Friday, April 30, 2010

Adaptation as Proof of Evolution

In 1831 Charles Darwin boarded the HMS Beagle to gather biological information from around the world. It was a wonderful opportunity for the young naturalist, and Darwin saw many fascinating wonders. The voyage is best known for its stop at the Galápagos Islands off the coast of Ecuador. There Darwin observed finches, mockingbirds and tortoises that varied distinctly from island to island. Some finches lived in coastal areas on the ground, others lived in forest trees, yet another lived in bushes. And the diet of these varieties varied considerably. One of the species ate buds and fruit, another prickly pear, others ate seeds and others were insectivores. And one of the insectivores even used a twig to fish out insects from crevices in the tree bark. Nicholas Lawson, the vice-governor who entertained Darwin over dinner claimed that so distinct were the tortoises from island to island that given the tortoise shell he could identify the island of origin.

Since then the Galápagos Finches in particular have become a celebrated icon of evolution. From academic dissertations and research papers to award-winning books and documentaries, they have been watched, dissected, analyzed, and praised. As science writer Jonathan Weiner put it, the changes in the beaks of the finches show us “Darwin’s process in action.” There’s only one problem: How did evolution create the process?

After Darwin, the twentieth century revealed the details of what should have been obvious. If Darwin’s evolutionary change brought about those different Galápagos Finches, it was driven by a profoundly complex process of chromosomes, genes and an army of molecular machines. We’re still learning about what Weiner calls “Darwin’s process” and it shows no sign of having evolved.

Consider the curious case of Carpodacus mexicanus (house finches) which began spreading throughout the United States in the 1940s from Mexico and the southwest. The beaks of these birds adapted to their new environments with great speed. Within a decade or so their beaks had adjusted to the new habitats. How could this occur to rapidly? Certainly not by evolution’s random mutations and natural selection. It was, as one science writer put it:

a complex interplay of processes … Interacting embryonic processes result in an initial level of phenotypic variation greater than what would be predicted from underlying genotypic variation alone.

In other words, complex embryonic machinery produce biological variation that responds to the environmental challenge far more efficiently and rapidly than evolution’s random mutation plus natural selection ever could. And that’s good because otherwise the birds would have failed in their new environments—evolution doesn’t work, but nature’s built-in adaptation machine does.

But in spite of this non evolutionary story of adaptation, evolutionists claim adaptation as proof of their idea. According to Ernst Mayr, “evolutionary change is also simply a fact owing to the changes in the content of gene pools from generation to generation.” Likewise, Isaac Asimov claimed that the peppered moth’s adaptation to industrial pollution proves evolution. And Steve Jones informed his readers that the changes observed in HIV (the human immunodeficiency virus) contain Darwin’s “entire argument.”

Such claims persist and even today evolutionists routinely claim examples of adaptation, from bacteria to birds, as evidence or even proof of evolution. It is another example of how vulnerable science is to simple and straightforward blunders in our thinking. This is not a complex scientific miscalculation or a clever logical fallacy. This is a blunder that is striking not for its subtly but for its transparency. Evolutionists cannot drop their theory though the science doesn’t support it, so they are driven to reprehensible reasoning. Religion drives science, and it matters.

Thursday, April 29, 2010

How Evolution Explains a Complex Immune Response

Fascinating new research suggests that the mere sight of a sick person can trigger an immune response. When test subjects viewed photos showing symptoms of infectious disease, their immune systems responded more aggressively compared to test subjects who viewed other types of photos (including photos of people bearing firearms). It is the first hard evidence that visual cues alone can influence the immune system. Evolutionists have no difficulty explaining this new finding, but that may not be a good sign for Darwin’s theory.

Biological designs that appear to be inefficient or useless are, not surprisingly, explained by evolutionists as a consequence of the blind, happenstance process of evolution. But it is also easy for evolutionists to explain profound designs and complexity, such as the immune response discovered by this new research.

This immune response begins with the viewing and processing of symptoms of infectious disease. These are complex visual scenes that easily can be confused with scenes having nothing to do with disease, infectious or otherwise. Other research suggests that persistent priming of the immune system is not good, so this visual processing needs to be reasonably accurate.

Next in line is a link to the immune system. Once the visual processing identifies a scene as containing signs of infectious disease, then signals need to be sent to the immune system to trigger an appropriate response. Of course, the response should not be too aggressive.

Certainly this immune response to the sight of sickness is not a trivial design. But divining an evolutionary explanation is a simple matter. Why? Because the design works. And anything that works is said to be a consequence of selection, for if it works, then of course it would be selected. Useless junk is due to evolution’s ineptitude—profound designs are due to evolution’s efficiency. As one science writer put it:

Having this immune response may have had its advantages in the days of early humans - even though they may have recoiled at the sight of other sick people too, their immune responses would have helped them live in proximity with others.

There you have it—evolution happens. But such facile explanations are too easy. For while it certainly seems obvious that selection would select what works, it is not obvious how what works arises in the first place. This is the elephant in the room that is so often conveniently ignored in evolutionary just-so stories.

In fact, there is no scientific reason to think that this incredible physiological response would just happen to arise occasionally, and then patiently await selection’s nod. But scientific reasoning is not the driving force.

Wednesday, April 28, 2010

New DNA Damage Repair Mechanism Must Have Arisen Early

DNA damage repair is a fascinating topic in cell biology. Fascinating because the cell's repair mechanisms are so incredible. What's more the mechanisms are coordinated in a sophisticated control network. As one researcher put it, "it’s almost as if cells have something akin to a computer program that becomes activated by DNA damage, and that program enables the cells to respond very quickly."

Now a new mechanism has been discovered which repairs DNA alkylation damage (the erroneous addition of carbon groups to DNA bases). The new mechanism links two previously known mechanisms. Here is how one science writer describes these two mechanisms:

The DNA repair process that removes such toxic "lesions" is known as base repair, and uses a protein called AGT (O6-alkylguanine DNA-alkytransferase) to remove the alkyl group before DNA replicates. The protein essentially sticks a chemical finger inside the DNA to flip the damaged [base] out from the DNA helix structure so that its adduct is exposed and can be transferred from the [base] to a part of its protein structure. The [base] is now repaired and can rejoin cytosine with three hydrogen bonds linking them.

AGT is believed to act alone, but there is another, unrelated repair process—nucleotide excision repair (NER)—that uses lots of proteins in its pathway. This repair occurs when bulky adducts stuck to bases distort the sleek shape of the DNA helix. Then a whole group of proteins come in and remove a patch of bases that includes the adduct, and DNA polymerase follows and fills in the patch while adding the correct base back.

The new mechanism uses alkyltransferase-like proteins (ATLs) which are similar to the AGT protein. Like AGT, ATL attacks the DNA base that has suffered alkylation damage. But the ATL protein distorts the DNA structure significantly, and thus triggers the nucleotide excision repair (NER) mechanism.

This sophisticated and coordinated repair sequence was found in all three domains of life (prokaryotes, eukaryotes and archaea). For evolutionists this forces the absurd conclusion that such a sophisticated DNA repair interaction evolved early on. Before there was so much as an amoeba, evolution had worked wonders. The earliest crude cells must not have been so crude after all. Evolution incredibly worked miracles in those heady days of early life. As the researchers write:

Our analysis of lesion-binding site conservation identifies new ATLs in sea anemone and ancestral archaea, indicating that ATL interactions are ancestral to present-day repair pathways in all domains of life.

This conclusion that complexity comes early is often forced on evolutionists, in spite of the evolutionary expectations to the contrary.

Tuesday, April 27, 2010

Some Good News for Biology Students

Evolutionists have complained bitterly that some states are requiring biology classes to present evolution from a theory-neutral perspective--that is, the evidence should be presented without first presenting evolution as true. And evolutionists have mounted an offensive against such efforts.

