Francisco Ayala: I Don’t Answer Questions on My Personal Beliefs

Here is an interview with evolutionist Francisco Ayala where he does not give answers about his personal beliefs.

You won [a Templeton prize] for arguing there is no contradiction between science and religion. Many disagree.

They are two windows through which we look at the world. Religion deals with our relationship with our creator, with each other, the meaning and purpose of life, and moral values; science deals with the make-up of matter, expansion of galaxies, evolution of organisms. They deal with different ways of knowing. I feel that science is compatible with religious faith in a personal, omnipotent and benevolent God.

This view that science and religion address different types of problems is known as the compartmentalization model. It ignores the vast and substantial body of theological claims made by scientists, and material claims made by religions.

Why do you say creationism is bad religion?

Creationism and intelligent design are not compatible with religion because they imply the designer is a bad designer, allowing cruelty and misery. Evolution explains these as a result of natural processes, in the same way we explain earthquakes, tsunamis or volcanic eruptions. We don’t have to attribute them to an action of God.

So god does not create calamity.

Do you believe in God?            

I don’t answer questions on my personal beliefs.

The evolutionist thinks his theodicy is not a personal belief. After all, isn’t it obvious that god would not create calamity? It reminds me of what Edwin Burtt wrote about positivism:

[T]he lesson is that even the attempt to escape metaphysics is no sooner put in the form of a proposition than it is seen to involve highly significant metaphysical postulates.

For this reason there is an exceedingly subtle and insidious danger in positivism. If you cannot avoid metaphysics, what kind of metaphysics are you likely to cherish when you sturdily suppose yourself to be free from the abomination? Of course it goes without saying that in this case your metaphysics will be held uncritically because it is unconscious; moreover, it will be passed on to others far more readily than your other notions inasmuch as it will be propagated by insinuation rather than by direct argument. That a serious student of Newton fails to see that his master had a most important metaphysic, is an exceedingly interesting testimony to the pervading influence, throughout modern thought, of the Newtonian first philosophy.

Now the history of mind reveals pretty clearly that the thinker who decries metaphysics will actually hold metaphysical notions of three main types. For one thing, he will share the ideas of his age on ultimate questions, so far as such ideas do not run counter to his interests or awaken his criticism. No one has yet appeared in human history, not even the most profoundly critical intellect, in whom no important idola theatri can be detected, but the metaphysician will at least be superior to his opponent in this respect, in that he will be constantly on his guard against the surreptitious entrance and unquestioned influence of such notions. In the second place, if he be a man engaged in any important inquiry, he must have a method, and he will be under a strong and constant temptation to make a metaphysics out of his method, that is, to suppose the universe ultimately of such a sort that his method must be appropriate and successful. Some of the consequences of succumbing to such a temptation have been abundantly evident in our discussion of the work of Kepler, Galileo, and Descartes. Finally since human nature demands metaphysics for its full intellectual satisfaction, no great mind can wholly avoid playing with ultimate questions, especially where they are powerfully thrust upon it by considerations arising from its positivistic investigations, or by certain vigorous extra-scientific interests, such as religion. But inasmuch as the positivist mind has failed to school itself in careful metaphysical thinking, its ventures at such points will be apt to appear pitiful, inadequate, or even fantastic. [The Metaphysical Foundations of Modern Science, Revised Ed., Doubleday Anchor, 1954, p. 228-9.]

Like a fish that doesn’t know it is in water, those who are most indebted to metaphysics are the least aware.

Arthur Caplan on the Elasticity of Evolution

Years ago, in response to worries that evolution was not falsifiable, an evolutionist assured me the theory was indeed falsifiable. Functionally unconstrained DNA, he explained, should not be conserved in distant species. Such a finding, he assured me, would absolutely refute evolution. Such claims of falsifiability can suffer from two potential problems: they can be too hard, or they can be too easy.

Falsifiability claims can be too hard in the sense that the finding in question is not likely to be discovered. Darwin made this move when he explained that his theory “would absolutely break down” if it could be demonstrated that “any complex organ existed, which could not possibly have been formed by numerous, successive, slight modifications.” Not surprisingly Darwin concluded that he could find out no such case. What he didn’t tell the reader is that his falsification criteria was impossible.

