Saturday, February 7, 2009

Tonya's Comments on Chapter IV

Chapter IV - Natural Selection

p81) This preservation of favourable variations and the rejection of injurious variations, I call Natural Selection.

Hmm, I was once told that nothing can be selected for, only against because basically, if you don't have the right stuff you die.

p82) ...a change in the conditions of life, by specially acting on the reproductive system, causes or increases variability...

Lamarkism, or Darwin just trying to make sense of what he didn't know?

p87) What natural selection cannot do, is to modify the structure of one species, without giving it any advantage, for the good of another species.

Maybe not on purpose, but there must be some examples of co-evolving species that shows modifications of one species being good for another?

p106) Generalists versus specialists!

...forms produced on large areas...will give rise to most new varieties and species.

I know you people discussed this but I would really like to see the data on that because even though it sounds logical, maybe it isn't true.

p107) Do all 'living fossils' come from inhabiting a confined area?

p108) That natural selection will always act with extreme slowness, I fully admit.

Opposite of punctuated equilibrium?

p109) I can see no limit to the amount of change, to the beauty and infinite complexity of the coadaptations between all organic beings, one with another and with their physical conditions of life, which may be effected in the long course of time by nature's power of selection.

I absolutely love this quote. Is there a limit to the amount of change? I can think of possibly two: 1) organisms will retain their use of DNA; 2) organisms will never be found in a gaseous state. I am iffy on point 1.

The section on extinction gets me excited for some reason :). What IS the maximum amount of species that existed on the earth at one particular time? Min.? How would we ever know? Does the number of species fluctuate with the earth's changing climates and habitats????? Can someone please build me a time machine?

p110) Hence, rare species will be less quickly modified or improved within any given period [compared to common species] and they will consequently be beaten in the race for life by the modified descendants of the commoner species.

This seems like a reasonable assumption for Darwin to make, but how often does this really occur? Maybe sometimes rare species are modified more quickly with changes in habitat.

p119) The modified offspring from the later and more highly improved branches in the lines of descent, will, it is probable, often take the place of, and so destroy, the earlier and less improved branches...

Again, this is always implied but is this really how evolution always works? I know it's hard to get actual data on this but it is really very important. But then Darwin goes on to explain anagenesis, where "the process of modification will be confined to a single line of descent". However, what about multiple lines of descent where the ancestor is not "destroyed". Also on p121, Darwin states "the original parent-species itself, will generally tend to become extinct". Generally, but not always? But then, maybe to hedge his bets, on p122 Darwin states that if "...the modified offspring of a species get into some distinct country, or become quickly adapted to some quite new station, in which [both] do not come into competition, both may continue to exist."

p121) ...the species, which are already extremely different in character, will generally tend to produce the greatest number of modified descendants.

This could easily be tested. Did Darwin already have the data?

Tonya's Comments on Chapter III

Chapter III - Struggle for existence

p61) I have called this principle, by which each slight variation, if useful, is preserved, by the term of Natural Selection, in order to mark its relation to man's power of selection.

It seems that even the name emphasizes (hu)man's power. Was this something Darwin was thinking about when he came up with the name for his idea? Not that humans had any power in natural selection of course, but that people would associate the power of 'nature' with the power already held by humankind?

p62) We behold the face of nature bright with gladness... :)

p63) There are different kinds/gradients of 'struggle'.

p66) ...the average number of any animal or plant depends only indirectly on the number of its eggs or seeds.

Yes, I understand that he is discussing k- verses r- selected organisms but I think this is quite a generalized statement and a lot of other factors determine the average number of them.

p68) Climate plays an important part in determining the average numbers of a species, and periodical seasons of extreme cold or drought, I believe to be the most effective of all checks.

Will this be a check of humans???

p70) ...that a plant could exist only where the conditions of its life were so favourable that many could exist together, and thus save each other from utter destruction.

This statement stood out for me for some reason. Has this been tested? Is this sort of like the school of fish hypothesis? Can anyone elaborate on this for me?

p73) Food Webs!

