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.)

Return to Origin part 1

Introducing my new pet project

The Mammal has had an idea to boost her productivity! (OK, I’ve actually had this idea pretty much since I started CM. Speed has never been among my selling points 😛 ) Since most of the posts I start writing about current science seem to die in their cradles these days, I have decided to go back to Ye Olde Science and try my hands at an Origin of Species re-read. Because Origin is one of the foundational works of my discipline, and it proved to be a lot more interesting than a callow undergraduate student of evolutionary biology had expected. Also, there is a lot of material in it, and on previous reads I’ve had no shortage of thoughts about it. There is a faint chance it can sustain a few months of blog posts 🙂

I’ve never been too bothered about reading “the classics”. The classics of literature that school forced me to read often turned out to be terribly written, boring tomes whose “profound” meanings held little interest for a young person. Much of my higher education gave me the feeling that biology is such a fast-moving field that anything older than a decade or so is probably of little value except as a historical curiosity. I was, it turns out, very wrong about that for more than one reason. First, you don’t really start appreciating the value of older literature until decades-old, obscure zoological papers are the only place you can find any information at all about the question you are researching. Biology may move fast when it comes to the genetics of well-known model organisms, but it sure as hell takes its time in investigating the development and regeneration of serpulid opercula.

Second, history can be interesting in itself. Science is not a series of independent discoveries; it is a complex, organic growth cultivated by interconnected minds embedded deep in their respective societies. Which ideas get picked up and which ones are forgotten doesn’t just depend on the quality of the evidence but also on the zeitgeist. (The first example I thought of was, disturbingly, the triumph of Lysenkoism over real genetics under Stalin. I guess straight-up imprisoning or executing anyone who doesn’t like your pet advisor’s pet theory kind of counts as an effect of the zeitgeist?)

I first decided to read Darwin’s Origin a number of years ago out of curiosity. I was, after all, studying for an evolutionary biology degree, and Origin was kind of the book that kicked it all off. (I think it might have been on offer at the university bookstore when I went to buy some textbooks, too.) To be honest, I fully expected a boring, painfully outdated, horribly convoluted book. I expected reading it to be a chore. I certainly didn’t expect to find beauty – never mind revelations – in it.

Suffice to say I was pleasantly surprised. While Darwin’s writing style can be a drag for a modern reader with an attention span trained on Facebook posts and cat memes (he’s waaaaaay more fond of run-on sentences than I am, and I have to actively restrain myself from letting them grow out of control), it is quite beautiful at times. What’s more interesting from the scientist’s perspective – while a lot of Origin is indeed outdated, there are some surprisingly “modern” ideas that I never would have expected to find in a 19th century book. The third major surprise of my first read was the sheer amount of data involved. I suppose I’d always known that Darwin didn’t pull his theory out of thin air, but I hadn’t realised just how much careful observation went into his best-known work. No wonder it took him decades to finish [1].

And so, from the vantage of a few more years of learning, I decided to give Origin of Species another read and document my thoughts along the way. I have no idea if this is going to work out, but hopefully publishing the first part will give me the incentive to carry on.

Origin saw six editions altogether. The version I have, the 1985 Penguin Classics edition, contains the text of the first edition, but also includes the Historical Sketch that Darwin added later. The Sketch itself went through a number of revisions; I’m not entirely sure which version my copy has. (Origin can be read free of charge in several places online, including TalkOrigins and Darwin Online. TalkOrigins’s version is also a first edition text with the Sketch added.) It is with this Sketch that I’m going to kick off the re-read.

I won’t even attempt to summarise chapters, and I might have to split most of them into multiple posts for sheer length. Comments might be a bit disjointed, since they reflect thoughts that came into my head as I was reading – sometimes connected, but often quite scattered and tangential. Any page numbers refer to my Penguin edition, but I’ll try to remember to give some pointers (paragraph descriptions, section headings, quotes) for anyone reading a different version.

Darwin on the shoulders of giants – the Historical Sketch (pp53-63)

I find the Historical Sketch (hereafter: HS) tremendously interesting. I’m not entirely sure why it appeared in later editions of Origin; I had assumed that it was a response to claims that he was ripping people off, but googling the subject yielded surprisingly little information. Johnson (2007) calls its origin “somewhat obscure,” and Darwin’s own statements on the matter contradictory. Darwin’s correspondence doesn’t even clarify when the HS was written, let alone why. Similar historical introductions, Johnson notes, are not uncommon in scientific writings of the era, and it is quite possible that Darwin was already drafting one for his “big species book” (of which Origin was the abridged version) years before the publication of Origin, but not much evidence remains to fill in the details.

