His Own Judge

After preaching ad nauseam (which you can read about here, here, here and here) on proper religion Jerry Coyne now feigns innocence and asks the question "what on earth is 'proper' religion?" in response to the preaching of his fellow priest, Francisco Ayala. Coyne convicts Ayala of his own crime. What is proper religion? Read your own book.

A Compass That is Never Right

What good is a compass that is never right? Evolution certainly is not that bad, but it is telling how often Darwin’s idea, mandated to be a fact, is so far off base. Consider for example the kangaroo genome, which turned out to be similar to the human genome. As one evolutionist explained:

There are a few differences, we have a few more of this, a few less of that, but they are the same genes and a lot of them are in the same order. Which really surprised us, we thought they’d be completely scrambled, but they’re not, there’s great chunks of the human genome which is sitting right there in the kangaroo genome.

It was a surprise because under evolution humans and kangaroos must be quite distant relatives. Evolutionists believe a small mouse-like species split into two lineages—the marsupials and the placentals—about 150 million years ago. And according to evolutionists that mouse-like species eventually turned into, among other things, a kangaroo in the one lineage and into a human in the other.

With that much evolutionary distance the kangaroo and human genomes should have evolved substantial differences. Sometimes evolution gets it right but often the theory, which evolutionists claim is mandatory for making sense of all of biology, just looks foolish.

See No Evil, Hear No Evil, Speak No Evil

Just as Charles Darwin dealt with difficulties with his theory of evolution in Chapter 6 of Origins, so too Denis Alexander deals with objections in Chapter 6 of his book Creation or Evolution. And just as Darwin’s logic was often questionable, so too is Alexander’s. The chief problem is Alexander’s rather selective presentation. For an author of a book about the origins controversy, Alexander seems to be remarkably unaware of the actual debate.

Alexander begins with the objection that evolution is a protected theory, and so not subject to objective criticism. Not at all, explains Alexander:

It is every biologist’s dream to make discoveries that would upset some cherished theory. If you do that then your career is made for life. If you found rabbit fossils in the pre-Cambrian era, or indubitable evidence for human dna dinosaur fossils in the same sedimentary layer, or evidence for new forms of life from the bottom of some deep ocean that displayed a different genetic code, or solid evidence for the inheritance of acquired characteristics, then your first author paper in Nature or Science is assured and you can live happily ever after.

Alexander goes on to exhort skeptics to become “a member of the scientific research community” and publish “results in peer-reviewed journals.”

This is a two-dimensional view of science. It reminds me of that seventh grade unit on how science works, which portrayed scientists as objective truth-seekers, toiling away in their white lab coats.

To be sure, scientists do toil away, and some even wear white lab coats. But this is only part of the story. Alexander seems ignorant of the realities of science that occur between the snapshots. Yes, some scientists do want to upset cherished theories, but many have no such dream. In fact science can be quite a conservative discipline. There is substantial risk in going against the accepted wisdom. More typically scientists seek new and better explanations, but within unspoken boundaries. Stray off of the playing field and you place your reputation (and funding) at risk.

One can find no better illustration of this than in one of Alexander’s own examples: the inheritance of acquired characteristics. “Solid evidence” for this phenomenon has been known for years, but evolutionists made it the third rail of the life sciences. The few scientists who dared touch it paid the price.

Alexander’s portrayal of science as easily accepting new findings—all that is needed is the evidence and a scientist to explain it—is again simplistic. The theory of evolution for example, developed by Darwin and Alfred Wallace, was not a revolutionary new idea that arose from the evidence, as evolutionists are fond of thinking. It built upon centuries of theological and philosophical thought that was increasingly influencing science. This Enlightenment influence was by no means dominant in Darwin’s day, but it was rapidly gaining among the elites in politics, culture and science. It is hardly a surprise that Darwin and Wallace concluded for transformationism even without knowing how such change could occur.

Alexander also seems to be ignorant of the many mechanisms in the culture of science that enforce conformity. He exhorts skeptics to become “a member of the scientific research community” and publish “results in peer-reviewed journals.” But there are myriad barriers that ensure skeptics are filtered out at every stage. Everything from passing grades and letters of recommendation to tenure and funding are strongly contingent on conformity. Dissenters are blacklisted so they never have a chance to raise objections.

None of this is to say science is not successful or that scientists should not receive credit for their contributions. Scientists work hard and usually do a good job. But they do not transcend politics or culture and, in fact, they have real bodies.

A New Model for Evolution: A Rhizome

Evolutionists have a problem. Their theory doesn’t fit the facts, yet it must be true. They have to constantly change their story, all the while insisting it is a fact. Like a Heraclitean flux, it is constantly changing and yet always called the same thing. Evolutionists are continually surprised by the science, yet they euphemistically call this “progress.” A recent article in The Lancet, suggesting that evolution is like a rhizome, is a good example of evolution’s folly that is so obvious.

In 2009, with the 200th anniversary of Darwin's birthday, the concept of Darwinism became so popular that it was celebrated in most biological journals. However, the Darwinist theory of evolution is associated with the scientific knowledge and outdated beliefs of the 19th century. The theory is characterised by a description of life as a tree in which all living organisms are thought to have a single ancestor and where each node represents a common ancestor (Darwin's tree) … The structure of our current knowledge base has changed substantially. …

Darwin was certain god would not have created the nested hierarchy pattern the species were thought to form. Today we know that pattern is a crude and inaccurate model.

In the 21st century, the genomic revolution has brought about an important change in the way we think about life, which has forced us to reconsider the way we describe evolution. Genomic data have gradually accumulated and show that there were multiple original sources of the genetic information of living organisms, with inheritance occurring not only vertically but also laterally. Such lateral gene transfer, initially observed only in bacteria, was quickly identified in all living organisms. For example, the human genome is a mosaic of genes with eukaryotic, bacterial (in the mitochondria and the nucleus), and viral origins. …

Multiple origins, vertical, lateral, gradual, punctuated, backwards, forwards. Got it.

Thus we cannot currently identify a single common ancestor for the gene repertoire of any organism. Comparative genome analysis shows not only a substantial level of plasticity in the gene repertoire, but also provides evidence that nearly all genes, including ribosomal genes, have been exchanged or recombined at some point in time. Overall, it is now thought that there are no two genes that have a similar history along the phylogenic tree.

So why do we need the nineteenth century dogma again?

Moreover, there are some genes that do not have a single history, due to the occurrence of intragenic recombinations. Therefore the representation of the evolutionary pathway as a tree leading to a single common ancestor on the basis of the analysis of one or more genes provides an incorrect representation of the stability and hierarchy of evolution. Finally, genome analyses have revealed that a very high proportion of genes are likely to be newly created through gene fusion, degradation, or other events, and that some genes are only found in one organism (named ORFans). These genes do not belong to any phylogenic tree and represent new genetic creations.

When the evolutionist states that the genes that appear out of nowhere are “likely to be newly created through gene fusion, degradation, or other events,” he means as opposed to having evolved by the conventional common descent narrative, or via horizontal gene transfer. Those avenues are ruled out, so the evolutionist must resort to unlikely schemes. He then labels them as “likely” not because science and mathematics reveals this to be so, but because evolution must be true.