On the other hand, falsifiability claims can be too easy in the sense that if the finding in question is discovered it can easily be accommodated by adjusting the theory. Evolution is constantly under revision due to the steady stream of unexpected scientific findings. When the evolutionist told me that evolution would absolutely break down if functionally unconstrained DNA was found to be conserved in distant species, I thought it was too hard. Given what we knew at the time, it seemed such a finding was unlikely. But then when it was discovered, the falsification criterion was revealed to be too easy. The discovery of so-called ultra conserved elements (UCEs) certainly was unexpected. As one evolutionist put it, “I about fell off my chair.” But of course, as with all the other unexpected findings, UCEs could do no real damage to evolutionary belief.

The seemingly infinite resiliency and elasticity of evolution is an indicator that there is more than mere science at play. Commentators have noticed this peculiar property of evolution for many years now. Philosopher Arthur Caplan once summarized these concerns as follows:

1. Evolution is rarely sullied by any specific predictions or retrodictions.

2. Evolution seems to possess a disquieting amount of elasticity. Anything and everything in the empirical biological world seems to be compatible with evolutionary explanations. Refuting evidence or crucial experiments that could realistically jeopardize an evolutionary account seem extremely few and far between.

3. Evolutionists seem willing to assume and postulate mechanisms, variables and conditions almost willy-nilly in their attempts to explain evolutionary changes. In evolutionary explanations the theorist simply assumes everything he needs to make the explanation work.

4. Evolution does not measure up to theories from other domains of scientific inquiry. Evolution is significantly poorer in its capacity for empirical refutation, falsifiability and testability.

Caplan noted that philosophers such as Michael Ruse had attempted to defend evolution against such charges. Caplan was not impressed with such attempts and concluded that perhaps we need to go easy on how we criticize theories such as evolution. Perhaps evolution is a different kind of theory, and needs to be treated as such.

Yes, evolution is a different kind of theory. Evolution is a religious theory. I once debated Ruse, but it was more of a discussion than a debate. I explained the metaphysics of evolution and Ruse explained the metaphysics of evolution. My point was that evolution is metaphysical and therefore a different kind of theory. Ruse point was that evolution is metaphysical and therefore true. He made the powerful point that without evolution we would be left with the foolish idea that god made this gritty and evil world.

There is no escaping the religion of evolution. Without it atheists would have to face the specter there is a God. And theists would have to face the specter there is the wrong kind of God. Better to believe the world spontaneously arose all by itself. Religion drives science, and it matters.

The Woodpecker Inspires High-G Engineering Designs

Recently research has shown the risk of concussion to football players. Even at the high school level helmet-to-helmet collisions can produce acceleration levels approaching 100 g's. Amazingly, woodpeckers can experience head collisions of 1200 g's, and at more than 20 times per second, as they peck at trees. New research is uncovering how the woodpecker manages to sustain such shocks and nature's design is inspiring a range of improvements to engineered systems.

The new research has found that woodpeckers have a shock absorber system that consists of four components.The woodpecker has an elastic beak that helps reduce the shock, a soft structure underlying the tongue, spongy bone in its skull, and a vibration-suppressing interaction between the skull and spinal fluid.

Discovering this system is only the first step. Researchers are now investigating how to take advantage of this design. In one experiment the woodpecker-inspired design was used to protect microelectronic circuitry. The entire system was fitted inside a bullet and the microelectronic were protected in impacts of up to an amazing 60,000 g's.

This technology has potential applications in airborne flight data recorders (which can withstand shocks of 1000 g's), automobiles and spacecraft. As one engineer observed:

This study is a fascinating example of how nature develops highly advanced structures in combination to solve what at first seems to be an impossible challenge. It may inform our thinking on regenerative dampers for vehicles, redirecting the energy into a form more easily recoverable than dumping it to heat. Ultimately, we need to learn from the woodpecker to recover energy and not give the driver a headache.

