Evolving Thoughts

Evolution, culture, philosophy and chocolate! John Wilkins' continuing struggle to come to terms with impermanence... "Humanus sum, nihil humanum a me alienum puto" - Terence

Friday, December 10, 2004

The Call of the Christian Wild

Why do some people insist that without the Bible as a moral authority, there is no moral code? Because for them, without the Bible, or even with it, they act like this.


The URL is no longer active. It described the bullying of atheist children by Christian children, with the tacit approval of Chrsitian school authorities.

One Flew over the Deist's Nest

Doing the rounds at the moment is this, seen on a few newsgroups:

Top atheist and professor Anthony Flew has finally admitted the obvious--that life is too complex to have arisen by natural causes. He now believes in the essentials of Intelligent Design theory and a "limited God", based on scientific evidence.

The greatest scientific deceit in history has been dealt a serious blow.

Rubbish. Flew's deism is antithetical to Christian and Islamic theism, for a start (Flew says as much) and all he is claiming is Spinoza's god - the distant and first causing god who has no personal agenda or relationships. And his reason is surprisingly weak - he cannot conceive how DNA got going.

Now I think there is a flaw here. It is often said (for example by Dawkins) that evolution got going when the first molecule acquired (by "chance") the property of being able to replicate itself. So for evolution to begin there had to be, it is said, a first replicator.

But this is a mistake - replicators are a sufficient cause of evolution, but they are not, in my opinion, necessary for it. And if they are not necessary for it (and in particular not necessary for natural selection) then they can themselves evolve using ordinary Darwinian processes of optimisation of fidelity of reproduction by selection.

If the original protobiological reactions generated copies of themselves, there will be differences in the stability and fidelity of copying for the different elements of that reaction cycle. Variants that are more stable will generate more copies, and variants that are more high fidelity than others will generate more copies like themselves. Selection will do the rest, and the end product will be replicators (RNA initially, followed by DNA). So there is a (feasible) argument that accounts for the evolution of replicators before there were any. Hence, the conclusion is based on an argumentum ad ignoratium.

There is no logical conundrum here. It concerns me that Flew does not see this, but then he is only following the standard opinion of hard selectionists like Dawkins. But his argument is an argument from ignorance. He may find it compelling personally, but it is not compelling logically.


... have always been regarded with suspicion:

Christmas presents for your biology teachers

Colin Purrington is an associate professor of biology at Stawrthmore College in Pennsylvania, and he is increasingly displaying the personality traits that we Australians refer to fondly as "shit stirring". Colin is responsible for the extended "textbook disclaimers" that have had a fair bit of press lately. He also did a genealogy of textbook disclaimers that found its way into the New York Times, with the help of cartoonist Felix Stockwell.

Now he has turned his satirical talents at listing present suggestions for beleaguered high school biology teachers who may be feeling the pressure from creationist parents and school board members. We sometimes forget these poor folk on the front line. Buy one of these items today for your child's biology teacher...

Wednesday, December 08, 2004

One Nation, Under the Designer

In a recent blog on the Phi Beta Kappa website, the international Professional Association for Educators, Mark Terry, who heads a school science department just up the road from Disco (the Discovery Institute, as they call themselves), put the Wedge Strategy into context, both politically, and what I am more interested in here, historically.

Terry rightly observes that what we are witnessing here is not merely a rejection of a single scientific theory, nor even the rejection solely of science, but an attempt to return to the days when the church controlled all intellectual life.

In short, the Wedge is about a return to Christendom - and the abandonment of the past three centuries of science and arts. Of course, that is not how it is put by Disco, or by the conservative Christians bankrolling this movement in the US or the UK or anywhere else, but that is what it means.

The person who, more than anyone else, overcame the religious patronage of science system that prevailed in Britain during the first half of the nineteenth century was Thomas Henry Huxley - Darwin's bull dog. Huxley, not born to a position of privilege like his later nemesis Sir Richard Owen (then just Richard), fought to make science a professional and independent institution, and as a result, Britain, science and society in the west flourished. Owen, indebted to and controlled by religious patronage, was unable to pursue his initial speculations on the matter of evolution. Later, he claimed to have both thought of it first and shown it to be wrong, neither of which were true. The point, however, was that had science been independent of the church then, we might now be discussing Owenism.

