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.

Background

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.

Summary

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.

Saturday, November 28, 2009

A Non Genetic Protein Translation Mechanism Adds More Complexity to Cellular Adaptation

Biology's sophisticated adaptation machine has now been discovered to be even more sophisticated. In recent years the types of adaptation often claimed to be examples of evolution in action have been found to be driven by complex mechanisms that respond to environmental pressures. It was yet another falsification of evolutionary expectations. Organisms responded far more quickly than neo Darwinism predicted, and this was because the responses were not the result of evolution's blind variation, but rather of directed mechanisms. Gene regulation and even gene modification mechanisms have been discovered which not only implement helpful adaptations, but they implement adaptations that are heritable.

Now we can add another chapter to the adaptation story. New research has found that proteins are modified as they are being constructed to help them fend off a virus, bacteria or toxic chemical. Proteins are constructed by glueing amino acids together in a string. The type of amino acid to use at each position is specified by a gene, as interpreted according to the DNA code.

The new research found that during this construction stage proteins may be modified if the cell is under stress. Specifically, the amino acid methionine is used at certain points in the sequence of amino acids even though it is not called for. Methionine can help provide protective armor due to the sulfur atom it carries in its side chain. It seems that some mechanism is intentionally inserting methionine in spite of what the genetic blueprint for the protein says. As was reported this week:

These "regulated errors" comprise a novel non-genetic mechanism by which cells can rapidly make important proteins more resistant to attack when stressed.

It is yet another finding that not only was not expected by evolution, but is difficult for evolution to explain with anything more than just-so stories.

Friday, November 27, 2009

De Novo Genes: What are the Chances?

We have been discussing the de novo gene T-urf13 found in the mitochondrial genome of certain varieties of corn. Readers have asked about the evolutionary claim that the gene arose via blind evolution, and in particular about the role of mutations. Let's have a look.

First, the time frame over which T-urf13 arose is too short for mutations to play a significant role. The evolutionary explanation is that existing, non proteins coding, DNA sequences in the corn mitochondrial genome provided the raw material for the new protein-coding gene, T-urf13.

Under evolution non protein coding DNA sequences are not supposed to carry a pre-planned protein coding information layer. Such information layers are common. For instance, in a communication system it is possible to transmit multiple messages simultaneously. Several telephone conversations or Internet users could, for example, share a single wire. In other words, there can be multiple messages superimposed on a signal.

And just as multiple messages can be transmitted in a wire, so too there can be multiple messages, or layers of information, in a DNA sequence. Of course evolution expected no such level of cleverness. Hence the surprise when overlapping genes were discovered in DNA. In recent years DNA has been found to contain several layers of information.

Could it be that there is another such layer of information that the cell uses to create new genes? Apparently so, for we now find de novo genes such as T-urf13. But because evolution dogmatically rejects any possibility of design, it does not allow non protein coding DNA sequences to carry a preplanned protein coding information layer.

Instead, such protein coding information must exist only by random chance. And when chance rearrangements occur, and a complete protein sequence just happens to form, then de novo genes can appear. A sophisticated protein such as URF13 may appear to be designed, but such an appearance must be deceptive. Such events must occur by chance, not by design.

And what are the chances of this occurring? The corn mitochondrial genome is about half a million base pairs in length. That is enough room to contain about 2,000 T-urf13 sized genes. This number can be increased by accounting for DNA's six different reading frames, and decreased by accounting for the fact that only part of the corn mitochondrial genome is available. It can also be increased by allowing for some overlap in the hidden genes.

Let's be conservative and say there is room for 100,000 such genes in the corn mitochondrial genome. Nonetheless this is seven orders of magnitude shy of the million million sequences needed for any hope of obtaining a functioning gene, as found in one experiment. And even that estimate was conservative because only the minor function of ATP binding was required.

In contrast, the URF13 protein is a far more complex, cleverly designed machine. It is designed such that several copies fit together to form a protein machine. And that machine fits into the inner mitochondria membrane, a very complex environment. And the machine provides a channel that allows only certain types of chemicals to pass through the membrane. And did I mention the channel is gated, with a molecular switch to open the gate?

