(1) Why does natural selection occur? (2) How does it occur? (3) What kinds of traits are most likely to be affected? (4) What are the effects of simultaneous natural selection of many traits and of the interactions among them? (5) What are the evolutionary dynamics of selected traits? (6) Are genera that are most prone to exhibit natural selection also those that are currently radiating most rapidly?³

1. Natural selection was the primary mechanism at every level of the evolutionary process. Natural selection caused genetic adaptation . . . . 4. Evolution of phenotypic characters such as eyes and ears, etc, was a good guide to protein evolution: or, protein evolution was expected to mimic phenotypic evolution. 5. Protein evolution was a good guide to DNA sequence evolution. Even Lewontin and Hubby thought, at first, that understanding protein evolution was the key to understanding DNA evolution. 6. Recombination was far more important than mutation in evolution. 7. Macroevolution was a simple extension of microevolution. 8. Definition of "species" was clear[--]the biological species concept of Dobzhansky and Mayr. 9. Speciation was understood in principle. 10. Evolution is a process of sharing common ancestors back to the origin of life, or in other words, evolution produces a tree of life. 11. Inheritance of acquired characters was impossible in biological organisms. 12. Random genetic drift was a clear concept and invoked constantly whenever population sizes were small, including fossil organisms. 13. The evolutionary synthesis was actually a synthesis.⁸

Explaining exactly how the great complexity and diversity of life on earth originated is still an enormous scientific challenge. ... There is the widespread attitude in the scientific community that, despite some problems in detail, textbook accounts on evolution have essentially solved the problem already. In my view, this is not quite correct.¹³

The vast majority of biologists engaged in evolutionary studies interpret virtually every aspect of biodiversity in adaptive terms. This narrow view of evolution has become untenable in light of recent observations from genomic sequencing and population genetic theory. ... What is in question is whether natural selection is a necessary or sufficient force to explain the emergence of the genomic and cellular features central to the building of complex organisms.¹⁴

Darwin's theory states that the unguided force of natural selection is supposed to be able to do what the intelligent breeder can do. But even a process of careful, intentional selection encounters limits that neither time nor the efforts of human breeders can overcome. Consequently, critics argue that by the logic of Darwin's own analogy, the power of natural selection is also limited. (EE, pg. 91)

This does not detract from the significance of artificial selection as an assay for genetic variation in natural populations. [Artificial selection] means the potential for a response to selection. Though evolution may not be as rapid in natural populations, the time spans for selection to operate are much longer.²⁰

George John Romane's famous treatise on evolution from the late 19th century, Darwin and After Darwin, states that "the process of artificial selection is precisely analogous to that of natural selection."²²

Biologist George St. Clair's 1873 book Darwinism and Design states, "The experimental argument which lies at the very base of Mr. Darwin's theory is that man's process in forming new breeds of pigeons is the analogue of nature's process in evolving new forms from old--the one is artificial selection, and the other natural selection."²³

Similarly Charles Clement Coe, in his 1895 Nature Versus Natural Selection: An Essay on Organic Evolution, refers to the "Analogy Between Natural and Artificial Selection."²⁴

In more modern times, Mark A. Largent's chapter in The Cambridge Companion to the "Origin of Species" (co-edited by Michael Ruse) discusses "Darwin's Analogy between Artificial and Natural Selection in the Origin of Species."²⁵

In the 2003 The Cambridge Companion to Darwin, C. Kenneth Waters notes that, "Darwin argued for the adequacy of natural selection by appealing to the analogy between artificial and natural selection."²⁶

A chapter in the National Academy Press volume In the Light of Evolution: Adaptation and Complex Design observes that "In the opening chapter of the Origin of Species, Charles Darwin introduced the idea of natural selection with an analogy to domestication."²⁷

M.J.S. Hodge observes in the 1992 Harvard University Press book Keywords in Evolutionary Biology that Darwin coined the term "natural selection" as an analogy for artificial selection: "To understand the history of the term 'natural selection' both before and after this moment in the Origin, we have, therefore, to look not for a sequence of explicit definitional equations but, rather, for the reasons why people, starting with Darwin himself, have felt themselves able to grasp and wield the concept adequately in the absence of consistent, authoritative definitional analyses of the term. In Darwin's own case, the term itself was a secondary matter; what really counted was his argument for the analogy that the term was coined to signify, the analogy between man's selection and nature's."²⁸

Explore Evolution asks, "But can this three-step process construct organs as complex as an eye?" This hackneyed canard about the alleged irreducible complexity of the eye rises again.

One of the most important questions in evolution is: How can new adaptations originate? This is a difficult question, because most evolutionary novelties, such as the eye or the wing, involve the orchestrated expression of many different loci, a number of which act in the expression of multiple phenotypes. Conventional explanations that randomly generated advantageous changes in complex characters accumulate one locus at a time are unconvincing on both functional and probabilistic grounds, because there is too much interconnectivity and too many degrees of mutational freedom.²⁹

began with a crude light-sensitive organ consisting of a layer of light-sensitive cells sandwiched between a darkened layer of cells and a transparent protective layer above. The simulation, therefore, does not cover the complete evolution of an eye. To begin with, it takes light sensitive cells as given ... and at the other end it ignores the evolution of advanced perceptual skills (which are more a problem in the evolution of the brain than the eye).³⁰

And where did the "little cup" come from? A ball of cells--from which the cup must be made--will tend to be rounded unless held in the correct shape by molecular supports. In fact, there are dozens of complex proteins involved in maintaining cell shape, and dozens more that control extracellular structure; in their absence, cells take on the shape of so many soap bubbles. Do these structures represent single-step mutations? Dawkins did not tell us how the apparently simple "cup" shape came to be.³⁷

Light strikes the eye in the form of photons, but the optic nerve conveys electrical impulses to the brain. Acting as a sophisticated transducer, the eye must mediate between two different physical signals. The retinal cells that figure in Dawkins' account are connected to horizontal cells; these shuttle information laterally between photoreceptors in order to smooth the visual signal. Amacrine cells act to filter the signal. Bipolar cells convey visual information further to ganglion cells, which in turn conduct information to the optic nerve. The system gives every indication of being tightly integrated, its parts mutually dependent.

The very problem that Darwin's theory was designed to evade now reappears. Like vibrations passing through a spider's web, changes to any part of the eye, if they are to improve vision, must bring about changes throughout the optical system. Without a correlative increase in the size and complexity of the optic nerve, an increase in the number of photoreceptive membranes can have no effect. A change in the optic nerve must in turn induce corresponding neurological changes in the brain. If these changes come about simultaneously, it makes no sense to talk of a gradual ascent of Mount Improbable. If they do not come about simultaneously, it is not clear why they should come about at all.