Whenever institutions like the church or government has tried to control science for their own ends, the results have been moribund and degenerate science, or worse. Terry is to be commended for bringing this to our attention. Go read it.

Did Darwin explain the origin of species in On the Origin of Species?

There is a repeated canard that Darwin did not account for the origin of species in his book (repeated by, among others, Futuyma). He did.

There is a similar canard that Darwin had no definition of "species" and indeed that he denied that species were real. This, too, is false.

On the latter, allow me to quote from Michael Ghiselin's Triumph of the Darwinian Method (1984 edn, chapter IV):

It is not difficult to find passages in Darwin's writing suggesting that he considered species to be purely artificial constructs. For instance: "In short, we shall have to treat species in the same manner as those naturalists treat genera, who admit that genera are merely artificial combinations made for convenience. This may not be a cheering prospect; but we shall at least be freed from the vain search for the undiscovered and undiscoverable essence of the term species."[26] On the basis of statements such as this, Mayr and others have come to the conclusion that Darwin upheld a morphological, as opposed to a biological, species concept.[27] That is, they maintain that he looked upon species as merely classes of organisms having a given degree of similarity and difference in the observed properties of their members. But there are certain other passages in Darwin's writings which show that the problem is more complicated. In his second notebook on the transmutation of species, Darwin says: "As species is real thing with regard to contemporaries - fertility must settle it."[28] The reality of species is affirmed in a letter to Gray written in 1860, in which Darwin severely criticizes some assertions of Louis Agassiz. The following statement is particularly relevant to the question at issue: "How absurd that logical quibble - 'if species do not exist, how can they vary?' As if any one doubted their temporary existence."[29] It appears that there is at least one sense in which species are thought to be real, although it is evident that there is a sense in which they are held to be not real. This being the case, any citation of statements by Darwin in support of his holding one or another point of view must be buttressed by a demonstration of the sense which he intended.

Ghiselin's footnote references are:
26 Origin, p. 485.

27 Mayr, "Isolation."

28 Second Notebook, p. 99. (The view expressed here was later modified.)

29 Life and Letters, II, 333.

Ghiselin, Michael T. 1969. The triumph of the Darwinian method. Berkeley: University of California Press, 1984 edition.

I have around 37 pages of Darwin's comments on species - so far as I can tell he always thought that species were contemporaneously real things, that were temporary. Interfertility is not, as Ghiselin suggests, a view Darwin later abandoned, but it is only a test, and not the cause of species in his later view.

He thought that species were formed from selection favouring varieties within a species. Although he flirted with geographical isolation as a cause before the Origin, after it, he thought selection, and only selection, caused new species, and he had a debate with Moritz Wagner, who proposed geographical isolation, on the matter.

Darwin appears to have been correct that selection can cause species, but incorrect in thinking that other factors such as geographical isolation cannot, and that all speciation is driven by selection. However, it does seem like all speciation is followed by selection as novel species adapt to different circumstances (including different mates).

Darwin explained speciation by what we would now call sympatric speciation (that term was invented much later, by EB Poulton). His mechanism was abandoned for a long time after around 1904 (Poulton's paper) in favour of Wagner's geographic isolation hypothesis (JT Gulick's work was pretty convincing to most).

Poulton, Edward Bagnall. 1903. What is a species? Proceedings of the Entomological Society of London: 1946-1994, reprinted in Poulton, Edward Bagnall. 1908. Essays on Evolution. Oxford: Clarendon.

However there are the following points to make:

1. Darwin did give an answer to the origin of species in The Origin of Species.

2. Recent work shows that in fact his mechanism does, realistically, generate new species from time to time (reviewed nicely by Schilthuizen 2001).

