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.

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.

Why Evolutionists Say Evolution is a Fact

Evolutionists say evolution is a fact, every bit as much as gravity is a fact. That is remarkable. We see and even feel gravity everyday. Evolution, on the other hand, entails rather dramatic, one-time, events that were supposed to have occurred long ago, when no one was around to witness them. How could we be sure of such a theory? There must be some extremely powerful and compelling scientific evidence for evolution to make it a fact as gravity is a fact. That is what one would think. But, surprisingly, there is no such evidence. When evolutionists try to explain why evolution is a fact, it is a tremendous anticlimax. Consider this example from evolutionist Massimo Pigliucci:

Consider the following: if there is any obvious evidence of the fact that evolution has occurred, it ought to be the impressive and worldwide consistent fossil record. Moreover, using the geological column as a way to date events during the history of the earth predates Darwin (i.e., it was invented by creationists), and we keep discovering new intermediate fossils further documenting evolution every year.

This is astonishing.

The fossil record, of course, is not "obvious evidence" of the fact of evolution. If we want to speak of facts, the fossil record provides a wide spectrum of data which do not prove evolution. Indeed, the fossil record falsified several fundamental predictions of evolution. That is a fact. Another fact is that evolutionists make startling truth claims and then back them up with weak or even contradictory evidences. This raises the question of how evolutionists could have such certainty in light of such skimpy evidence?

Scientific American: The Banality of Evil (ution)

Katherine Pollard's Scientific American article from last year, about what makes humans different from chimpanzees, is an unfortunate example of the banality of evolution. Charles Darwin's theory, updated to account for a variety of surprise evidences, is taken as fact and this leads to a remarkable level of credulity. Whatever we find in biology, it must be the product of evolution. This leads evolutionists away from a whole range of possible investigations and interesting questions. Instead, they drone on with the same, tired, evolutionary explanations that are so predictable. Here are a few passages of note from Pollard's article:

Six years ago I jumped at an opportunity to join the international team that was identifying the sequence of DNA bases, or “letters,” in the genome of the common chimpanzee (Pan troglodytes). As a biostatistician with a long-standing interest in human origins, I was eager to line up the human DNA sequence next to that of our closest living relative and take stock. A humbling truth emerged: our DNA blueprints are nearly 99 percent identical to theirs. That is, of the three billion letters that make up the human genome, only 15 million of them—less than 1 percent—have changed in the six million years or so since the human and chimp lineages diverged.

Humbling? Why is Pollard humbled? Did the brain evolve the feeling of humility to be activated upon learning of similarities with other species? If you think this is sarcasm check out what evolutionists have had to do to explain human behavior. It isn't your Daddy's evolution anymore. It seemed that evolution was as silly as could be. It was story telling on steroids. But then came the updated version of the theory, and evolutionists became their own best parody.

Evolutionary theory holds that the vast majority of these changes had little or no effect on our biology. But somewhere among those roughly 15 million bases lay the differences that made us human. I was determined to find them. Since then, I and others have made tantalizing progress in identifying a number of DNA sequences that set us apart from chimps.

Tantalizing progress? You've got to be kidding me. This "progress" is based on yet another evolutionary fumble; namely, an extreme over emphasis on DNA. In evolution-dom, DNA is king. Long ago evolutionists latched onto DNA as a Hail Mary explanation of how the information for macro evolution could be stored and passed on. Ever since then DNA has been viewed as the blueprint for biological design. Like a computer program, DNA was forced into the role of the biological "program" that determines the nature of an organism. The other parts of the organism, as with the computer, are viewed as merely mechanically performing tasks and following instructions.

Evolutionists need DNA to fulfill this role because they need unguided change to be heritable. Such change was viewed as created by DNA mutations, which could then be passed on to offspring. Scientific problems with this dogma are mounting, but evolutionists will be slow to adjust and reconcile such a fundamental failure.

Until recently the DNA dogma was even more narrow, as evolutionists viewed only the genes within the DNA as important. The remainder of the DNA (the vast majority) was often thought of as useless junk. Now that science, no thanks to evolution, is discovering that "junk" DNA can actually be important, evolutionists changed their view to include more of the DNA.

Now science is taking the next step, again no thanks to evolution, in finding that the nature of an organism may be influenced by players outside the exalted DNA. One obvious suggestion for this comes from precisely the data Pollard analyzes: the human and chimp DNA which are so similar. But Pollard's story is firmly rooted in the DNA dogma. Evolutionists make the absurd claim that a handful of genes, which stand out in humans, are the source of so much of the human-chimp difference.

