant appeals to democracy and freedom, such information-controlling interests are no better than the totalitarian regimes they profess to hate. Food for thought.

¹If you're unfamiliar with the sheer number of preposterous allegations made by the extreme right fringe during the 90s, you should pick up one of Al Franken's books. The number of people the Arkansas police are said to have murdered at the direct command of their former Governor is quite shocking.

Work/Social/Home Balance...

2009-11-29T08:00:00.001-05:00

The difficulty associated with balancing work and life when doing a postdoc is notorious. One tends to spend so much time working and/or thinking about work, that simple chores tend to pile up unfinished. I certainly don't think that I'm working too hard (many people work harder than I, and I'm sure that as my project 'ramps up' so too will my work), but I have been doing a lot of social activities involving both getting to know fellow postdocs and exploring DC. It's very typical for me to leave for the lab at 7:30 in the morning, only to arrive back home at 11 pm.

However, my intent in this post is not to complain, but rather to air my thoughts about how I need to better 'balance' my work/social/home life. Meeting people and exploring the city are certainly a lot of fun (I'm going to the Museum of Modern Art today with some friends, for instance), however, they cannot continuously come at the expense of laundry, vacuuming, and preparing meals for the next day. That last one in particular gets to be rather expensive: during the busiest periods of my Ph.D., I often failed to cook food and purchased many meals on campus.

Here's a lame segue-way: One of the major impediments to spending a lot of time at home when moving to a new city is the lack of 'cozyness' associated with a new place. When I first began blogging at the beginning of my Ph.D., I lived in an empty attic with 1) a mattress on the floor, and 2) an IKEA fold-out chair. Picking up shitty furniture off of the street was worthy of a blog post. Thus in an attempt to increase my own desire to spend more time at home, and to improve that great feeling associated with vegging out in front of the TV, I have acquired a couch and love seat combo:

The one major piece of furniture that did not come with me to the US was a couch - I've been sitting on a Snuggie™ draped dining room chair for all of my TV watching up until this point. The act of moving to a new country is not without considerable expense, and thus it's taken until now for me to save up enough money to pick up a decent couch.

I've grown somewhat tired of living the 'student life', and thus I actually wanted to pick up something that looked half-decent and presentable. Plus, chocolate brown suede hides dirt quite well... As you can see, my next purchase definitely needs to be a coffee table.

So if parking my butt on the couch in order to read papers, write blog posts, or play the occasional video game makes me spend more quality time at home, then this will be money well-spent.

So a Turkey, a Duck, and a Chicken walk into an oven1...

2009-11-27T22:29:00.014-05:00

Yesterday was my first American Thanksgiving. Given the 'specialness' of the occasion, I decided that a simple turkey would not suffice. We eat Turkeys on Thanksgiving in Canada, a day that's rather meaningless in our holiday pantheon. Thanksgiving here in the States is a much bigger deal, and thus deserved a much bigger feast! Thus, a buddy from the lab and I decided to make a Turducken:

A turducken consists of a turkey, that is stuffed with a duck, that is itself stuffed with a chicken. In order to pull off such a poultr-a-polcalypse, all three birds must have their rib cages and backbones surgically removed. This took a lot of time.

Here you can see all three de-boned bird carcasses. The two cooks were both evolutionary biologists, therefore we spent a bit of time remarking on the various homologies of avian form during our dissection.

Now, the big 'trick' to the turducken involves the fact that each layer of poultry is separated by a different layer of stuffing. Counting the stuffing that's in the central chicken, that's three separate stuffings that need to be made: a Southern cornbread stuffing, a traditional bread stuffing, and a cranberry stuffing made by mixing the previous two.

The entire monstrosity has to be pinched closed using skewers, and then flipped over in the pan.

It is then coated in browning sauce, and seasoned appropriately, then put into a pre-heated oven for 4 hours, with basting at regular intervals.

The finished masterpiece looks like this.

Give thanks to the turducken! Note the other excellent Thanksgiving fixings, such as a scrumptious green bean casserole (something very traditional here in the US, but that I'd never tried before) and mashed potatoes.

The final product ends up tasting much like a regular turkey with added pizazz. In particular, the duck layer is especially tasty (duck always is), and the three different stuffings certainly create a symphony of flavor that would otherwise be absent from a more traditional meal. This being said however, it's a huge amount of preparation - most recipes rightly recommend that the stuffings be prepared the night before cooking - so it's not something you'd want to eat often. Regardless, I'm quite proud that it turned out so well in the first attempt, and I'd certainly like to make such a birdstravaganza again.

¹An alternate title for this post would have been: Highlander 4: The Turduckening.

Book Club: The Black Hole Wars...

2009-11-26T09:22:00.003-05:00

A couple of weeks ago I was browsing the science section at the local Barnes & Noble when I suddenly felt that I fancied a bit of astrophysics. Reading books about biology is almost endlessly entertaining, but every once in a while, it's nice to see what the other sciences are up to.

Thus I picked up Leonard Susskind's The Black Hole War (BHW; 2008; Back Bay Books), which chronicles his ~20 year struggle to convince the physics community that a conjecture made by Stephen Hawking in the early '80s - that information entering a black hole is lost to the universe forever - was incorrect. This 'war' was a bit esoteric as even the author admits, but it did involve something a lot more fundamental than a simple question about what happens beyond the horizon of a black hole.

According to the author, the stakes were the following: One of the most fundamental concepts of all of physics, the law of conservation of information, states that information (in the form of entropy of a system) can never be destroyed. Physics had shown that anything crossing the horizon of a black hole was lost to the outside universe, however, Hawking had discovered that black holes evaporate. Thus, the question was: what happens to the information sequestered within a black hole? If, as Hawking suggested, information entering a black hole is lost to the universe forever upon evaporation, then the most fundamental underpinnings of physics, the laws of thermodynamics, were no longer absolute 'laws'. According to the author, only a few physicists seemed concerned with this revelation, probably because it involved such a special case that they felt it didn't really impact their work.

I'm not going to bother trying to explain the details of the physics, but over a period of two decades, Susskind and the Nobel Laureate, Gerard t'Hooft, succeeded in persuading the physics community that this was an issue deserving serious attention. The issue was finally resolved when, using the complex mathematics of string theory, it was shown that the information contained within a black hole could be radiated to the outside via quantum mechanical processes during its evaporation. Very heady stuff.

I found the book quite interesting simply because it describes a 'war' among academics, which, while tempers occasionally flared and egos were bruised, remained quite cordial over the entire interval. These disagreements over fundamental concepts of physics essentially occurred among people that consider one another 'friends'. Some of what the author commits to the page could be taken as somewhat insulting - Stephen Hawking is portrayed as a somewhat egotistical attention seeker, and we're constantly reminded of his stubbornness in accepting that his pet theory about the loss of information was on the verge of being disproven. However, it is a far cry from the ridiculous arguments that erupt among say, political pundits, over far more trivial issues.

I do have to admit though, that the book lost me on some of the finer details of the underlying physics. The author spends a considerable amount of time going into detail about the classical physics calculations relating to black holes, which is extremely helpful. Unfortunately, once we enter the realms of quantum mechanics, and especially string theory, we're treated to a lot more 'you'll have to take my word for it' type exposure. As a scientist of a somewhat classical bent (i.e., testable hypotheses define science), I must admit that I have a deep-seated distrust of string theory, firstly because it appears to be untestable, but secondly because most of the physics books I've read completely gloss over its principles and ask the reader to take the authors at their word. The one notable exception to this is Lee Smolin's The Trouble with Physics, which did a good job of explaining string theory, though not favorably.

Regardless, the book is both well written and entertaining, and while it may not have the same impact on non-physicists that it would were it being read by someone more familiar with the source material, it does present a situation where the march of scientific progress evidently worked properly. Many such disagreements in science, at least from my perspective, do boil over into impassioned emotional arguments rather than reasoned debate, and it's nice to read about a situation where empiricism took the day.

Demystifying phenotypes: the comparative genomics of evo-devo…

2009-11-22T23:49:00.004-05:00

I said that I’d blog about the short review article that I wrote for the new Drosophila journal, Fly. Now that I'm back from my weekend spent convocating in Canada (more on that in a future post), here it is. Essentially, my Ph.D. supervisor and I were invited to write this article because of the (small) buzz generated by a manuscript we published in BMC Biology last summer (Artieri et al. 2009. BMC Biology 7:42). These invited commentaries, called ‘Extra Views’ by Fly, give you 1,000 words plus a figure in order to talk about a paper you’ve recently published, and contextualize it within its field. I’ve already blogged about the article itself, so here I’ll focus on the latter.

Evo-devo, or the attempt to unite evolutionary and developmental biology is a fascinating field; however, I’d argue that while it’s certainly easy to understand how it is related to developmental biology – many of its tools and techniques are those of developmental genetics – it’s evolutionary component is somewhat independent of ‘mainstream’ evolutionary biology.

I’ll be a bit more specific in a moment, but first I’d like to explain why this is. At the turn of the 20th century, there was a fairly significant split between the fields of evolutionary and developmental biology. A lot of this stemmed from an over-reliance of developmental evolutionists during the day, notably Ernst Haeckel, on 'just-so stories', lacking any type of rigorous empirical foundation. Experimental embryology, on the other hand, was in the process of making significant developments and discoveries, and its practitioners became disillusioned with the descriptive work coming out of evolution.

However, the ‘deal’ was sealed between evolution and development during the ‘modern synthesis’ of Darwinian Evolution and Mendelian Genetics, one of the offshoots of which is the field known as population genetics (pop gen). Pop gen subsumed all of development into the abstract value of ‘fitness’, which turned a lot of developmental biologists off. To this day, I still read papers from developmental biologists predicting the imminent demise of the entire field of pop gen.

The synthesis of evo-devo, which began in the late 1970s , largely ignored any of the insights derived from population genetics. At the cost of hyperbole, it’s somewhat like re-inventing the wheel, and in a strange twist of fate, some evo-devo papers are creating the very just-so stories developmental biologists were originally dissatisfied with.

For instance, very few, if any, evo-devo papers even discuss the idea of within-species variation. In fact, most interest in the field of evo-devo involves comparisons between taxa that are so distantly related (e.g., HOX gene conservation between flies, nematodes, and humans) that there’s pretty much no way to predict the selective ‘forces’ or situations that led to current phenotypes. It’s one thing to infer that changes in this or that gene have led to changes in segmentation patterns of distantly related arthropod lineages, but it’s another thing entirely to test how these changes came about.

In many ways, the language of these extremely distant species comparisons is almost ‘Goldschmidtian’ in that, in the absence of understanding how selective forces shape variation into alternative body plans and morphologies, we subconsciously assume that such changes were saltatory, occurring in a single mutational jump (sometimes such assumptions are not subconscious at all). While rapid evolution is a possibility, some of these theories are strongly in conflict with what we’ve gleaned from decades of study of evolutionary biology.

Thus, the major thrust of this short article is to echo the sentiments of previous publications (e.g., Johnson and Porter 2001) and argue that population genetics has much to contribute to evo-devo synthesis by studying divergence in developmental patterns between closely related species, allowing us to understand the selective forces and ecological pressures leading to altered phenotypes.

It’s unfortunate that there still remains such a divide between these two biologies. Though I spent my Ph.D. doing the evolution ‘thing’, I’m moving a lot further into developmental biology territory with my postdoc, and I’ve already found that we have much to teach one another.

Conservative American Journalism...

2009-11-19T08:02:00.002-05:00

I've blogged about how I find the media here in the States a bit difficult to understand; although I'm sure there are alternatives, the papers I've come across firmly support one political party or the other. I just wanted to post a link to The Washington Examiner's editorial from yesterday:

'Stop bowing, stop apologizing'.

This is Washington, D.C.'s free conservative paper, and stuff like this runs every single day. It's not like I disagree with everything in the editorial, but there seems to be more than a tinge of xenophobic nationalism running through it.

Thoughts?

Rant: Attack Critcism...

2009-11-17T23:00:00.001-05:00

This post was supposed to be about the review paper on the 'comparative genomics of evo-devo' that I recently wrote for Fly, however, I've been working long postdoc hours and getting home quite late, so that'll have to wait until next time. Despite my rather positive week (I got the good news that another review that I've co-written was also accepted), I feel the need to rant.

I've already written about scientific criticism, a topic upon which I don't feel that scientists really take enough time to think about. My thesis is as follows: I think that as scientists, we become so accustomed to being constantly criticized about our work and questioned to death about every little detail, that we forget that junior scientists, or Darwin forbid, the general public, are not used to experiencing such a phenomenon. I'm sorry to say but, if you take a step back during some of these criticism sessions, I think that you'll realize that scientists often come off looking like jerks.

I once sat through a presentation given by an undergraduate student who was thinking about doing an M.Sc. in one of my previous labs. Said student spoke about the work that they were doing during their honors thesis, and, as is often the case, the project was fairly simple and the presentation needed some work - that's the point of learning, of course. However, one of the attendees tore this kid apart, literally asking the student why in the heck they'd ever thought that such a project could actually work. Did any of us really think that that this student had designed the project all by themselves? Would it even matter in the first place? No one expects an undergraduate designed project to win a Nobel prize.

Actually, there's something specific about this kind of criticism that really bugs me, and that's when the criticism is completely non-constructive. It's easy to point out all of the flaws in a particular technique or analysis, but it's often much more difficult to figure out how to fix them.