Nevertheless so profound is our ignorance, and so high our presumption, that we marvel when we hear of the extinction of an organic being; and as we do not see the cause, we invoke cataclysms to desolate the world, or invent laws on the duration of the forms of life!


humble-bees! :)

"In England, these insects used to be called Humble Bees, and they were the stuff of which legends were made. In The Origin of Species, Charles Darwin related a story that asserted that old maids were the real power behind the British Empire. The reasoning behind this remarkable claim was that the British army lived on beef; to raise beef you must have clover; and clover, particularly red clover, is pollinated only by humble bees. When field mice are abundant, they often break into the nests of humble bees to steal the honey pots, thus killing the bees. Old maids keep cats, and cats kill mice; hence the bee population, the clover crop, and the beef supply all depend on the number of old maids— well, you get the idea. It’s the food chain in action again." B. Meredith

p76) ...but probably in no one case could we precisely say why one species has been victorious over another in the great battle of life.

Any papers on this?

Chapter VI

Since last Wednesday, I have thought often of Chapter VI. I must express my amazement at Mr. Darwin's boldness of inserting a chapter which highlights the difficulties of his theory. The move is endearing for its honesty. If the reader had not already thought of these objections himself, the reader's attention was drawn to them nevertheless. It is quite clear Darwin himself had long wrestled with these questions he had yet to fully answer. However, last Wednesday I raised the prospect of another motive for the chapter: Did he insert the chapter as a clever device to pre-empt his critics? Did he intend to shoot down contradictory arguments, to reduce them to flames and wreckage, before they had even been lifted off the ground and put into the air?

I doubt it. I cannot help but notice in the chapter Darwin gives a fair-minded deference only to the scientific objections which the reader could level at his theory, for instance, the absence of transitional organisms in the fossil record. Nowhere in the chapter does he address the question concerning man's origins, religion, and so forth. Those issues were omitted. Yet those issues were potentially of greater interest to a wide range of readership, in view of the response to the book, the vast mass of people not being interested or trained in biology (their loss). Those issues were the largest obstacles to widespread acceptance of his theory. Further, the people who entertained these questions infused their criticisms of Darwin with considerably more fire than is common in polite academic debate. Even geologist Adam Sedgwick, by no means a religious fanatic but nevertheless a proponent of natural theology, wrote he read the Origin with "more pain than pleasure. Parts of it I admired greatly, parts I laughed at till my sides were almost sore; other parts I read with absolute sorrow, because I think them utterly false and grievously mischievous. " He then compared Darwin's theory to a contemporary idea to use a steam train to fly to the moon, saying the two possessed about the same amount of logic and inductive reasoning. Ouch! That sounded like it was meant to sting! Now, if Darwin were to head off all his critics at the pass, he would almost definitely have addressed the religious question or even have defended the merit of his logic. Yet the chapter is silent on this.

I can only conclude Darwin was interested in factual, scientific, and more clinical objections to his theory and not a wider realm of unresolvable debate. What would be the point of addressing those questions? A fanatic, after all, is one who won't change his mind and won't change the subject. Darwin would have made better use of his time employing his head in an aggressive fashion toward a brick wall. No chapter would have softened the impact of his work. No chapter would have quelled debate and made the Origin less controversial at that time and at that place. In laying forth in an honest and humble fashion the gaps in his theory, Darwin had in mind those who would approach the topic along the lines of his own logic, deeply embedded in evidence, the scientific method, and the facts. In light of the violent response to his work Darwin must no doubt have anticipated at the time of writing, it is not surprising he should isolate himself to a certain degree from those who had no interest in discussing the topic scientifically. I read in Browne's literary biography that Darwin generally left polemical debate on 'larger' questions to others like Huxley. Furthermore, his disdain for his "theological and metaphysical" critics I thought was plainly apparent in a quote from last week's readings in response to Sir Wyville Thomson, (who has my every sympathy for his first name, Victorian parents were cruel, I once read of a man named L.G. Trotter, or Lemuel Gungulfus): "This is a standard of criticism not uncommonly reached by theologians and metaphysicians when they write on scientific subjects, but is something new as coming from a naturalist." This gently implies, of course, that one, Sir Wyville's criticisms were unworthy of his standing at a naturalist, and two, the standard of criticism of theologians and metaphysicians were smitten by some form of infantile paralysis of the intellect.