A post-Darwinist concept of the living species can be proposed, to integrate the theories of multiplicity and de-novo creation … I believe that the evolution of species looks much more like a rhizome (or a mycelium). Consequently, this view of evolution resembles a clump of roots that considers the occurrence of multiplicities. Emerging species grow from the rhizome with gene repertoires of various origins that will allow, under favourable environmental conditions, the multiplication and perpetuation of this species. As such, potential new species and new genes are continuously appearing.

A good example of how evolutionary thought makes a mockery of science.

I suggest we respect the revolutionary mind of Darwin and allow the theory of evolution itself to evolve from a tree to a rhizome.

There’s not much to respect. Darwin was not an intellectual revolutionary. The theological and philosophical heavy lifting was done long before Darwin got in a boat and went anywhere. Darwin had good command of the science, but turned it upside down to fit the metaphysics of the day.

DNA Rules of the Road and Incredulity

Every biology student learns of two massive machines that operate on the DNA molecule. There is the transcription machine that makes a single-stranded copy of a gene, and there is the replication machine that makes a double-stranded copy of the DNA double helix. The former is the first step in the protein synthesis process while the latter is part of the cell division process. But what happens when these different machines meet as they operate on the same stretch of DNA? What are the rules of the DNA road?

New research suggests that the highly intricate replication process is not destabilized by head-on collisions wth the transcription machine, but merely pauses while it displaces the intruder. To do this it uses a protein that otherwise helps with transcription repair. As the paper explains:

These findings demonstrate the intrinsic stability of the replication apparatus and a previously unknown role for the transcription-coupled repair pathway in promoting replication past a RNAP [replisome and RNA polymerase] block.

It is research that is both important and interesting. And, as with any new finding, it may be relevant to the question of evolution. For instance, perhaps the theory of evolution had led us to predict this finding. Or, almost as good, perhaps the finding is reasonably inferred from the theory.

In this case a such a retrodiction would go something like this: If evolution is true then we would expect the replication machine to oust the transcription machine because random mutations could lead to such a design, but not to other conceivable designs.

But what if, on the other hand, evolution did not favor such a design? What if there was no such prediction, or retrodiction? Then it would be more difficult to enlist the design as support for evolution. In fact, what if evolution has no plausible explanation for the design?

In this case, perhaps the replication and transcription machines successfully negotiating their way in the crowded environment, resolving head-on collisions, and having an established “rules-of-the-road” is not likely given evolution’s random biological variation under the winnowing hand of natural selection. Here we would have a finding which does not fit evolutionary explanation, and the evidence shifts over from the plus column to the minus column.

What is interesting is how evolutionists routinely react to such findings. When presented with such designs, evolutionists almost invariably erect a series of fallacious roadblocks. You can see these same roadblocks used repeatedly, and they speak volumes about evolutionary thought.

One such fallacious roadblock is that placing such evidence in the minus column amounts to an argument from incredulity. “You can’t imagine how evolution could possibly have created such a design,” say evolutionists, “and so you think it is evidence against evolution.” It is a strange argument that places the burden on the one evaluating a theory also to defend the theory.

In fact anyone can “imagine” how evolution might have constructed the design, but what is needed is a plausible explanation. Evolutionists want us simply to accept an empty narrative. The problem is not incredulity on the part of the evaluator but credulity on the part of the evolutionist. “Don’t worry, it evolved” is not a plausible explanation.

This fallacious complaint of evolutionists also is another sign of the protectionism that runs through evolutionary thought. If findings that a theory does not explain are not allowed in the minus column, then what could possibly harm the theory? It is the ultimate form of unfalsifiability. Evidences that the theory explains make it a fact and DNA rules-of-the-road don’t count because that would be an argument from incredulity.

Forget About the Book, Just Read the Title

The title of Steven Shapin's new book is cogent:

Never Pure: Historical Studies of Science as if It Was Produced by People with Bodies, Situated in Time, Space, Culture, and Society, and Struggling for Credibility and Authority

Horizontal Gene Transfer and the Evolution of Evolution: You Can’t Make This Up

What do bacterial resistance to antibiotic drugs and the universal genetic code have in common? They both have been explained by horizontal gene transfer, a mechanism that evolutionists are increasingly using to explain the origin of the species. And what’s wrong with that? First, it makes evolution superfluous and second, it makes evolution ridiculous.

In the last century widespread use of antibiotics led to widespread resistance to antibiotics. Sometimes the resistance was rapid and so indicated a transfer of resistance between bacteria rather than independent adaptations. We now understand that bacteria, as well as higher organisms, can trade genetic material via several different mechanisms collectively referred to as horizontal gene transfer. As one science writer put it:

This seems to be a crude analogue of social learning, in which one species can learn the good tricks already discovered by another … the apparent ubiquity of horizontal gene transfer implies that microorganisms have an impressive capacity to actively alter their genomes in response to environmental stresses or opportunities.

This provides evolutionists with a convenient explanatory device for the many instances where the genetic sequence data do not cooperate with evolutionary expectations. Various studies have found that bacterial sequences often do not form the predicted evolutionary tree, and in such cases horizontal gene transfer is the typical explanation.

But while such explanations make sense, they also make evolution vulnerable to Occam’s razor. For when evolutionary predictions fail, as they often do, we find scientific explanations that are independent of evolution. Organisms intelligently adapt to environmental challenges and genes show up in the wrong place. We now understand that epigenetic and horizontal gene transfer mechanisms, respectively, often account for such phenomena. And while evolution requires such mechanisms to save it from its failures, those mechanisms do not need evolution. As we increasingly explain life with empirically observed, non evolutionary, mechanisms, why do we drag along with them the unwieldy nineteenth century Victorian doctrine?

The least of its problems

But horizontal gene transfer’s making evolution superfluous is the least of its problems. For in order for the evolutionary story to make sense, we must believe that evolution created horizontal gene transfer. This mechanism, increasingly understood to be a crucial player in adaptation, is not simple. Unlike the bumper sticker’s reminder, horizontal gene transfer is not something that just happens. It is a consequence of various complex mechanisms for which evolution has no explanation beyond the usual speculation.

So we must believe that evolution, sans horizontal gene transfer, somehow happened upon such a facility which then allowed for more evolution. Apparently we are living in the right multiverse.

This incredible level of serendipity has evolutionary theory looking increasingly ridiculous. Recently this reached a fever pitch when horizontal gene transfer was employed to explain the universal genetic code. The code is essentially the same across all species and yet it is profoundly robust and efficient. Compared to randomly selected codes the actual code is a standout. Now, to account for the codes “universality and optimality,” recent evolutionary speculation calls for a massive level of horizontal gene transfer which was “likely to be present in early communal life” and led to “innovation-sharing protocols.”

And how do we know such a world was “likely”? Because it is needed to evolve the genetic code. The evolutionists explain that traditional evolutionary theory doesn’t account for how the code could have arisen. Amazingly, following Francis Crick, evolutionists have often ascribed such marvels as the genetic code to accidents of history. But if that is excessive serendipity, so is the new idea.