But here's some good news. Some evolutionists, rather than using political manipulation, say they are going to use science. The new standards call for science, and to the science they will go.

Ken Miller and Steve Nowicki, for instance, authors of Prentice Hall and Holt McDougal texts, respectively, are looking forward to beefing up the scientific description and evidences for evolution. As Nowicki says:

I understand that there may be a political agenda behind the standards, but I am taking them at face value. If a state thinks students need more information to understand evolution, I am happy to provide that.

You mean there actually are evolutionists who will follow the standards (which call for science class to present science), rather than impute false motives and engage in political offensives? That is terrific news and Nowicki needs to be applauded. Last time I reviewed a Holt text it was, frankly, pathetic. The publisher's response to my review was equally disappointing. We look forward to better things.

Monday, April 26, 2010

A "Malfunction" That Helps: Induced Adaptation in Yeast Cells

When yeast cells face environmental stress, such as exposure to hydrogen peroxide, their internal operations can begin to malfunction. For example, a particular protein misfolds and no longer functions as well. This hardly seems surprising, but as usual there is more to the story. It seems that the misfolded protein normally helps to terminate the synthesis of new proteins. But when it is misfolded, some of the newly formed proteins end up a bit longer, with more information added. And the added information is not just random garbage--it helps the cells adjust to the environmental stress which brought about the change in the first place.

Hints of this adaptation mechanism appeared with researchers found that yeast cells faced with environmental stress do not slow down or fail to function--they modify. As one writer put it, phenotypic variation in the yeast cells comes "out of the woodwork." It seems that previously hidden variation emerges, and sometimes it is advantageous in dealing with the new environmental conditions.

Furthermore, these design changes have been found to be inheritable. They can persist across generations. As one researcher summarized it, this adaptation mechanism and inheritance "allows yeast cells to exploit pre-existing genetic variation to thrive in fluctuating environments."

New research is now adding more details. It seems that the yeast has proteins that help to fine tune the process. They inhibit the protein misfolding until the environmental stress reaches critical levels. At that point the protein misfolding occurs and helps to adapt to the environmental stress. As the researchers concluded:

we find that [protein misfolding] provides yeast cells with an adaptive advantage under oxidative stress conditions, ... [protein misfolding] provides a mechanism for uncovering genetic traits that aid survival during oxidative stress conditions.

This story of yeast adaptation is one example of epigenetics--mechanisms that help organisms adapt to changing conditions, and that may pass that change along to later generations. And it is another example of the falsification of evolution's fundamental prediction that biological variation is independent of need. What we now must believe is that evolution produced sophisticated mechanisms by which evolution can occur. The absurdity of evolution is reaching new heights. Religion drives science and it matters.

Sunday, April 25, 2010

It’s Not Just Science

The influence of evolutionary thought reaches far beyond science. Consider, for example, the histories we are given of how the theory of evolution arose. Charles Darwin and co-founder Alfred Wallace were deeply influenced by non scientific considerations and these influences have, to a certain extent, been explored. Janet Browne, Peter Bowler, Michael Ruse, Keith Thomson, Neal Gillespie, Adrian Desmond and James Moore are but a few of those who have elucidated the cultural, political and other non scientific forces that influenced Darwin and Wallace. As Bowler explains, historians are now far more concerned about the social environment within which scientific knowledge was generated, and far more willing to admit that the development of science is not the inevitable triumph of a series of factually true assertions about the natural world. That sounds like good, solid historiography. But there’s a catch.

Today’s history tellers cannot avoid the undeniable non scientific influences in evolutionary thought. But they do avoid the obvious implication; namely, that evolution entails non scientific premises. It is, as it were, a social construct. Evolution is a theory created by humans, out of human concerns that have very little to do with science.

All of this is plain to see. Every proof for evolution hinges on deep metaphysics that are independent of any scientific experiment ever conducted. As Stephen Jay Gould explained:

Odd arrangements and funny solutions are the proof of evolution—paths that a sensible God would never tread but that a natural process, constrained by history, follows perforce. No one understood this better than Darwin. Ernst Mayr has shown how Darwin, in defending evolution, consistently turned to organic parts and geographic distributions that make the least sense.

The strong arguments for evolution, as Elliott Sober has explained, incorporate assumptions about nature, design and god. If evolution is true it would be a remarkable triumph of philosophical and theological (not scientific) thought.

So why don’t our history tellers tell us these things? Why don’t they explain that evolution is not merely contingent on the history of ideas, but that evolution is, itself, just another one of those ideas? Every time evolutionists proclaim evolution to be a fact they are demonstrating their metaphysical influences. Why don’t our history tellers tell us this?

The answer is simple: our history tellers are, themselves, evolutionists. Their not too subtle explanations of the rise and success of evolution are filled with the very metaphysical influences that mandate evolution in the first place. Michael Ruse argues evolution is necessary to resolve the problem of evil and Peter Bowler repeats that creationism and design are clearly false. Thomson drives home the point in a passage worthy of Darwin himself:

We adopt the noble lion as a metaphor for strength and bravery, but there is little nobility in being the deer (or child) that is ripped apart by the lion and eaten while its viscera are still quivering in the dust. It is hard to see a divine utilitarian goodness in venomous snakes, stinging wasps, mosquitoes and poisonous plants, or in leprosy, malaria and cancer, or in the miseries of old age and the death of the very young. For humans, ugliness, disharmony, war, tyranny, famine, viciousness, greed, racism, inter-religious and intra-religious conflict seem to be at least as common a part of our conditions as goodness, happiness, peace and beauty.

This is the stalemate debated in every pulpit, denied at the hospital bed, eluded at every graveside – an acid eating away at the faith of young and old. A benign and loving God has somehow to be squared with all the slings and arrows of outrageous fortune that flesh is heir to. If God has not created all this misery and evil, and if they do not flow as some natural consequence of his creation, we would have to accept that it has some other cause. In that case, God would not be the only First Cause, but one of many possible causes. Given the premises on which it was based, natural theology could not avoid the challenge of finding an explanation of this paradox, to provide a new explanation of why good and evil are equally God's work. This was its Achilles heel, and in the attempt to produce a rational scientific explanation of misery, want and evil, a door was opened for Darwin.

These histories are evolutionary. They are told from the perspective of the history of ideas that led to evolution. They effortlessly transition from a telling of the history to a preaching of the message. Evolutionary thought has influenced far more than just science.

Saturday, April 24, 2010

Like Confessing a Murder

Think you receive too much email? Charles Darwin and his friend Joseph Hooker exchanged over 1,400 messages (they called them letters back then). In all Darwin exchanged over 15,000 letters with his list (er, correspondents). Here's one from January 11, 1844 in which Darwin raised the specter of his new idea:

At last gleams of light have come, & I am almost convinced (quite contrary to opinion I started with) that species are not (it is like confessing a murder) immutable.

It wasn't the first time Darwin revealed how significant the doctrine of immutability was in mid nineteenth century thought, and it demonstrates once again the importance of historical context.

To understand the evolution genre one must understand the history of thought behind it. In this case, one of the several metaphysical motivations for evolution was (and is) the claim 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 evolutionist 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 behind Darwin's concerns. And it explains why today evolutionists casually claim their theory is a fact--after all, we have discovered adaptation. 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.

Friday, April 23, 2010

A Suave Slug: How Evolution Imitates Mythology

In the dense tropical rainforest of Borneo live species unknown to science. One new find is Ibycus rachelae, a slug that, like the mythological Cupid, shoots its mate with an arrow of love. The dart injects an amorous hormone into its reluctant partner to liven things up.

And how does evolution explain this suave strategy? It would be something like this. First, the hormone happened to evolve and somehow served some purpose in the hapless slug. But the hormone also happened to work wonders when the lights were low. On those rare occasions when the slug was lucky, the hormone might somehow transfer to its partner when there was physical contact.

