Transposable Elements: From Junk DNA to Evolution Mechanism

Imagine if, back in 1859, Charles Darwin explained that evolution proceeds in fits and starts. Species rapidly appear as if planted there, and then go unchanged for eons. There would have been, as we say today, no bounce. In fact Darwin would have been laughed off the stage, and he knew it. Darwin had to present a narrative of gradualism. Funny thing is, the fits-and-starts narrative is today precisely what evolutionists tell us.

It seems strange that the absent minded process of evolution would leave a trail of contradictory evidence. For instance, evolution has not squared very well with the fits-and-starts pattern of the fossil record. Why should biology's evidence make evolution appear to be unlikely? Is evolution trying to deceive us? Or perhaps it is merely testing our faith. Well now we know. Enter junk DNA.

As I have mentioned before, a few years back evolutionists began to think that retroviruses could play important roles in evolution. This idea has now taken hold in a much bigger way, with the discovery of Genomic Drive. Amazing new research found that transposable elements, comprising about half of our genome and once thought to be so much junk, are the drivers behind evolution itself.

Now it makes sense that species suddenly appear and then don't change for eons. It is because those transposable elements occasionally awaken to action. The once junk DNA has gone from the dog house to the starting lineup. It turns out that transposable elements supply the genomic drive behind biology's wonders. Mutations are out, jumping genes are in.

In fact, this junk DNA is now thought to have a critical role in ensuring the survival of biological lineages. And how do they work their magic? The answer is easy. Transposable elements, they say, "do their survival work by reformatting and rearranging DNA genomes to sometimes create significant adaptive mutations that undergo natural selection." It is amazing that evolution so cleverly created its own Genomic Drive. Now, evolution is even more of a fact.

Research Into How Science and Evolutionary Beliefs Relate

Michael Reiss has published important new work on the relationship between biology and religion. It's good to see these important religious influences being investigated. Here is a summary of this important relationship and influence:

Belief in evolution is widespread and gaining significance in a number of countries. My research examines the characteristics of science and of evolutionary beliefs and the possible relationship between science and religion. I argue that evolution is sometimes best seen not as a misconception but as a worldview. In such instances, the most to which a science educator (whether in school, college or university) can normally aspire is to ensure that students with evolutionary beliefs understand the scientific position. In the short term, the scientific worldview is unlikely to supplant an evolutionary one for students who are firm evolutionists. We can help students to find their biology courses interesting and intellectually challenging without their being threatening. Effective teaching in this area can help students not only learn about biology but better appreciate the way science is done, the procedures by which scientific knowledge accumulates, the limitations of science, and the ways in which scientific knowledge differs from other forms of knowledge.

The damage from religious beliefs seems to be spreading faster than it can be contained. But there is reason for hope. Such beliefs can be countered with rational thinking and science. Do not give up.

More Accelerated Sequence Evolution

Evolutionists have a wide range of explanatory mechanisms from which to draw when trying to figure out how the species evolved. But sometimes these supposed mechanisms look more like a cover-up than an explanation. For instance, the differences between the human and chimp DNA instructions are not sprinkled, more or less at random, throughout our genome. Rather, these differences are found in clusters. Even more interesting, at these locations the chimp's genome is quite similar to other primates--it is the human that differs from the rest, not the chimp. Evolutionists refer to these clusters as human accelerated regions (HARs) because they believe the human genome evolved from a human-chimp common ancestor. These HARs cause several problems for evolution. For instance, we must believe that evolution magically caused rapid changes to occur right where needed to improve function and eventually create a human. As one evolutionist wrote:

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.

This is truly a whopper of a just-so story and you can read more here and here.

Now, evolutionists are again appealing to this accelerated evolution "mechanism" to explain the origin of a toxic protein found in the saliva of a North American shrew. The protein chops up other proteins using a novel mechanism, and evolutionists are saying that it "evolved adaptively via acquisition of small insertions and subsequent accelerated sequence evolution."

There you have it--evolution happens. But that's not all. Evolution implemented the same clever design in a Mexican lizard. Amazing.

This is yet another example of a striking design repeat in biology, but this time it is via accelerated evolution. Evolutionists have not calculated the probability of blind mutations doing this not once but twice, probably because it doesn't matter. After all, evolution is a fact.

