New Research: Retina Wiring Architecture Crucial in Image Processing

Our different senses rely on a complex process known as cellular signal transduction which converts an external stimulus, such as sound or light, to a nerve signal. But the nerve signal doesn’t go straight to the brain. In the case of mammalian vision the massive data stream emanating from the millions of photoreceptor cells undergoes substantial signal processing before the information is sent to the brain. New research is now providing more information about the cellular architecture involved in this intermediate processing stage.

Seeing the light

At the molecular level vision begins with a complex signal transduction cascade. As photons enter your eye they interact with light-sensitive chromophore molecules in the photoreceptor cells. The interaction causes the chromophore to change configuration and this, in turn, influences the large, trans-membrane rhodopsin protein to which the chromophore is attached.

The chromophore photoisomerization is the beginning of a remarkable cascade that causes action potentials to be triggered in the optic nerve. In response to the chromophore photoisomerization, the rhodopsin causes the activation of hundreds of transducin molecules. These, in turn, cause the activation of cGMP phosphodiesterase (by removing its inhibitory subunit), an enzyme that degrades the cyclic nucleotide, cGMP.

A single photon can result in the activation of hundreds of transducins, leading to the degradation of hundreds of thousands of cGMP molecules. cGMP molecules serve to open non selective ion channels in the membrane, so reduction in cGMP concentration serves to close these channels. This means that millions of sodium ions per second are shut out of the cell, causing a voltage change across the membrane. This hyperpolarization of the cell membrane causes a reduction in the release of neurotransmitter, the chemical that interacts with the nearby nerve cell, in the synaptic region of the cell. This reduction in neurotransmitter release ultimately causes an action potential to arise in the nerve cell. The next step is to process these nerve signals.

Image processing

A variety of signal processing, involving different types of cells, takes place downstream of the photoreceptor cells, before the vision information is sent to the brain. For instance, the signals from different photoreceptor cells are processed together to derive image information. In addition to this spatial processing, temporal processing derives motion information.

The amacrine and ganglion cells are important components in this processing stream. But this processing stream is not merely a massively parallel operation, where the signal from each photoreceptor cell is individually and simultaneously processed.

For instance, by the time they reach the ganglion cells, signals from the different photoreceptor cells are mingled. The result is that a given ganglion cell receives information for a circular image area. And different types of ganglion cells are sensitive to different spatial and temporal image patterns within that area.

What the new research discovered is that the signals feeding the ganglion cells sensitive to temporal image patterns (that is, motion) have intricate connection patterns. Specifically, if the ganglion cell detects motion from left to right, then it is connected to dendrites which extend from the amacrine cell in the opposite direction. As the researchers concluded, “Our findings indicate that a structural (wiring) asymmetry contributes to the computation of direction selectivity.”

Meanwhile evolution is left only with its foolish dogma. Evolutionists have long since committed themselves to the insistence that evolution is fact. Like the marching band that took a wrong turn down a dead end alley, they have no graceful exit. This is not going to end pretty.

Steve Clarke: Naturalism Can’t Be Sure

In his paper Naturalism, Science and the Supernatural, philosopher Steve Clarke argues that naturalism has a problem. Naturalism, Clarke points out, defers to science. And while fringe movements such as intelligent design appeal to the supernatural, mainstream accepted science does not. There are no contemporary examples, Clarke makes clear, of an explanation that appeals to the supernatural which is the best scientific explanation of some natural phenomenon. But such appeals have been made (and accepted) in the past, and there is no guarantee they won’t be in the future as well. Therefore naturalism, by deferring to science, cannot conclude against the supernatural. It is an interesting paper which raises, and misses, some important points.

Is science complete?

First, Clarke’s assurance that there is no contemporary explanation that appeals to the supernatural which is the best scientific explanation of some natural phenomenon, is rather obvious and practically a truism. Of course appeals to the supernatural don’t work for natural phenomenon. Natural phenomenon, by definition, are described by natural laws. Any appeal to the supernatural, by definition, will fail on Occam’s razor.

So yes, science has appealed to the supernatural in centuries past, but only because the phenomena in question was deemed to be supernatural. For example, it seemed to Newton that the best explanation for the origin of the solar system was that the creator placed the planets in their particular orbits. Likewise, it seemed to Paley that the best explanation for the origin of biological complexity was a designer. The origin of the solar system and biological complexity were deemed to be supernatural events.

This raises the thorny question of how one determines whether a phenomenon is natural. For instance, evolutionary philosopher Barbara Forrest states that science must be restricted to natural phenomena. In its investigations, science must restrict itself to a naturalistic methodology, where explanations must be strictly naturalistic, dealing with phenomena that are strictly natural.

But how do we determine whether a phenomenon is natural? If genuine science is to be restricted to natural phenomena, then how do we demarcate this genuine science from the pseudo science? It has been almost 30 years since Larry Laudan showed the severity of the demarcation problem which evolutionists continue erroneously to use as justification for their unlikely thesis.

