Domestication.

Those of you who have read Darwin will know that he had a strong interest in domestication and artificial selection. People have argued about how important this was in his development of the idea of natural selection, but there is no doubt that it was at least relevant in his explanation of the mechanism. It is the first topic he discusses in the Origin, and the only subject that he meant to cover in greater detail that he actually returned to in a later publication (the two-volume The Variation of Animals and Plants under Domestication, 1868).

I wrote a paper about domestication and what it can teach us about natural selection for the recent issue of Evolution: Education and Outreach, and I now see that Michael Purugganan and Dorian Fuller have authored a paper on this topic for the Feb. 12 issue of Nature (Darwin Day). I didn’t know about their paper, so it isn’t cited in my article, but I can at least give a link below. Another one that I learned about too late but which is recommended is by Melinda Zeder from a couple of years ago.

Gregory TR. 2009. Artificial selection and domestication: modern lessons from Darwin’s enduring analogy. Evolution: Education and Outreach 2: 5-27.

Purugganan MD and Fuller DQ. 2009. The nature of selection during plant domestication. Nature 457: 843-848.

Zeder MA 2006. Central questions in the domestication of plants and animals. Evolutionary Anthropology 15: 105-117.

For many more, see the references cited in my paper.

Jerry Coyne on Darwinism.

It’s great to know that Jerry Coyne has a blog — I certainly plan to read it and you should too.

However, I have to confess that I tend not to agree with him on a lot of points. His criticism of evo-devo, his opinion that punctuated equilibria is saltationist, and his apparent belief that there is nothing new under the sun in evolutionary biology that is worth getting too excited about.

I also disagree that “’Darwinism’” is a compact, four-syllable term for ‘modern evolutionary theory’”. No, it isn’t. It may be a synonymn for “adaptive change due to the process of natural selection”, but even that would be stretching it. There is a LOT in modern evolutionary theory that is well outside anything Darwin considered, and thus is not “Darwinism” in any sense. Genetic drift, everything to do with mutation, allopatric speciation, mass extinctions, developmental regulatory genes, genome duplication, population genetics, the list goes on. There is also a lot that Darwin considered, including use and disuse, pangenesis, and other components of what should also be included in “Darwinism”, that are not part of evolutionary theory.

I repeat the advice given by Scott and Branch for historic, scientific, and practical reasons: Don’t call it “Darwinism”.

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UPDATE: See also Larry Moran‘s thoughts.

What Darwin didn’t know.

As you may know, I have be (re-)reading the On the Origin of Species as part of a small discussion group made up of students from my most recent evolution course. I am always struck by how much Darwin knew, not only in terms of his enormous collation of specific facts, but also of the concepts that he introduced that are still easily recognizable. Read Chapters 3 and 4 of the Origin, and you will encounter not only natural selection, but the basics of what we now call competitive exclusion, coevolution, r- and K-selection, succession, phylogenies, gene flow (minus the genes), and many others.

Of course, there is a lot (read: a LOT) that Darwin didn’t, and couldn’t, know. How inheritance works, for example. Not surprisingly, evolutionary theory has advanced enormously since Darwin’s time, and many of his more specific ideas have been expanded, supplanted, or simply rejected. For this reason, it is quite inaccurate to use “evolutionary biology” and “Darwinism” interchangeably, even without the fact that anti-evolutionists use the latter term for rhetorical purposes.

While some have used the (obvious and inevitable) incompleteness of Darwin’s early ideas to sell magazines through sensationalism, I am nonetheless glad to see that others have taken a more measured approach in reminding readers that science has come a long way since 1859.

Here are some examples…

Modern Darwins
by M. Ridley, National Geographic

What Darwin Didn’t Know
by T. Hayden, Smithsonian Magazine

Let’s get rid of Darwinism
by O. Judson, New York Times blog

Don’t call it “Darwinism”
by E.C. Scott and G. Branch, Evolution: Education and Outreach

Also…

Can we please forget about Charles Darwin?
by S. Jones, Telegraph

Darwinism Must Die So That Evolution May Live
by C. Safina, New York Times

The latter two articles are a bit extreme, as Brian Switek, PZ Myers, John Hawks, and Jerry Coyne pointed out. It isn’t necessary to remove Darwin from the picture, and it certainly remains appropriate to celebrate his 200th birthday and the 150th anniversary of the On the Origin of Species this year. One excellent way of doing this is to actually read the Origin and to take note both of what Darwin knew and what we have learned in the subsequent 150 years.