Placental Evolutionary Tree: Example of Theory Complexity

It has long been understood that elaborate explanations can always be contrived in order to explain observations. But why should we believe they are true? The backward motion of planets can be explained by a series of epicycles, designed specifically to fit the peculiar motion. But with heliocentrism no such adjustments are required—the backward planetary motion is a natural outcome. So while complicated narratives are needed for bed-time stories and soap operas, parsimony is valued in science. Nature, and only nature, should be explained. Scientists become suspicious when a theory becomes increasingly complex to accommodate failed expectations—when particular explanations are needed to adjust to contradictory findings.

Falsifications can also be a sign of problems if they are common. If a theory makes predictions that are consistently wrong, then suspicion again arises. Regardless of how much complexity is needed to explain the contradictory findings, a steady stream of such findings, in itself, can indicate weakness.

Evolution has a long history of false predictions leading to rising complexity. The evolutionist’s claim that all of this is a sign of good science, of learning how evolution actually occurred, is not consistent with evolution’s many falsified predictions and complex adjustments.

One example of this is the evolutionary history of placental mammals. In recent decades this history was investigated by comparing the DNA sequences from different placentals. But the results were conflicting. Now, recent research has once again investigated this evolutionary history, this time using the much touted DNA retroelements which promise to provide a much clearer picture. But again, evolutionists must resort to convoluted explanations in order to fit the data to their theory:

We believe that the most parsimonious interpretation of the current data is that the ancestral placental populations were characterized by severe ancestral subdivisions and rejoinings, leading to a complex mosaic of phylogenetic relationships in recent species. Effects of alternating divergence, hybridization, introgression, and incomplete lineage sorting might complicate our search for a clear dichotomy at the base of this tree and leave us with an indistinct, effective “soft” polytomy, leading sometimes to one or the other solution depending on the size of the data set and the particular markers examined.

Evolution is now its own best parody. Evolutionists think nothing of these sorts of explanations and repeatedly use them when needed. But elaborate explanations can always be contrived in order to explain observations. Why should we believe they are true? As with heliocentrism, evolution erects so many "epicycles" in order to fit the data. Religion drives science and it matters.

The Persistence of Saltationism

One of Charles Darwin's predictions was that evolution occurs gradually via variations within populations. His friend Thomas H. Huxley was concerned that Darwin had assumed "an unnecessary difficulty in adopting Natura non facit saltum [nature does not make leaps] so unreservedly." But Darwin's theory would have been much less compelling without it. Imagine if evolution had included the caveat that saltations—rapid leaps—can occur by unknown mechanisms such that new fossil species can appear fully formed. This would have destroyed Darwin's premise that species evolve by natural processes and we wouldn’t be talking about him today. Yes the fossil record suggested that nature does take jumps, but it was safer for Darwin to question the data than to admit them into his theory.

In order for evolution to succeed Darwin would need to steer clear of the supernatural, or anything that could be interpreted as supernatural, and argue for a strictly naturalistic origin of species. Darwin could hardly argue for a naturalistic origin, and then propose a theory that suggested a supernatural interpretation.

In its first century evolution maintained Darwin's hope that the fossil record was incomplete. Aside from a few heretics such as Richard Goldschmidt and his hopeful monsters, most evolutionists carefully avoided the problem of stasis and abruptness in the fossil record. But scientific evidence doesn’t go away.

Today the specter of saltational evolution persists, and probably is here to stay. In recent years evolutionary studies have increasingly appealed to saltational evolution to explain a variety of biology’s wonders. For the angiosperm flower to Cirripedes (a Darwin favorite) and the turtle, evolutionists are saying saltational evolution should be considered in addition to the many other explanatory mechanisms.

Of course the appeal to hopeful monsters is certainly not evolution’s first or only use of one-time or strange events. From history changing endosymbiosis events to meteorite impacts, evolution is the story of contingencies. So why not a saltational event now and then? As evolutionist Ernst Mayr wrote, "Laws and experiments are inappropriate techniques" for explaining evolutionary events and processes. Anything can happen in this theory.

Important New Paper on Evolutionary Explanation

Evolutionist Marc Hauser has an important new paper on: The Origins of Evolutionary Storytelling: Evolved Adaptation or By-Product? The work is, as usual, extremely sophisticated and complex. As a service, here is a summary of the research and findings, without all the big words:

Considerable debate has surrounded the question of the origins of evolutionary storytelling. One proposal views evolutionary storytelling as an adaptation for cooperation, whereas an alternative proposal views evolutionary storytelling as a by-product of evolved, non-storytelling, cognitive functions. We critically evaluate each approach, explore the link between storytelling and mendacity in particular, and argue that recent empirical work in the history of mythology provides stronger support for the by-product approach. Specifically, despite differences in mythological background, individuals show no difference in the pattern of their preference for unfamiliar mythological scenarios in particular, and level of mendacity in general. These findings suggest that evolutionary storytelling evolved from pre-existing mythology and proclivity toward mendacity, but that it may then have been subject to selection, creating an adaptively designed system for solving the classic problem of looking in the mirror.

