Return to Origin part 2

In which Darwin’s Introduction sends me off on tangents about academic writing, gender and the nature of explanations.

The Origin of Species reread returns! Eventually! So much for increasing my productivity, but hey, at least I didn’t give up after the first one! (For the record, this post has been 99% written for the past month. It only took me that long to convince myself that hitting the “publish” button won’t turn me into the laughing stock of the universe.)

This won’t be as long as Part One, since the Introduction isn’t as long as the Historical Sketch either. In comparison with modern scientific works, the Intro is basically the abstract of Origin, mixed with a few acknowledgements. It covers pp. 65-69 of my copy.

It’s amusing and endearing how much of the first couple of pages is spent swearing up and down that Darwin didn’t pull his theory out of his backside. Also, the “sorry I couldn’t give you all the facts, I had to be brief” apology always cracks me up – if 400 pages full of facts is your idea of brevity, man, you should be writing epic fantasy, not science 😛 (Also: perfectionist much?)

I have written my own handful of scientific articles in my time as a PhD student, which definitely gives one a different perspective on some of the writing conventions in such works. (It should go without saying, but this is my individual perspective; I certainly don’t claim to represent all writers of scientific articles.) When authors talk about caution and caveats and more data being needed, I think most of the time they are both sincere and not. Scientists – the ones I’ve met, at least – generally seem like decent people who honestly worry about getting stuff right and not letting wishful thinking get in the way of good science.

However, when you’re preparing a manuscript for a peer-reviewed academic journal, there is always an element of satisfying reviewers, and if you sound more confident than the reviewers think your data warrant, they will comment on that. Adding caveats is not just a sign that you understand the limitations of your work, it is also insurance against being hassled by editors and reviewers. (And then there’s always throwing a bone to your worst enemies just in case they try to sabotage your paper, because scientists can be just as petty and occasionally awful as humanity at large, and often, anonymity doesn’t actually make it that much harder to figure out whose paper you’re reviewing.)

With all that said, it never occurred to me that Darwin wasn’t perfectly sincere in his numerous apologies for not providing even more evidence. He just doesn’t seem like that kind of guy. Please don’t disillusion me. I’m a giant ol’ sap at heart, okay?

P65 has another shoutout to Wallace, and p66 a huge acknowledgement to Hooker (an eminent scientist in his own right). This Darwin-Hooker bromance is making me all mushy inside! (See above: giant, sappy)

Pp66-7 contain, aside from another little dig at the Vestiges of Creation, some first-class philosophy fodder. Here, Darwin emphasises the importance of providing mechanisms when positing a new phenomenon. Lots of people, he says, might look at the similarities among species and conclude that different species have descended from common ancestors. “Nevertheless,” he continues, “such a conclusion, even if well founded, would be unsatisfactory, until it could be shown how the innumerable species inhabiting this world have been modified, so as to acquire that perfection of structure and coadaptation which most justly excites our admiration.”

Do we agree with this assessment? How much is suggesting a “what” worth without an accompanying “how”? And how necessary is a mechanism for the acceptance of a new scientific idea? The simple, distilled high-school science class version of the story of continental drift, for example, tells you that Alfred Wegener was laughed out of the room because he couldn’t say what force might make continents waltz across the surface of the planet. Then someone came up with mantle convection, and Wegener’s idea finally triumphed. The actual story, as is usually the case, seems a bit more complicated than that, but it does sound like the general acceptance of the idea needed that mechanistic underpinning that its proponents couldn’t quite provide at first.

While looking for scientific ideas that might have been widely accepted without that underpinning, I found myself getting really philosophical and wondering what counts as a mechanism. Perhaps this is easier to answer in biology, where most explanations can at least be conceptualised. One doesn’t have much difficulty imagining some individuals being better at procreation than others, and babies resembling their parents (the very dumbed-down essence of natural selection). What about physics, where shit gets really weird and soon leaves the realm of human experience when you start digging deep enough? Did physicists accept concepts like gravity, dark matter and dark energy because the maths worked out, because the observations were so bloody obvious that something had to be going on, or because “attractive force”, “weakly interacting massive particle” or “vacuum energy” make sense to human brains? (Of course, I wouldn’t expect a physicist to accept anything based solely on the third, but where the maths could go multiple ways, as – so far as I understand – on the boundaries of modern cosmology, is it easier to lean towards the equations that correspond to concepts that make the most sense?)

