Neo-Darwinism: The Current Paradigm
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Darwin, courtesy of the Henry E. Huntington Library and Art Gallery

Charles Darwin championed the theory of common descent and evolution by natural selection among descendants with slight variations on the ancestors' features. The concept of natural selection springs from artificial selection, a procedure breeders use to enhance desired characteristics such as stamina, color, size, yield, and so forth, in animals and plants. Darwin thought that a similar process happens in nature. There is nothing to disagree with here. Natural selection can bring about evolution in a fashion similar to artificial selection. But animal breeders and plant breeders have always known that artificial selection has limits. Wholly new characteristics never emerge from artificial selection; they will never breed a dog with antlers. The same kind of limit applies to all natural selection operating on the available genetic material.

Genetics

Mendel

Darwin actually knew very little about genetics. The great pioneer of that field was Gregor Mendel, whose work was contemporary with Darwin's. Now the theory of evolution incorporates Mendel's genetics into Darwin's framework; the combined theory was called "neo-Darwinism." (Recently, that cumbersome term is being replaced by the simpler "Darwinism".)

According to this paradigm, evolution is driven by chance. Chance mutations affect one or a few nucleotides of DNA per occurrence. Bigger changes come from recombination, a genetic process in which longer strands of DNA are swapped, transferred, or doubled. These two processes, mutation and recombination, create new meaning in DNA by lucky accidents. According to the prevailing paradigm, this is the mechanism behind evolution.

One problem with this story is that it is implausible. It is analogous to saying that a great work of literature such as Moby Dick could emerge from lesser preexisting books, if there were enough typos and swapping of paragraphs along the way. The trouble is, when this process is actually attempted with text, it never succeeds. Only with guidance can random processes lead to meaningful sentences or paragraphs. But plausibility in the current paradigm of evolution is apparently unnecessary. We are told by Richard Dawkins, "The general lesson we should learn is never to use human judgment in assessing such matters" (3).

Ordinary people are under the impression that there are examples in nature which prove that chance mutation and recombination can create new meaning in genetic code — new genes. Yet the alleged examples of the phenomenon do not actually exemplify it. Consider the ability of bacteria to become resistant to antibiotics. Salvador Luria and Max Delbrück proved in 1943 that the resistant bacteria descended from preexisting strains; the genes for the resistance were already available in the gene pool. Although some have disputed this interpretation of their experiments, it is now well established. And today we know that bacteria often acquire whole new genes conferring resistance to antibiotics; the genes are imported on "resistance plasmids" (3.5).

Another example of similar "evolution" in eukaryotic cells is described in Renato Dulbecco's The Design of Life. This time the genes for the new characteristic are already present in the organism (4):

...Trypanosomes [are] small eukaryotic parasites that in Africa cause sleeping sickness in humans and some animals. The animal responds by producing special protein molecules—antibodies that bind to the coat of the parasite and stop its growth.... But when the antibodies have almost gained control, parasites with a different coat make their appearance.... When the new antibodies are produced, the second wave of parasites disappear, but yet another kind emerges, with coat molecules different from the first two.

The study of this phenomenon has uncovered an amazing organization in the parasite's DNA. Radioactive probes ... have revealed that a hundred or more genes are devoted to coat variation, each gene specifying one kind of coat molecule.... Only one is active at a time.

The moth that has evolved to blend in with the sooty walls and treetrunks of modern industrial cities is another example of evolution in our time. Again, the genes for darker coloring in the moth were already available in the gene pool. Yes, there are a few documented examples in which a simple mutation in a bacterium brings about antibiotic resistance, but in these cases it does so by reducing or eliminating the affected gene's function, not by creating a new function. Among viruses, mutations can even alter a coating protein and thereby temporarily disguise the virus (4.5). But again, no new function is created. Such mutations could not drive the evolutionary progress we observe in the fossil record.

Of course, there are many examples of genes that have mutated slightly in the course of evolution without losing their original functions. And other examples, fewer in number, apparently indicate that genes may mutate slightly and acquire different but closely related functions. The globin family of genes are in this category. And in a third category, a handful of examples may indicate that a gene mutates slightly and acquires a wholly new function. These finally seem to be examples in which mutations create new meaning, but we are not sure this third account is accurate. The number of changed essential nucleotides in new genes that supposedly arose this way is still in the dozens at least, whereas the number of possible genes that would differ from a given average-size gene by only half-a-dozen essential nucleotides is enormous, on the order of 10^14. Blindly traversing even this short distance in sequence space so large requires incredible luck.