But this occurred rarely and so didn't help too much. That is, until the randomly designed slug happened to develop an arrow. The arrow worked wonders when it happened to fire at a prospective partner, and it happened to be armed with the hormone. That slug's wild success would proliferate into generations of gigolos.

That's how evolution works. Things that work luckily arise sometimes, and they are then selected.

This slug-turned-Cupid tale is typical of evolutionary storytelling. Stories such as these are told over and over. From textbooks to peer reviewed journals, just-so stories, as with the process of evolution, arise and persist.

But don't evolutionists ever tire of absurdity? Don't they ever think twice about their silliness? Or are they just winking at each other while taxpayers fund their imaginations? Either way, who needs Cupid, evolution is our new mythology.

Thursday, April 22, 2010

Why David Coppedge is Guilty

In our on-going investigation of the David Coppedge case we have uncovered some rather sordid details that suggest Coppedge has far more to hide than his misdeeds that are now so well known.

Not only did Coppedge actually loan DVDs that do not mandate evolution (something Jay Richards incredibly suggests may not even be a crime), but we are now learning that while in college Mr. Coppedge, then in his Sophomore year, once argued late into the night with his roommate and one other student (from down the hall) about various political issues.

Mr. Coppedge, according to our sources who are very reliable, expressed various opinions that were well known to be completely false. Coppedge provided various evidences to support his views, but that was irrelevant. On another occasion Mr. Coppedge was seen entering a bookstore on campus. Our source, who was naturally curious, ascertained that Coppedge browsed several controversial books in the Philosophy section of that bookstore.

If we were able to learn of such incriminations within our limited means, imagine what other crimes lurk in Mr. Coppedge's sordid past. Do we really need any more evidence? This case has guilt written all over it. Obviously the Jet Propulsion Laboratory acted in its great wisdom.

Wednesday, April 21, 2010

Codon Correlations: Molecular Recycling

It is well known that the genetic code translates DNA genes into proteins. But the process is immensely complex and new research is revealing some fascinating and challenging details. This process of protein synthesis begins with the unwinding of the DNA double helix. The two strands are separated and an incredible protein machine makes a copy of one of the strands. The copy contains the appropriate gene and, after some editing, the copy is sent to the ribosome where it provides the needed instructions.

The copy of the DNA strand is simply a sequence of nucleotides glued together. At the ribosome the nucleotides are read three at a time. Each triplet of nucleotides is called a codon because it codes for one of the 20 amino acids, according to the genetic code. There are four different nucleotides, so a codon has 64 different possible sequences of the three nucleotides. Since there are only 20 amino acids, several codons code for the same amino acid. In other words, the genetic code is degenerate.

At the ribosome there is a small army of molecular machines, called tRNAs, that read the codons and supply the appropriate amino acid, as per the genetic code. These tRNAs have a codon reader on one end and the corresponding amino acid glued to the other end. (The amino acids are glued onto the tRNAs by an army of proteins--the masters of the genetic code).

The tRNA machines are not always restricted to reading a particular codon, and in general there is not a one-to-one relationship between the codons and the tRNAs. For instance, a particular type of tRNA may read two of the six different codons that code for the serine amino acid. Also, the different tRNA machines are not in equal abundance. Instead, some are common and others are more rare.

One consequence of all this is that a given amino acid sequence (to be used in a protein) can be coded for by many different sequences of codons, which in turn could be read by different tRNAs. Therefore, a given amino acid sequence can use very different tRNAs, depending on the codon sequence used.

It has long been known that the different possible codons, which code for an amino acid, are not merely used at random in gene sequences. Instead, there are patterns though they vary across different genes and different organisms.

For instance, some codons appear more often than others, and genes that are used frequently tend to show a marked preference for the more common codons. And of course this means that certain tRNAs tend to be in greater demand.

The new research has now found another pattern: correlations in the sequence of codons used for a given amino acid along the protein sequence. For instance, consider all the serine amino acids in a protein sequence. What codons are used to code for those different serines?

The research found that the particular codon used for one of the serines, to stay with our example, influences the codon used at the next serine in the sequence. And what is this influence? The two codons tend to be either identical or, if not identical, they tend to be two codons that are read by a common tRNA machine. In other words, gene sequences tend to use the same tRNA machine for successive occurrences of an amino acid--tRNAs tend to be conserved.

This influence tends to wane as the distance between the two codons grows, in the protein sequence. And, as usual, the correlation is by no means consistent across genes or organisms. But the correlation is statistically significant, and the researchers showed that is is not merely a consequence of the well known codon bias.

Indeed, the correlation seems to be stronger in genes that need to be expressed quickly, such as those contributing to rapid growth or to acute stress responses. And finally, the researchers found this pattern of tRNA conservation is strongest for rare tRNAs, particularly in highly expressed genes.

Though many questions remain, all of this makes sense for enhancing the speed and fidelity of protein synthesis. What doesn't make a great deal of sense, as usual, is evolution. With evolution we must imagine a micro world of profound complexity--which we still do not fully understand--just happened to emerge.

Tuesday, April 20, 2010

The Stickleback and Confirmation Bias

Species of stickleback fish can rapid adapt to new environments. Such adaptations can range from minor adjustments to body shape and size to the complete loss of major structures such as the pelvis. It is an example of rapid, intelligent adaptation, not the sort of change expected by evolution.

This is not the only surprise for evolutionists. Recent research has found that these adaptations are controlled by different genes. That surprised evolutionists because they expect the same genes would control the same changes in related species. A basic prediction of evolution is that related species should be genetically similar, because they have been evolving independently for only a relatively short period. But this expectation is routinely contradicted by biology, which seems to be unaware of the theory of evolution.

Another interesting example of this in stickleback fish are the sex-determination genes, which are located on different chromosomes in different species. As one evolutionist admitted:

This is very surprising because these species are fairly closely related.

Evolutionists believe that significant differences such as these must have somehow evolved. Evolutionists may not have a clear or compelling explanation for how or why the change came about, but not surprisingly, they believe evolution did the job. Since these differences do not fit the evolutionary expectation, they are viewed as anomalies, whereas the similarities that are expected are viewed as more informative of evolutionary relationship. It is the latter, not the former, that are more often used when evolutionists create their evolutionary trees.

This pre screening of data is known as confirmation bias. It is a well known tendency in science. Proponents of a theory are less likely to dwell on, or perhaps even acknowledge, contradictory data. Those data are viewed as outliers. This is one reason why objective theory evaluation is difficult. Don't expect evolutionists to tell us one day that their theory may not be a fact after all, even though that is what the science tells us.

Monday, April 19, 2010

Histone Variants: The Incredible Story of Gene Regulation

Proteins are constructed from a string of amino acids, and the amino acid sequence is coded in a gene. But how does the cell know which of its many genes to use in synthesizing proteins? Gene regulation is accomplished via a number of complex mechanisms. For instance, methyl groups are used to tag both the DNA as well as the histone proteins about which the DNA is wrapped. You can read more about histones here and here. In addition to such methylation, histones can also vary by tiny differences in their amino acid sequence. Such histone variants serve as yet another type of tag used for gene regulation. Now new research is revealing the profound complexity of this mechanism.

Histone variants are not merely static sign posts that influence gene expression. These variants are moved, by other proteins, between different locations in the genome. The new research elucidates the migration patterns of a histone variant during mouse embryonic development. Cells differentiate over time in the growing embryo, and in this process the histone variant migrates to different genomic locations. And the research indicates these movements are orchestrated by three different proteins. As one researcher put it:

Our work shows that the regulation of histone variant localization -- the shape of the so-called epigenetic landscape at different regions of the genome -- is more complex than previously thought.