The researchers set up a virtual world to rerun history multiple times and test out different ideas. As one report explained:

Starting with a random initial population of codes being used by different organisms - all using the same DNA bases but with different associations of codons and amino acids - they first explored how the code might evolve in ordinary Darwinian evolution. While the ability of the code to withstand errors improves with time, they found that the results were inconsistent with the pattern we actually see in two ways. First, the code never became shared among all organisms - a number of distinct codes remained in use no matter how long the team ran their simulations. Second, in none of their runs did any of the codes evolve to reach the optimal structure of the actual code. “With vertical, Darwinian evolution,” says Goldenfeld, “we found that the code evolution gets stuck and does not find the true optimum.”

The results were very different when they allowed horizontal gene transfer between different organisms. Now, with advantageous genetic innovations able to flow horizontally across the entire system the code readily discovered the overall optimal structure and came to be universal among all organisms. "In some sense," says Woese, "the genetic code is a fossil or perhaps an echo of the origin of life, just as the cosmic microwave background is a sort of echo of the big bang. And its form points to a process very different from today's Darwinian evolution." For the researchers the conclusion is inescapable: the genetic code must have arisen in an earlier evolutionary phase dominated by horizontal gene transfer.

In other words, a population of organisms that just happened to arise, also just happened to develop advanced genetic codes--a large number of codes. And they then just happened to trades parts of their codes with each other, taking the good and leaving off the bad. This all just happened to happen. And fortunately incredible horizontal transfer mechanisms just happened to arise, to facilitate all this.

Evolutionists are now making the Greek myth makers appear downright sober. In an all-time understatement they do admit that pinning down the details of that early process remains a difficult task. This work augments the already rampant evolutionary serendipity with absurdity. Evolutionary theory is not merely superfluous, it is ridiculous.

The Human Epigenome Project: Darwinian-Free Science

About twenty five years ago Lars Olov Bygren discovered that feast and famine years can affect not only those who endure them, but their progeny as well. Bygren was not the first to observe that environmental influences can be transmitted to subsequent generations. And as with the earlier discoveries, even in recent decades such empirical findings have not been welcomed by evolutionists. Why? Because such findings go against evolutionary theory. As a recent Time magazine article explained:

Could parents’ experiences early in their lives somehow change the traits they passed to their offspring?

It was a heretical idea. After all, we have had a long-standing deal with biology: whatever choices we make during our lives might ruin our short-term memory or make us fat or hasten death, but they won’t change our genes — our actual DNA. Which meant that when we had kids of our own, the genetic slate would be wiped clean.

What’s more, any such effects of nurture (environment) on a species’ nature (genes) were not supposed to happen so quickly. Charles Darwin, whose On the Origin of Species celebrated its 150th anniversary in November, taught us that evolutionary changes take place over many generations and through millions of years of natural selection. But Bygren and other scientists have now amassed historical evidence suggesting that powerful environmental conditions (near death from starvation, for instance) can somehow leave an imprint on the genetic material in eggs and sperm. These genetic imprints can short-circuit evolution and pass along new traits in a single generation.

Such imprinting is the subject of epigenetics—the study of changes in gene activity that do not involve changes to the DNA yet in some cases may be passed down to successive generations. And although various epigenetic phenomena have been observed for over a century, and even the molecular details have been outlined for several decades, basic and applied research in the field has been slow to progress. Only in recent years have epigenetic-based therapeutics begun to appear. As the article explains:

Geneticists are quietly acknowledging that we may have too easily dismissed an early naturalist who anticipated modern epigenetics—and whom Darwinists have long disparaged. Jean-Baptiste Lamarck (1744-1829) argued that evolution could occur within a generation or two. He posited that animals acquired certain traits during their lifetimes because of their environment and choices. The most famous Lamarckian example: giraffes acquired their long necks because their recent ancestors had stretched to reach high, nutrient-rich leaves.

In contrast, Darwin argued that evolution works not through the fire of effort but through cold, impartial selection. By Darwinist thinking, giraffes got their long necks over millennia because genes for long necks had, very slowly, gained advantage. Darwin, who was 84 years younger than Lamarck, was the better scientist, and he won the day. Lamarckian evolution came to be seen as a scientific blunder. Yet epigenetics is now forcing scientists to re-evaluate Lamarck’s ideas.

Though in decades past evolutionists ridiculed scientists who dared suggest this heresy, at this point the evidence is undeniable. Through a great variety of complex mechanisms, organisms not only respond intelligently to the environment, they can pass response information on to their progeny. Evolutionists long since resisted such findings, for aside from their immense complexity, such mechanisms mean that evolution somehow created response mechanisms with future environments in mind. Not exactly the stuff of unguided mutations. It is yet another falsification of a fundamental expectation of evolutionary theory.

Now, in spite of evolution, science is pursuing the epigenome—the map of how the genome is marked, modified and influenced in response to the environment. As the article explains:

Remember the Human Genome Project? Completed in March 2000, the project found that the human genome contains something like 25,000 genes; it took $3 billion to map them all. The human epigenome contains an as yet unknowable number of patterns of epigenetic marks, a number so big that Ecker won't even speculate on it. The number is certainly in the millions. A full epigenome map will require major advances in computing power. When completed, the Human Epigenome Project (already under way in Europe) will make the Human Genome Project look like homework that 15th century kids did with an abacus.

But the potential is staggering. For decades, we have stumbled around massive Darwinian roadblocks. DNA, we thought, was an ironclad code that we and our children and their children had to live by. Now we can imagine a world in which we can tinker with DNA, bend it to our will. It will take geneticists and ethicists many years to work out all the implications, but be assured: the age of epigenetics has arrived.

Epigenetics has become, as past Director of the National Institutes of Health Elias Zerhouni recently remarked, “a central issue in biology.” It seems that the long-standing claim of evolutionists, that “nothing makes sense in biology except in the light of evolution,” needs to be revised.

Hibernation: Evolution Confirmed Again

As all school children know, many warm-blooded animals slip into an sleep-like state to pass part of the winter season. There is little food and the temperatures are cold, so a long nap seems like a great idea. Amazingly many of the animal’s processes shut down, including the immune system. Could this make the animal vulnerable to infection during its hibernation? And could this be the reason why animals sometimes wake up for brief periods?

Recent research suggests that hibernating animals have solved the tradeoff between activating the immune system to ward off infection and conserving energy to survive the winter. As one of the researchers explained:

Our model, which is confirmed by field data, shows that torpor patterns generally seen in some hibernating animals may be an evolutionary adaptation to help protect them from bacteria that grow well in low temperatures.

So, long ago some mutations happened to create a hibernation behavior, and it worked. That is no big deal when you consider that mutations created the animal in the first place. Then some later mutations fine-tuned the behavior. This included the waking up to solve the tradeoff between fighting infections and surviving the winter. Again, not a big deal as mutations are constantly trying out new designs anyway. Once again the evidence confirms evolution.

Biological Innovations and the Fact of Evolution

Evolutionists insist that evolution is a fact even though there is much debate about how it occurred. But if they debate the question of how evolution occurred, that means it is an open question. And does this not, in turn, mean that whether evolution occurred is also an open question? No, evolutionists assure us, there is no question that evolution occurred—it is a fact—because we observe it occurring. But therein lies the rub:

It is not clear that the mechanisms we observe are capable of causing the origin of species. What we observe are mechanisms that help species to adapt. Whether or not these mechanisms are capable of the larger-scale change evolution requires is in question.

