Book Club: Natural Acts...

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...

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...

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...

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...

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...

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...

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.