Eigen

Neo-Darwinism can rebut this line of criticism in two ways: 1) almost any gene will work — a "many-worlds" theory of biology, or; 2) there is a guided mutational pathway, as Manfred Eigen described in 1987 (5), leading from the first set of primitive genes to all of the genes subsequently used in biology. But, since 1987, Eigen's model has not been fleshed out. Furthermore, that kind of evolution would be ultra-gradual, unlike what we see in the fossil record. Neither of these two alternatives has any analog in the world of other codes such as text or computer programs. A theory that avoids these difficulties should be considered.

Thanat Chookajorn et al., "Epigenetic memory at malaria virulence genes" [abstract], 10.1073/pnas.0609084103, Proc. Natl. Acad. Sci. USA, online 5 Jan 2007. "The malaria parasite Plasmodium falciparum can switch its variant surface proteins ...to evade the host immune response. ...The gene family is enormous with a virtually unlimited number of members. ...Control of var gene transcription and antigenic variation is associated with a chromatin memory...."
26 Sep 2005: Common bacteria share an infinite gene pool?!
...African trypanosome source of scientific insight, The Rockefeller University, 25 Nov 2002.

The Origin of Antifreeze Protein Genes

The April 15, 1997 issue of Proc. Natl. Acad. Sci. USA contains a report with strong evidence — sequence similarities — linking two genes with different functions in a common Antarctic fish. One gene codes for trypsinogen, an enzyme produced in the pancreas. The other codes for a protein called antifreeze glycoprotein (AFGP) that keeps the fish's blood from freezing.

The related sequences are so similar that the biologists, from the University of Illinois, Urbana, date the divergence of the sequences as only five to 14 million years ago. This timing coincides with the independently estimated time when the Antarctic Ocean was frozen. "Selective pressure" would have favored the creation of an antifreeze gene then. The report makes a strong case that the antifreeze gene evolved from the trypsinogen gene by a series of steps including whole gene duplication; the deletion, insertion, duplication, and amplification of smaller sequences; and a frameshift mutation.

Proc. Nat. Acad. Sci., USA

It is possible to estimate the likelihood of creating a new gene this way. One could estimate the actual rate at which the steps listed above occur in the fish germline cells and the fish population at the time when the Antarctic Ocean was freezing. From there one could straightforwardly calculate the approximate number of trials of new genes that could have occurred, during a reasonable time window, to produce an antifreeze protein gene in the fish. One could also estimate the number of different actual genes that would code for antifreeze proteins. Other work by the same authors in the same issue (8) makes this estimation seem possible. Finally, a mathematician could, with little trouble, count the number of possible different genes that could be created from the trypsinogen gene and other possible precursor genes by the steps listed above. These estimates would enable one to calculate the probability that an antifreeze gene would be found by trial and error in the time available.

The last estimate, however, turns out to be lethal to our chances. The number of possible different genes that could be created by only a handful of steps from the list above is enormous. For example, consider a gene of 2,500 nucleotides, allowing a 75% error rate (625 essential nucleotides.) The number of possible different genes that could be created by deleting a single essential nucleotide and inserting it elsewhere in the same gene, five successive times, is 10^28. When sequences for insertion into the target gene can be any length, and can come from any of thousands of other genes, the possibilities quickly approach the theoretical maximum — in this example 4^625 or about 10^370. So the proposed mechanism does not increase the probability of arriving at a wholly new gene by chance. It's still monkeys writing Shakespeare, only now they have word processors with "cut and paste" functions.

The authors are aware of this problem and postulate other roles for genetic intermediates between the two genes. However, they seem to realize that this speculation is inadequate, because they conclude [the second article] by saying, "The selection of an appropriate permutation of three codons... was likely shaped by the structural specificity required for antifreeze ice interaction to take place." This sounds like teleology.

After the careful analysis by Chen et al., one might understand if a neo-Darwinists lost patience at this point in the discussion and simply asserted that it must have happened as they describe. Any reasonable person would admit that genetic sequences may gradually diverge over time, as in the antifreeze gene example. Cosmic Ancestry does not dispute that genetic sequences can gradually diverge over time, and that genetic recombination occurs. But for the discovery of lengthy new sequences with new meaning, the math in the example still doesn't work. And a model for this process in text, without guidance, will not succeed.

If the antifreeze gene was composed by the process Chen et al. describe, perhaps antifreeze activity is so non-specific that "almost any gene will do," as considered above. But if the precise antifreeze sequence was required (allowing only normal error tolerance), the composition process would have to have been guided somehow. Neo-Darwinism allows guidance by a chain of hypothetical intermediate steps (but not by teleology). Cosmic Ancestry would explain such guidance only by other instructions already in the genome; however, this concept is undeveloped.