More Doubts About Primordial Soup

You were probably taught in high school biology class that life arose from a primordial soup--the twentieth century's rendition of Darwin's "warm little pond." Most textbooks show pictorial-type drawings of the early earth as a dynamic environment, full of activity. Sunlight is beaming through the clouds with its all important energy-bearing ultra violet rays; rain is pouring down as lightning strikes bring more needed energy to the surface; volcanic activity creates hot spots with yet more energy and a few stray comets might be seen bringing their organic chemicals to seed the life-giving processes. The evolution machine is revving up its engines. Another figure might have illustrated an experimental arrangement mimicking those early-earth conditions. A primordial soup of various organic compounds brewed as sparks were set off in a gaseous mixture above steaming water. There's only one problem: it doesn't work.

Charles Darwin had speculated that life may have begun in a warm little pond with protein compounds ready to undergo more complex changes. Strangely enough, a century later experiments were found to confirm this vision. It appeared that Darwin just happened to be right and the headlines proclaimed that scientists had created "Life in a test tube."

But a plethora of problems were ignored in the process which textbooks eventually had to acknowledge. The 2004 version of George Johnson's high school text, published by Holt, Rinehart and Winston, for instance, includes the primordial soup section but adds a caveat.

In its Principles of Evolution unit, the student reads the usual narrative of organic molecules forming spontaneously in chemical reactions activated by energy from solar radiation, volcanic eruptions, and lightning. The text recounts the success of primordial soup experiments in synthesizing certain organic compounds and concludes:

These results support the hypothesis that some basic chemicals of life could have formed spontaneously under conditions like those in the experiment.

But this traditional life-in-a-test-tube narrative is then followed by an awkward caveat. As the next section explains,

Recent discoveries have caused scientists to reevaluate [the experiment]. We now know that the mixture of gases used in [the experiment] could not have existed on early Earth. ... Some scientists argue that the chemicals were produced within ocean bubbles. Others say that the chemicals arose in deep sea vents. The correct answer has not been determined yet.

That's a refreshing admission. Now a new evolution paper goes further. As one author put it, commenting on the paper:

Despite bioenergetic and thermodynamic failings, the 80-year-old concept of primordial soup remains central to mainstream thinking on the origin of life. But soup has no capacity for producing the energy vital for life.

"It is time to cast off the shackles of fermentation in some primordial soup," commented another author.

These evolutionists believe deep sea vents are the answer. The vents provide chemical gradients that early life would have used before learning how to create their own gradients. Of course we have no idea, beyond speculation, how this actually could have happened. The cell's energy transfer process (referred to as chemiosmosis), using nutrients to synthesize its own chemical energy (ATP), is astonishingly complex. But no matter, it must have happened:

Far from being too complex to have powered early life, it is nearly impossible to see how life could have begun without chemiosmosis ...

The eighteenth century philosopher and evolutionary thinker David Hume argued that the problem of evil trumped the problem of complexity. Nature may be complex, but it must have evolved because god would not have created this wretched world. Now, two centuries later, complexity is simply dismissed because evolution must have occurred.

Barbara Herrnstein Smith: A Thoughtful Voice

Barbara Herrnstein Smith’s recent piece in the New York Times on the interaction between religion and science is worth the time. Smith, literary critic at Duke and English professor at Brown, has several thoughtful observations on this often inflammatory topic. For instance, Smith urges that apparent conflicts between science and religion

need not exist in the ongoing lives and experiences of individuals. For neither logic nor rationality requires that all our ideas, impulses, affections, and acts be mutually aligned all the time.

Yet she rightly suspects problems in approaches that compartmentalize religion versus science, or attempt to make them complementary.

The former, as exemplified in Stephen J. Gould’s nonoverlapping magisteria, fails to capture the relation between them and “though seeking to counter views that lead to the dismissal of religion in the name of scientific knowledge, goes some distance to reinforcing them.” Smith continues:

Indeed, I’m inclined to say that Gould’s proposed partition of the territory (that is, facts and accounts of the natural world to science, values and instructions for moral conduct to religion) is, like many political partitions, objectionable in principle and unworkable in practice.