The same problem reappears at the level of biochemistry. Dawkins has framed his discussion in terms of gross anatomy. Each anatomical change that he describes requires a number of coordinate biochemical steps. "[T]he anatomical steps and structures that Darwin thought were so simple," the biochemist Mike Behe remarks in a provocative new book (Darwin's Black Box), "actually involve staggeringly complicated biochemical processes." A number of separate biochemical events are required simply to begin the process of curving a layer of proteins to form a lens. What initiates the sequence? How is it coordinated? And how controlled? On these absolutely fundamental matters, Dawkins has nothing whatsoever to say.³⁸

The biochemical evolution of the fundamental ability to sense light

The origin of the first "light sensitive spot"

The origin of neurological pathways to transmit the optical signal to a brain

The origin of a behavioral response to allow the sensing of light to give some behavioral advantage to the organism

The origin of the lens, cornea and iris in vertebrates

The origin of the compound eye in arthropods

Douglas Futuyma, Evolution (Sinauer, 2005)

Holt's Life Science (Holt, Rinehart, and Winston, 2001)

Sylva S. Mader, Essentials of Biology (McGraw Hill, 2007)

Strauss and Lisowski, Biology: The Web of Life (Addison-Wesley, 2000)

Glencoe's Biology: The Dynamics of Life (Florida Edition, 2006)

Sylvia S. Mader, Biology (10th ed., McGraw Hill, 2007)

Scott Freeman, Biological Science (3rd ed., 2008)

Kenneth Miller and Joseph Levine, Biology (Pearson/Prentice Hall, 2008)

David Savada, H. Craig Heller, Gordon H. Orians, William K. Purves, David M. Hillis, Life: The Science of Biology (8th ed., Sinauer, W. H. Freeman, 2008)

Douglas Futuyma, Evolution (Sinauer, 2005)

Holt's Life Science (Holt, Rinehart, and Winston, 2001)

Sylva S. Mader, Essentials of Biology (McGraw Hill, 2007)

Strauss and Lisowski, Biology: The Web of Life (Addison-Wesley, 2000)

Glencoe's Biology: The Dynamics of Life (Florida Edition, 2006)

Modern Biology (Holt Rinehart and Winston, 2002)

Raver's Biology: Patterns and Processes of Life (J. M. Lebel, 2004)

Collen Belk & Virginia Borden Maier, Biology: Science for Life (Pearson / Benjamin Cummings, 2010)

Sylvia S. Mader, Biology (10th ed., McGraw Hill, 2007)

Glencoe's Biology: An Everyday Experience (Glencoe, 2003)

Scott Freeman, Biological Science (3rd ed., 2008)

Explore Evolution argues that if natural selection cannot produce a certain change in a matter of decades, it could never produce that change. This is nonsensical on its face, and does not accurately reflect basic knowledge about natural selection and population genetics stretching back to the 1920s. It also misstates the effects that animal husbandry has been shown to have on domestic species.

[Gaffney and Cunningham] end the paper stating, "We conclude that the explanation for the lack of progress in winning times is not due to a lack of genetic gain in the thoroughbred population as a whole." Genetic gain in the population as a result of selective breeding is the very definition of artificial selection.

...breeders and horse-racing enthusiasts state they pay little attention to winning times. Instead, riders, horse owners, breeders, and bettors are rewarded for horses that win races, regardless of time, and little effort is made to "beat the clock."⁴⁵

But at the same time these same investigators reported that winning times have not improved significantly during the last 50 years for ''classic races,'' for example, races designed to match the best horses each year. Cunningham noted that winning times had been especially static for distance races and suggested that a physiological limit might have been reached, for example, for dealing with lactic acid buildup in muscle during performance. Therefore, although horses exhibited genetic variation for racing performance and the population continued to exhibit genetic gain during the period of study, the best times did not improve.⁴⁶

It is therefore impossible to know whether contemporary horses would run faster than famous racehorses like Seabiscuit or Secretariat if they ran against one another, or whether contemporary horses as a whole are faster in absolute terms than horses were 70 years ago.

In this regard, Jim Rooney (pers. comm., this conference), an expert on biomechanics of the horse, noted that if there is a limit on performance of the racehorse, it may be on the ability of the horse to remain sound in the face of the tremendous stresses of racing.⁴⁷

[Bailey] then wrote: "Consequently, track surfaces are often treated to be softer, slower, and (thus) less likely to cause stress on the horse."  If surfaces are slower and there is less stress on the horses, why are there (allegedly) more breakdowns today than in the past?

Also, [Bailey's] thought is a disconnect with the sentence that preceded it. It presumes that race track superintendents, realizing that their fast surfaces may have been causing injuries, reacted to that realization by "slowing" the surfaces down. I want to see his sources for this "thought" that he presents as fact. Obviously, I disagree with the thought and I believe that ninety-nine percent of the trainers would agree with me.

The reality is quite the opposite. In the mistaken belief that faster times make more people come to see Thoroughbreds run, the track supers are constantly grooming their surfaces in an effort to produce that "best" surface that allows the horse to run faster than ever before. They are NOT intentionally trying to cause breakdowns. They ARE intentionally trying to make their surfaces both faster and yes, safer. But I don't think there's a track super in the USA who intentionally makes his surface "slow."

[Bailey] concluded with: "Thus, modern racetracks may be slower than the tracks of 50 years ago." He conveniently used the word "may" which, I suppose, gets him off the hook. Remove that word and this statement simply cannot be true because the "science" of maintaining a race track today is so much better than it was 50 years ago. So are the materials used in the cushion and so is the equipment that is used in the maintenance. I 100 % disagree and would require that he cite "chapter and verse" and prove his conclusion with verifiable, expert evidence.

In the 1950s and '60s, any Thoroughbred (racing anywhere other than California) who could run three-quarters of a mile (six furlongs) in less than 1:12 was considered a pretty good horse, and one who could go in ten and change, or faster, was considered to be very fast.   Today, horses routinely go in 1:10 and change and nobody blinks an eye, and they run in 1:08 in CA, even on the artificial surfaces.

"Slower" surfaces today? Not on your life!"⁵¹

The following are three major areas of misconception among the Neo-Darwinists... Artificial selection on quantitative traits was taken as a model of the evolutionary process. It was easily shown, in agriculture or in the laboratory, that populations of most organisms contain sufficient additive genetic variance to obtain a response to selection on quantitative traits, such as measures of body size or increased yield of agriculturally valuable products such as milk in dairy cattle or grain size in food plants. Generalizing from this experience, it was assumed that natural populations are endowed with essentially unlimited additive genetic variance, implying that any sort of selection imposed by environmental changes will encounter abundant genetic variation on which to act. Moreover, this model was extended to evolutionary time as well as ecological time. This way of thinking ignored the substantial evidence from selection experiments that the response to selection on any trait essentially comes to a halt after a number of generations as the genetic variance for the trait in question is depleted; thereafter, further progress depends on the introduction of new variants either through outcrossing or new mutations (Falconer, 1981).⁵²

Some enthusiasts have claimed that natural selection can do anything. This is not true. Even though "natural selection is daily and hourly scrutinizing, throughout the world, every variation even the slightest," as Darwin (1859:84) has stated, it is nevertheless evident that there are definite limits to the effectiveness of selection.⁵³

The existing genetic organization of an animal or plant sets severe limits to its further evolution. As Weismann expressed it, no bird can ever evolve into a mammal, nor a beetle into a butterfly. Amphibians have been unable to develop a lineage that is successful in salt water. We marvel at the fact that mammals have been able to develop flight (bats) and aquatic adaptation (whales and seals), but there are many other ecological niches that mammals have been unable to occupy. There are, for instance, severe limits on size, and no amount of selection has allowed mammals to become smaller than a pygmy shrew and the bumblebee bat, or allow flying birds to grow beyond a limiting weight.⁵⁵

The most revolutionary feature of Darwin's On the Origin of Species (1859) was to propose natural selection as the single unifying mechanism that causes both micro- and macroevolution. Darwin argued that macroevolution is just microevolution writ large, or that the process we see and study as the cause of microevolution will, given sufficient time, also cause everything that we attribute to macroevolution. He argued that natural selection, which causes the evolution of the adaptations discussed throughout this essay is also responsible for the origin of all levels of biological complexity and for the origin of biological diversity, or all the species that have been found on the earth throughout its history.⁵⁹

What these data show is that dog breeders have already managed to produce animals which break new morphological ground. Whatever limits might seem to exist if we look at the shapes and sizes of wild canids have been surpassed by the work of dog breeders. Whatever limits natural selection has, they have prevented the evolution of variation beyond that seen within the rest of the entire order Carnivora (dogs, cats, bears, foxes, weasels, etc.), all within the last few thousand years. Natural selection may well have limits, but if the limits are that loose, they would not prevent the diversification of life as we know it over the course of several billion years.