Clarke’s criticism of naturalism too soft

Clarke’s thesis that naturalism’s deference to science renders it vulnerable to a possible, future appeal to the supernatural in the sciences is too conservative. Evolutionists motivate and justify evolution with several claims about the supernatural. Richard Dawkins, for instance, argues god would never have designed the blind spot in our retina. Such metaphysical truth claims are by no means limited to outspoken evangelists such as Dawkins. From seventeenth century tracts to today’s textbooks, evolution entails claims about the supernatural.

The fact that some of these evolutionists are atheists does not relieve them of their truth claims about the supernatural. They know god doesn’t exist, but they know a lot about him if he did exist. Such contradictions, or complexities to be more generous, in the naturalist’s position does not ease their predicament.

Clarke’s thesis that naturalism’s deference to science renders it vulnerable to the supernatural is not just a theoretical problem. That deference to science means that naturalism already today must acknowledge a commitment to metaphysical claims about the supernatural. How can they know such truths?

Making the World Safe for Empiricism

A Texas lawmaker is proposing legislation to protect college professors and students from view point discrimination regarding theories of origins:

An Arlington lawmaker has filed a bill aimed at protecting Texas college professors and students from discrimination because they question evolution.

The Fort Worth Star-Telegram reported that the measure from Republican state Rep. Bill Zedler would block higher education institutions from discriminating against or penalizing teachers or students based on their research into intelligent design or other theories that disagree with evolution.

Zedler said he filed the bill because of cases in which colleges had been hostile to those who believe that certain features of life-forms are so complex that they must have originated from a higher power.

It is good to see law makers addressing academic discrimination and blackballing, but if we’re going to pass laws, I would like to explicit protection for empiricism which has been under so much attack. How about something like this:

Discrimination and blackballing of people who believe scientific theories should account for the empirical data shall be illegal in publicly funded academic institutions.

Let’s make the world safe for empiricism again.

Anthropomorphic Terminology: Obstacle or Enabler?

As Bioessays Editor-in-Chief Andrew Moore reports, the lack of public acceptance of evolution is a fundamental misunderstanding of its core concepts. In fact, in the latest Bioessays Jacques Dubochet contends that many people think of evolution as producing modifications with an aim. They think of eyes as having evolved in order to see, and legs having evolved for walking, rather than in terms of directionless variation, and natural selection without motivation, design or strategy. “It is about time,” warns Moore, “that we stopped such anthropomorphic terminology and thinking, and confronted the likelihood that – far from being ‘excusable shorthand’ – it is an important contributor to a false impression of evolution among many non-scientists.” But Moore has it backwards.

Moore laments the use of anthropomorphic terminology in the evolution literature and rightly points out it misrepresents evolutionary theory:

There have even been meetings organized under titles such as “Molecular Strategies in Biological Evolution.” This and other examples impose a fallacious sense of direction of causality in evolution, and that is completely consistent with a common misconception of evolution facilitating organisms towards certain aims or goals. Another concept that arises from the “anthropomorphisation” of evolution is the “problem”: in other words, an organism or system evolves towards what we, retrospectively, identify as a barrier, or “problem” that had to be “solved,” and we wonder how it was overcome. Nature doesn’t solve anything. “Evolved towards” is another trap: we can only say “towards” in retrospect. The system cannot actually evolve towards anything.

But why would Moore think that such an error has led to the lay public rejecting evolution? I know people who are skeptical of evolution, and believe me this misconception (whether they hold it or not) is not the reason.

In fact, quite the opposite, it is precisely non evolutionary language that makes evolution more palatable. Anthropomorphic and Lamarckian terminology allows us to escape evolution’s foundational claim, and ultimate absurdity, that the biological world spontaneously arose by itself. Indeed, that very phrase, spontaneously arose by itself, while a scientifically accurate description of evolutionary thinking, is almost universally rejected by evolutionists as a straw man rendition of their theory. It is always interesting to see how evolutionists react when confronted with their own ideas, sans the euphemisms.

Consider this example conclusion from research involving the third eye:

A G_o-mediated phototransduction pathway might already be present in the ciliary photoreceptors of early coelomates, the last common ancestor of lizard (vertebrate) and scallop (mollusk), because both have this pathway. Later, the ancestral vertebrate photoreceptor acquired a second G protein, either gustducin or transducin, for chromatic antagonism and perhaps other purposes. The parietal photoreceptor evolved subsequently and retained these ancestral features.

This anthropomorphic and Lamarckian language is important in the evolutionary genre. Imagine if evolutionists reported that random biological variation produced a phototransduction pathway, and then produced myriad new proteins, which fortunately just happened to include a second G protein, which fortunately just happened to ... well you get the point.

Andrew Moore is correct that anthropomorphic and Lamarckian descriptions are misleading accounts of evolution. But he underestimates their important role as a necessary literary device to suppress the underlying absurdity. Far from an obstacle, they help enable acceptance of evolution.

A Professor's Evidence For Why Evolution is a Fact

I asked a professor why evolution is a fact and he listed off several evidences. Was he correct, is evolution a fact? The answer ultimately depends on you because there is no objective criteria for facthood. So there is bound to be disagreement, but let’s at least agree on our disagreement.