Finally and most seriously, I think that the idea of science and religion as counterpoised monoliths deepens prevailing misunderstandings of both. As I emphasize throughout the book, the kinds of things that can be assembled under the term “religion” are exceptionally diverse. They range from personal experiences and popular beliefs to formal doctrines, priestly institutions, ritual practices and devotional icons — Neanderthal burial rites to Vatican encyclicals. The same can be said of “science,” a term that embraces a wide range of quite different kinds of things — general pursuits and specialized practices, findings and theories, instruments and techniques, ideals and institutions (not to mention a share of devotional icons and ritual practices).

Smith also laments how her thoughtful views (my description, not hers), and the nuanced topic of the interaction between religion and science itself, are so often caricatured. Comments to an earlier column so often missed the point:

A good number consist of off-to-the-races polemics on science and religion having little to do with either the book or column. Others object to my presumed views based on inappropriate surmise.

Welcome to the debate. From newspaper headlines and TV news reports to blog comments, the complexities of both religion and science, not to mention their interaction, are so often lost. But complex they are:

Science and religion, in Gould’s account, are nicely balanced and occupy equally valuable pieces of land, but they remain monoliths — precisely, as one commentator puts it, “rocks of ages.” In “Natural Reflections,” I seek to pulverize both of those rocks, not in order to annihilate them but in order to reveal their complex, copious, varied, and changing composition.

And one of those complexities, so often ignored from the start, is the religion that makes its way into the column labeled as science, and the science that makes its way into the column labeled as religion.

Do You Believe in Magic? How Evolution Creates Evolution

New research is suggesting yet another twist on how evolution creates itself. The research tells us more about epigenetics, so first we need to review how epigenetics has already falsified much of evolutionary theory. I’ve written this before but it bears repeating. The adaptation of species to environmental pressures would seem like obvious evidence for evolution. But in recent years we have begun to understand the enormous complexity of adaptation. It is not a story of natural selection acting on undirected biological variations (that is, variations that are blind to environmental pressures). This sort of undirected process has been the evolutionary dogma for the past century. In what was known as the Modern Synthesis, biological adaptation was described as resulting from blind variations resulting, for instance, from genetic rearrangements or unguided mutations. No thanks to evolution we are now beginning to understand the real version of biological adaptation. What we are seeing is an incredibly complex adaptation machine that tweaks the designs of organisms in response to environmental pressures.

It is not a simple story as there are a variety of different ways such adaptations can occur. These mechanisms, broadly labeled as epigenetic inheritance, can regulate the expression of genes as well as redesign the genes. The bottom line is that the adaptations are not unguided, they benefit the organism, and they are extremely complex. The evolutionary story is completely wrong. As one evolutionist admitted, the Modern Synthesis:

states that variations are blind, are genetic (nucleic acid-based), and that saltational events do not significantly contribute to evolutionary change. The epigenetic perspective challenges all these assumptions, and it seems that a new extended theory, informed by developmental studies and epigenetic inheritance, and incorporating Darwinian, Lamarckian, and saltational frameworks, is going to replace the Modern Synthesis version of evolution.

A new extended theory? This should be interesting, for it would have to explain how evolution creates mechanisms which, themselves, cause evolution (in the form of adaptation). I sense a just-so story coming on. In fact, evolutionists are already explaining this without losing a step. For instance (from the same paper):

Epigenetic inheritance should be favored in fluctuating environmental conditions that last for more than one generation (but not for very long) and may be particularly important in the type of environments experienced by many microorganisms. In such fluctuating environments, efficient epigenetic inheritance is likely to evolve (i) if the parental environment carries reliable information about the offspring’s environment, (ii) when the response to induction is lengthy and incurs a very high cost, and (iii) when recall is not an option or incurs too high a cost.

See, that was easy. Evolution just happens. So long as there is an advantage to a new design, then it will appear. That's how evolution works.

One of the best known epigenetic mechanisms is DNA methylation in which a methyl group is added to cytosine, one of the four DNA chemical letters. The methyl group is a sort of marker that can help to regulate the expression of genes. DNA methylation is accomplished via the action of a complicated molecular machine (DNA methyltransferase) that adds the methyl group at precisely the right location in the DNA strand.

So evolution configured DNA methyltransferase and the associated molecular information that tells it where to add the methyl group, so that later the organism and its offspring could benefit when certain environmental pressures arose. That's good planning--evolution is almost as smart as evolutionists are.