Or as one writer explained, these findings “hint at an unimagined complexity of the genome.” Nothing in biology makes sense in the light of evolution.

Sunday, April 18, 2010

The Problem of Evil Atheism

From antiquity to today, the evil in the world has always been a powerful mandate for evolutionary thinking. God would not have designed or created this evil world, so it must have originated by the blind play of natural law. For centuries this solution has fueled atheism, but from where did evil-ness come?

The evil in the world is obvious and upsetting. Atheists, no less than others and perhaps even more so, are exercised by creation's terrors. Earthquakes and tsunamis kill thousands, diseases terrorize, floods destroy and droughts starve. Then there is the seemingly unending narrative of predation in the biological world. Nature is red in tooth and claw, as Lord Tennyson put it.

Atheists often proclaim this problem of evil as a justification for their beliefs but ironically this evil is as much a problem for atheism as it is a motivation. The problem is that atheism fails to explain the existence of evil.

Atheists say that we are able to identify evil as evil because the knowledge of what is evil evolved in our brains. But if that is true then there is no such thing as objective evil. Instead, evil is subjective. We may generally agree that something is evil, but that is only because of similar molecular interactions in our brains that happened to evolve, not because that thing is itself evil. There is no immaterial, objective standard which defines evil-ness.

One might think that atheists could agree with all this, but it is not so simple. Atheists could dispose of objective evil, but then they lose their raison d' etre. God is no longer responsible for creating or allowing evil because there is no such thing as true, objective evil. It is all just in our heads.

In fact, atheists very much do believe there is an objective standard. And they very much hold God to that standard. As PZ Myers wrote:

We go right to the central issue of whether there is a god or not. We're pretty certain that if there were an all-powerful being pulling the strings and shaping history for the benefit of human beings, the universe would look rather different than it does.

This is religion and it is the driving issue. It is no different than what David Hume and thousands of other atheists have been saying for centuries. God wouldn't do it that way and so our only option is atheism. This is what animates atheists. They cannot then turn around and drop their weapon, as though they never used it.

Friday, April 16, 2010

The Amazing Stickleback

It's worth repeating that if Charles Darwin had explained that evolution proceeds in fits and starts, his theory would have been ridiculed from the start. Imagine if Darwin had explained that, according to his theory of evolution, species rapidly appear as if planted there, and then go unchanged for eons. Darwin would have been laughed off the stage. Darwin had to present a narrative of gradualism. Funny thing is, the fits-and-starts narrative is today precisely what evolutionists tell us.

Evolutionists have tried to justify the fits-and-starts narrative with evidence of rapid changes in fish morphology. Problem is, those rapid changes are too rapid. They are a sign of a built-in adaptive capability rather than a lucky accident which evolutionists envision. New research on stickleback fish continues to tell this story. As one evolutionist explained:

There are six and perhaps eight stickleback species, all in the Northern Hemisphere. They live in Europe; coastal North America north from northern Mexico on the Pacific and north from New York on the Atlantic; and all over coastal northern Asia. Like salmon, many live in the sea and swim upstream to spawn. Others live in lakes.

After Ice Age glaciers started melting some 15,000 to 20,000 years ago, sea-going sticklebacks swam up streams to newly formed lakes. Many populations of ninespine and threespine sticklebacks were trapped in lakes, creating an experiment in evolution.

They adapted very quickly and dramatically to these new freshwater environments," says Shapiro. "Some of the changes include shifts in body shape and size, the amount of armor on their bodies and, occasionally, complete loss of major structures like the pelvis. That's the equivalent of us losing our legs."

Such rapid adaptations do not help us understand why the fossil record is characterized by the rapid appearance of new species followed by eons of no change.

Thursday, April 15, 2010

How to Convince Students of Evolution

Sometimes the most ardent evolutionists are those who understand it the least. Many who are not life scientists take evolution to be the gospel truth—after all, evolutionists have told them it is a scientific fact. And unlike the life scientists who at least are familiar with the evidential quandaries, those more distant from the data are blissfully ignorant. For them evolution is all the more an unquestionable truth. Evolutionists have misrepresented science and now we are paying the price with increasing scientific illiteracy. Consider a recent peer-reviewed paper on how to succeed in convincing students that evolution is true. The authors consider the problem of consciousness:

Historically and currently, one of the greatest obstacles to acceptance of evolution is the claim that human thought is a product of it. Alfred Wallace, who discovered natural selection independently of Darwin, was never able to accept that it applied to minds, which he thought had an irreducible spirituality. Students today find that the most implausible aspect of Darwin’s theory is the suggestion that it could provide a way of accounting for the operations of human minds. Here students have a double difficulty: not only is evolution an emergent process on the Darwinian account, but thinking is also an emergent process on the account currently being developed in neuroscience. … Thus the human mind is an emergent process resulting from an emergent process! So it is small wonder that students and ordinary people, not to mention many contemporary philosophers, have great difficulty imagining how mind could be the result of brain structures arising from natural selection.

Amazing how evolution works. Fortunately they have already solved much of the problem:

Thagard and Aubie (2008) offer a neuro computational model of emotional consciousness that explains how many interacting brain areas can generate such emotions as happiness.

It’s good to know happiness is no longer an issue. Nonetheless, there remains the problem of the actual evidence for free will:

Third, within our lifetimes, people are not completely constrained by the kinds of physical and biological forces that generated evolution, but rather operate by free will. Not only is free will supported by our subjective experience of having genuine choices to make, it also fits with our preferred view of ourselves and others as responsible agents.

But of course free will is an illusion and students need to understand this. Ultimately, evolution must be shown to be true in the same old way it has always been shown to be true, by comparing it with those “competing hypotheses” such as creationism. Religion drives science and it matters.

Wednesday, April 14, 2010

DNA Repair With a Molecular Tool

The threats to the DNA in our cells are incredible. Radiation, carcinogens and even chemicals produced within the cell attack the DNA thousands of time every day. What is more incredible though is the cell’s DNA repair system, which you can read more about here and here. The worst kind of DNA damage is the so-called double-strand break where both strands of the double helix break. In response the cell mounts a swift and sophisticated response which new research is helping to elucidate.

One of the key proteins involved in this DNA repair, known as CtIP, has a 49 amino acid DNA-binding segment that has an important role in the repair job. Interestingly, this segment appears to be normally buried within the interior of CtIP. It is exposed when chemical signals indicating DNA damage modify the CtIP structure. The tool is now flipped open and ready to do its job.

Obviously this repair kit wouldn’t work without the CtIP protein. But it also wouldn’t work without the chemical signal that opens it up. Remove either one and the repair kit doesn’t work very well. Of course CtIP needs to have a binding site for the chemical signal, and CtIP needs to undergo just the right conformational change under the influence of the binding.

This is only the beginning of the repair kit’s complexity. There are several more important players in the choreography, without which the repair job would suffer. Nothing in biology makes sense in the light of evolution.

Monday, April 12, 2010

Flexoelectric Motors of the Inner Ear

One of the many fascinating designs in biology is the workings of our senses. Here, for example, is a description of recent findings on the actions of hair cells in the inner ear. It is yet another example of incredible biology at work:

Microvilli (stereocilia) projecting from the apex of hair cells in the inner ear are actively motile structures that feed energy into the vibration of the inner ear and enhance sensitivity to sound. The biophysical mechanism underlying the hair bundle motor is unknown. In this study, we examined a membrane flexoelectric origin for active movements in stereocilia and conclude that it is likely to be an important contributor to mechanical power output by hair bundles. We formulated a realistic biophysical model of stereocilia incorporating stereocilia dimensions, the known flexoelectric coefficient of lipid membranes, mechanical compliance, and fluid drag. Electrical power enters the stereocilia through displacement sensitive ion channels and, due to the small diameter of stereocilia, is converted to useful mechanical power output by flexoelectricity. This motor augments molecular motors associated with the mechanosensitive apparatus itself that have been described previously. The model reveals stereocilia to be highly efficient and fast flexoelectric motors that capture the energy in the extracellular electro-chemical potential of the inner ear to generate mechanical power output. The power analysis provides an explanation for the correlation between stereocilia height and the tonotopic organization of hearing organs. Further, results suggest that flexoelectricity may be essential to the exquisite sensitivity and frequency selectivity of non-mammalian hearing organs at high auditory frequencies, and may contribute to the “cochlear amplifier” in mammals.