When I asked the professor why evolution is a fact he focused specifically on the evolution of humans and offered seven evidences: biogeographical data, fossils, genetic similarities between species in protein coding DNA, genetic similarities between species in non coding regions, genetic similarities between species involving transposons and retro viruses, and the fusion of human chromosome #2.

But there are two problems here. First these evidences are decidedly mixed, and second they are also selective. If these evidences make evolution a fact, then a great many things most people consider unlikely are, in fact, facts.

The evidence for evolution is mixed

In mandating evolution, the professor cited genetic similarities between the human and chimpanzee. There are indeed great similarities. In fact these two genomes are so similar it suggests there are other reasons for the human and chimp differences. Furthermore the DNA differences we do find don’t fit the expected evolutionary pattern.

It turns out that 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. Often these HARs are found in DNA segments that do not code for genes (the majority of the genome does not code for genes). These HARs cause several problems for evolution. For instance, we must believe that evolution 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.

Furthermore, some HARs are found in DNA segments that do code for genes, and here we find another story of contradictions.

Of course the evolutionary expectation was that humans evolved from the chimp-human ancestor via natural selection acting on mutations, to improve the genes. That is, mutations happen to occur in the genes and occasionally a mutation was helpful or at least not harmful (neutral). In those cases it may well persist and eventually become established in the population.

But findings published earlier this year reveal nothing of the kind. Assuming evolution is true, the HARs that were found in protein coding genes showed evidence not of mutations that had been selected because they were genetically helpful, but rather the exact opposite. The genetic changes showed evidence that they were, in fact, at least slightly deleterious. They had become established in the population not because they were helpful (or not harmful), but in spite of being deleterious. As the evolutionists concluded, the results led to:

the provocative hypothesis that many of the genetic changes leading to human-specific characters may have been prompted by fixation of deleterious mutations.

Once again the results make little sense under evolution.

Another problem with this genomic comparison evidence is that amongst the primates it often does not correlate well with morphological differences, as evolution would predict. For instance the orangutan looks and acts more like humans than do chimps. As one evolutionist admitted, if it weren’t for DNA, it would be the orangutan rather than the chimp pictured next to the human in the evolutionary tree. Contra the DNA evidence, only a handful of visible characters make it look like humans are most similar to chimps, whereas many more characters point to orangutans being more similar to humans than chimps. As one researcher put it:

There remains, however, a paradoxical problem lurking within the wealth of DNA data: our morphology and physiology have very little, if anything, uniquely in common with chimpanzees to corroborate a unique common ancestor. Most of the characters we do share with chimpanzees also occur in other primates, and in sexual biology and reproduction we could hardly be more different. It would be an understatement to think of this as an evolutionary puzzle.

Yet once again we find conflicting characters when trying to align the species to an evolutionary tree. Even presupposing that evolution is true, we are left with an array of contradictory data. Here is how one evolutionist summed it up:

revisiting the red ape is a useful reminder that not everything to do with morphology can be attributed to the closeness of a genetic relationship. We can evolve likenesses even to our more distant cousins if both sets of ancestors faced similar problems.

You can read more about this here.

The professor also mentioned the fusion of human chromosome #2. It would have been a problem for evolution if apes and humans had different number of chromosomes without any fusion events. We do have fewer chromosomes, but a fusion event was discovered. So evolution escaped what presumably would have been a problem. But the fusion event itself has nothing to do with evolution. We infer that such an event occurred, but there is no need for evolution to be true for the event to occur. So the evidence is interesting, and evolution escapes a problem, but there is nothing powerful here in support of the theory. Yet the professor described this evidence as demonstrating an evolutionary relationship: You can read more about the human chromosome #2 here, here and here.

A similarity does not demonstrate an evolutionary relationship. This is a misrepresentation of the scientific evidence. The fact that we share the same number of chromosomes with apes, or that we have a similar body plan, or that species share the same genetic code, or that different species of fish share similar gills, and so forth, does not demonstrate evolution.

There is of course much more that could be said about the scientific evidence. And it is not all bad for evolution. There are supporting evidences for evolution, and it has its successful predictions. But there are substantial scientific problems within the empirical evidence. While the evidence may be mixed, there is no question that evolution does not qualify as a scientific fact in the same sense that gravity or the round shape of the earth are facts. There is, however, an entirely different problem with the evidence that evolutionists set forth.

The evidence for evolution is selective

The evidence provided by the professor is selective. Yes, there is some supporting evidences within the professor’s categories, but he omitted entire categories that present substantial problems for evolution. This is a long story, but one rather obvious problematic category is that of mechanism. How is it that a living cell arose from inorganic chemicals? How did that population lead to multicellularity? How did fish arise, and then amphibians and birds and mammals? How did everything from the cardiovascular system to the brain arise?

There are few detailed answers to such questions. What we have mainly is speculation based on the assumption that evolution must be true. Evolution cannot even explain how proteins initially arose. The empirical evidence, rather, points to how astronomically unlikely their evolution would be. You can read more about this here, here, here, here, here and here.