General observations

Regardless of where it comes from, the HS is an intriguing little run-down of the history of evolutionary ideas as Darwin saw it. If there is one take-home message from this brief preface to Origin, it is that no scientific advance is a lightbulb suddenly blinking on in the dark. Ideas have roots, and complicated ideas come together from many different roots, some of them, in this case, going right back to antiquity.

Any good biology curriculum includes some of the researchers and thinkers featured in the HS – who hasn’t heard of Lamarck and his silly-silly inheritance of acquired characteristics, for example?[2] However, schools tend to gloss over the sheer quantity of evolutionary thinking going on in late 18th and early- to mid-19th century biology. Well, in his ten-and-a-half-page summary, Darwin discusses 34 authors, all of whom entertained the idea that species might change over time, and many of whom considered possible mechanisms for such change. Most of these guys I’d either never heard of at the time I first read Origin, or I’d never known they had a connection to evolution. All in all, the HS definitely gives the impression of a biological community ripe for an evolutionary revolution.

Finally: oh GODS, some of this is so funny. The HS exhibits some prime examples of the kind of borderline impolite academic snark that you can also find in today’s scientific debates. Having done research and written a few papers myself, I find academic snark doubly entertaining; just how many ways can you call someone an idiot while maintaining that essential veneer of professionalism?

A page-by-page trip through Tangentia

A.k.a. any old silliness that popped into my head along the way.

Victorian titling conventions: clearly long before the invention of clickbait! The full title of Origin is the unwieldy The Origin of Species by Means of Natural Selection, or The Preservation of Favoured Races in the Struggle for Life. [3] The HS is technically called An Historical Sketch of the Progress of Opinion on the Origin of Species Previously to the Publication of the First Edition of This Work. Quite a mouthful, but at least it tells you exactly what to expect. None of this “You Won’t Believe What This Man Found in His Soup!” nonsense!

Right off the bat, on p53: giant footnote that takes up half the page AND some of the next page. The HS has several of those, and I’m not entirely sure why they aren’t simply part of the main text. Luckily, the rest of the book is blissfully devoid of them.

By the way, this first footnote is pretty interesting. To me, anyway, since I spent a lot of time interacting with creationists, and by the quotes Darwin gives here, Aristotle (!) got something right that most creationists (or most people?) struggle with to this day. That being the idea that the traits of organisms do not arise in order to fulfil some goal – they just are, and if organisms seem well-adapted to their circumstances, that is because any that weren’t were exterminated by said circumstances.

P55, the discussion of Étienne Geoffroy Saint-Hilaire (the guy who sort-of invented dorsoventral inversion) and his ideas about the descent of species from original “types”: I love how Darwin just assumes that his readership knows French. This isn’t the last untranslated French quote in this book by a long shot. (This particular one, Google Translate tells me, basically boils down to “we need more research”.)

Also on the same page, in the next paragraph about WC Wells’s views – I honestly hadn’t known that “negroes and mulattoes [enjoying] immunity from certain tropical diseases” was already established in the early 19th century. Darwin doesn’t detail which diseases – wonder if malaria is among them? Seeing as sickle cell trait and malaria immunity is one of the textbook examples of heterozygote advantage in modern courses on evolution. I’m quite impressed (though maybe I shouldn’t be) that not only were scientists aware of differences in disease susceptibility, but also attributed these to something akin to natural selection. (Although I’m pretty certain that an understanding of the genetics was far out of reach for the naturalists of the time.)

On the next couple of pages, there are at least three allusions to archetypes that related species are thought to have diverged from. There seems to be a theme running through all of these “type” concepts, although Darwin doesn’t always give direct quotes, so I don’t know how accurate his descriptions of his colleagues’ views are. In connection with Geoffroy Saint-Hilaire, he mentions related species being “degenerations of the same type”; W. Herbert supposedly suggested “highly plastic” original forms to be the ancestor of each plant genus, and Rafinesque (this is a direct quote) wrote that “varieties are gradually becoming species by assuming constant and peculiar characters”, that is, “except the original types or ancestors of a genus”.