This claim is related to the "young earth" creationist belief that the earth is only a few thousand years old. In this belief system, there has not been enough time for speciation to occur, given the rate of change that we can observe in most populations. So it is necessary for them to deny reality (observations of speciation) in order to validate a creationist perspective on the age of the earth. An age, by the way, that is about 0.00000002% of the approximately 3 billion years over which biological evolution has proceeded.

String A: SHANNONINFORMATIONISAPOORMEASUREOFBIOLOGICALCOMPLEXITY

String B: JLNUKFPDARKSWUVEYTYKARRBVCLTLODOUUMUEVCRLQTSFFWKJDXSOB

[N]either RSC [Random Sequence Complexity] nor OSC [Ordered Sequence Complexity], or any combination of the two, is sufficient to describe the functional complexity observed in living organisms, for neither includes the additional dimension of functionality, which is essential for life. FSC [Functional Sequence Complexity] includes the dimension of functionality. Szostak argued that neither Shannon's original measure of uncertainty nor the measure of algorithmic complexity are sufficient. Shannon's classical information theory does not consider the meaning, or function, of a message. Algorithmic complexity fails to account for the observation that "different molecular structures may be functionally equivalent." For this reason, Szostak suggested that a new measure of information--functional information--is required.⁷³

[L]iving organisms are distinguished by their specified complexity. Crystals are usually taken as the prototypes of simple, well-specified structures, because they consist of a very large number of identical molecules packed together in a uniform way. Lumps of granite or random mixtures of polymers are examples of structures which are complex but not specified. The crystals fail to qualify as living because they lack complexity; the mixtures of polymers fail to qualify because they lack specificity.⁷⁶

A large portion of the information needed to construct an organism (with its various traits) is stored in the molecule DNA. Some scientists refer to this information as "assembly instructions" or "a genetic program." Just like a computer program, DNA contains the biological equivalent of lines of computer code. Evolutionary zoologist Richard Dawkins states, "The machine code of the genes is uncannily computer-like." (EE, pg. 94)

[The conservation of biochemistry throughout life] and the universality of the genetic code lead one to believe that life on earth had a beginning and (to use a computer analogy) a basic program of genetic messages originated to form some ancient primitive organism, namely, the protobiont. The biochemical unity of this basic program has been retained throughout evolution in some cases with little modification, and new subroutines have been added. ... In the following we will resort to illustrating our points by reference to the properties of language. It is important to understand that we are not reasoning by analogy. The sequence hypothesis applies directly to the protein and the genetic text as well as to written language and therefore the treatment is mathematically identical. ... The so-called "instructions in the amino acids themselves" which, it is proposed, generate the first informational biomolecules actually merely play the role of grammar, spelling rules, etc. in ordinary language. Grammar and spelling are autonomous and independent of meaning, so it is clear that it is impossible that the genome of the protobiont could have appeared in a "primitive soup" in this way [a self-organization scenario].⁷⁷

The first use of the term code to look at is one that seems most consonant with the notion many have of g: [DNA language] à [Amino acid language] as a ''genetic program''--as the manner by which data and instructions are represented in a programming (computer-like) language. ORFs are often said to constitute the symbolic text for gene products and the interactions of the latter, and in that sense we are told the genome is software.⁷⁹

Genes and emergent gene networks represent programming. These algorithms are written in a pre-existent operating system environment. As in computer science, this language is used by the programmer. We must not only find models for specific genetic programming, but for the genetic operating system. ... The algorithmic complexity of life puts our finest computers to shame.⁸⁰

[I]n information theory, adding random noise actually increases the amount of information being transmitted. Whether that information is useful or not to a listener is a separate matter. We usually have a very specific expectation for information transmitted over a telephone line, so random static on the line reduces the amount of information we had hoped to get.

DUPLICATINGTHISSTRINGDOESNOTGENERATENEWCSI

DUPLICATINGTHISSTRINGDOESNOTGENERATENEWCSIDUPLICATINGTHISSTRINGDOESNOTGENERATENEWCSI

[G]ene duplication is, presumably, not to be taken too seriously. If you count copies as new information, you must have a hard time with plagiarism in your classes. All that the miscreant students would have to say is 'It's just like gene duplication. Plagiarism is new information- you said so on your blog!'⁸²

A major hindrance to progress has been confusion regarding the role of positive (Darwinian) selection, i.e., natural selection favoring adaptive mutations. In particular, problems have arisen from the widespread use of certain poorly conceived statistical methods to test for positive selection. Thousands of papers are published every year claiming evidence of adaptive evolution on the basis of computational analyses alone, with no evidence whatsoever regarding the phenotypic effects of allegedly adaptive mutations. ... Contrary to a widespread impression, natural selection does not leave any unambiguous ''signature'' on the genome, certainly not one that is still detectable after tens or hundreds of millions of years. To biologists schooled in Neo-Darwinian thought processes, it is virtually axiomatic that any adaptive change must have been fixed as a result of natural selection. But it is important to remember that reality can be more complicated than simplistic textbook scenarios. ... In recent years the literature of evolutionary biology has been glutted with extravagant claims of positive selection on the basis of computational analyses alone ... This vast outpouring of pseudo-Darwinian hype has been genuinely harmful to the credibility of evolutionary biology as a science.⁸⁵

Although useful for determining lines of descent ... comparing sequences cannot show how a complex biochemical system achieved its function--the question that most concerns us in this book. By way of analogy, the instruction manuals for two different models of computer put out by the same company might have many identical words, sentences, and even paragraphs, suggesting a common ancestry (perhaps the same author wrote both manuals), but comparing the sequences of letters in the instruction manuals will never tell us if a computer can be produced step-by-step starting from a typewriter. ... Like the sequence analysts, I believe the evidence strongly supports common descent. But the root question remains unanswered: What has caused complex systems to form?⁸⁶

[M]odern Darwinists point to evidence of common descent and erroneously assume it to be evidence of the power of random mutation.⁸⁷

(1) Take a gene you've observed in some organism. We'll call it Gene B.
(2) Find another gene similar to Gene B. Let's call it Gene A.
(3) Claim that at some time in the past, Gene A duplicated so then there were two copies of Gene A.
(4) Then assert that one of Gene A's duplicates evolved into Gene B.

Given the known effects and rates of mutations, what were the odds of Gene A and Gene Z suddenly being rearranged next to one-another so that they could now function together as one single new gene product, Gene B?

Did the rearranged gene product B start out functional? If not, how quickly could it gain function? How was it preserved from loss until it became functional?

Are proteins really as malleable as this story would suppose or would the new combined gene encounter folding or other contextual problems?

What mutational pathway was taken to evolve Gene A and Gene Z into a new gene with function B?

What selective advantages were gained at each small step of this evolutionary pathway?

Were any "large steps" (i.e., multiple specific mutations) ever required to gain a selective advantage along the evolutionary pathway? Would such "large steps" be likely to occur?

Could all of this happen on a reasonable timescale?

Gene Evolution Game Rule 1: Whenever you find sequence homology between two genes, just invoke a duplication event of some hypothetical, ancient ancestral gene, and you can explain how two different genes came to share their similarities.

Gene Evolution Game Rule 2: When you need to explain how a gene acquired some new function, or evolved differences from another gene, just invoke the magic wand of natural selection. No need to demonstrate that there is any benefit to the new gene, or that a step-wise path to adaptation exists. Finally, natural selection is especially useful when part of your gene appears unique--since natural selection can change anything, just conclude that natural selection changed your gene so much that it no longer resembles its ancestor.

Gene Evolution Game Rule 3: When a gene seems to be composed of the parts of several genes, just invoke duplications and rearrangements of all the DNA sequences you need, so you can get them all together in the right place. If you need to delete parts of a gene, or invert them, or transpose to a new location, just invoke different types of rearrangements as often and as liberally as you wish, and ba-da-bing, you've got your new gene!

