Monday, December 28, 2009

The Cambrian Explosion Finally Explained: Got Calcium?

More than half a billion years ago most of the major animal groups appeared abruptly in what is known as the Cambrian Explosion. It initiated virtually all the major designs of multicellular life with barely a trace of evolutionary history. In a geological moment, the fossil species went from small worm-like creatures and the like to a tremendous diversity of complex life forms.

Evolutionists have had little success explaining this onetime event. Thomas H. Huxley likened it to a barrel that is filled rapidly with apples. Then it takes longer to fill the remaining spaces with pebbles, sand and finally water. Today’s explanations are more technical-sounding but no less reliant on speculation as opposed to direct description. Steven Stanley compared it to the introduction of bacteria croppers which prey on dominant species which previously had suppressed diversity. J. J. Sepkoski compared it to rapid growth of bacterial populations in a virgin petry dish. Were the Precambrian oceans a virgin ecosystem with the raw materials of oxygen and food supplied by ancient bacteria? Steve Jones wondered if the Cambrian explosion reflects some crucial change in DNA—life’s genetic material. "Might a great burst of genetic creativity," asks Jones, "have driven a Cambrian Genesis and given birth to the modern world?"

Now, thanks to new research, we have yet another explanation: calcium. Evolutionists are now saying that a rise in ocean calcium levels may have triggered the assembly of unicellular organisms into multicellular organisms and the rest, as evolutionists say, is history. As one report explained:

the question of what was the trigger for the single cell microorganisms to assemble and organize into multicellular organisms has remained unanswered until now.

What is astonishing is that there is anyone left out there who questions evolution. Can't they see that these guys are doing the heavy lifting? This is just rock solid investigative research, the kind we've come to expect from evolutionists.

Sunday, December 27, 2009

Richard Lenski on the Fact of Evolution: A Teaching Moment

Evolutionist Richard Lenski explains that evolution is both a fact and a theory. Lenski's reasoning is typical of evolutionary thinking and therefore useful in understanding this genre of thought. Lenski begins by defining evolution as biological change over time. Since such change is not controversial, it follows that evolution is a fact:

It is an incontrovertible fact that organisms have changed, or evolved, during the history of life on Earth.

Readers who first encounter such passages in the evolution literature may be surprised. Is this not a radical broadening of the very definition of evolution? How can mere change over time, which even the Genesis account calls for, be counted as evolution? This may seem to be a concession. Have evolutionists dropped the claim that strictly naturalistic explanations are sufficient to account for the origin of species?

No, evolutionists have made no such concession. It is typical to find in the evolution genre apparent logical disconnects such as this. In his article, Lenski explains evolution as the usual unguided biological variation coupled with natural selection (along with dozens of other occasional mechanisms, as needed).

So how should the reader understand and interpret the apparent disconnect. How can Lenski define evolution as mere change over time, but then swap back to the traditional understanding of evolution as strict naturalism? Is this an equivocation—a cheap ploy to prove evolution while bypassing its massive scientific problems?

No, this is not an equivocation. To understand the evolution genre one must understand the history of thought behind it. Even evolutionists are often not completely aware of this history, but the equating of evolution with mere change over time is shorthand for a centuries old metaphysical claim that underwrites evolution. The claim is that if God created the species they would be fixed. Indeed, divine creation would produce a static, unchanging world.

This thinking is often associated with the great eighteenth century Swedish botanist Carl Von Linne, or Linnaeus. At one time he advocated the fixity of species concept and later was troubled when he discovered hybrids—species that are produced by the crossing of two related species.

Linnaeus softened his doctrine of fixity of species, but this was inconsequential. His system with its conception of species became deeply rooted, and the nineteenth century began with the notion of species as immutable still strongly in place. This notion was increasingly being challenged but it was nonetheless a major obstacle for Darwin to overcome.

It was therefore highly significant when Darwin became persuaded that related populations of birds he saw at the Galapagos were actually different species. If there was the slightest foundation for this idea, Darwin had anticipated in a famous notebook entry, it "would undermine the stability of species."

Today's readers often fail to understand the significance. After all, what can be so important about some different birds on some islands? Certainly the birds did not suddenly reveal to Darwin how fishes could change to amphibians, or how amphibians could change to reptiles, or how reptiles could change to mammals. Rather, the revelation was that the idea of divine creation was suddenly becoming untenable. The crucible for Darwin was not an abundance of positive evidence for evolution but rather negative evidence against creation.