Schilthuizen, Menno. 2001. Frogs, flies, and dandelions: the making of species. Oxford: Oxford University Press.

3. Many new species are formed either by polyploidy or in allopatry, in fact.


4. Darwin explained some, but not all speciation.

The myth seems to be that Darwin did not even try to explain new species in TOoS. He did. He gave a good explanation - it just happens that it does not explain most speciation.

OK, now to what Darwin did say on the subject (6th edition used - so far as I can tell he does not change his views on this from 1859-1882. Page numbers in original edition):

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 from the struggle for life. Owing to this struggle, variations, however slight and from whatever cause proceeding, if they be in any degree profitable to the individuals of a species, in their infinitely complex relations to other organic beings and to their physical conditions of life, will tend to the preservation of such individuals, and will generally be inherited by the 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 Natural Selection, in order to mark its relation to man's power of selection. [Chapter III, p51f]

And in chapter IV, he notes

In order that any great amount of modification should be effected in a species, a variety, when once formed, must again, perhaps after a long interval of time, vary or present individual differences of the same favourable nature as before; and these must be again preserved, and so onward, step by step. [p66]

Reproductive isolation maintains the subsequent species:

Intercrossing plays a very important part in nature by keeping the individuals of the same species, or of the same variety, true and uniform in character. It will obviously thus act far more efficiently with those animals which unite for each birth; but, as already stated, we have reason to believe that occasional intercrosses take place with all animals and plants. Even if these take place only at long intervals of time, the young thus produced will gain so much in vigour and fertility over the offspring from long-continued self-fertilisation, that they will have a better chance of surviving and propagating their kind; and thus in the long run the influence of crosses, even at rare intervals, will be great. With respect to organic beings extremely low in the scale, which do not propagate sexually, nor conjugate, and which cannot possibly intercross, uniformity of character can be retained by them under the same conditions of life, only through the principle of inheritance, and through natural selection which will destroy any individuals departing from the proper type. If the conditions of life change and the form undergoes modification, uniformity of character can be given to the modified offspring, solely by natural selection preserving similar favourable variations. [p79]

Darwin at the time of the sixth edition thought that the formation of species did not rely on isolation and here he takes Moritz Wagner's view to task. Isolation does, he thought, make species formation easier, but he cannot agree it is required, as Wagner thought. And if the isolated population is too small, then isolation can in fact prevent speciation from occurring due to a lack of variation. The founder effect or drift through biased sampling has not occurred to him, as it later did to Weismann.

Isolation, also, is an important element in the modification of species through natural selection. In a confined or isolated area, if not very large, the organic and inorganic conditions of life will generally be almost uniform; so that natural selection will tend to modify all the varying individuals of the same species in the same manner. Intercrossing with the inhabitants of the surrounding districts will, also, be thus prevented. Moritz Wagner has lately published an interesting essay on this subject, and has shown that the service rendered by isolation in preventing crosses between newly-formed varieties is probably greater even than I supposed. But from reasons already assigned I can by no means agree with this naturalist, that migration and isolation are necessary elements for the formation of new species. The importance of isolation is likewise great in preventing, after any physical change in the conditions such as of climate, elevation of the land, &c., the immigration of better adapted organisms; and thus new places in the natural economy of the district will be left open to be filled up by the modification of the old inhabitants. Lastly, isolation will give time for a new variety to be improved at a slow rate; and this may sometimes be of much importance. If, however, an isolated area be very small, either from being surrounded by barriers, or from having very peculiar physical conditions, the total number of the inhabitants will be small; and this will retard the production of new species through natural selection, by decreasing the chances of favourable variations arising. [p79f]