… I guess what I’m saying is that this stuff is fascinating to ponder, and if anyone points me to a readable discussion of the subject by someone who actually knows what they’re talking about, I might well put it on my ever-expanding reading list…

P67 then reminded me how times have changed since Darwin’s day. Here, he discusses “man” and his “great power” in “accumulating slight variations”. Every time he talks about something humans did, it’s always a “he” (well, at least up to the end of the next chapter 😛 ). We’ve certainly come a long way when it comes to recognising the rest of humanity’s role in history…

This is where I decided that I needed to keep an eye out for any mention of female scientists (or just women in general) – women of science have existed for as long as science itself, but I’m curious whether Darwin drew on the work of any. It’s always satisfying to see women’s achievements recognised by their male contemporaries, especially in times when it wasn’t fashionable to do so. It would be extra satisfying to see it from a man I like and admire in his own right.

There is not much to say about the rest of the Introduction, except to note that it’s a decent summary of Darwin’s evolutionary theory. He lists the basic elements of the theory (variation + competition = natural selection + extinction), the main categories of evidence he used to come to his conclusions (artificial selection, embryology, ecology, biogeography, fossils) and the main questions that the theory must answer (novelties of morphology and behaviour, the sterility of hybrids, and the gaps in the fossil record). All of these will make extended appearances in the course of the book.

The last paragraph of the Intro is such a typical conclusion to a scientific abstract that I had to smile when reading it. There is still much to be learned, but the author is convinced that he is right about X, Y and Z. Not saying this is a bad way to conclude an introduction – all I’m saying is that for me, it’s a well-worn trope of academic writing that echoes with the voices of a thousand other works.

Next time, we’ll get into the meat of Origin proper. It turns out that the meat in Origin is often pigeon. (Seriously. Darwin was obsessed with pigeons.)

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In which fangirling turns into philosophy

Textbooks may portray science as a codification of facts, but it is really a disciplined way of asking about the unknown. — Andrew Knoll, Life on a Young Planet

Some books change your life. When I was 12 or 13 or thereabouts, SJ Gould and others’ Book of Life rekindled my interest in prehistoric life, introduced me to the Cambrian explosion, and opened my eyes to a whole new worldview. It’s one of the reasons I hold a degree in evolutionary biology.

Life on a Young Planet was not a life-changer, precisely. That’s not why I love it to pieces. By the time I read it, I’d gained an appreciation of just how complex and full of uncertainty natural science was, and the book was permeated by an awareness of this complexity. Also, it was simply beautiful writing.

(I can’t emphasise the importance of good writing enough. I’ve read too many papers and books [Crucible of Creation and The Plausibility of Life, I’m looking at you] that had good information but were so atrociously written that I nearly put them down despite being fascinated by their subject.)

Last month, the author of Life on a Young Planet, Harvard professor Andy Knoll, came to visit my university. I was practically bouncing with excitement from the moment I saw his name on a newsletter. He gave four lectures in total; until the very last one, I actually contemplated getting my copy of the book signed. Or, to be a fangirl and a nerd, my printout of his lovely biomineralisation review. (I still can’t decide if I made a mistake. Damn, I didn’t even ask a stupid question. Four lectures, and I just sat there and drooled over my notebook.)

Knoll is nearly as good a speaker as he is a writer. He doesn’t have the liveliest voice and speaks quite slowly, but if you can get past that, his lectures are really good. (I’m glad of that; I really don’t like losing my illusions!) They are solid structures that you have no difficulty following the logic of.

Let me put it this way – Andy Knoll is an excellent storyteller.

That got me worrying, because I’m a sceptic and (truth be told) a little bit of a cynic at heart, and because over the years I’ve done a lot of navel-gazing about belief and knowledge and conviction. I have a tendency to grow suspicious when I feel too certain about something.

Am I – are we – too often blinded by good storytelling? How often do we get so enamoured of good ideas that we try to force them on situations they don’t fit? And how often do we doubt something just because it sounds too neat?

Here’s the specific example from the Knoll lectures that made me think of this. Knoll is a champion of the oxygen + predation explanation of the Cambrian explosion. (I didn’t realise he was involved in that paper until it came up in the lectures…) He is also an advocate of a similar explanation for the diversification of single-celled eukaryotes 250 million years before the Cambrian. He convinced me well enough, but then I immediately thought – really? Is it really that simple? Does one size really fit both events?

I often take note of these “pet ideas” as I read scientific literature. A group of phylogeneticists uses microRNAs to tackle every tough problem ever. A palaeontologist interprets every squishy-looking Cambrian weirdo as a mollusc. Researchers in the biomineral field look for slushy amorphous precursors to crystalline hard parts everywhere. (Remember, all generalisations are false ;))

Just to be clear: I’m not at all saying that being a “pet idea” automatically makes something wrong or suspicious. For instance, the hunters of amorphous biominerals have some good theoretical reasons to look, and they often do find what they’re looking for. Likewise, I’m impressed enough with Andy Knoll’s pet hypothesis about the Cambrian that I’ve rethought my own pet ideas about the subject.