Evolutionist Ernst Mayr has pointed out that Darwin's conversion from creationist to materialist was due to three key scientific findings and later reinforced by several additional findings. These scientific findings were all findings against creation. In other words, the key evidence that swayed Darwin was not direct evidence for evolution but rather evidence against creation that indirectly argued for evolution.

And as Mayr further points out, the doctrine of fixity of species was a key barrier to overcome in order if the concept of evolution was to flourish:

Darwin called his great work On the Origin of Species, for he was fully conscious of the fact that the change from one species into another was the most fundamental problem of evolution. The fixed, essentialistic species was the fortress to be stormed and destroyed; once this had been accomplished, evolutionary thinking rushed through the breach like a flood through a break in a dike.

The pre-Darwinian metaphysic was that species were fixed and essentialistic. Evidence for small-scale change argued against the old view and in so doing became an important proof text for evolution.

This is the story between the lines when evolutionists casually associate their theory with change over time. It is shorthand for a long-held tradition in the history of thought. If there is change, then divine creation is false, and if creation is false then evolution, in one form or another, is true.

Metaphysical claims such as these mandate evolution. They underwrite the fact of evolution. The rest is just research problems on how evolution occurred—the theory of evolution. As Lenski explains, evolution is both fact and theory. Religion drives science, and it matters.

The Amazing Mantis Shrimp

You have probably heard of polaroid sunglasses which reduce glare. You may also know that if you rotate the glasses (or your head while you're wearing the glasses) the glare becomes stronger. This is because the sunglasses reduce glare in only one dimension. Light waves can have any orientation. Like waves in a pond, light waves can move upward and downward as the light travels forward. But unlike waves in a pond, light waves can also move from left to right and back, as the light travels forward. These two orientations are referred to as vertically and horizontally polarized light, respectively. But light is not restricted to one or the other--in general a light wave consists of both a vertical and a horizontal component. Purely vertical and horizontal light waves are special cases. And if you combine the vertical and horizontal components you obtain a wave that rotates as it travels forward. For example, the wave can rotate in a circle. But again, this is special case. In general, a light wave maps out an ellipse as it travels forward.

If all of this is confusing, don't worry. All you need to understand is the general idea that light waves can be polarized in different, complicated ways. These concepts are important to engineers and physicists who, for example, work in communications. Television and radio station transmitters and antennae, cell phones and transmitters, and the many other conveniences we enjoy are all carefully designed incorporating these concepts. For instance, CD and DVD players need to convert the vertically or horizontally polarized light to circular polarization.

But once again, after we understand and develop a new technology we find it was present all along in nature. In this case, mantis shrimps not only control the polarization of light waves, but they do it better than our best devices. The CD and DVD players, for instance, use a quarter-wave retarder that converts the polarization but only at a single color of light. The mantis shrimp makes the conversion across a broad spectrum of colors. Here is the abstract of a recent paper on the exploits of the mantis shrimp:

Animals make use of a wealth of optical physics to control and manipulate light, for example, in creating reflective animal colouration and polarized light signals. Their precise optics often surpass equivalent man-made optical devices in both sophistication and efficiency. Here, we report a biophysical mechanism that creates a natural full-visible-range achromatic quarter-wave retarder in the eye of a stomatopod crustacean. Analogous, man-made retardation devices are important optical components, used in both scientific research and commercial applications for controlling polarized light. Typical synthetic retarders are not achromatic, and more elaborate designs, such as, multilayer subwavelength gratings or bicrystalline constructions, only achieve partial wavelength independence. In this work, we use both experimental measurements and theoretical modelling of the photoreceptor structure to illustrate how a novel interplay of intrinsic and form birefringence results in a natural achromatic optic that significantly outperforms current man-made optical devices.

You can go here for a good description of the amazing mantis shrimp (optics is not its only speciality) and its most advanced vision system.

And what does evolution have to say about this? Only that it all evolved, somehow. Some mutations happened to occur, fantastic new designs emerged, and they stuck.

As silly as that sounds, it gets worse. As we have discussed before, the amazing optics hardware is only one of the essential components of the design. Without the processing logic and hardware, and behavior algorithms that use the processed signals, the upfront optics hardware, as fantastic as it is, is as useless as a jet engine is without the jet.