So the general thrust of this seemingly fashionable idea is that the ancestors of living species were more variable and less specialised than their descendants. Does anyone hear definite SJ Gouldian undertones here? Isn’t this basically the late great Gould’s view of the Cambrian Explosion in a nutshell? I guess I should have expected this idea to go very far back, what with Platonic ideals and all that, but it still took me by surprise to find it in this context.

… also, it took me until this point, nearly halfway through the HS, to realise that Darwin was going in chronological order. I blame sleep deprivation.

P57 is where I had a sudden “I really should know this” moment. I’m reading this bit and thinking, who the fuck wrote the Vestiges of Creation? I distinctly remembered hearing about it in class years ago, but I couldn’t for the life of me attach a name to it. For the record, Vestiges, a pop-sci book about the evolution of everything (written by a Scotsman named Robert Chambers) was originally published anonymously, so I’m not going to feel too bad about not remembering the author.

Here comes our first example of wonderful academic snark. Vestiges, by Darwin’s account, sounds like a big heap of vitalistic mumbo-jumbo, complete with ladder-thinking and generally likely to make me tear my hear out should I ever be brave enough to read it. I get the distinct impression that I share this opinion with one Mr Darwin – heck, I’m just going to quote his description of Vestiges in its full glory:

“But I cannot see how the two supposed ‘impulses’ account in a scientific sense for the numerous and beautiful co-adaptations which we see throughout nature; I cannot see that we thus gain any insight how, for instance, a woodpecker has become adapted to its peculiar habits of Life. The work, from its powerful and brilliant style, though displaying in the earlier editions little accurate knowledge and a great want of scientific caution, immediately had a very wide circulation. In my opinion it has done excellent service in this country in calling attention to the subject, in removing prejudice, and in thus preparing the ground for the reception of analogous views.”

So: it’s an overenthusiastic pile of pseudoscience that fails to actually explain anything, but I guess it’s… well-written? Oh, ol’ Chuck, you’re such a diplomat.

(Totally random aside: despite leaning towards biology and occasionally astronomy from an early age – so, definitely NOT chemistry – my first real encounter with vitalism, the belief that living things run on some kind of special life force, was in a book about the history of chemistry. Specifically, I learned how the first synthesis of an organic compound – urea – from completely inorganic sources dealt a great blow to the whole life force thing. The book in question was written in 1960s socialist Hungary and was, if memory serves, quite ideologically charged in places. That book would make for another interesting re-read, though probably not for anyone besides myself…)

Immediately after delivering third-degree burns to Vestiges, Darwin unleashes his diplomatic snark on Richard Owen, who was a bit of a… character. He has a reputation for trying to pass other people’s discoveries off as his own, and apparently Darwin’s natural selection was one of his targets. In the HS (p59 of my copy), Darwin summarises his take on Owen thusly:

“It is consolatory to me that others find Professor Owen’s controversial writings as difficult to understand and to reconcile with each other, as I do. As far as the mere enunciation of the principle of natural selection is concerned, it is quite immaterial whether or not Professor Owen preceded me, for both of us, as shown in this historical sketch, were long ago preceded by Dr Wells and Mr Matthews.”

Or: Owen, WTF are you on about?

P60 – It appears that Herbert Spencer was the granddaddy of evolutionary psychology, in that he was the first to propose that mental capacities could evolve gradually in the same way physical characteristics can. Cool.

(Also in this general area: more untranslated French quotes. From Geoffroy Saint-Hilaire, not Spencer.)

P61: Add Naudin to the “plastic archetypes” fan club. And have YET MORE French.

There is an interesting, if only tangentially related, footnote here. All through my reread of the HS I was waiting for Darwin to explain why his take on evolution was special and important, and contrary to my hazy recollection, he never does. (Not in the HS, anyway; my memory of Origin proper is not good enough to recall whether he does it later.) The closest he gets is in the p61 footnote, where he notes that 27 of the 34 authors he discusses “have written on special branches of natural history or geology”, which I interpret to mean that a general discussion of evolutionary theory had been lacking up to that point. So Origin’s perk is the breadth of its coverage? I’m not going to disagree with that…

(Our regular scheduling is interrupted for more French quotes. *le sigh*)

On p62, we finally get to the “other guy”, Alfred Russel Wallace, whom everyone always forgets about. Darwin doesn’t go into great detail; I suppose he figured the fact that they kind of published their theories of natural selection together sufficed. However, he does praise Wallace’s 1858 essay that made its way into the Journal of the Linnean Society for its “admirable force and clearness”. Darwin does seem like a guy who gives credit where credit is due.