Seeking agreement

In spite of these well known evidential issues the professor was insistent that evolution is a fact beyond all reasonable doubt. It is, he explained, a fact because what we observe shows it to be a fact. The scientific evidences say evolution happens and has happened, and we are relatives of many other living species, if not of all, in the planet. Of course these high claims are typical. Evolutionists say their theory is compelling and that it would be perverse and irrational to doubt it.

Obviously evolutionists have very unusual logic for determining what qualifies as a scientific fact. I’m not expecting them to change their minds about this, but perhaps we can understand that very different reasonings are at work. Perhaps we can agree about our disagreement.

Abby Hafer: Human Body Reveals Unintelligent Design

Last week Curry College anatomy and physiology professor Abby Hafer explained why evolution is the only genuinely scientific origins theory. In her lecture at the University of Connecticut, Hafer explained that our photoreceptor cells are backwards:

Another mechanical mishap is how the design of our eyes actually impedes our sight because the “wiring” of nerves is placed in front of the photoreceptors. These photoreceptors are crucial because they recognize light and discern the world around us. If other animals, such as the cuddle fish, can have the wiring in the back, why is ours in the front? It seems like a poor choice, unless “the creator,” as Hafer called it, which intelligent design points to, favors squids and octopi over humans.

Hafer added several other examples leaving no doubt about evolution’s scientific status. She pointed out the male reproductive system is “a very bad design” whereas frogs, for example, have no such liabilities. Or again, babies heads are too large, another poor design example.

Hafer also used the whale respiratory system to illustrate more Homo sapiens dysteleology. The whale has separate tubes for breathing and eating leaving no chance of food or drink going down the wrong pipe—another design flaw we are all familiar with.

The presentation was a tremendous educational event, helping the university’s young students to understand what real science is all about:

Students enjoyed her straightforward approach, and brother and sister Kevin and Kristina Breuninger, a 2nd-semester undecided major and an 8th-semester biology major, respectively, said they had “heard these points before, but she made them into simple scientific arguments.”

And there is no substitute for truly scientific arguments. Fortunately evolutionists such as Hafer are taking the time and effort to demonstrate true science in action.

Biology Teacher Jennifer Miller: Scientism in Action

Pennsylvania public school teacher Jennifer Miller testified at the famous Kitzmiller v. Dover trial five years ago. She teaches honors biology, anatomy and physiology at Dover Area Senior High School and for the past four years has chaired the school’s science department. Recently she had this to say to Scientific American:

How has teaching evolution in your classroom changed in the five years since Kitzmiller v. Dover?

Since Kitzmiller v. Dover I’ve definitely changed how I teach. The biggest thing is probably that evolution used to be the last thing we got to in the semester. Sometimes we maybe had one week or two weeks to cover it. Now I put evolution first, and I refer back to it to show how important it is to all topics of biology.

The other thing that I really think has changed is how I cover evolution. I'm no longer afraid to cover it in depth and to have in-depth conversations about evolution. I make sure I hit [the concept of] what is science and what is not, and how a scientific theory is very different from a "theory" that we use in everyday conversation.

A lot of teachers are wary of teaching evolution because of the controversy, and I was in that group—I didn't know if I could cover it, what I could say or couldn’t say. Now I do cover intelligent design, why it is not science, and why it should not be taught in a science classroom.

So intelligent design is not science and evolution is science. Continuing:

What are some common mistakes that teachers make in teaching evolution?
[…]

How do you see teaching evolution in schools changing in the next five years?
I wish that there were a lot more seminars so that people had more background in it. Maybe as we train new biology teachers—make sure that we give them what they really need to know—new teachers can arm themselves with the evidence that's out there. There is tons and tons of evidence for evolution, and it keeps piling up. As a teacher it’s hard to stay on top of that.

Tons and tons of evidence for evolution? That is certainly a happy coincidence.

What if the imposter had the “tons and tons of evidence”? And what if it was the “scientific” theory that was contradicted by the evidence? It’s a scary thought to be sure, but fortunately creationism is not only bogus science, it is also false. We all know the universe arose all by itself.

Fortunately we have public school teachers like Miller, backed by the wisdom of Judge Jones, to enlighten our children about these modern truths.

The Daffodil's Trumpet: A New Flower Part

The most common evidence for evolution are all the similarities between different species. Biology’s ubiquitous similarities are one of the reasons evolutionists say you can’t do research in the life sciences without evolution as your starting point. These similarities trace out evolutionary history, showing how different species are supposed to have evolved from each other. But what happens when biology reveals differences?

Botanists explain that flowers have four basic parts: sepals, petals, stamens and carpels. But new research shows that the daffodil’s trumpet is a fundamentally different thing. If similarities are such powerful evidence for evolution, then are differences such as the daffodil’s trumpet evidences against evolution? Of course not. As lead researcher, Oxford’s Professor Robert Scotland, explains:

The fascination for me has been because there are only four organs to most flowers, and because there’s so many different types of flowers and that basic system is highly conserved. The evolution of novelty within such a highly conserved but diverse system is interesting.