Mitotic Bookmarking Facilitates Transmission of Genetic Programming

As you read this many of the cells in your body are in a gradual process of division which results in the production of two daughter cells. In this process, known as mitosis, the cell duplicates its contents, including its DNA, before dividing. But the hardware is only part of a cell. Like a computer the cell contains programming information. For instance, tiny chemical signals—methyl groups—may be added to certain proteins or DNA sequences. You can read here about one way that this programming information is passed on to later generations. New research is now elucidating a different mechanism for preserving the cell's programming information.

Before the cell divides the DNA condenses and the various protein machines that normally bind to the DNA (to makes copies of the DNA genes, for instance) move away. The new research, however, found that one protein, known as MLL, remains connected to the condensed DNA. MLL connects to the DNA sequence adjacent to genes to influence the expression of the gene.

But during the process MLL moves to those genes that were most active. In this way MLL serves as programming information. MLL apparently identifies the genes that need to activate first in the new daughter cell. As the researchers wrote, "These findings implicate mitotic bookmarking as a component of ... gene regulation, which may facilitate inheritance of active gene expression states during cell division."

Indeed, it appears that MLL "bookmarks" active genes so they can quickly be identified in the daughter cell. It is another example of the additional layers of information in molecular biology, beyond the DNA itself.

It is also another example of the continuing failure of evolutionary theory where we must believe all this just happened to happen. MLL must have been created, or "recruited" as evolutionists prefer to imagine (who did the recruiting?). MLL must have luckily been coordinated with connecting and signaling molecules so as to attach to DNA. Even luckier, signaling molecules must have influenced MLL to switch to the active genes at just the right time. Then in the new, daughter, cell, the right molecules acted on the presence of MLL to activate those genes.

Impossible? Of course not. With enough multiverses anything can happen. A fact? Evolutionists think so. Religion drives science, and it matters.

Sunday, April 11, 2010

Darwin's Take-Home Message: The Great Contrast

Charles Darwin spent many years working on his ideas about evolution before publishing them in 1859. Darwin continued with revisions for another 17 years, finally stopping with his final edition, six years before he died. In his heartfelt introduction to his tome Darwin provided the reader with a context. Many readers would not make it through the lengthy work, but they would read the Introduction. So not surprisingly Darwin finished his introduction with his take-home message. If you go no further, this is what you needed to know. Here is how Darwin finished that first chapter:

No one ought to feel surprise at much remaining as yet unexplained in regard to the origin of species and varieties, if he make due allowance for our profound ignorance in regard to the mutual relations of the many beings which live around us. Who can explain why one species ranges widely and is very numerous, and why another allied species has a narrow range and is rare? Yet these relations are of the highest importance, for they determine the present welfare, and, as I believe, the future success and modification of every inhabitant of this world. Still less do we know of the mutual relations of the innumerable inhabitants of the world during the many past geological epochs in its history. Although much remains obscure, and will long remain obscure, I can entertain no doubt, after the most deliberate study and dispassionate judgment of which I am capable, that the view which most naturalists until recently entertained, and which I formerly entertained—namely, that each species has been independently created—is erroneous. I am fully convinced that species are not immutable; but that those belonging to what are called the same genera are lineal descendants of some other and generally extinct species, in the same manner as the acknowledged varieties of any one species are the descendants of that species. Furthermore, I am convinced that Natural Selection has been the most important, but not the exclusive, means of modification.

That final paragraph to his Introduction is, in many ways, an excellent summary of evolutionary thought. Darwin here explains that there is much that we do not understand about the origin of species, but what is plainly obvious is that the species were not independently created and immutable.

Darwin lays before the reader the contrast that has been running through this genre of thought for centuries. There is much we cannot explain, but this we know. We may not know how it happened, but we know how it didn't happen.

It could have been written 150 years earlier by Leibniz who couldn't explain the solar system design very well, but he knew how it wasn't designed. And it could have been written today by an evolutionist such as Francis Collins who, like Darwin, cannot explain how biology's marvels arose, but he knows how they didn't arise.

The uncertainty that science leaves us with is, by now, not too surprising. Yes we make great progress. But for every answer there seem to be two new questions. It is hardly a revelation that science has not yet revealed all.

What is more of a revelation is the certainty part of the equation. Yes there is much we don't understand, and we have all heard that before. But listen to the evolutionist's pronouncement of certainty in the face of such unknowns. This is astonishing.

How is it that they, with no more scientific knowledge than the rest of us, can suddenly find such truth?

The answer, of course, is that to evolutionists the world does not look designed. God would never have created this mess, so therefore it must have evolved, somehow. The paragraph, as with the book (and legacy) that follow, reveals ignorance followed by metaphysical certainty. We don't know how evolution occurred, but we know this world was not designed so evolution must have occurred.

Such metaphysical certainty trumps all manner of scientific problems. What we do understand from science does not bode well for evolution and common descent, but so what? Such ideas face tremendous scientific barriers, but they are puny compared to the overwhelming certainty that they are true. This much we know.

Saturday, April 10, 2010

The View From Nowhere

The objective of science is to be objective. Measurements, observations, explanations, hypotheses, theories, and laws should be free of personal opinion. Science should not depend on one's perspective, but rather it should escape parochial viewpoints. It should take on, as Thomas Nagel put it, the view from nowhere.

Some may argue that such objectivity is impossible. Others may contend it is not even desirable. Perhaps so, but nonetheless many scientists do strive for such objectivity.

Evolutionists, no less than others, claim their methods are objective. Indeed, evolutionists not only claim their science is independent of parochial viewpoints, they claim evolution is an inescapable, objective, fact, every bit as much as gravity is a fact.

This means that the scientific evidence, interpreted from a theory-neutral perspective, necessarily requires us to conclude for evolution. As Ernst Mayr put it, the fact of evolution is so overwhelmingly established that it would be irrational to call it a mere theory.

Strangely enough, these same evolutionists use subjective arguments to prove their point. As Stephen Jay Gould explained:

Odd arrangements and funny solutions are the proof of evolution—paths that a sensible God would never tread but that a natural process, constrained by history, follows perforce. No one understood this better than Darwin. Ernst Mayr has shown how Darwin, in defending evolution, consistently turned to organic parts and geographic distributions that make the least sense.

This is about as far from objectivity as a science can go.

And stranger yet, after making such parochial arguments evolutionists accuse dissenters of their own crime. True, the dissenters make no such subjective claims, but evolutionists say they do so secretly. It is their religious beliefs that drive them, say the evolutionists, whether they admit it or not. Pay no attention to the dissenters—what they say doesn't matter, it is obvious they have ulterior motives.

In making these accusations, evolutionists are their own judge. They pronounce subjective arguments, such as religious claims, as scientifically out of bounds. They rule themselves to be non scientists.

There is an obvious way out for evolutionists. They can exonerate themselves with one simple move. All they need do is to prove their claim. The key to their innocence lies in the objective, scientific data. All that is needed is an explanation of why the scientific evidence makes evolution a necessary conclusion from a theory neutral perspective. Why is evolution true from the view from nowhere?