Saturday, December 26, 2009

To Die is Gain

Can death ever be a good thing from an evolutionary perspective? Even though natural selection is all about survival and reproduction, the death of individual cells within a multicellular organism can be beneficial. For example, as the organism grows or when in stressful environments, some cells are no longer needed. Without the ability to kill off such cells organisms suffer. Indeed, such an inability leads to cancer. And so it is not surprising that plants and animals regularly kill off unneeded cells. In fact, their cells have an elaborate and sophisticated programmed cell death (PCD) apparatus. When the signal is given an amazing process of dis assembly begins where the cell's molecular structures are chopped up in an orderly manner. Like the engineers who know just where to dynamite a bridge, the PCD apparatus destroys the cell with remarkable efficiency.

PCD is yet another example of biology's elaborate and sophisticated designs that evolution struggles to explain. But new research has added yet more trouble for evolution. It turns out that PCD in plants and in animals have some similarities that further indicate, from an evolutionary perspective, that PCD was present in the common ancestor of plants and animals.

But the common ancestor of plants and animals was not a multicellular organism--it was a unicellular organism. Why would evolution design a cell that can kill itself?

It is yet another example of an evolutionary expectation gone wrong. And, in turn, evolutionists will react with another silly just-so story. Perhaps it will go something like this:

Competition for resources was fierce even in the early phases of evolutionary history. Before cells aggregated to form multicellular life, they existed in tightly knit communities, which provided various benefits including easier defense against predators, reduced susceptibility to environmental threats, and the facilitation of resource sharing as an insurance against the spatial or temporal resource famines that cells going it alone might face.

The cost of such cellular communities was that particular cells may need to be sacrificed occasionally for the good of overall community. For instance, perimeter cells facing environmental threats would have an increased chance of death and so their resource consumption would be inefficient. Better for them to cease consumption and conserve resources needed by the remainder of the community. Also, cells in the crowded interior of the community may occasionally face resource deficits and, again, cell death would improve the fitness of the remainder of the community.

These scenarios parallel the altruism that has been observed in insect communities, and there is no reason such evolutionary dynamics were not present in the unicellular world. This is an instance where evolutionary theory sheds light on itself, as what we learn about the evolution of observable extant species may apply to the evolution of unobservable, deep-time, species.

Of course the evolution of unicellular PCD relied on environmental signals to initiate the PCD. Such signals could not be too predominant or community wide, for they would have the potential to kill off the entire community. Nor could the PCD signaling be too rare. Most importantly, of course, the selected PCD signals would need to correlate with threats and stresses that could be countered with PCD. Resource concentration reduction is an obvious candidate PCD signal, but our research investigates several other, more subtle and more discriminating, environmental signals which could have led to the evolution of PCD in early life.

See how easy bad science is? One could get used to it.

Friday, December 25, 2009

The Problem(s) With Penguins

Penguins have always been a problem for evolution. Their flippers, for instance, are supposed to be the vestiges of wings. "Say again ...?" you say? That's right, according to evolution penguins are supposed to have evolved from an earlier bird with wings. The bird morphed into a penguin and the wings morphed into the penguin's flippers. Anyone who has seen a penguin swim knows its flippers are not just a happenstance design. The penguin is an incredible swimmer and the last thing that comes to mind is that its flippers somehow evolved from a wing. Of course for evolutionists this transition is a fact, even though they don't know how it happened.

Now penguins have been discovered to defy the much touted molecular clock. The molecular clock is simply a measure of the time that two species diverged from their common ancestor, as determined by their genetic differences. In other words, like the ticking of a clock, the steady stream of mutations, which help drive evolutionary change, accumulate and can be measured. Sometimes evolutionists have an idea of the supposed time since divergence from the fossil record. They use such cases to compute the rate at which the mutations accumulate, and once they know the rate they can use it in cases in which only the genetic data are available.

Evolutionists have been using this concept of the molecular clock for almost fifty years. But the clock is consistently wrong and the concept is becoming increasingly suspect. As with the steady ticking of a clock, problems with the molecular clock concept have slowly but surely continued to mount. Indeed, molecular clock predictions have been falsified many times over. Here's one example of many.

Early on it was found that the molecular clock varies dramatically depending on context. It would be like the clock in the kitchen running twice as fast as the clock in the living room. For instance, if evolution is true then we must believe that this molecular clock varies dramatically for different types of proteins. The histone IV protein, for example, shows only a few changes

Evolutionists concluded that histone IV must have a highly constrained design. Histone IV is involved in DNA packing, and surely that role is too important to monkey with. As evolutionist Thomas Jukes wrote:

... the histones are a class of proteins that are bound to DNA in cells that possess a nucleus. They take part in the formation of nucleosomes. Any change in histones could therefore have a destructive effect on the integrity of the cell.