As this BBC video explains, the daffodil’s trumpet is an “example of evolution in action.” This reminds me of a debate I had with a professor who first claimed similarities between species were evidence for evolution, and then claimed differences between species were also evidence for evolution. I guess everything is evidence for evolution—that’s why it is true.

Unexpected Role for Ciliary Photoreceptor Cells in a Brachiopod

New research has discovered ciliary photoreceptor cells providing directional light detection in the brachiopod Terebratalia transversa. This unexpected finding further complicates the already circuitous evolutionary narrative of the origins of vision at the cellular level.

Background

At the molecular level vision begins with a complex signal transduction cascade. As photons enter your eye they interact with light-sensitive chromophore molecules in the photoreceptor cells. The interaction causes the chromophore to change configuration and this, in turn, influences the large, trans-membrane rhodopsin protein to which the chromophore is attached.

The chromophore photoisomerization is the beginning of a remarkable cascade that causes action potentials to be triggered in the optic nerve. In response to the chromophore photoisomerization, the rhodopsin causes the activation of hundreds of transducin molecules. These, in turn, cause the activation of cGMP phosphodiesterase (by removing its inhibitory subunit), an enzyme that degrades the cyclic nucleotide, cGMP.

A single photon can result in the activation of hundreds of transducins, leading to the degradation of hundreds of thousands of cGMP molecules. cGMP molecules serve to open non selective ion channels in the membrane, so reduction in cGMP concentration serves to close these channels. This means that millions of sodium ions per second are shut out of the cell, causing a voltage change across the membrane. This hyperpolarization of the cell membrane causes a reduction in the release of neurotransmitter, the chemical that interacts with the nearby nerve cell, in the synaptic region of the cell. This reduction in neurotransmitter release ultimately causes an action potential to arise in the nerve cell.

This is the beginning of vision. And while there are variations on this remarkable sequence, it is found throughout the wide variety of vision systems found in biology. It is even found in the relatively simple, non image forming, third-eye. You can read more about this here.

Phylogenetic duplicity

Because this signal transduction cascade is so widespread, evolutionists must envision it to be present in the earliest organisms with vision capabilities. This need for evolution to have created unimaginable complexity early on is a consistent theme in evolutionary theory. Over and over, the fascinating designs found in biology must have, according to evolution, appeared early on, even before any need for such marvels.

For vision, this theme of early complexity is repeated at the cellular level, where two distinct photoreceptor cell morphologies—rhabdomeric and ciliary—are found. These two morphologies have different membrane folding strategies as well as biochemical pathways. But their widespread presence in organisms forces evolutionists to conclude they both must have been present in the last common bilaterian ancestor. Rhabdomeric photoreceptor cells are often associated with invertebrates and ciliary photoreceptor cells with vertebrates, but both invertebrates and vertebrates have cells with both morphologies.

And so both morphologies must trace back to that last common bilaterian ancestor. While it may stretch common sense for early evolution to create such complexity in duplicate, if you believe it can perform the feat once, then why not twice?

But there is more to the story. In invertebrates the ciliary morphology plays a lesser role. It is not found to provide directional light detection, but in more rudimentary light detection roles. So how then does it emerge as the chief architecture in vertebrate vision systems? The evolutionary narrative calls for a migration of the ciliary photoreceptor cells to the retina where they overtake the rhabdomeric photoreceptor cells while attaining new visionary skills. Why (and how) this would happen is anyone’s guess.

Only a few years ago evolutionists were confident of this narrative. It was, according to evolutionists, a compelling story that reaffirmed the truth of evolution. These amazing claims were yet another demonstration of how evolutionists interpret unlikely data into a favorable apologetic.

But now the story has become even more unlikely. The new research has indeed found ciliary photoreceptor cells providing directional light detection in Terebratalia transversa, an invertebrate. The narrative of ciliary photoreceptor cells migrating to the retina in vertebrates suddenly makes little sense. Evolution needs a new narrative, and as usual it is more complex:

The presence of ciliary photoreceptor-based eyes in protostomes suggests that the transition between non-visual and visual functions of photoreceptors has been more evolutionarily labile than previously recognized, and that co-option of ciliary and rhabdomeric photoreceptor cell types for directional light detection has occurred multiple times during animal evolution.

In other words, yes that evolutionary scenario we were so confident of must be discarded, but so what? We can always add more drama to the plot line. Whatever biology reveals, it must have evolved—theory respectability is not important. Religion drives science, and it matters.

A Protein Folding Experiment Shows Secondary Structure Does Not Form Before Tertiary Structure

Your cells create proteins, which then perform various function, via an intricate sequence of steps. Proteins open the DNA molecule exposing the genetic information, a protein machine then copies the sequence of exposed DNA nucleotides, the resulting transcript is edited and then passed to a ribosome, at the ribosome the universal genetic code is used to translate nucleotide triplets into amino acids, the amino acids are attached together in a line like train cars hitched together, the amino acid chain folds up and is transported elsewhere where it performs a precise function, probably after forming a multi-protein machine.