In fact, the scientific evidence suggests that they don’t. So the fact that we observe adaptations is not proof that evolution is a fact. Such a claim amounts to an equivocation on evolution. It could be that the mechanisms we observe are up to the task, but we don’t know that they are.

The question of how evolution occurred is very much relevant to whether evolution occurred. And after centuries of research, we certainly do not know how evolution could have occurred. Here is how one research paper described the problem:

As encompassed by the ‘Synthetic Theory’ (or ‘Modern Synthesis’) of evolutionary biology, the 20th century has provided a thorough understanding of the mechanisms of microevolution (Dobzhansky, 1937; Mayr, 1942; Simpson, 1944; Mayr and Provine, 1980). It is relatively well known how organisms adapt to their environment and, arguably, even how new species originate. However, whether this knowledge suffices to explain macroevolution, narrowly defined here to describe evolutionary processes that bring about fundamental novelties or changes in body plans (Theissen, 2006), has remained highly controversial.

How fundamental innovations (or novelties) originate in evolution remains one of the most enigmatic questions of biology. According to the proponents of the Synthetic Theory, the gradual process of evolution by natural selection that operates within populations and species also creates the unique traits recognizable at higher taxonomic levels, meaning that macroevolution is just microevolution extended over relatively long periods of time.

However, it has been repeatedly pointed out that innovation is different from adaptation, and that the Synthetic Theory, which is largely based on population genetics, falls short of explaining innovations, novelties, and the evolution of body plans (Riedl, 1977; Gilbert et al., 1996; Bateman et al., 1998; Erwin, 2000; Wagner, 2000; Haag and True, 2001; Wagner and Müller, 2002; Wagner and Laubichler, 2004; Müller and Newman, 2005; Theissen, 2006). These are not the only shortcomings of the Synthetic Theory. It considers evolution as the result of changes in allele frequency due to natural selection that engender subtle modifications of phenotype. According to the Synthetic Theory evolution always occurs gradually, in a countless number of almost infinitesimally small steps. Given sufficient time, these gradual changes accumulate and result in the larger differences that typically separate higher taxa. The fossil record, however, with its often abrupt transitions, provides limited evidence for the gradual evolution of new forms (Gould and Eldredge, 1993). In addition, the branching patterns of higher taxa in both animals and plants, as revealed by cladistics, do not support the view that the major features of body plans and their constituent parts arose in a gradual way (Vergara-Silva, 2003).

How fundamental innovations (or novelties) originate in evolution remains one of the most enigmatic questions of biology. But that is the heart of evolution. When evolutionists say evolution is an undeniable fact, they very much are including innovations and novelties. And in doing so, they damage the reputation of science.

Whether or not evolution occurred is another question entirely. But if we want to speak of facts, the fact of the matter is we do not know how, or even whether, evolution occurred. That is a scientific fact, and to claim otherwise is to harm science. Evolutionists accuse skeptics of doing damage to science. If they are genuinely searching for threats to science they should look closer to home.

Cricket Songs and Evolution in the Details

Male crickets attract females with their chirping, but some males are incapable of chirping. Now, new research shows that those silent males are affected by their singing comrades. Specifically, silent males that develop in the presence of abundant male song tend to be larger, with more reproductive potential, than male crickets growing up in a silent environment. Insects are more complicated than thought. As one researcher explained:

people often think of insects, especially the non-social insects, as mindless automatons, pre-programmed to carry out simple procedures throughout their lives

Of course, after all they simply happened to evolve.

Our research shows quite the opposite, and demonstrates how even small, inconspicuous animals respond to the vagaries of their social environment by capitalizing on conspicuous signals that are intended for a different receiver.

So now we know that a blind mutation made the crickets sensitive to the songs in their environment. And another blind mutation connected that sensitivity to increased growth and reproductive potential. This research demonstrates the power of evolutionary change.

Nuclear Power: A New Movement You Won’t Believe

I am going to tell you something unbelievable. It will sound like hyperbole or a parable contrived to make a point. It isn’t—it is true. You have heard of the many crazy things people believe but, believe it or not, there is a group that is certain that there is a way for the four fundamental forces of nature (gravity, electromagnetism, the weak nuclear force and the strong nuclear force) to rearrange fundamental particles to form spaceships, nuclear power plants and computers. I am indebted to Granville Sewell for this information, and why it is important.

This group does not merely assert that the four fundamental forces can rearrange fundamental particles to have the form of spaceships, nuclear power plants and computers, they actually believe that the four fundamental forces can rearrange matter to have the function of spaceships, nuclear power plants and computers. That is, the four fundamental forces create actual spaceships, nuclear power plants and computers.

Sometimes the more extreme and absurd a belief, the more firmly it is held. This seems to hold true in this case as Sewell was unsuccessful in trying to talk some sense into these people. He explained to them that their belief is highly unlikely given the second law of thermodynamics which states that things tend toward disorder, not order.

It may seem silly to use a scientific argument for such an obviously surreal belief. But the group tends to be scientifically oriented, so Sewell thought the second law would help them to see their colossal blunder.

No such luck. Their response, amazingly, was that sunlight makes all the difference. That’s right, they believe that the four fundamental forces, with the addition of solar radiation, can create spaceships, nuclear power plants and computers.

If you are interested in learning more about this group go here to see the writings of one its leaders.

If This Were Science

The twentieth century's revolution in molecular biology has produced volumes of sequence data which evolutionists have marshaled in defense of their theory. One high-profile example is the molecular similarity between humans and chimpanzees. First proteins and later the genomes of these two species were found to be practically identical. These findings have often been touted as compelling confirmations of evolution. But there are also differences—significant differences. One example is the differences in the Y chromosome, which recent research has elucidated. These differences are explained by evolutionists, of course, as arising from various evolutionary processes. But the differences are significant and the evolutionary scenarios are speculative. In fact a recent paper appealed to several different mechanisms in order to explain the differences. Of course none of this is impossible, but the ease with which evolutionists can explain observations that are at various points in the spectrum (such as high similarity and significant difference) is an example of why some observers view evolution as a tautology. When I pointed this out evolutionists responded with a variety of protectionist maneuvers. Here is an example.

Background

You may recall from your biology class that most mammal species have two sex-determining chromosomes labeled X and Y. A pair of X chromosomes makes for a female whereas an X and Y pair makes for a male. Unlike the other chromosome pairs in which the two chromosomes are highly similar, the X and Y chromosomes are quite different. The most obvious difference is in their sizes—the Y chromosome is quite a bit smaller than the X chromosome. And not surprisingly the Y chromosome contains genes that are male-specific.

Focusing on the Y chromosome, it is comprised of half-a-dozen different types of regions, distinguished both by differences in structure as well as content. For instance, the ampliconic regions contain long, repeated sections, often arranged in molecular palindromes. The X-transposed regions contain genes that are highly similar to counterparts in the X chromosome, and the X-degenerate regions contain gene remnants.