Jukes had no empirical evidence for this claim. It was based solely on the assumption that evolution is true. It is one example of many of how evolution corrupts science. In this case, laboratory research showed that cells sustain histone IV changes with fewer problems than expected. And the other histones sustain changes even more readily.

It was yet another example of evolution interfering with scientific progress in general, and of a molecular clock failure in particular. Now we are learning of dramatic failures of the molecular clock in penguins. These data are interesting because they are from penguin remains as old as 44,000 years. These remains allow for empirical comparison of old and current genomes (mitochondrial in this case), and the differences are several times off the molecular clock prediction.

Religion drives science and it matters.

Thursday, December 24, 2009

Is Design Theory Scientific? A Case Study

Evolutionists often say design theory does not qualify as legitimate science because it is not strictly naturalistic. Science, they say, must rigidly adhere to methodological naturalism, and restrict all explanations and causes to natural processes. This naturalism mandate renders evolutionists vulnerable to charges of (i) atheism and (ii) stacking the deck. Is not the naturalism-only mandate an obvious sign of atheists at work and, furthermore, is it not simply a ploy to define competing theories as unacceptable to begin with? Actually, no. Certainly some evolutionists are atheists, and perhaps some evolutionists stack the deck when they argue, but neither of these are entailed in arguments for evolution--the problems with the naturalism-only mandate are far more severe.

To understand the problems with the naturalism-only mandate, one must understand just what is being mandated. Some evolutionists appear to make the bare assertion that only rigidly naturalistic explanations can qualify as genuine science. As wiith most bare assertions this one doesn't work very well. For instance, it is easily countered by the bare assertion that rigidly naturalistic explanations are not required for genuine science (so there!). Some design critics, such as Taner Edis, warn evolutionists against making such an assertion for it does not allow for design theory to be rejected by according to the evidence.

But more thoughtful evolutionists, such as Joe Felsenstein, provide an underlying reason for the mandate. Felsenstein explains:

what he has just done is to admit that the hypothesis of a Designer is not science, as it predicts every possible result. If you predict every possible outcome, the ones that are seen and the ones that are not, then you have not predicted anything! ...

If there are none, then the Design he speaks of is an infinitely flexible hypothesis that predicts nothing, and thus is really not a scientific hypothesis at all … which is what I originally said.

In other words, in order to qualify as legitimate science a theory must distinguish between different outcomes. Naturalism is needed because otherwise each outcome is equally probable and the theory is not true science.

Deciding what does and does not qualify as legitimate science is notoriously difficult. There seem to be exceptions to every rule. But perhaps Felsenstein's criterion is reasonable. Shouldn't a scientific theory say at least something about the probabilities of what we might observe in the data?

Evolutionists say this test shows their theory to be the perfect model of true science. Consider, for example, the recurrent laryngeal nerve. As evolutionist Jerry Coyne explains:

The reason why the recurrent laryngeal nerve, for example, makes a big detour around the aorta before attaching to the larynx is perfectly understandable by evolution (the nerve and artery used to line up, but the artery evolved backwards, constraining the nerve to move with it)

In other words, historical contingencies and constraints play an important role in evolutionary explanations. Today's designs are not independent of their history. When we see obvious similarities between species evolutionists make the historical connections.

But special creation and design theory have no such basis from which to draw. Designs are independent. God could have created the species in any fashion, so there is no way to distinguish outcomes. Are not all designs equiprobable? As Coyne explains, the recurrent laryngeal nerve

makes no sense under the idea of special creation ... No form of creationism/intelligent design can explain these imperfections

Evolutionists use such examples to argue that their theory is scientific whereas creation and design are not. Now let's look at the facts.

These claims of evolutionists are false and hypocritical. Evolution does not distinguish different outcomes for the recurrent laryngeal nerve. When incredibly fantastic, mind boggling designs are found, they ascribe the wonder to natural selection. When similarities between species are found, they ascribe them to historical contingencies.

And evolutionists have a seemingly never ending list of mechanisms they use to explain everything in between. Whatever we find in biology, evolutionists say it must have evolved. Their predictions and expectations are often falsified and they have to patch their theory repeatedly. And there is no distinction between a new, fantastic design and a repeated design--both are equiprobable under evolution.