Although isolation is of great importance in the production of new species, on the whole I am inclined to believe that largeness of area is still more important, especially for the production of species which shall prove capable of enduring for a long period, and of spreading widely. Throughout a great and open area, not only will there be a better chance of favourable variations, arising from the large number of individuals of the same species there supported, but the conditions of life are much more complex from the large number of already existing species; and if some of these many species become modified and improved, others will have to be improved in a corresponding degree, or they will be exterminated. Each new form, also, as soon as it has been much improved, will be able to spread over the open and continuous area, and will thus come into competition with many other forms. Moreover, great areas, though now continuous, will often, owing to former oscillations of level, have existed in a broken condition; so that the good effects of isolation will generally, to a certain extent, have concurred. Finally, I conclude that, although small isolated areas have been in some respects highly favourable for the production of new species, yet that the course of modification will generally have been more rapid on large areas; and what is more important, that the new forms produced on large areas, which already have been victorious over many competitors, will be those that will spread most widely, and will give rise to the greatest number of new varieties and species. They will thus play a more important part in the changing history of the organic world. [p80f]

Ironically, as Kottler (1978: 285-288) noted, Darwin in the Notebooks believed that isolation was a sine qua non for speciation, in part following the views of Leopold von Buch. By this later stage, Darwin appears to have made Natural Selection the primary cause of species, requiring that variation needs to occur in situ as it were, and so needing larger populations to give it opportunity to do so.

Kottler, Malcolm J. 1978. Charles Darwin's biological species concept and theory of geographic speciation: the Transmutation Notebooks. Annals of Science 35:275-297.

[Thanks to Mike Syvanen and John Harshman for discussion]

Monday, December 06, 2004

The history of "species"

It occurs (was pointed out) to me that I have talked about everything but what I did my thesis on. So you must now suffer...

I make two historical claims, and a philosophical one. The philosophical one has been published, and is on my website (go to Published Papers) and so we can leave it for now that I think the general meaning of "species" is, and always has been, "differentiated lineage".

The historical claims are this:

1. The Received View that prior to Darwin or modern biology, biological species were essentialistic is historically false. While an essentialistic notion of logical species was the default opinion from Aristotle onwards, even he allowed that living beings would vary "the more and the less" from the logical type. Instead, contrary to Mayr's historical revisionism, typology was generally not essentialistic, as Polly Winsor is demonstrating in paper after paper these days.

Winsor, Mary Pickard. 2001. Cain on Linnaeus: the scientist-historian as unanalysed entity. Studies in the History and Philosophy of the Biological and Biomedical Sciences 32 (2):239-254.
———. 2003. Non-essentialist methods in pre-Darwinian taxonomy. Biology & Philosophy 18:387-400.
———. 2004. Setting up milestones: Sneath on Adanson and Mayr on Darwin. In Milestones in Systematics: Essays from a symposium held within the 3rd Systematics Association Biennial Meeting, September 2001, edited by D. M. Williams and P. L. Forey. London: Systematics Association.

In fact, it appears to me, on the basis of a little sampling, that essentialism in biology arises after Darwin, and in reaction to him. I have found examples in Catholic texts published around 1890. Possibly this is part of a Thomist revival in biology at a time when the Catholic Church had proscribed transmutationism (which was not its traditional view anyway). This was taken up and discussed (and dismissed) by HWB Joseph's Introduction to Logic, first edition 1906, second 1916.

Joseph, H. W. B. 1916. An introduction to logic. 2nd ed. Oxford: Clarendon Press.

Possibly this found its way into the discussions of the species concept and systematics in general at the early part of the 20th century, thence into Stresemann's book

Stresemann, Erwin. 1975. Ornithology from Aristotle to the present. Translated by H. J. Epstein and C. Epstein. Cambridge MA: Harvard University Press.

Stresemann wrote this during the second world war. He was Mayr's teacher before the latter made his way to America.

2. That there always was what I am calling a generative conception of species. It is implicit in Aristotle, but the best example is found in Epicurus' philosophy. I shall quote from Lucretius' On the Nature of Things to illustrate:
If things could be created out of nothing, any kind of things could be produced from any source. In the first place, men could spring from the sea, squamous fish from the ground, and birds could be hatched from the sky; cattle and other farm animals, and every kind of wild beast, would bear young of unpredictable species, and would make their home in cultivated and barren parts without discrimination. Moreover, the same fruits would not invariably grow on the same trees, but would change: any tree could bear any fruit. Seeing that there would be no elements with the capacity to generate each kind of thing, how could creatures constantly have a fixed mother? But, as it is, because all are formed from fixed seeds, each is born and issues out into the shores of light only from a source where the right ultimate particles exist. And this explains why all things cannot be produced from all things: any given thing possesses a distinct creative capacity.
(Lucretius 1969: 38, Book I. 155-191)

Lucretius. 1969. On the nature of things (De rerum natura). Translated by M. F. Smith. London: Sphere Books.