And how do evolutionists explain the development of such "highly advanced structures in combination"? They say that random biological variation, such as mutations, just happened to produce this system. They say that fortunately, there just happened to be a long series of gradual improvements leading to the final design. They don't know what those intermediate designs were, and there must have been many, but they are sure they exist. Somehow, amazing designs over and over just happen to be in a long series of useful, though unknown, intermediates.

Did the Seabird Evolve Head Feathers as Sensory Device?

New research shows that without their head feathers seabirds such as Aethia cristatella can’t find their way through tight spaces as well:

Crested and whiskered auklets nest in hollows on rocky islands in the remote northern Pacific Ocean. To see if their elaborate headdresses helped the birds make their way through the rocks to their nests at night, Jones and Seneviratne went to the Aleutian Islands, captured wild birds and put them in a darkened maze – but first they taped down some birds' decorative feathers.

Infrared camera recordings showed that whiskered auklets (Aethia pygmaea) bumped their heads nearly three times more often if their long head feathers were taped down. Crested auklets (A. cristatella), suffered similarly with their crests taped down, but adding an artificial crest to the naturally unadorned least auklet (A. pusilla) – which also nests on the islands but in more open areas – didn't help these birds avoid bumps. Moreover, Sereviratne says, "birds with longer crests had greater difficulty in navigating inside the maze" when their crests were taped down.

The evolutionary origin of the birds' elaborate head feathers supports the idea that their first job was sensing, says Seneviratne. He adds that the auklets' crests evolved from filoplumes, long hair- or thread-like feathers that lack normal feather structures and are attached to pressure-sensitive cells so they can detect touch. In many birds these feathers are hidden by larger contour or wing feathers, but in the auklets they stick out proudly where they can detect obstacles.

The auklet’s head feathers clearly are not just for looks. But evolutionary theory was not needed to make this discovery, nor does it help in explaining the feathers, or the cellular pressure-sensing mechanisms. In fact, beyond empty speculation evolution has no explanation for how such mechanisms could have arisen on their own. It is a typical example of how evolution is a gratuitous explanation, adding nothing but a “multiplied entity” as Occam put it. We may as well say, with the Aristotelians, that fire is hot because it has the quality of heat. Not only has evolutionary theory badly failed, it is not particularly helpful in doing science. It simply becomes more and more complex as we learn about the world.

Creation Versus Evolution: The Real Story

Creationist Ken Ham, president of Answers in Genesis, has been disinvited from homeschooling conferences over comments he made about evolutionist Peter Enns. Both Ham and Enns are conference speakers. As conference organizer Brennan Dean wrote:

Our expression of sacrifice and extraordinary kindness towards Ken and AIG has been returned to us and our attendees with Ken publicly attacking our conventions and other speakers. Our Board believes Ken's comments to be unnecessary, ungodly, and mean-spirited statements that are divisive at best and defamatory at worst.

An Answers in Genesis spokesman, however, explained that they were unaware there was a problem and that conference organizers should not have been surprised by Ham’s warnings that evolution compromises God's word.

On the surface this story appears to be about yet another tiff between creationists and evolutionists. The creationists may use it to remind us that scripture must be vigorously defended while the evolutionists may use it to make yet more appeals for nuanced readings of scripture. And those outside the debate undoubtedly will call for unity. But while all these points are perfectly valid, they miss the real story.

Can scripture accommodate evolution?

Evolutionists sometimes ask me if my religious beliefs can accommodate evolution. Do I criticize evolution objectively, they ask, or do I have religious motives? The answer is that my religious beliefs do not accommodate evolution, but not for the suspected reason.

When evolutionists ask this question they are thinking about the material aspects of evolution. Can your religious beliefs accommodate an old earth and species arising via natural processes rather than miraculous intervention? To this I say sure. With thinkers ranging from BB Warfield to the Roman Catholic Church, I don’t have a particular problem with God creating through his natural laws.

I’m not saying this is easy. True, Genesis does speak of the earth bringing forth some of the species. Is this not at least suggestive of natural processes? And even creationists appeal to limited amounts of evolutionary change. But I do not find either of these very compelling. Scripture does not seem to be easily adaptable to the evolutionary narrative. But saying this is different than saying scripture definitely excludes evolution. For me evolution is not a likely interpretation of scripture, but it is not out of the question. And if it is not out of the question, then it must be considered.

