Anthony Hopkins Schools Charlie Rose on the Religion in Science

As if we needed more evidence that myths abound regarding how science handles religion, Charlie Rose supplied it in abundance in his interview with legendary actor Anthony Hopkins last week. Fortunately Hopkins was able to disabuse the audience of Rose’s misconceptions, though it is not clear Rose was the better for it. Here is the relevant discussion, beginning at the 11:25 mark of the interview:

CR: You see it’s fascinating to me, because I’ve had, in a variety of television series—things that I have done having to do with scientists—and scientists can’t go there, because they can’t prove it—

AH: Can’t go where?

CR: To faith! Because they’re not willing to—most of them, certainly there are exceptions—but I mean people like, you know Nobel Laureates. They can’t go there, because they can’t prove it … Scientists in the end say “I can’t go there,” because they can’t prove it, and their intellectual—their whole being as a scientist—

AH: But there are many physicists who do believe. Dealing in particle physics for example, people are getting close to the essence of power of the—

CR: Well that’s part of what they’re working on in Geneva, is sort of the duplicating creation—

AH: And Einstein said … I don’t believe in a personal god, I believe in the god of Spinoza, where there’s an intelligence and a supreme awe-inspiring design at the back of the cosmos, starting from the Big Bang. Charles Darwin was a staunch member of his own church—he was a protestant. And when he went on the voyage of the Beagle it astonished him, the extraordinary range of life, and the power of life itself. And he never gave up his faith. Galileo was a man of the church—never opposed the church, but he got into a lot of trouble because he said things that upset the apple cart.

Hilarious. In response to Rose’s mythical meanderings, the actor Anthony Hopkins, without a moment of preparation, launches into a perfectly cogent discussion of the relationship between science and religion. In the space of 1 minute and 16 seconds Hopkins effectively deconstructs the media’s mythology. He begins with the diagnosis, cutting to the core with the simple question: “Can’t go where?” From there he begins with today’s scientists, and then progresses through classic historical examples (in order!) of Einstein, Darwin and Galileo—three of the most influential scientists in the history of modern science, each with their own different faith. Yes, his description of Darwin’s faith commitment may have been slightly off, but his overall thesis was spot on. I’m sure the audience learned something, but I doubt the myth makers did.

The Enduring Warfare Thesis Theses

Though historians tell us that the warfare thesis—the idea that the relationship between science and religion has been mostly one of conflict—is discredited, there seems to be a great many who have not yet learned of its demise. Not only is the warfare thesis alive and well in popular culture, it is also promoted by those who probably should know better. In fact in the origins debate each side has its own version. Why is the warfare thesis so enduring? One reason is that, like any good lie, there is some truth to it. Probably a better reason is its rhetorical power. But perhaps the main reason is that we need it—our religion demands it.

The warfare thesis is usually identified with a nineteenth century evolutionary movement that cast evolution skepticism as religiously driven. Men such as Darwin confidant Thomas Huxley, chemistry professor John Draper and Cornell University cofounder Andrew White promoted the warfare thesis as a general trend in the relationship between religion and science.

A popular prooftext is the Galileo Affair. But the seventeenth century debate about geocentrism versus heliocentrism, involving Galileo and the Roman Catholic Church, was hardly obvious. Subtleties in both the science and religion make simple stereotypes difficult to come by. Rather than serving as supporting evidence, the Galileo Affair is one of many problems with the warfare thesis.

Of course there are people who oppose strong scientific findings on religious grounds. Geocentrism still has its proponents. But the relationship between science and religion has generally been far more complex than one of simple obstructionism and conflict.

What the warfare thesis did provide, nonetheless, was powerful evolutionary rhetoric. This is exemplified no better than in Jerome Lawrence’s and Robert Lee’s Inherit the Wind. I once debated an evolutionist professor directly following the staging of this fictionalized account of the 1925 Scopes Monkey trial. It was like arguing against a war after a propaganda film. I made some powerful scientific points but they were met with empty stares while the professor’s metaphysical mandates for evolution received approving nods all around.

It was yet another example of the complexity of the relationship between science and religion. I, though billed as the “science skeptic,” made scientific arguments whereas the professor, though billed as the “science defender,” made religious arguments.

Historians note that religion has provided ideas for science. Did not Darwin learn about scarce resources from the cleric Thomas Malthus? But evolutionary thought does not merely draw on a few religious ideas for inspiration. Evolution rests on a religious foundation and mandate that dates back long before Darwin and remains crucial today.

In evolutionary thought, the relationship between science and religion is better modeled according to the centuries old adage: Theology is queen of the sciences. This view, of course, badly damages evolution’s claim to be a scientific fact and hence the warfare thesis. How better to handle a liability than to assign it to the opposition? Evolutionists need the warfare thesis, their religion demands it.

The other warfare thesis

But evolutionists are not the only ones who have a warfare thesis. Evolution’s skeptics also have one. While evolutionists blame the skeptics for being religious, the skeptics blame evolutionists for not being religious. Consider the seventeenth century Anglican cleric Thomas Burnet who was accused of atheism by Richard Bentley. Burnet was widely read and had lasting influence. He presented a variety of evidences and arguments that god would only use natural laws and processes to create the world. One may agree or disagree with his ideas, but Burnet certainly was no atheist.

A century later the equally religious James Hutton endured the atheist accusation, and after Darwin it became common for skeptics to equate evolution with atheism or naturalism. Most recently Albert Mohler writes:

The debate over Darwinism rages on, with almost every week bringing a new salvo in the great controversy. The reason for this is simple and straightforward – naturalistic evolution is the great intellectual rival to Christianity in the Western world. It is the creation myth of the secular elites and their intellectual weapon of choice in public debate.

In some sense, this has been true ever since Darwin.  …

Darwin’s central defenders today oppose even the idea known as “Intelligent Design.” Their worldview is that of a sterile box filled only with naturalistic precepts.

From the beginning of this conflict, there have been those who have attempted some form of accommodation with Darwinism. In its most common form, this amounts to some version of “theistic evolution” – the idea that the evolutionary process is guided by God in order to accomplish His divine purposes.

But evolutionary thought does not stem from naturalistic precepts. True, evolutionists insist on strict secondary causation in their explanation of origins, but the motivation and justification for this dogma is religious. And just as the evolutionary warfare thesis holds scientific concerns to be inconsequential compared to the supposed religious motivations, so too this warfare thesis holds religious arguments to be inconsequential compared to the supposed atheism or materialism. Such religious arguments are, according to this warfare thesis, nothing but mere accommodationism.

As before, there is much truth to this thesis. Certainly evolution has fueled atheism and materialism. And the growing atheism, in turn, promotes evolution. But evolution also fuels theism. Process theology, for instance, has strong influences from evolution. This is hardly surprising given the religious thought that mandated evolution in the first place. Any atheism to be found is parasitic on the underlying theism. Far from an attempt at accommodation, the theism is the driving force.

Consider, for example, the case of eighteenth century religious skeptic, David Hume. The influential Scottish philosopher promoted evolutionary thought and Darwin was well versed in Hume’s arguments which occasionally even show up in Origins, albeit with the usual Darwinian touch of subtlety.

If ever there was an opportunity to trace the path of atheism’s or naturalism’s influence it would be here. But what we find is exactly the opposite. Hume’s (and Darwin’s) arguments were mostly theological and occasionally philosophical, but never from atheism. Indeed, while Hume was a great rhetoritician and creative in his own right, many of his arguments can be seen in earlier theists.

It is not a large step to move from Malebranche’s and Leibniz’s naturalistic solutions to the problem of evil to Hume’s argument against a divine design of a world so filled with misery. And like any good student of debate, Hume could with equal skill marshal the opposing arguments. Arnauld’s rejection of such theodicies by appeal to the mysteries of the divine can be seen in Hume’s anthropomorphic warning. We must not think we can anywise conceive the perfections of god, so the design inference must be rejected. And Hume’s arguments against miracles came after decades of debate amongst theists.

Hume is by no means an isolated example. Today, for instance, Richard Dawkins argues god would never have designed the blind spot in our retina, and PZ Myers believes god would not have created this universe. And more important than the atheists are the theists who initiated and promoted the many metaphysical arguments that mandate evolution. For centuries they have insisted god would work strictly through secondary causes and be undetectable. This is the foundation of evolutionary thought. It is anything but atheistic.