The URF13 protein design dwarfs the experimentally screened function of ATP binding. And yet, even in that simple case, and with conservative assumptions, we find the probabilities of the T-urf13 de novo gene arising via blind evolution to be one in ten million (that is, 1 in 10,000,000). The real number undoubtedly has many more zeroes.

This is the story of evolutionary probabilities. Over and over we come up with so many zeros. In design after design, and species after species, evolution repeatedly draws upon unlikely events to create its marvels. Evolutionists now contemplate a multiverse--a super universe containing an untold number of unseen universes toiling away through the ages--in order to beat the odds. Sure these designs would never appear if there was just one universe, but what if there was a near infinity of universes? Surely one of them would get lucky.

Evolutionists do not worry that their story is unlikely. They insist de novo genes must, one way or another, be simply the result of blind processes. This is a good example of the absurdity of evolution. Like a robot that hits a wall but just keeps on trying, evolution cannot adjust to the scientific data. This is because evolution is not, at bottom, a scientific theory. It is driven by the metaphysical mandate that matter and motion must explain everything, regardless of the evidence. This mandate has arisen from a long history of thought in science, philosophy and theology. Religion drives science and it matters.

Thursday, November 26, 2009

Evolution and Medicine: Return of the Witch Doctor

Ever wonder what it would have been like to see a doctor in centuries past? How about the village witch doctor? From blood letting to rituals, it is sickening--no pun intended--to think of how ignorance and religious dogma have led to so much needless suffering. Now evolutionists want to bring their religious dogma into modern medicine. Today's doctor, they say, must be fully indoctrinated in their Darwinian ways. As one new "peer-reviewed" (sic) paper in a government funded journal explains:

Like other basic sciences, evolutionary biology needs to be taught both before and during medical school. Most introductory biology courses are insufficient to establish competency in evolutionary biology. Premedical students need evolution courses, possibly ones that emphasize medically relevant aspects. In medical school, evolutionary biology should be taught as one of the basic medical sciences. This will require a course that reviews basic principles and specific medical applications, followed by an integrated presentation of evolutionary aspects that apply to each disease and organ system. Evolutionary biology is not just another topic vying for inclusion in the curriculum; it is an essential foundation for a biological understanding of health and disease.

If you have ever wondered why history is important, wonder no more. Evolution has led the life sciences down so many false trails it is difficult even to keep track. Evolution is constantly wrong and evolutionists are always surprised by nature. And now they incredibly want to force modern medicine to go back in time and embrace absurd nineteenth century naivete. The last thing we want our doctors to be spending time and effort on is religiously motivated pseudo science.

If you don't understand why the controversy over evolution is important, then consider this: Evolutionists are not, and never were, content to be free to pursue their silly religious ideas. Like so many religious movements, they want you to be subject to their beliefs. They insist evolution is a fact to which every student must accede, every scientist must pay homage, and every medical doctor must be indoctrinated. And they will use your tax dollars to do so. Blood letting anyone?

Wednesday, November 25, 2009

Special Creation False: Your Tax Dollars at Work

Over at the National Science Foundation, where your tax dollars go to promoting Darwin's religious theory, evolutionist Jim Secord asks the question "Where did Charles Darwin become convinced of the truth of evolution?" That's a good way of putting it because Darwin and evolutionists ever since have indeed been convinced that evolution is true. It is, as they like to say, a fact every bit as much as gravity is a fact. That's quite a claim. You would think they might say it is a fact as much as are Alexander the Great's conquests or some other historical record. That would still be a misrepresentation of the scientific evidence, but it would not be as blatant. The comparison with gravity is downright ludicrous, and precisely for this reason it is a tipoff that evolution is not the product of empirical science. Experimental measurements and hypothesis testing do not produce metaphysical certainty.

As Secord explains, Darwin's observations led not to scientific conclusions but religious concerns:

The different varieties of tortoises and mockingbirds provided powerful evidence of the relations between the Galapagos fauna and that of nearby South America. In geographical space, as in geologic time, closely allied species emerged successively and in order, just as they did in the fossil record. These relations, which impressed Darwin throughout the voyage, suggested that species were not specially created.