Because most random genetic mutations neither benefit nor harm an organism, they accumulate at a steady rate that reflects the amount of time that has passed since two living species had a common forebear (this rate of change is often
spoken of as the “ticking of the molecular clock”).

Except that the "molecular clock" doesn't actually work. It is yet another false prediction that goes unmentioned.

Acceleration in that rate of change in some part of the genome, in contrast, is a hallmark of positive selection, in which mutations that help an organism survive and reproduce are more likely to be passed on to future generations. In other words, those parts of the code that have undergone the most modification since the chimp-human split are the sequences that most likely shaped humankind.

Do we really need evolution to tell us that the DNA segments with the most differences between the human and chimp are more important in understanding the sources of the human-chimp difference? Here we see the banality of evolution.

The fact that HAR1 was essentially frozen in time through hundreds of millions of years indicates that it does something very important; that it then underwent abrupt revision in humans suggests that this function was significantly modified in our lineage.

More banality. The gene is significantly different in humans as compared to a wide range of other species. So yes, this suggests its function is significantly different in humans. This conclusion is obvious and we don't need evolution to figure it out. The evolutionary wrapping is superfluous. The talk of how the gene is "frozen in time" and that it "underwent abrupt revision in humans" is gratuitous story telling. Science gives the important findings and evolution gives the meaningless extras.

In fact, what evolutionists do not mention is that HAR1 is yet another example of genome differences between species that are larger than evolution predicted. The human-chimp differences are more than an order of magnitude greater than what evolution predicts. Fortunately, this freak barrage of typos just happened to hit the mark, providing quantum leaps in design improvement leading to the human brain.

Furthermore, these typos simultaneously must have altered two other genes which overlap with HAR1. That's right, HAR1 lies in a region of overlapping genes. Imagine typing a paragraph which contains one message when read normally and a different message when read backward. Not only must evolution have created all of biology's genetic information, but it composed the information in overlapping prose. Someday evolutionists will figure out how.

It might seem surprising that no one paid attention to these amazing 118 bases of the human genome earlier. But in the absence of technology for readily comparing whole genomes, researchers had no way of knowing that HAR1 was more than just another piece of junk DNA.

It was technology, not evolution, that was needed.

The way to evolve a human from a chimp-human ancestor is not to speed the ticking of the molecular clock as a whole. Rather the secret is to have rapid change occur in sites where those changes make an important difference in an organism’s functioning. HAR1 is certainly such a place. So, too, is the FOXP2 gene, which contains another of the fast-changing sequences I identified and is known to be involved in speech.

I wish Charles Darwin could see the new levels of banality he has given us. The "fact" of his theory now underwrites the ascribing anything and everything to evolution, no matter how ludicrous. Evolution has become a tautology. Whatever we find in biology is simply chalked up to evolution's amazing powers. A core tenet of evolution is that the biological variation, upon which natural selection operates, is independent of need. This view has been falsified so many times that evolutionists such as Pollard no longer skip a beat when reporting on evolution's "secret" miracles. In this case, evolution's secret is to focus the multiple mutations where they are needed to construct jaw-dropping designs.

Evolution's Appeal

Scientific problems with evolution don't really matter. This genre of thought scratches too many itches to let science bring it down. Traditionally those itches have mainly been theological and philosophical. Now, as the evolutionary narrative subsumes human nature, new itches emerge. Geoffrey Miller, an evolutionary psychologist, provides a peek into this latest addition to evolution's appeal. This quote appears in a fancy, inside cover advertisement run by the John Templeton Foundation, in the May 2009 Scientific American:

In the last two decades, evolutionary psychology has cast new light on ever more facets of human nature. And contrary to popular critiques of the field, it has done so in way that are ever more intellectually thrilling, morally enlightening, spiritually satisfying, and socially progressive. What we mean by "evolution" and "human nature" continues to develop through mutual interaction, lie the passions of a whispering couple in a close-embrace tango.

What a coincidence that objective scientific research just happens to be "intellectually thrilling, morally enlightening, spiritually satisfying, and socially progressive." Any chance that is not really a coincidence? Any chance evolutionary research is not really scientific research? Miller continues:

During the 1990s, biologists developed a whole new toolbox of ideas about the nature of evolution, including theories based on life history, multi-level selection, strong reciprocity, good-genes sexual selection, and costly signalling. These terms may be unfamiliar to non-specialists, but they represent a revolution in Darwinian theory and have proven their value again and again in understanding aspects of human nature that defy simplistic "survival of the fittest" reasoning.