But while this warfare thesis may not be accurate, it is powerful rhetoric. How better to construct an enemy than to blame it on the secularists or atheists? As with the evolutionist’s warfare thesis, this one is an enduring theme.

And by blaming evolution on the atheists one can avoid the difficult metaphysical and theological issues evolutionists raise. What about Burnet’s and Kant’s greater god argument, and what about Leibniz’s problem of evil? And what about those fossils and design similarities? There is no need to address these evolutionary questions if it can all be dismissed as a secularist agenda. But it isn’t.

In the origins debate each side has its own warfare thesis, and these opposing theses serve many purposes. Unfortunately these theses are misconceptions at best, and self-serving religiously driven fictions at worst.

Insect Eyes Inspire More Efficient Solar Power

Moths not only see well in the night, they also keep a low profile and that technology is now making its way into solar cell design. As one report explains:

The eyes of moths, which allow them to see well at night, are also covered with a water-repellent, antireflective coating that makes their eyes among the least reflective surfaces in nature and helps them hide from predators in the dark. Mimicking the moth eye's microstructure, a team of researchers in Japan has created a new film, suitable for mass-production, for covering solar cells that can cut down on the amount of reflected light and help capture more power from the sun.

It is yet another example of nature’s remarkable designs finding application in engineering work.

The Hierarchy of Evolutionary Apologetics: Protein Evolution Case Study

A common retort from evolution’s defenders is that all those scientists can’t be wrong. Is it conceivable that so many scientific papers and reports, with their conclusions about evolution, are making the same mistake? Before answering this we first must understand the hierarchy of the evolution apologetics literature. At the base of the pyramid are the scientific papers documenting new research findings. Next up are the review papers that organize and summarize the state of the research. And finally there is the popular literature, such as newspaper and magazine articles, and books. Across this hierarchy evolutionists make different types of claims that should not be blindly lumped together. Yes, there are problems across the spectrum, but they tend to be different kinds of problems.

Background: The Hierarchy of Evolutionary Apologetics

Scientific papers document important and perfectly legitimate research. The results are usually presented carefully and rarely are they exaggerated. And it is difficult to find such papers claiming that evolution is a fact.

These papers do, however, discuss the results strictly in terms of evolution. No matter how unlikely evolution is given the results, they are interpreted as though evolution were the only explanation. Problematic results, and they are common, are not allowed to suggest epistemological challenges. They may only pose theoretical problems.

The authors cannot suggest that we may not, after all, know evolution to be a fact. They may only point out our ignorance of how it is supposed to have occurred. In all of this it is difficult to avoid misrepresentations of the research results, but such blunders are limited by the narrow scope of such papers.

Review and survey papers, on the other hand, do make more expansive evolutionary claims. These review papers draw on the vast body of research literature to organize and summarize the state of the research. They draw broader conclusions, and when discussing the subject of evolution these papers are more likely to make obviously unsupportable evolutionary claims.

Finally the popular literature is the next step beyond the review papers. If the review papers are summaries for scientists, the popular literature provides summaries for the non scientific audience. It is here that the dogmatic, sweeping evolutionary claims are most prevalent. Evolution must be a fact, all the scientific evidence unquestionably supports and proves evolution, doubters have nothing but nefarious motivations, there is war between science and religion, and so forth.

In terms of sheer magnitude, the first category—the narrowly focused research papers—dominates the literature. And here there is far less speculation and far more technical detail. Problems do arise in the evolutionary interpretations of the results, but such speculation is a minor part of the paper.

But like toxic pollutants that accumulate and reach increasing concentrations at higher levels of the food chain, the speculation becomes amplified in the review papers, and then even more so in the popular literature. Like a morphing rumor, what begins as tentative and unlikely speculation of how evolution might account for problematic findings ultimately becomes yet another evolutionary proof text in the popular literature.

So when evolutionists argue that those scientific papers and reports cannot all be wrong, we might agree with them. The technical details of the scientific research are certainly not wrong. True, there are misrepresentations of science when the results are force fit into evolution, but the far more egregious misrepresentations of science are found as one moves up the hierarchy of the evolution literature.

Case study: Protein evolution

Imagine a choppy ocean filled with waves for as far as the eye can see. Meanwhile the sky is dotted with an occasional jet airliner flying far above. This scene gives an idea of what science is telling us about protein evolution. A protein consists of hundreds of amino acids glued together in a long sequence. Because nature uses 20 different amino acids, the total number of possible sequences is astronomically huge. For a protein with 300 amino acids in all, for instance, there are 20^300 (roughly equal to a one followed by 390 zeros) different possible sequences.

It is an ocean of possibilities. But the vast majority of these possible amino acid sequences are worthless to evolution. Not only are they essentially dysfunctional themselves, but even as evolutionary starting points they don’t lead to much better designs. If you evolve a typical randomly selected amino acid sequence, you can improve the design a bit, but the search quickly stagnates.

Like the choppy ocean, the protein function landscape seems to be filled with a great many swells. Evolution can move up from the bottom of a swell to the top of a nearby wave, but this is only a minor improvement in the protein function. Go any further and evolution would fall into the neighboring swell, leaving it no better off than when it started.

Very rarely, in this seemingly endless sea of minor ups and downs, an extremely efficient, functional protein punctuates the protein function landscape. Here the landscape rapidly shoots up into the sky. This is not a gradual rise leading to these lofty and tiny regions of functional proteins. Rather, the landscape abruptly rises to heights far above the ocean’s surface. Like the jet airliners flying far above the ocean, proteins appear to be rare events in an otherwise non descript landscape.

Several types of protein studies point to this conclusion. Some of these studies begin with random amino acid sequences and attempt to evolve them toward nature’s proteins or something like them. These studies show that only minor functionality can be evolved from random starting points. Nature’s marvels, or anything like them, are so astronomically rare evolution would never find them using its blind, adaptive walk. (This is to say nothing of how the machinery for such a search could have evolved in the first place.)

Other studies begin not with a random amino acid sequence, but rather work backwards from a known protein. These studies show that proteins are quite sensitive. The function of a typical protein exponentially degrades as random mutations are introduced.

Whether we start at the beginning or the end, the science tells us that the protein function landscape is not one of smooth funnels leading to fantastic molecular machines, as evolution would expect.

And as it seems to be with so much of biology, when scientists work with nature’s designs some fascinating engineering can be done. Just as the design of a jet aircraft can be adjusted and augmented to meet a new performance requirement, so too proteins can be adapted to meet desired properties. And just as engines or other components can sometimes be swapped between aircraft, so too proteins are marvelously modular, allowing for new designs to be created by mixing and matching.

Unfortunately evolutionists routinely conflate such design engineering with evolutionary possibilities. Proteins are adaptable, so can’t they gradually evolve? Proteins are module, so can’t they just swap designs when gradualism fails? The science contradicts such conclusions, but evolutionists are driven more by their theory than by the data. Here are two examples.

An example research paper

In this research paper, evolutionists investigated how proteins might have evolved. They attempted to demonstrate the evolution of a virus—a molecular machine consisting of several proteins—in the laboratory. To simplify the problem they started with all but a small part of the virus intact. They randomized the amino acid sequence of one part of one of the viral proteins, and they repeatedly evolved that randomized segment in hopes of reconstructing the entire virus.

What they discovered was that the evolutionary process could produce only tiny levels of functionality (in this case the virus’ ability to infect a host). Their evolved sequences showed no similarity to the native sequence which is supposed to have evolved. And the best virus they could produce, even with the vast majority of the virus already intact, was several orders of magnitude weaker than nature’s virus.

The reason their evolutionary process failed was that the search for better amino acid sequences, that would improve the virus’ ability to infect the host, became too difficult. A possible evolutionary explanation for these disappointing results is that in such a limited laboratory study, the evolutionists were simply unable to reproduce what the vast resources of nature could produce. Perhaps in the course of time evolution could evolve what the evolutionists could not do in the laboratory.

But the results refuted even this fall back explanation. In fact, the evolutionists would not merely need an expanded study with more time in the laboratory, they would need more time than evolution ever had—many times over. The number of experiments they would need to conduct in order to have any hope of evolving a virus that rivals nature’s version is difficult to compute. But it is at least 10^70 (a one followed by 70 zeros).