Let's see now, where's that verse in Genesis about birds on islands being completely different than those on the nearest mainland? Oh well, in any case Darwin argued powerfully that special creation must be false. The evidence for evolution was weak at best, but it had to be true. Religion drives science and it matters.

Tuesday, November 24, 2009

De Novo Genes and Normal Science

Science can be wrong about some things and still make great discoveries and inventions. One can believe the earth is flat or that electrons are nothing more than tiny billiard balls and still make progress. The history of science is a fascinating story of erroneous theories and beliefs intertwined with remarkable progress. And even today’s life science research journals are full of asinine statements, arising from a belief in evolution, mingled with perfectly good scientific research. Most scientists can distinguish between the hard data gathered in the laboratory and the obligatory evolutionary framework into which the data are forced and presented. You focus on the former in order to make progress and tolerate the latter in order to get funded. Such are the practical realities of working in science.

But the origins debate is different. Here the evolution paradigm itself is questioned. That evolutionary framework and filter through which all data and hypotheses must fit is up for debate. Perhaps evolution, or at least core parts of the framework, are not true.

One may scorn at such folly and remain within the paradigm. Or one may argue against such folly. But one may not do both. It makes no sense to interpret the evidence from within the paradigm, and then argue that such interpretations prove the paradigm. In order to defend evolution as true, one must examine the evidence from a theory-neutral perspective.

Here is a simple example: A new horse fossil is discovered and evolutionists decide where it fits best amongst the already known fossils. It may not fit perfectly, and the evolutionists may be unsure about which twig in the evolutionary bush is right for this new fossil (or if perhaps a new twig should be hypothesized). But they believe evolution is true and so the fossil must fit somewhere. They announce to the world that horse evolution is now better understood and apologists then use the finding as an example of powerful evidence for evolution. After all, the evolution of the horse has been revealed.

But of course the fossil revealed no such evolutionary step—it was interpreted as an evolutionary step. Unfortunately this sophistry is common. All the time I see evolutionists making just this sort of argument. Arthur Hunt, for instance, uses de novo genes in just such an argument. Genes that are found in only one or a few allied species are sometimes thought to be newly evolved. Hunt realizes the evolution of such genes might seem “difficult to some” as there are “judicious” events that must have occurred.

Now from within the evolution paradigm, there is the question of whether such genes really are de novo. Could they not have evolved via some other mechanisms, such as lateral gene transfer. Evolutionists investigate such options, and sometimes can find none that work. In these instances they conclude a gene must be newly evolved. Hunt explains these issues and then erroneously argues that since the other evolutionary options have been eliminated for these genes, therefore they must be de novo genes, and therefore de novo genes do not pose a problem for evolution. He writes:

I would encourage readers to read the paper … This is the best way to appreciate that this one pillar of [design] thought, that new protein-coding genes cannot arise by “natural” means, is an illusion.

Design can occur by natural means but that is another story. What is even more problematic than this caricature of design is Hunt’s argument for evolution according to its own assumptions.

The paper, of course, provides no compelling explanation for the blind evolution of de novo genes. As usual the paper presupposes that such blind evolution must have occurred. Therefore the paper’s conclusions must be carefully weighed rather than simply employed as evidence for blind evolution. This logical fallacy is, unfortunately, pervasive in the origins discussion.

Monday, November 23, 2009

De Novo Genes: The Evolutionary Explanation

Cells have remarkable adaptation capabilities. They can precisely adjust which segments of the genome are copied for use in the cell. They can edit and regulate those DNA copies according to their needs. And they can even modify the DNA itself, such as with adaptive mutations, to accommodate environmental pressures. And in addition to these examples, cells can create completely new, de novo, genes in an evolutionary instant. It is yet another biological capability that reveals the scientific weakness of evolutionary theory.

One apparent de novo gene is T-urf13 which was found in certain varieties of corn. T-urf13 is not in the main genome in the cell’s nucleus, but rather in the smaller genome in the mitochondria. The mitochondria is the cell’s power plant which produces adenosine triphosphate (ATP) molecules—the standard unit of chemical energy.

