A Pyknon Prediction

The latest "junk" DNA finding is that pyknons have been found in the much studied plant Arabidopsis thaliana. Pyknons are short (about 20 nucleotides) DNA sequence patterns that are common, and show up in both genes and the "junk" regions of DNA (introns and intergenic).

In addition to their dual presence as (i) evolutionary "junk" (which increasingly is being found to be useful in spite of evolutionary expectations) and (ii) within genes, pyknons are also similar to regulatory RNA sequences, and have some interesting correlations and patterns regarding their chromosomal positioning.

So why are pyknons so prevalent in these "junk" DNA regions? The researchers think they are a by-product of the action of RNA gene silencing. In other words, it's just junk after all. If the history of evolutionary expectations is a useful guide, you can expect that this will be yet another one gone wrong.

McLeroy Does it Again

The much maligned Don McLeroy has a column in today's Bryan-College Station Eagle. Recall that McLeroy has been accused of a host of nefarious deeds, including recklessly disregarding the advice of education experts, causing the Texas State Board of Education to be “extremely dysfunctional,” fueling endless culture wars, and putting ideology and partisanship ahead of the schoolchildren of Texas. So what does McLeroy have to say for himself?

Well he starts right off with the ludicrous idea of teaching only science in science class. I can now see why everyone was so upset. McLeroy writes that there is no place for any ideology, religious or otherwise in science class. He obviously is up to no good. He also argues that students should be able to challenge untestable ideologies being taught as dogma. This of course will undermine the authority of the teacher and textbook.

We all agree with the need for, so-called, critical thinking. But McLeroy takes this to a dangerous extreme, essentially bringing anarchy to the classroom. Students need to be taught theories that everyone already knows are true. It profits no one for students to question the truth. Students may ask questions about theories, but not question the theories themselves. McLeroy fundamentally misunderstands what critical thinking is all about.

McLeroy's ulterior motives become all too obvious when he addresses the theory of evolution (which is really a fact). He thinks, of all things, that students should study evidence for common ancestry, such as in the fossil record. McLeroy would then allow these young, impressionable, students to question evolution.

It is hard to believe that we are even debating how to teach science. Students obviously need to be taught, and tested on, the truth. Questioning the truth will get them nowhere.

Hearing Design Research

One of the many fascinating designs in biology is the workings of our senses. Here, for example, is a description of new findings on the actions of hair cells in the inner ear. It is yet another example of biology leaving evolution in the dust:

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

How Future Scholars Will View Evolution

Centuries from now, here is how a history book is likely to describe the theory of evolution:

As with many new paradigms, evolutionary thought developed over a lengthy period. Within the period known as Modern Science, which had its beginnings in the middle of the second millennium, evolutionary thought began to emerge in the mid seventeenth century. At that time theologians and philosophers from various traditions strenuously argued that the world must have arisen via strictly naturalistic processes. These schools of thought contributed to what became known as The Enlightenment period in the eighteenth century which marked a major turning point in Western intellectual thought.

In The Enlightenment period theological and metaphysical positions became codified in Western thought. These positions became sufficiently accepted and familiar so as to be no longer in need of justification. Instead, Western thinking rapidly incorporated these positions as new truths. This new theology made strong commitments in the area of divine intent, action, and interaction with creation. The impact on science was profound as this theology mandated that God's interactions with the world was to be strictly via secondary causes (i.e., natural laws), and that all of history must be governed solely by such causes. This paradigm later became known as Evolutionary Thought.

In Evolutionary Thought, science implicitly incorporated these theological and metaphysical commitments. Western, and by now worldwide, thought entered a dark age of anti intellectualism in the nineteenth and twentieth centuries. In this period all findings were described as evolutionary. Needless to say this was cause for ever more strained explanations of the evidence. Nonetheless, a rigid social and financial structure enforced adherence, complete with implicit penalties and harassment of dissenters.

We now understand that a key enabler of Evolutionary Thought was the denial of its very foundation. In its Delusion of Objectivity, evolution denied any theological or metaphysical influence or commitment. Indeed, the very term Enlightenment is an anachronism. We still use this historical term, even though it was meant to convey the idea of objectivity and independence of religious assumption and authority. Indeed, The Enlightenment period was precisely the opposite. As with so many periods of history, The Enlightenment was strongly influenced by theology and metaphysics. The difference in The Enlightenment was its denial of such influence. This Delusion of Objectivity was the source of much of the justification for Evolutionary Thought, until its demise in the early twenty first century.