This high-level summary gives an idea of the immense complexity of proteins, but there are a great many more details. For instance, protein molecular structures fall into a four-level hierarchy. The line of amino acids attached one to the next is called the protein’s primary structure. This line forms repeating patterns (helices and strands) in the folded up protein called the protein’s secondary structure. The folded up protein is called the tertiary structure. And proteins binding together form the quaternary structure.

But these structures may not always appear in this order. For instance, the secondary structure may form as a consequence of the tertiary structure coming together, rather than forming before this folding up process. Also, the tertiary structure may not form until the protein binds with its partner to form the quaternary structure.

These two facts were used in new research. A peptide that forms its tertiary structure after binding with its partner was used to determine when the peptide's secondary structure forms. Such secondary structure might provide a good framework as the peptide binds to the protein. But the researchers found that the secondary structure is not present as the peptide is folding. Rather, it appears after binding with the partner protein, and after the folding process.

Richard Olson: An Educator Who is Trying to Educate

With the incessant drumbeat of the warfare thesis—the conviction that, where they interact, religion and science are in conflict—amongst pundits and the media, one occasionally wonders if historians are working hard enough. While academics write papers for each other explaining how deeply flawed is the warfare thesis, the nightly news hasn’t received the message. Are historians oblivious to the disconnect? No, at least Richard Olson isn’t. Here is what he says in his new Zygon paper:

I argue that for psychological and social reasons, the traditional “Conflict Model” of science and religion interactions has such a strong hold on the nonexpert imagination that counterexamples and claims that interactions are simply more complex than the model allows are inadequate to undermine its power.

Yes, well put. The warfare thesis indeed has such a strong hold on the nonexpert imagination that it seems to be impervious to facts.

Taxonomies, such as those of Ian Barbour and John Haught, which characterize conflict as only one among several possible relationships, help. But these taxonomies, by themselves, fail to offer an account of why different relationships prevail among different communities and how they succeed one another within particular communities ­that is, they contain no dynamic elements.

True, most taxonomies of the various ways religion and science interact are inadequate. They miss the most important interaction of all.

To undermine the power of the “Conflict Model,” we should be seeking to offer alternative models for science and religion interactions that can both incorporate the range of stances articulated by scholars like Barbour and which can offer an account of the process by which differing attitudes succeed one another.

Yes, and until historians more actively elucidate the most important interaction—where religion is the queen and science the handmaiden—progress will be limited. How are we to understand the evolutionist’s stream of religious mandates (such as here) followed by their insistence that evolution is nothing more than objective science (such as here and here)? I’m afraid all the alternative models historians can suppose will not help until the basic, fundamental assertions of evolutionary thought are acknowledged.

John Beddington and Intolerance of Pseudo-Science

It is good to see the growing impatience of religiously motivated pseudo-science. Too often science has been, and continues to be, religion’s handmaiden. In fact it is surprising there hasn’t been a stronger backlash. But now it may be coming on too strong—the backlash may be more of whiplash. Witness Government Chief Scientific Adviser John Beddington’s recent remarks:

In closing remarks to an annual conference of around 300 scientific civil servants on 3 February, in London, Beddington said that selective use of science ought to be treated in the same way as racism and homophobia. “We are grossly intolerant, and properly so, of racism. We are grossly intolerant, and properly so, of people who [are] anti-homosexuality...We are not—and I genuinely think we should think about how we do this—grossly intolerant of pseudo-science, the building up of what purports to be science by the cherry-picking of the facts and the failure to use scientific evidence and the failure to use scientific method,” he said.

Beddington said he intends to take this agenda forward with his fellow chief scientists and also with the research councils. “I really believe that … we need to recognise that this is a pernicious influence, it is an increasingly pernicious influence and we need to be thinking about how we can actually deal with it.

“I really would urge you to be grossly intolerant … We should not tolerate what is potentially something that can seriously undermine our ability to address important problems.

“There are enough difficult and important problems out there without having to … deal with what is politically or morally or religiously motivated nonsense.”

It is refreshing to see strong words against “religiously motivated nonsense,” but I am afraid this may be a sign of dangerous overreactions to come. Yes, evolution is every bit as dangerous as Beddington suggests. In fact it is arguably far more dangerous than racism and homophobia.

But evolutionists are not guilty of hatred as are racists. Yes evolutionists bring us “religiously motivated nonsense” as Beddington puts it. Yes they cherry-pick the facts, misrepresent science and have a pernicious influence. It is difficult not to be a little bit angry with them. But we must not overreact. Rather than speak of intolerance we must speak of forgiveness. We must exchange our anger for love. I do not urge you to be grossly intolerant.

This Just In: Plants Have Leaves—Evolution Must Be True

As if evolution was not silly enough already evolutionists are now claiming that the fact that different plants all have leaves is a compelling evidence for their belief that all of nature just happened to spontaneously arise, all by itself. I occasionally enjoy a good spoof, but this is no joke. You can see this evolutionary logic for yourself right here. Some may find this unbelievable but this example, while stupefying, is actually representative of evolutionary thinking.