That's another issue to this as well havignng to do with pointing out flaws in general. No project is ever going to be perfect. There will always be assumptions, caveats, and aspects of the experiment that cannot be accounted for. In some cases such problems completely undermine the original purpose of the work and are legitimate reasons to abandon the project in the first place; however, often they're simply part of the ongoing progress towards a better understanding of the world. I'm much more interested in making sure that people understand the limitations of their work and take into account the assumptions and caveats associated with their analyses than I am with making sure that everything they do is absolutely perfect. The latter is impossible and thus a complete waste of time.

This may seem obvious, but I see these types of unavoidable criticisms levied time and time again. In fact, I've taken classes wherein I've lost marks for not adding petty, useless criticisms to my review of a manuscript (I have a particular hatred of the over-used 'the authors should have also done experiments X,Y, and Z' on a paper that obviously constitutes years worth of work).

I guess my rant for today essentially boils down to the idea that I think that we scientists should attempt to use more common sense when it comes to criticism (some folks obviously do this already). Younger scientists should probably be eased into the scathing criticism, and we should probably hold back when it comes to correcting laypeople's mistakes and lack of understanding. However, it would probably pay all of us to attempt to make our criticisms more constructive. Everyone knows how frustrating it is to have reviewers casually dismiss your work - sometimes for good reason and sometimes having obviously not actually read your paper. I think that in many cases, we become so used to doling out and receiving criticism that we fail to think about its effect on others. In fact, I know that I'm guilty of this myself...

Hitting the Ground Running...

2009-11-11T21:33:00.002-05:00

I've been busy. On Monday I had my first lab meeting presentation since beginning as a postdoc here at the NIH. I have to admit that I faced this task with a bit of trepidation as I've never had 2.5 hour 'informal'¹ style lab meeting presentations before. We spend a lot of time on the details, and everyone contributes opinions about the relative merits of the project being presented. I think that my talk went over relatively well, and thus the project that I've proposed to undertake is ready to go.

It's a strange feeling, starting all over again after so many years. It's a strange sort of paradox in our field in that, as you advance in your career, you keep going through new cycles of being the junior member in a particular group. For instance, when I was finishing up my Ph.D., I'd built up a cachet of seniority in the lab - and among friends and fellows - only to drop back to the status of the 'new guy' in a new lab. However, this paradox only carries so far: I may be the 'new guy', but people speak to me in a manner that befits my experience. No matter how 'fresh' a postdoc you are, people care about your opinions, something that is not always the case when you're a new graduate student...

The other aspect to the newness is starting out on a new project. There's a definite security to having a pile of data and a few publications beneath your feet. Whenever you begin something new, you couple the excitement of learning new things about what it is you're studying to trepidation about whether or not your project is going to work. I don't think that my project is likely to fail, but it will certainly have its share of challenges, and all projects are like battle-plans: they rarely survive their encounter with reality unscathed. To quote the great pulp philosopher Yogi Berra: "In theory there is no difference between theory and practice. In practice there is."

Regardless, I'm quite excited about what I'm doing. During the course of my Ph.D., I became interested in the field of evolutionary developmental biology, or 'evo-devo' for short, a subject that's become somewhat of cultural darling in recent years. Big evo-devo papers come out continuously, and topics in this field tend to headline major conferences. While I think that the results coming out of the field are remarkable and exciting, I also think that there's been a lack of contribution from the 'evolution' side of the inter-disciplinary synthesis. Almost all of the work out of evo-devo has come from developmental biologists, and I think that evolutionary biologists, and in particular population geneticists and speciation geneticists have a lot to offer as well (which is part of what I plan to do in my new lab).

I happily found out that a mini-review I wrote last month was accepted for publication in the January issue of the new Drosophila journal Fly. This short piece covers a lot of my thoughts on how evolutionary biology can contribute to evo-devo, so I'll blog about it in a future post.

¹An 'informal' presentation (a.k.a., a 'chalk-talk') is one where the audience is free to interrupt the presenter with questions for clarification. This is opposed to a 'formal' presentation wherein the present goes through their talk and is then questioned. Obviously all lab meetings are somewhat informal; however, our lab covers roughly 12 slides in 2 hours, so they're really informal!

Book Club: Natural Acts...

2009-11-05T23:00:00.000-05:00

A friend once suggested to me that one of the big scientific associations, say the AAAS or the Royal Society, should place its 'stamp of approval' on all books that are legitimately scientific. Then, he reasoned, non-scientists wouldn't have to walk into a Chapters or Barnes & Noble science section wondering which books are 'real' science, and which ones are written by the Discovery Institute or Deepak Chopra.

Setting aside arguments about the potential for censorship or the logistics of setting up an office of people whose job it would be to read and vet these books, this would place books such as David Quammen's Natural Acts (NA; 2008; Norton), a collection of short pieces about nature, in a very awkward position. While there's nothing wrong with the information presented within the book, it's not science - in the same sense that almost everything presented on 'edutainment' channels (e.g., Discovery, The Learning Channel, etc.) isn't science. But back to that in a moment.

Quammen is a good writer, especially if you like the style of writing that appears in highbrow magazines - you know, the stories that begin in the middle and follow a Tarantino-esque non-linear plot that emphasizes the characters and atmosphere as much as the subject of the article itself? He's not a trained scientist, which is something that he admits in the introduction to the book, but he does quite a good job - as far as I can tell from the stories themselves - of getting the facts straight. Quammen does seem to care about making sure that the material is presented properly, and he does a better job than many at making the subjects interesting.

Speaking of subjects, the book's chapters cover a large range of topics without any real rhyme or reason. Some involve detailed descriptions of particular animals, such as mosquitoes or bats, while others are dedicated to wild and interesting people pursuing field work, such as Dr. J. Michael Fay, who spent 15 months walking a 1,200 mile transect of the African continent. Finally, other chapters are more like personal travel diaries involving interesting nature reserves. People who love descriptions of the wild and stories about foreign (or domestic) adventures should love it. However, as I said before, it's not science.

Science is not simply the dry presentation of facts. Rather, it is the attempt to test our interpretation of these facts. I'm certainly biased, but it's not enough for me to read that this species does X. Furthermore it's not sufficient for me to learn why X is done: I'd also like to know how we came to the conclusion that this species does X because of Y. Perhaps the use of Xs and Ys makes this more convoluted than I intended - the point is that science explains things and in doing so explains how we got this knowledge.

I can't fault Natural Acts for not going into more depth as this was obviously not its intention. However, with the exception of the extensive, and interesting, travel-log pieces at the end, I really could get any of these stories out of a non-science magazine. It's probably a personal bias, but I suppose that when I bother to read a book about biology, I'm looking for something with a little more detail than what I'd get on a typical Discovery Channel show.

I really hate to go back to him all the time, but I do think that Stephen Jay Gould was the master of taking random 'factoids' and using them in order to actually teach his readership about some of the more complex details in the fields of paleontology and evolutionary biology. It's not that every author needs to do exactly what Gould did, but I guess that I am looking for a bit more that 'golly-gee would you look at that!' type stories about how amazing nature is. I know how amazing nature is, now I want to understand why it's so amazing.

Rant: Literature...

2009-11-03T21:33:00.003-05:00

My book club post about David Quammen's Natural Acts is already written, and I was planning on posting it this evening. However, given my recent, awful weekend involving both swine flu and a very, very serious toe stubbing, I felt the need to rant.

When I was a in high school, I was more into English literature than was probably sensible for a teenage male. I really enjoyed Shakespeare, and while I wasn't a huge fan of the Victorian era, I did have quite a passion for early 20th century stuff like The Great Gatsby and all the myriad products of the distopian futurism age (1984, Brave New World, Anthem, etc.). There was quite a long period during which I seriously considered majoring in English. This was entirely, irrevocably destroyed during the very first English class I took in university.

Now I, as much as anyone, believe that writing, whether prose or poetic verse, is an art filled with symbolism. Alice in Wonderland may very well be an allegory for Lewis Carroll's many opium binges, and obviously most poems are metaphors for a great many aspects of the human 'condition'... or whatever. However, I simply refuse to believe, without some supporting evidence, that prolific authors have had time to imbue every single word of every single sentence they've ever written with multiple alternate meanings.

Seriously? The aged professor in this English class spent 8 months trying to convince me that every sentence in the 6 novels, 2 plays, and the giant anthology of poetry that we read was specifically constructed, word-by-word, in order to symbolize some specific facet of the universe. Metaphors and multiple meanings in the works of Lord Byron, Yeats, and Hemingway? Of course! But every single word being able to be interpreted in this specific way? Don't you think that sometimes these people were just, I don't know, trying to construct sentences?!?!?!

If you pour over the Bible trying to find secret meaning in every single syllable, people will probably call you insane. But do the same for Dickens and all of a sudden you're an English lit major! This may sound harsh, but I believe that a little skepticism is in order here. This could easily be resolved by a double-blind study wherein a poet makes notes of the actual meaning(s) behind his/her verses, followed by a reader trying to decipher those meanings. I'm willing to bet that there's a correlation between the number of decades that an author has been dead and the number of meanings that have been attributed to their work, though I'm not sure how a study could be designed to test that one.

Where did this all come from, you ask? Well, I've been reading some of the work of Franz Kafka - an oddball to be sure, but something that I felt I should be passingly acquainted with. The collection that I have, like all such classical compilations, begins with an introduction to the pieces wherein, like all such introductions, we're told that the author brilliantly sought to juxtapose this and that via this device or that metaphor, blah, blah, blah. Maybe he did. Or maybe Kafka sat down and wrote some interesting stories that meant something important to him, and we're now picking his tales apart and assigning arbitrary meaning to every single passage?

Brilliant minds are likely capable of producing brilliant literary works endowed with layers of metaphor, allegory, simile, and parable. However, I sometimes get the same feeling about these literary analyses that I get when I hear stoners discussing the lyrics to their favorite band's songs: did you ever think that sometimes the words were put there simply because they sound good together?

P.S. I still enjoy literature, and I don't think that all English profs are crazy! But man, sometimes those literary analyses are pretty wild...

Field Work...

2009-11-02T10:29:00.003-05:00

While laid up in bed here in my apartment, I've almost finished reading through David Quammen's new edition of Natural Acts, a collection of his essays about nature originally published in 1985, but reissued in 2008 with more recent material. I'll probably write up a book club about Natural Acts. In this post, however, I'd rather talk about a subject that comes out quite a bit in the course of the book: some people's fascination with field biology.

Now, admittedly, field biology makes for better public-targeted stories in magazines or on the National Geographic or Discovery Channels. There's something visceral about seeing nature 'in action' rather than in the lab. Well for some people, at least. I think that the underlying issue here isn't really nature vs. the lab, but really the abstract vs. the tangible. It's difficult to publicize the importance of individual sub-cellular components to people who have no experience with - or understanding of - them. That being said, I would point to Stephen Jay Gould as a popular science writer who was usually able to make any part of of the study of natural history relevant to the broader picture.

Lay people aside, there are also those actual biologists who have a penchant for fieldwork - I believe that TheBrummell is one of them. It's rather strange that I've never really had that desire. In fact, it's not until recently that I've actually become interested in 'Nature' more generally. It didn't bother me that during an entire 2 year long M.Sc., ostensibly spent working on the Atlantic salmon, Salmo salar, I did not see a single salmon in association with the lab (I did, however, eat an Artic charr towards the end of my degree).

I think that the desire to do fieldwork has a lot to do with the reasons that we got involved in science in the first place. Most biologists were likely pushed towards this field due to a love of some some stupid-looking endangered species or other (my first girlfriend in undergrad was completely obsessed with Manatees...), or because they just plain-ol' love hugging trees. Obviously I kid, except about how dumb Manatees are, but I think you get my point. I on the other hand, have always been interested in genetics, later switching to genomics. I swear that this interest dawned in me during my childhood obsession with the Teenage Mutant Ninja Turtles and the X-men, and my subsequent upsetting discovery that their definitions of 'mutation' were wildly heterodox by scientific standards. A more appropriate title for the former of my obsessions may have been Cancer Turtles - Age Notwithstanding.

Back to the fieldwork thing: Quammen's book documents numerous cases of people who seem to enjoy spending huge amounts of time alone in rather inhospitable places. Well, inhospitable to humans, at least. Don't these people have... umm, needs? Call me a slave to technology, but I'd probably go nuts if I had to spend a year isolated from electronics. I'd also like to consider myself a 'people-person' in that I don't enjoy spending long periods of time alone (hence why the swine flu is driving me crazy!!!). Perhaps it takes a certain type of personality to fly up to some dog-forsaken island up in the Canadian North and collect 'samples' whilst proudly growing a 'field beard'.

I'll admit that I've become much more interested in the organisms whose genomes I have studied. At the beginning of my scientific career, I didn't care about them beyond the As,Cs,Ts, and Gs that appeared on my screen. So I suppose that exposure to the general field of biology is having some sort of effect. But when it comes to fieldwork, I just don't know. I don't think I could be away from civilization for an extended period of time. I guess I'm just not cut out for it.

Brains...

2009-10-30T19:50:00.003-04:00

Via a cruel twist of fate, it turns out that I have likely contracted the dreaded 'swine flu'. My boss had it last week, and some people close to other folks in the lab have gotten it - now I feel awful as well. Great. My digital thermometer currently reads 101.4°F, which is apparently 'bad' (according to the pamphlet that came with the device). I hurt everywhere, for some reason especially in my coccyx, and I believe I'm on the verge of fever induced delirium. Now, the H1N1 isn't supposed to be a danger to strapping young late-20s lads such as myself; however, I think we can all admit to each other that I'm not going to pull through this. I've read the comics and watched the movies - aches, pains, fevers, chills - they're only the first wave of symptoms. You see dear reader, I've come to terms with the fact that I'm becoming a zombie.