For example, a rhodopsin from the Japanese conger eel with λ_max ≈ 480 nm achieved this sensitivity through the interaction of three different amino acid replacements (at sites 195, 195, and 292). There does not seem to be any way that natural selection could favor an amino acid replacement that would be of adaptive value only if two other replacements were to occur as well.⁹⁴

The mutation would have reduced the Darwinian fitness of those individuals. . . . It only would've become fixed if it coincided with mutations that reduced tooth size, jaw size and increased brain size. What are the chances of that?⁹⁶

Question 1: Is there a step-wise adaptive pathway to mutate from A to B, with a selective advantage gained at each small step of the pathway?

Question 2: If not, are multiple specific mutations ever necessary to gain or improve function?

Question 3: If so, are such multi-mutation events likely to occur given the available probabilistic resources?

If these changes come about simultaneously, it makes no sense to talk of a gradual ascent of Mount Improbable. If they do not come about simultaneously, it is not clear why they should come about at all.⁹⁸

As you might imagine, only a small fraction of the possible combinations of amino acids will fold spontaneously into a stable structure. If you make a protein with a random sequence of amino acids, chances are that it will only form a gooey tangle when placed in water. Cells have perfected the sequences of amino acids over many years of evolutionary selection...¹⁰²

The fact that very large population sizes--10⁹ or greater--are required to build even a minimal [multi-residue] feature requiring two nucleotide alterations within 10⁸ generations by the processes described in our model, and that enormous population sizes are required for more complex features or shorter times, seems to indicate that the mechanism of gene duplication and point mutation alone would be ineffective, at least for multicellular diploid species, because few multicellular species reach the required population sizes.¹⁰³

[Protein engineering research] does not mimic random mutation. It is the exact opposite of random mutation. ... What do the lab results tell us about whether random-yet-productive shuffling of domains "occurs with significant frequency under conditions that are likely to occur in nature"?  About whether that is biologically reasonable?  Nothing at all.  When a scientist intentionally arranges fragments of genes in order to maximize the chances of their interacting productively, he has left Darwin far, far behind. ... [Experiments that engineered proteins by shuffling domains] didn't just splice two genes together in a single step; they took several additional steps as well.  ... Remember the more steps that have to occur between beneficial states, the much less plausible are Darwinian explanations.  ... Domain shuffling would be an instance of the "natural genetic engineering" championed by James Shapiro where evolution by big random changes is hoped to do what evolution by small random changes can't.  But random is random.  No matter if a monkey is rearranging single letters or whole chapters, incoherence plagues every step.  ... One step might luckily be helpful on occasion, maybe rarely a second step might build on it.  But Darwinian processes in particular and unintelligent ones in general don't build coherent systems.  So it is biologically most reasonable to conclude that, like multiple brand new protein-protein binding sites, the arrangement of multiple genetic elements into sophisticated logic circuits similar to those of computers is also well beyond the edge of Darwinian evolution.¹⁰⁵

First, although a testes-specific promoter was essential for Sdic, this unusual regulatory region did not really "evolve." Instead it was aboriginal, created de novo by the fortuitous juxtaposition of suitable sequences. The more extensive evolutionary changes took place in Cdic intron 3, enabling an originally untranslatable sequence to become a new coding region whose product functions in the assembly of axonemal dynein.¹¹⁴

To consider the AFGP story as a special case of duplication and divergence would be oversimplifying; it is clear that the antifreeze function, or even a related function that could be converted to the purpose, was not present in trypsinogen. The molecular mechanisms involved in the formation of this gene were indeed more creative--making sense from nonsense--by calling into a functional coding capacity intronic DNA sequences.¹²⁵

As it has become more practical to trace the sequences of genes in multiple species, scientists have been able to identify genes which went through these processes, acquiring new functions within relatively recent history. That research systematically refutes the claim in Explore Evolution that "whether you're talking about artificial selection or about microevolution that occurs naturally, changes in the sub-population take place as genetic information is lost to that population" (p. 95).

exons may have been "recruited" or "donated" from other genes (and in some cases from an "unknown sou[r]ce");

there were vague appeals to "extensive refashioning of the genome";

mutations were said to cause "fortuitous juxtaposition of suitable sequences" in a gene-promoting region that therefore "did not really 'evolve'";

researchers assumed "radical change in the structure" due to "rapid, adaptive evolution" and claimed that "positive selection has played an important role in the evolution" of the gene, even though function of the gene was not even known;

genes were purportedly "cobbled together from DNA of no related function (or no function at all)";

the "creation" of new exons "from a unique noncoding genomic sequence that fortuitously evolved" was assumed, not demonstrated;

we were given alternatives that promoter regions arose from a "random genomic sequence that happens to be similar to a promoter sequence," or that the gene arose because it was inserted by pure chance right next to a functional promoter.

explanations went little further than invoking "the chimeric fusion of two genes" based solely on sequence similarity;

when no source material is recognizable, we're told that "genes emerge and evolve very rapidly, generating copies that bear little similarity to their ancestral precursors" because they are simply "hypermutable";

we even saw "a striking case of convergent evolution" of "near-identical" proteins.

On the other hand, each daughter population will have lost genetic information necessary for building certain other traits. The total biological information in the gene pool will have decreased, which limits how much the daughter population can vary and change in the future. Ultimately, this means that the isolated "daughter" populations are more vulnerable to environmental stresses (natural disasters or other changes in the environment). For this reason, small isolated populations are great candidates for extinction. In summary, whether you're talking about artificial selection or about microevolution that occurs naturally, changes in the sub-population take place as genetic information is lost to that population. (pg. 95)

These critics would say that natural selection works well as an editor, but not an author. It has a demonstrated capacity to weed out the failures from among what already exists, but it has not been shown to generate new biological information or structures. (EE, pg. 95)

You may be surprised to learn that most critics of neo-Darwinism agree with many of the arguments you have just read [from proponents of neo-Darwinism]. At least, up to a point. Few biologists today would argue over whether the different species of Galapagos mockingbirds (for example) descended from a common ancestor. (EE, pg. 79)

If Universal Common Descent is true, it must have a mechanism that can produce macroevolutionary change--that can transform one type of animal into a fundamentally different type of animal ... Since critics of the argument from biogeography see no evidence of large-scale change, or of a mechanism that can produce the new genes needed to cause such change, they doubt that the biogeographical distribution of animals supports Universal Common Descent. (EE, pg. 77, emphasis added)

The adaptive radiations of marsupials in Australia, finches in the Galápagos, honeycreepers in Hawaii, or cichlids in Africa's Rift Valley (to choose but a few examples) produced a range of variation equivalent to variation seen within vastly larger taxonomic groups. While the variation is not infinite, saying that these species are not fundamentally different from their ancestors ignores the basic biology.