I’m also not accusing these people of being closed-minded. Going back to Knoll, IMO he demonstrated ample healthy scepticism about his pets during his post-lecture Q&A sessions. (Which makes me a bit less nervous about the neatness of his stories.)

Someone better versed in the philosophy and sociology of science could probably write a long treatise involving paradigms and confirmation bias and contrariness here. I’m even less of a philosopher than I am a geologist, so I think I’ll leave the deeper insights to those who have them.

Meanwhile, I’ll continue to be a fan of Andy Knoll and appreciate a good scientific story. So long as I remember to look beneath the surface – both of good stories and of my own suspicion of them…

 

Jean-Bernard Caron likes molluscs!

A while back, I discussed the interpretation of the enigmatic Cambrian creature Nectocaris on this space. I just discovered that the same guy (or, well, one of the guys) who described the new Nectocaris fossils as the remains of a primitive cephalopod had also been part of a publication “molluscifying” another enigmatic Cambrian creature. In this somewhat earlier case, Caron et al. (2006) interpret Odontogriphus as a soft-bodied primitive mollusc. Something of a grand-uncle to everything molluscan that lives today. (Unlike Nectocaris, Odontogriphus did, apparently, have a radula.)

Needless to say, this interpretation was immediately contested by another Cambrian expert, Nick Butterfield (Butterfield, 2006). The radula of Odontogriphus (and of the more popular “spiny slug” Wiwaxia) aren’t necessarily true radulae, the serial gills of Odontogriphus need not be the specific kind of gills that molluscs have, etc. (This then triggered a response from Team Mollusc [Caron et al., 2007], but I digress :))

I’m beginning to see a pattern here, something much broader than J-B Caron vs. everyone else. It basically reminds me of the contrast the whole of Wonderful Life (Gould, 1991) was built on. To those who haven’t read the book, one of the central themes of Wonderful Life is the (re-)interpretation of Burgess Shale fossils. Initially, the fossils were all shoehorned into already known groups. Decades later, palaeontologists began to examine them more closely, and found that few of them truly fit into those groups. Out of these surprises grew Stephen Jay Gould’s brave new Cambrian world, the festival of freaks that later dwindled to the pathetic little remnant of its full diversity that populates today’s seas. (We’ll leave the discussion of how right or wrong either view is for another time ;))

Another parallel that comes to mind is the extreme range of interpretations of the earlier Ediacaran organisms, which researchers have flagged as everything from early members of living animal groups to a totally new form of life.

Also, somewhat, the lumper/splitter division that seems to exists in vertebrate palaeontology. There are the “lumpers” who want to group everything vaguely similar into the same taxon, and there are those that want to split everything vaguely unique into its own group. (It should go without saying, but there are also opinions in between. I don’t want you to come away thinking that palaeontology and taxonomy are just armed camps of lumpers and splitters shouting obscenities at each other across a barricade ;))

I get the impression that hardcore lumpers tend to consistently be lumpers and hardcore splitters tend to remain splitters.

Are there just some people who want to connect every new observation to something we’ve already seen? Are there just people with a natural tendency to emphasise the uniqueness of new observations? Or prefer to take the middle ground, as the case may be? Why? And more generally, what makes scientists pick one side – or refuse to pick sides – in controversial issues?

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References

Butterfield NJ (2006) Hooking some stem-group “worms”: fossil lophotrochozoans in the Burgess Shale. BioEssays 28:1161-1166

Caron J et al. (2006) A soft-bodied mollusc with radula from the Middle Cambrian Burgess Shale. Nature 442:159-163

Caron J et al. (2007) Reply to Butterfield on stem-group “worms”: fossil lophotrochozoans in the Burgess Shale. BioEssays 29:200-202

Gould SJ (1991) Wonderful Life. Penguin.