Like a dam that is full of water, mitochondria are filled with protons. And just as water flowing through the dam turns a turbine to produce electricity, protons flowing through a mitochondrial membrane turn a molecular turbine to produce chemical energy in the form of ATP. This molecular turbine, known at ATP synthase, is one of many types of transmembrane proteins—proteins that are imbedded in and span a membrane wall.

The T-urf13 gene produces another transmembrane protein—URF13. Multiple copies of URF13 group together to provide a channel opening in the membrane for water-loving molecules to cross. The URF13 channel is normally closed and opens only when certain molecules bind to the exterior side of the channel. (Yes, this is a complicated design.) The binding molecule serves to alter the URF13 structure so as to open the channel in just the right way. Unfortunately toxins from certain fungal pathogens also bind and open the URF13 channel. This wreaks havoc because it is like poking a hole in a dam.

This problem arose about forty years ago and since then we have learned much about the T-urf13 gene. It is found in only one corn line and appears to have arisen rapidly. A small part of the gene (about 15%) is highly similar to a small part of a different gene in the same mitochondrial genome. That other gene codes not for a protein, but rather for a ribosomal RNA. Most of the remainder of the T-urf13 gene is quite similar to a flanking sequence, just outside of that same ribosomal RNA gene. Finally, there is a small segment of the T-urf13 gene that has no matches elsewhere in the mitochondrial genome.

It appears that T-urf13 is a de novo gene, having been constructed mostly from two segments in or around a ribosomal RNA gene. It is intriguing that segments associated with an RNA gene would combine to form a protein-coding gene. It is another sign of the fascinating re-use and mixing and matching capabilities that seem to be built into the cell’s design.

Evolutionists, who see biology as a big fluke, don’t see it that way. They amazingly conclude that the T-urf13 gene, which produces such an incredibly complex protein, arose by random chance.

Their idea is that spontaneous genomic rearrangements blindly produce new segments of protein-coding DNA on a regular basis. And once in awhile even a blind process finds a marvel like T-urf13. Does this not suggest that the vast genome is a source of de novo genes? Evolution created genomes consisting of billions of nucleotides, and those DNA segments then become sources of future genes, so their thinking goes.

There’s only one problem: the idea makes little scientific sense. Even a random DNA sequence the length of the entire corn genome does not contain a single gene that likely would code for a functioning gene. One study, for instance, found that more than a million million random sequences were needed to find a single functioning protein. In that study, not only was the protein shorter than URF13 (URF13 is 50% longer and the chances likely degrade rapidly with length), but what qualified as “function” was quite modest (mild ATP binding was defined as function which, compared to the URF13 channel, is like a tricycle compared to a jetliner).

We may not be able to compute precisely the probability of evolution’s explanation for de novo genes such as T-urf13, but we do know the chances are not very good. And that is being kind. Religion drives science and it matters.

Saturday, November 21, 2009

De Novo Genes: What We Know and Don’t Know

I once debated an evolutionist who listed a dozen or so major areas of evidence he said proved evolution. The problem was each of the areas of evidence was problematic for evolution. True, one could find within those areas, as he did, supportive evidences. But the story was not so simple. In fact the areas of scientific evidence, when carefully examined from a theory-neutral perspective, reveal all kinds of problems for evolution. Is evolution false? Is it true? The answer is there are no easy answers. There certainly are substantial scientific problems with Darwin’s idea—that much we do know. If evolution is true then there is much we have to learn about science. But the scientific evidence can tell us something else, and with far more certainty. It tells us that we should not turn to evolutionists for a serious evaluation of the scientific evidence.

It is both shocking and disappointing how grossly evolutionists misrepresent science. This becomes painfully obvious when they, as with the evolutionist I debated, claim problematic areas of evidence as powerful proofs. Consider, for example, the findings of de novo genes.

One of the facts of biology that evolutionists claim as powerful supporting evidence is the many similarities in genes between the different species. There are many such similar genes, and they certainly do fall in the list of supporting evidence. But if such genomic similarities are powerful evidence for evolution, then what about the genomic differences?

There are, in fact, substantial genomic differences even between otherwise allied species. And it stands to reason that these evolutionary surprises would fall in the list of contradictory evidence, right?