If a new, fantastic design appears such as the trilobite eye, then evolutionists ascribe it to natural selection. If similar designs are found in different species, then it is ascribed to common descent. If later cousin species are found to lack the design, then common descent can be dropped as an explanation and the design can be said to have evolved independently. The evolutionary explanation is extremely flexible.

If distinguishing between outcomes is the hallmark of true science, then evolution is the theory that doesn't qualify.

As for design theory, while it does not rule out historical contingency as a possible explanation it, in any case, looks for a rationale for what we find in nature. The more probable outcomes are functional designs that require planning, foresight, mechanisms, and so forth. Design theory tries to figure out how nature works rather than viewing it as a fluke and accident of history. And the history of science is squarely on its side. Over and over evolutionary expectations that nature is a fluke are overruled by the evidence. Over and over we find function and fantastic designs which make no sense under evolution.

How do you want to do science? Do you want to constrain every explanation to an improbable theory, or do you want to figure out how nature works without a priori theoretical constraint?

Saturday, December 19, 2009

Jerry Coyne's Why Evolution is True, Part I

Some books are difficult to read because they are not well written while others are difficult to read because the ideas don't make sense. There is turgid prose and then there is turgid logic. I have finally finished Jerry Coyne's Why Evolution is True which, if Coyne was not a leading evolutionist of international repute, I would have dismissed after the first chapter. Coyne is an excellent writer but Why Evolution is True is a laborious read because it doesn't make much sense. Thumbing through my copy, I see page after page with margin notes indicating various fallacies and inconsistencies. More later on this, but for now here are some aggregate statistics.

By my count Coyne affirms the consequent 21 times throughout Why Evolution is True. He begs the question 33 times and makes 35 theological claims. Coyne fails to mention important scientific problems that bear on his points 31 times.

I finally tired of counting but the volume is a veritable treasure trove of evolutionary thought. There are the usual just-so stories, unfalsifiable claims, presumptuous statements, ad hominem criticisms and so forth. In the evolution genre you can hope for quality writing but it seems there is no escaping problems with the content of that writing.

Tuesday, December 8, 2009

A De Novo Gene: Unlikely and Very Unlikely

If you scramble about 90% of a protein sequence—randomly replacing amino acids with different ones—would the protein still work? That is what evolutionists are implying in order to make sense of their theory. The problem is that evolution’s explanations for de novo genes are unlikely and very unlikely. In the case of the T-urf13 de novo gene, the two choices seem to be (i) a one in ten million shot that protein coding sequences just happened to be lying around waiting for use or (ii) only about 10% of the T-urf13 sequence really matters and you can scramble the rest with no effect.


An obvious problem with evolution is that it calls for vast banks of biological programs to arise on their own. One example of this is the protein coding genes within DNA. Evolutionists usually say that these resulted from the reuse of existing protein coding genes. For instance, we are able to see in color because the photocells in our retina contain different proteins that are sensitive to different colors of light.

And how did the genes for these different proteins arise? Easy, take one such gene, duplicate it and throw in a few mutations to modify the color sensitivity. Of course there are massive problems with this narrative which evolutionists fail to recognize, but that’s another story.

Also, there is the question of from where did the first such gene come? If new genes come from pre existing genes, then from where did the first gene come? Ever since David Hume, evolutionists have argued against an infinite regress of causation so they have to have a starting point. But they have no explanation for such massive complexity beyond vague speculation which amounts to “See, poof, it happened.”

In an effort to bridge this enormous gap, evolutionists have constructed a new narrative based on de novo genes. These are genes that were not predicted but now, amazingly, evolutionists are using them as proof that evolution can indeed create new protein coding genes.

That is the argument evolutionists use for the de novo gene T-urf13 which was found in the mitochondrial genome of certain varieties of corn. The problem is that T-urf13 provides no such evidence. Indeed, if anything, it is yet another de novo gene that contradicts evolutionary theory. Let’s have a look.

Two choices: Unlikely and very unlikely

The T-urf13 gene sequence appears to come from two separate sequences already residing in the mitochondrial genome. The two sequences are in, and flanking, an RNA gene. In other words, it appears that two sequences came together, along with a short unidentified segment, to form this new gene.