New findings

Recently the chimpanzee Y chromosome was decoded and compared to its human counterpart. Unlike previous DNA comparisons between the two species that revealed high similarity, the two Y chromosomes show substantial differences. The cousin genes present in both chromosomes are highly similar, but about a third of the genes have no cousin in the other chromosome. Also there are no X-transposed regions in the chimp Y chromosome, and overall the chimp has significantly fewer genes. On the other hand, the chimp’s ampliconic regions contain about twice as many long palindromes as the respective human regions. As the paper explained, these chimp and human regions “differ radically in sequence structure and gene content.” The illustration below shows these differences in the chimp and human Y chromosomes.




A tautology?

Prior to these findings evolutionists had thought the pattern of diminished size of Y chromosomes was due to a decaying action that slowed over time. These new findings don’t fit that hypothesis as there is far too much difference between the human and chimp Y chromosomes. Consequently they need another explanation. In fact multiple explanations are required to explain the many differences. So evolutionists say these differences are a consequence of “rapid divergence” driven by various “synergistic factors.” There was, for example, the “brisk kinetics” of ectopic recombination, genetic hitchhiking, and the great competition for mates amongst chimpanzees.

Impossible? Not at all. Indeed, it certainly is true that the Y chromosome is a unique type of chromosome. But the ease with which evolutionists can swap in opposing hypotheses and explain findings from across the spectrum, feeds the view the evolution is a tautology. Whatever is found, some say, evolution has an explanation for it.

Criticism

When I pointed this out one evolutionist responded with harsh criticism. But he seemed more intent on protecting the theory of evolution rather than exploring possible implications of the new findings. His response was notable because he is well known for his intelligence and communication skills. This was not the diatribe of some unknown critic. And that is why his comments are important. Unfortunately, theory protectionism is too often the first response of evolutionists.

He wrote that my article was shameless, shocking and incompetent. He went on to write that “His views on this topic are about the equivalent of some college freshman who wrote an essay on a biological topic without doing the responsible thing and doing the basic background research first. In a student, it would excusable, kind of, but for a Ph.D. presenting himself as an expert, holding forth on a blog, and posting his stuff on other blogs, and generally on a mission to "inform" the public about evolution, it's incredible.”

But what was shameless, shocking or incompetent about pointing out the reaction of evolutionists to these new findings, and the context of their previous claims? In fact, his specific complaints did not back up his criticism.

For instance, he wrote that “there are a lot of standard, well-known population genetics reasons why things like the Y-chromosome should evolve rapidly.” But if it were so obvious then evolutionists would not have been surprised by the new findings. They would not have to replace their decay hypothesis with new mechanisms. Certainly evolution would not have been harmed if substantially greater similarity had been found.

He also wrote that “the subjective ‘amount’ of change is not the most important thing, especially because things like deletions can cause ‘a lot’ of ‘difference’ in sequence, but actually reflect a very few events. Others have already pointed out that the non-deleted sequence maintains quite high similarity.”

True, a single deletion can cause substantial change, but for now we do not even know what degree of the observed differences can be explained by deletions.

He next wrote “the amount of change also isn't the most important thing because common ancestry doesn't predict that everything will evolve at exactly the same rate (which is what Hunter, stunningly and ridiculously, implies), rather it predicts that, whatever the rate of sequence change, humans and chimps will usually be closest to each other, gorillas will be a little farther (but not much), then orangs, then gibbons, then old-word monkeys, then new world monkeys, then lemurs, then other placentals, then marsupials, etc.”

But I implied no such thing. The evolutionist finds my article to be shameless, shocking and incompetent, yet he works from a misreading of it. He next wrote that “There is a massive amount of literature just on the evolution of sex chromosomes, it's a classic example of a highly successful application of population genetics and evolutionary biology, and Hunter is embarrassing and discrediting himself and creationists in general by irresponsibly blathering about a topic like this when he clearly knows jack squat about it.”

While it is true that there is substantial evolutionary literature on the evolution of sex chromosomes, this body of work is based on the presupposition that evolution is true. That is understandable for practical reasons, but it means that heroic assumptions go unquestioned. This body of work is very much a part of evolutionary thought—it is not work done from a theory-neutral perspective.

Finally, he criticizes my article for not presenting its own prediction. Here the protectionism becomes obvious. The evolutionist's heated criticism has long since left the actual article. The article is said to be shameless, but yet it is nowhere to be seen in the criticism.

If this were science, evolutionists would acknowledge that their theory is not a fact as much as is gravity. But instead they make this claim, and they use protectionist moves to avoid criticism.

A Deep-Sea Snail and Evolution’s Superior Material Designs

Once again evolution has come up with an ingenious design, this time a multilayered protective material with a range of potential applications. The material was discovered in the shell of a deep-sea snail, Crysomallon squamiferum, which is able to withstand powerful crab attacks. Here is the summary of the new findings:

Biological exoskeletons, in particular those with unusually robust and multifunctional properties, hold enormous potential for the development of improved load-bearing and protective engineering materials. Here, we report new materials and mechanical design principles of the iron-plated multilayered structure of the natural armor of Crysomallon squamiferum, a recently discovered gastropod mollusc from the Kairei Indian hydrothermal vent field, which is unlike any other known natural or synthetic engineered armor. We have determined through nanoscale experiments and computational simulations of a predatory attack that the specific combination of different materials, microstructures, interfacial geometries, gradation, and layering are advantageous for penetration resistance, energy dissipation, mitigation of fracture and crack arrest, reduction of back deflections, and resistance to bending and tensile loads. The structure-property-performance relationships described are expected to be of technological interest for a variety of civilian and defense applications.

C. squamiferum’s shell is truly an evolutionary breakthrough providing material science with several new concepts for protective armoring. As one report explains:

the snail employs some unique tricks to protect itself. For example, the shell's outermost layer consists of strong particles of iron sulphide created in the hydrothermal vents, each around 20 nanometres across, embedded in a soft organic matrix secreted by the snail. This structure is designed to crack when hit, but in a way that absorbs energy.

Cracks spread only by fanning out around the iron sulphide particles. This "microcracking" not only absorbs energy, it also ensures that larger cracks do not form. What's more, the particles of iron sulphide may blunt and deform intruding claws …

A thick, spongy middle layer acts as padding to dissipate further the energy of the blow. This makes it less likely that the mollusc's brittle inner shell, which is made of calcium carbonate, will crack. …

Helmets, motorbikes and Arctic pipelines that collide with icebergs, leading to costly oil spills, could also benefit ...

C. squamiferum’s revolutionary shell design is yet another reason why evolution is so important to science as a whole.

Human-Chimp Genomic Differences

One of the most popular evidences proclaimed for evolution in recent years is the high similarity between the human and chimpanzee genomes. The cousin genomes are about 99% similar and this has repeatedly been expounded as an obvious proof text of evolution. But these comparisons did not include the finicky Y chromosome which only recently has been decoded from the chimp genome. These new results show an entirely different picture.

Scientific theories are used to make predictions. And when those predictions are confirmed they make a theory look good. Certainly evolutionists think that the 99% similarity between human and chimp genomes is a powerful confirmation of evolution. But there are two sides of the prediction coin—the more you gain on the upside, the more you can lose on the downside. If a successful prediction is compelling proof of a theory, then its failure is a strong falsifier. And we now know that the human and chimp Y chromosomes are highly dissimilar.

