Saturday, February 25, 2006


Symmetry Breaking and the Evolution of Development

Symmetry Breaking and the Evolution of Development

[Palmer, Science, Oct '04]

Because of its simplicity, the binary-switch nature of left-right asymmetry permits meaningful comparisons among many different organisms. Phylogenetic analyses of asymmetry variation, inheritance, and molecular mechanisms reveal unexpected insights into how development evolves. First, directional asymmetry, an evolutionary novelty, arose from nonheritable origins almost as often as from mutations, implying that genetic assimilation ('phenotype precedes genotype') is a common mode of evolution. Second, the molecular pathway directing hearts leftward - the nodal cascade - varies considerably among vertebrates (homology of form does not require homology of development) and was possibly co-opted from a preexisting asymmetrical chordate organ system. Finally, declining frequencies of spontaneous asymmetry reversal throughout vertebrate evolution suggest that heart development has become more canalized.

Books on Symmetry from the Science and Evolution Bookshop: UK | US

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Classic Papers on Human Origins from Nature Magazine

1) Dart, R. A. Australopithecus africanus:
The Man-Ape of South Africa
Nature 115, 195-199 (1925)
When Dart, an anatomist from South Africa, reported the first 'ape-man', he was derided by the same people who fell for the fraudulent Piltdown Man. But Piltdown was a fake and Dart was vindicated. The modern study of human origins starts here.

2) Leakey, L. S. B.
A new fossil skull from Olduvai
Nature 184, 491-493 (1959)
Fossil-hunter Louis Leakey had been scouring East Africa for clues about human origins in vain for 30 years before he (or rather, his wife) hit the jackpot at Olduvai Gorge in Tanzania. The new player on the fossil scene was lantern-jawed 'Nutcracker man'.

3) Leakey, L. S. B., Tobias, P. V. and Napier, J. R.
A new species of the genus Homo from Olduvai Gorge.
Nature 202, 7-9 (1964) Leakey scores again with fossils associated with primitive tools. He announces Homo habilis - 'handy man' - the first fossil member of our own genus; and with him, the first stirrings of technology.

4) Leakey, R. E. F.
Evidence for an advanced Plio-Pleistocene hominid from East Rudolf, Kenya
Nature 242, 447-450 (1973)
Richard Leakey - son of Louis - describes a skull as iconic as they come, but always known enigmatically as '1470'. Thought to belong to an early form of Homo (now Homo rudolfensis), this specimen is a key fossil in the understanding of human origins.

5) Johanson, D. C. and Taieb, M.
Plio-Pleistocene hominid discoveries in Hadar, Ethiopia
Nature 260, 293-297 (1976)
Donald Johanson pushes the human story back beyond the 3-million-year- mark with a skeleton, later assigned to Australopithecus afarensis. The skeleton is now known as 'Lucy', after Lucy in the Sky with Diamonds, the Beatles' tune popular in the field camp.

6) Leakey, M. D. and Hay, R. L.
Pliocene footprints in the Laetolil Beds at Laetoli, northern Tanzania
Nature 278, 317-323 (1979)
When a volcanic eruption sent a rain of ash over what is now Tanzania, an adult and child, probably both Australopithecus afarensis, set out to watch the show - leaving, as a poignant souvenir, perfect and very modern-looking footprints, preserved in the ashfall.

7) Brown, F., Harris, J., Leakey, R. and Walker, A.
Early Homo erectus skeleton from west Lake Turkana, Kenya
Nature 316, 788-792 (1985)
This report of a young but surprisingly tall young Homo erectus male raises many questions about our own African genesis, and the origins of that very human feature called 'childhood'.

8) Cann, R. L., Stoneking, M. & Wilson, A.
Mitochondrial DNA and human evolution
Nature 325, 31-36 (1987) A molecular bombshell that traces the human story by comparing mitochondrial DNA frrom modern humans. The message is clear - all modern humans have their roots in Africa, and surprisingly recently, between 100,000 and 200,000 years ago.

9) Arsuaga, J.-L., Martínez, I., Gracia, A., Carretero, J.-M. & Carbonell, A.
Three new human skulls from the Sima de los Huesos Middle Pleistocene site in Sierra de Atapuerca, Spain
Nature 362, 534-537 (1993) The 'Pit of Bones' near Burgos in Spain is a treasure-trove of information on the first Europeans. At around 300,000 years old, these skulls may have been close to the ancestry of the classic caveman, Neanderthal Man.

