Abiogenesis vs. evolution.

At The Panda's Thumb, Nick Matzke has a post about abiogenesis (the origin of life from non-life) and evolution. He, PZ, and others argue that abiogenesis is part of evolutionary biology and that it is a cop-out to deflect challenges about it from anti-evolutionists. Allow me a brief summary of my interpretation.

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Question: Do we need evolutionary biology to understand the origin of life?

Answer: Very probably. Early replicators, once they arise, would undergo evolution. Mutation, natural selection, etc., would have been important before cellular life as we understand it appeared. However, there are components to the issue that predate the occurrence of natural selection, which are more properly understood in terms of organic chemistry than biology. The line is not sharp, though, so keeping evolution out of abiogenesis research is unwise.

Evidence: Whether "cells" (membranes with stuff inside) or replicator molecules (e.g., RNA) appeared first, if there was heritable variation and reproduction and survival that differed among them, then selection would have happened.

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Question: Do we need to understand how life arose to understand the subsequent evolution of cellular life?

Answer: No.

Evidence: We have been studying evolution seriously for 150 years and understand quite a bit about how it happens, yet we don't know how life arose.

So, Nick and others are correct that we should not say that abiogenesis is independent of evolution. However, if they are implying that abiogenesis is part of — more importantly, a crucial part of — evolutionary theory, then I do not agree. The influence is one-way, and this is the opposite of the way anti-evolutionists perceive it. They argue that if we do not know how life started, then evolution is false. In actuality, knowing how life started has nothing to do with studying how life has evolved since the first complex cells appeared. However, understanding how complex cellular life evolves probably tells us something about how life arose because the same processes are relevant whenever there are variable replicating entities.

In my opinion, it remains a valid and useful argument to point out that uncertainty regarding the origin of life is irrelevant to the factual standing of evolution over the past 3.8 billion years.

 

Natural selection before Darwin.

Charles Darwin (1809-1882) opened his first notebook about "the species question" in 1837, not long after his return from the voyage of the Beagle. By 1838, he had developed the basic outline   of his theory of natural selection to explain the evolution of species. He spent the next 20 years developing the theory and marshaling evidence in favour of both the fact that species are related through common descent and his particular theory to explain this. After receiving word that another naturalist, Alfred Russel Wallace (1823-1913), had independently come upon the same theory, he assembled his work for publication, first in a joint paper with Wallace presented to the Linnean Society of London in 1858 and then his "abstract", On the Origin of Species, in 1859.

Some authors have argued that Edward Blyth (1810-1873), an acquaintance of Darwin's, developed the central idea of selection in an 1835 paper in the Magazine of Natural History. For example, Eiseley and Grote (1959) claimed that "the leading tenets of Darwin's work — the struggle for existence, variation, natural selection and sexual selection are all fully expressed in Blyth's 1835 paper", from which they then quoted the following:

It is a general law of nature for all creatures to propagate the like of themselves: and this extends even to the most trivial minutiæ, to the slightest individual peculiarities; and thus, among ourselves, we see a family likeness transmitted from generation to generation. When two animals are matched together, each remarkable for a certain given peculiarity, no matter how trivial, there is also a decided tendency in nature for that peculiarity to increase; and if the produce of these animals be set apart, and only those in which the same peculiarity is most apparent, be selected to breed from, the next generation will possess it in a still more remarkable degree; and so on, till at length the variety I designate a breed, is formed, which may be very unlike the original type.

As Eiseley and Grote (1959) and others have noted, however, Blyth's description applies to artificial selection, a process that had obviously been known to breeders long before. In terms of natural selection, Blyth suggested that it would be a conservative and not a creative process, acting to restore the original features modified by artificial selection; that is, it was not a process that caused change, but one that maintained stability within species. Neither Darwin nor Blyth considered this to have been an early example of Darwin's theory of evolution by natural selection (see Schwartz 1974).