Contemporary evolutionary biologists point to other biogeographical evidence in support of this view. For example, in the Hawaiian Islands, there are hundreds of species of the fruit fly genus Drosophila. These species are not found anywhere else in the world. Why are there so many different species of fruit fly in such a remote place? As the National Academy of Sciences argues, "The biological explanation for the multiplicity of related species in remote localities is that such great diversity is a consequence of their evolution from a few common ancestors that colonized an isolated environment." (EE, pg. 75)

critics note that the examples of mockingbirds in the Galápagos and fruit flies in the Hawaiian Islands show only small-scale variations in existing traits. Further, some geneticists think that these changes have occurred because the populations of these birds and fruit flies became isolated, and lost genetic information over time. (EE, pg. 77)

slightly different head dimensions and eye shapes

1 fork (Scaptomyza) vs. 2+ forks (Drosophila) on antennae bristles, known as arista

dull (Scaptomyza) vs. shiny (Drosophila) plates covering the middle of the thorax

2-4 (Scaptomyza) vs. 6-8 (Drosophila) acrostichal rows of hairs

differences in the shape of the male anatomy and some other internal anatomy, such as the spermathecae, testes, vasa deferentia, paragonia, ejaculatory apodemes, and Malphigian tubules

short (Scaptomyza) vs. long (Drosophila) egg filaments

Mockingbirds from the Galapagos Islands, not finches, gave Charles Darwin his ideas about evolution. ... Darwin's finches are the better-known birds connected with helping Darwin come to his conclusions on evolution. However, it was the little-known mockingbirds that were the key.¹⁵

[M]ost modern critics of neo-Darwinism accept the idea that all the mockingbirds of the Galápagos have a common ancestor. In their view, the evidence does support the idea that these birds have changed in response to their environment (Evolution #1), but it does not show that all creatures everywhere have a single common ancestor (Evolution #2). And that's the rub. These scientists accept that plants and animals of the Galápagos were transported or migrated to the islands and then adapted in some ways to their new environment. They point out, however, that migration and adaptation does not equal macroevolutionary change. (EE, pg. 76)

Hawaiian drosophilid fruit flies ... [and] Galápagan groundfinches ... are in reality modest in terms of species numbers and net rates of species formation.²¹

Since insects, too, are attracted to the nectar, it is not surprising to find that many nectar eaters are also insect eaters, and from this it is a short step to a diet of nothing but insects.³⁰

[T]hroughout such changes, the basic body type and structural features of the honeycreepers were preserved. In other words, there was diversification, but only within limited boundaries. Different forms of Hawaiian honeycreepers are (as far as we know) reproductively isolated from each other -- and are thus separate species according to the Biological Species Concept. Nevertheless, they differ from each other no more than, say, different breeds of dogs, which are all members of the same species. In fact, the morphological differences between some dog breeds are greater than the morphological differences between species of Hawaiian honeycreepers.³³

Why are marsupials mainly found on those two continents? Proponents of Common Descent offer this explanation. The first mammals with the marsupial's distinctive mode of reproduction arose on the ancient southern super-continent of Gondwanaland. Later, after this great land mass broke up into separate continents, the ancestors of the modern marsupials were separated from other mammals and evolved in isolation on the new continents of Australia and South America. The distinctive Australian marsupials--kangaroos and koalas, for example--are the result of that evolutionary process in an isolated locale. (EE, pg. 75)

In the Early Cenozoic of the Northern Hemisphere, as in the Late Cenozoic of South America, the arrival of placentals led to the elimination, or near-elimination, of the marsupials. Why, then, did Early Cenozoic placentals of Australia become extinct, leaving the monotremes and the marsupials as the only Late Cenozoic mammals of that continent?⁴⁶

Where did the modern lineages of placental mammals originate? Recent molecular data seemingly have overturned not only schemata of placental relationships based on morphological data, but also hypotheses about the time and place of origin of the modern lineages. The original hypothesis of Northern Hemisphere origin, based on the fossil record, has been replaced by a "Garden of Eden" hypothesis of origins on a southern continent, based on molecular phylogenies.⁴⁷

Convergence is a deeply intriguing mystery, given how complex some of the structures are. Some scientists are skeptical that an undirected process like natural selection and mutation would have stumbled upon the same complex structure many different times. Advocates of neo-Darwinism, on the other hand, think convergent structures simply show that natural selection can produce functional innovations more than once. For other scientists, the phenomenon of convergence raises doubts about how significant homology really is as evidence for Common Descent. Convergence, by definition, affirms that similar structures do not necessarily point to common ancestry. Even neo-Darwinists acknowledge this. But if similar features can point to having a common ancestor--and to not having a common ancestor--how much does "homology" really tell us about the history of life? (EE, pg. 48)

I have been particularly struck by the adjectives that accompany descriptions of evolutionary convergence. Words like "remarkable," "striking," "extraordinary," or even "astonishing" and "uncanny" are common place. It is well appreciated that seldom are the similarities precise, and this in itself is as concrete a piece of evidence for the reality of evolution as can be provided. Even so, the frequency of adjectival surprise associated with descriptions of convergence suggests there is almost a feeling of unease in these similarities. Indeed, I strongly suspect that some of these biologists sense the ghost of teleology looking over their shoulders.⁵²

Cladistics can run into difficulties in its application because not all character states are necessarily homologous. Certain resemblances are convergent--that is, the result of independent evolution. We cannot always detect these convergences immediately, and their presence may contradict other similarities, "true homologies" yet to be recognized. Thus, we are obliged to assume at first that, for each character, similar states are homologous, despite knowing that there may be convergence among them.⁵⁴

The same pattern of diversification and migration seen in marsupials can also be seen in other groups of plants and animals. That consistency between biogeographic and evolutionary patterns provides important evidence about the continuity of the processes driving the evolution and diversification of all life. This continuity is what would be expected of a pattern of common descent, and is not what would be expected with the creationist orchard scheme.

A classic problem in biogeography is to explain why particular terrestrial and freshwater taxa have geographical distributions that are broken up by oceans. Why are southern beeches (Nothofagus spp.) found in Australia, New Zealand, New Guinea and southern South America? Why are there iguanas on the Fiji Islands, whereas all their close relatives are in the New World?⁵⁷

The most biogeographically challenging aspect of platyrrhine evolution concerns the origin of the entire clade. South America was an island continent throughout most of the Tertiary, and most of the orders of mammals found in Paleocene through Miocene deposits are endemic families or orders almost exclusively restricted to that continent. Primates first appear in the Late Oligocene and become common only in the Early Miocene. Rodents also appear first in the Oligocene. Both groups are almost certainly immigrants from some other continent, and paleontologists have debated for much of this century how and where primates reached South America.⁶⁶

The origin of platyrrhine monkeys puzzled paleontologists for decades. ... When and how did the monkeys get to South America? Prior to about 1970, paleontologists invoked the concept of parallel evolution. ... It seemed so unlikely that monkeys from Africa could cross a water barrier like the Atlantic Ocean... Molecular evidence demonstrated that all monkeys shared a common ancestor prior to their separation. ... The "rafting hypothesis" argues that monkeys evolved from prosimians once and only once in Africa, and that it is a primitive monkey (parapithecid), and not a prosimian, that made the water-logged trip to South America. ... Other species colonizing South America must have arrived in similar ways over millions of years.⁶⁷

The case of platyrrhines is more difficult to explain as anthropoid primates have higher metabolic rates and do not have the ability for prolonged periods of topor. A two-week rafting event across the Atlantic must have involved a floating island with an adequate food and water supply.⁷¹

Lizards reaching South America⁷⁸

Large caviomorph rodents reaching South America⁷⁹

Bees arriving in Madagascar⁸⁰

Lemurs arriving in Madagascar⁸¹

The arrival of other mammals in Madagascar, including the Tenrecidae (hedgehoglike insectivorous mammals), aardvarks, the hippopotamus, and the Viverridae (cat-sized carnivorous mammals)⁸²

Dispersal of salamanders across the western end of the Mediterranean⁸³

Dispersal of certain lizards across the western end of the Mediterranean⁸⁴

The origin of certain lizards in Cuba⁸⁵

The appearance of elephant fossils on "many islands," which are said to have arrived by swimming⁸⁶

Dispersal of freshwater frogs across oceanic island chains⁸⁷

Certain frogs reaching Madagascar⁸⁸

The colonization of Anguilla by green iguanas⁸⁹

Appearance of certain South American insects⁹⁰

Dispersals of chameleons across the Indian Ocean⁹¹

Origin of certain insects in Caribbean islands⁹²

The origin of mantellid frogs found on the island of Mayotte in the Comoros archipelago, despite the fact that "[a]mphibians are thought to be unable to disperse over ocean barriers because they do not tolerate the osmotic stress of salt water"⁹³