And to further complicate matters, this molecular marker can, itself, be modified. That is, the mark can be marked, thus adding another layer of information to the epigenetic mechanism. In this case, the methyl group is hydroxylated. And of course a different complicated molecular machine is required for the task, and the information of when and where to go to work is needed.

Evolution must have created all these processes and molecular machines so evolution could occur. But that’s not all. Recently researchers found differing methylation patterns amongst mice from the same litter, reared in the same environment. As was reported:

[Researchers] found regions in the animal's genetic makeup with strikingly different patterns. Moreover, these regions occurred among genes responsible for determining anatomy during early development.

In other words, variably methylated regions of DNA have been discovered, and such variability could lead to increased trait variability. Evolutionists speculate that this could help the population survive:

We're proposing that certain gene variants contribute to heterogeneity in populations. In a fluctuating environment, this gives generations more opportunity to survive.

And perhaps this new capability could help answer long-standing questions about how it is that evolution could work so well. As the article explains:

For more than 100 years, mainstream science has embraced the basic tenets of Darwin's view that characteristics that increase an organism's ability to survive and reproduce will be passed from generation to generation. … Characteristics that affect an organism's ability to adapt and survive in times of environmental change have been thought to arise by chance through random mutations in an organism's DNA. However, this view could not explain how such mutations, which arise only rarely, help organisms of every size and variety adapt quickly enough through time.

We already knew evolution was plenty clever. It created genes, chromosomes and alleles, horizontal gene transfer, introns, DNA methylation, and its additional hydroxyl signal just to name a few structures and processes. Of course there is a dizzying array of molecular machines choreographing this drama at just the right moments. All this so more evolution could occur.

And now we add another miracle to the list: variably methylated regions of DNA so future generations could survive when some unforeseen environmental challenge arises. The levels of absurdity to which evolutionists will go is truly remarkable.

How to Read Darwin

The first two chapters of Origin are on the topic of biological variation. In the first chapter Darwin discusses what breeders had learned (Variation Under Domestication) and the second chapter discusses biological variability in the wild (Variation Under Nature). The two chapters serve as a good summary of what was known at the time, but it's slow going as the material does not seem to advance Darwin's thesis very well. In these chapters Darwin is, among other things, introducing the reader to the idea that what we observe today as distinct species, and the labels we give them, are rather arbitrary. What we are seeing is a snapshot at a particular point in time, but over eons of time the designs of the species are fluid. The boundaries shift and new species emerge as the picture gradually changes. The reading is a bit tedious, but as these first two chapters close Darwin pivots, and makes his first important move.

Darwin ends Chapter 2 with a section entitled Summary, but here he introduces a new, important idea. Yes, he summarizes what he has been discussing, but he provides a new, powerful interpretation:

In genera having more than the average number of species in any country, the species of these genera have more than the average number of varieties. In large genera the species are apt to be closely, but unequally, allied together, forming little clusters round other species. Species very closely allied to other species apparently have restricted ranges. In all these respects the species of large genera present a strong analogy with varieties. And we can clearly understand these analogies, if species once existed as varieties, and thus originated; whereas, these analogies are utterly inexplicable if species are independent creations.

Earlier in the chapter Darwin had made a few comments in passing about creationism, but nothing too significant. But here Darwin introduces the reader to the power behind his long argument. The pattern will repeat many times: long tedious passages followed by the powerful conclusion that nature's evidence falsifies divine creation.

Don't worry if you don't completely follow the observations Darwin discusses in the above quote. Here's what you need to understand. The take home message for evolutionists is that, as usual, there are no viable explanations other than evolution's. The observations may not be fully understood under evolution, but under creation or design the story becomes downright impossible. As Ernst Mayr wrote:

The greatest triumph of Darwinism is that the theory of natural selection, for 80 years after 1859 a minority opinion, is now the prevailing explanation of evolutionary change. It must be admitted, however, that it has achieved this position less by the amount of irrefutable proofs it has been able to present than by the default of all the opposing theories.

Indeed, but the default of those opposing theories is not a scientific conclusion. It was evolutionary metaphysics that dictated the outcome. This is the take home message for everyone else. Darwin's reasoning, such as in the passage above, is metaphysical.

The idea that the patterns Darwin was discussing are "utterly inexplicable if species are independent creations" is not from science. Nor did it come from creationists of the day. Nor was it merely a casual observation, made in passing. Then and today, these are the arguments that make evolution a fact. There is no proof that evolution is a fact that does not entail metaphysics. As Stephen Jay Gould observed:

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.

