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.)

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)

Enjoy!

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.

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).

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 advantage...by 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.

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 http://www.imdb.com/title/tt0974014/), 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. ;-)

Evolution and Art

I believe it was on the first day of this class, that Dr. Fox said something to the effect of:

Evolution affects every subject, with perhaps the exception of art...

After recently finishing a semester of studying art history, I wasn't sure this was true. I wanted to find this link. Last night I found it in the most unlikely place, "The Colbert Report".

Stephen T. Colbert's guest on January 28th 2009, was Dennis Dutton, who says that the appreciation of art has evolved as an evolutionary trait. He has written a book on why art is related to human evolutionary history called "The art of instinct".

You can see the episode on the CTV broadband network, under The Colbert Report.

Natural Selection VS Religion - Response to e-mail

In response to Mike's e-mail:

Thanks for the readings Mike, I will certainly go over them this weekend.

To add another angle to this look at the tense relationship of Darwin and Religion I would suggest some light google searching on some of the legal trails about teaching natural selection in the classroom. 

The classic historical case is the Scopes trial of 1926. Here, high school teacher John Scopes was charged by the State of Tennessee with breaking the "Butler Act"; which made it illegal "to teach any theory that denies the story of the Divine Creation of man as taught in the Bible, and to teach instead that man has descended from a lower order of animals". There are many websites that give different slants on the trail. Search "Scopes Monkey Trial" and you can pick what you wish to read.  

There have also been more recent trails using the "bacterial flagellum argument" in place of the 1800s "watchmaker/eye argument" see http://www.newscientist.com/

or watch this very good lecture by Dr. Kenneth R. Miller at Brown University and this more instructional animation of hypothesized and tested steps.

There have also been earlier public arguments like that between T.H. Huxley and Bishop S. Wilburforce at Oxford. I heard a funny recreation at Down House, it went something like this.

Above Pictures: Plaque designating Down House as an English Heritage Site (left); Darwin's gardens (right). Those hundreds of cabbages he mentions in chapter 3, they are still there.

A suggested reading for 02/04/09

As Josh notes, next week's supplementary reading is a very famous and controversial article that drew many responses. I highly recommend this 1996 American Scientist article from architectural historian Robert Mark, critiquing the use of the 'spandrel' metaphor by both Gould & Lewontin and their critic Daniel Dennett.

supplementary reading for 02/04/09

A classic paper from Gould and Lewontin.

Gould, SJ and RC Lewontin. 1979. The spandrels of San Marco and the Panglossian paradigm: a critique of the adaptationist programme. Proceedings of the Royal Society of London. Series B. Biological Sciences 205 (1161):581-598. (available at a lot of places as PDF, here's a copy from University of Illinois: Urbana-Champaign)

This paper isn't on the official menu but I think it's a good quasi-contemporary review of the Gould and Lewontin paper (as borrowed from the reading list of the evolutionary biology course I took once upon a time...)

Pigliucci, M and J Kaplan. 2000. The fall and rise of Dr Pangloss: adaptationism and the Spandrels paper 20 years later. Trends in Ecology and Evolution 15 (2):66-70 (pdf available here)

Further thoughts on Chapters III-IV

1. As an ecologist, I'm in total agreement with John Whitfield at Blogging the Origin when he says that reading Chapter III engenders the feeling that there's nothing new under the sun. An old joke in philosophy is that all philosophy is footnotes to Plato. After reading chapter III of the Origin, one could be forgiven for thinking that all ecology is footnotes to Darwin.

2. Chapter IV also has plenty of prescient bits, my personal favorite of which is the passage on p. 113 stating that it has been 'experimentally shown' that diverse mixed plots of grass will be more productive than plots sown with one species. The diversity-productivity relationship has been the subject of intensive recent research, and broadly speaking, Darwin turns out to have been right: more diverse plots are more productive. But the underlying mechanisms have been controversial (at least they were for a time). The main issue is/was how to distinguish between an effect of diversity per se on productivity from the effects of particular species (all else being equal, a more diverse plot is more likely to contain a dominant, highly-productive species). In my own work I've helped develop a solution to this issue. Interestingly, the solution is based on George Price's work on the mathematics of natural selection (see Fox 2005). Briefly, dominance of a mixed plot by a highly productive species turns out to be formally analogous to the increase in frequency of a trait favored by selection. We can use Price's mathematics to factor out this effect, leaving a remainder that isolates the effect of 'diversity' per se on productivity. So this little subfield of research has come full circle: Darwin raised the example of the diversity-productivity relationship because of its implications for his evolutionary ideas; it now turns out that Darwin's evolutionary ideas have implications for understanding the diversity-productivity relationship. Not sure how interesting this is to anyone besides me, but I assume if you've read this far you found it at least mildly interesting... ;-)

3. A historical note related to #2: Darwin doesn't cite the experiment to which he was referring, but my friend and former colleague Andy Hector recently identified it. It turns out to have been, as far as we know, the very first 'ecology' experiment ever conducted, predating Haeckel's coining of the term 'ecology' by several decades. See Hector and Hooper 2002 Science 295:639-640 for this interesting historical nugget.