Chances are good that you will soon see me ~~shambling~~ walking by on the street. Furthermore, given my well known propensity for ignoring the world in order to concentrate on the sweet sounds of 80s era heavy metal emanating from my iPod, you'll probably mistake the vacant, glassy look in my eyes as being normal. Perhaps you'll approach, wanting to strike up a conversation about nerdery, or science. However, the reply you will receive should immediately alert you to what's going on:

"B...R...A...I...NS..."

This is your cue to hightail it out of my vicinity. I've heard all sorts of people talk about their own personal zombie apocalypse survival plans. Hope is a powerful thing, even if obviously futile. As we all know, we zombies may be slow, but we're relentless, and it only takes one scratch (or evening of unprotected sex) to add your heroic-ass to our numbers. Instead, try to think of the loved ones you should be spending time with before you're all eventually eaten.

Despite the obvious zombifying pandemic sweeping the globe, I'll admit that I haven't yet caught site of the shambling horde myself. I assume that this is the result of the plague having a reanimating effect on only a small number of its infectees. We're growing in numbers until we'll suddenly burst out onto the street like a terrifying pride parade: We're dead and we're not going anywhere... and we're going to eat you!

"Carlo," you may ask, "why not take matters into your own hands and end your torment now, while you've still have control of yourself." In a kinder world, such a suggestion would have merit. However, I've seen those films too, and all I'd do is create an uglier zombie. Only the foolish could assume that eternal slumber offers respite from the shambling horde: we were dead to begin with for Pete's sake!

Regardless, I'm lying in bed, slowly typing at my PC, resolved to meet my fate - if not standing up, then at least with my eyes open. Thoughts geti... ng mu...dled, han.d..s hea...vy...

"B...R...A...I...NS..."

P.S. This post is in no way intended to make light of the toll that the H1N1 virus has already taken. Rather, I'm using humor to not focus on my own suffering!

Book Club: Tears of the Cheetah...

2009-10-29T23:30:00.001-04:00

It's like this. I wanna blog, I really do. I mean, I'm actually thinking of blogging about my own field (not my own work of course) - you know, telling the peeps out there about evolutionary developmental biology and my thoughts about it. But here's the problem: As compared to how things were for a good part of my Ph.D., my schedule here is totally out of whack. I'm getting home from the lab no earlier than 7 pm, and by the time I've cooked food and taken care of the things I need to take care of, it's usually around 9. That's a pretty late hour to begin thinking about the intricacies of science and, to be honest, I need to unwind. We'll see how things go - if I want to blog about science, maybe I could take notes about good blog post ideas while I'm reading the stacks of papers I've been pouring over lately? At least the project is coalescing much more rapidly than my Ph.D. did!

So let's take it easy tonight. I'm going to talk about a book I just finished: Tears of the Cheetah by Stephen J. O'Brian (ToC; 2003; St. Martin's Press). I've wanted to read this book for a while, but have refrained from doing so on account of some people whom I respect having told me that it wouldn't be worth my time. Unfortunately, I have to admit that they were at least partially correct.

ToC is a strange beast. On the one hand, it's a highly entertaining collection of tales involving ecological mysteries that were solved using molecular biology. This is significant in and of itself, because I've read a lot of popular books about science, and few of them go into any details about molecular evolution (I'm not sure that molecular work is a particularly complex field, however, it does require a certain amount of background knowledge about the basics of cellular biology in order to wade through its jargon). On the other hand, the book chooses a very curious middle ground between technical presentation for the specialist and sufficient explanation for the lay-person. I don't think it really satisfies either.

As I am want to say in casual conversation, 'here's the thing': I'm sure that many a layperson would read ToC and tell me that they understood it just fine. Unfortunately, I'd have a hard time believing them, because I could easily pick out parts of the book where people unfamiliar with fairly complex concepts of population genetics would be led astray. For example, a large portion of the book deals with the problem of inbreeding depression resulting from small population sizes of endangered mammals. Inbreeding depression, or the reduction in fitness caused by the increase in frequency of exposed recessive lethals as well as the loss of genomic diversity (which can increase the likelihood of parasite invasion), is well explained and presented in the book, and by the end of the first few chapters the reader is convinced that increasing the population sizes of endangered species is critical to maintaining these species (amazingly, some wrong-headed conservationists believe that it is sufficient to maintain the small existing populations). However, later in the book, we're suddenly told that species having too large population sizes is also bad because of the concept of genetic load. This isn't really correct, and genetic load is a much more complicated concept, from a theoretical standpoint, than is inbreeding depression. It depends on more factors, and really is more of a conceptual device used to explain a particular phenomenon: the difference between the actual mean population fitness and the theoretical fitness that would exist if all individuals had the fittest genotype.

The point is that, especially in the second half of the book, the author begins to delve a lot more deeply into the specific details of molecular tests and protocols. However, these molecular concepts become increasingly complex and detailed whereas the explanations become more cursory. I suppose it could be argued that there's really not a lot that ToC could have done: these concepts are complicated, and had to be presented somewhere. However, presenting concepts clearly and completely is part-and-parcel of scientific communication - it's not particularly helpful to public understanding if you gloss over the details. It's the intricacies of the techniques themselves that actually make up the science; just presenting the results is what the Discovery Network does.

So I guess I'd recommend Tears of the Cheetah to the rare people who have an interest in how molecular biology can aid in studies of ecology. Folks trained in science will probably enjoy many of the details of the work, however, while the book may be interesting to laypeople, I'm not sure if it's a good way to introduce them to the concepts it deals with. For that, I'd still recommend Dawkin's The Ancestor's Tale, or Carroll's The Making of the Fittest.

Peddling Woo...

2009-10-24T21:01:00.002-04:00

Sorry 'bout the lack of posts, but I haven't been 'round the PC much whilst the American odyssey continues. This week I was subjected to two separate physical examinations: one required by my employer and another by my new MD/health insurance provider because I am a new patient. Curiously, both medical doctors tried to peddle 'woo' to me - not just 'I'm a scientist and know that this doesn't work' woo, rather I'm talking whacked-out crazy garbage.

On Monday, my new doctor advertised the benefits of Laser Acupunture. LASER ACUPUNCTURE. From life123.com:

Laser acupuncture treatments are the latest approach to the many types of acupuncture. It was only a matter of time before the light therapy and technology of lasers brought acupuncture and laser use together. The results of this process have been lauded as formidable.

All forms of acupuncture stimulate specific points on the body as an effort to redirect chi (life energy) flow through the meridians of the body. The premise behind acupuncture is that the stimulation of these points will open up the channels of the body, encouraging the proper flow of energy, thereby stimulating the body’s innate ability to heal itself and to remain healthy. This stimulation has long been provided by tiny, thin needles, cupping, moxibustion and, now, through intense, low-level light lasers. These lasers stimulate the same points with light that a needle would. Needles are still used in laser therapy, but they are only placed on the stimulation points, not inserted into the skin.

I especially like the sentence about how it was 'only a matter of time' before acupuncture and lasers came together. If you'd care to, you can read this paper, wherein it's argued that laser acupuncture IS, in fact, traditional Chinese medicine. A buddy of mine and I had a rowdy laugh about how Confucius had actually invented Laser Tag™, in 500 B.C., but that it had been abandoned by the Emperor because it was more effective to actually kill people rather than have elaborate mock battles wearing stupid vests and helmets.

Laser Acupuncture!!! Anyways, I wasn't interested in that (nor do I think it's covered by my HMO), so I went my merry way with a prescription for actual medication.

During my second physical, the doctor asked me if I'd considered not taking drugs for various ailments, and try homeopathy instead. I was like, 'um... no'. Then she went on to point out that she knows that there are many people who don't 'believe' that ~~water~~ homeopathy works, but that she'd seen a homeopath herself, who had totally relieved her symptoms. I replied that the placebo effect was fairly remarkable. She 'agreed' by making some vague comment about the amazing ability of the mind to heal the body¹. Great. Is evidence based medicine just like, one facet of the overall medical curriculum or something?

I realize that a sample size of 2 is far too small to make sweeping generalizations about the medical profession, but it is rather disturbing that I was peddled woo twice in one week!

¹Don't get me wrong, there's a well documented relationship between mental, emotional, and stress states and patient's recovery ability, but I think we know what I'm talking about here. Relaxation techniques and 250 times diluted cow urine aren't going to cure lymphoma.

'Two-Tiered Science' and Research Interests...

2009-10-19T08:30:00.000-04:00

A friend of mine summed up the benefits of a career in academia by pointing out that it's one of the few ways that you can be (modestly) paid to learn. I'm still learning a lot, which should be obvious, because science continues to learn.

One of the the things that I've learned is that labs with access to expensive resources and large grants are able address some questions that are outside of the ability of typical, good-ol' NSERC-funded academic labs. I'm not referring to the debate as to whether more money produces 'better science', but rather simply to the observation that certain life-science technologies have seen tremendous improvements in recent years, opening entirely new avenues of research. So long as you can afford them.

Take genomic sequencing, for example. 10 years ago, people were working on perfecting Sanger sequencing, the standard method that had been available since the mid-70s. The last few years have seen the emergence of 'next-generation' sequencing technologies, which are mind-bendingly more efficient than what was available before. A single Illumina (Solexa) sequencing run can generate 56 gigabases of genomic reads, which means that sequencing whole-genomes - something that made headlines a decade ago - is now completely trivial¹. This depth-of-coverage is so good, in fact, that you can measure gene expression levels by direct RNA sequencing: the number of reads mapping to a given transcript (corrected for its length) is directly proportional to the abundance of the transcript in the cell. This technique is very precise, and can be calibrated to give estimates of the actual number of RNA molecules in the cell; unlike microarrays, which are used to measure relative expression. Microarrays will likely become a thing of the past.

The point I'm making is that, while amazing, these technologies require dedicated facilities and cost a fair amount of coin - though the price continues to decrease. There are some labs that have access to this stuff, and some that don't. Given that next-gen sequencing has been shown to be more accurate than microarrays (Marioni et al. 2008), it's already getting to the point where it's more difficult to publish microarray-based studies. As always, there are 'haves' and 'have-nots', I suppose. I don't quite know how to feel about that yet.

However, let me switch gears into something else I've learned that is somewhat related. Whenever you're writing a grant/scholarship proposal, you've gotta find ways to make your research 'sexy', and to convince the reviewers that what you're doing is going to provide information that will be of interest and use to the scientific community as a whole. I've found myself, in the past, leaning heavily on concepts such as the novelty and scope of my work. I think that I'm turning a bit of a new leaf on this one. I've been convinced that it's much better to argue for the biological interest and importance to the community of the work. Essentially, what unanswered scientific conundrum are you seeking to address, and how will your proposal generate the data required to tackle said issue?

In a way, I think that this relates somewhat to the 'have-not' labs. Having access to technology or resources that allow you to do something that no one has ever done (see above) is great, but the sole fact that you're doing something new or that it's bigger than previous studies is kind-of a scientific logical fallacy: it doesn't automatically mean that your work will actually produce anything valuable. The fact that we can now sequence any old genome isn't as compelling as the good reasons one should provide as to why we should sequence any particular genome.

I've seen, and probably contributed to, a lot of proposals that seemed to rely entirely on big numbers and impressive figures to woo audiences, without ever really addressing the ultimate point of the work. Having moved into a 'have' lab, the mere fact that this amazing technology is available has somewhat lost its luster - it's what we do with it that matters. My continued education has brought me to the following conclusion: I think that the arrival of the 'post-genomics era' should also signal the commencement of the 'post-gee-whiz era', wherein the simple fact that we're doing something that's beyond the scope of what could be done before is not sufficient scientific justification for doing it.

¹Assembling and analyzing them, however, is a completely different story.

Understanding the American Health Care Debate...

2009-10-18T11:21:00.002-04:00

The debate about the health care system here in the US is difficult to understand for 'aliens' such as myself (I've spoken to a few of my fellow aliens from other ~~planets~~ countries and they agree). I'm not necessarily speaking about the public vs. private issue, but rather the underlying logic behind the American private health care system. I understand the arguments behind a free-market driven system; what I don't understand is the level (patient/doctor/hospital/HMO) at which said competition takes place.

If, like me, you're curious about what's going on, I recommend downloading this week's episode of This American Life (TAL) here, or through iTunes. TAL is a little different from most podcasts in that the MP3 is only freely available for a week following the latest episode after which it becomes $1. NPR's gotta make money somehow, I guess. Anyways, this means that you've probably about 24 hours to get the most recent episode!

Pot-Pourri...

2009-10-17T21:05:00.003-04:00

I had a fear that this would happen. Moving to a new country and starting in a new lab has kept me very busy, thus I've had very little time to blog. Often I get home past 8pm, and by the time I've cooked food and relaxed, I'm way too tired to write. Hopefully, I'll establish some sort of routine soon. I'm too exhausted to blog about science - despite having a good idea for a post - so instead I'm just going to talk about bad drivers and politics.

I signed up for the gym here at the NIH, and have been going daily for the past four days. It's rather small compared to what I'm used to (I'd estimate that McMaster's gym is at least 10 times the size of the one at the NIH), however, it hasn't ever been busy when I've been there, so I've been able to work out and get out quickly. One big impetus for why I wanted to start going to the campus gym is the simple fact that I no longer want to jog outdoors near my place. It's somewhat frightening, but I cannot get over how little attention is paid to pedestrians here.