Darwin, it seems, was concerned with the realm of factual debate. He had little time or patience for controversy, notwithstanding how much of it his book produced. In writing Chapter VI he was concerned with the mechanics of his own theory, not with how others might perceive it. It is often a scholarly device to pre-empt objections by including such a section in this work, or at any rate having it exhibited meekly in a footnote. However, it takes a great deal of confidence to place it at great length in a full chapter, smack dab in the middle of his book. Had Darwin been less knowledgable about his theory, and less capable in its presentation, such a bold display in Chapter VI would have resulted in his theory sputtering out rather than gaining credibility. It would have confirmed doubts rather than encouraged discussion about their resolution. I have actually witnessed the former process in other works written by those a bit too confident in their ability to refute criticism. Those people should stick to their footnotes and endnotes. Darwin on the other hand, knew his subject, and was willing to receive criticism along technical lines. But it is apparent he was not very concerned with other kinds of reproach. The fact that non-technical objections would dominant the reception of his book by the public but had no place in his modest reappraisal shows that Chapter VI was by no means inserted to manipulate the reader. Above all, it demonstrates a devotion to the pursuit of the facts, which in my opinion is admirable.

(It was interesting to note that this "valiant seeking after truth" is often considered naive by many people today. But I suppose that is because we are in a profoundly advanced postmodern age, or so they tell me, where we cannot express the facts, but can only express arguments and theories convincingly disguised as the facts. What cynicism! That is probably why some including my-poor-jaded-self might suspect Chapter VI was designed as rhetoric to manipulate the reader. Admittedly we see it far too often nowadays - especially in history, take it from me. The problem today, it seems, is although people are usually far too smart to believe in rhetoric, they are not nearly stupid enough to believe in facts. And so they settle for rhetoric anyway.)

Friday, February 6, 2009

supplementary reading for Chapters 7+8

For those playing along at home, the supplementary reading for Chapters 7-8 of OTOOS

Mallet, J. 2007. Hybrid speciation. Nature 446(7133):279-283. (available as PDF)


Darwin's religious beliefs

Looking ahead to the session on evolution and religion, I thought folks might be interested in this brief popular article by John Brooke on Darwin's own religious beliefs. John Brooke is an Oxford don and one of the world's leading historians of science and religion. That's why we're so chuffed that he's going to be coming to Calgary in the fall to deliver the third talk in our upcoming public lecture series, Introducing Charles Darwin. Public discussions of evolution and religion tend to be dominated by extremists on both sides, and so have a black-and-white character. But as John Brooke points out (and will point out at greater length in his talk), Darwin's own beliefs evolved through various shades of gray.

Thursday, February 5, 2009

Science: special issue on speciation

This week's Science is a special issue devoted to speciation. Well worth checking out to get the current view on topics of central concern in the Origin. One of the review papers from this issue might be a good choice for a supplemental reading at some point. You can access Science via the library website (search for electronic journals).

Wednesday, February 4, 2009

Further thoughts on the spandrels of San Marco

First, let me say that this article is deservedly famous (cited 1873 times in ISI Web of Science, which is 10 times more than even quite famous and influential scientific papers of similar vintage). It reads best if read as an intentionally-provocative conceptual critique, and there's absolutely value in both intentional provocation and conceptual critique. Every student of evolution should (and probably does) read it.

Having said that, I think Gould and Lewontin deserve heaps of criticism, both of their ideas and of how they present those ideas. Put bluntly, I think they're full of ****. Below are my criticisms, none of which are unique to me, although perhaps the blunt language is. Sorry, but parts of this article really make me angry.

1. The spandrel analogy doesn't work, nor does the analogy of the gaps in fan vaulting, for reasons Robert Mark lays out. Maybe a better example of what Gould & Lewontin mean by a "spandrel" exists, but if so I can't think of one. The deeper problem here is that I simply don't know what is meant by "architectural by-product", and I'm not sure any example could make it clear. The notion of an architectural by-product seems to me to be very fuzzy, and a very poor analogy for any sort of constraint to which functioning organisms might be subject. Maybe this is a case where we'd be better served by actually thinking about functional biology, rather than analogies to functional biology. There are certainly times when a good metaphor or analogy clarifies an argument, but there are also times when a superficially-plausible metaphor or analogy serves only to hide unclear thinking.