Evolutionary cannot explain how a single protein first arose, much less molecular machines, cells, multicellular organisms, nervous systems, cellular transduction, and a thousand other designs. In fact biology is full of fantastic, unique solutions no one would have ever guessed. Consider all the different kinds of plants biology has to offer.

Cactus plant leaves, for instance, are like spines whereas poinsettia leaves are like flower petals. On the other hand the venus flytrap leaves are like jaws that close to catch insects, and the pitcher plant leaves form a pitcher to catch insects. Of course beyond unfounded speculation about blind mutations just happening to construct such marvels, evolutionists have no scientific explanation for how these arose. Yet amazingly, in biology’s unlikely designs such as these evolutionists are certain their idea is proven. They write:

In the following photos of plants, the leaves are quite different from the “normal” leaves we envision. Each leaf has a very different shape and function, yet all are homologous structures, derived from a common ancestral form. The pitcher plant and Venus’ flytrap use leaves to trap and digest insects. The bright red leaves of the poinsettia look like flower petals. The cactus leaves are modified into small spines which reduce water loss and can protect the cactus from herbivory.

Derived from a common ancestral form? And how do evolutionists know these radically different designs evolved from a common ancestor? Well, because they are homologous, that’s how. And after all, homologous structures share a common ancestor. Amazing.

The next example, the tetrapod forelimb, is equally silly. Take a look at the eusthenopteron forelimb and the rabbit forelimb, for instance, in the figure. Like the plant leaves, these designs are radically different.

Yet we are told this “demonstrates their common ancestry.” Demonstrates their common ancestry? How are these demonstrations of common ancestry? In fact there is no demonstration of common ancestry here. Evolutionists show some nice illustrations of radically different plants and animals, and simply assert that this is a demonstration of common ancestry. This is the height of absurdity.

The evolutionary argument is that evolution is restricted to certain designs. And while such designs evolve a bit, the underlying design framework is unchangeable. Evolution is stuck with it. Hence these similarities, even such remote similarities, are compelling demonstrations of evolution.

There are two problems here. First, the claim affirms the consequent. If a hypothesis successfully makes a prediction, that does not mean the hypothesis is correct. Second, the claim is false. Evolutionists routinely ascribe complete redesigns to evolution. Evolution is supposedly capable of complete makeovers. But then when a pattern is observed, we are told evolution is stuck with it. Evolutionists just make up whatever suits the moment. In fact if evolution is so stuck with designs, then it would clearly be falsified, as it wouldn’t be able to come up with all those new designs it is always devising.

But if all this seems unlikely, is it not better than separate ancestry? Using this reasoning, evolution, it turns out, is impervious to low likelihoods. It doesn’t matter if the evidence is astronomically unlikely. In fact, the more unlikely the better because the alternative is even worse. Evolutionary philosopher Elliott Sober has analyzed how common descent advances via this contrastive thinking. The powerful arguments and evidence do not actually bolster the theory but rather they rebuke the alternative. He explains it this way:

This last result provides a reminder of how important the contrastive framework is for evaluating evidence. It seems to offend against common sense to say that E is stronger evidence for the common-ancestry hypothesis the lower the value is of [the probability of E given the common-ancestry hypothesis]. This seems tantamount to saying that the evidence better supports a hypothesis the more miraculous the evidence would be if the hypothesis were true. Have we entered a Lewis Carroll world in which down is up? No, the point is that, in the models we have examined, the ratio [the probability of E given the common-ancestry hypothesis divided by the probability of E given the separate-ancestry hypothesis] goes up as [the probability of E given the common-ancestry hypothesis] goes down. … When the likelihoods of the two hypotheses are linked in this way, it is a point in favor of the common-ancestry hypothesis that it says that the evidence is very improbable. [Evidence and Evolution, p. 314]

In other words, it doesn’t matter that common descent is not a good theory. It must be true because the alternative is even worse. Sober refers to this mode of reasoning as Darwin’s Principle. It seems evolutionists can talk themselves into anything, including the claim that leaves prove their unlikely idea. Religion drives science and it matters.

Addendum:

An evolutionist commented that my Sober quote above is misleading, and my summary that it doesn’t matter that common descent is not a good theory is erroneous. He reasoning was that I took the Sober quote out of context and used an ellipses to manipulate the meaning of the quote.

This is yet another example of how evolutionists are unable to face the reality of their theory and its implications. No matter how much evidence they are presented with, evolutionists will never agree with the obvious. First the idea that the ellipses hides some crucial message from Sober that is the key to the passage, and without it I have manipulated the meaning, is pathetic. In fact, what I omitted were three sentences that further reinforce the point. I omitted them simply because they are redundant and full of jargon. Here they are:

An easy way to see this point is to imagine that Pr(1 --> 1) = 1, Pr(0 --> 1) = 0, and let Pr(Z = 1) = p, where Z, recall, is an ancestor of the observed species X and Y. Then the likelihood of CA is p and the likelihood of SA is p^2, so the likelihood ratio of CA to SA is 1/p. Now it is obvious how the evidence for CA gets stronger as p gets smaller.