As a disclaimer, I've never felt that drivers have been particularly good anywhere that I've lived. The reason for their awfulness may vary: on the East Coast, for example, they tend to be too slow and lackadaisical. But that's specifically in terms of their overall driving ability. I've never lived in a place where I was quite as terrified about crossing the street as I am now. If people are turning right at a green light, for example, you may as well let them go, because they ain't stopping for nobody. Oh well, so far I've been able to dodge getting hit...

Changing the subject: I've been trying to read the newspaper here in the States, but I'm having a tough time of it. I don't know if it's simply the papers that I'm reading, but I've noticed one of two features: 1) the newspaper will have a definite agenda. All stories will be presented from either the 'conservative' or 'liberal' perspective (usually conservative) without any real justification for why this particular opinion is being forwarded. For instance, the Washington Examiner recently had an editorial titled 'A Big Chill of Global Warming' where the entirety of climate research was called into question in a tiny article, lacking any significant detail. Pretty big allegations for four paragraphs. Or 2) The newspaper will not have an obvious overall agenda, but rather will present both the conservative and liberal opinions side-by-side without any interpretation of the 'data'. For example, I've seen a few papers that will have op-ed sections in the middle where the first page will present everything the Obama administration has done as being excellent (without real justification), while page two will argue that the Obama administration is about to destroy the country (again without real justification).

I asked a few fellow labmates about this and they've pretty much unanimously told me that they don't 'follow the news'. Wow. Actually, that's not entirely correct. One person suggested that I listen to NPR's This American Life, which I now agree is an excellent production. It's kind of entertaining because said person also warned me that This American Life is liberally-biased, so if I'm not into that, be careful. I reminded him that I was Canadian, and that our 'Conservative' Prime Minister would probably seem like a Pinko to most Republicans: leftist bias is all a function of where you place your center.

After reading the papers, I think I understand why politics are considered such a taboo subject in casual conversation here in America. You've got two choices and no matter which one you choose, you're going to get stuck with a lot of ideological baggage you probably don't care about. Issues have become so divisive that I figure most people just assume that the folks they're speaking to are either firmly on the side of one party or the other, and nothing they're going to say will change that. Better to avoid uncomfortable conversations. I'm pretty used to living in areas where people criticize the government all the time no matter what (how else would you even attempt to keep it honest). But simply, criticizing a Conservative party doesn't immediately mean you're a Liberal back home... you could, of course, support the NDP!

Things Left Behind...

2009-10-13T22:50:00.002-04:00

I've intentionally made an effort to keep my post-American move blog posts upbeat and positive. This is because, while it is certainly exciting to move into a new phase in one's career, it's also sad to leave things behind. I'm terrible at this. Not only have I left good friends back in Hamilton, Vancouver, Halifax, and Moncton, but my gf and I are now 'doing the long distance thing'. Thrice before I've moved hundreds if not thousands of kilometers away, and I've done a very piss-poor job of keeping in touch with the friends I'd made in my previous haunts. This was actually a major impetus for me to create this blog - in addition to being able to meet people and discuss science within the greater 'blogosphere', it's also provided a convenient way for old friends to keep up with what I'm up to, and get into contact with me.

I've done an excellent job of keeping myself positive; postdoc-ing is pretty much as much work as you can probably imagine that it is, thus I've kept myself very, very busy. However, I did have a bit of a moment of sadness when I read Necator's very eloquent post about our friendship, and how he's going to miss hanging out now that I'm gone. As I said in my comments to the post, I could easily write a similar (though I'm certain less poetic) take about what I myself am going to miss, but this would make me sad. And unfortunately, I am currently without a shoulder to cry upon ;-) .

So instead, I'll simply say thanks for the sentiments. I appreciate them very much. And don't worry, we'll keep in touch¹.

¹As evidence of this assertion, I'll point to the fact that TheBrummell and I have kept in regular contact for the past several years, despite numerous moves.

Rant: User Interfaces...

2009-10-11T19:35:00.002-04:00

As I sit here typing at my Mac, warmly wrapped in my ~~cult robes~~ snuggie, I'm reminded that the classic age of software engineers dictating to the consumer how he or she will interact with electronics is over. Forgive me, that was a strange sentence.

Let me rephrase it like this: there's a lot of competition in the consumer electronics/computers market nowadays. I am 1) surprised by the degree of variability that still exists when it comes to ease-of-use of these devices and 2) somewhat shocked that some companies persist in releasing products that remain difficult and unintuitive.

Here's an example, I think that, regardless of personal preferences, most people would agree that Apple has been the reigning champion of user interfaces for the past few years. Anyone who has used an iPod Touch or iPhone can attest to how intuitive the device is, especially given the degree of functionality it possesses.

On the other hand, I recently got a new cellular phone called the Samsung 'Rogue' that also has a touch screen and is supposed to be a complete multimedia device. Now, 9 times out of 10, I'll have my iPod on me, but I'll always have my cell on me, so I figured that I'd drop a few tunes on it just in case. Unfortunately, the software required to do so only works on PCs, not Macs. This is actually completely contradictory to what the guy at Verizon told me - namely that I could simply drag MP3s onto the memory card in the phone and play them directly. Yes, iPods require iTunes (or a number of other clients that emulate it), but does anyone really have any trouble using that software? There are even competent Linux programs that emulate the functionality of iTunes.

Furthermore, the touch-screen on the Rogue is pretty awful, especially as compared to Apple's efforts. It's not particularly sensitive, constantly reorganizes buttons on the desktop such that they're on top of one another, and seems to nest menus in such a way that frequently used features are buried unnecessarily. If this is what Samsung plans to use to compete with the iPhone (they're about the same price), they're insane.

However, Apple is not without its own closeted skeletons. I'm temporarily using an iMac in the lab that runs OS 10.4 'Tiger' and I can't stand it. I'm a recent Mac convert (less than a year) and much of the reason that I actually decided to move over to Macs had to do with all of the excellent productivity features of OS 10.5., most of them coming from various excellent Linux modules (e.g., Spaces and Exposé). Having multiple windows open in 10.4, which I always, always do while working, is a huge chore to navigate. And all of those Mac-isms that I hate, such as windows constantly resizing and the inability to properly maximize¹ are in full force. It's amazing to me, an outsider who recently began using Macs exclusively, how much of an improvement the new OSs are as compared to the old ones in terms of basic user interfaces.

Many companies seem to be obsessed with designing their own proprietary software that's required to use their device(s). Particularly bad about this is Sony, whose software is notoriously un-user-friendly and poorly coded. Sony frequently releases new multimedia products that fail utterly, and I'm sure they'd have greater success if they put a bit more effort into making the software as sleek as the product itself. Oh well.

Anyways, I suppose that this was a rather incoherent rant, which some may argue is implied in the very term 'rant'. However, it does strike me as strange that companies are still releasing products that are difficult if not tedious to use in a day and age when competition among such products is so fierce.

¹Brummell, before you go off on your anti-OS X rant, I'll point out that many of the complaints you've described to me don't apply to the newer versions of OSX. For instance, there is no 'line of single pixels' at the border of windows that you cannot maximize beyond. I can fully maximize my windows.

Book Club Duo and the Matter of Framing...

2009-10-08T20:30:00.005-04:00

I'm going to break with tradition a bit and discuss two books in one post. Furthermore, I'm going to gloss over the typical general overview I do on the blog and rather refer to a specific issue discussed in both of these books: that of framing.

The first book is Science Under Siege (2009; Prometheus), which is a collection of recent essays from the pages of the Skeptical Inquirer, edited by Kendrick Frazier. Each essay, or series, covers a different topic deserving of skeptical inquiry, and typically reveals the topic to be pure woo. It's very similar to something like Michael Shermer's Why People Believe Weird Things, however, it's slightly different in that the essays are mostly written by experts in the field of interest and tend to be more technical. All but a few are very well written, and overall the book opened my awareness to even more sad pseudoscientific junk, which is pretty surprising considering how much I read about this stuff.

A particular essay that caught my attention was titled 'Only a Theory? Framing the Evolution/Creation Issue' by David Morrison. The issue of framing has come up a lot on the science blogs of late, and Morrison recommended the short book Don't think of an elephant! by George Lackoff (2004; Chelsea Green) as a good primer for what this whole 'framing' issue is all about.

After reading Lackoff's book, I have to admit that I don't understand why so many of the science blogs are against the concept of framing (but more on this below). According to Lackoff, framing involves using language and metaphors in such a way that they evoke particular mental structures that influence how we see the world. This is the central issue in Morrison's article 'Only a Theory?'.

Scientists have a (mostly) accepted and understood definition of the word 'theory'. In fact, the scientific definition of theory actually represents the classical definition of the word: "a well-substantiated explanation of some aspect of the natural world; an organized system of accepted knowledge that applies in a variety of circumstances to explain a specific set of phenomena". However, modern parlance, and in particular American vernacular, has changed the definition of theory to something much more akin to, "a belief that can guide behavior", or something synonymous with a 'hunch'.

What Morrison argues is that, it's great and all that we know what we're talking about when we say 'The Theory of Evolution', but 99% of the American public does not. So the question is, why do scientists persist in referring to it as the 'Theory of Evolution' instead of just 'Evolution'. By adding the word theory into there, we're simply framing the issue in such a way that it immediately invokes uncertainty. Furthermore, scientists are being inconsistent in their defense of using the word theory because there are many other well-supported concepts that we rarely refer to (in public) as theories, such as gravity, relativity, atoms, etc.

So why not just start referring to it as 'Evolution'? That way, needless airtime on TV and radio, or page space in print, will not be wasted defining the word theory every single time. Bringing this back to Lackoff, he explains, via his own work, that if research has shown us anything, it's that it's very, very difficult to change people's frames. Also, simply presenting the facts will not induce people to behave rationally, and this has been demonstrated empirically time and time again.

I think that the debate regarding framing that I've read about on blogs seems to be a bit more complicated. For example, a lot of the discussion at Sandwalk seems to relate scientific framing to something akin to accomodationism, i.e., 'pretending' that science doesn't doesn't conflict with people's bogus, anti-scientific views. In this sense, separating science from atheism, for example, could be seen as a way to frame the debate such that it doesn't run up against conservative values.

Interestingly however, Don't think of an Elephant specifically cautions against this form of reasoning; the idea being that ultimately, you're never going to be able to give those you're mollifying what they expect (e.g., scientific proof of God, or whatever). Rather, what the book advocates is framing the debate in such a way that you present, in this case, evolution as something beneficial to what your audience cares about. Conservatives don't care about basic science and the best you can hope for is to convince their children of its value. However, the issue of whether or not America will be able to compete with other nations scientifically and its importance to the economy is another matter (here's a factoid: a full 65% of the postdocs at the taxpayer-funded NIH are foreigners). The point of framing, in Lackoff's presentation of the topic, is to avoid being reactionary and set the tone of the conversation such that it is couched in language that appeals to those we're trying to influence (instead of using language that immediately offends them).

Lackoff explicitly discusses the topic that framing is not lying (rather that's called lying), rather it's about using language and metaphors such that they advance your goals. In this respect, every single grant or fellowship application is framed. I know, I just wrote one.

Anyways, the point of this post was to address the differences between the concept of framing being presented in the books I've read versus that that has been discussed on the science blogs. I agree that I don't think science should be accomodationist, and I also agree that accurate presentation of the data, methods, and interpretations is paramount. If you change these aspects of the game, you're doing bad science. But carefully choosing our language such that it focuses on things that our audience actually cares about need not conflict with these values.

Snuggie!!!

2009-10-08T08:07:00.003-04:00

I walked into a local pharmacy here and discovered that they had a whole rack of 'Snuggies' that they were trying to get rid of, so I picked one up:

Guess I killed two birds with one stone: I've now got access to my hands while in a blanket and I have my Halloween costume covered. Sweet!

The Smithsonian National Museum of Natural History...

2009-10-06T18:53:00.009-04:00

I've wanted to visit the Smithsonian National Museum of Natural History (SNMNH) ever since reading Stephen Jay Gould's Wonderful Life. This place is a treasure, and all Americans should take great pride in the fact that they have free access to such an establishment (it's free for aliens like me as well!).

I have to admit that I had an almost spiritual experience while walking its halls (in the sense of it being uplifting and inspiring). What's glorious about the SNMNH is that, unlike so many similar museums - and that's somewhat of a misnomer because nothing is 'similar' to this in terms of scale - its mission is not about presenting factoids, but rather actual science. I was stunned by how many murals, videos, and demonstration kiosks were placed explicitly to explain how and why scientists have come to the conclusions that are being presented here. Take, for instance, a display of various meteorite fragments collected from different American locales ('Natural History' includes evolution/paleontology, geology, and astronomy). There's an explanatory video right next to it that explains how, based on impact dynamics and meteorological records, astronomers are able to trace its origins back to a particular region of the asteroid belt. Plate tectonics, seismology, minerology, paleontology, and yes, my darling evolution are explained in considerable detail!

It's amazing; like the sum toto of current human knowledge in a particular area of science is being packaged and lavishly presented for all to see. Doubt evolution??? Here's the f$%ing fossils. Go ahead and touch them! Come and see this whole wall dedicated to displaying a sequence of fossilized remains of transitional whales. That's right, it's all there, written in stone... and genes! There was also a special exhibit called 'The Evolution of Evolution' that did a good job of explaining how evolutionary biology has matured over the last 150 years. Unfortunately, I'm sure that Professor Moran would have been dismayed by the continued focus on selection and casual dismissal of drift (as am I)...