So what is the scriptural problem with evolution? The problem is that evolutionary thinking is, and always has been, motivated by non biblical claims about God. I have discussed this in this blog, but the best place to find these claims is in the evolution literature, both before and after Darwin. Simply put, evolutionary thought is motivated and justified by various claims about how God would create the world. God wouldn’t create all of the many lowly creatures—that is beneath him. God wouldn’t create evil or inefficiency—that would be against his nature. God wouldn’t create particular patterns—that would be capricious. And so forth. In all about a dozen theological and philosophical arguments, that mandate evolution, arose in the Enlightenment years before Darwin. And they were and remain today tremendously influential. They are the reason that evolutionists today insist evolution is a fact, not merely a theory. Evolution is, at bottom, a religious idea developed in polite Christian settings. Today’s atheists, like a conforming teenager who thinks he is in rebellion, rehearse these same arguments as if demonstrating a religious skepticism.

But the Bible will have none of this. Scripture presents a creator who is in control. This creator knows precisely what he is creating. He may use miracles, he may use natural processes, but there are no surprises in the end. This may sound evolution friendly but it is not. This view is not at all accommodative of evolutionary thought. For as evolutionist SJ Gould put it, “Odd arrangements and funny solutions are the proof of evolution—paths that a sensible God would never tread.” Both atheist and theist alike agree god would not have created this mess, and so evolution must be a fact. That is a religious claim that doesn’t pass the scriptural test. (And without its religious claims evolution is left only with its scientific claims which are prima facie absurd). Consider, for example, God’s message to Job regarding the unlikely ostrich:

      “The wings of the ostrich wave proudly,
      But are her wings and pinions like the kindly stork’s?

      For she leaves her eggs on the ground,
      And warms them in the dust;

      She forgets that a foot may crush them,
      Or that a wild beast may break them.

      She treats her young harshly, as though they were not hers;
      Her labor is in vain, without concern,

      Because God deprived her of wisdom,
      And did not endow her with understanding. [Job 39:13-17]

This and other passages do not give hints that creations arose in spite of the creator’s wishes.

The real story

And so the real story is not at the level of mechanism, but at the level of divine intent. And this brings us full circle back to the Ken Ham and the creationists. For while creationists and evolutionists argue about mechanism, they both agree about divine intent. God, they say, did not intend for this evil world. For creationists the problem is solved by the Fall. For evolutionists it is solved by natural law. But where it counts they agree. Consider, for example, how Ham responded to the killer tsunami in the Indian Ocean a few years ago:

Those of us who believe in a literal Genesis have a history, a history concerning the Fall, a history concerning the Flood. So when we look at this world, we’re looking at a fallen world. It’s not God’s fault there are tsunamis. … Death is not God's fault. [Christianity Today, April 24, 2006]

Creationists say God would not use long time periods to create. They say God would not use cruel processes to create. These are claims about divine intent, and that is the real story.

Does Religious Belief Drive Evolution Skepticism?

A typical evolutionary argument is that skepticism is driven by religious belief. As one evolutionist recently commented:

isn't it odd that essentially 100% of evolution deniers just happen to also be theists?

If you want to understand evolution, you need to listen to evolutionists. This example reveals their logic at work. Consider the facts. Atheists typically believe the world arose on its own. They believe in evolution, in one form or another. Theists, on the other hand, have a diversity of views. Christians in particular have the freedom to engage the broad spectrum of explanations, ranging from natural processes to miracles. Ever since Basil, Christians have considered origins narratives ranging from mostly secondary to mostly primary causation.

Given these facts, how could it be odd that "essentially 100% of evolution deniers just happen to also be theists"? How could this suggest religious belief drives evolution skepticism? Quite the opposite, it is what one would expect. There are few atheists who aren't evolutionists. So what?

Only evolutionary logic could force-fit the fact that skeptics are mostly theists, into support for evolution.