12 Nov 2006: The Making of the Fittest, by geneticist Sean B. Carroll, W. W. Norton, 2006.
Evolutionary Scrap-heap Challenge..., a Reply forwarded by Stan Franklin, 17 Apr 2006.
7 May 2004: Ultraconserved elements.
2003, November 20: In mammals, CNGs are more numerous and better conserved than genes — a hint of possible other instructions already in the genome.
1999, October 21: A blood protein arose from a digestive enzyme.

Punctuated Equilibrium

The usual procedure is to forget the difficulties, never to talk about them, and to proceed as if the theory were without fault. — Paul Feyerabend (9)

Darwin wrote that evolution was a gradual process, with infinitesimal changes accumulating over the ages to eventually yield major differences in living things. If evolution advances as Darwin says it must, only tiny steps would ever happen. He states in The Origin of Species: "If it could be demonstrated that any complex organ existed which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down" (10).

Evidence from fossils does not bear out Darwin's theory of gradual change. Instead, species remain relatively unchanged for long periods, and then suddenly, new kinds arise. Many bacteria today have apparently changed very little since they first appeared. Some archaebacterial species appear to be as old as life on Earth; they haven't evolved very far in almost four billion years. We know that bacteria were the only inhabitants of the earth until about 1.7 billion years ago. Apparently, no major evolutionary developments happened among the bacteria for the first two billion years of life—more than half of the time life has existed on Earth.

By contrast, the entire Cambrian Explosion of about 570 million years ago took only five to nine million years (11). All kinds of multicelled creatures, in astonishing variety, seemed to come at once out of nowhere (12). On the cover of Time we read this synopsis of the Cambrian Explosion: "New discoveries show that life as we know it began in an amazing biological frenzy that changed the planet almost overnight" (13).

Similar discontinuities can be seen on a finer scale in the individual histories of species. In fact, the sudden appearance of new kinds of creatures, without evidence of intermediate kinds, is more the rule than the exception. Examples of intermediate kinds, such as the dog-sized Mesohippus that preceded the horse are actually quite rare. Stephen Jay Gould calls this discrepancy between the theory (gradualism) and the evidence (big steps) the paleontologists' "trade secret."

Today there is still considerable discord over punctuated equilibrium. How real is stasis (the period without appreciable change), how gradual is punctuation, and how can neo-Darwinists account for them? One proposal is "species sorting" or "species selection." In general, the new idea is that big evolutionary steps occur gradually in small, isolated populations. When the evolutionary steps are complete, the small population with its new advantage quickly expands and replaces the bigger population. Thus, in the geological record the change looks instantaneous. This solution has some appeal, but it offers little more by way of explanation than that gradual evolution always takes place somewhere out of sight. In 1931, J.B.S. Haldane foresaw this problem. "The paleontologist can always postulate a slow evolution in some area hitherto unexplored geologically, followed by migration into known areas" (14). Perhaps punctuated equilibrium is a clue that the genetic mechanism underlying evolutionary progress is altogether different from the one currently in favor.

15 Jan 2008: Did meteors cause the Great Ordovician Biodiversification Event?
4 Jan 2008: A sudden diversification of life..., if confirmed,... reinforces the idea that major evolutionary innovations occurred in bursts.
Gene Hunt, "The relative importance of directional change, random walks, and stasis in the evolution of fossil lineages" [abstract], 10.1073/pnas.0704088104, p 18404-18408 v 104, Proc. Natl. Acad. Sci. USA, 20 Nov (online 14 Nov) 2007. "The rarity with which directional evolution was observed in this study corroborates a key claim of punctuated equilibria...."
Antonis Rokas et al., "Animal Evolution and the Molecular Signature of Radiations Compressed in Time" [abstract], 10.1126/science.1116759, p 1933-1938 v 310, Science, 23 Dec 2006. "The differences ...suggest that the early history of metazoans was a radiation compressed in time, a finding that is in agreement with paleontological inferences."
Ancient crustacean raises new questions, by Ivan Noble, BBC News Online, 19 July 2001: 511 million-year-old fossil supports Cambrian expolsion.
Carol Kaesuk Yoon, "Fossil Findings May Force Revisions in the History of Life" [text], The New York Times, 22 May 2001. "The real peak of life's diversity may have come and gone more than 400 million years ago."
1999, November 3: Fossils of primitive fish have been found in the Lower Cambrian.