The new research shows significant differences particularly between the male-specific regions of the human and chimp Y chromosomes—the MSYs. Unlike the prediction of highly conserved genomes over the 6 million years since the two species split apart, the new results indicate a “wholesale renovation” and “remodeling” in the respective lineages. Little change was predicted but what has been found is that more than 30% of the chimpanzee MSY region has no human counterpart, and vice-versa.

Furthermore, the human and chimp regions are not in the same order. Contrary to what was expected, “the chimpanzee and human MSYs differ markedly in sequence structure” reflecting “extensive rearrangement.” In all, the chimp and human Y chromosomes are “horrendously different from each other,” said one evolutionist.

And how did all this occur? These human and chimp regions differ radically in sequence structure and gene content, “indicating rapid evolution” explain evolutionists. It is an example of “rapid divergence” driven by various “synergistic factors.” There was, for example, the “brisk kinetics” of ectopic recombination, genetic hitchhiking, and the competition for mates.

So when genetic similarities are found they are powerful evidence for common descent, and when surprising differences arise they are examples “rapid evolution.” No wonder evolution has been called a tautology.

More Echolocation Convergence in Bats

For many years the molecular sequences in the bat genome have not been cooperating, and recent research continues to confirm these findings. If evolution is true, then we must believe that the incredible echolocation ability found in some bats arose multiple times, by evolving independently. That's not easy for evolutionists to explain. How could such uncanny design details repeat themselves via blind biological variation (no, natural selection doesn't help)?

On the other hand, perhaps instead of evolving independently, it only evolved once long ago, and then repeatedly was lost in particular lineages. That's another puzzle. If it was valuable enough to be selected, then why would it later disappear?

But of course if one believes in evolution, then problems such as these are minor. In fact, they are easy to explain. Echolocation evolved repeatedly due to similar environmental pressures. Or, on the other hand, echolocation could have been lost in different lineages due to shifts in environmental pressures. See, nothing in biology makes sense except in the light of evolution.

A Code That Isn't Universal

The DNA code, which translates DNA sequences into protein sequences, has always been claimed as extremely compelling evidence for evolution. The code was first described in the mid twentieth century and, among other things, was found to be universal, or nearly so. The same DNA code is used in the cells in your brain and your big toe. The same DNA code is used in different species. The same DNA code is even used across the major kingdoms. All tissues, all species use the same code? Surely they were not independently created—they must have evolved. And if the code varied, on the other hand, evolution would surely be falsified. In one fell swoop, the DNA code not only is another compelling evidence for evolution, it also demonstrates that evolution is falsifiable, a badge that is crucial for evolutionists who seek to distinguish themselves from those religious rascals. But now a new code has been discovered and, believe it or not, it is not universal.

Most people understand that genes are sections of DNA that code for molecular machines such as proteins. But what is less familiar is that in higher organisms many of the genes are broken up into expressed regions, or exons, which are separated by intervening regions, or introns. After the gene is copied the transcript is edited, splicing out the introns and glueing together the exons. Not only is it a fantastically complex process, it also adds tremendous versatility to how genes are used. A given gene may be spliced into alternate sets of exons, resulting in different protein machines. There are three genes, for example, that generate over 3,000 different spliced products to help control the neuron designs of the brain.

But how does the splicing machinery know where to cut and paste? The answer is that there is an elaborate code that exciting new research is helping to elucidate. The new massive study systematically analyzed how genes are alternatively spliced in four different types of mouse tissue: central nervous system tissue, muscle tissue, digestive system tissue, and whole embryos.

The study found significant signals that the splicing machinery seem to use to decide how to do its splicing. This splicing code is extremely complicated, using not only sequence patterns in the DNA transcript, but also the shape of transcript, as well as other factors.

What is also complex about the new code is that it varies substantially across the four tissue types. There is still much to learn, but there certainly is no question that this is no universal code. Is evolution still falsifiable?

The Green Sea Slug: An Animal With Photosynthesis

In his evolution apologetic, Science on Trial, Douglas Futuyma argued that the idea that the species were created is obviously false because they not well designed. Evolution, concluded Futuyma, must be true. For instance, Futuyma pointed out that photosynthesis is immensely useful, yet no higher animals have this mechanism. But new research is finding just that. The green sea slug, it seems, is part animal and part plant. As one report explained:

Pierce emphasized that this green slug goes far beyond animals such as corals that host live-in microbes that share the bounties of their photosynthesis. Most of those hosts tuck in the partner cells whole in crevices or pockets among host cells. Pierce’s slug, however, takes just parts of cells, the little green photosynthetic organelles called chloroplasts, from the algae it eats. The slug’s highly branched gut network engulfs these stolen bits and holds them inside slug cells.

Some related slugs also engulf chloroplasts but E. chlorotica alone preserves the organelles in working order for a whole slug lifetime of nearly a year. The slug readily sucks the innards out of algal filaments whenever they’re available, but in good light, multiple meals aren’t essential. Scientists have shown that once a young slug has slurped its first chloroplast meal from one of its few favored species of Vaucheria algae, the slug does not have to eat again for the rest of its life. All it has to do is sunbathe.

In fact the slug comes pre equipped with the necessary equipment to synthesize its own chlorophyll, the machine that captures energy from sunlight and makes plants green, and run the captured chloroplasts. As one researcher put it, “This could be a fusion of a plant and an animal—that’s just cool.” It certainly is, and for evolution it is bizarre. As one evolutionist put it, “Steps in evolution can be more creative than I ever imagined.”

Let the Worship Begin

In 1734 Daniel Bernoulli used cutting edge statistical methods of his day to prove that our solar system must have evolved as a result of a single cause. He who would deny this, concluded the scientist-mathematician, “must reject all the truths, which we know by induction.” Bernoulli’s high confidence was, of course, unwarranted as later years would reveal. But today, almost three centuries later, little has changed.

If you gaze at an illustration of our solar system you will immediately be struck by its clock-like regularities. The planets revolve about the sun in the same direction, and in the same plane—the sun’s equatorial plane known as the ecliptic. And as the planets race around the track they also spin like tops, and in the same direction. And their moons show the same patterns. The solar system seems to be one big, precise, clock-like machine. Well, almost.

In fact, imbedded in the solar system’s clock-like regularities are a great many anomalies, some of which were known in Bernoulli’s day. The comets do not travel in the ecliptic, many moons go their own way, and Venus and Uranus don’t spin like the other planets. And beyond the obvious anomalies there is a steady stream of less obvious, but no less vexing, deviations. For instance, while the planets do appear to travel in the ecliptic, in fact their orbits all deviate from that ideal, in varying degrees.

This is the puzzle of the solar system. It reveals striking patterns but also myriad and significant anomalies. Bernoulli was sure a single cause was behind all this, but his certainty was to give way, years later, to a variety of complex ideas with multiple causes that would be needed.

A comet may have collided with the sun or a cloud of material may have condensed. Instabilities may have caused some planets to form rapidly, planets and objects collided, moons formed, icy dust collected, planets perturbed and raced around each other, moons were captured, objects were ejected to the far reaches, the solar wind cleaned house, and magnetic braking slowed the sun. These is a bit of the pinball-machine like chaos that has been envisioned to account for the solar system. Hardly the single cause Bernoulli had “proven.” And today’s discoveries of other solar systems, with their variety of patterns, has complicated the picture even more.