Mazurek D and Zatoń M (2011) Is Nectocaris pteryx a cephalopod? Lethaia 44:2-4

What might have been possible

(Of fins, genes, fossils and the nature of evidence)

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Behold the lengthy going-on about limbs, developmental genetics and semi-philosophical stuff that I promised! I mentioned that this was long in the making. Ironically, that means I’m not sure I managed to make it coherent… Then again, my blog subtitle does warn you about certain “meanderings” 😉

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I previously mentioned that limbs kind of brought me to evo-devo. I haven’t closely followed the subject since, but a recent paper (Schneider et al., 2011) brought it back to my attention. Aside from the nostalgia, the evolution of limbs is also a perfect excuse for me to ruminate on some of the issues I consider important in evo-devo – such as the meaning of evidence, the role of “model organisms” and the nature of homology and novelty. (Some of this I touched on in my treehopper post)

I love developmental genetics. Davis et al. (2007), which through the blurred glasses of hindsight I’ll call the paper that made me an evo-devo nerd, is a genetic study. Genes are really exciting for us evolutionists because they obey different rules from the traits they control. Especially for regulatory genes – those that affect the activity of other genes –, gene sequence doesn’t correspond to the appearance of the organism in any straightforward way. The same circuitry of regulatory genes can also control the development of quite different structures, because most of the actual work is done by their target genes. Therefore, genes can often preserve connections we can no longer see in higher-level traits. (My favourite combination of evidence is genes plus fossils, but bear with me a little…)

The gist of Davis et al. (2007) is as follows. Hands and feet (collectively known as the autopod) are unique to tetrapods, or vertebrates with legs. There’s a special pattern of Hox gene activity that controls autopod formation. This pattern was missing from the fish that had been examined at the time. However, those fish are quite different from the distant ancestors they shared with tetrapods. There are living fish whose fin skeletons include bits that might correspond to digits, and there are many fossil examples. These include, as it later turned out, not just the iconic fishapod Tiktaalik, but also its slightly less tetrapod-like relative Panderichthys (Boisvert et al., 2008). Hence the question: did common lab animals like zebrafish lose the bones and the genetic circuitry, and did the bones of the autopod evolve from particular bones of the ancestral fin, or did tetrapods invent something new?

The answer is almost certainly the former, Davis et al. (2007) tell us after they find the tetrapod kind of Hox gene expression in the fins of a comparatively “primitive” ray-finned fish (Ray-fins are one of the two main groups of bony fishes. The zebrafish is a ray-fin, as are other familiar fish like cod and tuna. The other group – lobe-fins – include lungfish, coelacanths and tetrapods themselves). Around the same time, other teams found similar patterns in lungfish (Johanson et al., 2007), which are probably the closest living relatives of tetrapods, and sharks (Freitas et al., 2007), which are only distantly related to any of the creatures mentioned above.

Schneider et al. (2011), which caused this post, found that some DNA elements that regulate the Hox genes in the autopod are shared by tetrapods, ray-fins and sharks (ergo, probably all living vertebrates with fins or limbs). Together with the evidence from fossil and modern skeletons, this suggests that the digits of tetrapods evolved from pre-existing fin bones by tweaking an ancient genetic program. Fins and limbs really are variations on a single ancient theme. (Illustration of “fishapod” fins and early tetrapod limbs below is by Dennis C Murphy, from Devonian Times)

It is at this conclusion that we come to the stuff Hox gene expression can’t tell us. Knowing that radial bones (or cartilages, as the case may be) in fins and digits in limbs are “really the same thing” in some way is one thing. But radials and digits are not that similar, and neither is a shark’s fin and a newt’s leg. Maybe you’re interested in how one became the other, how fins suited to balancing and manoeuvring in water became limbs suited to plodding along on land. The autopod-like Hox pattern doesn’t say, since it’s basically the same in appendages that look very different, a perfect example of what I said about regulatory genes a few paragraphs back. Clearly, Hox genes define a distinct part of the fin or limb, but they don’t give detailed instructions on how to flesh it out. The details depend on the genes under Hox control.

Unseen ancestors

Now, fins and limbs are relatively easy, because we have a really quite awesome fossil record of their history (and also, some cool computer models :D). But the same lessons we can learn from their example apply equally to countless other cases where the fossil record is silent. Shared expression patterns of “master” genes and genetic pathways are often used to infer things about ancestors that aren’t known from fossils at all (De Robertis, 2008 is a nice review of such pathways). How far can we take such inferences? What does the fact that arthropods, vertebrates and segmented worms all seem to use some of the same genetic pathways to generate their bodies from repeating units (e.g. Stollewerk et al., 2003; Pueyo et al., 2008; Rivera and Weisblat, 2009)? Was their common ancestor as obviously segmented as an earthworm, did it just have a few repeated body parts like a chiton, or maybe nothing more than the basic ladder-like nervous system* of bilaterian animals? Or perhaps even less?

[*Photo of the nervous system of a planarian flatworm stained with a fluorescent dye, by the Agata group.]

The fossil record of early animal evolution (or rather, the lack of it) argues that this common ancestor was relatively small and simple (Erwin and Davidson, 2002). We know that quite different structures can be underpinned by the same “master” genes. Given this, can we really say anything meaningful about such long-extinct creatures? Well, we certainly can. They probably had the genetic circuitry their descendants share today. But what does that say about their body plans?