And yet, there it is. This relatively short sequence of amino acids exists as part of of the virus, with its fantastically high infection capabilities. And of course this is not merely a problem for a part of one protein, in one virus. It is a problem for all life, for proteins are crucial molecular machines throughout biology.

But not surprisingly the evolutionists interpreted their results according to their theory. The majority of the paper presents the detailed scientific results. There is no misinterpretation or exaggeration, until that is, the discussion of the implications for evolution. The evolutionists write:

Such a huge search is impractical and implies that evolution of the wild-type phage must have involved not only random substitutions but also other mechanisms, such as homologous recombination.

Homologous recombination? It would be difficult to imagine a more unlikely explanation. Homologous recombination is a complex genetic mechanism assisted by finely-tuned proteins. It is circular to recruit such a mechanism for the initial evolution of proteins—for no such mechanism is likely to have existed. And that is putting it mildly.

And even if homologous recombination could somehow have been in play, it wouldn’t help anyway. For while this is a clever mechanism for the swapping of nature’s protein modules, it does not help when used with sequences that are nowhere close to solving the problem. Jumping from one ocean wave to another doesn’t improve the odds in finding the astronomical, one-in-10^70, longshot.

The evolutionists found that it is impossible for evolution’s gradual search to solve the problem, even for the single module they were experimenting with (and all the other modules in the virus already at their native sequences). But if repeated attempts by evolution are going to fail, then the mixing and matching of those errant attempts will not help either. They merely represent another blind attempt. Unfortunately, it is unscientific conclusions such as these that inform the next level up in the apologetics hierarchy.

An example survey paper

This survey paper is entitled “Exploring protein fitness landscapes by directed evolution.” The paper discusses both the engineering problem of creating new proteins and its implications for how proteins evolved in the first place. For the most part this survey paper is a helpful and accurate summary of the relevant scientific findings at the time. The enormous complexity of the problem, and even the challenges for evolution are clearly stated. Here are several examples from the paper:

Notwithstanding significant advances, a molecular-level understanding of why one protein performs a certain task better than another remains elusive. This state of affairs is perhaps not surprising when we remember that a protein often undergoes conformational changes during function and exists as a dynamic ensemble of conformers that are only slightly more stable than their unfolded and nonfunctional states and that might themselves be functionally diverse. Mutations far from active sites can influence protein function. Engineering enzymatic activity is particularly difficult, because very small changes in structure or chemical properties can have very significant effects on catalysis. Thus predicting the amino acid sequence, or changes to an amino acid sequence, that would generate a specific behavior remains a challenge, particularly for applications requiring high performance (such as an industrial enzyme or a therapeutic protein). Unfortunately, where function is concerned, details matter, and we just don't understand the details. …

Although the distance between any two sequences is small (that is, equals the number of mutations required to interconvert them and is therefore ≤ L), this high-dimensional space contains an incomprehensibly large number of possible proteins. For even a small protein of 100 amino acids there are 20^100 (~10^130) possible sequences, or more than the number of atoms in the universe. Searching in this space for billions of years for solutions to survival, nature has explored only an infinitesimal fraction of the possible proteins. …

The vast size of sequence space makes it impossible to characterize (or even model) more than a minute fraction of this fitness surface. Despite this, several important features have emerged from accumulated experimental studies. The first is the low overall density of functional sequences: the vast majority do not code for any functional protein, much less the desired protein. …

Because most mutations are deleterious, the probability that a variant retains its fold and function declines exponentially with the number of random substitutions, and random jumps in sequence space uncover mostly inactive proteins. Thus new functions are extremely difficult to obtain without altering some aspect of the search. One approach is to create a new starting point, a parent protein with at least some minimal function, and improve that by directed evolution. …

An approach to making multiple mutations that is used extensively in nature is recombination. Naturally-occurring homologous proteins can be recombined to create genetic diversity within protein sequence libraries. …

Furthermore, natural evolution works on a different fitness landscape, and it is unclear how the protein fitness assayed during directed evolution is related to the organismal fitness that natural evolution optimizes.

These passages discuss some of the difficulties in using protein engineering as evidence for evolution, and some of the contradictory evidence protein engineering has produced. Unfortunately, none of this is interpreted outside of the evolutionary framework, and in fact the paper goes well beyond, and against, the scientific data in elaborating the evolutionary narrative:

Millions of years of life's struggle for survival in different environments have led proteins to provide diverse, creative and efficient solutions to a wide range of problems, from extracting energy from the environment to repairing and replicating their own code. …

Evolution, however, had no difficulty generating these impressive molecules. …

Evolution is unique because it works at all scales, from molecules to ecosystems — no other engineering design algorithm can make that claim. A simple algorithm of mutation and artificial selection has proved effective for everything from the selective breeding of plants and animals to discovering self-replicating nucleic acid sequences. …

Among the large number of mutational trajectories between a starting point and a solution, smooth uphill paths can often be found. …

Despite the vast size of sequence space and the complex nature of protein function, the Darwinian algorithm of mutation and selection provides a powerful method to generate proteins with altered functions.

This is the apologetics message of the paper that informs the popular literature. Whereas the research paper’s undefendable, non scientific statements were limited, now in the survey paper they frame the narrative from beginning to end. Evolution, one way or another, must have happened, so the evidence must support it. There can be no contradictory evidence.

To make this story sound scientific, the paper equivocates on evolution. It conflates the protein engineering findings that nature’s proteins can adapt with the evolutionary narrative:

Despite their complexity and finely-tuned nature, proteins are remarkably evolvable: they can adapt under the pressure of selection, changing behavior, function and even fold. …

Biological components and systems have shown a remarkable ability to adapt under the pressure of artificial selection, an evolvability that very likely reflects their own history of natural selection. …

Even the earliest directed evolution experiments noted how rapidly proteins could adapt to new selective pressures, indicating the ready availability of smooth uphill paths in the fitness landscapes. …

This simple uphill walk on a fitness landscape in sequence space works because proteins are wonderfully evolvable and can adapt to new conditions or even take on new functions with only a few mutations.

Proteins are remarkably evolvable along smooth uphill paths because, after all, their adaptation under artificial selection reflects their own history of natural selection? Of course the adaptation of native proteins proves no such thing. It is yet another rehearsing of Darwin’s flawed logic that animal husbandry and breeding provide a peek into the mechanisms of change that, by the way, created all of biology. Religion drives science and it matters.

New Genes: Putting the Theory Before the Evidence

Imagine that you have been falsely accused of a crime. The police department has identified you as the prime suspect and they are busy gathering as much evidence against you as possible. They have constructed a theory of your motivations and actions, and as they gather the evidence they interpret it according to their theory. Their process of working from a preconceived notion of your guilt leads the police investigators to explain even ambiguous or contradictory evidence in ways that support their theory. And so it is the theory that is informing the evidence, rather than the evidence informing the theory. As crazy as it sounds, this approach is standard for evolutionists and here are three recent examples dealing with protein evolution.

Example 1: Evolving a virus

In this study evolutionists investigated how proteins might have evolved. They attempted to demonstrate the evolution of a virus—a molecular machine consisting of several proteins—in the laboratory. To simplify the problem they started with all but a small part of the virus intact. They randomized the amino acid sequence of one part of one of the viral proteins, and they repeatedly evolved that randomized segment in hopes of reconstructing the entire virus.

What they discovered was that the evolutionary process could produce only tiny improvements to the virus’ ability to infect a host. Their evolved sequences showed no similarity to the native sequence which is supposed to have evolved. And the best virus they could produce, even with the vast majority of the virus already intact, was several orders of magnitude weaker than nature’s virus.

The reason their evolutionary process failed was that the search for better amino acid sequences, that would improve the virus’ ability to infect the host, became too difficult. A possible evolutionary explanation for these disappointing results is that in such a limited laboratory study, the evolutionists were simply unable to reproduce what the vast resources of nature could produce. Perhaps in the course of time evolution could evolve what the evolutionists could not do in the laboratory.

But the results refuted even this fall back explanation. In fact, the evolutionists would not merely need an expanded study with more time in the laboratory, they would need more time than evolution ever had—many times over. The number of experiments they would need to conduct in order to have any hope of evolving a virus that rivals nature’s version is difficult to compute. But it is at least 10^70 (a one followed by 70 zeros).