Regardless, the place is absolutely amazing. I spent ~4 hours there and barely got to see anything in detail. Next time, I'll plan my day a little better and pack a lunch. Flash photography is allowed, so I've uploaded a few of the pictures that I snapped:

Note how 2 of the entrance banners make explicit reference to evolution. There was no softened language in here, just hard science.

The Burgess Shale fossil of Anomalocaris canadensis from the Walcott collection. This was the specific reason that I came to the museum. I stood next to rocks containing the fossilized imprints of organisms that lived > 500 million years ago. I also have pictures of Edicaran fossils that are even older.

A fossil of the fabled Euryptids, or giant sea scorpions that went extinct in the Permian. There's also a really big, well preserved one at the Royal Ontario Museum in Toronto.

Here's a fossil of Zygorhiza kochii, one of those transitional whales I mentioned above.

This is an amazing fossil from the late Cretaceous because it actually reveals what kinds of marine species were predator vs. prey.

For the heck of it, here's the famous ~200 million dollar Hope Diamond.

I'll end with a photo from the geology section showing gold ore in various states of refinement. I'd like to spend a lot more time in the geology and astronomy sections of the museum, because I know I'd learn a lot.

Anyways, I seriously doubt that many creationists, particularly those of the young-earth type, frequent this wonderful establishment. At the same time, it's likely that they'd go on ignoring all of the evidence just like they always have. We can only hope that more people will take their kids there (it's free!) such that future generations will develop an affection for science.

New Country, New Look...

2009-10-04T21:56:00.005-04:00

Today I made my first foray into Washington, D.C. proper and visited the Smithsonian National Museum of Natural History, which was amazing. I'll post a more detailed account of it tomorrow, because I've realized that the blogosphere is rather low-key on weekends, and thus I should probably confine my Saturday/Sunday postings to more whimsical topics.

In this spirit I wish to relate the conclusion of one of my life 'quests', which involved the procurement of a fedora. Most people's fascination (if any) with the fedora obviously comes from the popular Indiana Jones films, and I do remember wanting to purchase a replica Indy fedora at Disneyworld when I was 16. However, my more recent love-affair with the hat has come from the picture on the bottle of the Italian beer, Moretti:

The Birra Moretti logo.

A former graduate student in the lab in which I did my Ph.D. pointed out the following: American and Canadian brands of beer advertise their products by implying that liquor will get you attractive scantily clad women. Not so with Moretti. I mean, look at this guy: He's just got off of a long, hard day of work. On the way home, he stops at the local pub and orders himself a glass of beer. That beer is obviously the best thing that's happened to the old guy all day. I want to be that guy.

I realize that I want to be that guy too, except for the green suit. He's obviously of Northern Italian ancestry - green tends to clash with my well tanned southern Italian skin.

Conveniently, I happened upon a haberdashery (I'm not just using this word to be a sophist; the shop actually billed itself thusly) and found myself a cheap fedora. I can't tell you how many times I've looked for one of these in vain back home. Either they're out of fashion (probably) or they're well hidden. Anyways, here it is:

I think it's rather dashing...

Evolution in America: The First 150 Years...

2009-10-03T08:05:00.003-04:00

A couple of days ago I attended a really interesting seminar here at the NIH titled 'Evolution in America: A Short History of the First 150 Years', presented by historian Barry Werth, author of Banquet at Delmonico’s: Great Minds, the Gilded Age, and the Triumph of Evolution in America. Werth went over a rather detailed historical overview of the history of the public perception of evolutionary theory since the publication of Origin in the States, which was rather illuminating.

I'd already read about much of the details that the speaker covered, however, he did postulate one interesting hypothesis that I felt was worth recounting. Werth noted that until the 1980s, the American public had never received details of Darwin's theory of evolution directly from reading Darwin himself, nor from evolutionary scientists. Rather, all knowledge of evolution had come through the filter of popular writers, who'd injected elements of their own biases and beliefs.

For instance, during Darwin's own day, most American's would have learned of his theory via the writings of Herbert Spencer, who was extremely popular on this continent. Spencer presented evolution in order to support his views of anti-government libertarianism, eugenics, and progressivism - to Spencer, evolution was not an undirected force. In fact, by the end of the 19th century, Americans viewed Spencer's doctrine as synonymous with Darwin's.

If you read SJ Gould's The Mismeasure of Man, you'll find out that these views actually continued unabated until the second world war, when the West learned what extreme eugenics entailed. Eugenics quickly fell out of favor, taking Darwinian theory with it in the mind of the public of the USA. It really isn't until Gould came along that evolutionary scientists began writing (relatively) unfiltered books on Darwin's theory for the public¹.

This can be contrasted with the situation in Europe, where figures such as Thomas Henry Huxley or Ernst Haeckel promoted Darwinian evolution directly to the public. Thus Werth argues that America's understanding of evolutionary theory has always been somewhat uniquely conflicted, which may explain why its acceptance to this day is so poor. The presentation did point out that the Sputnik crisis of the late 50s prompted a renewed dedication to science, that brought evolutionary theory back onto the main stage where it enjoyed a brief resurgence. However, this was somewhat quelled with the emergence of sociobiology in the mid-70s, bringing back a lot of the eugenics-based disenchantment felt by the public.

More direct communication with the public from scientists is needed regardless of whether Werth's interesting hypothesis is correct. But it's something to mull over nonetheless.

¹One notable exception to this was American botanist and evolutionist Asa Gray, who wrote quite extensively for the general public. However, Gray's evolutionary writings were largely molded by his own deeply religious views, and his actual view of evolution is somewhat confusing and muddled (see Gray's Darwinia).

Health Care...

2009-10-02T08:00:00.000-04:00

I've been in the States for just over a week, and I've already fallen in love with Barnes and Noble¹. There's a big one in a really nice part of town near the Bethesda metro station, and I see myself spending quite a bit of time there (or alternatively at another location about a 15 minute walk away from my place). I've also finally had the opportunity to try 'Pork Rinds', which aren't for me. They really do taste like a meal (e.g., pork tenderloin) and thus I can't see myself eating them as a snack. But this isn't the subject of this post.

Yesterday, I activated my health insurance here in the US, which included a ~1.5 hour long orientation session for foreigners - we were not referred to as aliens - explaining how health insurance works. Non-Americans seemed to find it rather complicated.

It is not my intent to comment on the current state of the ongoing American public health care debate, which, according to everything I've read and heard while here in the capital area, is quickly spiraling out of control and failing miserably. Ultimately I think that Americans need to do what's right for America, regardless of my own opinions. Also, the greater issue at stake here isn't really public vs private health care, but rather finding some system that curbs ever-rising health care costs, which have doubled in the last decade, and whose increases are predicted to soon outpace inflation. Rather, I'd like to blog about my experience with private health care (I've only ever known a public system up until this point).

My institute's health care coverage is apparently quite good, because it's nationwide and even international. Some of the other orientation attendee's who'd completed grad school in the States remarked that grad student insurance was typically limited to using the school's own hospital, even in cases of emergency. Our plan is nationwide, however, that doesn't mean you can just go anywhere (well you can, but see below). Rather, there's a website you need to use in order to determine what health care facilities are 'in-network': those are the ones you should use to pay the least amount of money. If you go to an 'out-of-network' facility, the insurance will still pay some of your fees, but very little (~20%). Furthermore, the first time each year that you use an out-of-network facility, you must pay a one time deductible of $250.

When using 'in-network' facilities, coverage is pretty much comprehensive (i.e., everything is covered), however, there is typically a small 'copay' fee, ranging from $10-25, that must be paid for each service. The largest copay comes from using an emergency room ($50) if you are not then subsequently admitted to the hospital for at least an overnight stay.

Probably the best feature of the plan (in comparison to the Canadian public health care system) is the prescription drug coverage. However, this is somewhat complicated by the fact that there is a long list of generic/preferred/non-preferred brands for each type of medication and the deductible fees vary based on which brand you use. I have no problem using generics (which have only a $5 copay), however, you need to request them specifically from your doctor because the pharmacist is required to dispense the brand written on the actual prescription. Regardless, prescription drug coverage is nice - though I've generally had it through private companies in Canada (in fact, the exact same provider that I have here in the States).

The total fee for this coverage is $355/month, or $4,260 annually, but I don't actually have to pay this because one of the benefits of being a postdoc at this institute is that your health care is provided as part of your contract and is not deducted from your negotiated salary. I only require individual care though; the family version of the plan runs in excess of ~$10,000 annually. This may seem like a lot, but it's important to keep in mind that we pay much higher taxes, particularly on income, than do Americans. However, the flip-side is that to get this coverage, I need to work here, so coverage at the level of the individual consumer when obtained outside of an employer plan is probably a whole 'nother ball game. Furthermore, accidentally (or in an emergency) going to the 'wrong' hospital, could prove financially disastrous, which is very different from what we're used to in Canada.

Anyways, I had no idea how it works, so figured I'd blog about it.

¹and, strangely, have joined the ACLU, thus ending my future conservative political ambitions...

The U.S. is Weird...

2009-09-29T21:19:00.003-04:00

Livin' in the U.S.A...

2009-09-29T10:17:00.004-04:00

I’d forgotten how brutal it was to go for a whole week without internet access. How did The Ancients™ (i.e., pre- ~1993) get by? Oh well, at least I’ve returned to cyberspace now.

The drive from Hamilton to the metro D.C. area was uneventful if a bit confusing. Apparently, many people travelling to Washington from Ontario go via Pittsburg. This adds a few hours to the total travel time, but it lets you remain on interstates the entire way, and makes for a straightforward ride. Our GPS, which incidentally was set to ‘avoid toll roads’, took us on a merry ~9 hour journey through the boonies and environs of various Pennsylvanian coal-mining towns. Being in the backwater led us to pursue a game of sorts in trying to find a roadside diner that served proper ‘grits’. Unfortunately, we’d left quite early in the morning and none of the family diners we came across opened before 11 am. What kind of family restaurant doesn’t serve breakfast??? I should also mention that one restaurant we passed by – and I mean literally passed along by without considering – was called ‘The Triple-K’. Seriously?

We made it to Rockville at about 3 pm and promptly moved all of my stuff into my new apartment, which happens to be both quite large and quite nice. I’d been warned by multiple people that the D.C. area is extremely expensive to live in, and while this is true, I think I lucked out in terms of value¹. I’m about a 10 minute walk from the nearest D.C. Metro station, which is an 8 minute subway ride to the lab.

I’ve spent only a couple of days in my new lab, which is impressively outfitted and in a new building, and instead have taken the past few days to procure amenities and secure services. Moving to a new country is surprisingly challenging, and most of the difficulties I’d heard about with respect to moving to the States proved to be accurate. On the positive side, the workarounds I’d come across were also accurate.

Two big issues surround the move. Firstly, it takes several weeks in order to get an American Social Security Number. This means that several services, especially those involving banking, will be locked out until this happens. Thankfully the Bank of America allows you to open a checking account without an SSN (something I’ve heard that most banks do not allow), meaning that you don’t have to spend the first month hiding your cash under a mattress. You’re not allowed to receive direct deposit from your employer without the SSN however, but if you’re lucky (and I happen to be in this case), your employer will cut you a check until you procure the number. You’re also unable to transfer funds online between American and Canadian banks without the SSN, which makes paying bills back home somewhat more complicated than necessary.

The second issue involves the simple fact that American and Canadian credit corporations are not united, and thus for the purposes of obtaining utilities, it can be surprisingly difficult. Many companies will require rather large security deposits for the first year (~$400), which is a real bummer. Thankfully, I’ve learned that some larger American companies will check and approve you based on your Canadian credit history. For instance, I was able to get a cellular phone through Verizon Wireless with very little fuss – the only inconvenience was the fact that the process took a little longer than it normally does.

Allow me to travel down a brief tangent here. Every time I’ve undertaken one of these long-distance moves, I’ve pretty much immediately sought out a Wal-Mart in order to pick up that standard junk that every house/apartment requires (e.g., broom, wastebaskets, cleaning supplies, hamper, cutlery drawer thingie, etc.). To my dismay, there are no Wal-Marts in the Metro D.C. area. I’m not joking: the nearest Purple-Paradise² is 20 kilometers away, and in no way accessible without a vehicle. I don’t think I’ve ever lived anywhere that didn’t have several Wal-Marts nearby. However, the U.S. has several Wal-Mart-like chains that are absent in Canada, and thus I was able to secure supplies at a local enormous ‘Target’.

The numbers on the map represent Walmarts. Notice how I'm some kind of strange 'dead zone'.

For the most part, America has been pretty much exactly like Canada, with only a few small exceptions. For starters, I need to get used to U.S. money. It would certainly help if the US followed the ‘Monopoly Money’ standard of coloring different bills like the rest of the world (they have begun putting a bit of color into them, so it’s a start). Also, they still use one dollar bills here, which is fine except for the fact that your wallet remains thick even after making several purchases: everything gets replaced by ‘Washingtons’, giving your ass-cheek a false sense of wealth and leading to much embarrassment when it’s time to actually produce the ‘scratch’. The other notable difference is the use of the Imperial system of measurements. I think I’m doing pretty well when it comes to distance and weight (inches and lbs are pretty common in Canada), but I don’t think I’ll ever get used to Fahrenheit. Thankfully I’ve got a conversion tool on my iPod.