We probably should not expect evolutionists to produce this new argument anytime soon. For centuries they have been making their high claims that evolutionary histories are undeniable, and each time they invoke subjective, parochial, interpretations. In fact, the stronger the proof, the more subjective the premises. Religion drives science, and it matters.

Friday, April 9, 2010

A Sound of Thunder: Another Fundamental Failure

One of the most fundamental premises of evolutionary theory is that the evolutionary process is indeterminate. The species arose via a process which did not have them in mind. This is because, from mutations to comet strikes, evolution depends on sporadic, unguided events that know nothing of making species. Evolution is contingent on random events and does not know where it is going—there is no teleology.

The cicada sings its song, the blue whale sprays a shower from its blowhole, the rattlesnake strikes at lightning speed, a dandelion turns toward the sun. These and all the other species just happened to arise. The designs were fortuitous for reproduction, but they were accidental.


Given the contingent nature of the evolutionary process, the theory predicts that what it produces is rather unpredictable. Unlike physics with its laws and predicted trajectories, the evolutionary process is more of a random walk. The biological design space is enormous and evolution traces circuitous veins through it, no more predictable than a the path of a bolt of lightning.

The prediction then is that evolution is unpredictable. We can observe what evolution produces but can hardly predict what it will produce. Theodosius Dobzhansky put it this way: “The evolution of every phyletic line yields a novelty that never existed before and is a unique, unrepeatable, and irreversible proceeding.” Likewise Ernst Mayr wrote that “Laws and experiments are inappropriate techniques” for explaining evolutionary events and processes.

Stephen Jay Gould explained that if evolution were replayed again it would go down a radically different pathway. It is a central tenet of neo Darwinism, explains Simon Conway Morris, that evolution is open-ended and indeterminate in terms of predictable outcomes.

Similarly Ken Miller wrote that chance “plays an undeniable role in history ... The twentieth century could easily have been very different—the next century more different still.”

Perhaps he read Ray Bradbury’s 1952 short story “A Sound of Thunder” which illustrated this evolutionary view. The story takes place in the mid twenty first century when time travel has not only become possible, it is rather mundane. Eckels, a cowardly but curious safari hunter, signs up to go on a safari back in time but doesn’t respect the hazards of time travel.

The safari company has carefully selected dinosaur targets for the hunt. The dinosaur must be one which is about to die from some natural cause such as drowning in a tar pit. They may kill the beast a moment before its death but otherwise they must leave the scene untouched. They use an anti-gravity metal path to walk about without touching the ground and they even recover the bullets after the kill.

But these precautions are lost on Eckels. Travis, the safari guide must explain to him the fragility of the future:

“A Time Machine is finicky business. Not knowing it, we might kill an important animal, a small bird, a roach, a flower even, thus destroying an important link in a growing species.”

“That’s not clear,” said Eckels.

“All right,” Travis continued, “say we accidentally kill one mouse here. That means all the future families of this one particular mouse are destroyed, right?”


“And all the families of the families of the families of that one mouse! With a stamp of your foot, you annihilate first one, then a dozen, then a thousand, a million, a billion possible mice!”

“So they’re dead,” said Eckels. “So what?”

“So what?” Travis snorted quietly. “Well, what about the foxes that’ll need those mice to survive? For want of ten mice, a fox dies. For want of ten foxes a lion starves. For want of a lion, all manner of insects, vultures, infinite billions of life forms are thrown into chaos and destruction. Eventually it all boils down to this: fifty-nine million years later, a caveman, one of a dozen on the entire world, goes hunting wild boar or saber-toothed tiger for food. But you, friend, have stepped on all the tigers in that region. By stepping on one single mouse. So the caveman starves. And the caveman, please note, is not just any expendable man, no! He is an entire future nation. From his loins would have sprung ten sons. From their loins one hundred sons, and thus onward to a civilization. Destroy this one man, and you destroy a race, a people, an entire history of life. It is comparable to slaying some of Adam’s grandchildren. The stomp of your foot, on one mouse, could start an earthquake, the effects of which could shake our earth and destinies down through Time, to their very foundations. With the death of that one caveman, a billion others yet unborn are throttled in the womb. Perhaps Rome never rises on its seven hills. Perhaps Europe is forever a dark forest, and only Asia waxes healthy and teeming. Step on a mouse and you crush the Pyramids. Step on a mouse and you leave your print, like a Grand Canyon, across Eternity. Queen Elizabeth might never be born, Washington might not cross the Delaware, there might never be a United States at all. So be careful. Stay on the Path. Never step off!”

But when Eckels sees the towering dinosaur up close he panics. “It could reach up and grab the moon,” exclaims the overwhelmed Eckels when he first sees the beast. The immense and terrifying dinosaur is too much for him and he must retreat to the safety of the time machine. But in his fright Eckels slips off the path and onto the ground. What has he done to the future?

The safari guides are livid. One wants to leave Eckels there in the past, but of course that would risk even greater changes to the future. They take Eckels back to the 21st century with them, only to discover a dead butterfly in the mud on Eckels's boot and along with it a different world.

Eckels killed the butterfly and altered the future. Bradbury’s tale captures the evolutionary view of natural history as a contingent process. As Miller put it, “The twentieth century could easily have been very different—the next century more different still”


The expectation that evolution is a contingent, unrepeatable, unpredictable, indeterminate process has been falsified by the many examples of repeated designs found in otherwise unrelated branches of life. Such repeated designs are not merely occasional. They are not the anomalous exceptions to the rule. Rather biology presents a seemingly unending stream of such repeated designs. They range from molecules to social systems and cognitive processes.

Such similarity, referred to as homoplasy, reveals not a random walk but consistent trends in life’s designs. As Conway Morris suggests, this prediction that evolution is open-ended and indeterminate is “now open to question.” Here is one example:

Consider, for example, the seemingly arcane area of frog ecomorphs. As befits an evolutionary laboratory, the frogs of Madagascar show a series of adaptive radiations, with the occupation of habitats as diverse as burrowing, as well as dwelling in trees, rocks and torrential streams. These ecomorphs find a series of striking convergences with the frogs of Asia (principally India), and so too in this latter region there are further episodes of parallel evolution (e.g., independent development of fangs). The comparisons between Madagascan and Asian frogs are all the more striking because they extend to the larval forms, but there is one striking omission. Thus, in Asia there is no counterpart to the iconic poisonous mantellids. So, the principle of the repeatability of evolution fails at the first hurdle? Not quite, because the mantellids display a series of striking convergences with the neotropical dendrobatids.

Homoplasy is ubiquitous in biology and Conway Morris has documented many examples in his book Life’s Solution.


While some evolutionists realize that the massive homoplasy observed in biology requires a rethinking of their theory, many simply ascribe homoplasy as a consequence of similar environmental pressures. Unfortunately this simple explanation does not help as it, itself, invokes the non evolutionary concept of environmental pressures inducing biological change. Also, homoplasy is not necessarily correlated with the environment.

To convert the explanation to an evolutionary one we must say that random biological changes just happened to converge to similar designs in distant lineages, over and over and over. Regardless of how evolution’s repeatability is explained, it falsifies a fundamental prediction of evolution.

Thursday, April 8, 2010

Bruce Waltke and the Scientific Orthodoxy

Bruce Waltke, a Professor of Old Testament, has parted ways with Reformed Theological Seminary, perhaps due to controversies over his sympathies with evolution. Rod Dreher at BeliefNet worries that this is a dangerous disregard for science:

it is all but incomprehensible that in 2010, any American scholar, particularly one of his academic distinction, could be so harshly bullied for stating an opinion consonant with current scientific orthodoxy.

I hope we can all agree with Dreher's opposition to bullying. But what about Dreher's and Waltke's high regard for "current scientific orthodoxy"?

Can we no longer confront the data on our own? Must we have evolutionists dictate the message? If only Waltke was familiar with the current scientific data, rather than the current scientific orthodoxy.