Religion drives science, and it matters.

Coyne: Evolutionary Arguments Not Theological

Evolutionists agree that their theory is a fact, every bit as much as gravity is a fact. It is not difficult to find proofs for this claim in the evolution literature. On the Internet, in magazine articles, in popular books, and in textbooks, proofs of the fact of evolution are common. In fact they date back to the beginning of modern science (or even to antiquity if one cares to take it that far). And these proofs are perfectly logical—there is nothing wrong with their reasoning. But a proof contains going-in assumptions, or axioms, and evolution’s axioms are metaphysical. That is, evolution incorporates axioms that do not come from science; rather, they drive the science.

Here’s an example. It has been known since Aristotle that species tend to cluster in a hierarchical pattern and in the eighteenth century Linnaeus saw it as a reflection of the Creator’s divine plan. Obviously this pattern does not force one to embrace evolution. But does it really look like a divine plan? Darwin argued it most certainly did not:

The several subordinate groups in any class cannot be ranked in a single file, but seem clustered round points, and these round other points, and so on in almost endless cycles. If species had been independently created, no explanation would have been possible of this kind of classification.

This argument about divine patterns did not begin with Darwin. It has complex theological roots, and today it continues as one of evolution’s many metaphysical axioms. Fifty years ago evolutionist George Carter explained that “If species are separately created there is no reason why they should be created in large groups of fundamentally similar structure.”

Niles Eldredge agrees that the pattern defies creationism and design:

Could the single artisan, who has no one but himself from whom to steal designs, possibly be the explanation for why the Creator fashioned life in a hierarchical fashion—why, for example, reptiles, amphibians, mammals, and birds all share the same limb structure?

Likewise Jerry Coyne explains that the appearance of species through time is “far from random” and “no theory of special creation, or any theory other than evolution, can explain these patterns.” [29] And why are species so similar? “There is no reason,” explains Coyne, “why a celestial designer, fashioning organisms from scratch like an architect designs buildings, should make new species by remodeling the features of existing ones.” [54]

Of course this claim about how the species would be designed does not come from science. Nor do the many other metaphysical claims that, over and over, prove evolution.

For instance, another common metaphysical mandate is that god or a designer would never draw up inefficient designs. A favorite example is the recurrent laryngeal nerve which, Coyne explains,

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

In fact evolution is drenched in metaphysics. From its early formulations in the Enlightenment years, to Darwin, to today’s refinements, evolution relies on non scientific assumptions. The “fact” of evolution has never been demonstrated without appeal to ultimate truths which are far beyond the halls of science.

Is this enough for us to convict evolution? Actually no, metaphysics is no sin. There’s certainly nothing wrong with holding religious beliefs. And is there anything wrong with viewing the world through the spectacles of one’s beliefs?

Indeed, who says there is anything wrong with allowing one’s beliefs to influence science? Well, in fact evolutionists say this, and herein lies the rub. The problem is not that evolution is a metaphysical theory or that evolutionists promote their metaphysical views. The problem is that evolutionists criticize others for precisely what they do. They even deny what they do. As Jerry Coyne explains, our metaphysics are really not metaphysics at all:

the argument from imperfection — i.e., organisms show imperfections of “design” that constitute evidence for evolution — is not a theological argument, but a scientific one. The reason why the recurrent laryngeal nerve, for example, makes a big detour around the aorta before attaching to the larynx is perfectly understandable by evolution (the nerve and artery used to line up, but the artery evolved backwards, constraining the nerve to move with it), but makes no sense under the idea of special creation — unless, that is, you believe that the creator designed things to make them look as if they evolved. No form of creationism/intelligent design can explain these imperfections, but they all, as Dobzhansky said, “make sense in the light of evolution.”

Should we laugh or cry? According to Coyne the design “makes no sense under the idea of special creation" and this "is not a theological argument, but a scientific one.” Coyne’s misrepresentations and sophistry are astonishing. You can read more about this here. The problem is not that evolutionists are metaphysicians—the problem is that they are in denial, and in the process make a mockery of science. Religion drives science and it matters.

Scientists (Do Not) Find a Fingerprint of Evolution

Did you know that most of the evidence claimed for evolution is actually not evidence for evolution? That's right, remember the mountain of evidence that evolutionists say is supposed to make evolution a fact? Well most of it consists of biological findings that merely have been interpreted according to evolution.