Coordinating Genes

We violate probability, by our nature. — Lewis Thomas

Richard Dawkins writes that the eye could evolve easily, by chance, in tiny steps. In an article entitled "The Eye in a Twinkling," he discusses how improvements of only one percent each could lead, in only some 400,000 generations, to the eye of a fish (15). He says eyes could have evolved many times, as they must have, because there are about 40 different kinds of eyes.

If eyes have evolved as Dawkins describes, by chance, then the genetic program to coordinate all the embryological steps in the growth of an eye (of each type) would evolve only after the genes for the steps themselves had evolved. Yet recently, scientists learned that the same gene coordinating the embryological steps in eye-making works in wasps and mice! The coordinating gene must have come first. "The observation that mammals and insects, which have evolved separately for more than 500 million years, share the same master control gene for eye morphogenesis indicates that the genetic control mechanisms for development are much more universal than anticipated" (16). In March, 1997, a group of scientists at the National Eye Institute in Bethesda, Maryland and the University of Basil in Switzerland reported that a gene controlling eye development is shared by fruitflies, mice, and squid (17). These startling developments have made theorists reconsider how eyes evolved (18).

A coordinating gene that works the same way in very different animals is not confined to the eye. Homeotic genes in the Drosophila (the fruitfly often used to study genetics) are known to control the expression of at least twenty of the fly's genes. Homeotic genes can be identified by the presence in them of a sequence 180 nucleotides long called a homeobox. "The big surprise concerning homeoboxes came in 1984 with the discovery of a homeobox, very similar to the Drosophila ones in a vertebrate, the toad Xenopus laevis. Soon afterwards the first mammalian homeoboxes were located..." (19). Coordinating genes appear to be standardized across a broad range of multicelled animals. And in March, 1997, biologists from the John Innes Centre for Plant Science Research in Norwich, England and Caltech found impressive similarities between homeotic genes in the fruitfly and a flowering plant (20).

It is difficult for neo-Darwinism to explain the appearance of embryological coordinating genes before the appearance of the embryological steps they coordinate. It's like saying that the blueprints for automobile manufacturing plants were on hand before the invention of automobiles.

25 Jun 2008: Vertebrate and jellyfish eyes use similar genes.
21 May 2005: The key to early eye evolution?
A highly conserved mechanism ...points to a common evolutionary origin of animal eyes. "The mechanisms used to control nerve cell formation in the zebrafish and fruitfly eyes thus appear to be exact copies of each other." Carl Neumann, Max Planck Institute for Developmental Biology, Tuebingen, 22 September 2000.

Convergent Evolution

"Convergent evolution" has been observed since the time of Darwin. It is the name given to apparent coincidences in evolution, such as the physical similarity between sharks (fish) and dolphins (mammals), or the parallelism in the cochlea of birds and mammals. A striking example is the resemblance between the Tasmanian wolf, which is an Australian marsupial "dog," and mammalian dogs common on other continents. Although the two would be very far apart on a phylogenetic tree, it takes a skilled zoologist to distinguish them by anatomical features like the skeleton. And examples of convergence also appear at the molecular level, as in similar antibody proteins carried by camels and nurse sharks. As The New York Times observes, "The more scientists look, the more examples of convergence they find" (21).

Neo-Darwinism accounts for the phenomenon by supposing that evolutionary options are often severely restricted by circumstances. "Convergences keep happening because organisms keep wanting to do similar things, and there are only so many ways of doing them," says molecular biologist Rudolf A. Raff of Indiana University (22). So the phenomenon has been named "the principle of convergence" or "convergent evolution." But naming the problem doesn't mean it has been explained. The renowned Harvard biologist Stephen Jay Gould believes that slight differences in the course of evolution should lead to totally different outcomes. If so, convergence is baffling. A discerning witness is justified in wondering if neo-Darwinism adequately explains convergence, or if another theory might account for it better.

28 Jan 2006: Important aspects of the history of life are replicable and predictable.
16 Mar 2005: Life’s Solution, by Simon Conway Morris.
Spider webs untangle evolution "...The concept that chance reigns supreme may ring less true when it comes to complex behaviours." Roxanne Khamsi, News@Nature.com, 1 Nov 2004.
Juan Carlos Santos et al., "Multiple, recurring origins of aposematism and diet specialization in poison frogs" [abstract], p 12792-12797 v 100, Proc. Natl. Acad. Sci. USA, 28 Oct 2003.
Moya Meredith Smith and Zerina Johanson, "Separate Evolutionary Origins of Teeth from Evidence in Fossil Jawed Vertebrates" [abstract], p 1235-1236 v 299, Science, 21 Feb 2003.
Poles apart, molars together "The teeth that might have allowed mammals to develop ...into today’s relative giants arose twice on different continents." Juliette Shackleton, Nature Science Update, 4 January 2001.