This deference to scientific orthodoxy is a consistent theme. From textbooks to church sermons it is a convenient way around the science. Imagine appealing to the "current scientific orthodoxy" to promote blood-letting or alchemy. Nonetheless, textbooks now routinely inform students that scientists now believe evolution is a fact, rather than explain just why it is evolutionists believe this. That would be rather awkward.

Wednesday, April 7, 2010

PZ Myers: The Anti-Authoritarian Authoritarian

Is there a religious influence and authoritarian tradition in science? Evolutionists such as PZ Myers reject any such notion. Though Myers relies on the usual theological truth claims that are fundamental to evolution, he is sure that science is free of all such nonsense. When he is not busy shutting down scientific inquiry with religious dictates, he reassures his readers that science is a process that empowers questioning and change.

Certainly that is what science should be, but it is precisely the opposite in the hands of evolutionists such as Myers. They believe evolution is a fact, based on religious dogma that goes back centuries. Far from the empowering the asking of questions when the evidence contradicts their theory, they protect evolution from harm. You can see examples of Myers' religious commitment here and here. Myers criticizes the religious ignorance and dogma he disagrees with, but he ignores the religious dogma that is foundational to evolution.

Tuesday, April 6, 2010

Simon Conway Morris: Darwin 1, Paley 0

Eighteenth century English natural theology reached a pinnacle in the work of William Paley who was decidedly optimistic about the world. Not only did creation prove design, it was also a very pleasant place. Here is how the Anglican described an English garden:

It is a happy world after all. The air, the earth, the water, teem with delighted existence. In a spring noon, or a summer evening, on whichever side I turn my eyes, myriads of happy beings crowd upon my view. The insect youth are on the wing. Swarms of newborn flies are trying their pinions in the air. Their sportive motions, their wanton mazes, their gratuitous activity, their continual change of place without use or purpose, testify their joy, and the exultation which they feel in their lately discovered faculties. A bee amongst the flowers in spring, is one of the most cheerful objects that can be looked upon. Its life appears to be all enjoyment; so busy, and so pleased: yet it is only a specimen of insect life.

It appears to be the very picture of what David Hume had in mind when excoriating the natural theologians for their neglect of the evil all around them. Paley, who came after Hume, is yet another reminder of the recycling of ideas in the history of thought. Did Paley not realize how well he caricatured Hume’s target? Did he not recall Hume’s retort that a perpetual war is kindled amongst all living creatures, and that nature is so arranged so as to embitter the life of every living being? Or was his English garden supposed to offset Hume’s vicious world?

Either way, it hardly matters. Regardless of the century, it seems the pious continue to exhalt nature’s harmony while the skeptics continue to complain of its evils. There are common threads running through our thinking that seem to transcend the traditions at hand. There will always be a Hume and a Paley.

The banality of (arguments about) evil

Unfortunately, consistency does not imply quality. For all of their fame, Hume and Paley presented remarkably naïve thought. “I find it astonishing,” commented one philosopher recently of Hume’s work, “how well posterity has treated ‘Of Miracles,’ given how completely the confection collapses under a little probing.”

I was also astonished when I first read Paley. He emphasized the happiness of nature’s creatures as evidence for God, and he even presented a proof for his cheery dictum that God “wills and wishes the happiness of His creatures.”

Paley began with the premise that when God created human beings He either wished for their happiness, or their misery, or He was indifferent. Paley then ruled out God wishing for our misery, for if that were the case He didn’t do a very good job. God certainly could have made things much more miserable. Likewise, if God were indifferent then why do our senses have the capacity to receive pleasure and why is there such an abundance of external objects fitted to produce it?

By the process of elimination Paley thought he had proved that God wills and wishes the happiness of His creatures. In a few short pages, and without reference to scripture, Paley reduced a profound theological question to a triviality. The implication, Paley concluded, was that “the method of coming at the will of God, concerning any action, by the light of nature, is to inquire into the tendency of that action to promote or diminish the general happiness.”

Next in line: Darwin

Darwin, as evolutionists will not let us forget, demolished Paley’s natural theology. True enough, but so what? Darwin, who was steeped in Hume and reused his arguments when convenient, was unfortunately no better than the Scottish philosopher. We might say that we find it astonishing how well posterity has treated ‘Origins,’ given how completely the confection collapses under a little probing. For instance, consider this Darwinian gem:

How inexplicable are the cases of serial homologies on the ordinary view of creation! Why should the brain be enclosed in a box composed of such numerous and such extraordinary shaped pieces of bone, apparently representing vertebrae? … Why should similar bones have been created to form the wing and the leg of a bat, used as they are for such totally different purposes, namely flying and walking? Why should one crustacean, which has an extremely complex mouth formed of many parts, consequently always have fewer legs; or conversely, those with many legs have simpler mouths? Why should the sepals, petals, stamens, and pistils, in each flower, though fitted for such distinct purposes, be all constructed on the same pattern?

Such pathetic rationalism is typical of Darwin’s confection. It was “one long argument” against Paley. As Simon Conway Morris recently wrote:

Curiously, it is seldom appreciated that whatever else [Darwin’s] masterpiece set out to achieve it was at heart an exorcism of William Paley. With consummate skill, and in striking contrast to the belligerent and graceless rhetoric of some of his intellectual descendants, he systematically dismantled Paley's creationism. But 150 years on the message has evidently failed to sink in.

Yes it has failed to sink in, but not as Morris thinks. Evolutionists such as Morris are concerned IDs have not yet read the memo. Don’t IDs know Darwin demolished Paley?

Of course they do.

What hasn’t sunk in is that it doesn’t matter. What hasn’t sunk in is that Darwinian thought is the height of rationalism, and that evolution is soaking in metaphysics. What hasn’t sunk in is that evolution, and its overwhelming evidence, hinge on the same old religious confection.

Monday, April 5, 2010

The Evolution of Evolutionary Thought: Why Historians Analyze Evolutionists But Not Evolution

One of the reasons evolutionists are convinced their theory is true is because of the way the species compare to each other. The patterns we find amongst the species, say the evolutionists, prove Darwin’s idea beyond a shadow of a doubt. Such arguments pervade the evolution genre—from textbooks to popular literature—but what exactly do they mean? To understand this we must understand the evolutionary mind. These arguments have circuitous histories and baked-in assumptions that are now long forgotten. But they are worth remembering. Here is one example.

In the early years of modern science it was argued that motion was caused by contact between masses. In this mechanical philosophy, influences in the natural world were assumed to be transmitted only by direct mechanical contact. And while this may seem intuitive, the related assumption that there can be no vacuum was less obvious. But it was taken to be a fact. As Rene Descartes wrote in 1644, “some make the mistake of imagining [the heavens] to be a totally empty space … there can be no such vacuum in nature.”

For Descartes the planets moved around the sun because they floated in a cosmic whirlpool. And although Isaac Newton later disproved any such Cartesian whirlpool effect, the Lutheran philosopher and mathematician Gottfried Leibniz later promoted Descartes’ ideas. As Leibniz explained in 1715, the principle of plenitude disproves the existence of vacuums in nature:

Now let us fancy a space wholly empty. God could have placed some matter in it without derogating in any respect from all other things. Therefore he has actually placed some matter in that space; therefore there is no space wholly empty; therefore all is full.

It was a good example of how rationalism can produce certainty in even the most obscure notions. Empirical evidence gives one a healthy respect for nature’s complexities, but thought experiments lead to tidy conclusions.

Not surprisingly this mechanical philosophy objected to Newton’s idea that gravitational attraction acted at a distance, and even through a vacuum. How could Newton, Leibniz asked, “have the sun to attract the globe of the earth through an empty space?” Such a notion, Leibniz objected, took on occult qualities.