The spread of flightless insects to the Chatham Islands⁹⁴

The origin of indigenous gekkos in South America⁹⁵

Origin of crocodile distributions⁹⁶

The appearance of sloths in South America⁹⁷

The origin of a group of Australian rodents⁹⁸

The appearance of land mammals of the Mediterranean islands (also suggesting that "Hippos, elephants, and giant deer reached the islands by swimming")⁹⁹

The origin of various land reptiles in Western Samoa¹⁰⁰

The presence of Crotalus rattlesnakes in Baja California¹⁰¹

(a) Scaevola (Angiospermae: Goodeniaceae) three times from Australia to Hawaii; (b) Lepidium mustards (Angiospermae: Brassicaceae) from North America and Africa to Australia; (c) Myosotis forget-me-nots (Angiospermae: Boraginaceae) from Eurasia to New Zealand and from New Zealand to South America; (d) Tarentola geckos from Africa to Cuba; (e) Maschalocephalus (Angiospermae: Rapateaceae) from South America to Africa; (f) monkeys (Platyrrhini) from Africa to South America; (g) melastomes (Angiospermae: Melastomataceae) from South America to Africa; (h) cotton (Angiospermae: Malvaceae: Gossypium) from Africa to South America; (i) chameleons three times from Madagascar to Africa; (j) several frog genera to and from Madagascar; (k) Acridocarpus (Angiospermae: Malpighiaceae) from Madagascar to New Caledonia; (l) Baobab trees (Angiospermae: Bombacaceae: Adansonia) between Africa and Australia; (m) 200 plant species between Tasmania and New Zealand; (n) many plant taxa between Australia and New Zealand; and (o) Nemuaron (Angiospermae: Atherospermataceae) from Australia (or Antarctica) to New Caledonia.¹⁰²

[H]istorical biogeography is the discipline that looks at how groups of organisms have evolved and how their geographic distributions have changed in relation to geological or climatic events. ... In phylogenetic analysis, the arbiter among competing hypotheses suggested by different character systems, i.e. incongruence among characters, is parsimony. The analogous problem in biogeography is what to do when one group suggests one biogeographic pattern, and another group suggests another.¹⁰³

"For a long time the holy grail was to build a tree of life," says Eric Bapteste, an evolutionary biologist at the Pierre and Marie Curie University in Paris, France. A few years ago it looked as though the grail was within reach. But today the project lies in tatters, torn to pieces by an onslaught of negative evidence. Many biologists now argue that the tree concept is obsolete and needs to be discarded. "We have no evidence at all that the tree of life is a reality," says Bapteste. That bombshell has even persuaded some that our fundamental view of biology needs to change.¹⁰⁶

The problems began in the early 1990s when it became possible to sequence actual bacterial and archaeal genes rather than just RNA. Everybody expected these DNA sequences to confirm the RNA tree, and sometimes they did but, crucially, sometimes they did not. RNA, for example, might suggest that species A was more closely related to species B than species C, but a tree made from DNA would suggest the reverse.¹⁰⁷

Syvanen recently compared 2,000 genes that are common to humans, frogs, sea squirts, sea urchins, fruit flies and nematodes. In theory, he should have been able to use the gene sequences to construct an evolutionary tree showing the relationships between the six animals. He failed. The problem was that different genes told contradictory evolutionary stories. This was especially true of sea-squirt genes. Conventionally, sea squirts--also known as tunicates--are lumped together with frogs, humans and other vertebrates in the phylum Chordata, but the genes were sending mixed signals. Some genes did indeed cluster within the chordates, but others indicated that tunicates should be placed with sea urchins, which aren't chordates. "Roughly 50 per cent of its genes have one evolutionary history and 50 per cent another," Syvanen says.¹⁰⁹

Darwin was using this evidence to challenge a theory that was popular in his day, but is almost unheard of now: the fixity of species. (EE, pg. 76)

Campbell, Reece, Mitchell, and Taylor's, Biology: Concepts and Connections (4th ed., 2003): "The Greek philosopher Aristotle, whose views had an enormous impact on Western culture, generally held that species are fixed, or permanent, and do not evolve. Judeo-Christian culture fortified this idea with a literal interpretation of the Book of Genesis, holding that all species were individually designed by a divine creator. The idea that all species are static in form and inhabit an Earth that is at most 6,000 years old dominated the intellectual and cultural climate of the Western world for centuries."¹¹⁶ "Aristotle and the Judeo-Christian culture held that species are fixed. Fossils suggested that life-forms change."¹¹⁷

Campbell and Reece's Biology (6th ed., 2002): "In this view of life, which prevailed for over 2,000 years, species are permanent, are perfect, and do not evolve."¹¹⁸

Campbell and Reece's Biology (7th ed., 2005): "Darwin's view of life contrasted sharply with traditional beliefs ... of life that had been created at the beginning and remained unchanged ever since. Darwin's book challenged a worldview that had been prevalent for centuries."¹¹⁹

Cecie Starr's Biology: Concepts and Applications (2006): "At one time Europeans viewed nature as a great Chain of Being extending from the 'lowest' forms of life to humans, and on to spiritual beings. Each kind of being, or species as it was called, was one separate link in the chain. All of the links had been designed and forged at the same time at one center of creation. They had not changed since. Once all the links were discovered and described, the meaning of life would be revealed."¹²⁰

Kenneth Miller and Joseph Levine's Biology (2008): "Most Europeans in Darwin's day believed that ... [s]ince that original creation, they concluded, neither the planet nor its living species had changed. A robin, for example, has always looked and behaved as robins had in the past."¹²¹

Scott Freeman's Biological Science (2005): "When Darwin published his theory in 1859 ... the leading explanation for the diversity of organisms was a theory called special creation. ... The theory of special creation also maintained that species were immutable, or incapable of change, and thus had been unchanged since the moment of their creation."¹²²

Sylva S. Mader's Essentials of Biology (2007): "Prior to Darwin, lay people had an entirely different way of looking at the world. They believed ... that since the time of creation, species had remained exactly the same. ... A noted zoologist at the time, Georges Cuvier, founded the science of paleontology, ... [Cuvier] believed in the fixity of species..."¹²³

Strickberger's Evolution (4th ed., 2008, by Brian K. Hall and Benedikt Hallgrimsson)

Evolution by Nicholas H. Barton, Derek E. G. Briggs, Jonathan A. Eisen, David B. Goldstein, Nipam H. Patel (Cold Spring Harbor Laboratory, 2007)

Evolutionary Analysis, by Scott Freeman and Jon C. Herron (3rd ed., Pearson/Prentice Hall, 2004)

Evolution: An Introduction by Stephen C. Stearns and Rolf F. Hoekstra (2nd ed., Oxford University Press, 2005)

Even John C. Briggs' treatise Global Biogeography does not list MacArthur and Wilson's book in its references.

Kenneth Miller and Joseph Levine's Biology (2008): "large-scale evolutionary changes that take place over long periods of time." Saying that macroevolution entails the origin of "large-scale" features, this textbook uses some of the very same language in EE.

Sylva S. Mader's Essentials of Biology (2007): "Large-scale evolutionary change, such as the formation of new species." Again, this textbook uses much the same language that EE does.

Campbell and Reece's Biology (5th ed., 1999): "Evolutionary change on a grand scale, encompassing the origin of novel designs..." Again, this fits neatly with EE's definition--a definition that looks at substantive innovations of biological novelty.

Belk & Maier's Biology: Science for Life (2010): "Large-scale evolutionary change, usually referring to the origin of new species." This is another example of a textbook using the same language about "large-scale evolutionary change" that EE does.