Patrick Matthew (1790-1874) did not feel the same way as Blyth, and was vocal in his belief that he had preceded Darwin as, according to calling cards he carried, "Discoverer of the Principle of Natural Selection". In fact, Matthew had proposed an idea similar to natural selection in his 1831 book On Naval Timber and Arboriculture,

There is a law universal in nature, tending to render every reproductive being the best possible suited to its condition that its kind, or organized matter, is susceptible of, which appears intended to model the physical and mental or instinctive powers to their highest perfection and to continue them so. This law sustains the lion in his strength, the hare in her swiftness, and the fox in his wiles. As nature, in all her modifications of life, has a power of increase far beyond what is needed to supply the place of what falls by Time's decay, those individuals who possess not the requisite strength, swiftness, hardihood, or cunning, fall prematurely without reproducing—either a prey to their natural devourers, or sinking under disease, generally induced by want of nourishment, their place being occupied by the more perfect of their own kind, who are pressing on the means of subsistence . . .

There is more beauty and unity of design in this continual balancing of life to circumstance, and greater conformity to those dispositions of nature which are manifest to us, than in total destruction and new creation . . . [The] progeny of the same parents, under great differences of circumstance, might, in several generations, even become distinct species, incapable of co-reproduction.

Darwin, like most others, was not aware of Matthew's book and he learned of it in 1860 when Matthew wrote a letter to the Gardners' Chronicle and Agricultural Gazette including excerpts from his book in response to a review of Darwin's On the Origin of Species.

In your Number of March 3d I observe a long quotation from the Times, stating that Mr. Darwin "professes to have discovered the existence and modus operandi of the natural law of selection," that is, "the power in nature which takes the place of man and performs a selection, sua sponte," in organic life. This discovery recently published as "the results of 20 years' investigation and reflection" by Mr. Darwin turns out to be what I published very fully and brought to apply practically to forestry in my work "Naval Timber and Arboriculture," published as far back as January 1, 1831, by Adam & Charles Black, Edinburgh, and Longman & Co., London, and reviewed in numerous periodicals, so as to have full publicity in the "Metropolitan Magazine," the "Quarterly Review," the "Gardeners' Magazine," by Loudon, who spoke of it as the book, and repeatedly in the "United Service Magazine" for 1831, &c. The following is an extract from this volume, which clearly proves a prior claim.

In a reply in the same magazine, Darwin said,

I freely acknowledge that Mr. Matthew has anticipated by many years the explanation which I have offered of the origin of species, under the name of natural selection. I think that no one will feel surprised that neither I, nor apparently any other naturalist, has heard of Mr. Matthew's views, considering how briefly they are given, and that they appeared in the Appendix to a work on Naval Timber and Arboriculture. I can do no more than offer my apologies to Mr. Matthew for my entire ignorance of his publication.

In terms of arguments that Matthew's contribution diminishes that of Darwin, I tend to agree with Peter Bowler, who said in his book Evolution: The History of an Idea,

Such efforts to denigrate Darwin misunderstand the whole point of the history of science: Matthew did suggest a basic idea of selection, but he did nothing to develop it; and he published it in the appendix to a book on the raising of trees for shipbuilding. No one took him seriously, and he played no role in the emergence of Darwinism. Simple priority is not enough to earn a thinker a place in the history of science: one has to develop the idea and convince others of its value to make a real contribution. Darwin's notebooks confirm that he drew no inspiration from Matthew or any of the other alleged precursors.

In any case, neither Blyth nor Matthew was the first to propose natural selection in very basic form. Another individual, an American physician of Scottish descent by the name of William Charles Wells (1757-1817), presented a paper in 1813 (published in 1818) that included a process of natural selection to account for differences in skin colour among people. Wells considered light skin to be the primitive condition, with dark skin a subsequent specialization.

Again, those who attend to the improvement of domestic animals, when they find individuals possessing, in a greater degree than common, qualities they desire, couple a male and female of these together, then take the best of their offspring as a new stock, and in this way proceed, till they approach as near the point in view, as the nature of things will permit. But, what is here done by art, seems to be done, with equal efficacy, though more slowly, by nature, in the formation of varieties of mankind, fitted for the country which they inhabit. Of the accidental varieties of man, which would occur amnog the first few and scattered inhabitants of the middle regions of Africa, some one would be better fitted than the others to bear the diseases of the country. This race would consequently multiply, while the others would decrease, not only from their inability to sustain the attacks of disease, but from their incapacity of contending with their more vigorous neighbours. The colour of this vigorous race I take for granted, from what has been already said, would be dark. But the same disposition to form varieties still existing, a darker and a darker race would in the course of time occur, and as the darkest would be the best fitted for the climate, this would at length become the most prevalent, if not the only race, in the particular country in which it had originated.