Something I found interesting a few paragraphs from the end of the HS: how the same “Great Man” can mean totally different things to different people. I know Karl von Baer as one of the founding fathers of evo-devo, with his famous laws of embryology. However, when Darwin mentions von Baer’s belief in common descent, he only says that it was based mainly on biogeography. Are we even talking about the same von Baer??

Finally, the HS concludes with a little hat-tip to Darwin’s long-time friend, correspondent and fellow nerd, Joseph Hooker. Hooker will make many more appearances in Origin if memory serves – he was the source of many of the observations on which Darwin built his mighty edifice. Those two: geeky bromance of the (19th) century.

Concluding thoughts

Reading this Historical Sketch again made me wonder why it is Darwin that we remember today as “the” father of evolution. Origin may not be a totally academic work, but it sure as hell isn’t light reading. Yet it was immensely popular – the first edition sold out as soon as it was published, and the book saw six editions during Darwin’s lifetime. Was it the completeness of his treatment? His excellent social network? Was it simply a case of right place, right time? I should probably let historians of science ruminate on that. Instead, I shall move on to the Introduction. But not today. Definitely enough meandering for today!

***

(Small) footnotes:

[1] Which, by the way, he still considered unfinished at the time of publication, but I’m jumping ahead of myself here. [Back to post]

[2] As we’ll (hopefully) see later in the re-read, this idea didn’t seem quite so silly at the time – Darwin himself didn’t fully discount it. He did scoff at other components of Lamarck’s theory of evolution, however. [Back to post]

[3] No, he does not use “race” in that sense. [Back to post]

***

Reference:

Johnson CN (2007) The preface to Darwin’s Origin of Species: the curious history of the “Historical Sketch”. Journal of the History of Biology 40:529-556.

A bit of Hox gene nostalgia

I had the most random epiphany over my morning tea today. I don’t even know what got me thinking about the Cambrian explosion (as if I needed a reason…). Might have been remembering something from the Euro Evo Devo conference I recently went to. (I kind of wanted to post about that, because I saw some awesome things, but too much effort. My brain isn’t very cooperative these days.)

Anyway.

I was thinking about explanations of the Cambrian explosion and remembering how the relevant chapter in The Book of Life (otherwise known as the book that made me an evolutionary biologist)  tried to make it all about Hox genes. It’s an incredibly simplistic idea, and almost certainly wrong given what we now know about the history of Hox genes (and animals)*. At the time, and for a long time afterwards, I really wanted it to be true because it appeals to my particular biases. But I digress.

Then it dawned on me just how new and shiny Hox genes were when this book was written. I thought, holy shit, TBoL is old. And how far evo-devo as a field has come since!

The Book of Life was first published in 1993. That is less than a decade after the discovery of the homeobox in fruit fly genes that controlled the identity of segments (McGinnis et al., 1984; Scott and Weiner, 1984), and the finding that homeoboxes were shared by very distantly related animals (Carrasco et al., 1984). It was only four years after the recognition that fly and vertebrate Hox genes are activated in the same order along the body axis (Graham et al., 1989; Duboule and Dollé, 1989).

This was a HUGE discovery. Nowadays, we’re used to the idea that many if not most of the genes and gene networks animals use to direct embryonic development are very ancient, but before the discovery of Hox genes and their clusters and their neatly ordered expression patterns, this was not at all obvious. What were the implications of these amazing, deep connections for the evolution of animal form? It’s not surprising that Hox genes would be co-opted to explain animal evolution’s greatest mysteries.

It also occurred to me that 1993 is the year of the zootype paper (Slack et al., 1993). Slack et al. reads like a first peek into a brave new world with limitless possibilities. They first note the similarity of Hox gene expression throughout much of the animal kingdom, then propose that this expression pattern (their “zootype”) should be the definition of an animal. After that, they speculate that just as the pattern of Hox genes could define animals, the patterns of genes controlled by Hoxes could define subgroups within animals. Imagine, they say, if we could solve all those tough questions in animal phylogeny by looking at gene expression.

As always, things turned out More Complicated, what with broken and lost Hox clusters and all the other weird shit developmental “master” genes get up to… but it was nice to look back at the bright and simple childhood of my field.