The answer may not be too far from “fuck all”. That’s why I chose a quote from Tabin et al. (1999) for the title of this post. I couldn’t agree more when they write, “developmental genetics only tells us what characters might have been possible”. I love finding out where we and the other creatures with whom we share this planet came from. That’s why I’m in this business. But there is only so much that any given type of evidence can tell us. And this is why I think the fossil record is so important. Like Erwin and Davidson (2002) argue, it can help us distinguish between “might have beens” in sometimes surprising ways.

Same difference

All of this puts the whole concept of homology into a slightly unsettling new perspective. Homologues (often spelled “homologs” nowadays) are supposed to be traits (genes, organs, behaviours etc.) that are derived from the same ancestral trait. The original concept of homology was defined for whole organs/body parts. Now, what do we do with organs that are made by the same genetic networks? Some of them show obvious historical continuity with the organs of other organisms. A bird’s wing is clearly homologous to my arm, on probably every level imaginable. They are connected by similar position on the body, similar basic structure, similar development and developmental genetics, and a rich fossil record. But that absolutely need not be the case.

Some butterflies use the same genetic circuitry to put eyespots on their wings that insects in general use to subdivide their wings into different regions (Keys et al., 1999). It would be quite absurd to call wings and eyespots homologous because of that – but in a very real sense, the gene network underpinning both is “the same thing”. And there is everything in between. Eyes, for example, share common “master” developmental genes including Pax6/eyeless. They were probably built around homologous cell types (i.e. photoreceptors) in most animals that have them (e.g. Arendt, 2003). Nonetheless, the highly complex eye structures of, say, a squid, a dragonfly and a falcon almost certainly evolved independently. And then there are the strange, confused identities of bird fingers that I talked about on previous occasions. Thus, when we ask the question: “are these two structures homologous?” – there is often no simple yes/no answer. At the very least, you have to ask: at what level?

An ode to diversity

The whole autopod business also highlights the dangers of extrapolation. Scientists believed that the autopod-specific Hox code was invented by tetrapods because their staple experimental fish didn’t have it. But life is a huge, diverse bush. Every twig has its own unique quirks, and we can’t take any of them to represent everything on its branch in every respect. In fact, some of the most popular lab animals – fruit flies, nematode worms, the aforementioned zebrafish – are also among the quirkier denizens of the planet. This is why I find it really really important not to limit ourselves to a few well-worn “model organisms”, not to draw sweeping conclusions from them. Although our common ancestry means that fruit flies or nematodes will in many ways help us understand ourselves, there is no guarantee. Comparative biology thrives on diversity.

(Of course, I say that as an evolutionary biologist working on a non-model organism. I may be somewhat biased ;))

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References

Arendt D (2003) Evolution of eyes and photoreceptor cell types. The International Journal of Developmental Biology 47:563-571

Boisvert CA et al. (2008) The pectoral fin of Panderichthys and the origin of digits. Nature 456:636-638

Davis MC et al. (2007) An autopodial-like pattern of Hox expression in the fins of a basal actinopterygian fish. Nature 447:473-476

De Robertis EM (2008) Evo-devo: Variations on ancestral themes. Cell 132:185-195

Erwin DH & Davidson EH (2002) The last common bilaterian ancestor. Development 129:3021-3032

Freitas R et al. (2007) Biphasic Hoxd gene expression in shark paired fins reveals ancient origin of the distal limb domain. PLoS ONE 2:e754

Johanson Z et al. (2007) Fish fingers: digit homologues in sarcopterygian fish fins. Journal of Experimental Zoology Part B 308:757-768

Keys DN et al. (1999) Recruitment of a hedgehog regulatory circuit in butterfly eyespot evolution. Science 283:532-534

Pueyo JI et al. (2008) Ancestral Notch-mediated segmentation revealed in the cockroach Periplaneta americana. PNAS 105:16614-16619

Rivera AS & Weisblat DA (2009) And Lophotrochozoa makes three: Notch/Hes signaling in annelid segmentation. Development Genes and Evolution 219:37-43

Schneider I et al. (2011) Appendage expression driven by the Hoxd Global Control Region is an ancestral gnathostome feature. PNAS 108:12782-12786

Stollewerk A et al. (2003) Involvement of Notch and Delta genes in spider segmentation. Nature 423:863-865

Tabin CJ et al. (1999) Out on a limb: Parallels in vertebrate and invertebrate limb patterning and the origin of appendages. Integrative and Comparative Biology 39:650-663