But if Bernoulli’s foray into cosmology was ill-fated, he did make a lasting, if unfortunately, contribution to the historical sciences. That would be his method of constructing and comparing different hypotheses. Hypotheses in the historical sciences tend to be dramatically underdetermined and so, it would seem, hardly able to be proven.

But if competing hypotheses could be constructed—and knocked down—then is not one’s hypothesis the obvious winner? In fact statistical probabilities could be calculated allowing us no option, as Bernoulli argued, but to accept the hypothesis unquestioningly. His was not the first use of such contrastive thinking, but the son of math’s first family brought the authority of numerical calculations and to the historical sciences.

Bernoulli’s mathematical version of contrastive proofs soon became standard fare in eighteenth century cosmology, and then no less so in the nineteenth century’s theory of evolution. After Darwin it continued to provide many of the key justifications of evolutionary thought. Now a new paper out this week in the elite journal Nature continues the tradition.

The new paper constructs several hypotheses for the early phases of evolution history and shows how universal common descent, in one variant or another, is the clear winner. And in the now well-established Bernoullian tradition, the results are grossly misinterpreted in favor of evolution. After showing that a comparison of 23 proteins—similar versions of which are found in many species—fit the universal common descent hypothesis far better than the hypothesized alternatives, the paper erroneously states that the results are “very strong empirical evidence” for universal common descent.

Not surprisingly the paper is an instant hit with evolutionists, celebrated everywhere from journals and popular science magazines to the blogosphere. One science newsletter proclaims:

First Large-Scale Formal Quantitative Test Confirms Darwin’s Theory of Universal Common Ancestry

Scientific American has informed its readers that “The Proof Is in the Proteins: Test Supports Universal Common Ancestor for All Life,” and National Geographic adds that:

All Species Evolved From Single Cell, Study Finds
Creationism called "absolutely horrible hypothesis"—statistically speaking.

In his blog PZ Myers, who with his Lutheran background believes god would never have created this world, applauds the big numbers that “support evolutionary theory.” And Nick Matzke, who also believes in the evolutionary metaphysics that god would never have designed what we observe in the biological world, is delighted that the new work debunks creationism.

Of course all of this is false. It is junk science at its worst. In a public discussion I asked the paper’s author about these problems. I reminded him that one hypothesis comparing well against others does not translate into very strong empirical evidence for the hypothesis. But he disagreed. He assured me that his analysis is fundamentally based on modern, cutting edge statistical methods, and that he firmly stands by his conclusions. Indeed, no scientist or statistician would find them to be controversial, he added.

I explained to him that the problem lies not with the statistical methods. Daniel Bernoulli also used cutting edge methods of the day (he was the first that I know of to use a null hypothesis based on random distributions). But when comparing such scores a scientist or a statistician would merely claim that the hypothesis with the significantly higher score is the winner of the group. That is entirely different than his high claim that the results constitute very strong empirical evidence for the hypothesis. That conclusion is simply false. The hypothesis may be true, it may not be true, but the study does not provide such powerful empirical evidence for it. Unfortunately, such misinformation fuels the kind of reporting we saw above.

But again the evolutionist continued to disagree. You are simply incorrect, he replied. From a model selection perspective, from a likelihood perspective, and from a Bayesian perspective, empirical evidence can only be evaluated relative to other hypotheses. That’s all we have. No hypothesis can be evaluated in isolation—such an idea is impossible and incoherent. This view is not from evolutionary biology—this is the standard non-frequentist statistical view (and even most frequentists have the same view). He suggested I read some introductory books on likelihood and Bayesian statistics.

Evolutionary thought, including its history, metaphysics and abuse of science, is a fascinating study. I replied that I was amazed. The lengths to which evolutionists must go is incredible. It is always striking to see the certainty with which evolutionists promote their philosophies and metaphysics. You can see it in the history of evolutionary thought, and today it just keeps on coming. They impose their philosophies, as though they were facts, on the world. Their faulty logic is exceeded only by their boldness.

I again explained that when one hypothesis beats out others you cannot make the claims you are making. What you have is very strong evidence that the hypothesis beats out the other hypotheses, period. You do not have very strong evidence for the hypothesis, as you are claiming.

And your appeal to the limitations in your confirmation methods doesn’t change the fact that you are making false claims, and celebrating them as valid findings. The fact that “That's all we have” hardly justifies the publishing and promotion of misinformation. The fact that “That’s all we have” ought to serve to temper the claims, not exalt them.

But contrastive thinking has been at the heart of evolutionary thought for centuries. From Kant to Darwin, and on up, what has always been rather revealing is how evolutionists have presented their proofs as though they were objective, undeniable findings. It is always a bit shocking to see such bold claims made on such faulty logic.

At this point the evolutionist turned the blame on me. We have, he explained, overwhelming evidence that universal common ancestry beats out competing multiple independent ancestry hypotheses. If you don’t consider that as evidence for universal common ancestry, then you are certainly entitled to that opinion. But the rest of us are not required to believe that your opinion makes any sense. Yours is a strange philosophy, to my mind, and I’m sure to most people who will read your words.

Repeatedly I have found that evolutionists are unable to see the problems and fallacies with their theory. And so when you point out those problems, the evolutionist ultimately can only conclude that the problem lies with you. You are an obstructionist, or biased, or anti science, or something.

This evolutionist was not being judgmental in any personal way. He threw up his hands and concluded that I am the problem, but his response was genuine, not contrived. It was not mean spirited. Just as Bernoulli proclaimed that anyone who would deny the obvious evolutionary conclusions “must reject all the truths, which we know by induction” so too evolutionists ever since can only understand skepticism as, itself, problematic.

Evolution is a metaphysically-driven tradition and like most such traditions has built-in protections against objective critique. The result, unfortunately, is junk science. This new paper will be erroneously celebrated far and wide as yet a new level of certainty for evolution. Let the worship begin.

Evolution v37.302

This blog is erroneous and I have retracted the offending section. Apologies for the false publicity.

two men say they’re Jesus one of them must be wrong—Dire Straits

Historian Stephen Brush points out that the origin of the solar system remains unsolved because, though textbooks will dogmatically present the current theory, in fact the “current” theory seems to be changing on a regular basis. All the more so for evolution, which seems to be pivoting at an ever increasing rate. Consider the origin of the complicated eukaryotes. Practically every permutation has been suggested on the basic model of an ancestor splitting three ways to give rise to bacteria, archaea and eukaryotes. Perhaps the archaea split off from the eukaryote lineage, or perhaps the bacteria split off from the archaea lineage. Perhaps the bacteria split off from the eukaryote lineage, or perhaps the archaea and bacteria lineages produced a fusion that led to eukaryotes. For being an undeniable fact, it’s amazing how little evolution fits the facts.

Recently however, it seemed that at least some of this ambiguity was finally resolved. That finicky eukaryote lineage was finally nailed down for good. There was no question about it, the eukaryotes arose from a unique fusion event between a lonesome bacteria and archaea. Here is what I wrote just a few months ago:

I wish I had a nickel for every statement of evolutionary certainty that later had to be dropped. Carl Zimmer’s recent piece on how eukaryotes are supposed to have evolved quotes Eugene Koonin as stating that “it is certain” that a long time ago, in a warm pond far far away, two cells (an archaea and a bacteria) symbiotically merged to form the first eukaryote. The rest, as they say, was history, as from that humble eukaryote sprung everything from the trilobite to the tyrannosaurus.