CBC Sunday Edition on Darwin.

Today’s Sunday Edition on CBC was about Darwin. Guests included Brian Alters, Ken Miller, and Ruth Padel. (Padel is Darwin’s great-great-granddaughter and has a book entitled Darwin: A Life in Poems).

A schedule of the program is available here. The podcast is not up yet, but when it is, it will be here.

On the Origin of Species – Chapter 3.

Chapter 3 – Struggle for Existence

This is the chapter in which Darwin really picks things up. Whereas the first two may have been more like, in Darwin’s own words, “a dry list of facts”, this one is written in a very passionate tone. Having established that individuals vary both in domesticated breeds and in nature, he now moves into the second major ingredient of natural selection: overproduction.

Some important things in this chapter:

1) Darwin strongly emphasizes adaptation. This is not very surprising, given that he considered natural selection as the main (but not only) mechanism of evolution.

“But the mere existence of individual variability and of some few well-marked varieties, though necessary as the foundation for the work, helps us but little in understanding how species arise in nature. How have all those exquisite adaptations of one part of the organisation to another part, and to the conditions of life, and of one distinct organic being to another being, been perfected? We see these beautiful co-adaptations most plainly in the woodpecker and missletoe; and only a little less plainly in the humblest parasite which clings to the hairs of a quadruped or feathers of a bird; in the structure of the beetle which dives through the water; in the plumed seed which is wafted by the gentlest breeze; in short, we see beautiful adaptations everywhere and in every part of the organic world.”

2) We may think life is well balanced and peaceful, but there is carnage going on all around, if not right this moment then at the very least during difficult seasons.

“We behold the face of nature bright with gladness, we often see superabundance of food; we do not see, or we forget, that the birds which are idly singing round us mostly live on insects or seeds, and are thus constantly destroying life; or we forget how largely these songsters, or their eggs, or their nestlings, are destroyed by birds and beasts of prey; we do not always bear in mind, that though food may be now superabundant, it is not so at all seasons of each recurring year.”

“Although some species may be now increasing, more or less rapidly, in numbers, all cannot do so, for the world would not hold them.”

3) The struggle for life can be against the environment (e.g., surviving in cold or dry habitats), but the major factor is the biotic environment. He also points out that what matters more than survival is reproduction.

“I should premise that I use the term Struggle for Existence in a large and metaphorical sense, including dependence of one being on another, and including (which is more important) not only the life of the individual, but success in leaving progeny. Two canine animals in a time of dearth, may be truly said to struggle with each other which shall get food and live. But a plant on the edge of a desert is said to struggle for life against the drought, though more properly it should be said to be dependent on the moisture. A plant which annually produces a thousand seeds, of which on an average only one comes to maturity, may be more truly said to struggle with the plants of the same and other kinds which already clothe the ground. The missletoe is dependent on the apple and a few other trees, but can only in a far-fetched sense be said to struggle with these trees, for if too many of these parasites grow on the same tree, it will languish and die. But several seedling missletoes, growing close together on the same branch, may more truly be said to struggle with each other. As the missletoe is disseminated by birds, its existence depends on birds; and it may metaphorically be said to struggle with other fruit-bearing plants, in order to tempt birds to devour and thus disseminate its seeds rather than those of other plants. In these several senses, which pass into each other, I use for convenience sake the general term of struggle for existence.”

4) Darwin considers extinction to be gradual, not catastrophic (he acknowledges what we now call background extinction but not mass extinctions).

“Battle within battle must ever be recurring with varying success; and yet in the long-run the forces are so nicely balanced, that the face of nature remains uniform for long periods of time, though assuredly the merest trifle would often give the victory to one organic being over another. 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!”

5) Darwin recognizes different strategies of reproduction (what we now call r-selection and K-selection).

“A large number of eggs is of some importance to those species, which depend on a rapidly fluctuating amount of food, for it allows them rapidly to increase in number. But the real importance of a large number of eggs or seeds is to make up for much destruction at some period of life; and this period in the great majority of cases is an early one. If an animal can in any way protect its own eggs or young, a small number may be produced, and yet the average stock be fully kept up; but if many eggs or young are destroyed, many must be produced, or the species will become extinct.”

6) Competition is most intense between members of the same species because their requirements are so similar.

“But the struggle almost invariably will be most severe between the individuals of the same species, for they frequent the same districts, require the same food, and are exposed to the same dangers.”