That's true, there has been a revolution in Darwinian theory. And the just-so stories have become even more unbelievable. This new toolbox of ideas does explain many aspects of human nature, but so does astrology. Ever since Darwin, evolution has become increasingly complex and circuitous. Today it looks like one massive Rube Goldberg machine, ready to collapse on itself.

Histone Inspectors: Codes and More Codes

By now most people know about the DNA code. A DNA strand consists of a sequence of molecules, or letters, that encodes for proteins. Many people do not realize, however, that there are additional, more nuanced, codes associated with the DNA. For instance, minor chemical modifications (such as the addition of a methyl group) to the DNA provide bar-code like signals to the protein machinery that operate on the DNA. This DNA methylation influences which genes, along the DNA strand, are read off. And this DNA methylation itself may be modified to provide additional information.

Or again, the DNA is wrapped around histone proteins, and these histones are also bar-coded. The histones have a hub, around which the DNA wraps, and a tail that sticks out on which chemical tags are attached. Again these tags are signals for the protein machinery. Furthermore, these tags are removed as well. Such modifications and removal of these chemical tags means that these codes are dynamic, and there are protein inspectors that double-check these complex encodings.

These subtle codes are also context dependent. In one type of cell a histone modification may turn off a gene whereas in another type of cell the same histone modification may turn on the gene.

New research has elucidated some of the structural details of the histone inspectors. This is important research because these subtle codes, and associated machinery and mechanisms, are not yet fully understood. They have profound biological impact, but we still have much to learn about how it all works.

Needless to say the idea that all of this arose on its own, as a consequence mutations and the like, luckily putting together such intricacies, is beyond silly. Religion drives science, and it matters.

Does the Evidence Support Evolution, or does Evolution Support the Evidence?

For all their disagreements, evolutionists strongly agree that evolution is a fact, just as gravity is a fact. There is no question that evolution occurred. And since evolution is as certain as gravity, those who do not assent must not be rational, or they must have ulterior motives. If there are scientific questions about evolution (and there are), they merely relate to the question of how evolution occurred, not whether evolution occurred. Those who point out that the scientific evidence does not bode well for evolution must understand that such evidence can in no way call the fact of evolution into doubt. The scientific evidence can only bear on questions of how evolution occurred.

Now this logic might be reasonable if the scientific problems with evolution were minor compared to the supporting evidence. We certainly do not doubt the fact of gravity even though we do not understand the details of how it works. But then again, the evidence for gravity is rather strong. In the case of evolution, it is the other way around. In the case of evolution, it is the problems which are rather strong.

We don't understand how life could have first evolved, we don't understand how multicellular organisms could have evolved from unicellular organisms, we don't understand how identical unconstrained DNA sequences could be conserved in distant species, we don't understand how shocking differences could have evolved in otherwise similar species, we don't understand how consciousness could have evolved, we don't understand how adaptive mechanisms could have evolved, we don't understand how a thousand and one complex structures, superior to our best military machines, could have evolved, we don't understand how ..., well you get the idea.

In light of the scientific evidence, the fact that evolutionists shout down any dissent makes them look more like the Wizard of Oz than sober scientists. Consider, for instance, the problem of how multicellular organisms could have evolved from unicellular organisms. Bob Holmes reported on this last year in The NewScientist. One problem is that such an evolutionary move must have occurred quickly, without leaving any evidence. As one evolution admitted, "The different branches of the animal tree evolved very rapidly in a short period, a long time ago."

Another problem is that reconstructions of the evolutionary tree are not stable. Was the ancestor of multicellular organisms a choanoflagellate? Or was it a placozoan, or a ctenophore, or even a sponge larva? Different methods lead to different reconstructions. And of course the move to multicellular organisms required more complex designs. Not surprisingly, the details of early animal evolution are still hotly debated.

While evolutionists can provide plenty of guesses about how multicellular organisms could have evolved from unicellular organisms, the fact is evolutionists have no idea how they actually evolved. And if evolutionists have no idea how they evolved, can we really be sure that they did evolve? Evolutionists scoff at such skepticism. It is unwarranted, they say, because evolution is a fact. It seems that rather than the scientific evidence putting to rest problems with the fact of evolution, it is the fact of evolution that is putting to rest problems with the scientific evidence.