Wrong. With evolutionists, all evidences support evolution, one way or another. Evolutionist Arthur Hunt, for instance claims that the findings of de novo genes refutes the notion that evolution alone can’t do the job “in no uncertain terms.” The idea that proteins can’t arise from scratch, explains Hunt, “is an illusion.

And just how did evolution perform this feat? According to Hunt and the evolutionists, at some point in evolutionary history a segment of DNA recruited the machinery needed to begin coding for a protein. Fortunately that DNA segment contained the proper message so the resulting peptide was indeed a functioning protein. And of course subsequent mutations may have enhanced or modified the newly minted molecular machine.

There you have it. No details regarding how likely (or should I say unlikely) a non coding segment of DNA just happens to code for a functioning protein. No details on how often this would have to occur in order to evolution to get lucky.

Now don’t get me wrong—I’m not saying this evolutionary interpretation is impossible. I wasn’t there and, frankly, I don’t know enough to calculate the probabilities. (I don’t think any else does either which would explain why evolutionists haven’t provided them).

We do have some relevant experimental data. A functioning protein arising from a random DNA sequence of about 400 base pairs is extremely unlikely. Even shorter sequences need millions upon millions of tries to get anything even slightly functional.

But of course mere function isn’t good enough in the evolutionary world. Becoming fixed in the population requires useful function, or luck, or some combination of the two. And then there is the recruitment of the machinery to make the sequence code for a protein. How many times would that have to occur, and what are the probabilities?

Impossible? Certainly not, but we’re a long way from certainty. Unfortunately, certainty is precisely what Hunt and the evolutionists have. We can argue about what the scientific evidence implies, but it does not give us certainty about questions of origin. We are simply nowhere close to the evolutionist’s claim that their theory is a fact just as much as is gravity.

The claims of evolutionists are both shocking and disappointing. We scientists have the serious responsibility of public trust. Others depend on us for a fair and honest assessment of what the scientific evidence reveals—and what it doesn’t reveal. We do them, and science, an injustice by providing anything less.

Wednesday, November 4, 2009

RNA Repair Better Than New

One of the many examples of incredible complexity in biology is the DNA repair system. It is also an example of incredible complexity that appeared incredibly early in the history of life. If complexity evolves from simplicity, then it does so at an astonishing pace. As amazing as this story is, it is only the beginning. We now know that DNA's transcript--its sister molecule RNA--has its own repair system which also must have arisen early.

Not surprisingly the RNA repair system is immensely complex. But an interesting twist is that after the RNA molecule has been repaired it is sealed with a methyl group, making it stronger than it was in the first place.

It is just the sort of thing we would never expect with evolution. A complex and esoteric design appearing very early in the history of life. With evolution we must imagine that such an intricate and precise sealing capability just happened to arise for no reason in some of the earliest cells. The blind dart thrower just happened to hit the bull's eye.

And of course if that's true, then the walls must be covered with all the darts that didn't hit the mark--the only way a blind dart thrower could luckily hit the mark is with a great many tries. Evolution must have produced bizarre and useless designs at an unheard of pace.

It is an aspect of evolution that evolutionists don't often discuss: if precise designs arose by chance, then how many tries were required? Such awkward questions are often covered over with Lamarckian language. It is said that environmental pressures brought about the designs. This may sound good, but there is one problem. With evolution environmental pressures do no such thing. The jaw-dropping designs must arise for no reason. It's amazing how well evolution works.

Tuesday, November 3, 2009

Transposable Elements in the Rice Genome: New Data for an Old Theory

Evolution has many false predictions to its credit, but for every false prediction there is an adjustment. Evolution's expectations are constantly being upended, but each time the unabashed evolutionists simply add another patch to their theory. They never stop to consider that there could be a problem--after all, evolution is a fact.

Consider, for example, the evolutionary expectation that biological adaptation is, like water eroding rock, a long slow process requiring eons of time. Only by the magic of natural selection acting on blind mutations are species able to adapt to environmental pressures. Only rarely does a mutation serendipitously cause a helpful change, and even then it might not spread through the population. It's amazing that species have survived at all.