Biogeography Workshop at Evolution2009

Next week's evolution2009 conference offers a K-12 educators workshop entitled "Evolution 101: Evolution and Biogeography." The announcement explains that:

Biogeography is traditionally a keystone approach to evolutionary biology, as seen in the works of Charles Darwin, Alfred Russell Wallace and Henry Bates.

The works of Darwin and Wallace? The Darwin-Wallace paradigm was a restrictive dogma, not a keystone, in biogeography. It took a century to exorcise but now, fifty years later, is it resurrected as good science.

In addition to brainwashing, workshop participants will also receive a small library of evolution propaganda, including the National Academies of Science's Science, Evolution and Creationism. This handy booklet is packed with evolutionary newspeak, such as the wonderfully freeing thought that evolution is true regardless of the evidence. "Even if their negative arguments against evolution were correct," the NAS informs young scientists, it would not matter because evolutionists can always contrive alternative explanations. Now that's hard science.

Also, Mike Webster and Louise Mead will lead a session on "tree-thinking." Apparently unaware of the scientific evidence, and that even evolutionists are admitting that tree-thinking needs a reassessment, Webster and Mead will "use simple games and simulations to demonstrate why it is that evolution leads to tree-like patterns of relationships among species." If that is true then evolution is false.

And of course do not miss the Gould Lecture that evening where Eugenie Scott will be rewarded for her tireless efforts in saving the world for evolution. Scott will bemoan the public's "high incidence of rejection of evolution" and encourage teachers to do what they can to dispel such ignorance. The problem, as Scott sees it, is that people just don't understand the basic ideas of evolution.

Don't understand the basic ideas of evolution? How could that be? In fact we are, and have been for many years, awash in evolution education. Public school classes, with their highly produced textbooks, have been inculcating tender minds for generations. And our media, legal system, entertainment, and cultural elites are all dominated by a positive, evolutionary-is-good-science, mindset. TV specials, museums, science and popular magazines--everywhere we look we are told about the virtues of evolution and the nefarious motives of those who doubt.

The problem is not that folks do not understand evolution well enough, the problem is that folks understand evolution too well.

PZ Myers: The Anti-Authoritarian Authoritarian

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

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

Did Vision Evolve?

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

Second, if a new vision capability did just happen magically to arise, it would be worthless since there would be no interpretation of the new signals 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 incoming signals that must be changing too fast.

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.

Groups That Laugh Together Stay Together

Evolutionists group species by similarities, thinking this reveals patterns of common descent. Then they find another similarity (not surprisingly with the same pattern) and they conclude it must have evolved. After all, it fits the pattern.

The logic is laughable, and here's a funny example. Evolutionists are now concluding that laughter evolved in a common ancestor of the great apes and humans. And how do they figure this? First, they tickled 22 apes and three humans (your tax dollars at work). Then they discovered similarities. As the BBC reports:

Because the sounds of the most closely related apes matched most closely in the analysis of the laughter, the researchers believe the work is proof of laughter's shared evolutionary origin, followed by adaptation to its form in the species we see today.

Should we laugh or cry?

Pure Dogma

Once upon a time scientists were supposed to be skeptical. Scientific theories, we were taught, were to be questioned. Yes scientists were to formulate theories, but they were also to search for evidence against theories, even their own. And while such a noble action as searching for problems with one's own theory might be too much to ask, certainly scientists were never to protect a theory against contradictory evidence or mislead the public. That would be the ultimate scientific sell out. Scientists were to be objective, and to follow the evidence where ever it may lead.

Those days are gone--long gone. Misleading the public, covering up evidence, protecting theories--that is all standard fare today. We have now arrived at the sad state where evidence that is contrary to evolution--any contrary evidence--is not allowed. Consider this recent exchange between Yudhijit Bhattacharjee of Science magazine and evolution crusader Eugenie Scott:

Science magazine: How has this battle changed in the past 20 years?

Eugenie Scott: The enemy has become more diverse. When I started, it was just creation science. Now we have creation science, intelligent design [ID], and straight-up antievolution in the form of "evidence against evolution."