Junk DNA: The Real Story

By now you have probably heard about so-called junk DNA. In recent decades the genomes of a growing number of species have been mapped out. Not surprisingly, scientists did not understand how many of these DNA sequences worked. For instance, repetitive sequences are common, but what do they do? As these data accumulated evolutionists increasingly viewed such sequences as useless junk. Then, years later, various functions began to emerge as our knowledge grew. This junk DNA story is the latest version of what seems like a repeating bad dream that goes like this. Scientists discover something new in biology but don't understand it. Evolutionists, unaware that they are staring at a design whose complexity dwarfs their puny understanding, decide it is a useless evolutionary leftover. Such a useless design is pressed into service as an evolution apologetic. Later, when the function is eventually uncovered, evolutionists automatically claim the design as an evolutionary achievement. The structure goes from junk to treasure without a second thought.

A recent finding of "junk" DNA function involves repetitive elements which have been found to be active in certain tissues. The researchers concluded that this activity "has a key influence" on the overall activity of the mammalian genome. As one evolutionist admitted, "As a class [repetitive elements] are not just a junk DNA. They're not just parasites, but they can shape the architecture of the genome."

So what is the story here? That biological designs are complex? That evolutionary thinking does not anticipate nature very well? That evolutionists should think twice and speak once, rather than the other way around? Yes, these are all good lessons for us, but these are not the real story behind junk DNA (and the other rags-to-riches stories in the history of evolutionary thought).

The real story behind junk DNA is not that it is a show stopper for evolutionary theory. In fact, evolution never predicted junk DNA. And it can get by just fine, thank you, if there is no such thing as junk DNA. But if evolution is so ambivalent toward junk DNA, then why is it such a powerful apologetic? If the science doesn't hinge on the efficacy of DNA, then why is that very efficacy so important? And why is the finding of function so important to evolution's opposition?

Here we find the real story behind junk DNA. Junk DNA (and all examples of evil and dysteleology in nature), proclaim evolutionists, contradicts creation. The message seems so obvious and instinctive that it is not even thought through clearly. Is not junk DNA clear evidence for the scientific theory of evolution? No. The junk DNA apologetic is a religious statement about God. It is that simple.

Junk DNA mandates evolution because it denies creation on the basis of religious beliefs. God would never create DNA with no function. Such beliefs are not open to scientific rebuttal. Science has nothing to do with it. I cannot even begin to recount the number of scientists, professors and pundits I have heard proclaim, in the name of science, such religious conclusions as proof of evolution. They should be wearing a tiara and holding a scepter. This is the real story behind junk DNA.

Evolution: A One-in-a-Billion Shot

It is no surprise that there are scientific problems with evolution. Its predictions are continually turning out to be false. It undoubtedly ranks number one in faulty expectations. For instance, one of its primary predictions, common descent, has badly failed. The reconciliation of the molecular and the visible, morphological, features has been a major problem in trying to resolve the evolutionary tree. The molecular and morphological features often indicate "strikingly different" evolutionary trees that cannot be explained as due to different methods being used.

The growing gap between molecular analyses and the fossil record, concluded one researcher, "is astounding." Instead of a single evolutionary tree emerging from the data, there is a wealth of competing evolutionary trees. And often what evolutionists conclude is downright strange. Over time insects must have evolved wings, then lost them in the evolutionary process only then later yet again to evolve them (or less parsimoniously, the wings could have disappeared over and over throughout the tree). Or again, bats must have independently evolved, in separate lineages, the same intricate echolocation capability.

As one researcher put it, "Phylogenetic incongruities can be seen everywhere in the universal tree, from its root to the major branchings within and among the various taxa to the makeup of the primary groupings themselves." These are not minor statistical variations and the general failure to converge on a single topology has some researchers calling for a relaxation from "tree-thinking."

And this is but a sampling of the many falsified predictions of evolution. There are many more where these came from as evolutionists are constantly surprised. You can see 14 basic predictions that were falsified here. Predictions which evolutionists are absolutely sure of are routinely found to be false. "I about fell off my chair" is the typical refrain of evolutionists.