But biology reveals that species adapt rapidly, enacting adaptations that help deal with the environmental pressures. In many cases selection has nothing to do with it, and it doesn't require eons of time. You can read more about this false prediction of evolution here.

Research continues to fill in our understanding of this intelligent adaptation capability. For instance, new findings are now revealing more about how rice can rapidly adapt. In this case the smart adaptations were caused by transposable elements which are small segments of DNA that evolutionists thought inconveniently plopped themselves down in the genome whereever they happened to land. The transposable elements would help only rarely when a lucky insertion occurred.

But instead, the research demonstrated a transposable element that not only does not act randomly, but provides rapid resistance to environmental pressures (low water and high salt environments were tested). As the lead researcher explained:

What we discovered was brand new and really stunning.

What is equally stunning is how conservative and resistant to change are evolutionists. Evidence like this makes no difference for religion, not science, drives evolutionary thinking.

Monday, November 2, 2009

Complexity: A Prediction of Evolution

How can evolutionists explain biology's complexities such as the sonar tracking capabilities that outperform our best military equipment? One argument is that we must never doubt evolution, for such doubt is a science stopper. Another argument is that we mustn't think of God as a designer, for that is to anthropomorphize God. Aside from such philosophical and theological arguments, evolutionists also turn this apparent difficulty into a success story. That's right, evolutionists claim complexity as a fulfilled prediction. As Jerry Coyne writes in his book Why Evolution is True, "The deepest (and oldest) layers of rock would contain the fossils of more primitive species, and some fossils should become more complex as the layers of rock become younger." [17]

But this is not a prediction of evolution. Believe me, evolution would not skip a beat if we found primitive life forms on a distant planet that had not changed for billions of years. Evolution makes no prediction that complexity should emerge.

Perhaps what Coyne and the evolutionists mean is that given that complex life exists today, then we should see it emerge from primitive forms. In other words, evolution predicts simple, not complex, beginnings.

But in that case, the prediction has not been a fruitful one. From the trilobite eye to the DNA code, early life does not show signs of simplicity. In fact, evolutionary reconstructions of what the ancient common ancestor to all life would have looked like come up with more complexity than simplicity. As evolutionist Nick Lane recently wrote:

There is no doubt that the common ancestor possessed DNA, RNA and proteins, a universal genetic code, ribosomes (the protein-building factories), ATP and a proton-powered enzyme for making ATP. The detailed mechanisms for reading off DNA and converting genes into proteins were also in place. In short, then, the last common ancestor of all life looks pretty much like a modern cell.

Similarly the cell's proteins, often referred to as the building blocks of life, do not reveal simple beginnings if evolution is true. As one evolutionist admitted last year:

It is commonly believed that complex organisms arose from simple ones. Yet analyses of genomes and of their transcribed genes in various organisms reveal that, as far as protein-coding genes are concerned, the repertoire of a sea anemone—a rather simple, evolutionarily basal animal—is almost as complex as that of a human.

You can read more about the failure of this evolutionary expectation here. Dogma doesn't help science.

Wednesday, October 28, 2009

Shifting the Burden of Proof

Evolutionists say their theory is a fact but they don't know how it happened. Beyond vague speculation about natural selection acting on blind biological variation, evolutionists have no idea how most of biology's wonders arose. Some animals are equipped with their own sonar tracking kits that outperform our best military equipment. Did this just evolve? Perhaps, but we don't have scientific evidence for it. Evolution does not seem like a good theory so evolutionists, like a good debater, shift the burden of proof.

One argument Darwin used is the anthropomorphic warning which you can read about here. Another argument Darwin used is that there really isn't any problem for evolution so long as evolution cannot be disproved.

Can you imagine a scientist proposing a dubious theory and then claiming it is true because an impossible falsification criterion has not been met? This is precisely what Darwin did. He wrote:

If it could be demonstrated that any complex organ existed, which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down. But I can find out no such case.

This was hardly a concession. Darwin may sound generous here, allowing that his theory would “absolutely break down,” but his requirement for such a failure is no less than impossible. For no one can show that an organ “could not possibly” have been formed in such a way. So in short order Darwin reduced what seemed to be a dilemma for his theory into a logical truism.