Here is an example that I've discussed before at Evolution News & Views. A prestigious scientific journal, the Proceedings of the National Academy of Sciences, published detailed findings about how DNA information is used to make proteins in our cells. The research team, led by Cold Spring Harbor Laboratory professor Michael Zhang, discovered subtle signals in the DNA that help guide incredibly complex molecular machinery when editing the DNA information. The findings are not in any way evidence for evolution, and yet the headlines proclaimed “Scientists Find a Fingerprint of Evolution Across the Human Genome.”

This was not merely a case of journalistic naivete. One can hardly blame the science writer when the journal paper itself presented the results as elucidating the evolutionary process. The paper's title alone (“RNA landscape of evolution for optimal exon and intron discrimination”) suggests a new finding about evolution, and the paper concludes that human genes seem to have been optimized “during evolution.”

But the “during evolution” part is gratuitous. The key findings are about how the genetic signals work, not that they evolved. There is, in fact, nothing in the findings to indicate evolution. The science writer concluded that “the researchers found signs that evolution rejects some types of mutations,” but there simply was no such finding. What the researchers actually found was the presence of certain subtle signals in the genome. They found no evidence that the signals were produced by evolution.

This dynamic is common and, not surprisingly, influences popular thinking. For reports such as this are taken to be objective, scientific confirmations of evolution. They often find their way into the popular literature, text books, Internet discussions, origins debates and so forth. Because evolution is believed to be a fact, we have lost the ability to rightly evaluate scientific evidence. All evidence must point to evolution, even if it doesn’t. This is yet another way that evolution harms science.

Reverend Jerry Coyne: Lanugo and Epistemology

You probably have never seen the words lanugo and epistemology in the same sentence. But to understand the power of evolutionary thinking we need to understand both words. Lanugo is a fine hair we grow about six months after conception and then lose before birth. Epistemology, on the other hand, is the theory of knowledge. How do we know what we know? How can we know that what we know is true? It's a complicated subject and science avoids many of the quandaries by simply positing hypotheses that make predictions. Think of the process as an IF-THEN statement. IF the planets circle the sun, THEN we should observe retrograde motion. Epistemologically speaking, the IF-THEN statement is very safe. It makes no claims about ultimate truth, it simply states that if a particular hypothesis is true, then a particular event should be observed. And if the event is observed then the hypothesis may or may not be true. All we can say is that it has not been falsified. If the event is not observed, on the other hand, then the hypothesis is false or at least needs to be modified. As you can see it is not easy to make progress with the IF-THEN statement. If all we can do is not falsify a hypothesis how can we ever establish any truths? This is where evolutionary thinking comes in.

Evolutionary thinking smashes through the IF-THEN log jam by instead using the IF-AND-ONLY-IF-THEN statement. Here's an example: If and only if it is Friday, then evolutionists play poker. In this example, if we observe evolutionists playing poker then it must be Friday. There is no other possibility. Unlike the IF-THEN statement, the IF-AND-ONLY-IF-THEN statement allows you to establish truths.

Evolutionists have used this powerful technique to establish the truth of evolution. Consider perhaps the most famous phrase in evolution today: "Nothing in biology makes sense except in the light of evolution." This was written by the famous twentieth century evolutionist Theodosius Dobzhansky and the phrase continues to be celebrated by evolutionists today. It is equivalent to claiming that "Everything in biology only makes sense in light of evolution," or in the IF-AND-ONLY-IF-THEN statement format as: "IF-AND-ONLY-IF evolution is true, THEN will we find what we find in biology."

It is all suddenly so simple--of course evolution is true. It is a wonder that creationists ever doubted this obvious truth. From where else can you get that kind of certainty except evolutionary thought?

The power of the IF-AND-ONLY-IF-THEN statement, as you can see, is that it covers the water front. It provides knowledge of all possible explanations. Evolution, and only evolution, can explain biology. No other explanation works.

Philosophers such as Kyle Stanford have worried that science is vulnerable to the problem of unconceived alternatives. How can we really know that no other explanation works? How can we even know what are all the possible alternatives? But as usual philosophers fail to comprehend the power of evolutionary thought.