Next, note the evolutionist's use of the word "denier." This is a strong word, but why apply it to skeptics of the dogma that the world spontaneously arose? Evolutionists insist their idea is a scientific fact, and they fail to support this claim. In fact there are monumental scientific problems with this claim. Cannot people be skeptical without being labeled as a "denier"? If one wants to use the D word here, it would seem that those insisting evolution is a scientific fact are the ones who are in denial.

But on the other hand, those who accept evolution come from all sorts of religious backgrounds; over 40% of scientists are professing believers of some sort or another. If religious/anti-religious sentiment were driving acceptance of evolution what are we to make of the religious diversity in the evolution crowd, and the very distinct lack of religious diversity in the anti-evolution crowd? Another coincidence?

Again, the evolutionary logic misses the mark. Where it counts there is little religious diversity in evolutionary thought. Yes there are atheists and various types of theists, but there is a conserved metaphysical view. Christians such as Francis Collins and atheists such as PZ Myers agree that god would not have created what we find in this world.

Skeptics, on the other hand, have tremendous diversity. Their religious views range from young earth creationism to the very theological naturalism that drives evolution. In the latter case, many skeptics of evolution agree with evolutionists that natural processes must have played a significant role in creating the species because god would not have created what we see in biology. But they also realize that those natural processes are, alone, not up to the task.

And of the Christians who do accept evolution, do you think they are on average more, or less educated than their brothers and sisters who don't accept evolution? Care to take a guess? Is that a coincidence as well?

So what does that tell us about the state of our educational system?

Isn't the high correlation between education and acceptance of evolution a little odd? It's almost as if the more people learn about the subject, the more likely the are to accept it.

The correlation between education and acceptance of evolution is not necessarily a plus for evolution, as though good science is up for a vote. In fact, our education system does not teach critical teaching regarding evolution. Instead, it dogmatically instructs students that evolution is a fact using the usual combination of faulty science and metaphysical reasoning. You can read more about this here, here, here, here, here, here, here, here, here and here.

It is hardly surprising that there might be a correlation between education and acceptance of evolution.

I guess education is a bad thing, a temptation from the devil, perhaps. Maybe they're just being brainwashed in institutions of higher learning, and it's a happy accident that they are able to so effectively add to mankind's body of knowledge.

Here we have both a straw man argument and circular reasoning that are all too common amongst evolutionists. Clearly the education system is badly failing and we ought not try to cover that over with hyperbole.

Secondly, there is no happy accident with evolution. It has not added to "mankind's body of knowledge." Only the evolutionist's erroneous claim that evolution is good science can lead to this conclusion.

did you ever stop and think how odd it is that you're smarter than 99.9 percent of all professional biologists? (and around 98 percent of all other scientists?) ... Supernatural explanations are ruled out, as a matter of practicality. Science is about testing claims. Call us when you can test supernatural causes. A design claim that had either a testable agent, or a testable mechanism would be considered.

Finally the serendipity of evolutionary thought is clear. Naturalism is mandated and luckily enough, it also turned out to be a fact. Naturalism is mandated and isn't it strange that all those scientists just happen to be evolutionists? Naturalism is mandated and incredibly enough, all those journal articles support evolution. Naturalism is mandated in our schools and amazingly there is a correlation between education and acceptance of evolution. Evolutionists aren't fooling anyone but themselves.

The Evolution of Homoplasies

It is one of the fundamental concepts of, and evidences for, evolution: similarities found in different species. These similarities, or lack thereof, are used to construct evolutionary trees which show how the species are evolutionarily related. Species sharing many similarities are close neighbors while species sharing fewer similarities are distantly related. And according to textbooks such relationships are obvious. Those textbooks show clean and compelling illustrations of evolutionary trees. But the biological data are not so cooperative. One problem is the many uncanny similarities found in what otherwise must be, according to evolution, more distant species.

Similarities in otherwise distant species are known as homoplasies. They are, as one paper explained, not the expected outcome:

Phenotypes and taxa are expected to diverge as evolution proceeds. Thus, when divergent lineages are found to be morphologically similar, explanation is needed. Homoplasy is similarity that is the result not of simple ancestry, but of either reversal to an ancestral trait in a lineage or of independent evolution. …

However, one does not seek homoplasy—it “finds” the researcher and compels one to ask appropriate questions.