Evolution was protected from criticism and all that was needed to explain complexity was a clever thought experiment. Darwin so lowered the requirements that anyone with a pen and a vivid imagination can now claim to have solved the problem of complexity. It is now common to see in the evolution literature vague explanations, which rely on such dubious mechanisms as “chance” or “opportunism,” put forth as though they are solutions to the problem of complexity.

Monday, October 26, 2009

Anthropomorphic Warning, Part II

It's not my dog, it didn't bite you, and besides you hit the dog first anyway. --Anon

An evolutionist has criticized my previous post about Darwin's warning that we must not anthropomorphize God. Darwin argued repeatedly that God would never have created this inefficient and capricious world, but when it came to complex designs such as the eye, Darwin suddenly backtracked.

In his book Darwin made several failed attempts to reckon with the problem of how his blind process of evolution could create such wonders as the eye. The idea that the eye evolved on its own seemed absurd, but Darwin argued that while it is tempting to see God as the master engineer who crafted complex organs such as the eye, this would make God too much like man.

Darwin agreed that the perfection of the eye reminds us of the telescope which resulted from the highest of human intellect. Was it not right to conclude that the eye was also the product of a great intellect? This may seem the obvious answer but Darwin warned against it, for we should not "assume that the Creator works by intellectual powers like those of man." Better to imagine the eye as the result of natural selection's perfecting powers rather than having God too much involved in the world.

So according to Darwin, God would never create inefficient designs, God would never create capricious patterns, and besides we can't know the mind of God anyway. It seems contradictory but nonetheless my critic complains:

Religion drives your 'science' Mr Hunter (although you don't ever seem to have really done any) every bit as much as the people at Answers In Genesis or ICR. You have an agenda, an a priori commitment to defending your favourite set of ancient fables, and folklorish poetry.

So in other words, I believe in ancient fables and folklorish poetry, these beliefs drive my scientific research, and besides I haven't done any scientific research anyway.

It's not my dog, it didn't bite you, and besides you hit the dog first anyway.

Sunday, October 25, 2009

The Contradiction of Darwin's Anthropomorphic Warning

It's not my dog, it didn't bite you, and besides you hit the dog first anyway. This funny example of childish reasoning is reminiscent of the arguments for evolution. For example, evolutionists say that God would never create inefficient designs, God would never create capricious patterns, and besides we can't know the mind of God anyway. In other words, we must not think this complex world was designed or created because there are inefficiencies and confusing patterns, and besides we could never know how God would design a world anyway. Evolutionists simultaneously claim (i) we know how God would create and (ii) we can't know how God would create. And why can't we know? Because to know how God would create it is to project human qualities onto God and, evolutionists warn, we must not do that.

The anthropomorphic warning

This anthropomorphic warning can service several needs. In the seventeenth century Spinoza used it to defend his pantheism. Were not theists making out God to be something like themselves but with a deeper voice? "I believe," Spinoza wrote to a friend, "that if a triangle could speak, it would say, in like manner, that God is eminently triangular, while a circle would say that the divine nature is eminently circular."

On the other hand, Antoine Arnauld warned that the seventeenth century theodicies (solutions to the problem of evil) were guilty of anthropomorphizing God. The Jansenist rejected the theodicies of Malebranche and Leibniz which he thought subjected God to human reasoning.

But it was in the hands of the eighteenth century philosopher David Hume where the anthropomorphic warning found its application in evolutionary thought. Hume had argued that God could not have designed this world for all its misery. After all, wrote Hume, "A perpetual war is kindled amongst all living creatures," and nature is so arranged so as "to embitter the life of every living being."

Hume obviously was not concerned about Arnauld's warning as he assumed he knew what God would and would not create. Indeed, Hume amazingly retooled Spinoza's version of the warning to attack design from the rear. Not only did the problem of evil rebuke design, but any such appeal to design was faulty to begin with because we can't know God anyway:


we ought never to imagine that we comprehend the attributes of this divine being, ... let us beware, lest we think that our ideas anywise correspond to his perfections ... He is infinitely superior to our limited view and comprehension; and is more the object of worship in the temple, than of disputation in the schools.