And yet, there it is. This relatively short sequence of amino acids exists as part of of the virus, with its fantastically high infection capabilities. And of course this is not merely a problem for a part of one protein, in one virus. It is a problem for all life, for proteins are crucial molecular machines throughout biology.

Did the evolutionists conclude that proteins did not evolve? Did they suggest their findings are a problem for evolution? Did they even do so little as discuss the possibility that this one particular protein they studied may not have evolved?

No. There is not even a hint from the evolutionists there is a problem. In fact, the results are, in typical fashion, interpreted according to evolution. As usual, the evolutionists simply explained that evolution must have, somehow, solved the problem:

Such a huge search is impractical and implies that evolution of the wild-type phage must have involved not only random substitutions but also other mechanisms, such as homologous recombination.

But other mechanisms, such as homologous recombination, do not help. Homologous recombination, or any other mechanism that evolutionists can imagine, does not provide some ingenious end around the problem. Evolution cannot somehow brilliantly find the one in 10^70 long shot. The evolutionists rosy report is not data-driven, but theory-driven.

Example 2: Evolving a simple function

In this study evolutionists attempted to evolve a protein that binds to a simple, common chemical group. This function is so simple even random polypeptides sometimes have slight binding affinities. Using their laboratory process the evolutionists were able to evolve minor improvements to a random polypeptide’s binding affinity. But these small binding levels are hardly detectable. So not only is the function trivial (in order to improve fitness a protein needs to do more than merely bind to a chemical), but the levels observed are likely too small to make a difference anyway.

As with Example 1 the evolved amino acid sequences showed no similarity to nature’s sequences and when the evolutionists tried using a larger number of trials there was no sign of improved results.

Despite these feeble results the evolutionists made remarkable conclusions:

The ease of the functional development within a small sequence variety implies that enzyme evolution is prompted even within a small population of random polypeptides. … These results mark the implementation of Darwinian evolution in the system.

There is no comparison between the evolution of an enzyme and their polypeptides with minor binding affinities. And there certainly was no Darwinian evolution demonstrated in their results, for such evolution requires tangible fitness improvements which can be selected. It was good research work, but the interpretation was according to evolution.

Example 3: New genes

This example deals with new genes. When a gene is found in a large number of species, evolutionists assume it came from the common ancestor of those species, which would date far back into evolutionary history. But when a gene is found in only one or a few species, evolutionists must conclude it arose in the common ancestor of only those few species, and therefore more recently.

But how can a new gene arise so quickly? Genes that code for proteins are difficult to evolve in any case (see here and here), but the problem is accentuated when the time frame is shortened.

How a gene could have evolved is not the only problem with new genes. Such new genes, however they were supposed to have evolved, were expected to be less important. But in this study evolutionists noticed this wasn’t so.

The evolutionists compared what they assume to be new and old genes, and found no statistical difference in the importance of their functions. Knockout a new gene, and you are just as likely to kill the organism as when you knockout an old gene. In fact, the proportion of genes that are essential is similar in every assumed evolutionary age group they examined.

But once again, evolutionists do not hesitate in fitting awkward results into their framework. “These data,” the evolutionists deftly concluded, “suggest that new genes frequently and rapidly evolve essential functions and participate in development.”

In fact, outside of evolutionary theory, there is no reason to think these genes are any newer than other genes. And inside of evolutionary theory there is no scientific explanation of how proteins arise in the first place. Evolutionists are hardly in a position to assert that these data, or any other data for that matter, suggest new genes frequently and rapidly evolve, period. With little more than a bare assertion the evolutionists convert yet another unexpected finding into an evolutionary proclamation.

Evolutionists are bound to the preconceived notion that evolution must be a fact. It drives their thinking in spite of the scientific evidence, and they interpret any and all evidence in this light. It may sound crazy, but it is the theory that informs the evidence, rather than the evidence that informs the theory.

Protein Evolution: A Problem That Defies Description

Charles Darwin’s theory of evolution is scientifically unlikely. The idea that all of biology just happened to arise spontaneously over long time periods (yes, that is what the theory of evolution says) is not motivated by the scientific evidence. This can be seen at all levels of biology including, more prominently in recent years, at the molecular level. A good example of this is the scientific evidence on proteins, and what it says about evolution.

It is not that the scientific evidence reveals proteins to be particularly unlikely on evolution. Proteins are not known to be any less likely to have evolved than, say, DNA repair mechanisms, cellular signal transduction, the electron transport chain, neurons, cardiovascular systems, mice or blue whales. But proteins are a bit more amenable to analysis. As mysterious and difficult as proteins are, molecular biology can at least provide some data on their supposed evolution. In the digital molecular world experiments can show how profoundly evolutionary expectations have failed, and how much more faith required to continue with the theory.

One way to understand how unlikely is protein evolution is in their sensitivity to change. Proteins generally do not tolerate much change to their design. Their designs can vary, but not much. In the vast universe of all possible protein designs, they are not vast oceans but more like the tiny holes in a golf course. This evidence indicates the evolutionary process is unlikely to find them.

Another way to understand protein evolution is to start at the beginning rather than the end. That is, rather than analyzing nature’s proteins, one can start with a non functional, random chain of amino acids to see how easily it can migrate toward functional proteins via evolution’s processes of natural selection or drift. These experiments confirm that the evolution of a protein is scientifically unlikely.

Such experiments reveal what seemed rather obvious from biochemistry: evolutionary schemes are not likely to find the highly complex protein designs we find in nature. The results of such experiments fall short of anything close to the real thing. The resulting sequences of amino acids look nothing like what we find in nature, and the resulting functions are orders of magnitude short of what real proteins do.

In fact, such experiments typically need all kind of advantages to show much progress. For instance, some experiments only attempt to evolve a part of a protein, while the rest of the protein is already at nature’s design at the beginning of the experiment. And some experiments apply artificial selection on low levels of trivial functions which otherwise would not improve fitness at the organismal level.

But even with these advantages the results demonstrate the failure of evolutionary expectations. Unfortunately, evolutionists are less than forthright in their representation of what science is telling us. For example, here is how one journal paper reported its results:

By extrapolation, we estimated that adaptive walking requires a library size of 10^70 [a one followed by 70 zeros] with 35 substitutions to reach comparable fitness. Such a huge search is impractical and implies that evolution of the wild-type phage must have involved not only random substitutions but also other mechanisms, such as homologous recombination.

Here the evolutionists must admit the obvious, that the envisioned protein evolution via gradual changes and natural selection does not work. In fact it is ridiculously unrealistic. But they then deny the gravity of the problem. With nothing but speculation they resolve their astronomical long shot with “other mechanisms” such as homologous recombination.

It is one of the great tragedies of our time that most people lack the scientific training to appreciate the incredible absurdity of evolutionary thought. The suggestion that homologous recombination could resolve this astronomical long shot is the height of absurdity. This is not hyperbole.

What cannot be solved with a library size of 10^70 is not magically going to be resolved with homologous recombination. And this is not to mention that homologous recombination would not have even existed when proteins first evolved. Indeed, an army of specialized proteins is required before homologous recombination is even possible. If homologous recombination was the key to evolving proteins, then aircraft carriers were the key to winning the battle of Trafalgar.

Indeed, it is a difficult task to describe the immense magnitude of this evolutionary folly. Here’s my attempt: It would be like throwing a paper airplane from the top of a skyscraper and explaining that it will make a hole-in-one at a golf course on the other side of town. On second thought, that still does not do the job—the evolutionary folly is far greater than this.

It Didn’t Begin (or End) With Darwin

By far the most amazing aspect of evolution is not its idea that all things just happened to arise spontaneously but—even more eyebrow raising—its claim that all of this is a scientific fact. It would be irrational and perverse to deny it, insist evolutionists. Evolution is, they say, beyond any shadow of a doubt, as certain as gravity, nay even more certain. This claim is so obviously false that it begs the question: what are evolutionists thinking?

Evolutionists say their idea is an obvious scientific fact and they have explained why over and over. In fact, the reasoning was already well established when Charles Darwin wrote Origin a hundred fifty years ago.