4. Given Darwin's prescience in so many areas, I was a little disappointed to see that his theory of the origin of species relies so heavily on the principle of divergence of character (i.e. you'll be fitter if your offspring are more variable). It certainly wouldn't have been beyond Darwin to have thought up more modern ideas, such as that widespread species often comprise geographically-separated subpopulations living in different environments and therefore subject to different selection pressures, which will drive them apart in the long run as long as rates of gene flow among subpopulations are sufficiently low. I was expecting to see a clear statement of this idea, and I never did. EDIT: whoops, Darwin does indeed hit on this idea. On pp. 107-108 he refers to subsidence converting a continent into large islands, thereby isolating separate populations of the same species. And then he says "...after physical change of any kind, immigration will be prevented, so that new places in the polity of each island will have to be filled up by modifications of the old inhabitants; and time will be allowed for the varieties in each to become modified and perfected." And of course, this passage is a summary of what has come before. I suppose I missed it because Darwin often intermingles this idea with other distinct but related ideas (e.g., on p. 103, when he talks about the spatial scales on which we should expect to see variation within highly-mobile species like birds vs. less-mobile species).

5. The later parts of chapter IV (pp. 116-130), on the 'tree of life' and the problem of classification, was interesting to me as proposing a solution to a problem that, as modern readers, we don't even recognize as a problem. The Linnean system of classification is hierarchical: species are nested within genera, which are nested within families, etc. What justifies (or maybe better, 'motivates') a hierarchical classification system? After all, there are many non-hierarchical possibilities. One could, for instance, group organisms into 'functional groups' based on their ecological 'roles' (e.g., herbivores, carnivores), and these groups would not be hierarchical but rather overlapping (e.g., some organisms are both herbivorous and carnivorous). I'm sure that various non-hierarchical classifications schemes were proposed at some point in the history of science (anyone know anything about this?). But if all life really does comprise a single branching evolutionary 'tree', that's a strong motivation for choosing a hierarchical classification system which reflects the hierarchical nature of 'tree-like' branching. This gets to philosophical issues regarding 'natural kinds'. Nature is full of variable 'things' that are similar in some respects and different in others. Is there ever a 'natural' way to classify these things, to 'cleave Nature at the joints'? Or is classification merely a human construct, something we do strictly for our own convenience?

supplementary paper for this week

Price, GR. 1995. The Nature of Selection. Journal of Theoretical Biology 175(3):389-396. (pdf here)

At the end of this course I will add in all of these links into the main supplementary readings post down below. Somewhere. Down there.

Tonya's Comments on the Introduction and Chapters I-II

My turn :)

p5) As many more individuals of each species are born than can possibly survive, there is frequently a recurring struggle for existence

This idea of a struggle for existence can mean many things. For instance, it can be an aggressive struggle such as when a food supply diminishes, or it can be a passive struggle (e.g. individuals being killed off by a deadly virus).

Natural selection almost inevitably causes much Extinction of the less improved forms...

Does he really have to use the term 'less improved'? Yes, I agree in a certain context they are less improved because they went extinct in a certain situation, but perhaps if the situation would be different then they would be the improved form.

I'm not really liking the subchapter headings posted at the top of each chapter and not above the paragraphs associated with each topic. I guess I am supposed to guess which paragraph goes with each topic (not that it is hard, it is just annoying).

p7) [individuals of the same variety or sub-variety of older cultivated plants and animals] generally differ much more from each other than do individuals of any one species or variety in a state of nature.

What?! Maybe I am not understanding this correctly but this cannot be true, can it?

Darwin thinks it is absurd that some people thing that every race which breeds true has had a wild prototype (p19) :)
Darwin also believes it is always best to study some special group (p20). Yay beetles!

p26) it is difficult, perhaps impossible, to bring forward one case of the hybrid offspring of two animals clearly distinct being themselves perfectly fertile.

Can anyone please explain this sentence to me?????

p36) Interesting tidbit: the barbarians of Tierra del Fuego would rather eat their old women over their dogs in dismal times. Hmm.

p40) We know nothing about the origin or history of any of our domestic breeds.

Awe Darwin, if only you knew how far we have come.

p42) Facility in preventing crosses is an important element of success in the formation of new races

Prezygotic and postzygotic mating barriers!

Interesting tidbit #2: cats are valued by women and children, not by men.

p52) I was very impressed with Darwins understanding of incipient species and that not all must attain the rank of species but there are a multitude of situations that can occur.

Here, Darwin describes a species as: a set of individuals closely resembling each other

p54) What does he mean when he states "plants low in the scale of organization". This is an odd way of writing about a plant with uncomplicated morphology, if that's what he even means.

p56) ...where many species of a genus have been formed, on an average many are still forming...

Is this an active area of modern research? Very interesting!

p57) ...in large genera the amount of difference between the species is often exceedingly small.