Oh yeah, another notable, positive difference between our two nations is the ridiculously low sales taxes here (~5%) and the somewhat philosophically related extremely low liquor prices. Coronas are less than $1 per bottle, and, if one has absolutely no desire for quality, a 26er (750 ml) of whisky can run as low as 5 US dollars. I’m not exaggerating about that last one. A bottom of the barrel 26er of hard liquor back home will run you ~$20 CDN. Not that any of this matters as postdocs do not have time to drink…

I’ve not yet had the time to really explore the capital, nor have I really even explored the area around my apartment. I’ve had quite a few things to take care of in terms of both administration and work (I’ve got a review paper that must be submitted by October 1st), but I’m sure I’ll get the chance to do some exploring soon. As soon as I get settled, I’ll have the opportunity to get back into the routine. I’m alone here in the US (the gf and I are doing the long-distance thing) so I’m going to take the opportunity to immerse myself more deeply into science, including blogging about it.

¹This is the third time that I’ve picked up and moved hundreds of kilometers into a new apartment of which I didn’t know what to expect. This also happens to be the first that doesn’t seem to be a total disaster in that the first time (when I moved to British-Columbia) my roommate committed suicide within a few weeks of my moving there, and when I subsequently moved to Ontario, my apartment was such a dive that I could literally see my breath upon waking in the Winter months.

²I’m not the only person who’s noted the strange increase in the proportion of people wearing purple clothing at Wal-Marts when compared to the general population…

Off the Grid for a bit...

2009-09-20T14:58:00.008-04:00

I'll be moving to Maryland on Tuesday. Between now and then, things are going to be extremely busy, and I obviously won't have time to blog. Furthermore, I'm not sure how long it'll take me to get the internet set up at my new place, so the blog may not be updated this week.

You'll also notice that I've already changed my profile. My new place of employment requires that I put a disclaimer on my blog stating that it doesn't represent the views of the NIH, so there it is.

I'll see y'all on the blogosphere in a little bit!

P.S. In honor of the move to America, I present Rammstein:

And in typical fashion, here's a map of the move:

And so it Begins!

2009-09-17T21:22:00.004-04:00

Today was a long day. My gf and I got up really early and drove down to the the Peace Bridge border crossing - connecting Fort-Erie, Ontario to Buffalo, New York - so that I could obtain my work visa.

Thankfully, the application went off without too much difficulty (only a couple of hours of waiting), based largely on the fact that I pretty much brought every document that I thought could be remotely relevant. I didn't have transcripts from all my universities, so it was a good thing that I actually had the degrees.

As an aside, there were quite a few people that were complaining about being asked to wait at the US Customs and Border Patrol station while their cars were being searched, or their documents were being checked. I wanted to point out to these people that the CBP officers don't 'owe' them anything. It's not like our Canadian tax dollars pay their salaries, and we didn't elect the government that hired them. Sure, tourism dollars are important, but that's more of an issue with New York State Tourism authority. I didn't think our wait time was particularly long, considering that this is one of the busiest border crossings between our two countries, furthermore, all of the staff were quite friendly. Oh well.

I'll be working as a postdoc under the NAFTA TN visa. All temporary work visas have pros and cons. This one's a little more work to upkeep (it must be renewed annually), but it's the most flexible depending on what happens in the future - my intent is to return to Canada, but if a future postdoctoral opportunity or temporary job opens in the States, this visa will make transitioning to something like that easier.

Now that the visa is stapled to my passport, this means that I'll be leaving for the Metro DC area in 5 days! I've already begun packing and I think that my affairs are all in order, but I've still got quite a few things to take care of in the next few days. It's always important to make sure that you leave your lab with everything taken care of (e.g., samples, stocks, etc.) so I've gotta go in and fix that all up.

I'll try to keep blogging over the weekend, but then expect a brief blackout on my end until I can get my stuff set up in the USA.

Rant: Clothing...

2009-09-15T10:13:00.004-04:00

I realize that the title of this post suggests that its contents will be something akin to the mad ravings of a nudist. (Un)fortunately, such is not the case.

I imagine that many people make fun of my wardrobe. I'm highly cognizant of the fact that I do not dress with any particular 'style', nor do I have a particularly large number of different outfits. I've frequently, for example, owned multiple pairs of the same jeans, such that it probably seemed to others as though I was wearing the exact same pair of pants for weeks on end. Yes, I'll admit that this probably makes me 'uncool'.

Are any of my readers familiar with the concept of 'Gradwear'? I was introduced to this term at the beginning of my M.Sc. Essentially, Gradwear is a blanket term for clothing that's comfortable for use while doing the type of work that you do in the lab. I worked in a Drosophila lab wherein our main fly incubator was broken (we had a smaller incubator for specific experiments). Thus, it was decided that we'd keep the ambient lab temperature at a balmy 25ºC - the temperature at which most fly stocks are maintained. This may seem like only a few degrees above room temperature, but I frequently found myself sweating while doing routine work. It was uncomfortable as hell, and given that I was spending 6 or 7 days a week in the lab, I only purchased the loosest sub-tropical clothing and wore all year round. My gf, for instance, frequently complained that I'd wear my crappy T-shirts during the Winter instead of sweaters, or long-sleeve shirts. The weather outside didn't matter; it was always sweltering in the lab.

Anyways, now that I'll be postdoc-ing and making a bit more dough, I've resolved myself to increase the quality of my wardrobe, at least to the level that it was during my M.Sc., but this brings up a small issue: While I enjoy the act of buying new clothing, I thoroughly dislike the process of shopping for clothing.

Here's an example of why: I am not a large person, nor am I particularly skinny either. If I go to Tommy Hilfiger and try on a shirt, I will typically fit into a small size, and sometimes even this will be slightly too big. However, striding across the mall's concourse to Bluenotes, a medium T-shirt will be so tight that I won't be able to move my shoulders without tearing the thing apart. A large shirt from the same store will feel like I'm wearing a bed sheet. I'm certain that more savvy fashionistas will be well aware of the lack of standards among brands, but it irks me (my gf informs me that I should know that Bluenotes caters to tweens and thus their clothing is smaller. I'm pretty short [5'7''] so I don't see how teenage guys would be that much smaller than I am).

Here's another strange issue: Yesterday I tried on a pair on pants that seemed like they were designed by some extremely repressed pre-Vatican II Catholic nun. In terms of the dimensions of the legs and waist, I could easily fit into them. However, I was unable to actually pull them all the way up because the groin was obviously designed for use by a eunuch or the front-man of a 'screamo' band:

Please visit www.yourscenesucks.com for hours of entertainment!

So yeah, now that I'm no longer a grad student I feel that I must break the chains of Gradwear and buy some decent clothing. Like many former grad students, however, I'm no longer sure what to wear as I started university when 'Airwalks' and 'Doc Martens' were all the rage (a buddy of mine frequently complains that he began university during the 'grunge' period and thus his fashion sense is even more screwed up). I suppose I'll just read People magazine and find out what's hot.

Now that I'm a doctor though, I must admit that I've developed a strange fascination with tweed jackets and leather patches...

Moving South...

2009-09-13T18:01:00.002-04:00

I have to admit that I've begun to get a bit antsy about moving to the States. Perhaps I was being naïve, but I figured that as long as I had my affairs in order here in Canada (i.e., no outstanding bills, all services appropriately canceled, etc.) as well as an appropriate visa, all I had to do was move to my new apartment with a wad of ready cash on hand, and get settled there. However, I've been doing some reading on the internet - because I had some questions about the visa process - and I've found quite a few websites offering advice that would suggest that things are not so simple.

For instance, multiple Canadian expats have complained about the fact that it was extremely difficult to get access to utilities and banking services. According to these folks, as a general rule, American banks and utility providers will not accept a Canadian credit history and thus will require large, up-front deposits if they're to sign you on to a telephone plan, for example. Also, quite a few people in an expat discussion forum wrote that while they were able to open US bank accounts, they were unable to obtain American credit cards. I'm going to sit down with a 'financial advisor' here in Ontario next week to see what I can do about this.

Another issue involves the American Social Security Number. You generally can't get paid until you get one, and you're not allowed to apply for one until 2 weeks after you move across the border. While the online information assures you that this number is provided quite promptly, some people claim that it took over two months before they saw their first paycheck due to delays in processing their SSN (this shouldn't be a big problem because I've got access to emergency funds if I need them).

Anyways, I guess I'm throwing out a post to solicit advice from people who have lived in the States under temporary visas. Is there anything I should know? Stuff I should plan for? Details I should be aware of? etc. I don't have a large readership, but if you know anyone who may have any insight pass them my way.

The Great Controverted Question...

2009-09-09T10:53:00.003-04:00

As a graduation gift, a friend of mine got me a collection of Thomas Henry Huxley's writings called Essays upon Some Controverted Questions (1892; Cambridge University Press) that I've been reading. I haven't finished the dense book yet, but since it's a collection of independent essays loosely tied together to a particular topic (see below), I figured that I'd write some thoughts out on it.

The long introduction to the book frames its overall thrust: The controverted question of the age is as follows, "if Scripture has been discovered not to be worthy of unquestioning belief, faith in the Supernatural itself is, so far, undermined." Reading the subsequent arguments really struck home the fact that a) Huxley's views very closely match my own, and that b) the nature of the debate has not changed 1 iota in ~130 years.

Huxley complains that Christian apologists (more specifically non-Anglican Protestants) run into the dilemma of wanting to 'have their cake and eat it too'. The argument runs as follows: if the Bible is unerringly accurate with regards to what is verifiable by human observation, then you need only assume that it is also accurate with regards to what cannot be verified to use it as a moral and spiritual guide. If, on the other hand, the Bible is inaccurate with regards to its verifiable claims, then you're making the assumption that it is accurate with regards to its unverifiable claims, despite knowing that it is false in at least some of its claims. More simplistically, I've always looked at it like this: If you pick and choose which passages of the Bible you want to follow and believe, you're simply creating your own completely illegitimate religion.

As Huxley points out, the first option is untenable, both intrinsically and extrinsically. Intrinsically because the Bible, both Old and New Testaments, are full of obvious, irreconcilable contradictions (if you need to prove this to yourself, read Genesis chapters 1 and 2, or the Gospel of Matthew followed by Paul's letter to the Galatians). Now, 'irreconcilable' here requires a caveat that explains why this is a bigger problem for Protestants. This is because the Catholic, Anglican, Greek Orthodox, etc. churches never claimed that the Bible could be read without the need of interpretation as do the Protestants. This does not solve the problems, however, because the interpreters run straight into the legitimacy problem noted above: they're still picking and choosing what passages they want to believe in.

The extrinsic problems appear to make up the major focus of the essays in the book as Huxley argues that the historical accounts of Genesis are not supported by modern science in any way. A big issue regarding apologists of the day was their argument that the Bible was not supposed to be read literally, but rather metaphorically, e.g., the order of the acts of creation in Genesis records the order of first appearance of fossils in the geological record. However, as the author observes, this is not the case, no matter how 'metaphorically' one wants to interpret these passages (unless of course one wants to interpret them completely ass-backwards).

Another interesting, close-to-home, argument that Huxley makes is the nonsensical nature of the word 'supernatural'. If natural includes everything that we can interact with, test and verify, and supernatural involves the alleged existence of things that can neither be felt, tested, or verified, then what's the point? What was the original evidence for the existence of the supernatural? By definition, there was no evidence to ever suggest the existence of the supernatural at all. Of course, there are alternative ways to define supernatural such that it can interact with the natural; however, at that point it should be verifiable if not just 'natural' in the first place. I think the point of the original definition (and the one that's bandied about by the Catholic Church, for example) is that it removes even the possibility that divine revelation could be subject to scientific scrutiny. However, by Huxley's view, it inevitably undermines itself.

Anyways, it's just interesting (disturbing?) to see that the same arguments have been going back and forth regarding the legitimacy of religion since Darwin's days (most of the essays were written in the 1870s-80s). It really does seem, as Dawkins has often claimed, that a major focus of the 'evidence' for religion used to be the existence of life. This 'non-evidence based' approach appears to be a more recent thing. It's difficult to shoot out a 'book club' post on collections of essays, so if any of the individual essays warrant further discussion, I'll blog about them individually.

Ph.D. Thesis Wordle...

2009-09-08T08:23:00.002-04:00

I told BB that I'd run my Ph.D. thesis through Wordle once it was done. Unfortunately, I got caught up in the whole defense thing and forgot. Better late than never! Here it is:

I think it's pretty darned cool.

Big Idea Syndrome...

2009-09-07T10:07:00.006-04:00

Big Idea Syndrome: “Whatever I study is the most important thing in evolution — in fact, the driving force of evolution.”

I learned about 'big idea syndrome' via Jerry Coyne's blog in his discussion about a ridiculous paper that got published in PNAS¹:

Williamson, DI. 2009. Caterpillars evolved from onychophorans by hybridogenesis. Proc Natl Acad Sci USA. Online advanced access.

The article essentially argues that species with complex life cycles - specifically those that go through a larval growth stage before metamorphosing into an adult mating stage as happens in holometabolous insects - evolved via that fusion of the genomes of a species with a larval-like morphology (e.g., onychophorans) with that of a species with a morphologically complex adult stage (e.g., butterflies). Let us put this into perspective:

The relationship between the onychophorans (velvet worms) and the arthropods (insects, chelicerates, crustaceans, etc.) has been a matter of debate for some time. Velvet worms are obviously segmented, though without the same degree of chitinous exo-skeleton that distinguishes the arthropods, and for some time it was thought that onychophorans represented a link between arthropods and segmented worms:

An onychophoran. Image cred here.