For instance, Darwin agreed that the perfection of the eye reminds us of the telescope which resulted from the highest of human intellect. Was it not right to conclude that the eye was also the product of a great intellect? This may seem the obvious answer but Darwin warned against it, for we should not “assume that the Creator works by intellectual powers like those of man.” Better to imagine the eye as the result of natural selection’s perfecting powers rather than having god too much involved in the world.

This warning against anthropomorphizing god came right out of the Enlightenment philosopher David Hume whose writings Darwin was well familiar with. It was a reaction to English natural theology that argued the world looks designed by god. Hume argued this made god out to be too much like His human creatures. For example, the natural theologians were fond of comparing the human body with machines such as clocks. No one doubts that a clock was designed, so why not the body as well? Hume used the problem of evil to negate this argument. Better to view god as distant and unknowable, and a creation that somehow arose on its own. Hume had no problem with god being infinitely powerful and wise, but he must also be transcendent and incomprehensible:

But as all perfection is entirely relative, we ought never to imagine that we comprehend the attributes of this divine being, or to suppose that his perfections have any analogy or likeness to the perfections of a human creature. Wisdom, thought, design, knowledge; these we justly ascribe to him; because these words are honorable among men, and we have no other language or other conceptions by which we can express our adoration of him. But let us beware, lest we think that our ideas anywise correspond to his perfections, or that his attributes have any resemblance to these qualities among men. He is infinitely superior to our limited view and comprehension; and is more the object of worship in the temple, than of disputation in the schools.

Far more lasting and influential than this anthropomorphic warning argument were the various arguments from evil, inefficiency and dysteleology. God would never have created this gritty world. These arguments had been developed and tested in the seventeenth and eighteenth centuries, and by Darwin’s day a foundation had been laid.

The predation and bloodshed in nature was an obvious example of a creation that seemed unbefitting of a loving god. But Darwin added a great many examples of nature’s designs that seemed to be better explained as a consequence of the blind interplay of natural laws than intelligent design.

Darwin presented these arguments throughout his book, with great conviction that they made his theory compelling. The first one appears at the end of the second chapter.

The first two chapters of Origin are on the topic of biological variation. In the first chapter Darwin discusses what breeders had learned (Variation Under Domestication) and in the second chapter he discusses biological variability in the wild (Variation Under Nature). The two chapters serve as a good summary of what was known at the time.

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

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

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

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

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

Or as Stephen Jay Gould put it:

Odd arrangements and funny solutions are the proof of evolution—paths that a sensible God would never tread but that a natural process, constrained by history, follows perforce. No one understood this better than Darwin. Ernst Mayr has shown how Darwin, in defending evolution, consistently turned to organic parts and geographic distributions that make the least sense.

Designs that make the least sense. They are one of the keys to understanding evolutionary thinking. In addition to the other arguments for why evolution is a fact, I examined this argument from dysteleology ten years ago in my book Darwin’s God: Evolution and the Problem of Evil, and others such as Paul Nelson had discussed it earlier. And so I was delighted to see this key evolutionary argument for the fact of evolution elaborated in the prestigious science journal, Proceedings of the National Academy of Sciences, a year ago.

The paper was written by philosopher Elliot Sober who for years had been analyzing evolution’s arguments in great detail. In that paper Sober points out that while one of the main objections to evolution, both when Origin was published and in the minds of many present-day Creationists, is the idea that species are separated from each other by walls. Darwin, Sober explains, overcame this with those designs that make the least sense:

Darwin thought he had strong evidence for common ancestry. This is enough to show that insuperable species boundaries (and insuperable boundaries between “kinds”) are a myth; if different species have a common ancestor, the lineages involved faced no such walls in their evolution. …

Adaptive similarities provide almost no evidence for common ancestry while similarities that are useless or deleterious provide strong evidence for common ancestry.

And why are useless or deleterious similarities so helpful? It is not because they raise the probability of common ancestry, but rather because they lower the probability of separate ancestry. In other words, the reason common descent is a no-brainer is that the alternative, separate ancestry, is extremely unlikely. Sober call this Darwin’s Principle.

I referred to this analysis and Sober’s paper in my previous posting and several evolutionists commented that I had misrepresented Sober. Here are some of their comments:

False. Sober said no such thing in that book. In fact, he said the opposite.

Darwin’s principle refers to the notion that traits that are not selectively advantageous are better evidence for common descent than are traits that are selectively advantageous. He says this in the context of comparing common descent to separate ancestry.

You are quite fond of misunderstanding Sober, aren’t you?

But in fact Sober did say such a thing. In the paper Sober clearly explains that Darwin’s Principle, which demonstrates species are not separated by insuperable boundaries, is based on the ratio of (i) the probability of evidence on common ancestry divided by (ii) the probability of evidence on separate ancestry. The key is that the argument is compelling not because of the former being high, but because of the latter being low. It is not a direct argument for common ancestry, but rather an argument against separate ancestry.

As Mayr and Gould explain above, evolution is a fact because design or creation is false, as demonstrated by so many inefficiencies and bad designs that make the least sense. Over and over, Darwin made arguments against divine creation as his proofs for evolution.

Sober explains this argument in great detail in his book Evidence and Evolution. Here is how he summarizes the paradox that common descent can be found to be a fact though the evidence is unlikely:

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. [Sober, 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.

As Sober explains his PNAS paper, the key is designs that are have low probability on separate ancestry. He gives examples such as gill slits in the human embryo and our tail bone, but Darwin used dozens of examples in addition to the Chapter 2 example above. These are classic examples used by evolutionists to show how compelling is evolution. The probability on common descent may be weak, but it must be true because the probability on design or creation is zero. Here are representative embryology and gill slit quotes from leading evolutionists:

How does God’s plan for humans and sharks require them to have almost identical embryos? [Douglas Futuyma, Science on Trial: The Case for Evolution, p. 48]

The passage through a fishlike stage by the embryos of the higher vertebrates is not explained by creation, but is readily accounted for as an evolutionary relic. [Tim Berra, Evolution and the Myth of Creationism, p. 22]

Now, we’re not absolutely sure why some species retain much of their evolutionary history during development. The “adding new stuff onto old” principle is just a hypothesis—and explanation for the facts of embryology. It’s hard to prove that it was easier for a developmental program to evolve one way rather than another. But the facts of embryology remain, and make sense only in light of evolution. [Jerry Coyne, Why Evolution is True, p. 78-9]

These evolutionary arguments certainly are powerful, but their power comes from their metaphysics. If the evolutionists are correct in their theological and philosophical premises then of course evolution is correct. Its likelihood would be a number divided by zero. And that is infinity. Granted the numerator may be small, but the denominator is zero. So it does not matter how ridiculous evolutionary theory is—it must be a fact.

All arguments for the fact of evolution are metaphysical. From the seventeenth century to today, evolutionists gain their tremendous confidence from their religious convictions. That doesn’t mean they are wrong, but it does place a tremendous burden on their metaphysics.

Sober does not approve of such metaphysics. Do they not make objective analysis impossible? In his book he first levels this criticism at creation and design. As I wrote in my review of his book:

Sober next presents what he takes to be a “devastating objection” to the design argument, first raised by David Hume in the eighteenth century. Sober argues that evolutionists should not make theological claims in proving evolution. Likewise, Sober finds the same defect in the design argument. For when Paley argued that the complexity of the eye implies a designer, was he not assuming knowledge of what God would design? [126, 141-147] Ultimately Sober concludes that creation and ID cannot even follow basic scientific protocol. [356]

And Sober agrees that evolutionists should not use such metaphysics as well. But Sober’s disapproval does not remedy the problem. As Gould and Mayr document, Darwin’s argument rested on the low probability of the alternative. This has not changed since Darwin and today, though evolutionists insist their idea is a scientific fact, it would be better characterized as a religious mandate. Every argument for why evolution is a fact is metaphysical. That doesn’t mean it is false, but it should not be thought of as a scientific fact.