(And my bright and simple childhood. I read The Book of Life in 1998 or 1999, not entirely sure, and in between Backstreet Boys fandom, exchanging several bookfuls of letters with my BFF and making heart-shaped eyes at long-haired guitar-playing teenage boys, I somehow found true, eternal, nerdy love. *nostalgic sigh*)

***

*Caveat: it’s been years since I last re-read the book, and my copy is currently about 2500 km from me, so the discussion of the Cambrian explosion might be more nuanced than I remember. Also, my copy is the second edition, so I’m only assuming that the Hox gene thing is there in the original.

***

References:

Carrasco AE et al. (1984) Cloning of an X. laevis gene expressed during early embryogenesis coding for a peptide region homologous to Drosophila homeotic genes. Cell 37:409-414

Duboule D & Dollé P (1989) The structural and functional organization of the murine HOX gene family resembles that of Drosophila homeotic genes. The EMBO Journal 8:1497-1505

Graham A et al. (1989) The murine and Drosophila homeobox gene complexes have common features of organization and expression. Cell 57:367-378

McGinnis W et al. (1984) A conserved DNA sequence in homoeotic genes of the Drosophila Antennapedia and bithorax complexes. Nature 308:428-433

Scott MP & Weiner AJ (1984) Structural relationships among genes that control development: sequence homology between the Antennapedia, Ultrabithorax, and fushi tarazu loci of Drosophila. PNAS 81:4115-4119

Slack JMW et al. (1993) The zootype and the phylotypic stage. Nature 361:490-492

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…

 

Wheeee!

… sorry, guys. I did say something about squee and headdesk moments on my about page. ^_^;

It’s nothing big, really. I just got my hands on a book I’ve had on my wishlist for years, read a couple of chapters, and so far all I keep thinking is “neeeeeat!”

Dear editors and contributors, you all are officially making me happy. So happy that only the yay turtle can properly express my feelings!

(Seriously, who came up with this picture? It’s just perfect.)

We’ll read the rest of the book, and then we’ll see if Embryos in Deep Time is also as awesome as it sounds…

A small planet hidden in plain sight, and a must-read book

Random squeey post!

Squee number one: Dumusque et al. (2012) found a probably earth-sized planet literally next door to the solar system. The newly announced rockball orbits α Centauri B, one of the three(?)* stars making up the star system closest to the sun. Alas, it’s unlikely to harbour life of any kind given its very close orbit – it goes around a star not much cooler than our sun in slightly over 3 days. However, the authors point out that small planets are most likely to be found in multiplanet systems, and given the difficulty of finding this one, the star may well have even harder to detect, more distant companions. I think this is a nice reminder of how much more we need to learn about other solar systems – this little guy has been circling there, a mere four point something light years from us, and we only found it now. Keep it up, planet hunters, you’re doing amazing stuff!

Reference: Dumusque X et al. (2012) An Earth-mass planet orbiting α Centauri B. Nature advance online publication available online 17/10/2012, doi: 10.1038/nature11572

*I’ll let the real astronomers argue whether Proxima Centauri is part of the α Centauri system…

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Squee number two: I totally must read this book. It’s the ultimate evo-devo book: it’s about fossilised development, basically. It seems overwhelmingly vertebrate-centred based on the review in Developmental Dynamics, but hey, there is an invertebrate chapter and I take what I can get 😀

And wow, it’s not even that expensive as far as university-published hardcover sciencey books go! Hmm. Shall we give in to temptation right now or save it for a Christmas present?

 

The folly of hindsight

Recently, I’ve been re-reading Life on a Young Planet. As I said before, it’s an excellent book. It is beautifully written, cleverly structured, and the author is obviously knowledgeable about the subject (which, sadly, isn’t always true in popular science). Most importantly, it emphasises the process of science, as opposed to the actual knowledge gained through that process. “How do we know what we know?” is a question at least as important to Andrew Knoll as “What do we know?” As he so eloquently puts it, “[t]extbooks may portray science as a codification of facts, but it is really a disciplined way of asking about the unknown.” This is an attitude I share with him, and probably a big part of the reason the book has such a special place in my heart.

So, I was surprised to discover on this re-read that Knoll falls into one of the most common traps of talking about evolution: teleological thinking. In Chapter 11, “Cambrian Redux”, he writes that “[f]orty million years after the Cambrian began, evolutionary way stations still played a major role in the ecology of marine environments.” He is discussing the Cambrian explosion, of course, and here he is talking about stem groups of living phyla living alongside the crown groups [1]. I don’t think he means to convey a sense of goal-orientation, but the wording does exactly that. It sounds as if, say, Anomalocaris was just something evolution had to pass through to get to arthropods, not a successful animal in its own right. It suggests that the eventual supplanting of these now-extinct lineages was meant to happen.