Obviously the scientific evidence does not bode well for evolution. One way to evaluate the theory is with Bayes' theorem which states that for any given scientific observation, O, the probability a theory, T, is true, given that observation, is the probability of the theory prior to the observation multiplied by the probability of the observation given that the theory is true, divided by the probability of the observation without knowing whether the theory is true or not. It sounds complicated but the formula is simple:

P(TO) = P(T) * P(OT) / P(O)

Bayes' theorem gives us a way to evaluate a theory given a series of observations. A difficulty, however, is that the probabilities are difficult to gauge. What is P(T), P(OT) and P(O)? What we can do is use a conservative computation, giving evolution favorable treatment at every turn.

Consider the ratio P(OT) / P(O). If an evolutionist is certain that observation, O, will not be observed, then the numerator should be quite low, say one in a million or one in a thousand. If P(O) is 0.5 then the ratio would be 0.000002 or 0.002, respectively. But to be conservative, and give evolution favorable treatment, let's set the ratio to 0.2, orders of magnitude greater than is reflected in the evolutionists expectations.

For our 14 falsified predictions, using these extremely conservative values, Bayes' theorem tells us that evolution is a one-in-a-billion shot. This calculation is conservative, and there are many more falsified predictions for which to account. But you can see the religion behind evolution did not lead to a very good scientific theory.

Evolution and Evolvability: A New Kind of Science

The basic idea behind evolution is rather simple: in times of difficulty not everyone survives, or at least not everyone reproduces. Those who are faster, bigger, taller, stronger, smarter, or whatever it is that makes for successful reproduction, will do just that. And those who lack the requisite capabilities will not reproduce, or not reproduce as prolifically. One way or another, the result is that, in those difficult times, future generations are more representative of the winners. The traits of the successful reproducers are passed on more often. This means the population undergoes a change—it evolves.

Just this sort of change has been demonstrated by the breeders and Darwin surmised that nature could do the same thing, except to a greater degree given long time periods and the ruthless, unending battle for survival. In all of this there is, however, the basic assumption that populations just naturally have significant variation.

Evolution relies on the fact that populations consist of individuals of various sizes, shapes and skills. For a given environment some individuals are going to be better reproducers than others. It is a simple fact that seems so obvious no one ever much questioned it.

But in the twentieth century a great deal was learned about genetics and how such biological variations arise in populations. It isn't simple.

Biological variation arises as a consequence of a profoundly complex Mendelian machine consisting of genes and their interactions, molecular machines that replicate and copy the DNA, other machines that translate the copied DNA into proteins according to the genetic code, and so forth. If the resulting biological variation is the fuel of evolution, then how did the variation, and its underlying machines, arise in the first place?

With evolution we must believe that evolution just so happened to create elaborate machinery which just so happened to enable further evolution to occur. Evolvability must have evolved.

I say "just so happened" not in derision, but rather to describe evolutionary theory. Remember, the idea behind evolution is that a population will change because the winners are better represented in future generation. In other words, we can expect the future generations to be better at reproducing. That does not mean we should expect more biological variation via incredibly complex molecular machines acting in coordinated fashion. As one evolutionist admitted in a recent paper:

If evolvability represents the long-term evolutionary potential of a population, there is no reason why individual selection will necessarily maximize it. On the contrary, logically, individual selection could have the effect of destroying evolvability. … one can imagine that fixation of the fittest genotype from those presently available might have detrimental effects on the population’s evolvability—its ability to adapt in the future. … It could be that individual species show a tendency to evolve towards an inability to respond adaptively to subsequent environmental changes—at the level of individual selection, non-evolvability could, in principle, be favoured.

This reveals a profound serendipity in evolutionary theory. Evolution relies on a biological variation machine which did not need to be present. It just so happened that evolvability evolved so evolution could occur.

But this is not all. This problem of complex biological variation, which has been known for many years, is now being amplified by new research showing that biological variation is not only awfully convenient, but that this variation in populations actually responds to environmental challenges.

When there is an environmental shift species amazingly, in direct contradiction to evolutionary theory, respond rapidly and effectively to the new challenge. Sometimes the response is an invisible molecular adjustment that alters the metabolism; in other instances the organism's entire body plan is modified. From molecular to morphological change, biological adaptations are rapid and effective.

As if evolution was not silly enough already, science increasingly reveals its absurdities. Only religious convictions can find such mythology to be fact. Evolutionists now speak of adaptive mutations and adaptive substitutions. And they wonder how their blind process could design such intelligence. How could differential reproductive success lead to organisms that amazingly adapt to change? How could evolution produce machines tuned and ready to adjust to the environment? Like physiological changes that adjust an individual to environmental changes, adaptive changes adjust a population to environmental changes. In both cases biology relies on profoundly complex mechanisms.