Frankly, at one level there may not be much further debate about biogeography. Unless somebody, somewhere, makes an astounding discovery on one side or the other, the issue is likely to remain exactly where it is. (EE, pg. 79)

How much creative power do evolutionary mechanisms possess? That is a key question in the current controversy about Darwinian evolution. Since understanding this mechanism is vitally important to our understanding of the history of life, and since Darwin and modern neo-Darwinists have claimed that natural selection can indeed produce large-scale biological change, the next part of this book will examine the arguments for and against the creative power of this mechanism. (EE, pgs. 79-80)

By making such a sweeping and imbalanced generalization, Explore Evolution misinforms students about the actual evidence at hand. By making the claims without explaining the basis for them, Explore Evolution makes it impossible for students to explore these ideas in any additional depth, once again hindering inquiry, rather than encouraging and supporting true scientific investigation.

First, contrary to the key assertion [of EE], scientists have been aware of natural genetic code mutants since at least the 1960s, and the actual molecular mechanism of some of these mutations (such as "suppressors of amber") was elucidated in both bacteria and yeast (Goodman HM, Abelson J, Landy A, Brenner S, Smith JD. "Amber suppression: a nucleotide change in the anticodon of a tyrosine transfer RNA." Nature. 1968; 217:1019-24; Capecchi MR, Hughes SH, Wahl GM. "Yeast super-suppressors are altered tRNAs capable of translating a nonsense codon in vitro." Cell. 1975; 6:269-77.) Amber suppressor mutations change the read-out of certain codons from STOP to an amino acid by altering the structure of one of the transfer RNAs. This tRNA recognizes the codons in messenger RNAs and allows the addition of the correct amino acid during protein synthesis.

These mutants showed how new variant genetic codes can evolve, and what kind of selective pressures can favor such changes (in this case, the need for reversion of point mutations which introduce deleterious STOP codons in critical genes). (emphasis added)

Therefore, it was recognized fairly early that the genetic code did not need to be absolutely invariant to be fundamentally shared between all organisms ("universal").

Consider what might happen if a mutation changed the genetic code. Such a mutation might, for example, alter the sequence of the serine tRNA molecule of the class that corresponds to UCU, causing them to recognize UUU sequences instead. This would be a lethal mutation in haploid cells containing only one gene directing the production of tRNAser, for serine would not be inserted into many of its normal positions in proteins. Even if there were more than one gene...this type of mutation would still be lethal, since it would cause the simultaneous replacement of many phenylalanine residues by serine in cell proteins.

The standard view of the evolution of the genetic code had been that, once the code became fixed in some primitive lineage of organisms, then any coding change would be precluded because the transitory coding stage that a population must experience to change its code would be lethal. Consider, for example, mutations that change the charging specificity of a tRNA aminoacyl synthetase, such that it charged a glycyl-tRNA with arginine instead. Suddenly glycines are replaced by arginines throughout the genome, which would undoubtedly cause irreparable cellular chaos. This could be thought of as the quintessential case of stabilizing selection: a 'Death Valley' in the adaptive landscape. (2001, R63; reference numbers omitted)

If organisms had arisen independently they could perfectly well have used different codes to connect the 64 trinucleotide codons to the 20 amino acids; but if they arose by common descent any alteration of the code would be lethal, because it would change too many proteins at once. Hence the finding of the same genetic code in microbes, plants and animals...spectacularly confirms a strong evolutionary prediction.

1. Start with the universal code: UGA, UAA, UAG → stop, and Tt-eRF1 recognizes all three stop codons. 2. Tt-eRF1 would then have evolved to be specific to UGA. 3. UAA and UAG would have been removed from the termination sites of any gene where they existed, and become unassigned, i.e., untranslatable nonsense codons. 4. Then the gene for tRNAgln, with the anticodon UmUG, would have duplicated. 5. The duplicate mutated to UmUA, pairing with UAA and UAG so that these now are translated as Gln. (Osawa 1995, 99)

The model outlined by Jukes and Osawa . . . would lead to a potentially awkward intermediate stage where some genes end in [UAA and UAG], but neither [UAA or UAG] recognizing tRNAs nor...release factors exist in the cell. The outcome of this state in eukaryotes is not known, but in eubacteria the cognate tRNA of the penultimate codon remains covalently attached to the carboxyl-terminus of the protein. (Keeling 1997, 208) . . . during the appearance of code deviations, ancient termination codons are acquiring a new sense and new UAA and UAG codons are accumulating in the reading frames. This will generate ambiguity in the length of translation products. (Cohen and Adoutte 1995, 105)

Creationist X wrote about topic Y.

EE discusses topic Y.

Therefore, EE recycles a creationist argument (topic Y), which does not belong in public school science classrooms.

Karl Marx wrote about capitalism.

Milton Friedman discussed capitalism;

Therefore, Milton Friedman had Marxist sympathies.

a creationist attack on science

classic creationist strategy

the critics are creationists...motivated by a religious agenda

a classic creationist falsehood

long-discredited creationist claims

common creationist talking points

a creationist Senator

a bogus creationist model

a long history of creationist misrepresentation

the modern creationist strategy

the usual creationist focus

a dolled up creationist model

a petty creationist caricature

a common creationist trope

some hackneyed creationist claims

a rehash of older creationist arguments

He is also apparently a creationist [this refers to a professor of biology at the University of San Francisco]

creationist canards

simply restatements of long-discredited creationist falsehoods

the erroneous creationist canard

a whole stable of intelligent design creationist writers

a Creationist cause célèbre

a flawed creationist interpretation

a lightly repackaged creationist attack on science

Another creationist canard

a common creationist strategy

a restatement of the creationist doctrine

typical creationist ploy

ID promoters and other creationists

a common creationist assertion

creationist misrepresentations

creationist errors

With the possible exception of behavior, evolutionary biology is treated unlike any other science. Philosophers, sociologists, and ethicists expound on the central role of evolutionary theory in understanding our place in the world. Physicists excited about biocomplexity and computer scientists enamored with genetic algorithms promise a bold new understanding of evolution, and similar claims are made in the emerging field of evolutionary psychology (and its derivatives in political science, economics, and even the humanities). Numerous popularizers of evolution, some with careers focused on defending the teaching of evolution in the public schools, are entirely satisfied that a blind adherence to the Darwinian concept of natural selection is a license for such activities.

If this scientific idea were false, how would we know it?

We tested this theory and the evidence supports it.

Just got my first look at the tome today. I can sum up my feelings in one word:

BWA HA HA HA HA HA AH AH A !!!!!!!!!!!!!!!!!!!!!!!!!

This proposition [of common ancestry] is central because it is presupposed so widely in evolutionary research. When biologists attempt to reconstruct the phylogenetic relationships that link a set of species, they usually assume that the taxa under study are genealogically related. Whether one uses cladistic parsimony, distance measures, or maximum likelihood methods, the typical question is which tree is the best one, not whether there is a tree in the first place.

Despite the large volume of publication, however, the underlying reality remains unchanged: everything we know is circumstantial and indirect, and what actually occurred remains unknown.

Apparently, the coelacanth, lungfish, and tetrapod lineages diverged within such a short time interval that at this level of analysis, their relationships appear to be an irresolvable trichotomy. (2004, 1512)

Thus there are significant variations regarding conclusions derived from molecular biological data sets, and differences between various parts of the morphological and molecular data sets.

The living lungfishes and the coelacanth represent tiny, randomly selected remnants of ancient groups that were numerous, varied, and widely distributed in the Devonian. One can only wonder at how accurate, or even relevant, the relationships that we estimate to exist between these organisms today may be with respect to the actual phylogenetic relationships of their basal groups. (1999, 340)

First, since the analyses [of tetrapod relationships] were all done cladistically, the underlying phylogenetic model in all cases was monophyletic. A single "main line" of tetrapod evolution is assumed to have existed in all cases. Possible polyphyletic scenarios were methodologically and philosophically excluded as implausible.