Darwin added an acknowledgment of Wells's work beginning with the 4th edition of the Origin in 1866,

In 1813 Dr. W.C. Wells read before the Royal Society 'An Account of a White Female, part of whose Skin resembles that of a Negro;' but his paper was not published until his famous 'Two Essays upon Dew and Single Vision' appeared in 1818. In this paper he distinctly recognises the principle of natural selection, and this is the first recognition which has been indicated; but he applies it only to the races of man, and to certain characters alone.

What Darwin (and until recently, most historians) did not realize was that the general notion of selection had already been proposed by 1794. In an review in Nature in 2003, Paul Pearson pointed out that James Hutton (1726-1797), considered the Father of Modern Geology, postulated something similar to natural selection in An Investigation of the Principles of Knowledge. (Pearson also noted the interesting bit of trivia that Hutton, Wells, Matthew, and Darwin all attended the University of Edinburgh).

As Hutton (1794) said,

 …if an organised body is not in the situation and circumstances best adapted to its sustenance and propagation, then, in conceiving an indefinite variety among the individuals of that species, we must be assured, that, on the one hand, those which depart most from the best adapted constitution, will be most liable to perish, while, on the other hand, those organised bodies, which most approach to the best constitution for the present circumstances, will be best adapted to continue, in preserving themselves and multiplying the individuals of their race.

Now, if those organised bodies shall thus multiply, in varying continually according to the particular circumstances in which are found the necessary conditions for their life and propagation, we might expect to see, in this world, a variety in the species of things, which we might term a race; varieties which do not affect the species of things, but which, upon many occasions, might appear to us as being a different race of the same species, whether of plant or animal. But, such things are every where observed; consequently, we have reason to conclude, it is truly in this manner, that are naturally produced those various races of plants and animals, which we find naturally upon the surface of this earth. Each of those races of things, therefore, would appear to us to be wisely calculated, by nature, for the purpose of this world.

Hutton used the examples of fast running and a strong sense of smell in dogs to illustrate the mechanism. He did not, however, accept the notion that new species could form by this or any process. For Hutton, this was limited to creating varieties only and not species.

 

It is important to note that Darwin himself recognized that others had discovered natural selection at least in basic outline before (and after) he had. He did not avoid sharing credit to the extent that it was due. In light of this history, one could argue that because natural selection as a mechanism had been proposed by several authors that it would have been discovered and recognized as important eventually, even without Darwin's input — and, indeed, it probably would have, as would Newton's laws of motion, Einstein's theory of relativity, and other fundamental principles describing the natural world. On the other hand, the idea had been around for at least six decades before Darwin published the Origin, and it was not until someone of Darwin's genius developed the idea that evolution assumed its position as the underlying theme of all biology.

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Epigenetics and Neo-(Neo-)Lamarckism.

A very brief comment on a complicated topic…

New Scientist has a story in the current issue about epigenetics — differences in gene expression that are not due to changes in the gene sequences themselves — and how non-genetic variation can be both influenced environmentally and, in some cases, inherited.

The New Scientist story, which is entitled Rewriting Darwin: the new non-genetic inheritance, is another example of the “reporting on a revolution” and “underdog vindicated” fallacies so common in science reporting.

 Half a century before Charles Darwin published On the Origin of Species, the French naturalist Jean-Baptiste Lamarck outlined his own theory of evolution. A cornerstone of this was the idea that characteristics acquired during an individual’s lifetime can be passed on to their offspring. In its day, Lamarck’s theory was generally ignored or lampooned. Then came Darwin, and Gregor Mendel’s discovery of genetics. In recent years, ideas along the lines of Richard Dawkins’s concept of the “selfish gene” have come to dominate discussions about heritability, and with the exception of a brief surge of interest in the late 19th and early 20th centuries, “Lamarckism” has long been consigned to the theory junkyard.