7) At higher levels, closely related species experience more intense competition than distantly related species, again because their requirements are similar.

“As species of the same genus have usually, though by no means invariably, some similarity in habits and constitution, and always in structure, the struggle will generally be more severe between species of the same genus, when they come into competition with each other, than between species of distinct genera.

Some famous quotes:

“Again, it may be asked, how is it that varieties, which I have called incipient species, become ultimately converted into good and distinct species, which in most cases obviously differ from each other far more than do the varieties of the same species? How do those groups of species, which constitute what are called distinct genera, and which differ from each other more than do the species of the same genus, arise? All these results, as we shall more fully see in the next chapter, follow inevitably from the struggle for life. Owing to this struggle for life, any variation, however slight and from whatever cause proceeding, if it be in any degree profitable to an individual of any species, in its infinitely complex relations to other organic beings and to external nature, will tend to the preservation of that individual, and will generally be inherited by its offspring. The offspring, also, will thus have a better chance of surviving, for, of the many individuals of any species which are periodically born, but a small number can survive. 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. We have seen that man by selection can certainly produce great results, and can adapt organic beings to his own uses, through the accumulation of slight but useful variations, given to him by the hand of Nature. But Natural Selection, as we shall hereafter see, is a power incessantly ready for action, and is as immeasurably superior to man’s feeble efforts, as the works of Nature are to those of Art.”

“We can dimly see why the competition should be most severe between allied forms, which fill nearly the same place in the economy of nature; but probably in no one case could we precisely say why one species has been victorious over another in the great battle of life.”

On the Origin of Species – Chapter 2

Once again, this is just a repost of what I wrote in my book club discussion forum.

Chapter 2 – Variation Under Nature

This is a fairly short chapter, with much less information than the discussion of variation under domestication. In part, this is because a lot more was known about variation in domesticated animals and plants than in natural species. However, it wasn’t considered by everyone to be a good approach — Wallace always thought Darwin’s argument was weakened by relying so much on domestication as an analogy with natural processes.

Some things I found interesting in this chapter:

1) Species are hard to define. We talked in class about how there is no clear definition of species and how this causes problems in biology. Well, Darwin recognized the difficulty very early (p.67).

“Nor shall I here discuss the various definitions which have been given of the term species. No one definition has as yet satisfied all naturalists; yet every naturalist knows vaguely what he means when he speaks of a species.”

2) Darwin begins to suggest that the variation within species (e.g., varieties) is the same stuff that turns into differences among species. He introduces the term “incipient species” to indicate this. However, not all incipient species will become species — some may go exinct and some may not change further (p.76).

“Hence I believe a well-marked variety may be justly called an incipient species; but whether this belief be justifiable must be judged of by the general weight of the several facts and views given throughout this work.

It need not be supposed that all varieties or incipient species necessarily attain the rank of species. They may whilst in this incipient state become extinct, or they may endure as varieties for very long periods.”

3) Sometimes daughter species can co-exist with parental species — it is not always a gradual change of one species into another. In other words, Darwin recognizes cladogenesis (indeed, something compatible with punctuated equilibria) and not only anagenesis (p.76) .

“If a variety were to flourish so as to exceed in numbers the parent species, it would then rank as the species, and the species as the variety; or it might come to supplant and exterminate the parent species; or both might co-exist, and both rank as independent species.”

4) Nevertheless, Darwin does not think that species are real. They are just convenient constructs (p.76).

“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. The term variety, again, in comparison with mere individual differences, is also applied arbitrarily, and for mere convenience sake.”

UPDATE: John Wilkins does not think that this and similar passages indicate that Darwin considered species as mere conveniences, only that he considered the distinction between varieties (which he called “incipient species”) and species to be mainly arbitrary. He may have a point.

5) Darwin suggests that widespread, numerous species are likely to produce more daughter species (p.77). This would seem to contradict later models of speciation involving geographic isolation, especially ones based on drift in small isolates.

“Hence it is the most flourishing, or, as they may be called, the dominant species,— those which range widely over the world, are the most diffused in their own country, and are the most numerous in individuals,—which oftenest produce well-marked varieties, or, as I consider them, incipient species.”

6) Darwin has compiled a series of data (he doesn’t show them here) comparing genera that are diverse (lots of species) and those that are not, and argues that larger genera include species that themselves include more varieties. He argues on this basis that dominant lineages will become more dominant, since these varieties are incipient species. However, he also notes that this does not continue indefinitely because some previously dominant lineages disappear and some small genera can expand.