10) White, T. D., Suwa, G. and Asfaw, B.
Australopithecus ramidus, a new species of early hominid from Aramis, Ethiopia
Nature 371, 306-312 (1994) Now known as Ardipithecus ramidus, this extremely primitive creature was the first member of the human family known from beyond 4 million years ago. Still controversial, its affinities with the new finds from Chad have yet to be investigated.


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Friday, February 24, 2006


An Error In Associating Lamarck With 'Adaptive Mutations'?

An Error In Associating Lamarck With 'Adaptive Mutations'?

Words frozen in time should be differentiated from those carved in stone:

In 1640 Galileo Galilei wrote a letter to Fortunio Liceti in which he said:

"If Aristotle were to see the new discoveries recently [made] in the heavens, whose immobility he had asserted, because no alteration had previously been seen in them, he would now without doubt state the contrary." ['Galileo Galilei - Towards a Resolution of 350 Years of Debate', Paul Cardinal Poupard].

The above statement highlights the danger of placing dependence on words frozen in time without taking into account how different those words might be if their author had had access to the discoveries that have since been made.

Lamarck, for example, published his "Zoological Philosophy" in 1809 and is today popularly associated with "the inheritance of acquired characteristics" whereby organisms somehow direct their own evolution. On the basis of Galileo's words, however, it could be argued that had Lamarck been alive in the 1890s, over thirty years after publication of Darwin's "On the Origin of Species", his views would have progressed from the moment in time in which they had been caught.

With access to the discoveries and discussions that occured throughout the 19th Century it is conceivable that Lamarck might even have reached broad agreement with J. Mark Baldwin over the latter's proposal of an indirect factor in evolution, known today as the "Baldwin Effect", and described in the 1896 paper "A New Factor in Evolution" [American Naturalist].

Pure speculation of course, but if sufficient to illustrate a general principle (that "words frozen in time should be differentiated from those carved in stone"), then the inappropriateness of interpreting new discoveries or proposals in 'Lamarckian terms' is readily apparent.

John Latter

Model of an Internal Evolutionary Mechanism:

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Thursday, February 23, 2006


Birds that make teeth (Press Release + Summary)


1) Birds that make teeth
(Press Release)

Gone does not necessarily mean forgotten, especially in biology. A recent finding by researchers at the University of Wisconsin, Madison, and colleagues from the University of Manchester have found new evidence that the ability to form previously lost organs--in this case, teeth--can be maintained millions of years after the last known ancestor possessed them.

Birds do not have teeth. However, their ancestors did--about 70 - 80 million years ago. The evolutionary loss of teeth corresponded to the formation of the beak that is present in all living birds. Nonetheless, it has been known that if mouse tooth-forming tissue is in contact with bird jaw tissue, the bird tissue is able to follow the instructions given by the mouse tissue and participate in making teeth, and that these teeth look very much like those of mammals. However, Drs. Matthew Harris and John F. Fallon and colleagues have found that modern birds retain the ability to make teeth even without instruction from their tooth-bearing cousins.

Full text at:

2) The Development of Archosaurian First-Generation Teeth in a Chicken Mutant

[Harris et al., Current Biology, Feb '06]


Modern birds do not have teeth. Rather, they develop a specialized keratinized structure, called the rhamphotheca, that covers the mandible, maxillae, and premaxillae. Although recombination studies have shown that the avian epidermis can respond to tooth-inductive cues from mouse or lizard oral mesenchyme and participate in tooth formation 1; 2, attempts to initiate tooth development de novo in birds have failed. Here, we describe the formation of teeth in the talpid2 chicken mutant, including the developmental processes and early molecular changes associated with the formation of teeth. Additionally, we show recapitulation of the early events seen in talpid2 after in vivo activation of β-catenin in wild-type embryos. We compare the formation of teeth in the talpid2 mutant with that in the alligator and show the formation of decidedly archosaurian (crocodilian) first-generation teeth in an avian embryo. The formation of teeth in the mutant is coupled with alterations in the specification of the oral/aboral boundary of the jaw. We propose an epigenetic model of the developmental modification of dentition in avian evolution; in this model, changes in the relative position of a lateral signaling center over competent odontogenic mesenchyme led to loss of teeth in avians while maintaining tooth developmental potential.

Summary available at:

One of the authors (John F. Fallon) sent me a copy of the full paper yesterday. His email address is at the link above. Contact me here if you have any difficulty.

John Latter

Model of an Internal Evolutionary Mechanism

Books on Evolution from the Science and Evolution Bookshop: UK | US


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Wednesday, February 22, 2006


UCSD Study Shows 'Junk' DNA Has Evolutionary Importance (News + Article)


1) UCSD Study Shows 'Junk' DNA Has Evolutionary Importance (Press Release)

Genetic material derisively called "junk" DNA because it does not contain the instructions for protein-coding genes and appears to have little or no function is actually critically important to an organism's evolutionary survival, according to a study conducted by a biologist at UCSD.