Evidence against evolution? Is there something wrong with that? Yes, there is for evolutionists. Science, in the hands of evolutionists, is something to be manipulated. Scientists who want to examine the evidence are ridiculed and marginalized. If you doubt evolution you are considered to be the enemy. Motives are assigned to you, and you are stereotyped. This is pure dogma. Religion drives science, and it matters.

The Three Fallacies of Evolution

We routinely hear that the biological evidence proves evolution, beyond any shadow of a doubt. Recently PZ Myers made this claim for the fossil evidence and Sean Carroll for the molecular evidence. These evidences are often debated and discussed, but what is often missed is that this evolutionary reasoning is illogical to begin with. Philosophical failure is not a good starting point for discussion. Any debate needs to start with a clear understanding of the evidence and what it means. Unfortunately, such a starting point is difficult to come by. In fact, three different fallacies are routinely at work in the evolution genre. Here are quotes from Myers and Carroll, and an explanation of the fallacies.

In his book The Making of the Fittest: DNA and the Ultimate Forensic Record of Evolution, Carroll discusses the use of genetic markers such as LINEs and SINEs (long and short interspersed elements, respectively) to reconstruct evolutionary relationships. He concludes:

biologists have sufficient forensic evidence to determine species' kinship beyond any doubt. [99]

Similarly, Myers derives similar certainty from the fossil evidence:

The evolution of whales is also a matter of fact and evidence. We have the fossils; we can see a pattern of change across geological time, from those hooved terrestrial quadrupeds to flippered ambush predators adapted to living in the shallows to four-flippered, paddle-tailed swimmers to obligate water-dwellers with flukes and no hind limbs, with many stages in between. It is a beautiful and strongly-supported example of macroevolutionary change. So yes, we believe it — you'd have to be blind to ignore the testimony of the rocks.

Fallacy #1: Affirming the consequent

These types of truth claims are consistent in the evolution genre. The first, and most important fallacy is that these arguments affirm the consequent. This fallacy states that if P implies Q, then Q implies P. For instance, if a theory predicts that it will rain next Tuesday, that does not mean that if it rains on Tuesday the theory is true. But this is precisely the logic of evolution. If evolution is true then we expect fossil sequences and genetic similarities to fall into the expected evolutionary patterns. Evolutionists such as Carroll and Myers have found such patterns in the fossil and molecular data and claim, as above, that they prove evolution to be true.

Fallacy #2: Confirmation bias

A common motif in the evolution genre is the elevation of confirming evidence. As in the examples above, the patterns that fit the evolutionary expectations are touted as proof texts. But there are plenty of evidential problems as well. Often these problems are in the same data in which the evolutionists find their persuasive patterns. Yes, many fossils fall into the expected pattern, but many do not. Likewise for the molecular data. These uncooperative data are often not considered when evolutionists formulate their proofs of why evolution is a fact. This fallacy is known as confirmation bias.

Fallacy #3: Evidence denial

Because there is so much uncooperative data, evolutionary expectations have become quite flexible. In fact, sometimes it is difficult to identify just what constitutes the expected evolutionary pattern. In the fossil record, for instance, increasing complexity, decreasing complexity, rapid appearance, trees, bushes, diversity explosions, stasis for eons can all fit within evolution's broad and flexible imagination of what natural forces can do. Therefore, when evolutionists find great significant in evidences that fulfill some particular evolutionary pattern, they are ignoring the many other patterns that evolution also expects.

Evolutionists consistently make eye-brow raising claims. Evolution, they say, is a fact beyond any shadow of a doubt, as obvious as gravity, and so forth. These claims are perceived to have the full faith and backing of modern science. But they do not. Behind such unbelievable claims is, not surprisingly, any number of logical fallacies that cannot stand up to even modest scrutiny.

Behavior Solutions

Behind all the incredible structural designs in biology are the amazing behavioral designs. They expose evolution’s absurdities perhaps even more than do the structures. As one evolutionist admitted, the theory is in disarray. And so it is good to see that an understanding of behavior is emerging that is free of the evolutionary dogma, such as in Nature's I.Q., where, according to the publisher, “Hungarian scientists Balazs Hornyanszky and Istvan Tasi ... point out how Darwinian 'just so' stories fail to explain these irreducibly complex instincts and behaviors.”