Of course evolutionists have answers for those questions. These unexpected similarities may have independently evolved from scratch. Or perhaps the trait disappeared in one lineage, only to later reappear much later. To elucidate such details evolutionists construct evolutionary trees. As the paper explains:

Phylogenetic analysis is necessary to show that derived similarity is not the simple result of common ancestry of taxa being compared.

But the process of constructing evolutionary trees, using phylogenetic analysis, presupposes that evolution occurred. In other words, in order to demonstrate that a trait independently evolved in different lineages, evolutionists begin by assuming evolution. This assumption, however, is implicit rather than explicit. It is unspoken. When reporting that they have discovered that a trait, such as the vision system, independently evolved several times, evolutionists do not explain that they began by assuming evolution is true. Without that assumption there is no scientific reason to think these homoplasies evolved—independently or otherwise.

In fact, there are plenty of scientific reasons to think they did not evolve. Specific designs, where many are possible, are not likely to repeatedly arise by chance (no, selection does not help).

In some cases these homoplasies develop in the embryonic stages via similar pathways. For instance, the Pax6 master control gene plays an important role in the development of the different vision systems that are supposed to have independently evolved. This means that Pax6 must predate the evolution of these different vision systems. This is yet another example of the serendipity that pervades evolutionary theory. In this case, we must believe that genes such as Pax6 first evolved when no vision system existed. Then later it enabled such phenomenal designs to arise:

The image-forming eyes of invertebrate and vertebrate taxa are convergent organs that share some core developmental genetic mechanisms that exemplify deep homology. All eyes, invertebrate and vertebrate, develop through a cascade of similar transcription factors despite vast phylogenetic distances. These networks include genes (e.g., Pax6) that have been deployed in different ways at different times, and specific pathways that have re-evolved in different lineages by mutation, gene duplication, and intercalary evolution. The networks and cascades, which contain homologous genes and members of the same gene families, are not genetically identical. Thus, the end phenotypes might be general homologs at a deep hierarchical level but convergent with respect to end phenotype and phylogeny. Indeed, what has historically been termed “convergence” and attributed to independent evolution in unrelated taxa has a common genetic system associated with trait development.

Such pre adaptation narratives are ubiquitous in the evolution literature. All kinds of profoundly complex designs arise only much later to be recruited as a crucial component in some even more complex design.

Plant and animal defense systems

Or consider the striking similarities in how plants and animals defend against pathogens. In this case various homoplasies are found, calling for various evolutionary explanations. As one paper explained, a clear, irrefutable picture has emerged. “Plants and animals use similar types of cell surface sensors to detect conserved microbial signatures.”

These different types of cell surface sensors work rather well in helping to defend against pathogens. This is why they evolved independently according to evolutionists. But in fact what such findings reveal is the tight design requirements. Apparently only a limited set of cell surface sensors can do the job.

This runs counter to the typical evolutionary explanation that the impossible probabilities they must surmount don’t really matter because there must be a great many different, as yet unknown, designs that evolution could have luckily hit upon. Yes, the chances of any one design is remote, but there must be a great many different designs that all could do the job. Apparently not in the case of these cell surface sensors.

Evolutionary trees are not the clean, compelling result as they too often are represented to be. Homoplasies, which strain the evolutionary probabilities even further, are yet another example of this. Yes the similarities between the species can be modeled with evolutionary trees, but such a conclusion has substantial scientific problems.

Parasitic Insects and Evolution

Would God really want to take credit for the mosquito? Natural theology, which reigned before Charles Darwin introduced his theory of evolution, argued that creation demonstrated the power, wisdom, and goodness of God. But what about nature’s evils? Consider for example the ichneumonoidea, wasps that inject their eggs into a host insect. They also inject a chemical that paralyzes the host without killing it. Aside from providing an incubator for the wasp’s eggs, the host also becomes the first meal for the newly hatched wasp, which carefully consumes the host so as to keep it alive a long as possible. As is so often observed in nature, profound levels of evil are accompanied by profound levels of complexity. Evil, it turns out, is not always banal.