Yes, (with my very limited experience) I would agree with this statement as this is true in Nicrophorus (Silphidae: Coleoptera) which has many species; however, the opposite is not true because in Brychius (Haliplidae: Coleoptera), there are only three species and they are really hard to tell apart.

Introduction and Chapters I-II notations

Some of a host of random notations and questions I had while reading through the first ~60 pages of OTOOS

p3) Naturalists continually refer to external conditions ... as the only possible cause of variation

Is this statement true? Did no one before Darwin publish an explanation for variation that relied on factors intrinsic to organisms?

p6) Furthermore, I am convinced that Natural Selection has been the main but not exclusive means of modification.

From the get-go, Darwin is making it clear that he thinks NS works in concert with other natural phenomena to modify the species of the world. It takes a while to get out of him what he thinks these other natural phenomena are but eventually he talks about them.

p8) But I am strongly inclined to suspect that the most frequent cause of variability may be attributed to the male and female reproductive elements having been affected prior to the act of conception.

Okay, in Chapter I he starts laying down the framework for how he thinks variability in organisms occurs. The problem is that ...this is massively generalistic and begs big questions. The (to use the modern terminology) gametes are affected? By what? By ...the organism's thoughts? By actions of the environment? By use and disuse? The answer here can't be NS because that's not going to affect reproductive elements, NS is only acting on whole organisms, not parts of them.

p11) Nevertheless some slight amount of change may, I think, be attributed to the direct action of the conditions of life -- as, in some cases, increased size from amount of food ...

So the conditions of life cause variation in organisms. Is this limited to that one individual in its life or is this something that becomes inheritable, e.g., an acquired characteristic? I'd say it's not but then a few sentences later...

The great and inherited development of the udders in cows and goats in countries where they are habitually milked ... is another instance of the effect of use. Not a single domestic animal can be named which has not in some country drooping ears; and the view suggested by some authors, that the drooping is due to the disuse of the muscles of the ear ... seems probable.

This is the beginning of a book full of comments that show that Darwin did not have a scientific problem with acquired characteristics; he just didn't think that they alone explained variation. If promoting acquired characteristics makes one a Lamarckist than Darwin is being a Lamarckist in OTOOS. (and I use the term Lamarckist in its general sorta pop-sci understanding of the term. Even wikipedia tells me that's too simplistic but ...just go with it)

p20-29 I won't quote but basically Darwin gives a great litany of well thought-out reasons why domesticated pigeons, even though they show amazing amounts of variation, must be descended from one ancestral species. It's weird reading this in a book full of Darwin deferring to popular opinion at the time that domesticated dogs must have descended from several ancestral species.

p32-42 Darwin is doing the best job he can at explaining out artificial selection as the driving force behind variation in domesticated species. And it's a great job: he establishes that breeders are picking up tiny, minute differences in their animals. He establishes that not all of these animals breed. He makes it certain to explain that breeders don't aim to make a new variety of, say, dog. No one sat down and decided to make a Dalmatian. But breeders picking small changes in generation after generation will eventually produce a new breed of dog. Artificial selection may be intelligently-driven but it does not have directionality, since breeders can't control what the next generation of bred organism will look like. Or, more to the point, breeders can't create novel features, they can merely select for them.

All Darwin has to do now is replace the word "artificial" with "natural" and "breeders" with "nature" and he can convince the reader that NS occurs.

p43) No one supposes that all the individuals of the same species are cast in the very same mould.

This became part of discussion today because the Mayr introduction to this OTOOS publication mentions how Darwin took species away from typological understanding into a population-level understanding. There was a lot said today about this and ...a lot more can easily be said about it. I don't have much to add.

p46) I am inclined to suspect that we see in these polymorphic genera variations in points of structure which are of no service or disservice to the species, and which consequently have not been seized on and rendered definite by natural selection.

Later in the text Darwin will come back to this with his commentary on how one should make phylogenetic trees (although, of course, he doesn't use that terminology.) But, when I read this, I fail to see how Kimuran neutral theory (or at least the first assertation of it) is in anyway contradictory to natural selection. DNA and RNA aren't organismal structures (they literally build strucutres) but if they're not under selection than they can be as neutral as they want to be.

Chapter II is generally a long discussion on how the "What is a species?" discussion will never have any definite winner. To cut to the chase...

p52) From these remarks it will be seen that I look at the term species, as one arbitrarily given for the sake of convenience to a set of individuals closely resembling each other, and that it does not essentially differ from the term variety, which is given to less distinct and more fluctuating forms.

In our modern biological world we could probably argue that species have definite molecular markers and that we could use those to define a "species", but even in that case there might be more unsampled populations out there which actually show a marker that is 'partway' between one defined species and another.

Embracing Darwin's worldview partially means embracing the idea that species are abstracts. In a Darwinian world, species barriers "break down" as we take modern-day populations of organisms and expose them to the fourth dimension. In so doing we see that somewhere the species we are tracing back in time start off as a 'variety' of another species, and that species the same, and so on and so on etc.

four-dimensional populations of organisms that are all more re n