The Unavoidable Teleology

Evolution is constantly force-fit into roles it was not designed for. We often see explanations such as: “Evolution uses strategy X to create fantastic design Y.” Such design language is not merely convenient shorthand or sloppy thinking. It is the only way to imagine how evolution could work, in many instances, but of course it makes no sense. Consider this latest teleological description of evolution’s creation of the amazing squid’s vision systems, provided by Margaret McFall-Ngai:

Evolution has a “toolkit” and when it needs to do a particular job, such as see light, it uses the same toolkit again and again. In this case, the light organ, which comes from different tissues than the eye during development, uses the same proteins as the eye to see light.

How clever of evolution to create a “toolkit” that it could then use when the need arises.

Religion Masquerades as Science in Forbes Magazine

Michael Ruse has a piece in Forbes magazine about the recent hype over the Darwinius masillae fossil. I’m not sure what a business magazine finds interesting about the 47-million-year-old primate fossil, but I’m sure it isn’t interested in promoting the religion that underwrites the theory of evolution. Like most evolutionists Ruse doesn’t hide his theological convictions. I once debated Ruse but it was hardly a debate. I explained that evolutionists mandate naturalism for religious reasons such as the problem of evil, and Ruse argued that evolution is mandated for religious reasons such as the problem of evil. Such convictions provide evolutionists with a metaphysical certainty that evolution is true. As Ruse writes:

Thanks to the Origin and to the huge amount of research done in the subsequent century and a half, we have massive evidence–from paleontology, biogeography, anatomy, embryology and every other branch of biology–putting the fact that organisms evolved well beyond reasonable doubt. This is as certain as that the Earth goes around the sun or that water is composed of oxygen and hydrogen. Other than the aforementioned biblical literalists, no one doubts this fact. Nor should they.

Evolution is a fact, and is well beyond reasonable doubt? It may sound like science but it is not—this is religion in disguise. This level of certainty comes from metaphysics, not measurements. From a scientific perspective the evidence presents a plethora of problems for evolution. But from a religious perspective the evidence is conclusive. Consider the evidence from biogeography. Elsewhere Ruse has written that:

Given an all-wise God just why is it that different forms appear in similar climates, whereas the same forms appear in different climates? It is all pointless without evolution.

Here we have the strength of the argument, and the mandate for evolution. It really doesn’t matter if evolution struggles with the evidence. It must be true. You can read the rest of the biogeography story here. Religion drives science and it matters.

David Penny: Religion Can be Subtle

At next week’s evolution2009 conference, David Penny will give the Society of Systematic Biologists Presidential Address. Penny’s talk has the engaging title: “Why we should finally take Darwin 100% seriously: who's afraid of the big bad ID’er.” It should be interesting. As an evolutionist, Penny is an advocate of religious interpretations of the scientific evidence. Often this religious influence is obvious but sometimes it is subtle, as in a paper that Penny and coworkers published in Nature magazine.

In that 1982 paper, Penny responded to Sir Karl Popper’s occasional criticisms of evolution, such as that it is not falsifiable and is a metaphysical research program. Penny responded with the classic random-design-as-null-hypothesis argument which dates back to the eighteenth century when it was introduced by Daniel Bernoulli, and elaborated by Immanuel Kant and Pierre Laplace.

That’s quite a trio and the argument, though it is deeply theological (simply put, it claims God would not create patterns in nature), soon became standard fare in science. And the argument had the virtue of sounding scientific when carefully restated. As Penny declared:

Clearly we can reject any idea that the trees from the different sequences are independent.

Independent? What does that mean? This is a subtle, but deeply metaphysical interpretation of the evidence (See Science’s Blind Spot for more details). It is used as a consistent and powerful proof in the evolution literature, and it is not scientific. Ironically, in attempting to rebut Popper’s observation that evolution is not falsifiable and metaphysical, Penny instead confirmed these very points. Religion drives science and it matters.

Wiker's New Book

The history and philosophy of science, as they relate to theories of origins, are largely sympathetic to evolution. The history of how Darwin's theory arose and its subsequent acceptance often carries with it the implicit assumption that evolution is true. Many questions that a curious historian would naturally explore if evolution was viewed merely as a theory, rather than a fact, go unasked. Likewise, important philosophical issues are left untouched because, if evolution is true they are less interesting. All of this helps to fuel a climate of anti intellectualism. But there are some historians and philosophers who are willing to suspend the assumption that evolution is true. One such scholar is Benjamin Wiker and you can see his new book, The Darwin Myth: The Life and Lies of Charles Darwin, here.