In the October 20 issue of Nature, Peter Andolfatto, an assistant professor of biology at UCSD, shows that these non-coding regions play an important role in maintaining an organism's genetic integrity. In his study of the genes from the fruit fly Drosophila melanogaster, he discovered that these regions are strongly affected by natural selection, the evolutionary process that preferentially leads to the survival of organisms and genes best adapted to the environment.

Full text at:

2) Adaptive evolution of non-coding DNA in Drosophila (Article)

A large fraction of eukaryotic genomes consists of DNA that is not translated into protein sequence, and little is known about its functional significance. Here I show that several classes of non-coding DNA in Drosophila are evolving considerably slower than synonymous sites, and yet show an excess of between-species divergence relative to polymorphism when compared with synonymous sites. The former is a hallmark of selective constraint, but the latter is a signature of adaptive evolution, resembling general patterns of protein evolution in Drosophila. I estimate that about 40-70% of nucleotides in intergenic regions, untranslated portions of mature mRNAs (UTRs) and most intronic DNA are evolutionarily constrained relative to synonymous sites. However, I also use an extension to the McDonald-Kreitman test to show that a substantial fraction of the nucleotide divergence in these regions was driven to fixation by positive selection (about 20% for most intronic and intergenic DNA, and 60% for UTRs). On the basis of these observations, I suggest that a large fraction of the non-translated genome is functionally important and subject to both purifying selection and adaptive evolution. These results imply that, although positive selection is clearly an important facet of protein evolution, adaptive changes to non-coding DNA might have been considerably more common in the evolution of D. melanogaster.

Full text at:

PDF versions:

John Latter

Model of an Internal Evolutionary Mechanism

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Tuesday, February 21, 2006


Darwinism's Rules of Reasoning: Phillip Johnson on Pierre Grasse

From "Darwinism's Rules of Reasoning" (Chapter 1 of "Darwinism: Science or Philosophy") by Phillip Johnson:

"MY STARTING POINT is a book review that Theodosius Dobzhansky published in 1975, critiquing Pierre Grasse's The Evolution of Life.{1} Grasse, an eminent French zoologist, believed in something that he called "evolution." So did Dobzhansky, but when Dobzhansky used that term he meant neo-Darwinism, evolution propelled by random mutation and guided by natural selection. Grasse used the same term to refer to something very different, a poorly understood process of transformation in which one general category (like reptiles) gave rise to another (like mammals), guided by mysterious "internal factors" that seemed to compel many individual lines of descent to converge at a new form of life. Grasse denied emphatically that mutation and selection have the power to create new complex organs or body plans, explaining that the intra-species variation that results from DNA copying errors is mere fluctuation, which never leads to any important innovation."

Full text at:

[For more on Grasse see: Grasse, Behe, and "Irreducible Complexity"]

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Grasse, Behe, and "Irreducible Complexity"

Dr Pierre-Paul Grasse (editor of the 28-volume "Traite de Zoologie",
ex-president of the Academie des Sciences, etc.) is considered to
have been one of the most eminent of French zoologists.

I am currently* reading his "Evolution of Living Organisms: Evidence
for a New Theory of Transformation," (Academic Press: New York NY,
1977) with a view to summarizing the reasons why he should feel
that 'internal factors' are involved in evolution.

At the moment, however, I am quite intrigued by the following two

"Life is an epiphenomenon arising from a COMPLEX, structural, and
autonomous system forming an object endowed with an IRREDUCIBLE
individuality" (my capitals) [p.172]


"The system has become functional only when all its components
have come together and adjusted themselves to one another. The
Darwinian hypothesis compels us to postulate a preparatory period
during which selection acts upon something that does not,
physiologically speaking, yet exist. Under the necessary conditions
of the postulate, the action can only have been prophetic! Any
explanation ruling out the active intervention of the organism in the
acquisition of regulating systems may be regarded as inadequate.