Another theological objection was that Newton’s solar system was, ultimately, not stable. Over eons to time it could occasionally become chaotic. While Newton allowed that God could fix things when needed, this was unacceptable to the rationalists. God was not an unskilled designer who would create a faulty machine. Therefore God would not use miracles to fix nature, and whoever thinks otherwise, Leibniz said, “must have a very mean notion of the wisdom and power of God.”

Despite the many theological objections Newton’s new physics was compelling. But as Newton cautioned, while it explained the motion we observe, it did not explain the origin of that motion. Newton could explain how the planets moved, but not how they got going. That question was attempted by a series of brilliant thinkers in the eighteenth century.

In 1734 Daniel Bernoulli wrote an award winning paper on the origin of the solar system. His explanation, that the sun’s atmosphere caused the planetary motions and alignments, was reminiscent of Descartes’ whirlpools. And while Bernoulli’s explanation was eventually discarded, he introduced a powerful argument that became crucial in evolutionary thought and remains pervasive today.

The planetary orbits were aligned so as to form a striking pattern. Surely this could not have arisen by chance, argued the great mathematician. Bernoulli posited random design as the null hypothesis. Either the planets fell into their orbits by chance or some mechanism caused their alignment. Bernoulli used a calculation to show the long odds of random design, thus proving beyond a shadow of a doubt that a mechanical cause did the job. He who would deny this, the Christian argued, “must reject all the truths, which we know by induction.”

Twenty years later Immanuel Kant elaborated Bernoulli’s argument. Why do planets revolve about the sun in the same direction? “It is clear,” explained the great philosopher, “that there is no reason why the celestial bodies must organize their orbits in one single direction.” If God had directly arranged their orbits then we would expect them to reveal deviations and differences:

Thus, God’s choice, not having the slightest motive for tying them to one single arrangement, would reveal itself with a greater freedom in all sorts of deviations and differences.

Theology was not discarded in the Enlightenment, as is often said, it was internalized. Buffon and Laplace followed with their versions of Bernoulli’s random design null hypothesis calculation, and cosmic evolution became accepted fact. The details were yet to be worked out, but it was a fact. Sound familiar?

Not surprisingly Bernoulli’s random design null hypothesis became a key argument in Darwin’s new theory of biological evolution. For like the planets, the species show striking patterns. Over and over, they are “aligned.” As Darwin pointed out, “We never find the bones of the arm and forearm, or of the thigh and leg, transposed.” If God created the species, the evolution inventor pointed out, then we should find “a sudden leap from structure to structure?”

Such rationalism was rampant in Darwin’s thought, and it is pervasive in the literature today. Biological patterns, and there are many, disprove creation and therefore prove evolution. Mark Ridley, in his textbook Evolution, explains to the student that protein comparisons between 11 different species should not reveal the patterns we find if they did not evolve:

If the 11 species had independent origins, there is no reason why their [traits] should be correlated.

This is nothing more than seventeenth century rationalism in the guise of twentieth century molecular biology.

This is but one example of the many metaphysical arguments motivating and mandating evolution. Why don’t the historians explain this, you might wonder. The answer, it seems, is that historians allow themselves to analyze the evolutionists, but not their arguments—at least not from a theory-neutral perspective.

One helpful exception is Neal Gillespie’s Charles Darwin and the Problem of Creation. Gillespie reveals many of Darwin’s metaphysical arguments, and he explores their context to a limited extent. But the Enlightenment and earlier influences, and the place and importance of metaphysics in today’s theory, are outside the scope of Gillespie’s fine work. And of course those subjects would have raised awkward questions about the theory’s scientific status—and that is not allowed.

Friday, April 2, 2010

DNA Methylation in Bacteria

How do bacteria respond to environmental challenges and signals so quickly and effectively? In addition to genetic modifications there are a series of non genetic, or epigenetic, modifications. Genetic modifications change the sequence of nucleotides that, for instance, comprise a protein-coding gene. In that case the resulting protein is modified to better handle the environmental challenge. Epigenetics, on the other hand, involves various other types of modifications. For instance, the three-dimensional structures of proteins may be dramatically altered, or tiny chemical signals—methyl groups—may be added to certain proteins or DNA sequences. As with genetic modifications, many of the epigenetic modifications are heritable, so the adjustments are passed on to later generations.

Consider the methylation of DNA. This occurs at certain target sites along the DNA sequence where specific short DNA sequences appear. These sequences are found by special proteins as they move along the DNA. The special proteins search for these sequences and add a methyl group to the adenine base that appears within the sequence. The protein binds to the DNA, twists the helix so the adenine base rotates into a precisely shaped pocket in the protein, and the protein then facilitates the transfer of the methyl group from a short donor molecule to the adenine.

The short donor molecule does more, however, than just supply a methyl group. It also actually helps to control the special protein. How does this work? Of course the short donor molecule binds to the pocket of the special protein so the methyl group is ready for transfer. But the donor molecule also binds to another site on the protein. This binding serves to alter the structure of the protein, enhancing its function. So the special protein is designed to do its job when it is charged with a donor molecule.

But not all of the DNA target sequences are methylated. This complex DNA methylation function doesn’t occur if the target sequence is protected by another protein that binds to the sequence. This protein binds to some of these DNA target sequences but not all. The result is a particular DNA methylation pattern which influences which genes are expressed, and therefore how the bacteria interacts with the environment.

This DNA methylation pattern is propagated to the daughter cells when the bacteria divides. When such division occurs the DNA must, of course, be replicated. The double helix is separated and new complementary strands are synthesized on each strand. At the DNA target sequences there is an adenine on both strands. If both adenines are methylated, then after replication the two newly formed DNA helices will each contain only a single methylated adenine—the original adenines are methylated but the new adenines that were added are not.

These hemimethylated sequences are rectified by other proteins, which methylate the lone, unmethylated, adenines. The result is that after cell division, the two new bacteria cells have inherited the full DNA methylation pattern established in the original cell. You can read more about this and other bacterial epigenetic mechanisms in this review paper.

This is one small chapter of the epigenetics story that helps to explain the incredible adaptation capabilities we observe in both single and multiple cell organisms. The idea that such capabilities evolved is, of course, not motivated by science. Evolutionists once claimed that adaptation was obvious proof of evolution, but in fact biological adapation is yet another massive problem for evolution.

Thursday, April 1, 2010

What You Think You See is Not What You See

Those textbook diagrams showing the supposed evolution of vision reveal a real blind spot, for there are big problems with this evolutionary narrative. For instance, the biochemistry, even in primitive eyes is numbingly complex. The notion that it evolved is nowhere motivated by the scientific evidence.

Second, the sensing of light signals, alone, does nothing for it needs to be interpreted in the brain. And third, speaking of signals, the signal processing that goes on between the initial signal transduction and the brain is profound. The signal transduction, as phenomenally complex as that is, is only the beginning.

The incoming light is converted into an electrical signal (action potential) and then undergoes massive processing before making its impact on the brain. And new research is revealing new levels of complexity in this processing. If you stare at a horizontal line first, then a circle appears stretched out, like an ellipse. This simple fact was ingeniously used in an experiment to study how the processing deals with the rapidly changing incoming signals.

Our eyes move several times per second. If we were aware of what our eyes were seeing we'd have difficulty making sense of such rapid movements. As it is we don't sense such movements, and one theory held that the signal processing in our vision system deleted certain scenes to keep the image steady in our brains. But when subjects were shown a horizontal line too quickly to be sensed, they nonetheless then saw a circle as an ellipse.

In other words, even those scenes of which we are not aware have an effect on the scenes that we do see. Our vision system is even more complex than we thought, and the evolutionary narrative, that a few mutations created and modified a few genes from which arose fancy new vision capabilities, has become that much more absurd.