The consistent elements of the generative conception are that form is reproduced consistently. It often has a sexual element, and so it is a kind of Biological Species Concept, despite Mayr's claim that this was not discovered until the 20thC and perfected by him. Almost everywhere you look, in naturalists or philosophers, the generative conception is a consistent thread running from that day to this. It is in John Ray, Linnaeus, Buffon, Lamarck, the 19th century naturalists, in Mill, in Locke and so forth.

There is a consistent tendency in science to see only that which has contributed to the current consensus, and to over-estmiate the originality of modern work. Mayr's is an egregious example, but he is not alone; on this subject alone, Simpson, Cain and others have all roughly committed the same mistake under the Received View. And it exists in other sciences. It derives, I believe, from the fact that science has different exigencies and interests than historical research (let's not get into whether history is a science or not. It is, and it is not. Leave it there).

Sunday, December 05, 2004

Of course we are still evolving

A common riff on the role of medical and technological advances is that they have somehow insulted humanity from evolution, or the ordinary course of evolution. This is an old canard - it goes back to the days before Darwin, and is a basic justification of eugenics programs (not just the Nazi horrors, but the more "positive" programs of encouraging the "better" kind of humans to interbreed).

If medicine has interfered with the selective pressures we faced in the past, it is thought, we will face degeneration, or be in control of our own evolution, or something, that will interfere with the "normal" course of evolution.

A very nice article by Gabrielle Walker in Prospect Magazine, a UK publication of The Independent, discusses this in some detail.

You'd think that after we encountered AIDS, MRSA (multiply resistant Staphylococcus aureus), bird flu, swine flu, Nile River fever, and the host of new and altered diseases that occur, we would not be so sure. But there is more.

It is overlooked, in part because we think of what we humans do as being not a part of Nature, but of Art (the division is as old as Greek philosophy - Art is techne in Greek) that our own cultural activities both constructs a niche to which we will eventually become adapted, if it persisted long enough, and also provides new selective pressures.

For a start, there has been extensive selection against diseases that only get a purchase in urban environments in Europe. Alleles that confer resistance to bubonic plague are widespread - I wonder why? Is there any reason to think that if a disease hit us today, we would not change our allele frequencies so that resistant alleles would become widespread, to the point where the disease was unable to spread, vaccines and antibiotics notwithstanding?

Moreover, there is selection against lactose-intolerance that has been applied in a very brief period, in evolutionary terms. All through Asia now, this selection pressure is being applied. You don't need to die for selection to apply, just do slightly worse at raising children and grandchildren and greatgrandchildren, etc., than those who do not have the gene you do.

Even if we can manage to modify genes directly, this does not stop evolution. One of two things can happen, or both. The genes we use will have been "tested" elsewhere before we use them, in other humans or other organisms, in which case this is still just a spread of gene alleles through selection - the fact that scientists rather than gametes spread the genes is largely irrelevant, as what happens after those genes are introduced will be independent of the scientists anyway - they are, evolutionarily speaking, a blip.

The other is that introducing these genes individually into a complex developmental program will have massive unlooked-for effects - the Pandora Principle. Biology is replete with things that are massively interlinked - if you, for example, reactivated the fossil gene for the production of Vitamin C, it may turn out that in certain environments this caused liver failure. These things are not easily predictable, if at all. And no matter how much is predictable, some will always not be.

So have we stopped evolving? We have not! Evolution is affected by behavior, as we know under the principle of the Baldwin Effect. It is time to lay this mistake to rest once and for all.