2. As we discussed in class, complaining in a generic way about "atomizing" organisms into traits is useless. We can't do without atomization; the phenotype of an organism is too complex to summarize in one number. Fortunately, there are objective strategies available to us to identify which (arbitrarily-individuated) "traits" are correlated with which others, and to what degree. But Gould and Lewontin aren't in the business of talking in a specific way about the practical research approaches real scientists use or could use in order to address precisely this or any other of the issues the article raises. Nor do Gould & Lewontin talk in a specific way about how one would go about actually studying adaptation of integrated whole organisms. I have more to say below about Gould & Lewontin's refusal to come down from the rhetorical clouds and actually engage with how to do science.

Nor can natural selection due without atomization (this is what justifies individuation of traits by scientists). As Lewontin himself once pointed out in print, an organism that wasn't atomized into independent traits couldn't evolve by natural selection, because beneficial mutations would be all but impossible (any mutation would almost certainly just lead to a non-viable organism). Of course, this doesn't mean that natural selection "sees" individual traits. It is indeed true that natural selection only "sees" the whole organism. Specifically, all that natural selection "sees" is (relative) fitness, which is an integrated measure of how well the whole organism is adapted to its current environment. Natural selection only acts indirectly on every other trait, however those traits are individuated. And you know who emphasized this point most keenly? Architect of the Modern Synthesis and famous arch-selectionist R. A. Fisher. Welcome to the selectionist camp, Gould & Lewontin! Nice of you to join us!

3. We shouldn't tell stories about how every feature of every organism is adaptive, say Gould & Lewontin. Fine (obvious, but fine). So presumably that means we should be better adaptationists, and you will describe specific research approaches by which we can achieve that goal? No? You say all you plan to do is tell stories like how the chin isn't an "atomic" trait (despite the fact that one could very well perform an artificial selection experiment to increase or decrease chin size)? Stories like how the small forelimbs of Tyrannosaurus must be an example of correlated growth, without explaining how one would go about testing this hypothesis? I see. Can I make a suggestion, gentlemen? The same storytelling approach that delights readers of popular science columns in Natural History magazine may not go down so well with Ph.D. scientists who understandably will be looking for a little more rigor. Especially when your goal is to argue against the use of story-telling in science!

Gould & Lewontin's lack of willingness to actually say anything about the practical conduct of science is why the last paragraph on p. 151 pisses me off so much. Here, Gould & Lewontin go beyond intentionally-provocative into borderline offensive. Gould & Lewontin complain about how adaptationists admit genetic drift, allometry, etc. in principle, but dismiss their importance in practice and then congratulate themselves for being such undogmatic and ecumenical chaps. To which the only possible response is: How dare you? How dare you tar every single working evolutionary biologist with the same broad brush, without having the guts to actually quote even a single example of anyone dismissing alternative hypotheses to natural selection without evidence? Your claim here is far stronger than the weak, uninteresting claim that some scientists have sometimes drawn mistaken or overhasty conclusions. Your claim here is that the entire field of evolutionary biology is systematically and willfully biased. Which is complete and utter crap. Science is hard, scientists mostly do their best, and their best is mostly pretty good (or do you think we haven't learned anything about how the world works since the 17th century?) How dare you criticize others for how they choose to pursue their science, without saying one word about how to pursue the alternative research program you suggest? Could it be that we do in fact routinely test for and reject some of the hypotheses you claim are ignored (no population geneticist can publish a paper claiming selection on a trait without ruling out drift)? More broadly, could it be that history has shown that a research program focused on testing adaptationist hypotheses is actually a productive way to make progress? And by the way, I love that passage on p. 157 where you point out in passing that correlations of growth (allometric patterns) are themselves subject to selection, only to immediately go back to focusing on non-adaptive hypotheses. I love how you set such a good example for the rest of us by taking alternative hypotheses so seriously.

4. Gould's idea that there's an important distinction between adaptations and exaptations (i.e. traits co-opted by selection to perform a new function) is worthless. As is patently obvious, all adaptations are exaptations if one looks back far enough in the history of life. I'm suspicious that Gould was only able to push this idea (which he did in in several publications) because of how famous he was.

5. Gould & Lewontin claim that drift, developmental constraints, correlations of growth, etc. may well be collectively so important that their effects should be regarded as the "main story" of evolution, with adaptation by natural selection becoming a relatively unimportant detail. What they never bother to explain is how the heck we ever got complex, functioning organisms that could experience genetic drift and exhibit developmental constraints and correlations of growth in the first place? Seriously, how in the name of Darwin was that supposed to happen, except via natural selection?