Does Microevolution Explain Macroevolution?

Ernst Mayr's 1988 classic, Toward a New Philosophy of Biology, asks the question, "Does Microevolution Explain Macroevolution?" (24). The issue came into sharper focus after Niles Eldredge and Stephen Jay Gould introduced the concept of "punctuated equilibrium" into the discussion of evolution. Microevolution would occur during stasis, and macroevolution at the punctuation points. This scenario is inconsistent with neo-Darwinian gradualism, according to which macroevolution is simply cumulative microevolution over long periods of time. The question challenges standard neo-Darwinism at its heart.

In our opinion, neo-Darwinism adequately accounts for microevolution. Changes in existing allele frequencies are already known to cause microevolution such as the darkening of the English moth's wings. A single nucleotide substitution can alter a virus's protein coat into one that the host's immune system doesn't recognize. The insertion or deletion of a single nucleotide causes a nonsense mutation that would disable, for example, a promoter or repressor sequence, thereby switching other whole genetic programs off or on.

Macroevolutionary progress such as the evolution of photosynthesis, on the other hand, requires wholly new genes with lengthy new instruction sequences. Whereas a new gene can be activated by a single point mutation, as mentioned above, there is scant evidence that new genes can be composed by Darwinian random point mutations and recombination events. Examples supporting this composition method are very few and weak.

Notice the term "progress" in the preceding paragraph. Any significant advance in evolution requires new genes. But loss of function, of course, can occur without new genes. So, macroevolutionary loss of function is not hard to explain. The real question is, "Does microevolutionary progress explain macroevolutionary progress?"

An excellent example of microevolutionary progress was discovered in 1999, by geneticists and ophthalmologists at University College London. From sequences of opsin genes they have deduced a plausible way for trichromatic vision in the howler monkey to have evolved from dichromatic vision by neo-Darwinian gene duplication and random mutation. Their analysis of the control regions of the genes, which are upstream of the coding regions, confirms the duplication. Interestingly, of the approximately 80 nucleotides from the coding region of the two genes that were compared, only one nucleotide was not identical. This plausible mutation causes a single amino acid substitution in the second howler opsin that changes its color sensitivity. The changed gene makes 3-color vision possible (25). In a recently discovered closely related example only two amino acid substitutions account for the blue-shifted vision of coelacanths (26).

The howler monkeys' acquisition of trichromatic vision represents evolutionary progress, unquestionably. But the same neo-Darwinian microevolutionary mechanism has not been shown to be capable of manufacturing the wholly new genes necessary for macroevolutionary progress. We believe that another source for these new genes is necessary.

Gerald H. Jacobs et al., "Emergence of Novel Color Vision in Mice Engineered to Express a Human Cone Photopigment" [abstract], 10.1126/science.1138838, p 1723-1725 v 315, Science, 23 Mar 2007. And commentary by Patrick Goymer, "Evolution: Colour vision for mice" [abstract], 10.1038/nrg2106, p 324-325 v 8, Nature Reviews Genetics, May 2007.
12 Nov 2006: The Making of the Fittest, by geneticist Sean B. Carroll, W. W. Norton, 2006.
23 Sep 2005: Today's protein families have been fine-tuned from ancient templates.
Shozo Yokoyama and Naomi Takenaka, "The Molecular Basis of Adaptive Evolution of Squirrelfish Rhodopsins" [abstract], p 2071-2078 v 21 n 11, Molecular Biology and Evolution, Nov 2004: well-documented microevolution.
15 Jan 2004: Are normal microevolutionary processes sufficient to account for human origins?
Uwe Stolz et al., "Darwinian natural selection for orange bioluminescent color in a Jamaican click beetle" [abstract], Proc. Natl. Acad. Sci. USA, online 17 Nov 2003: typical example of microevolution.
2003, April 7: Stephen Jay Gould's account of macroevolution, in a new Encyclopedia of Evolution....
Macroevolutionary Progress Redefined..., 4 Sep 2002.