Evolutionists and the Giraffe’s Recurrent Laryngeal Nerve

In a recent university level evolution textbook the author rehearses the usual religious mandates for evolution in a chapter entitled “The Evidence for Evolution.” As Elliot Sober has observed, Darwin’s Principle (as Sober referred to it) is that biological inefficiencies and bad designs are powerful evidence for the fact of evolution because they show how unlikely are the creation or design alternatives. And so it is no surprise that, like Darwin’s book and the evolutionary apologetic literature since Darwin, the textbook is loaded with nature’s bad designs as the proof texts of evolution. Here is what the author writes about a typical example, the giraffe’s recurrent laryngeal nerve:

However, there are some homologies that do look positively disadvantageous. One of the cranial nerves goes from the brain to the larynx via a tube near the heart. In fish this is a direct route. But the same nerve in all species follows the same route, and in the giraffe it results in an absurd detour down and up the neck, so that the giraffe has to grow maybe 3-5 meters more nerve than it would with a direct connection. The “recurrent laryngeal nerve,” as it is called, is surely inefficient. It is easy to explain such an efficiency if giraffes have evolved in small stages from a fish-like ancestor; but why giraffes should have such a nerve if they originated independently … well, we can leave that to others to try to explain. [Mark Ridley, Evolution, Blackwell, p. 50, 1993]

It is yet another example of how evolution’s religion harms science. Let’s have a look.

Having it both ways

Evolutionists say that everything in the universe, indeed even the universe itself, just happened to spontaneously arise. And when dramatic differences are discovered in otherwise similar species, evolutionists do not lose a beat. Though evolutionists maintain that evolution is constrained by law, they are always able to imagine new contingencies to explain such dramatic changes.

Yet here, in the example of the giraffe’s recurrent laryngeal nerve, we are told that evolution was simply not able to remedy this gross inefficiency. Now of course there is no falsifying this account. Certainly, it is possible that the evolutionary account occurred as evolutionists imagine. But evolution’s ability to turn on a dime, switching from a new-designs-rapidly-appear narrative to an evolution-is-constrained narrative, depending on the problem at hand, makes the argument not as compelling as evolutionists insist it is.

Furthermore, in spite of the usual bold evolutionary claims, evolution in fact does not explain how the giraffe’s recurrent laryngeal nerve, or any nerve for that matter, evolved. The textbook informs the student that the inefficiency is “easy to explain” as a product of evolution, but in fact evolutionists provide nothing more than vague speculation. That last thing nerve cells look like is a product of evolution.

Nerve cells: More than just a wire

Nerve cells have a long tail which carries an electronic impulse. The tail can be several feet long and its signal might stimulate a muscle to action, control a gland, or report a sensation to the brain.

Like a cable containing thousands of different telephone wires, nerve cells are often bundled together to form a nerve. Early researchers considered that perhaps the electronic impulse traveled along the nerve cell tail like electricity in a wire. But they soon realized that the signal in nerve cells is too weak to travel very far. The nerve cell would need to boost the signal along the way for it to travel along the tail.

After years of research it was discovered that the signal is boosted by membrane proteins. First, there is a membrane protein that simultaneously pumps potassium ions into the cell and sodium ions out of the cell. This sets up a chemical gradient across the membrane. There is more potassium inside the cell than outside, and there is more sodium outside than inside. Also, there are more negatively charged ions inside the cell so there is a voltage drop (50-100 millivolt) across the membrane.

In addition to the sodium-potassium pump, there are also sodium channels and potassium channels. These membrane proteins allow sodium and potassium, respectively, to pass through the membrane. They are normally closed, but when the electronic impulse travels along the nerve cell tail, it causes the sodium channels to quickly open. Sodium ions outside the cell then come streaming into the cell down the electro-chemical gradient. As a result the voltage drop is reversed and the decaying electronic impulse, which caused the sodium channels to open, is boosted as it continues on its way along the nerve cell tail.

When the voltage goes from negative to positive inside the cell, the sodium channels slowly close and the potassium channels open. Hence the sodium channels are open only momentarily, and now with the potassium channels open, the potassium ions concentrated inside the cell come streaming out down their electro-chemical gradient. As a result the original voltage drop is reestablished.

This process repeats itself until the impulse finally reaches the end of the nerve cell tail. Although we’ve left out many details, it should be obvious that the process depends on the intricate workings of the three membrane proteins. The sodium-potassium pump helps set up the electro-chemical gradient, the electronic impulse is strong enough to activate the sodium channel, and then the sodium and potassium channels open and close with precise timing.

How, for example, are the channels designed to be ion-selective? Sodium is about 40% smaller than potassium so the sodium channel can exclude potassium if it is just big enough for sodium. Random mutations must have struck on an amino acid sequence that would fold up just right to provide the right channel size.

The potassium channel, on the other hand is large enough for both potassium, and sodium, yet it is highly efficient. It somehow excludes sodium almost perfectly (the potassium to sodium ratio is about 10000), yet allows potassium to pass through almost as if there were nothing in the way. The solution seems to be in the particular amino acids that line the channel and their precise orientation. For potassium, moving through the channel is as easy as moving through water, but sodium rattles around—it fits in the channel but it makes less favorable interactions with the amino acids.

Nerve cells are constantly firing off in your body. They control your eyes as you read these words, and they send back the images you see on this page to your brain. They, along with chemical signals, control a multitude of processes in our bodies. And no, they most certainly do not look as though they evolved.

Is the recurrent laryngeal nerve “surely inefficient”?

Evolutionists interpret biology, not surprisingly, according to evolution. They see biology as a series of kludges and flukes that just happened to come together. Naturally, they view the giraffe’s recurrent laryngeal nerve as an evolutionary blind alley. The nerve pointlessly got stretched. But in fact, on its long journey around the giraffe’s heart, the recurrent laryngeal nerve is hard at work. Gray’s Anatomy explains that as it winds around the subclavian artery the nerve sends several filaments to the cardiac plexus. It also sends branches to the mucous membrane, the oesophagus, and trachea. In fact, there is nothing like biology to remedy evolutionary misconceptions. Perhaps the recurrent laryngeal nerve is inefficient, perhaps it isn’t. But let’s try understanding it first before making theory-laden conclusions.

Nonetheless, this is what evolutionists believe. As evolutionist Jerry Coyne explains, the giraffe’s recurrent laryngeal nerve “makes no sense under the idea of special creation ... No form of creationism/intelligent design can explain these imperfections.” As he further explains in his book, Why Evolution is true:

One of nature’s worst designs is shown by the recurrent laryngeal nerve of mammals. Running from the brain to the larynx, this nerve helps us speak and swallow. The curious thing is that it is much longer than it needs to be. ... In giraffes the nerve takes a similar path, but one that runs all the way down that long neck and back up again: a distance fifteen feet longer than the direct route! ... This circuitous path of the recurrent laryngeal nerve is not only poor design, but might even be maladaptive. That extra length makes it more prone to injury. It can, for example, be damaged by a blow to the chest, making it hard to talk or swallow. But the pathway makes sense when we understand how the recurrent laryngeal nerve evolved. ... But the particular bad designs that we see make sense only if they evolved from features of earlier ancestors. If a designer did have discernable motives when creating species, one of them must surely have been to fool biologists by making organisms look as though they evolved. [82-5]

Or again, here is how evolutionist Richard Dawkins puts it:

The recurrent laryngeal nerve is a remarkable piece of unintelligent design. The nerve starts in the head, with the brain, and the end organ is the larynx, the voice box. But instead of going straight there it goes looping past the voice box. In the case of the giraffe, it goes down the full length of the giraffe’s neck, loops down one of the main arteries in the chest and then comes straight back up again to the voice box, having gone within a couple of inches of the voice box on its way down. No intelligent designer would ever have done that.

Some people are not quite sure what to make of this evolutionary metaphysics. In order to understand evolution, one needs to listen to what the evolutionists are saying. You may not agree, but this is what evolutionists believe. What if you believed the things evolutionists insist must be true? It may be difficult, but pretend for a moment that you actually believed as Darwin and the evolutionists do. Then, of course, you would say evolution is a fact. You would have to agree that the details are not well understood, but so what? So what if the theory is bizarre given the science—it must be true, one way or another.

This is rationalism.

When I pointed out this recurrent laryngeal nerve argument in my previous posting, a professor commented that this is not a problem for evolution, but rather a problem for me:

1. Either there is no prediction of what an omnipotent, designer would do,

2. ... or there is a prediction.

In the former case it is then clear that there is no prediction, the assumption of such a Designer makes no predictions about anything, and if so this hypothesis is not science.