Since evolutionists are convinced their idea must be a fact, they must believe this all makes perfect sense. Somehow, in this mockery of science, evolvability evolves. For instance:

For Kirshner & Gerhart (1998), the developmental process, in animals in particular, is such as to enhance the probability that new mutations changing phenotype will be adaptive, and the adaptive substitutions occurring serve to reinforce the ability of the developmental process to subsequently change adaptively. Draghi & Wagner (2007) have argued on theoretical grounds that adaptive substitutions will tend to increase future adaptability.

Amazing. I guess we're just living in the right universe. Religion drives science, and it matters.

The Genome of a Microbial Eukaryote: You Can't Make This Stuff Up

New research is confirming the evolutionary conundrum of early complexity. The research shows that a microbial eukaryote, Naegleria gruberi, shares a large number of genes in common with other eukaryotes. And why is this a problem? Evolutionists have resorted to many incredible just-so stories of convergence. From intricate spider web designs to entire vision systems, evolutionists have been forced to say such designs, because they are found repeated in distant species, have evolved more than once. And while the supposed independent evolution of these striking designs is silly, even these evolutionists have not yet said that similar genes evolve independently. Until and unless they resort to such a fantasy they must say that similar genes in different species have arisen from a common ancestor. And that leads to another problem.

According to evolution, similar genes in different species have a common ancestral gene. But a great many similar genes are found in a great many different species. Consequently evolutionists are forced to conclude the common ancestor was a super ancestor. For decades now evolutionists have been jacking up the capabilities of early life. All the high-tech innovations of biology were, apparently, produced in those warm little ponds of early life.

The new research tells us that with evolution we must believe that the last common ancestor of the eukaryotes must have had at least 4133 genes. This is up from the earlier estimate of 3417, and it is a lower bound. For several reasons the number must even be significantly greater than 4133 genes if evolution is true. This continues the theme of, as one evolutionist put it, "The Incredible Expanding Ancestor of Eukaryotes."

These gene numbers alone force evolutionists to conclude that the last common ancestor of eukaryotes was already a complex organism. This is also the conclusion when the biology is compared. That early eukaryote must have had not only the vast majority of the complex DNA replication, RNA splicing and interference, and protein translation machinery, it was also capable of advanced movement and was equipped with versatile energy conversion systems.

This is truly an astonishing story evolutionists are telling us. Incredible biological capabilities, crucial to advanced life, just happened to arise rapidly in those heady days of early evolution. It was, as evolutionists now say, a giant step to an amoeba, yet a small step to man. Right. I can hear the ball bearings already.

The Religion Behind Skepticism of Evolution

If evolution is motivated by religious thought then what about skepticism of evolution, is it not also religiously motivated? Yes, there is religion behind evolution skepticism, but not in the way we are told. The constant drumbeat of evolutionists and their media groupies is that skepticism is all about creationism. I have lost track of how many times I have been called a creationist. In one debate I was asked if I accept the fossil record, as though it must conflict with my religion. Evolutionists never seem to tire of erroneously labeling their detractors as creationists.

It is not true that evolution skepticism is grounded in creationism any more than evolution is grounded in atheism. But skepticism does have a religious motivation, of a sort. Simply put, we do not accept that the religious mandates for evolution are necessarily true.

How did Charles Darwin know that God would not create the species as we find them? He argued over and over that the biological evidence disproved divine creation, and so evolution (somehow) must be true. Similar arguments were used by evolution co-founder Alfred Wallace. They were foundational and remain crucial today. How does Ken Miller know that God would not create the mosquito? How does Jerry Coyne know God would not design the sort of embryos we find?

The evolutionists may well be correct in their assertions, but we don't know they are correct. We believe the evolutionist's mandate that God would create the world according to their sentiment is an over reach. Our religious belief, on the other hand, is more of a minimalist approach. Yes, scripture tells us some things, but it does not tell us everything.

But you won't learn that from the nightly news or the evolution literature. You will be told that evolution skepticism has a religious ax to grind. A friend of mine was interviewed by NBC Nightly News. It was a lengthy interview but his scientific problems with evolution were not what the journalists were looking for. Not surprisingly he was not included in their lead story which informed viewers about "The Battle Between Science and the Bible."