But the story is more complicated than the mere reuse of pre existing coding sequences. Under the theory of evolution, the RNA and flanking sequences are not designed to have a role in coding for proteins. Evolution does not have the foresight, for instance, to imbed secondary functions for future use in the DNA information.

Evolutionists therefore cannot say the T-urf13 gene arose from the duplication of an existing protein gene. They could say that T-urf13 is a lucky strike—that the RNA and flanking sequences just happened to have protein coding properties even though they were not designed or used as such. As explained elsewhere this is unlikely (probably far worse than a one in ten million shot).

Or evolutionists can agree that, yes, the RNA and flanking sequences were not originally protein-coding like segments, but mutations evolved them into a protein coding sequence. The problem here is that we don’t find very many mutations at work. This is a difficult argument for evolutionists to make because there is so little sequence information added to the sequence. What we find is a couple dozen point mutations out of about 340 nucleotides (about 93% of the nucleotides are conserved), along with several insertions and deletions.

This second option is probably worse than the first option. For evolutionists would have to say that a sequence that has no protein-coding properties—that was not designed or selected for such information and therefore is no better than a random sequence insofar as protein-coding is concerned—can be converted into a protein-coding gene by swapping only a relatively few nucleotides. The resulting protein would have only a few percent of the amino acids modified, along with some insertions and deletions.

One way to test this evolutionary hypothesis would be to introduce mutations at those T-urf13 nucleotide sites that share identity with the original RNA and flanking sequences. In other words, scramble the majority of the T-urf13 gene. While we cannot know for sure, certainly our current knowledge suggests the resulting gene would be junk. You cannot scramble ninety percent of a gene and reasonably expect a folding, functioning, fitness-adding protein.

And if the mutated gene is junk, then we would conclude that T-urf13 owes its protein-coding abilities, probably in large part, to those original RNA and flanking sequences and that the evolutionary hypothesis makes little sense.


Evolution is not well supported by the scientific evidence. Yet evolutionists continue to reinterpret the evidence in creative ways to prop up the theory. In the case of the T-urf13 gene evolutionists have claimed that, in spite of the science, the gene is a result of a routine evolutionary capability to produce new genes.

Monday, December 7, 2009

Headline: No Such Thing As 'Junk RNA'

New research has found that very short RNA strands, as small as 15 nucleotides, are not junk as evolutionists had expected but instead perform regulatory roles. As one writer explained:

Tiny strands of RNA previously dismissed as cellular junk are actually very stable molecules that may play significant roles in cellular processes, according to researchers at the University of Pittsburgh School of Medicine and the University of Pittsburgh Cancer Institute.

Many of these so-called usRNA molecules interact with proteins that in turn interact with other RNA molecules that regulate cellular processes.

All of this was a big surprise to evolutionists but since evolution is a fact they know that it blindly arose, one way or another. The only remaining question is how it evolved, but that is less important than knowing that it did evolve. That's what scientific progress is all about.

The Evolutionist's T-urf13 Silence: Day 10

Conservative estimates are that the chances that the de novo gene T-urf13 blindly evolved are one in ten million. For all we know they are probably far worse. But are the estimates valid? Evolutionists have rejected them as flawed. One evolutionist called them "ridiculous" and another called them "unsupported," promising to reveal all at some later time. Many other evolutionists have ridiculed the entire idea as obviously in error while making all manner of ad hominem attacks.

But none have shared their wisdom on exactly why the estimates are so wrong. As usual, evolutionists attack the messenger rather then address the message.

The problem seems to be straightforward. Evolutionists have claimed T-urf13 as evidence that evolution creates new genes with ease. But it seems to be another unlikely just-so story that fills the evolutionary narrative. What are we missing? The silence is deafening.

Joe Felsenstein: Just Look at the Evidence

As a follow-up to his earlier comments that design is not a legitimate scientific hypothesis, evolutionist Joe Felsenstein adds this comment:

Thanks to Cornelius Hunter for quoting my comment at Panda's Thumb in its entirety, without emendation (he did add some emphasis, in color, but not in a way that changed my meaning).

My comment was not responsive to the origin of T-urf13 but was intended as a response to many other comments Hunter has made on this blog (and at Uncommon Descent) in which he argues that one cannot predict what a Designer would do, and thus that arguments that she would not make bad design are invalid.

As should be clear from my statement, I was pointing out that this makes the hypothesis of a Designer not a scientific theory, and thus not a credible alternative to naturalist explanations.