In the latter case, there is a prediction and the giraffe’s recurrent laryngeal nerve is evidence against it.

We’ve been over this ground here many times. Cornelius has never explained what, if any predictions the hypothesis of Design makes.

The problem is that opponents of evolutionary biology want to have it both ways. In other cases they try to make predictions that an omnipotent Designer would not make certain kinds of designs. The simplest example is junk DNA. People who argue that there is evidence for Intelligent Design often say that it does make a prediction—that there will not be junk DNA. They never, ever, say where in their theory this prediction comes from, because to do so would be to admit that its origin is in theology. An intelligent, benign Designer would just not do it that way, they are arguing.

Cornelius continues to be caught on this dilemma and continues to try to argue that there is no prediction from Design, but continues to try to maintain that Design is science. He’s stuck. We’ve been over this ground many times here, and he is still stuck. He can get unstuck by disavowing the junk DNA prediction, but then he’s ultimately going to have to admit that his Design hypothesis is not science.

Rationalists place their need to know above limitations of their knowledge. If you point out the limitations they will criticize you for violating science’s intellectual necessity. They will even turn their dilemma onto you, assuming you face the same problem (no, I do not have a “Design hypothesis” as the professor thinks).

But how can we possibly know how the giraffe’s recurrent laryngeal nerve (or DNA that evolutionists label as junk, or a thousand other structures) ought to be designed? We barely understand how it even works. I would be the first to agree, indeed the first to argue, that our ability to judge and predict how an omnipotent designer would and would not make certain kinds of designs is limited. I will be happy when we can simply understand how those designs work.

I will be even happier when evolutionists cease their claims that evolution is a scientific fact based on metaphysical claims. If the professor is sure the design theory fails to qualify as science because it argues nature looks like it was designed, then why does he not also hold that evolution fails to qualify as science because it argues nature looks like it was not designed? Is it OK to argue what a designer would not do, but not OK to argue what a designer would do?

Evolutionists are fond of declaring what is and is not legitimate science, but their arguments are hypocritical. Science must stick to what is testable, they insist, but they then make all manner of untestable, metaphysical claims.

Evolutionists have taken science far afield. They have immersed science in their religious and philosophical concerns. And when you point it out they blame you for causing the problem. Religion drives science and it matters.

Professor: God Would Not Create the Giraffe’s Recurrent Laryngeal Nerve

One thing evolutionists agree on is that evolution is not only a theory, it is also a scientific fact. It is a curious point of consensus given that, of all the many, many evolutionary claims, it is the one that is most obviously and undeniably false. It is not that evolutionists fail to prove evolution to be a fact. They most definitely have done so, many times over. But their proofs are not scientific.

Evolution may or may not be true, but it is not a scientific fact. No one knows for certain whether evolution is true or not, but we certainly do know what is the state of our knowledge. The claim that evolution is a scientific fact is a claim about the state of our knowledge. And while there is uncertainty about evolution, there is no uncertainty about our knowledge.

We all know what the state of our knowledge is and, from a scientific perspective, that knowledge does not indicate evolution to be a scientific fact. Not even close.

We do not know evolution to be an obvious, compelling explanation of the data—beyond any shadow of a doubt. Yet this is precisely what evolutionists claim.

This simply is not the case. In fact, truth be told, there are tremendous scientific problems with the theory of evolution. We can argue about just how badly evolution fares on the evidence, but the evolutionary claim that it is a scientific fact is an obvious misrepresentation of the science.

But of course the evolutionist’s claims do not stem from science in the first place. For centuries evolutionists have presented a metaphysical—not scientific—certainty. You can find this in the seventeenth century literature, you can find it in today’s literature, and you can find it anywhere in between. Here, for example, is what one professor recently wrote to me:

An omnipotent god could do anything (we guess), but one who is omnipotent, serious, and thoughtful (at least as serious and thoughtful as an exemplary human) would not route wiring from giraffe’s larynx around its aorta

Such truth claims are standard amongst evolutionists. They rush in where wise men fear to tread. They do not hesitate to make claims that no one can demonstrate to be true or false. Such claims are metaphysical, and they are unfalsifiable.

How does the professor know that an omnipotent, serious, and thoughtful god would not route wiring from the giraffe’s larynx around its aorta?

What does the professor know about omnipotent, serious, and thoughtful gods? And what does the professor know about creating giraffes? Precious little, I’m afraid, in both cases.

Evolutionary thought is the height of hubris. It would be difficult to imagine a more anti intellectual tradition within the history of thought.

Of course evolutionists do not know that the many ultimate truth claims they make, which motivate and justify their thinking, are true. Obviously for them evolution must be a no-brainer—their theology demands it. Given such metaphysical axioms then, yes, evolution is a fact. But evolution is not a scientific fact, and that is a fact.

Post Synaptic Proteins Intolerant of Change

Proteins are very unlikely machines but post synaptic proteins are even more unlikely.

Background: Neurons and synapses

The human brain is, as one science writer put it, “truly awesome”:

A typical, healthy one houses some 200 billion nerve cells, which are connected to one another via hundreds of trillions of synapses. Each synapse functions like a microprocessor, and tens of thousands of them can connect a single neuron to other nerve cells. In the cerebral cortex alone, there are roughly 125 trillion synapses, which is about how many stars fill 1,500 Milky Way galaxies.

And as one researcher explains:

One synapse, by itself, is more like a microprocessor—with both memory-storage and information-processing elements—than a mere on/off switch. In fact, one synapse may contain on the order of 1,000 molecular-scale switches. A single human brain has more switches than all the computers and routers and Internet connections on Earth.

Neurons are the body’s wiring. They carry electrical signals called action potentials. When an action potential reaches the end of a neuron it is passed on to another neuron or to tissue, via the synapse. First, the action potential causes voltage-controlled calcium channels, located at the end of the neuron, to open. Positive calcium ions on the outside stream into the neuron throught the open channels. The calcium ions influence special proteins just inside the neuron, which in turn cause small bubbles to dock with the cell membrane. The bubbles contain a neurotransmitter chemical which is released to the outside of the cell.

The neurotransmitter chemical floats across the synaptic gap between the cells, and attaches to the other cell, setting off the desired action. It is here where thousands of different proteins work in tight coordination to handle the incoming signals. These proteins form visible blobs called post synaptic densities (PSDs).

New findings: PSD protein designs

New research now emphasizes PSD complexity and the tight tolerances of the PSD protein designs. In fact, a wide range of mutations in these proteins are known to cause a variety of neurological and psychiatric diseases. And the new research finds that these proteins are highly conserved across species, suggesting they are highly sensitive to mutations. Here is how the New York Times described the findings:

The work should help in understanding how the synapse works in laying down memories, as well as the basis of the many diseases that turn out to be caused by defects in the synapse’s delicate machinery.

The research team, led by Seth Grant of the Sanger Institute near Cambridge, England, compiled the first exact inventory of all the protein components of the synaptic information-processing machinery. No fewer than 1,461 proteins are involved in this biological machinery, they report in the current issue of Nature Neuroscience.
…
Each neuron in the human brain makes an average 1,000 or so connections with other neurons. There are 100 billion neurons, so the brain probably contains 100 trillion synapses, its most critical working part.
…
These receptors feed the signals they receive to a delicate complex of protein-based machines that process and store the information.

The complex of proteins involved in this information processing is known to neuroanatomists as the post-synaptic density, because the proteins stick together as a visible blob, but the name does scant justice to its critical function.

The 1,461 genes that specify these synaptic proteins constitute more than 7 percent of the human genome’s 20,000 protein-coding genes, an indication of the synapse’s complexity and importance.

Dr. Grant believes that the proteins are probably linked together to form several biological machines that process the information and change the physical properties of the neuron as a way of laying down a memory.

The tolerances of these machines seem to be very fine because almost any mutation in the underlying genes leads to a misshapen protein and, consequently, to disease. Looking through a standard list of Mendelian diseases, which are those caused by alterations in a single gene, the Sanger team found that mutations in 169 of the synaptic genes led to 269 different human diseases.