The headlines won't tell you this but our religious motivation, as it were, is to keep a lid on religious beliefs that are unsupportable.

The Evolution of Venomous Proteins

Imagine a Star Trek movie in which two strikingly similar planets are discovered. The planets are in different corners of the universe, yet their coastlines, mountain ranges, inhabitants and cultures are amazingly alike. Or again, imagine a new, yet fully-formed, planet is discovered. The planet was not there a few years earlier, but there it is, complete with inhabitants and civilizations. These two phenomena--convergence and rapid appearance--are common in biology and, needless to say, they contradict evolutionary expectations. These surprises are not often seriously reckoned with. Evolutionists do not engage the implications of these findings, and sometimes they even avoid or deny the findings altogether.

To explain convergence and rapid appearance evolutionists tack on unlikely and complex explanations to their their theory. These epicycles are, themselves, a sort of measure of the truth value of a theory. A large number of epicycles suggests the theory is merely a tautology--a description of what we observe rather than an explanation of an underlying fundamental aspect of nature. A recent study of animal venom is the latest example of this pattern of epicycles and denial.

The study compared toxic proteins across a wide spectrum of species. These molecular assassins are cleverly designed. In World War II, the Allies bombed German ball bearing factories as a way of disabling its larger war machine. Obviously such a strategy required detailed knowledge of the war machine, how it works, the single point failures, where they are located, how they can be disabled, and so forth. Similarly, these biological toxins are finely tuned to disable crucial processes, such as the conversion of food energy to chemical energy, or the nervous system to paralyze the prey. Beyond vague speculation, evolutionists have no explanation for how such finely tuned toxins could have evolved.

Beyond the problem of how such designs evolved, these toxic proteins also reveal patterns of convergence and rapid appearance. Evolutionists are trying to figure out how very different types of animals have such similar venomous proteins. And some of the proteins appear to be completely new, as there are no known proteins in biology that share any significant degree of similarity. This implies a massive degree of evolutionary change in a relatively short period of time (something the study fails to mention), ending with a finely tuned molecular machine.

How can evolutionists present such findings within their framework? A common literary device in the evolution genre is the use of teleological language, such as "evolution designed the hemoglobin molecule to perform several important functions." Of course evolutionists do not literally mean that evolution consciously designed anything. Their teleological language is useful shorthand. Useful because it masks the absurdity of the notion that the blind, unguided process of evolution stumbles upon incredibly complex designs, again and again.

And so, not surprisingly, in this study the evolutionists use a plethora of teleological language in their peer reviewed paper. The reader is told, for example, that the study "confirms that convergent protein recruitment" spans all major animal phyla. We also learn that "the proteins chosen" in the evolutionary process are from widely dispersed protein families. Such literary devices are ubiquitous in the evolution genre and crucial to maintaining a credible narrative.

Gene Expression and Evolvability

The twentieth century unveiled the world of molecular biology, including DNA, the genetic code, proteins, and the molecular basis for modern genetics. Such findings, according to Neo Darwinists, nicely supported evolution. Evolutionary change was fueled by variation arising from genetic mutations. How the genes, and their supporting cast, arose in the first place was a more difficult question. But given their existence the evolutionary narrative was held with great confidence. This straightforward narrative is now understood, however, to be too simplistic. For instance, we now understand that biological variation often arises not from changes in the genes but rather from changes in the expression levels of the genes. Even those celebrated beaks of Darwin's finches appear to be changing via variation in gene expression levels. And more significant variation, such as body plan differences in related insects, also correlate with varying gene expression levels. These new findings do not bode well for traditional evolutionary theory.

From yeast to humans, studies reveal that biological variation can correlate with gene expression levels. Interestingly, as one recent paper explains, these varying levels of gene expression repeatedly show up in some genes but not others. The mechanisms that control the gene expression levels, though varied, focus on these genes.

For instance, recent studies have found that the similar genes in similar species may have substantial differences in expression levels, while other types of genes share conserved expression levels.

In fact, varying expression levels correlate with changes even within a species. New research published this week reveals that gene expression levels can vary significantly between people who otherwise, of course, share extremely similar genomes. As one researcher explained:

the bulk of the differences among individuals are not found in the genes themselves, but in regions we know relatively little about. Now we see that these differences profoundly impact protein binding and gene expression.