Now all that is changing. No one is arguing that Lamarck got everything right, but over the past decade it has become increasingly clear that environmental factors, such as diet or stress, can have biological consequences that are transmitted to offspring without a single change to gene sequences taking place. In fact, some biologists are already starting to consider this process as routine. However, fully accepting the idea, provocatively dubbed the “new Lamarckism”, would mean a radical rewrite of modern evolutionary theory.

The article includes an interview with Eva Jablonka, who is one of the Altenberg 16 who are, as we speak, revolutionizing evolutionary theory (just kidding, but see here for a summary of what she had to discuss).

So, is this “neo-Lamarckism” and is it going to require “a radical rewrite of evolutionary theory”? Some thoughts:

1) There already was a neo-Lamarckism in the late 1800s and early 1900s. So this would be neo-neo-Lamarckism if anything.

2) Epigenetics, by definition, involves modifications of the expression of genetic systems. If heritable, they would be subject to natural selection, drift, etc., when they arise within a population. So, while this is certainly interesting, it will be a welcome expansion of existing theory rather than a revolution.

3) The inheritance of acquired characters was not original to Lamarck (it was the predominant view in his era), and in any case this by itself does not make a theory of evolution “Lamarckian”. Lamarckian evolution a) considers adaptation as the result of use and disuse in response to need b) leading to enhancements of particular features that c) improve an organism’s fit to its environment, which d) are then passed on and e) accumulate in each generation, f) leading to progressive increases in complexity, with g) no extinction, and h) simple forms produced anew by spontaneous generation.

4) Lamarck rejected the notion that the environment would directly affect organismal traits — the point was that organisms responding to the environment led to adaptive changes that were passed on.

It is now necessary to explain what I mean by this statement: The environment affects the shape and organization of animals, that is to say that when the environment becomes very different, it produces in the course of time corresponding modifications in the shape and organization of animals. It is true, if this statement were to be taken literally, I should be convicted of an error; for, whatever the environment may do, it does not work any direct modification whatever in the shape and organization of animals. [Translated as in Kampourakis and Zogza (2007)]

One person who postulated heritable, acquired, undirected variation was Darwin.

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See also:

The imaginary Lamarck by M. Ghiselin

Shades of Lamarck by S.J. Gould

Students’ preconceptions about evolution: How accurate is the characterization as “Lamarckian” when considering the history of evolutionary thought? by K. Kampourakis and V. Zogza

The early history of the idea of the inheritance of acquired characters and of pangenesis by C. Zirkle

Functional redundancy.

The move from Blogger to Scientific Blogging has been good overall, and I am certainly enjoying more hits and a broader readership from outside the normal blogosphere. However, I have also noticed that bloggers and blog readers have more or less dropped off. I think it would be useful for Genomicron to reach both audiences, but it seems that one Genomicron can’t serve that function yet. Perhaps when the new format of SB is operational it will. Meanwhile, I am opting to resurrect the pseudoGenomicron and have it persist as a functionally redundant parablog. That is to say I will be cross posting everything on both sites, and blog readers who like this one better can read it and people who want links to lots of other interesting stuff can visit the other one. It will be a little more work, but worth it I think. The Feedburner feed will use the original Genomicron so it can have full posts.

If you prefer the other version, it’s here.

Birds and dinosaurs, collagen, and Huxley.

I have already blogged about this topic in a short post [Yet another link between dinosaurs and birds], so I will just point out the existence of another paper along these lines using phylogenetic analyses of collagen amino acid sequences recovered from T. rex fossils to demonstrate a close affinity between theropod dinosaurs and birds (Organ et al. 2008), a link first proposed by T.H. Huxley in 1868. This newest analysis was led by Chris Organ, who also did the dinosaur cell/genome size estimation study (Organ et al. 2007; Zimmer 2007). They also looked at mastodons. The data from mastodons and dinosaur aren’t new (Asara et al. 2007; Schweitzer et al. 2007) — the main update is the inclusion extant species and of a phylogenetic component.


There are plenty of news stories about it, including the following.

Molecular Analysis Confirms Tyrannosaurus Rex’s Evolutionary Link To Birds (ScienceDaily)

From T. Rex to Chicken: The Dino-Bird Connection(Discovery News)

T. rex confirmed as great granddaddy of all birds (New Scientist)

Phylogenetic Tree: Dinosaurs, Alligators And … Ostriches? (Scientific Blogging)

Gunk in T. Rex Fossil Confirms Dino-Bird Lineage (LiveScience)

Finally, a reminder about how species names should be listed.
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References

Asara, J.M., M.H. Schweitzer, L.M. Freimark, M. Phillips, and L.C. Cantley. 2007. Protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry. Science 316: 280-285.