So the brain and its circuitry is phenomenally detailed and complex, the different parts are tightly integrated, and they have a low threshold to change. This adds yet more problems to the evolutionary narrative. The PSD proteins are even more sensitive to change than typical proteins (see here and here). Evolutionists must believe that these proteins underwent huge changes in their evolution. Not only is there scant evidence of intermediate designs leading to the known proteins, but the evidence we do have is that these proteins do not tolerate change.

So the evolutionary narrative, as usual, must believe that the biological world underwent radical, unheard of levels of change, though mysteriously today such change is not tolerated. All the while luckily creating an astonishing world of biological wonders.

The Miracle of Ribosome Assembly Evolution

New research is uncovering the details of how the cell’s protein factory—the ribosome—is constructed. The ribosome translates messenger RNA molecules—edited copies of DNA protein-coding genes—into a string of amino acids, according to the genetic code. The ribosome has two major components (one smaller and one larger), each made up of both RNA and protein molecules, and is constructed via a complex sequence of events.

The RNA components of the ribosome are copies of DNA genes. These ribosomal RNA molecules—known as rRNAs—are initially in a raw copy of DNA which eventually is edited. For instance, one of these copies of DNA may contain many rRNAs, separated by spacer segments. The spacer segments need to be removed, leaving the individual rRNAs ready for assembly.

One of the findings of the new research is that in the early stages of assembly, one of the DNA copies folds up such that a spacer segment binds to one of the rRNAs. In particular, the spacer binds to the special segment of the rRNA that reads the messenger RNA molecules, in the final, assembled ribosome. When the spacer is removed, the rRNA switches to its correct shape, for function in the ribosome. One implication of this finding is that ribosome construction can be regulated by this switch. Remove the spacer and ribosome construction proceeds. Leave the spacer, and ribosome construction halts. As the researchers concluded:

our data show that the intrinsic ability of RNA to form stable structural switches is exploited to order and regulate RNA-dependent biological processes.

RNA tends to fold up into a variety of shapes. In this case, as lead researcher Katrin Karbstein suggests, RNA folding properties are part of the design:

Perhaps, nature has found a way to exploit RNA’s Achilles’ heel—its propensity to form alternative structures … Nature might be using this to stall important biological processes and allow for quality control and regulation.

But of course this mechanism brings yet more complexity:

What is interesting is that as the organism becomes more complex, the number of cleavages needed increases. This may make the process more accurate and that may be an evolutionary advantage, but even in bacteria this cutting is not done in a simple way. We still don’t know exactly why that is.

Karbstein suggests that the strictly ordered cutting and pasting steps in ribosome assembly are introduced to produce singularly perfect intermediates. As she explains:

Ribosomes make mistakes rarely, on the order of one in 10,000 amino acid changes. A lot of this accuracy depends on conversations between different parts of the ribosomes, so if the structure of the RNA isn’t correct, these conversations can’t happen. And that means more mistakes, and that’s not good because it can lead to any number of disease states.

Ribosomes don’t just happen. They are not easily assembled and the evolution of this choreography calls for several just-so heroics. Yes, this fine-tuned set of mechanisms makes for fantastic regulation of the cellular protein making factory, but it means that evolution must have gone through a stage where life didn’t work. For the spacer segment that binds to the rRNA is a show-stopper. It would be selected against instantly.

The only way to resolve this problem is to have the spacer removal mechanism already in place, before the spacer sequence itself evolved. As usual, evolutionists would need to rely on the needed mechanism just happening to serve some other useful purpose, and when the spacer sequence happened to arise for no reason, the removal mechanism found new work for itself. In other words, mutations arose that caused the DNA copy to fold, rendering ribosome synthesis—and life itself—impossible. But as luck would have it, there just happened to be the right molecular machine lying around that removed the problematic segment at just the right time and place. Not only was the fatal flaw obviated, but a brilliant new means of regulation invented. Amazing. Over time, further mutations happened to refine its actions and today we have the fine-tuned ribosome assembly process.

There you have it—evolution’s just-add-water version of science. For the umpteenth time evolution becomes a charade. Behind the scenes, in deep-time where no one can see it working, evolution once again performs miracle after miracle.

Entropy and the Distinction Between Operation and Origin

In the seventeenth century Isaac Newton figured out how the solar system worked. The same gravitational force that makes apples drop to the ground also steers the planets in their orbits about the sun. But the English physicist warned against over estimating the power of his new laws. Though the planets “persevere in their orbits by the mere laws of gravity,” Newton concluded, “yet they could by no means have at first derived the regular position of the orbits themselves from those laws.” Gravity alone can maintain an orbit about the sun, but not establish such an orbit. In the centuries since Newton evolutionists have constructed a solar system origin narrative replete with contingent events and all manner of natural law heroics.

There is much more to the history of solar system theorizing and its underlying metaphysics. For our current purposes, what is important about Newton’s warning is his distinction between nature’s operation and its origin. He could explain the former with his laws of gravity, but not the latter.

In the three hundred years since Newton, science has grappled with many more fantastic operations of nature. One that has commanded much attention in recent years is the protein folding problem. About fifty years ago it became apparent that proteins, consisting of hundreds of amino acids chained together, are champions of entropy. They routinely defeat nature’s tendency toward disorder as they find their correct three dimensional shape in a universe of failures.

In 1969 Cyrus Levinthal noted that since proteins fold in a fraction of a second, they cannot explore any significant portion of the universe of possible shapes. Somehow the protein knows how to go from the unfolded to correct folded state—two very different structures—in a short time. Levinthal concluded that the folding of proteins must be directed rather than random. But the speed and accuracy of the process seemed like a paradox.

Like Newton’s solar system problem, the operation of protein folding is a great story of science’s discovering nature’s complexity and fantastic operation. And as with the solar system, there is a distinction between the operation and the origin of proteins.

The operation of the protein is due to its amino acid sequence and its surrounding environment. The origin of the protein deals with how that rare amino acid sequence arose in the first place.

But recently physicist Ard Louis has said that the operations of proteins should give us confidence in their evolution. “If I look at something like the bacterial flagellum motor,” notes Louis, “one question is how has it evolved, another question is how does it self-assemble.”

True enough, but since we now better understand the self-assembly of these proteins, Louis has greater confidence they arose via strictly naturalistic causes (that is, that they evolved):

And so the fact that it took us quite awhile to understand these principles, makes me think that we could do the same over evolutionary time, over a much longer period of time. There’s no reason why, if we think about this long enough, we may not find the answer.

No reason? Why does Louis conclude there is no reason we may not find an evolutionary explanation for proteins and the machines they form? I can think of a reason straight off: What if proteins did not arise from strictly naturalistic causes? That could make it pretty difficult to find evolutionary solutions.

Louis concludes there is no reason we may not find a strictly naturalistic explanation for the origin of proteins because we find strictly naturalistic explanations for the operation of proteins.

But this makes no sense. Just because science succeeds on some problems doesn’t mean it will succeed on other problems. But it’s worse than this. For the particular success we are talking about—explanations for the operation of proteins—does not in the slightest suggest a solution for the origin of proteins.

In fact, what we are learning about the operation of proteins is that it so strongly hinges on the design of the protein. The incredible protein folding and other operations are pre programmed in the protein’s amino acid sequence. Understanding these principles does not suggest the protein evolved; rather, it suggests even more so how unlikely such an evolution would be.

What we have learned about the operation of the protein does not make evolution any more likely or probable. It does not point to a strictly naturalistic narrative because, after all such an approach worked for the operation of the protein. In fact, it was the very design of the protein that proved so crucial in understanding its operation.

A child does not understand how an automobile operates. When he eventually learns the automobile works according to natural law, that does not give him confidence that the origin of the automobile was also according to natural law. And yet this is Louis’ logic.

When I pointed this out here and here, evolutionists wrote to me defending Louis. One explained that Louis was merely pointing out that we ought not to think complex designs are impossible without intervention. The bacterial flagellum is complex, yet it self-assembles.

But such self-assembly is possible only because the constituent proteins have rare amino acid sequences. From where did those amino acid sequences come? The problem of operation of the flagellum points back to the problem of its origin.

This evolutionary argument that naturalistic operation implies naturalistic origin tramples on Newton’s distinction between the two. None of this is to say that the naturalistic origin of proteins is impossible. Perhaps evolution can create all of biology, but that is not what the science is telling us. And fallacious philosophical arguments don’t change that fact.