Summary

Artificial selection never produces wholly new characteristics. Without the input of new genes, there is no evidence that natural selection does either.
The notion that mutation and recombination can compose new genes is implausible.
There is scant evidence that mutation and recombination can compose functional new genes that differ from any known predecessor by more than, say, a dozen essential nucleotides.
The evolution of antifreeze glycoproteins in Antarctic cod presents problems for both Darwinism and Cosmic Ancestry.
Evolution does not appear to be gradual, contrary to Darwin's firm prediction.
The standard theory cannot explain why the coordinating genes that control the development of embryos and major features are often very similar across totally different species.
Convergent evolution is a surprise not well-explained by neo-Darwinism.
Macroevolutionary progress is not accounted for by neo-Darwinian microevolution.

What'sNEW (More new items follow subtopics above.)

Elizabeth Pennisi, "Deciphering the Genetics of Evolution" [link], doi:10.1126/science.321.5890.760, p 760-763 v 321, Science, 8 Aug 2008. "Powerful personalities lock horns over how the genome changes to set the stage for evolution."
Ben-Yang Liao and Jianzhi Zhang, "Null mutations in human and mouse orthologs frequently result in different phenotypes" [abstract], doi:10.1073/pnas.0800387105, p 6987-6992 v 105, Proc. Natl. Acad. Sci. USA, 13 May (online 5 May) 2008. "...We find that >20% of human essential genes have nonessential mouse orthologs."
Todd A. Sangster et al., "HSP90-buffered genetic variation is common in Arabidopsis thaliana" [abstract], doi:10.1073/pnas.0712210105, Proc. Natl. Acad. Sci. USA, online 19 Feb 2008. "...HSP90 is likely to occupy a central position in the translation of genotypic variation into phenotypic differences."
Todd A. Sangster et al., "HSP90 affects the expression of genetic variation and developmental stability in quantitative traits" [abstract], doi:10.1073/pnas.0712200105, Proc. Natl. Acad. Sci. USA, online 19 Feb 2008.
Shocking Evolution Into Action, by Nicole Giese, Whitehead Institute for Biomedical Research, 18 Feb 2008 | also on Newswise.com. "The abundance of naturally occurring genetic variation that is affected by Hsp90 was remarkable."
Inheritance via RNA is the subject of a Reply from Stan Franklin, 4 Jan 2008.
Committee on Revising Science and Creationism, Science, Evolution, and Creationism [link], ISBN: 0-309-10587-0, National Academies Press, 2008.
19 Dec 2007: The ancestor of earthly life was molecularly complex.
Anthony Poole and David Penny, "Eukaryote evolution: Engulfed by speculation" [text], 10.1038/447913a, p 913 v 447, Nature, 21 Jun 2007. "The onus is on proponents, not sceptics, to find evidence for their theories."
Exploring the Dark Matter of the Genome, Physorg.com, 15 Jun 2007.
Rajkumar Sasidharan and Cyrus Chothia, "The selection of acceptable protein mutations" [abstract], 10.1073/pnas.0703737104, Proc. Natl. Acad. Sci. USA, online 31 May 2007. "This work implies that commonly allowed mutations are selected by a set of general constraints that are well defined and whose nature varies with divergence."
Jicheng Wang et al., "Evidence for mutation showers" [abstract], 10.1073/pnas.0610902104, Proc. Natl. Acad. Sci. USA, online 7 May 2007. "We conclude that mutation showers exist...."
Andrew Hendry, "The Elvis paradox" [text], 10.1038/446147a, p 147-149 v 446, Nature, 8 Mar 2007. Estes and Arnold consider the "paradox of stasis" in The American Naturalist.
Jun Gojobori et al., "Adaptive evolution in humans revealed by the negative correlation between the polymorphism and fixation phases of evolution" [abstract], 10.1073/pnas.0605565104, Proc. Natl. Acad. Sci. USA, online 26 Feb 2007.
No Missing Link? Evolutionary Changes Occur Suddenly, Professor Says, ScienceDaily.com, 12 Feb 2007.
Scientists Discover Parallel Codes In Genes, ScienceDaily.com, 9 Feb 2007.
Genetic information: Codes and enigmas, doi:10.1038/444259a, by Helen Pearson, News@Nature.com, online 15 Nov 2006.
Christopher D Herring, Anu Raghunathan, Christiane Honisch et al., "Comparative genome sequencing of Escherichia coli allows observation of bacterial evolution on a laboratory timescale" [abstract], 10.1038/ng1906, Nature Genetics, online 5 Nov 2006. "We obtained proof that the observed spontaneous mutations were responsible for improved fitness by creating single, double and triple site-directed mutants...."