Worship God, yes, but do not peer into the mysteries of the divine. Except, that is, when it comes to the problem of evil. It's not my dog, it didn't bite you, and besides you hit the dog first anyway.

Christ in the House of His Parents

The anthropomorphic warning reached a fever pitch a decade before Darwin published his book when the child prodigy John Millais unveiled his painting, Christ in the House of His Parents, first exhibited at the Royal Academy in 1850. Look carefully at the painting (above) before reading further.

In his painting, Millais portrays the young boy Jesus as, well, a young boy. He is very human and in fact has injured his hand in his father’s carpentry shop. Mother Mary attends to the boy while Joseph continues with his work; outside the door sheep patiently await their future savior. The scene is both symbolic and realistic, with wood scraps lying all about and workers going about their duties.

But the setting was altogether too realistic for a culture that separated the creator from the creation. The scriptures said that God became flesh and dwelt among us. He knew anxiety, sorrow, pain, temptation and joy. But this view of God was lost on the Victorians. They emphasized God’s wisdom, power and transcendence. Could he really have bruised his hand in a messy carpenter’s shop?

The Times complained that the painting was revolting, for its "attempt to associate the holy family with the meanest details of a carpenter’s shop, with no conceivable omission of misery, of dirt, even of disease, all finished with the same loathsome meticulousness, is disgusting …" Blackwood’s Magazine said "We can hardly imagine anything more ugly, graceless and unpleasant," and Charles Dickens called the painting "mean, odious, revolting and repulsive."

Next stop: Darwinism

According to many Victorians we ought not to think that God is like us and it is hardly surprising that Darwin would reuse Hume's argument. In Chapter Six of Origins Darwin made several failed attempts to reckon with the problem of how his blind process of evolution could create such wonders as the eye. It seemed absurd, but Darwin argued that while it is tempting to see God as the master engineer who crafted complex organs such as the eye, this would make God too much like man.

Darwin agreed that the perfection of the eye reminds us of the telescope which resulted from the highest of human intellect. Was it not right to conclude that the eye was also the product of a great intellect? This may seem the obvious answer but Darwin warned against it, for we should not "assume that the Creator works by intellectual powers like those of man." Better to imagine the eye as the result of natural selection's perfecting powers rather than having God too much involved in the world.

After Hume, Darwin had made strong arguments that God most certainly would never have created this world. There were, for example, many similar crustaceans, fish and other marine animals inhabiting the seas off the eastern and western shores of North America, the Mediterranean and Japan, and the temperate lands of North America and Europe. This, Darwin argued, was "inexplicable on the theory of creation" because God never would have used such a capricious design.

We cannot rationalize such similarities as due to the nearly similar physical conditions of the areas for elsewhere we find similar physical conditions (such as South America, South Africa and Australia) with utterly dissimilar inhabitants. Likewise, deep limestone caverns on different continents presented nearly identical conditions yet harbored dissimilar species.

Another problem for the doctrine of creation was that native plants and animals were often overtaken by those introduced by man. Darwin pointed out that many of "the best adapted plants and animals were not created for oceanic islands; for man has unintentionally stocked them far more fully and perfectly than did nature." If God had created the species they would have been optimally designed for their specific environments.

Similarly, frogs, toads and newts were only found on certain islands, such as New Zealand, New Caledonia, and the Andaman Islands. Darwin argued these were not genuine oceanic islands. Aside from these islands, the lack of frogs, toads and newts was "very difficult to explain" on the theory of creation.

These are but a few of the dozens of such religious arguments Darwin used to prove his new theory. The science was weak but the religion was strong. Like Hume, Darwin knew what God would and would not design.

And yet, on the other hand, when all else failed Darwin, after Hume, invoked the anthropomorphic warning. The eye may appear to be designed, but surely such thinking is guilty of anthropomorphizing God. It's not my dog, it didn't bite you, and besides you hit the dog first anyway.

Hume critic John Earman recently lamented, "I find it astonishing how well posterity has treated 'Of Miracles,' given how completely the confection collapses under a little probing." Unfortunately the confection did not end with Hume. Religion drives science and it matters.