The parasitic wasp

In Darwin’s day the entomologist (and Reverend) William Kirby pointed out the amazing complexities of such parasites. How did the parasitic wasp know how to avoid injuring the vital organs? He wrote:

In this strange and apparently cruel operation one circumstance is truly remarkable. The larva of the Ichneumon, though every day, perhaps for months, it gnaws the inside of the caterpillar, and though at last it has devoured almost every part of it except the skin and intestines, carefully all this time it avoids injuring the vital organs, as if aware that its own existence depends on that of the insect upon which it preys!

But Kirby’s views were not shared by those who felt god would never create such a horrifying world. Centuries earlier Thomas Burnett, Ralph Cudworth, John Ray and others had called for a distancing of God at the sight of far less wrenching evils. Imagine what their response would have been to nature’s new round of atrocities being uncovered by science.

It probably would have been similar to Darwin’s response, who argued in his book on evolution that the instinctive hatred of the queen-bee for her own fertile daughters and the parasitic wasp feeding within the living bodies of caterpillars were yet more proofs for his new theory. It seemed that Darwin was, as one historian put it, “yearning after a better God than God.” As Darwin wrote to Asa Gray in 1860:

I own that I cannot see as plainly as others do, and as I should wish to do, evidence of design and beneficence on all sides of us. There seems to me too much misery in the world. I cannot persuade myself that a beneficent and omnipotent God would have designedly created the Ichneumonidae with the express intention of their feeding within the living bodies of caterpillars, or the cat should play with mice.

Science and religion were “thoroughly interwoven in Darwin’s life and thought,” but this was hardly unique to Darwin. It is not surprising that many theologians gave a warm welcome to Darwin’s theory. Nor is it surprising that Darwin’s theory would lend itself to a new round of theological naturalism. Theological naturalism had argued for a distancing of the Creator from creation. Now Darwin’s theory was filling in the details. It was natural selection, not a divine finger, that did the job. Darwin’s idea provided a new framework for continued theological speculation.

The mosquito

More disgusting than the parasitic wasp is the mosquito, which brings misery and death to hundreds of millions of people every year. As evolutionist Ken Miller rhetorically asks, would god really want to take credit for the mosquito? Of course if Burnett, Darwin, Miller and the rest don’t believe god would create such evils, then evolution must be true, one way or another.

But like the parasitic wasp, the mosquito is complex. For instance, a few years ago Chinese researchers discovered that mosquitoes have an amazing ability to land, walk and take-off from water. Of course mosquitoes are not the only insect that can move about on the water’s surface, but the buoyancy of a mosquito’s leg—about 23 times the mosquito’s body weight—and its nanostructures are remarkable.

Blood-feeding insects also have exquisitely designed carbon dioxide sensors to home in on their prey. Research has identified two dedicated neural receptors that together cause nerve signals to be sent when carbon dioxide is present. The experiments found that the presence of both receptors is required—either one alone failed to sense the carbon dioxide.

As one scientist explained, such molecular sensor systems are “exquisitely sensitive” to carbon dioxide levels we don’t even notice. They are, indeed, “wonders of natural engineering.”

Given such an exquisite design, and given that both receptors are required because a single receptor working alone is ineffective, one might think that evolutionists might struggle to explain this engineering marvel.

But evolutionists have no such problem. After all, would god really want to take credit for the mosquito?

Philosophers to Discuss the Metaphysics of Evolutionary Naturalism

Don’t be fooled by the upcoming conference on “The Metaphysics of Evolutionary Naturalism” at the American University of Beirut. In spite of the title the conference is not about the metaphysics of evolutionary naturalism, it is about the metaphysical implications of evolutionary naturalism. As the conference description explains:

From the perspective of the history of philosophy, evolutionary theory raises some very fundamental questions indeed.

Indeed yes, but they won’t be asked at this conference. Here are some questions that won’t be asked:

1. Can a strictly naturalistic research program enjoy guarantees of completeness and realism?

2. Is a strictly naturalistic approach required for legitimate science? If so, can the resulting explanations be objective facts?

3. Is it serendipity that the strictly naturalistic origin of life narrative is (i) required for science and (ii) a fact?