Orkun S. Soyer and Sebastian Bonhoeffer, "Evolution of complexity in signaling pathways" [abstract], 10.1073/pnas.0604449103, Proc. Natl. Acad. Sci. USA, online 23 Oct 2006. "...Pathways could be driven toward complexity via simple evolutionary mechanisms...."
3 Oct 2006: Can plants overwrite unhealthy genes?
P M Brakefield and V French, "Evo-devo focus issue: Editorial" [text], 10.1038/sj.hdy.6800878, p 137-138 v 97, Heredity, Sep 2006. "...The basic mechanisms of embryonic development are extremely ancient and have been highly conserved.... Evo-devo... should continue to reveal how genetic change in the processes of development can lead to the abundant diversity in form that we observe in nature."
7 Jun 2006: Blowflies were preadapted for the rapid evolution of insecticide resistance.
Daniel M. Weinreich et al., "Darwinian Evolution Can Follow Only Very Few Mutational Paths to Fitter Proteins" [abstract], p 111-114 v 312, Science, 7 Apr 2006. About optimization: 5 certain a-a substitutions could theoretically be reached 5!=120 ways, but only 10 of them are likely to be permitted by natural selection.
T. Martin Embley1 and William Martin, "Eukaryotic evolution, changes and challenges" [abstract], p 623-630 v 440, Nature, 30 Mar 2006.
19 Feb 2006: Why has there has been so little change in major body plans since the Early Cambrian?
14 Feb 2006: Researchers evolve a complex genetic trait in the laboratory?
5 Jan 2006: "Evolution in Action" was the number one "Breakthrough of the Year" according to Science.
31 Oct 2005: The Plausibility of Life: Resolving Darwin’s Dilemma, by Marc W. Kirschner and John C. Gerhart, Yale University Press, 2005.
30 Sep 2005: The chimp genome has been sequenced. At least seventeen human genes contain exons missing in chimps.
Could evo-devo account for genetic novelty? Stan Franklin wonders, 25 Jul 2005.
14 Jul 2005: The World Summit on Evolution in the Galapagos Islands, 8-12 June 2005.
University of Chicago study overturns conventional theory in evolution, by Catherine Gianaro, EurekAlert!, 7 Jun 2005.
Alarm pheromone causes aphids to sprout wings, by Lynne Miller, EurekAlert!, 18 May 2005.
Tohru Sugawara et al., "Parallelism of amino acid changes at the RH1 affecting spectral sensitivity among deep-water cichlids from Lakes Tanganyika and Malawi" [abstract], p 5448-5453 v 102, Proc. Natl. Acad. Sci. USA, 12 Apr 2005. "...The number of genetic changes underlying the appearance of similar traits in cichlid diversification may be fewer than previously expected."
24 Mar 2005: Plants can overwrite unhealthy genes.
15 Mar 2005: "Biology today is no more fully understood in principle than physics was a century or so ago."
Andrew P. Hendry, "The power of natural selection," p 694-695 v 433, Nature, 17 Feb 2005. "We are only deluding ourselves that we have a good handle on the typical power of selection in nature."
16 Feb 2005: Fitness Landscapes.
I King Jordan et al., "A universal trend of amino acid gain and loss in protein evolution" [abstract], doi:10.1038/nature03306, p 633-638 v 433, Nature, 10 Feb 2005.
4 Feb 2005: Ernst Mayr died yesterday at 100 years of age.
H. Allen Orr, "The Genetic Theory of Adaptation: A Brief History" [open access], doi:10.1038/nrg1523, p 119-127 v 6, Nature Reviews Genetics, Feb 2005. Our comment — adaptation has a very short reach.
Rachel B. Brem and Leonid Kruglyak, "The landscape of genetic complexity across 5,700 gene expression traits in yeast" [abstract], 10.1073/pnas.0408709102, Proc. Natl. Acad. Sci. USA, online 19 Jan 2005. "Most detected QTLs (quantitative trait loci) have weak effects."
Kenneth M. Weiss and Anne V. Buchanan, Genetics and the Logic of Evolution, ISBN: 0471238058, Wiley-Liss (John Wiley and Sons, Inc.), 9 Jan 2004.
21 Nov 2004: Vertebrate photoreceptor cells in a primitive invertebrate.
14 Nov 2004: The birth of a new gene unique to apes and humans....
Sinéad Collins and Graham Bell, "Phenotypic consequences of 1,000 generations of selection at elevated CO2 in a green alga," p 566 - 569 v 431 Nature, 30 Sep 2004. "...Selection lines of the unicellular green alga Chlamydomonas failed to evolve specific adaptation to a CO2 concentration of 1,050 parts per million."