The notion that species may change through time and that living organisms are related to one another through common descent...species have changed over time and are connected by descent from common ancestors.

Evolution #1: "Change over time" First, evolution can mean that the life forms we see today are different than the life forms that lived in the past. (EE, p. 8)

...we have to make an important distinction between the terms common descent and Universal Common Descent. You may think the terms mean the same thing. They don't. As we've just seen, it's possible to think that some organisms share a common ancestor without thinking that all organisms are descended from a single common ancestor. (EE, p. 10)

The millions of diverse living species we find around us in the modern world are descended from a common ancestor that lived in the remote past. (Ayala and Valentine 1979, 1)

Evolution asserts that the pattern of similarity by which all known organisms may be linked is the natural outcome of some process of genealogy. In other words, all organisms are related. (Eldredge and Cracraft 1980, 2)

It is important to realize at the outset that evolution is not "just a theory." It is, again, a theory and a fact...[N]ew forms of life are continually generated by the splitting of a single lineage into two or more lineages. This is known as "speciation." About five million years ago, a species of primates split into two distinct lineages: one leading to modern chimpanzees and the other to modern humans. And this ancestral primate itself shared a common ancestor with earlier primates, which in turn shared a common ancestor with other mammals. The earlier ancestor of all mammals shared an even earlier ancestor with reptiles, and so on back to the origin of life. Such successive splitting yields the common metaphor of an evolutionary "tree of life," whose root was the first species to arise and whose twigs are the millions of living species. Any two extant species share a common ancestor, which can in principle be found by tracing that pair of twigs back through the branches to the node where they meet. (Coyne 2005, 23; second emphasis added)

...it is generally assumed that, in principle, the TOL [Tree of Life] exists and is resolvable although, in practice, full resolution might never be attained and, furthermore, might not even be particularly important for understanding the actual events that transpired during the respective transitional stages.

Here, I argue for a fundamentally different solution, i.e., that a single, uninterrupted TOL does not exist, although the evolution of large divisions of life for extended time intervals can be adequately described by trees. (2007, 3; reference numbers omitted)

We're just at the tip of the iceberg of what the [genetic] divergence is on this planet... One question is, can we extrapolate back from this data set to describe the most recent common ancestor. I don't necessarily buy that there is a single ancestor. It's counterintuitive to me. I think we may have thousands of recent common ancestors and they are not necessarily so common. (Brockman 2007, p. 42)

Traditional approaches to characterizing prokaryote genome evolution focus on the component of the genome that fits the metaphor of a tree. The issue is how large that component is over the fullness of evolutionary time. Although there can be little doubt that a considerable component of prokaryote genome evolution over recent evolutionary time scales is fundamentally treelike in nature, differences in gene content exceeding 30% among individual strains of E. coli demonstrate that LGT [lateral gene transfer] has substantial impact on genome evolution even at the species level. Our findings indicate that, over long evolutionary time scales, the cumulative role of LGT leaves almost no gene family among prokaryotes untouched....When all genes and genomes are considered, the tree paradigm fits only a small minority of the genome at best; hence, more realistic computational models for the microbial evolutionary process are needed. (Dagan et al. 2008, p. 10043; note numbers omitted)

The fact that evolution was accepted while selection remained under suspicion shows that we must evaluate developments in the scientific community at different levels....There was no simple conversion to a monolithic theory brought about by the weight of evidence.

Although the biologists accepted evolution and common descent almost unanimously, most of them had reservations with respect to natural selection....None of the opposition to Darwin was as serious as that coming from his own profession. In the 80 years after 1859, the non-Darwinian biologists were decidedly in the majority. (1982, 120)

In reality, anyone who denies the logical link between genetic changes within a population ("microevolution") and speciation ("macroevolution") is similar to someone who watches the sun come up in the east and move west across the sky, but denies that it will set in the west. The only difference between genetic changes within a population and generation of a new species from that population is time. Given enough time, the sun will set in the west.

Here is a question of utmost importance for our understanding of what has been called the 'big picture' of evolution (Simpson 1944, 1953): are the divergences that lead ultimately to higher-level groups, such as those that would typically be labeled as orders, classes, and phyla, qualitatively or quantitatively different from those that lead to low-level sister groups, such as races, species and genera? (2008, 30)

contrary to classic evolution theory, the processes that drive the small changes observed as species diverge cannot be taken as models for evolution of the body plans of animals. These are as apples and oranges, so to speak, and that is why it is necessary to apply new principles that derive from the structure/function relations of gene regulatory networks to approach the mechanisms of body plan evolution. (2006, 195)

A persistent debate in evolutionary biology is one over the continuity of microevolution and macroevolution--whether macroevolutionary trends are governed by the principles of microevolution....The continuity of selective processes over microevolutionary and macroevolutionary time continues to be a source of disagreement in evolutionary biology (Solé et al. 1999; Erwin, 2000; Carroll, 2001; Plotnick & Sepkoski, 2001), one that Maynard Smith (1989) described as 'unsatisfactory.' In dispute is whether the effects of selection operating over microevolutionary time, or at the population level, account for observed trends over macroevolutionary time.

Macroevolution is evolution "above the species level," that is, evolution that supersedes that of interbreeding populations, the domain of microevolution. Just the fact of a break in the interbreeding continuity of genetic lineages at speciation demonstrates a level of phenomena of evolutionary interplay that is not microevolutionary. And this level clearly has its own patterns and processes. If we proceed from the data base, rather than from an assumption of extrapolationism, we might get a crack at understanding what these processes are.

Even on his own terms, Levinton has missed the process of macroevolution as he defines it. In supporting the conventional extrapolationist view of evolution, he excludes a lot of problems that simply have no counterpart in the orthodox literature of the Modern Synthesis. How do major evolutionary changes get started? Does anyone still believe that populations sit around for tens of thousands of years, waiting for favorable mutations to occur (and just how does that happen, by the way?), then anxiously guard them until enough accumulate for selection to push the population toward new and useful change? There you have the mathematical arguments of neodarwinism that Waddington and others rightly characterized as "vacuous." The attention is on the gauges, not on the machinery. For example, the soles of the human feet and the ventral callosities of the ostrich begin to thicken before birth; how did the response first engendered by post-natal wear become anticipatory, captured by the genome? What is the interplay between morphogenesis and genetics, and how does an organisms phenotypic behavior translate through developmental change into the hereditary program? If feathers did not evolve "for" flight, of what use is a neodarwinian explanation that demonstrates that they could evolve gradually from scales? What does that explain?

I would like to see a new evolutionary synthesis that approaches questions of how morphogenesis constructs new features, and how it does it so well, so often, and so quickly. (1989, 77)

Scientists who support a polyphyletic view differ on how many trees one should expect to find in the "orchard" of life. Some, such as microbiologist Carl Woese of the University of Illinois, argue that life on earth is descended "not from one, but from three distinctly different cell types" ("On the evolution of cells," Proceedings of the National Academy of Sciences 99 (2002):8742- 77; 8746). Others, including Malcolm Gordon of UCLA and Christian Schwabe of the Medical University of South Carolina, think there might be a greater number of separate trees.

Against this background of high variability between relaxins from purportedly closely related species, the relaxins of pig and whale are all but identical. The molecules derived from rats, guinea pigs, man and pigs are as distant from each other (approximately 55%) as all are from the elasmobranch's [shark's] relaxin. ... Insulin, however, brings man and pig phylogenetically closer together than chimpanzee and man. (Schwabe 1994, 171-2)

Why didn't you mention in your Schwabe post that his claim of pig relaxin in Ciona is probably due to contamination? It's dishonest not to. Particularly when you lecture your readers on the importance of data, you can't let something like this go unmentioned. A vague reference to Hafner & Korthof just doesn't cut it.