4. Are contrastive approaches to theory evaluation, such as likelihood ratios, undermined by the problem of unconceived alternatives?

5. Does the infinite regress make design impossible? Non scientific? Both? If so, does this mandate evolution as is claimed?

6. Would an all-good, all-powerful, all-knowledgeable creator never intend this world as evolutionists claim?

7. Can atheists make metaphysical assertions, such as that god would never create this world, without contradicting themselves?

How can one be a naturalist after Darwin? On the ancient teleological naturalist picture, namely that of Aristotle, the goal of the study of the physical world, organic and inorganic, was to reveal the ultimate purposes of things. This teleological world-view was then coupled with the belief in a unified deity, and resulted in the belief that the study of the physical world offers a window into the mind of God.

Darwin completed a revolution in the sciences that was begun by Galileo. Galileo’s mathematization of physics removed Aristotelean final causes from the inorganic part of the natural world. Darwin’s theory of natural selection removed those final causes from the organic part of the natural world as well. The implications of such a radical shift in world-view are still vague, especially the implications concerning metaphysical commitments.

But the implications of Darwin’s theory on metaphysics are uncannily similar to the pre Darwin metaphysics from which Darwin argued. Today we conclude that it is a greater god who does not intervene, but this is precisely what Leibniz and others vigorously argued. Shouldn’t the metaphysical inputs be considered as well as the metaphysical outputs?

Given all the advances in science, it seems that we cannot answer the traditional philosophical problems concerning consciousness, freedom or even religion but through this new Darwinian naturalist lens.

But the naturalist lens was crafted from philosophical and theological concerns, long before Darwin got in a boat and went anywhere. Religion drives science, and it matters (but don’t tell the philosophers).

Simon Conway Morris: Convergence Solves Complexity

Imagine a future space explorer who travels to a distant galaxy and discovers an inhabited planet with an advanced civilization. In his visit he tours a great art museum. The halls are adorned with many beautiful paintings, but as the traveler walks through the museum an eerie feeling of deja vu overtakes him. The various exhibits he observes show different styles and movements that are uncannily similar to what he is familiar with from his home planet. Even particular paintings are incredibly similar to what he remembers. This would be eerie because this high similarity has occurred for no apparent reason. A million different paintings are possible, the traveler would never expect to see such similarity in independent masterpieces. Well we don’t need to wait for space travel to test for such a strange occurrence—we see it everyday in biology.

The level of convergence in biology has been found to be amazing in recent decades. Strikingly similar designs run all through the biological world. Such similarities do not bode well for evolution because (i) they are supposed to be independently created by chance events, (ii) often they must have arisen in different initial conditions, (iii) often they are found in different environments and (iv) the design space is large. How can we understand these strikingly similar masterpieces?

Well it really isn’t so difficult after all. You see, if our eye evolved once, then why not twice? Evolution is a story of serendipity, so why not add a bit more? Accepting the evolution of life requires a credulous mind. Once evolution is accepted as fact, all kind of events can be accommodated.

Consider how evolutionist Simon Conway Morris explains convergence at the Map of Life website that documents convergences. Incredibly, for Morris, not only is convergence not a problem for evolution, it actually is yet another proof text. The message from biology’s massive convergence is “First, that evolution is true.” And how do these convergences help support such an amazing conclusion? Morris explains that biology’s very complex structures, such as the bacterial flagellar motor, “evolved independently at least twice.”

In other words, if you think complexity argues against evolution, just look—convergence reveals independent versions, which of course must have evolved. Such independent evolution proves such structures can’t be too complex. So rather than a question mark, convergence actually serves to remove a different question mark: complexity.

I guess the complexity of the eye is even more deceptive given how many times it converged:

The Map of Life documents many more examples of convergence for you to explore, and in fact in the case of the camera-eye alone there is much more to be said. The camera-eye has actually evolved at least seven times, most extraordinarily in a group of jellyfish known as the box-jellies (or cubozoans). Although these jellyfish have a nervous system, they don’t have a brain, and furthermore they belong to a phylum known as cnidarians, widely agreed to be amongst the most primitive of animals.

The more people learn about evolution, the more amazed they are. Religion drives science, and it matters.

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.