So in this example, Sober argues that the common ancestry hypothesis (CA) improves as its likelihood decreases. It is no different than the surrounding passage. His reasoning is that as the likelihood of CA decreases, the likelihood of the separate ancestry hypothesis (SA) decreases even more. So when compared to SA, CA looks better when the evidence says it is even more unlikely. It is an example of how evolutionists use pretzel logic to try to make their idea attain that status of a fact.

But the evolutionist complained that "It's a pretty big stretch (to put it mildly) to take this specific argument about probabilities of character states and represent it as referring to the entire theory of common descent."

But of course I did not represent it as referring to the entire theory of common descent. As I explained above, the Sober analysis applies to the evolutionist's silly arguments that plants having leaves demonstrates common descent. In fact, I was quite clear about this: I wrote:

But if all this seems unlikely, is it not better than separate ancestry?

In other words, I first explained that the evolutionist argument appears silly, and I then provided a particular evolutionary interpretation of the evidence to which the Sober analysis directly applies.

This is a good example of how debates and discussions go with evolutionists. They begin with a religiously motivated, unscientific idea, and from there is it absurdities, fallacies and canards, one after the other.

John Lynch on The Voyage that Shook the World

The National Center for Science Education, whose mission is to defend the teaching of evolution in public schools, recently published a review of the film Darwin: The Voyage that Shook the World. The review was written by John Lynch, an evolutionary biologist and historian of science, and Jim Lippard, a student, both at Arizona State University. Aside from misrepresenting science, the review also misrepresents my views and contribution to the film. Lynch and Lippard write:

Near the end of the film, it is stated that in Darwin’s time, science was only beginning to emerge from philosophy, and that Darwin’s project was philosophical and anti-religious as much as it was scientific.

Lynch and Lippard then suggest that this position was probably inspired by me. I was of course surprised to read such a blatant misrepresentation of my view. After all, I have written several books, websites, and blogs on the fact that evolution entails religious and metaphysical premises.

In fact, in the film I made this quite clear. Near the end of the film, I stated that:

150 years later, it is clear that Darwin’s theory of evolution is really not about science, it’s about god.

How could the historian of science Lynch possibly foul this up. Not only did I not say Darwin’s project was anti-religious, I clearly and unambiguously stated the exact opposite. Darwin’s writings are chocked full of religious and metaphysical concerns and arguments. And they build on religious sentiment that had been influencing studies of the nature for two centuries leading up to Darwin. But Lynch is an evolutionist, and for evolutionists the warfare thesis is standard fare. Religion drives science, and it matters.

Like Not Believing in Algebra

Though evolutionists insist evolution is a fact many life scientists do not share their conviction. Our entire existence including all of biology, according to evolutionists, just happened to arise on its own—somehow. Nothing in biology makes sense, they claim, except in the light of evolution. But such dogma has badly failed. Not only are their claims not scientific to begin with (“Nothing in biology makes sense except in the light of evolution” is equivalent to an if-and-only-if statement which is impossible within the bounds of science), but evolution’s fundamental predictions are consistently proven wrong. It is hardly surprising that many life scientists hold a more tentative view. But one recent survey revealed that even biology teachers routinely fail to carry out their duties of indoctrinating young students. The responses of evolutionists are telling.

A recent Pennsylvania State study by two political scientists reveals that most US public high school teachers are either uncomfortable with teaching evolution or doubtful of its accuracy. Clearly teachers are not carrying the water for evolutionists and something must be done. In lamenting this state of affairs Nature blogger Adam Mann begins with yet another erroneous reference to the Scopes Monkey Trial:

Almost a century after the famed Scopes Monkey Trial, battles over teaching evolution versus creationism in US public schools persist - but they have shifted to individual classrooms where teachers have a vast influence over whether evolution is present, a new study finds.

Of course the Scopes Monkey Trial was not simply a battle over teaching evolution versus creationism. It was an ACLU-spearheaded advocacy for the religious thinking that is the heart of evolutionary thought, as made obvious in the famous grilling of William Jennings Bryan by Clarence Darrow on the Bible’s foolishness.

Next Mann erroneously equates intelligent design with creationism to present the usual black/white picture to the reader. There are the bad guys over there seeking to spread dangerous lies, and then there are evolutionists—the vanguard of scientific truth and justice. Mann quotes William Wallace of the National Association of Biology Teachers to elaborate on this dangerous state of affairs:

Since evolution is the fundamental concept unifying biology, it is surprising how many high school biology teachers are unaccepting or uneasy with it, says William Wallace, the Washington D.C. representative of the National Association of Biology Teachers. “It’s like a math teacher not believing in algebra,” he says. Better instruction during a prospective biology teacher's college training could help mitigate this fact, he says, a position the researchers advocate for as well.

Not believing that evolution is an undeniable fact is like not believing in algebra? Given evolution’s substantial failure and algebra’s foundational status, it would be difficult to imagine a less appropriate comparison. Algebra is a branch of mathematics, evolution is a religiously-driven theory that contradicts the empirical evidence. If evolutionists are concerned about the  harmful effects of religion on science they should look closer to home.