Oh, and it should be clear that naturalism does *not* create an "intellectual necessity" of evolution. There are explanations that might be advanced that are not evolutionary but are natural. It is the evidence, not simply naturalism itself, that is the basis for concluding that life has evolved.

Unfortunately these misrepresentations are typical of evolutionists. Not only are evolution's metaphysical arguments from dysteleology, or bad design, perfectly valid, they can also be quite powerful. Felsenstein's strawman that we say otherwise would be bizarre if it wasn't so common.

Next Felsenstein explains that his message is that he thinks that the hypothesis of a Designer is "not a scientific theory, and thus not a credible alternative to naturalist explanations."

Yes, that is precisely the point. The intellectual necessity is a metaphysical argument for naturalistic explanations. As with all the dozen or more metaphysical mandates for evolution, the argument attacks design or creation using non scientific premises that a design or creation advocate would not recognize.

Felsenstein next writes that "naturalism does *not* create an "intellectual necessity" of evolution." Of course it doesn't and it is a wonder that Felsenstein arrived at such a backward reading. The mandates for naturalism and evolution come from religious and philosophical traditions entailing non scientific premises.

Evolutionists consistently mischaracterize criticism to convert serious problems into so many strawmen to knockdown.

Finally Felsenstein appeals to the evidence. Evolutionists are notorious for their claims that the science proves evolution to be a fact. But such proofs always rely on metaphysics. The number of evolutionists who have explained how the science proves evolution is precisely zero.

And, to forestall the usual response, no one is misunderstanding what "fact" means. Evolutionists say their theory is a fact as much as is gravity or the round shape of the earth. That is an absurd claim which, not surprisingly, has never been justified scientifically.

I have tremendous respect for Felsenstein's smarts as a scientist and the quality of his work. But so often we see world-class scientists appear foolish propping up evolution. Religion drives science and it matters.

Saturday, December 5, 2009

Joe Felsenstein: De Novo Genes Trumped by Metaphysics

Evolutionist Joe Felsenstein sounded a familiar note recently when he appealed to evolution's intellectual necessity in response to scientific criticism. I pointed out here that the blind evolution of the de novo gene T-urf13 is highly unlikely. In typical fashion, the evolutionist completely ignored the scientific issue at hand and skipped straight to the metaphysics. There are about a dozen metaphysical arguments mandating evolution. They fall into the two categories of theology and philosophy and provide the foundation of evolutionary thought going back several centuries. You can see my reconstruction of the evolution of evolutionary thought here. There is much cross fertilization between these traditions which form a sort of tapestry in the history of thought. Of course these arguments are not scientific, but they are extremely powerful. They are why evolutionists confidently know their theory must be true. Therefore empirical evidence is not an epistemological problem, but merely a scientific problem. No observation can harm our knowledge that evolution is a fact. Hence Felsenstein goes straight to the underlying philosophy:

A simple way to state the problem with Cornelius Hunter’s argument is that he is arguing that a Designer could do anything, so a Designer cannot be refuted by any observation. He is happy to have thereby refuted all the people who point out bad design.

But he doesn’t get it that what he has just done is to admit that the hypothesis of a Designer is not science, as it predicts every possible result. If you predict every possible outcome, the ones that are seen and the ones that are not, then you have not predicted anything!

Unless you have some information about the Designer’s intentions, her powers, how frequently she acts, and where, and on which organisms and which phenotypes, you ain’t got nothin’, no scientific hypothesis at all.

In other words, not only is evolution true, it also is necessary for proper science. That's convenient.

This argument that strictly naturalistic explanations are mandated in the historical sciences traces back to the nineteenth century before Darwin though, as with several of evolution's metaphysical planks, it gained momentum from Darwin's theory as much as it fueled Darwin's theory in the first place.

Darwin's main concern was that people accept evolution. Which subhypothesis of evolution one accepts, explained Darwin, "signifies extremely little in comparison with the admission that species have descended from other species, and have not been created immutable: for he who admits this as a great truth has a wide field open to him for further inquiry."

Evolution was needed for scientific research as that was yet another spot where creation failed. As he wrote in Origins:

On the ordinary view of the independent creation of each being, we can only say that so it is;—that it has pleased the Creator to construct all the animals and plants in each great class on a uniform plan; but this is not a scientific explanation.