To take as an evident truth the fact that the control mechanisms
attenuating or neutralizing the actions of the environment (these
are, let it be remembered, complex systems having several coordinated
elements) could have been assembled by successive and lucky strokes
of chance without the slightest need for the organism to play any
role whatsoever, is to sacrifice objective scientific analysis to a
wholly verbal magic trick" (Grasse's italics) [p.152]

I haven't read Michael Behe's "Darwin's Black Box: The Biochemical
Challenge to Evolution" but a TalkOrigins article [1] provides the
following quote:

"By irreducibly complex I mean a single system composed of
several well-matched, interacting parts that contribute to the basic
function, wherein the removal of any one of the parts causes the
system to effectively cease functioning. An irreducibly complex
system cannot be produced directly (that is, by continuously
improving the initial function, which continues to work by the same
mechanism) by slight, successive modifications of a precursor system,
because any precursor to an irreducibly complex system that is
missing a part is by definition nonfunctional. An irreducibly complex
biological system, if there is such a thing, would be a powerful
challenge to Darwinian evolution. (Behe's italics) [p.39]

This article describes irreducible complexity as "essentially a
rehash of the famously flawed watchmaker argument advanced by William
Paley at the start of the 19th century" and comments elsewhere liken
the concept to "The old 'chicken-and-egg' question". Even so, I can't
help wondering if Behe had been inspired by Grasse's words!

From a wider perspective I found it interesting that Grasse
was arguing the case for 'internal factors' while others are using
similar reasoning to argue for external ones..

John Latter

*Grasse, Behe, and "Irreducible Complexity" first appeared here and was written in 2002.

[1] Irreducible Complexity and Michael Behe:


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Sunday, February 19, 2006


To See or Not to See: Evolution of Eye Degeneration in Mexican Blind Cavefish

To See or Not to See: Evolution of Eye Degeneration in Mexican Blind Cavefish [Jeffery et al., Integrative and Comparative Biology Vol 43 #4, '03]


The evolutionary mechanisms responsible for the loss of eyes in cave animals are still unresolved. Hypotheses invoking natural selection or neutral mutation have been advanced to explain eye regression. Here we describe comparative molecular and developmental studies in the teleost Astyanax mexicanus that shed new light on this problem. A. mexicanus is a single species consisting of a sighted surface-dwelling form (surface fish) and many blind cave-dwelling forms (cavefish) from different caves. We first review the evolutionary relationships of Astyanax cavefish populations and conclude that eye degeneration may have evolved multiple times. We then compare the mechanisms of eye degeneration in different cavefish populations. We describe the results of experiments showing that programmed cell death of the lens plays a key role in controlling eye degeneration in these cavefish populations. We also show that Pax6 gene expression and fate determination in the optic primordia are modified similarly in different cavefish populations, probably due to hyperactive midline signaling. We discuss the contributions of the comparative developmental approach toward resolving the evolutionary mechanisms of eye degeneration. A new hypothesis is presented in which both natural selection and neutral mutation are proposed to have roles in cavefish eye degeneration.

Full text at:


A couple of news stories regarding some of Jeffrey's earlier work:

Blind fish reveal eye growth factors (July '00)

UM Scientists Find Clue to Blindness in Cavefish (Oct '04)

[apoptosis, teleost, genes, biology]

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Origination of Organismal Form: The Forgotten Cause In Evolutionary Theory

Origination of Organismal Form: Beyond the Gene in Developmental and Evolutionary Biology (Gerd B. Müller (Muller) and Stuart Newman)

Chapter 1:

Origination of Organismal Form: The Forgotten Cause In Evolutionary Theory

Evolutionary biology arose from the age-old desire to understand the origin and the diver-sification of organismal forms. During the past 150 years, the question of how these two as-pects of evolution are causally realized has become a field of scientific inquiry, and the standard answer, encapsulated in a central tenet of Darwinism, is by "variation of traits"and "natural selection." The modern version of this tenet holds that the continued modification and inheritance of a basic genetic tool kit for the regulation of developmental processes, directed by mechanisms acting at the population level, has generated the panoply of organismal body plans encountered in nature. This notion is superimposed on a sophisticated, mathematically based population genetics, which became the dominant mode of evolutionary biology in the second half of the twentieth century. As a consequence, much of present-day evolutionary theory is concerned with formal accounts of quantitative variation and diversification. Other major branches of evolutionary biology have concentrated on patterns of evolution, ecological factors, and, increasingly, on the associated molecular changes. Indeed, the concern with the "gene" has overwhelmed all other aspects, and evolutionary biology today has become almost synonymous with evolutionary genetics.

These developments have edged the field farther and farther away from the second initial theme: the origin of organismal form and structure. The question of why and how certain forms appear in organismal evolution addresses not what is being maintained (and quantitatively varied) but rather what is being generated in a qualitative sense. This causal question concerning the specific generative mechanisms that underlie the origin and innovation of phenotypic characters is probably best embodied in the term origination, which will be used in this sense throughout this volume.

Full text of Chapter 1 available at: link:

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