Recent molecular and morphological phylogenetic evidence do not support the hypothesis that velvet worms are such a link, but it does suggest that they are closely allied with the arthropods: they may have an archaic relationship with the chelicerates (spiders, scorpions, horseshoe crabs) (Strausfeld et al. 2006).

What does this mean in terms of that awful paper cited above? Well, all the evidence at our disposal seems to point to the idea that onychophorans are closely related to arthropods, but diverged from the other arthropods quite basally in the tree:

A phylogeny of the arthropods as inferred from mitochondrial sequences. From Hassanin 2006.

Do you see where chelicerates are on that tree relative to insects? Everything we know would argue that onychophorans and butterflies are hundreds of millions of years diverged! It's hard enough to get hybrids between species of fruit flies that are a few millions of years diverged, but this paper is suggesting that hybridization occurred between members of separate phyla!

This doesn't even take into account the question as to how the new hybrid's genome, which would have been a complete clusterf#$k of genes and chromosomal organizations from highly diverged species, somehow 'knew' how to express the velvet worm morphology genes first, followed a subsequent metamorphosis into a butterfly. If neither the onychophorans nor the butterflies actually underwent metamorphosis prior to the supposed fusion, where did the genes required for said metamorphosis come from? That's the problem with these saltatory theories of evolution - everything would have had to have been in place for the transition to have occurred in one generational step.

As Jerry Coyne points out, this hypothesis is quite easily testable: if correct, then butterflies should have a large number of genes that are more similar to onychophorans than their fellow arthropods (I assume that all holometabolous species must have acquired their larval stage from such a fusion, and thus we'd have to compare the butterflies to non-metamorphosing arthropods).

However, the bigger problem is that such a ludicrous idea was ever published in the first place. Science progresses by building upon the foundation of previous discoveries and accrued knowledge. This paper basically ignores everything we already know about developmental genetics and speciation. However, it was pushed through by Lynn Margulis, the scientist who originally proposed the endosymbiotic theory of the origin of mitochondria and chloroplasts, and now seems to think that hybridization can explain everything. Big idea syndrome indeed.

¹Proceedings of the National Academy of Sciences of the USA is considered to be one of the upper tier scientific journals.

Genomfart...

2009-09-05T15:00:00.001-04:00

Genomfart is Swedish for 'passage' or more specifically 'thoroughfare'.

With all of my US visa woes out of the way (for now), I should be moving down to Maryland in about 2 to 2.5 weeks time - assuming my understanding of the entire process is correct. In the meantime I've got a few things that I've got to wrap up in the lab here - the major one being submitting my final research paper for publication. In doing some background reading in order to beef up its discussion, I came upon a really interesting chapter in Dr. Micheal Lynch's book The Origins of Genome Architecture (2007; Sinauer) titled 'Genomfart' (it's the final chapter of the book).

In under 30 pages, Lynch does an amazing job of describing the essence of modern molecular evolutionary biology, its caveats, and most interesting to me, the other life science disciplines that are legitimately interested in evolutionary biology, but don't seem to really understand exactly what studying evolution entails.

What Dr. Lynch points out is that proper evolutionary biology is not a comparative discipline. Simply pointing out the similarities and differences between two separate taxa does not 'complete the evolutionary story'. The only way that one could think that such a cursory overview was sufficient to describe the evolutionary process would be to assume a priori that each difference between species was obviously driven by adaptive evolution.

An entire page of the chapter is devoted to presenting unsubstantiated claims that have been made regarding the evolutionary process - some of which enjoy a lot of cachet in the popular and technical literature. For instance, that genome size is modulated in order to optimize cell size and replication rate, that gene network modules serve as plug-ins that enable saltatory evolution, or that introns exist to enhance the production of new genes by exon shuffling. The commonality among all such claims is that they ignore 3 of the 4 primary forces governing evolution: mutation, recombination, and drift. They focus exclusively on selection.

It's amazing that while the issues surrounding the use of 'just-so stories' in the interpretation of evolutionary history have been well established and appreciated for decades (as always, consult Gould and Lewontin 1979 for an excellent treatment), it seems as though many of the sub-disciplines of biology and the life sciences - especially those that aren't directly connected with evolutionary biology - don't seem to be in the business of hypothesis testing when it comes to evolutionary musings. Simply pointing out an observed phenomenon as well as a plausible mechanism explaining its origin says nothing about the reality of said mechanism. Another criticism leveled by Lynch, however, concerns the observation that some of these mechanisms aren't plausible at all! The power of selection is formidable indeed, however, its efficiency is strongly reduced in species with low effective population sizes. In order to account for many of the theories involving human evolution - take evolutionary psychology, for example - selection on all of these supposed adaptations would have to be extremely strong in order to overcome the effects of random genetic drift.

Unfortunately, understanding the effects of drift (and biased mutation) underlies much of the problems associated with unrestricted evolutionary musings. Drift takes place in any population, regardless of the conditions, owing to the stochasticity of genetic transmission. Selection, on the other hand, requires specific conditions, available variation, or the input of the requisite mutations. Thus, as population geneticists have been taught for some time now, non-adaptive processes should be the default, i.e., null, hypothesis for comparative observations (I'm not even going to touch upon the issue of correlated traits). Only when the action of non-adaptive processes can be rejected should selection be invoked. Only in such a manner does evolution constitute a valid, hypothesis driven enterprise in which further hypotheses regarding the specific mechanisms driving evolutionary change can be subsequently tested.

What is the null hypothesis about how specific human behavioral traits diverge? We can claim, for example, that humor is an adaptive trait, and that it helps humans cope with difficult lives (or whatever). But how are we supposed to test this hypothesis? Of course we would further claim that a trait as complex as this behavior could not have arisen via chance processes, but this would be specious: we know next to nothing about the underlying genetic basis of these traits. There's abundant evidence that complex systems can arise through non-adaptive processes (think of gene duplication followed by subfunctionalization - new genetic information is created without the need for adaptive evolution to be invoked). Furthermore, such processes are more likely to occur in species with small population sizes, like humans.

In the course of the chapter, Lynch forwards the suggestion that the biological fields most hostile to population genetics and molecular evolution - particularly evo-devo - tend to be those interested in traits wherein the underlying genetic basis is unknown or poorly understood, or that the population level processes remain a mystery. Some of these just-so stories involve traits of which we know nothing about the genes involved, the level(s) intraspecific variation, or even their supposed utility. As the chapter notes: "The population genetic basis of evolutionary change is now so well established that those who claim its inadequacy should certainly bear the burden of explanation."

Every now and then I come across a paper or a book that does a really good job of synthesizing a large body of information into a series of easily understood points. These tend to make good learning tools, and I like to save them away somewhere (for the journal articles this is easy because I use Papers). Genomfart is one such learning tool, and I think I'm going to pick up the whole book once I've saved a bit of dough (hopefully it'll come out in paperback!).

Rant: In Which I Get One Last Potshot from the University Administration...

2009-09-03T19:24:00.004-04:00

As some may have noticed, I've changed the description of my blog to indicate that I am "[c]urrently in the interim between having graduated and moving on to a postdoc." The reason that I haven't begun my postdoc is simple: in order to move to the USA, I need to obtain an American work visa.

This shouldn't be a problem, the only thing I need to provide to my new employer, so that they will sponsor my application, is proof that I've obtained my Ph.D. Seems reasonable enough. However, since obtaining that proof requires dealing with university administration, it's never so simple. See here's the problem, they've written me a letter containing the following: "Subject to senate approval, the [Ph.D.] will be conferred at our fall convocation in November 2009." Unfortunately, this is an issue because my employer requires a letter indicating that I have obtained my Ph.D. - it's not a problem that it will conferred at a later date, but the 'subject to senate approval' implies that some evaluation remains (i.e., I still could not get it).

So I went to see the folks at graduate studies who informed me that a) this wording absolutely had to go on the letter, and that b) this indicates a formality wherein, twice a year (November and June) the University Senate holds a special meeting wherein they 'bulk-endorse' all of the degrees that people have completed. Great! I paid over $24,000 in tuition and expenses, plus printing and binding fees for my thesis, and the university is going to make me wait in limbo for three months because of some ceremonial procedure? Give me a break!

I put in my dues! I passed with commendations! Not a single person would ever imply that I didn't work my butt off in order to get to this position, and now the school is telling me that I have to wait for three months in order to move onto my next job because of a formality? I'm lucky that I'll still have a position in my current lab if worse comes to worse¹ (though I won't have a place to live), but what would happen if our lab didn't have the funds? Am I then supposed to get a part-time job for a few months in order to pay the bills because of bureaucratic nonsense? Everything is already cleared in the Registrar's computer: it says 'clear to graduate'!!!

To be fair, the people at the School of Graduate Studies did sympathize with me. In fact, apparently I'm not the first person this has happened to, and it's even worse if you graduate in July or January. They told me that the subject of changing this particular policy has come up in meetings before - wherein you would still graduate in November, but would have your degree conferred as soon as the paperwork was done - but it doesn't seem to have had an effect.

I love what I do and all that, I really do. But I've really had nothing but problems when it comes to dealing with the university admin since entering grad school (for some reason I never had issues during my undergrad at Dalhousie). Many times I feel as though the people I speak to in admin are out of touch with the 'real world' - you know, like in assuming that forcing you to completely change your living and employment arrangements for a four month stretch isn't a big deal. The Ivory Tower culture can be a blast, but by Huxley's sideburns it can be frustrating.

¹I doubt it will come to this, I've still got options at my disposal, and my boss is backing me up.

Book Club: The Book Nobody Read...

2009-08-31T13:00:00.000-04:00

The Book Nobody Read (BNR; 2004; Penguin) is arguably a bit nerdy, even by my standards. It chronicles the attempt of Harvard Emeritus Professor of Astronomy and History of Science, Owen Gingerich, to identify, inspect, and chronicle every extant copy of Copernicus's De revolutionibus orbium coelestium (On the Revolutions of the Heavenly Spheres) - the seminal 16th century manuscript (1543) that is considered to have pushed the concept of a heliocentric cosmology into the European public consciousness. While the bulk of the book is a description of the most interesting surviving manuscripts (interesting because of their history or what the annotations within them reveal about astronomical thought of the era), the book's 'subplot' involves reflecting upon Arthur Koestler's¹ claim that nobody read Copernicus's book when it was first published, but rather that the heliocentric system developed independently among subsequent thinkers.

Although the large sections of the book pertaining to the purchase and sale of classical texts are fascinating in their own right - for instance, very few copies of the first edition of De Revolutionibus remain in private hands, and one will run upwards of $500,000 at auction - I was personally more interested in Gingerich's overall discussion about what the original owners' annotations found within the texts say about 16th century science.

It's only as I've become older and more experienced that I've begun to appreciate what these classical figures actually accomplished. For instance, Copernicus's heliocentric cosmology was not obviously superior to most people in comparison to the established Ptolemaic model - in fact they both fit and predicted the same observations. However, Copernicus' model was arguably 'simpler'² due to its elimination of the equant, thus favoring uniform circular motion. It wasn't necessarily obvious to the average astronomically inclined person that Copernicus had actually produced something worthy of a revolution in thought and it wasn't until Johannes Kepler published his Astronomia nova (1609) arguing for the elliptical orbit of planets that a simpler heliocentric system that also made more accurate predictions arrived.

An interesting detail with regards to the Copernican vs. Keplerian systems comes from some annotations found in one of the manuscripts suggesting that Copernicus may have been considering elliptical orbits. The author argues that this is very unlikely because, unlike most pictures in high school physics and astronomy textbooks would have you believe, the orbits of the 5 planets known at that time are only very slightly elliptical. This eccentricity has a noticeable effect when attempting to predict the exact positions of planets years into the future, however, Copernicus' lack of a telescope would have led to these deviations being well within his own measurement error.

Oddly, while the book is titled The Book Nobody Read specifically in reference to Koestler's claim, BNR very quickly drops any explicit discussion about the effect Copernicus' model on the European academic scene. The discussion of how the annotations found in many copies reveal who read it and what they thought of it gives us some clues about its impact, but in the end we're told quite quickly that it had obviously been read, and that Koestler 'was wrong. Dead wrong.' I hate for this to sound like a review, but it would have been very useful in my overall appreciation of the work had a final chapter been added that synthesized what we'd learned about Copernicus' impact over the course of Gingerich's very impressive 30 year, globe-trotting endeavor. Oh well.

It's nice to get back to reading for pleasure again.

¹Koestler was a prolific and respected writer who produced a biography of Kepler in 1960. However, in the latter half of his life, he became increasingly fascinated with pseudo-science and the paranormal, especially parapsychology. In my own field of biology, I've come across his name in some old books in reference to the fact that he was still actively promoting the possibility of Lamarckian inheritance well into the 1970s.

²I'm no physicist, so don't quote me here. However, the point is made in the book.

Can Amateurs Still Contribute to Science? and Other Musings...

2009-08-29T11:25:00.005-04:00

amateur (n): someone who pursues a study or sport as a pastime.

Anyone who's read up on the history of science will know that its progress is littered with significant contributions made by amateurs, or people who did not pursue research as their primary means of employment, nor necessarily obtained advanced degrees. Important examples include Gregor Mendel's discovery of genetics, or Abbott Handerson Thayer's contribution to our understanding of animal coloration.

That being said, it's hard to ignore the fact that much of science has become increasingly technical, either requiring expensive, specialized equipment, or analysis techniques that are unlikely to be grasped by people to which they haven't been taught professionally. Thus the question may be asked: can amateurs still contribute to scientific knowledge? That they can meaningfully contribute to the culture and dissemination of science is without question.