Evolutionists have powerfully used the IF-AND-ONLY-IF-THEN statement for centuries to prove their ideas. They have provided true-truth like no other tradition in the history of thought. And for that we must thank them gratefully. To fully appreciate the power, and simplicity, of evolutionary thought, here is how the Reverend Jerry Coyne applies this logic to lanugo. Here is the Word of Coyne:

One of my favorite cases of embryological evidence for evolution is the furry human fetus. We are famously known as "naked apes" because, unlike other primates, we don't have a thick coat of hair. But in fact for one brief period we do--as embryos. Around sixth months after conception, we become completely covered with a fine, downy coat of hair called lanugo. Lanugo is usually shed about a month before birth, when it's replaced by the more sparsely distributed hair with which we're born. ... Now, there's no need for a human embryo to have a transitory coat of hair. After all, it's a cozy 98.6 degrees Fahrenheit in the womb. Lanugo can be explained only as a remnant of our primate ancestry: fetal monkeys also develop a coat of hair at about the same stage of development. Their hair, however, doesn't fall out, but hangs on to become the adult coat. And, like humans, fetal whales also have lanugo, a remnant of when their ancestors lived on land. [80:1]

As usual Coyne skillfully presents evolutionary truths with a gentle and loving message. How obvious it now is that lanugo can only be explained by evolution (or in other words, IF-AND-ONLY-IF evolution is true, THEN will we have lanugo). Now you can see why evolution is true.

Modular Evolution: All of The Benefits, None of the Risk

You have probably heard that evolution has difficulty explaining the origin of amazingly complex designs. It turns out that evolutionists have quietly solved the problem while we weren’t paying attention. With little fanfare, they have rolled out modular evolution. This new kind of evolution is truly astonishing. What it does is, well, it creates complexity just like that. Evolutionists once thought that biology’s miracles evolved more or less one step at a time. But such staid ideas about evolution have long since become, as J. D. Hooker probably would say if he were around today, “old stick-in-the-mud doctrines.” If bankers can liven things up then why not evolutionists?

Modular evolution creates new complexity not the old fashioned way, but by a new type of go-go evolution. Like a bank that makes millions without taking any of the risk, modular evolution doesn’t worry about creating complexity, it just does. As the theory goes—and this is a very theoretical piece of work—modular evolution assembles different design components (or modules) that have already evolved. Kind of like putting an engine and a transmission together, modular evolution skips over the intermediate steps and goes right for the finished design. How clever.

And now a new fossil finding in China has confirmed just this type of advanced evolutionary process. The fossil reveals a flying reptile which has been appropriately christened Darwinopterus because, after all, Darwin invented evolution. As evolutionist David Unwin explains:

Darwinopterus came as quite a shock to us. We had always expected a gap-filler with typically intermediate features such as a moderately elongate tail—neither long nor short. But the strange thing about Darwinopterus is that it has a head and neck just like that of advanced pterosaurs, while the rest of the skeleton, including a very long tail, is identical to that of primitive forms.

There you have it—go-go evolution proceeding by leaps and bounds. The design obviously gave Darwinopterus great new capabilities which would have been selected by evolution, so there’s really nothing to question here. Like bankers, evolutionists have learned to focus on benefits rather than risks.

An Oracle of the Reverend Jerry Coyne

The Reverend Jerry Coyne has condescended to reveal a treasure of timeless truths in his little revelation entitled Why Evolution is True. That these truths are metaphysical--they cannot be deduced from science--make them especially precious. In his revelation Reverend Coyne illuminates a wide range of truths for us to revere. Here is an oracle of Coyne on bad design:

What I mean by "bad design" is the notion that if organisms were built from scratch by a designer--one who used the biological building blocks of nerves, muscles, bone, and so on--they would not have such imperfections. Perfect design would truly be the sign of a skilled and intelligent designer. Imperfect design is the mark of evolution. ...

Flatfish are born as normal-looking fish that swim vertically, with one eye placed on each side of a pancake-shaped body. But a month thereafter, a strange thing happens: one eye begins to move upward. It migrates over the skull and joins the other eye to form a pair of eyes on one side of the body, either right of left, depending on the species. The skull also changes its shape to promote this movement, and there are changes in the fins and color. In concert, the flatfish tips onto its newly eyeless side, so that both eyes are now on top. ...

If you wanted to design a flatfish, you wouldn't do it this way. You'd produce a fish like the skate, which is flat from birth and lies on its belly--not one that has to achieve flatness by lying on its side, moving its eyes and deforming the skull. Flatfish are poorly designed. ...

the particular bad designs that we see make sense only if they evolved ... [81:3-85:3]

As the Most High Coyne reveals, perfect design is, truly, truly, a sign of a skilled designer. No designer would design the species we find. Evolution must be true. Such ultimate truths can only come from a prophet. Amen.