6. Gould & Lewontin go on and on about how important forces besides natural selection are, but they completely miss all kinds of interesting questions that can be asked about the interplay between multiple evolutionary "forces". They talk as if these other forces are alternatives to natural selection, when in fact it's typically the case that all these forces co-occur and really surprising phenomena arise from their interplay (it's not always that the "strongest" force just swamps all the others). For instance, developmental systems themselves vary and variation in developmental outcomes has fitness consequences, so developmental systems are subject to selection. So how do developmental constraints themselves evolve? Can organisms evolve to become more "evolvable" (e.g., to have more atomized traits)?

Unfortunately for Gould (though not for Lewontin, who was trained as a mathematical population geneticist), developing sensible hypotheses about these kinds of feedbacks between development and evolution pretty much requires mathematical models. Gunter Wagner's work is a good recent example of this kind of modeling. While Gould was famous for knowing a lot about all sorts of subjects, math was a notable gap in his expertise, at least as far as can be judged from his publications. I think this is a very important limitation of Gould's entire approach to science (of which the spandrels paper is merely one particularly famous example). Gould thinks big, but he doesn't think quantitatively (Darwin doesn't either, but Darwin had a good excuse). Reasoning with mathematics is very different than reasoning with analogies and metaphors. Math forces you to be much more explicit and precise in your assumptions and in the logic with which you derive your conclusions, and doesn't leave much room for you to show off your rhetorical skills or your superficial knowledge of architecture. Things like "developmental constraints" and "correlations of growth" have very precise definitions in the context of mathematical models like those of Gunter Wagner, which makes metaphors and analogies superfluous. I don't claim that mathematical modelling necessarily eliminates conceptual arguments or alleviates conceptual confusion (witness ongoing conceptual debate about the interpretation of quantum mechanics), but it often helps a lot, by forcing precision and explicitness.

I'll conclude with a final irony. A hot area of current research is explaining where "correlations of growth" actually come from in the first place. After all, these correlations exhibit some striking quantitative patterns (which I won't review here; take my word for it). Why these particular patterns and not some others? This isn't about whether selection can or cannot modify pre-existing correlations--it's about why these particular correlations exist at all. And were he alive, Gould probably wouldn't have liked the (tentative) answer. All the best-supported current hypotheses argue that observed correlations of growth (i.e. the allometric relationships Gould loved to appeal to so much as an alternative to adaptive explanations) are themselves ultimately a by-product of natural selection on some other organismal feature. For instance, allometric scaling of metabolic rate with body size may well be a by-product of selection for optimizing the functioning of closed circulatory systems (see West et al. 1994 Science). So maybe the biggest constraint on adaptive evolution is ultimately...adaptive evolution. Oh the irony.

Further thoughts on Chapters V-VI

1. I was stunned that Darwin could attribute the eyelessness of cave-dwelling animals to disuse (p. 138), only to later hit on the correct explanation in the context of a discussion of why parasites lack organs that their free-living relatives need (p. 148). "Now the saving of a large and complex structure, when rendered superfluous...would be a decided less nutriment being wasted in developing a structure now become useless." How could he not see that this argument about parasites applies equally well to eyeless cave-dwellers, and indeed to many cases of apparent "loss by disuse"?

2. That quibble aside, I found much of chapters V-VI to be very strongly written and argued. Darwin's best writing seems to go hand in hand with his best science--the writing flows well when Darwin knows what he's talking about. Hard to pick highlights, but I'll suggest a few and other folks can add their own favorites:

-p. 190, where Darwin points out that organs that perform multiple functions, and multiple organs performing the same function, provide fertile raw material for the evolution of new functions. This is exactly the same argument used today to counter Michael Behe's claims of the "irreducible complexity" of cellular biochemistry.

-p. 140, where Darwin writes, "We have reason to believe that species in a state of nature are limited in their ranges by the competition of other organic beings quite as much as, or more than, by adaptation to particular climates." Spot on. Unfortunately, many modern ecologists who work on describing species' ranges with respect to climate variables, and predicting future ranges under climate change, proceed as if this weren't true. They make the mistake of assuming that, because species' range boundaries often are coincident with some change in climate (e.g., "the northern range limit of species X coincides with the latitude at which minimum winter temperatures drop below zero), they are caused by that same change in climate ("therefore, this species must not be able to tolerate temperatures below zero"). Yes, the fallacy of "correlation implies causation" is alive and well in the science of range limits. Correlation is an especially poor guide to causation in this context because latitudinal and altitudinal range limits are almost necessarily coincident with some change in climate or other. If only everyone would read the Origin!