Richard Dawkins called this “the conceit of hindsight” and complained about it at length in the introduction to his (also really good) book The Ancestor’s Tale. Dawkins characterises such thinking as “seeing the past as aimed at our own time, as though the characters in history’s play had nothing better to do with their time than foreshadow us.” (In this particular case, he’s talking about ordinary history, as a prelude to introducing the same problem in evolutionary history.) It’s a very common way of thinking about evolution (just look at any of the traditionalmarch of progressimages), and it’s also totally wrong.

If you’ve been in prolonged contact with creationists, you’ve almost certainly encountered conspicuous examples of this common misconception. Types of questions I’ve personally seen include “what use is half a wing/[insert transitional feature here]?”, “why didn’t all X evolve into Y?”, and “how did X know they were evolving into Y?” At the heart of each lurks the idea that evolution works towards goals. That it doesn’t seems to be one of the most difficult aspects of evolutionary theory to grasp, and it’s especially hard to escape when we are looking at the past.

Simply put, evolution has no foresight. Rather than working towards something, the process always reacts to something. Rather than looking ahead, it constantly lives in the present, though it’s often saddled with the baggage of the past. The kinds of things that cause mutation (such as replication errors, radiation and chemical damage) have random effects [2]. Moreover, the processes that sort among mutations, such as natural selection, are similarly blind. Because the mechanisms of evolution are not thinking entities, the only traits that get passed on are traits that help their owners reproduce in the here and now. Any long-term trend is the outcome of repeated rounds of selection on the same traits. Evolution has no goal in the same way a snowflake doesn’t aim for your nose, though in retrospect you can perhaps reconstruct the path it took to get there.

That’s the problem with history: we are looking back on processes whose outcomes we already know. It’s so tempting to view the preceding events as mere stages in a journey aimed at those outcomes. After all, we humans work with goals in mind all the time (ironically, nowadays we might use evolutionary principles to attain those goals!). Unfortunately, viewing evolution in this way can lose sight of the process by focusing on the endpoint – and then people start asking about half wings.

It’s important to remember that the ancestor of the wing was not “half a wing”. It was just a modified arm that had some advantage over its ancestor, e.g. large feathers to help a dinosaur keep her eggs warm, or (closer to “wingness”) glide from tree to tree. These animals weren’t half-functional fliers, they were fully functional at whatever they were doing. If an alien scientist looked around in a Middle Jurassic forest, it might have marvelled at the exquisite gliding adaptations of small dinosaurs much like Microraptor [3], but it surely wouldn’t have focused on how bad they were at flying.

(Also, always remember that when you are the only one who can do something, by definition you’re the best at it!)

I wish we could just drop the teleological language altogether. It’s surprisingly difficult even when you actively try, though. It could be something about the way language works (at least the two I know well). Somehow, it seems much easier to say things like “X evolved to do Y” in them than to give a more accurate description of the evolutionary process. I’m sure that says something profound about human minds…

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[1] In systematic jargon, a crown group is the last common ancestor of all living members of a group, and all of its descendants (including extinct ones). The corresponding stem group (stem groups are always relative to a crown) includes anything extinct that’s more closely related to the crown group in question than to any other living lineage. For example, all non-avian dinosaurs were stem birds.

[2] We have to be precise about the meaning of “random” here. Some mutagens cause very specific mutations. “Random” refers to their fitness effects, not the chemical changes that happen or even the places where they happen (though the latter is largely random, except for trivial constraints). The same mutation in different parts of the genome can be beneficial, harmful or have no effect at all, and conversely, the same is true for different mutations at the same spot – and all of this is uncontrollable. If you keep your study organisms in a hot environment, they won’t suddenly start producing more mutations that make them heat-resistant. That’s the main thing we mean when we say mutations are random.

[3] Microraptor itself is Early Cretaceous – birds were already around when these guys inhabited the forests of China. The first part of the Jurassic – i.e. the time between early dinosaurs and Archaeopteryx – doesn’t have a great record of dinosaur fossils, so most of what we know of the origin of birds comes from relatives of birds that persisted alongside birds later on. However, a few very bird-like fossils are contemporaneous with, or older than, Archaeopteryx. Like Microraptor, some of these creatures have long leg feathers (unlike Microraptor‘s, theirs aren’t very aerodynamic) , so that may be something ancestral for the “birdy” lineage.