As Darwin’s friend J. D. Hooker put it, if theories of divine creation are "admitted as truths, why there is an end of the whole matter, and it is no use hoping ever to get any rational explanation of origin or dispersion of species—so I hate them."

Thirty years later evolutionist Joseph Le Conte argued that the origins of new species, though obscure and even inexplicable, must have a natural cause. To doubt this, he warned, is to doubt "the validity of reason, and the rational constitution of organic Nature." For Le Conte divine creation was not rational. Evolution, he triumphantly concluded, "is as certain as the law of gravitation. Nay, it is far more certain."

Needless to say this metaphysical sentiment only grew stronger in the twentieth century. Evolutionists, under the guise of science, continued to issue this non scientific mandate for evolution. As Niles Eldredge wrote more recently:

But the Creator obviously could have fashioned each species in any way imaginable. There is no basis for us to make predictions about what we should find when we study animals and plants if we accept the basic creationist position. … the creator could have fashioned each organ system or physiological process (such as digestion) in whatever fashion the Creator pleased.

Felsenstein's metaphysic is nothing new. It falls into well defined clade in the history of evolutionary thought. Of course there is nothing wrong with metaphysics, per se. But let's not pretend we're doing science.

Wednesday, December 2, 2009

De Novo Genes: Criticism From Nick Matzke

On a day when President Obama once again called for civility and unity I am reminded how difficult this is to achieve in the origins debate. Intellectual discussions with evolutionists are about as likely as intellectual discussions with the Wizard of Oz. Rarely have I been able to cajole an evolutionist into reasoned discussion of the scientific evidence. Instead the evolutionist mischaracterizes science and deploys metaphysical justifications while accusing the skeptic of all manner of misdeeds. This infinite loop was replayed again last week on an evolutionary blog when Nick Matzke criticized recent posts here, here and here on T-urf13. I explained that the de novo gene T-urf13 is unlikely to have blindly evolved. I concluded the chances of that occurring are substantially worse than one in ten million. In return I received several pages of bizarre and irrelevant vitriol which managed to avoid the science at hand.

This is a genre that evolutionists seemed to have honed, and I was quickly reminded of it in Matzke's opening where he labelled me as a "young-earth creationist." Not only am I not a young-earth creationist, I have never even written about the topic. But accuracy and truth are not prominent in this genre.

For evolutionists the "young-earth creationist" label carries immense rhetorical value which outweighs any loss of credibility that may result. After all, the evolutionist can always respond to correction with taunts of secrecy, denial, and so forth. Indeed, I am routinely labelled as a "closet young-earth creationist."

And if I am hiding a secret religious belief then, of course, whatever I have to say in response to such charges is nothing more than a tired cover-up to which no one should pay heed. The verdict has been rendered: The evolution skeptic is an unscientific, religious zealot and therefore evolution remains a scientific fact. As Matzke pronounces:

as with many creationists, Hunter thinks his ridiculous little trope is actually a silver bullet that can be used to effortlessly kill any evolutionary evidence, thus saving his tender innocent brain the trauma of actually having to come up with a better explanation than the evolutionary one.

So much for truth and accuracy. And of course the fact of evolution stands firm:

Well, how does Hunter react to this empirical evidence on the origin of a new gene? He simply ignores the overwhelming sequence evidence right in front of him, and instead claims, based on typical creationist “it must have come together all at once from completely random sequence” assumptions, that the natural origin of T-urf13 is too improbable to be believed.

Matzke misrepresents both the science and my points. Far from ignoring the sequence evidence, it is precisely that evidence that is problematic for evolution. Protein coding sequences are extremely unlikely but here we find a significant part of one in a non-coding region.

And Matzke's quote is a silly and fictitious strawman. Of course the de novo gene arose from the pre existing sequences rather than "all at once from completely random sequence." The problem is that evolutionists are now claiming from unclear evidence that evolution is clearly capable of producing de novo genes.

Yes, some sequences came together to form a new gene. But that does not automatically demonstrate evolution any more than would a population responding to an environmental shift. Sure we can imagine how these sequences came together, but the elephant in the room is "how do lengthy protein coding sequences arise in non coding regions?"

Evolution predicts this should not happen and does not explain it. We may find an answer to this question, but for now it is not immediately obvious. At best it appears that evolution will be left with the usual "new proteins arise from the cutting, copying and pasting of pre existing proteins, with a few mutations thrown in here or there." But that hardly makes a de novo gene, such as T-urf13, evidence that evolution creates new proteins.