-p. 193-194, the discussion of convergent evolution, using the example of electrical organs in fish. Is there any better summary of convergence than Darwin's? "I am inclined to believe that in nearly the same way as two men have sometimes independently hit on the very same invention, so natural selection, working for the good of each being and taking advantage of analogous variations, has sometimes modified in very nearly the same manner two parts in two organic beings, which owe but little of their structure in common to inheritance from the same ancestor."

Convergent evolution is a huge thorn in the side of those (such as Gould) who want to argue against the importance of natural selection or for the importance of some other putative cause of adaptation. Gould liked to claim that, if you "rewound the tape of life" and played it again, it would come out completely differently--that the history of life is a unique sequence of historical contingencies. He used the bizarreness (to our eyes) of the Burgess Shale fossils of the Cambrian explosion to argue for this point of view. Many of the "body plans" that evolved in the Cambrian explosion were not passed down in the subsequent history of life, and we can't see any functional (i.e. selective) reason why some forms passed down and others did not, suggesting that the persistent forms were just lucky. Of course, one can interpret the Burgess Shale in other ways, as Simon Conway Morris does. And presumably, even if the particular adaptations observed over the history of life are contingent on ancient chance events, any possible history of life would presumably be filled with adaptations of some sort or other. So Gould's interpretation of the Burgess Shale fossils doesn't imply much of anything about the importance of natural selection in shaping the history of life. But leave all that aside. Instead of arguing about fossils that are so ancient we'll never be able to have much sure knowledge about them, why not look to other sources of evidence, sources that are readily accessible--such as living electric fishes? Convergent evolution is direct evidence against Gould's claim of radical contingency, and we don't lack for examples of it. Gould wrote a huge amount on evolution, but if you go through his writings you will find very few mentions of convergence. Gould deployed many rhetorical strategies, but raising objections to his own position in order to refute them was not one of them.

I'll put up a separate post on the Gould & Lewontin article. I'm glad we read it, I think it's a great article for students to grapple with. That doesn't mean I agree with a word of it.

Sunday, February 1, 2009

Evolution inspiring art

Following up from the previous post, Darwin and his ideas certainly have been the subject of art (as opposed to influencing art). Darwin-related books and films with which I'm familiar:

-Famous Hollywood movie Inherit the Wind, about the Scopes trial

-Angels and Insects, an A. S. Byatt novella about a young Victorian naturalist not unlike a young Darwin, who falls in love with the daughter of his upper-class patron. The Victorian family dynamic is compared/contrasted with the dynamics of the ant colonies the naturalist is studying. A very good read, highly recommended. The book was made into a film of the same title which is well-worth seeking out, as it sticks very close to the book and is equally good.

-A Darwin biopic is slated for release this year: Creation (working title: Annie's Box). The film will focus on the tensions between Darwin's scientific ideas and his family life. The film is based on the Darwin biography Annie's Box. Paul Bettany will play Charles Darwin and Jennifer Connelly will play his wife Emma; they've both been in a bunch of movies you've heard of. Jon Amiel (Sommersby, and more unfortunately, The Core and The Man Who Knew Too Little) directs a script by John Collee (Master and Commander). The release date was supposed to be Feb. 12, but has been pushed back to Sept. 25 (see, which makes me wonder a little if it will end up being released at all (or maybe the studio thinks it's so good they want to set it up for Oscar buzz...)

-I was once given Mr. Darwin's Shooter as a gift but never read it (though I tried really hard). It's a literary novel told from the point of view of the boy assigned to serve as Darwin's shooter on the Beagle (i.e. it was his job to shoot whatever animals Darwin wanted collected). The boy is religious and has qualms about helping Darwin do science. Anyway, to borrow a line from Anthony Lane, I found the book so finely written as to be unreadable (it reads somewhat like Moby-Dick). But maybe that was just me.

-No, Planet of the Apes does not count as a movie about evolution. Nor does Jurassic Park. ;-)