Emma Marris, "Tibetans show 'evolution in action'" [story], 10.1038/news040913-20, News@nature.com, 16 Sep 2004. "A gene for well oxygenated blood is spreading in the Himalayas." (Once a gene is available, natural selection works on it.)
Flies with inner ears?, by David Secko, The Scientist, 13 Sep 2004.
25 Jul 2004: 100 years old, Ernst Mayr reviews the development evolutionary thought in Science.
David J. Amor et al., "Human centromere repositioning 'in progress'" [abstract], p 6542-6547 v 101, Proc. Natl. Acad. Sci. USA, 27 Apr 2004.
The Most Natural Selection, by Steven Kotler, LA Weekly, 18 Apr 2004. If evolution rewards only reproductive success, why does homosexuality persist?
16 Apr 2004: The rat genome has been sequenced.
14 Apr 2004: "Can we ever hope to pin down the genetic changes that underlie the big steps in evolution?"
24 Feb 2004: Evolution caught in the act?
Erik R. Zinser et al., "Bacterial Evolution Through the Selective Loss of Beneficial Genes: Trade-Offs in Expression Involving Two Loci" [abstract], p 1271-1277 v 164, Genetics, August 2003. Adaptation by gene loss can happen a third way.
2003, August 29: "...We must conclude that there are no detailed Darwinian accounts..." (Franklin M. Harold, 2001).
Redundant Evolution, by Leslie Mullen, Astrobiology Magazine, 28 Apr 2003.
2003, April 16: Point mutations are less important than rearrangements of longer DNA strands in evolution....
A new branch on the tree of life, by Lynn Yarris, ScienceBeat, 4 Apr 2003. "Nature, it seems, found two different ways to evolve six legs."
2003, March 25: Here Be Dragons, by David W. Koerner and Simon Levay.
2003, March 3: What Evolution Is, by Ernst Mayr.
2003, January 23: Wingless stick insects have re-evolved wings.
Testing Darwinism versus Cosmic Ancestry — a new CA webpage, 24 Nov 2002.
Steve Olson, "Seeking the Signs of Selection" [summary], p 1324-1325 v 298, Science, 15 Nov 2002.
Fossil protein breakthrough will probe evolution, by Fred Pearce, NewScientist.com, 13 Nov 2002. "...Osteocalcin can survive ...long enough to look back ...to the last common ancestor of humans and chimpanzees."
Paul Raeburn, "'Of Moths and Men': The Moth That Failed" (book review) [text], The New York Times, 25 Aug 2001.
Fossils Help Determine When Humans, Apes Diverged, nationalgeographic.com, 23 Aug 2002. "The gene,... was mutated (knocked out) in humans in comparison with the normal, intact gene in apes."
2002, July 14: Mouse vs Human
2002, Jul 7: Acquiring Genomes.
Science Mimicking, Perhaps Even Predicting, Evolution — about basic research that supports Darwinism, by Jonathan Sherwood, UniSci.com, 21 Mar 2002.
2002, Mar 2: Correction.
2002, Feb 8: Biologists demonstrate macroevolution and thus answer a major challenge to darwinism by creationists.
2001, December 21: A gene needed for multcellularity is present in a single-celled organism.
Squirrels 'genetically altered' by forest. Actually they were altered by genes acquired from other squirrels. BBCNews, 21 Sep 2001.
Donald R. Forsdyke, The Origin of Species, Revisited [contents, publisher's promo], McGill-Queen's University Press, 2001.
2001, May 28: Eukaryote-to-prokaryote evolution in 15 days?!
2000, December 26: An email to Massimo Pigliucci recaps the argument against Darwinism.
2000, December 15: Mutation appears to double lifespan of flies.
2000, November 23: Monad to Man, by Michael Ruse, about evolutionary progress.
2000, September 27: Prions can turn on genetic programs.
1999, July 15: A recent issue of Science features evolution.
1999, June 3: Example of microevolution.
1998, August 25: We owe the repertoire of our immune system to one transposon insertion, which occurred 450 million years ago in the ancestor of the jawed fishes.
Was Darwin Wrong? The critics of evolution. Links to about two dozen even-handed book reviews by Gert Korthof. The reviews have further links.
The Tree of Life: an excellent growing illustrated resource on the classifications of life.
The Richard Dawkins Unofficial Website: a flashy site that thoroughly endorses Dawkins. It has good links and is kept current.
Enter Evolution: Theory and History. Evolutionary scientists before Darwin, from UC Berkeley.
Evolution, Science, and Society: a "white paper" on behalf of the field of evolutionary biology [Executive Summary] by Douglas J. Futuyma et al.

References