In fact, not only do gene expression levels vary between related species and individuals within the same species, they also vary within the same individual, for instance in response to different environmental changes. As one evolutionist explains, when the expression of a gene is strongly regulated between different conditions, it also evolves rapidly between related strains or species. It seems the line between physiology and evolution is blurred:

Thus, it is possible that genes differ in their capacity for expression flexibility, which is manifested at various timescales: during evolution in response to mutations; during physiological responses to environmental changes; and within a population of cells as a result of stochastic fluctuations.

He concludes:

As noted above, expression divergence (the extent to which expression of a gene evolves) correlates with expression responsiveness (the extent to which expression of a gene is changed in response to the environment). We believe that the promoter elements discussed above underlie expression flexibility of these genes on short timescales (responsiveness and noise), which are instrumental in the immediate response of a cell to the environment, as well as on longer timescales (expression divergence), which may allow evolutionary adaptation to novel conditions. In other words, the correlation between responsiveness and expression divergence may be due to their dependence on the same promoter properties.

But the mechanisms that influence the gene expression levels are not simple. They involve proteins and DNA sequences. With the traditional theory of evolution we must believe that mutations created such mechanisms, one step at a time while they had little or no ability to influence expression levels. We therefore must contrive imaginary functions that would conveniently lead to their powerful expression level control capabilities.

Furthermore these expression level mechanisms needed to be applied only to certain genes. Not only are the mechanisms complex, but they must arise in the right place.

But the problems do not stop there. For such mechanisms, even when fully operational, would have limited usefulness. They must await environmental challenges to reveal their true worth. When such challenges arise the expression levels of those certain genes must change in the right way. The mechanism, if it works correctly, becomes invaluable. But until then it waits.

So now evolutionists speak of the evolvability of gene expression. The right genes, they say, have an inherent capacity to evolve its expression. In other words, evolution created the mechanisms which caused more evolution to occur—evolution creates evolution.

The Scandal of the Evolutionary Mind

I once had a discussion with an evolutionist who, not surprisingly, claimed that evolution is fact. “Have you ever seen a sea lion try to move across a beach?” It is obviously not a good design, he argued, and so must have evolved. The sea lion’s “design is not intelligent, but rather is a product of evolution,” he concluded, for “design would attempt to produce something that works well, if it is intelligent design, and this does not work well and so is not intelligent design.”

This evolutionist also made a series of erroneous claims about the evidence for evolution. He began with the remarkable statement that “DNA sequences provide an absolute and irrefutable record” that evolution is a fact. “Virtually every single gene sequence we examine,” he explained, “can be seen to be represented in closely related species and in more distantly related species with increasing numbers of nucleotide changes as we look at more distant species.”

It was, he triumphantly concluded, “absolute proof, in hard copy, reiterated in every single gene of every single organism.” It sounded good but it was wrong. The real data, in the real world, simply do not fit the evolutionary pattern as evolutionists envision.

He also claimed that every piece of evidence in biology supports the conclusion that evolution is a fact. But how could this be? I responded that there are many evidences that do not support this conclusion, such as (i) nonhomologous development pathways, (ii) the abrupt appearance of fossil species in the geological strata and (iii) the complexity and circularity of cellular protein synthesis.

To this he responded that these three examples “are not facts.” But these are facts—well known facts. It would be non scientific to say that the abrupt appearance of fossil species, nonhomologous development processes and the complexity and circularity of cellular protein synthesis are not facts. Protein synthesis in the cell is “circular” because it requires pre existing proteins. A leading undergraduate textbook calls the process “inexplicably complex.”

His claim that my examples are not facts, coupled with his insistence that evolution is a fact, raised questions about how he was arriving at his conclusions. How could an evolutionist possibly state that such well known and well documented biological phenomena are not to be considered as facts?

We can argue about what these observations portend. We can debate how well they do, or do not, comport with evolutionary theory. But not facts?

Was this some anonymous internet rant? Was I wasting my time with an ignorant and dogmatic lurker who had nothing to offer but silly and fallacious canards? Hardly. This was a life science professor at a university who was chair of the Biology department. Yes, chair of the Biology department. And his arguments were, unfortunately, typical. I have seen them, or arguments like them, over and over.

This extreme level of anti intellectualism is the scandal of the evolutionary mind. It is always the first shock to those who allow themselves to question the paradigm and venture into the debate with skepticism. Evolutionists are full of bluster, but their position is astonishingly dull.