This issue popped into my mind whilst pursuing something of an infrequent hobby of mine: random internet searches coupled to relentless link clicking¹. It turns out that while the general consensus may be that amateur contribution to science, at least at the level that was possible in the past, is an aspect of days gone by, the attempt to contribute to ~~pseudo~~ science is alive and well.

Before I discuss the strange, I need to make an important point to my readers who have previously found my rants about science fiction to be tiresome. The issue that I take with regards to sci-fi isn't the existence of speculative fiction or even completely unrealistic 'space sagas'. Rather, it's the confusion that people and the popular press demonstrate about whether speculative fiction is actual science. On posts on my own blog, people have argued that this distinction is crystal clear: science fiction is 'just' fiction, etc. However, my reading of the situation consistently reveals a desire within the sci-fi community to attribute actual scientific contributions to their favorite authors. This post isn't intended to be a continuation of the any previous arguments, however, while speculative fiction contributes general ideas, science is all about the details. Simply drawing a faster-than-light engine on a page and attaching fancy names to its components doesn't hold a candle to actually explaining how it works. Also, I'd like to avoid stuff like this in the headlines:

Michael Crichton, Novelist, Scientist and Creator of Hit-series "ER" Dead at 66

Anyways, link-clicking brought me into contact with the International Fortean Organization (INFO) which, according to the Wikipedia: "The Fortean Society was started in the United States in 1931 by Tiffany Thayer in order to promote the ideas of American writer Charles Fort", who "was an American writer and researcher into anomalous phenomena."

Reading Fort's Wikipedia page is a bit of a microcosm of the disconnect between the perception of science and its practice. We're told that:

Fort's relationship with the study of anomalous phenomena is frequently misunderstood and misrepresented. For over thirty years, Charles Fort sat in the libraries of New York and London, assiduously reading scientific journals, newspapers, and magazines, collecting notes on phenomena that lay outside the accepted theories and beliefs of the time.

This is later referred to as Fort's 'data collection technique'. As far as I'm aware, Fort never actually produced any data to support his fascination with the paranormal (a term as useless as 'supernatural'). Instead, what he's more remembered for is his repeated condemnation of mainstream science, and its susceptibility to bias. As someone put it "People with a psychological need to believe in marvels are no more prejudiced and gullible than people with a psychological need not to believe in marvels." Except for the actual data, I suppose - go look up Fort's 'theory' of the Super-Sargasso Sea for a picture of his nihilistic contributions.

Anyways, I'm getting a bit off-topic here, but 'crankery' is unfortunately one of the most prominent forms of amateur 'contribution', and its modus operandi reveals the misunderstanding that many people have with the concept of evidence. For something to be considered 'scientific', it requires repeatable, controlled, empirical² evidence. I'm strongly inclined to believe that Fort's 'data', for example, is based on anecdotal evidence³. Up to 40,000 people are claimed to have witnessed the miracle at Fatima, for example; however, their accounts vary, and there are plausible non-miraculous explanations for what (may have) occurred. Testable, repeatable evidence always counts for more than any number of anecdotes.

It may have occurred to the reader that this post appears to be more of a rant about pseudo-science rather than an actual reflection about amateur contributions to science. But in reading more random links online, it struck me as to how rigorous the methods of science actually are as compared to all of the new-age quackery (please consult timecube.com). It's unfortunate that the 'paranormal' seems so tantalizing to general public, and it's explanations often seem simple and comforting, while complicated, dry science is apparently boring. One need only look at the phenomenon surrounding The Secret in order to get some idea of the supernatural's appeal.

Nonetheless, there's certainly opportunity for lay-people to contribute meaningfully as a hobby in the descriptive wings of fields such as ecology and astronomy, where independent observation of many locations greatly helps in efforts to catalog a wide variety of phenomena. However, it seems rather unlikely that it's easy for people to make contributions to physics, chemistry, or molecular biology on their spare time.

As a final thought, I wonder if the increasing technicality and breadth of required jargon within most fields is partially responsible for our having a difficult time disseminating an interest in these matters to the broader public? Most of science has probably been quite technical for a good century now (physics and astronomy for longer), however, there was not that long ago when all that was known about genetics, for example, could have been absorbed by any reasonably curious person. Just a thought.

¹Let the reader be warned! It is via this pass-time that I discovered furries, slash fiction, and very bizarre white power music. I'm not passing judgment (except on the racism, of course) but clicker beware, the majority of the internet is NSFW.

²Empirical can either indicate direct observation, or through the use of instruments or techniques whose information is acquired through means that are understood based on other scientific principles.

³Wow, I looked up the Wikipedia page on paranormal and found the line: Charles Fort (1874-1932) is perhaps the best known collector of paranormal anecdotes.

A Spectacular Gift!

2009-08-27T16:25:00.004-04:00

A good friend of mine got me a very nice gift for my defense:

It's an original 19th century United States 6th ed. of The Origin of Species by Means of Natural Selection as published by Rand, McNally & Company (before they transitioned exclusively into cartography)! We've done some internet scouring in order to get some info about this edition of the manuscript; it's odd because it does not feature a publication date. Some classic booksellers list it as published in 1872-73 (the original publication was made in 1872 in England by John Murray & Sons); however others suggest that Rand McNally may have acquired the rights to publish the book a little later. There were multiple American publishing houses issuing the book.

Interestingly, the first page is signed "Edwin A. Howes Jr." with "Feb. 12, '98", which we've assumed refers to 1898:

A little bit of internet searching reveals that Edwin A. Howes is a relatively popular name, however, there is one Edwin Alliston Howes Jr. who was a tax attorney and author who lived during the appropriate period. Unfortunately, I have been unable to find any details beyond that.

Regardless, it's an amazing gift and the perfect thing to get a book obssessed nerd such as myself. I already own copies of the 1st and 6th editions of The Origin, perhaps it's time to read it again?

In other news, the thesis was printed and handed in yesterday, thus making my Ph.D. official. Furthermore, I went to the clinic here at Mac and talked to a doctor about my 'thesis wrist'. Thankfully, it appears to be the coupling of a minor case of tendonitis as well as something else I can't pronounce, but it should go away in a few days so long as I take a regular dose of anti-inflammatory Advil, and sleep with the wrist brace. Better yet, the doc told me that I don't even have to give up playing video games (just 'take it easy'). So all is good, I'll try to get back to posting about science-specific topics tomorrow!

Finally got my Ph.D....

2009-08-25T19:48:00.003-04:00

The evening before my thesis defense, I had two separate nightmares about the thing. Standing up in front of a panel of critics and attempting to demonstrate that you are knowledgeable in a complex field is a fairly harrowing experience, you see.

As I said in my brief post yesterday, I expected the questions to be more general. For instance, several aspects of my thesis, especially with regards to the statistics underlying the analysis of patterns of molecular evolution or microarrays, have many different software tools available. Many of these programs operate under different assumptions, and there's a fair amount of debate in the technical literature about the relative pros and cons with regards to any particular technique. This provides fodder for questions: e.g., why did you choose this particular test/program instead of that one? While I certainly got a few of those, the majority of the questions were concerned with the details of my tables and figures, or the wording of various sections of the manuscript - particularly with regards to our assumptions and expectations.

I'm not complaining; I'm quite glad the thing is done! However, I think that this reaffirms my earlier point about how it's very difficult to predict the types of questions you'll be asked. All three of the molecular evolution/population genetics defenses that I attended in the past month were quite different in terms of the content and direction of the questioning. Thankfully, I received very few corrections (a few typographical issues and requests to add in a couple of references) and I was able to finish them all today - tomorrow I'll print it off and hand it in, thus 'sealing the deal'.

Last night, some friends from the department came by my apartment for a celebration, and I was finally able to crack open the specialty bottle of Jack Daniel's that TheBrummell had procured from Lynchburg, TN; subsequently gifting it to me with the stipulation that it be opened only after my defense. It went down nice and smooth, like sippin' whiskey should. During the celebrations, some people asked me if I felt any different, having now finished. Honestly, I didn't, and I still don't today.

I think that there was a big change in my knowledge and comprehension of my field, as well as my outlook on the direction of its research, during the course of the actual writing of my thesis. I'd felt the same way at the end of my M.Sc. as well. I remain convinced that there's something fundamentally valuable about taking the time and effort to properly situate the work you've been doing into a broader context - both in terms of the 'story' you've attempted to tell with your degree, and in the entire field as a whole. I'm quite disturbed by the few people I've spoken to who would prefer that we eliminate the practice of writing theses altogether because 'no one reads them'. I don't necessarily think that that was ever the point. Regardless, I feel about the same way now as I did when I handed in my thesis, just a lot more relaxed.

I suppose that this really is a milestone in my life. As my father has always said, education is the one thing that people can never take away from you. Once you get those letters stuck behind your name - B.Sc., M.Sc., Ph.D. - they become a permanent form of 'currency' in the market of human capital. While the real reflection of my abilities as a researcher may lay in my publication record, my ability to be recognized as an effective communicator at conferences and the like, and my capacity to come up with new and interesting avenues of inquiry, that Ph.D. is a necessary stepping stone advertising that I actually put in the hard work necessary to understand what I'm talking about. However, a Ph.D. is not a sufficient criterion for being respected in science, rather that requires regular demonstration of proficiency, and thus the adventure continues.

I'm glad I'm finally here: it was a long, hard road with many ups and downs, but I'd like to think that the former outnumbered the latter. It's difficult to believe that when I entered my undergrad, Clinton was still in power in the U.S., Wikipedia didn't exist, Geocities websites were all the rage, and I'd never heard of a blog. I've spent 10 years in university, most of the time living in residence or crummy apartments, while many of my friends went on to do things like get married, have kids, and secure real jobs. Once in a while, while things were rough, I'd envy them; but only rarely, and in the end I don't regret it for a moment. I know that I love what I do and the prospect of never having to work at a job that I hate is worth all of the blood, sweat, and tears.

(Raising a glass of Daniel's fine whiskey): To good friends and good science all along the empiricist's path.

Dr. Carlo!

2009-08-24T15:46:00.004-04:00

By the ecological explanatory power of Hamilton's theory of kin selection, the deed is done! I have successfully defended my Ph.D., thus completing a decade of post-secondary education. The questions posed during my defense were a bit more specific than I expected - almost everything involved me explaining specific details of my analysis. I'd really spent a lot of time preparing for general questions about the methodology. However, I was familiar with what I'd done, so overall I think I came off well.

I'm having a bunch of colleagues from the Dept. over this evening for a celebration, so I don't have time to write out a long blog post. I just wanted to say that it's done and that it went well. I'll write up a longer treatment tomorrow!

YAY!

Am I Ready?

2009-08-21T11:05:00.004-04:00

I've spent the entirety of the past week doing 3 things: 1) Reading over the key review and data papers relevant to the introduction to my thesis, 2) Reading over the details of the methods I've used, particularly the software and stats (I've got two bioinformaticians on my examination committee), and 3) finalizing and practicing my presentation.

The presentation is essentially done. As was the case during my M.Sc. thesis defense 4 years ago, I found putting together this talk especially tough. How does one summarize four years of work on a variety of subjects in 15 to 20 minutes? Actually, you're not supposed to summarize anything - the guidelines are as follows:

The Ph.D. Final Oral Examination on the thesis takes the form of a brief statement by the candidate and questioning by the Committee. You should prepare a statement which will take between 15 and 20 minutes to deliver. In preparing it, you should consider that you are speaking to an audience who have read your thesis. A simple summary is therefore neither necessary nor desirable. What you should endeavour to do is stress the main points of your contribution to the advancement of knowledge and the technical difficulties either of an experimental or theoretical nature which you have overcome. Notes or other aids may be used but the statement may not be read from a prepared script.

It's a 'statement', not a 'presentation', much like the statement made by the defendant at the beginning of a trial... Every single person from our department who has defended has essentially provided a summary of their work, followed by some comment about its significance. I will do the same. An email from my supervisor to the Dean of grad studies about why we aren't expected to summarize our work for the general audience led to a reply indicating that the grad studies committee is thinking about revising these rules, encouraging a summary. But I digress...

This morning my boss walked into the lab and asked: Are you ready for Monday? Well, I suppose that I'm comfortable with the materials contained in my thesis. I won't be able to go into the technical details of every single analysis I've used, but I think I understand their utilities and limitations. I've also tried to mull over ideas regarding the standard questions that one gets asked at these things like future directions, what I would have done differently, caveats to my analysis, etc. Also, my wrist continues to ache and I think I'm going cross-eyed from all the reading/note-taking I've been doing.

My experience regarding my M.Sc. defense is that I could anticipate a few obvious directions of questioning (e.g., anything that was rather equivocal in the thesis); however, the majority of the questions were unanticipated yet relevant, and I think I did a pretty good job answering most of them. Some things I didn't know, but that will be the case on Monday as well - my goal is to feel confident about my ability to answer the questions I definitely should know the answers to.

While I began stressing out about my M.Sc. thesis weeks in advance, I've only just begun to get nervous about the Ph.D. defense. It's easy to sit in the audience during a defense and cringe when someone cannot answer an obvious question; but it's another thing entirely to be standing in front of the firing squad while being asked the same thing yourself!

In the end, I suppose there's only so much you can do at this point. Most of the preparatory work should have been done in the past four years: a week before the defense isn't when one is supposed to start thinking about why things were done the way that they were! All that I hope for is that I'm led into the questioning with a few softballs, so that I can get my confidence up and establish a 'flow'.

We'll see if I throw up an 'I'M FREAKING OUT!' post during the weekend!