Huxley, T.H. 1868. On the animals which are most nearly intermediate between birds and the reptiles. Annals and Magazine of Natural History, Series 4, 2: 66-75.

Organ, C.L., A.M. Shedlock, A. Meade, M. Pagel, and S.V. Edwards. 2007. Origin of avian genome size and structure in non-avian dinosaurs. Nature 446: 180-184.

Organ, C.L., M.H. Schweitzer, W. Zheng, L.M. Freimark, L.C. Cantley, and J.M. Asara. 2008. Molecular phylogenetics of mastodon and Tyrannosaurus rex. Science 320: 499.

Schweitzer, M.H., Z. Suo, R. Avci, J.M. Asara, M.A. Allen, F.T. Arce, and J.R. Horner. 2007. Analyses of soft tissue from Tyrannosaurus rex suggest the presence of protein. Science 316: 277-280.

Zimmer, C. 2007. Jurassic genome. Science 315: 1358-1359.



Shedding light on Darwin.

Apparently shedding light on Darwin (for photography) is difficult.

Not enough:


Too much:


Incidentally, this statue of Darwin is located next to a small cafe at the back end of the first floor at the Natural History Museum in London. In the main hall, halfway up the central staircase and overlooking the reconstruction of Dippy (Diplodocus carnegii), is a bronze statue of Richard Owen. It seems the Natural History Museum forgot to expel this vocal opponent of “Darwinism”. I suppose the fact that he did real research and founded a real museum (namely, the NHM) had something to do with it.


Hiroshima.

The Skeptical Alchemist posted this video, which has some significance for me since I was in Hiroshima less than 2 weeks ago.

Say what you want about the need to end the war, the expected casualties during an invasion, or whatever other rationalizations you like. But consider this question, by Leó Szilárd:

“Suppose Germany had developed two bombs before we had any bombs. And suppose Germany had dropped one bomb, say, on Rochester and the other on Buffalo, and then having run out of bombs she would have lost the war. Can anyone doubt that we would then have defined the dropping of atomic bombs on cities as a war crime, and that we would have sentenced the Germans who were guilty of this crime to death at Nuremberg and hanged them?”


My growing respect for New Scientist.

I have said some nice things about New Scientist, such as noting that they printed one of the best popular treatments of “junk DNA” I have read [New Scientist gets it right]. On the other hand, I also criticized one of their headlines as perpetuating misconceptions about how evolution works [Chimps are not more evolved than humans or anyone else]. Today, New Scientist shows that they are far more worthy of endorsement than nitpicking in their publication of a special issue on evolution. Not only this, but the online version of one of the articles links to my aforementioned criticism, which I consider very decent.

My local bookstore does not have the April 19 issue yet, so I have not seen the print version, but their collection of 24 myths and misconceptions can be accessed freely online:

Shared misconceptions:

Everything is an adaptation produced by natural selection

Natural selection is the only means of evolution

Natural selection leads to ever-greater complexity

Evolution produces creatures perfectly adapted to their environment

Evolution always promotes the survival of species

It doesn’t matter if people do not understand evolution

“Survival of the fittest” justifies “everyone for themselves”

Evolution is limitlessly creative

Evolution cannot explain traits such as homosexuality

Creationism provides a coherent alternative to evolution

Creationist myths:

Evolution must be wrong because the Bible is inerrant

Accepting evolution undermines morality

Evolutionary theory leads to racism and genocide

Religion and evolution are incompatible

Half a wing is no use to anyone

Evolutionary science is not predictive

Evolution cannot be disproved so is not science

Evolution is just so unlikely to produce complex life forms

Evolution is an entirely random process

Mutations can only destroy information, not create it

Darwin is the ultimate authority on evolution

The bacterial flagellum is irreducibly complex

Yet more creationist misconceptions

Evolution violates the second law of thermodynamics

[Tipped hats to Panda’s Thumb and Sandwalk]