Fly Eyes Inspire Better Video Cameras

Evolutionists are always pointing out that evolution is a lousy process. Our aching backs, useless wisdom teeth, and backward wiring in our retinas are, they say, consequences of evolution's ineptitude. It is hardly the sort of thing that a designer would want to copy. Would you want to fly on an aircraft if its design was inspired by such a haphazard process? Of course not. And who can argue with the evolutionist’s logic. If life is the result of the random interplay of the laws of thermodynamics, motion, electromagnetism, gravity and so forth, then we would hardly expect anything that works very well, if at all. But if all this is true, then what about nature’s dazzling designs? If evolution is a lousy designer, then what can we say about biology’s many intricacies? In fact biology’s designs are not only incredibly complex (so much so we’re still trying to figure them out), they often are quite useful.

Biology is yielding a wealth of designs and structures that find a variety of practical applications. In today's engineering fields there is an emphasis on biologically-inspired designs. Courses, textbooks and conferences increasingly look to biology for design ideas and synergies.

Military researchers, for instance, have been on to this for years. If the bat's biosonar can perform ranging measurements several times more accurately than our best military equipment, then let's find out how they do it. Likewise, if bats can perform synthetic aperture imaging in a few seconds and simultaneously solve complex geometrical equations to optimally intercept their prey, then it is no surprise that the military is interested.

In fact biology offers a wealth of such high-tech productions. Consider the fly's advanced image processing capabilities. As one writer explained, the "pesky fly's eyes hold an important blueprint for creating better video cameras, military target-detection systems, and surveillance equipment." The potential applications are significant and include commercial (e.g., cameras and video cameras), security (e.g., improved detection of movements in shadows), and military (e.g., improved target detection and tracking).

Evolutionists say that evolution created the many biological marvels such as the bat's biosonar and the fly's vision system. They say that a lousy, undirected and haphazard process just happened to outwit the best scientists and engineers in the world—time and time again. According to Darwinists, biological structures with unknown function are useless and an obvious sign of an inept, undirected process. But biological structures with awesome designs are, on the other hand, also supposed to be the product of undirected biological change, such as mutations.

Claiming that the bat's biosonar or the fly's vision system is the result of evolution is more speculation than explanation. In fact, that is putting is nicely. How silly it would be to unequivocally claim that the most advanced, complex designs must have arisen as a consequence undirected biological change. A sequence of mutations just happened to produce the most accurate sonar system known to humanity.

This is so silly, in fact, that Darwinists usually refrain from saying this. It is their theory, but more often than not Darwinists use the less ridiculous-sounding Lamarckian language. The designs, they say, arose as a consequence of selection pressure. This explanation violates their own principle that biological change must not be initiated or crafted in response to need. According to evolution, biological change must be undirected. Selection must play a role only after the biological change occurs, not before.

Nor is gradualism a remedy to the problem. Construction of biosonar and advanced image processing, one undirected mutation at a time, is no better than all at once. In both cases the undirected biological change must hit upon the same phenomenal design. Gradualism, however, has the added burden that there must exist a very long sequence of finely graded useful intermediates, leading to the final design. We know of no such sequence, but we must believe it exists. All very amazing for such a lousy process.

Why Ken Miller is Right About Our Backward Retina

In the steady-stream of “not junk after all” findings it was inevitable that our backward retina would be discovered to work quite well, thank you. But if you think it is another icon of evolution that has been shattered, think again. Evolutionary explanations of vision go back to Darwin, and they haven’t changed much in spite of our much improved understanding of how vision actually works. And now new findings that the inverted design of our retina isn’t as bad as it looks, while interesting, are not much more than a yawner for evolutionists.

Darwin’s view of vision

In Chapter six of Origins Darwin addressed what he saw as the chief difficulties with his new theory. A good example to begin with was the eye. “To suppose,” wrote Darwin, “that the eye with all its inimitable contrivances for adjusting the focus to different distances, for admitting different amounts of light, and for the correction of spherical and chromatic aberration, could have been formed by natural selection, seems, I freely confess, absurd in the highest degree.”

But Darwin then abruptly pivoted. Anticipating the twentieth century’s non intuitive findings such as quantum mechanics and chaos theory, Darwin’s justification for evolution was that science is not always intuitive. Does the earth really hurtle at breakneck speed around the stationary sun? Vox populi, vox Dei, advised the sage of Kent, cannot be trusted in science. The next pivot was even easier:

Reason tells me, that if numerous gradations from a simple and imperfect eye to one complex and perfect can be shown to exist, each grade being useful to its possessor, as is certainly the case; if further, the eye ever varies and the variations be inherited, as is likewise certainly the case; and if such variations should be useful to any animal under changing conditions of life, then the difficulty of believing that a perfect and complex eye could be formed by natural selection, though insuperable by our imagination, should not be considered as subversive of the theory. How a nerve comes to be sensitive to light, hardly concerns us more than how life itself originated; but I may remark that, as some of the lowest organisms, in which nerves cannot be detected, are capable of perceiving light, it does not seem impossible that certain sensitive elements in their sarcode should become aggregated and developed into nerves, endowed with this special sensibility.

It is incredible that such non scientific conjecture continues to be taken seriously by anyone today. This nineteenth century thought experiment was conveniently oblivious to the biochemistry underlying vision. Even the relatively simple third eye vision cascade dwarfs anything of which Darwin could have dreamt. And it shows no sign of having evolved.

As if sensing a problem Darwin employed a deeply metaphysical argument from one of his favorite authors, David Hume’s anthropomorphic warning:

It is scarcely possible to avoid comparing the eye with a telescope. We know that this instrument has been perfected by the long-continued efforts of the highest human intellects; and we naturally infer that the eye has been formed by a somewhat analogous process. But may not this inference be presumptuous? Have we any right to assume that the Creator works by intellectual powers like those of man? If we must compare the eye to an optical instrument, we ought in imagination to take a thick layer of transparent tissue, with spaces filled with fluid, and with a nerve sensitive to light beneath, and then suppose every part of this layer to be continually changing slowly in density, so as to separate into layers of different densities and thicknesses, placed at different distances from each other, and with the surfaces of each layer slowly changing in form. Further we must suppose that there is a power, represented by natural selection or the survival of the fittest, always intently watching each slight alteration in the transparent layers; and carefully preserving each which, under varied circumstances, in any way or in any degree, tends to produce a distincter image. We must suppose each new state of the instrument to be multiplied by the million; each to be preserved until a better one is produced, and then the old ones to be all destroyed. In living bodies, variation will cause the slight alterations, generation will multiply them almost infinitely, and natural selection will pick out with unerring skill each improvement. Let this process go on for millions of years; and during each year on millions of individuals of many kinds; and may we not believe that a living optical instrument might thus be formed as superior to one of glass, as the works of the Creator are to those of man?

The Enlightenment supplied the gnosticism and Darwin supplied the just-so story. We must suppose “natural selection or the survival of the fittest” created the eye, our religion depends on it.

Dawkins and our backward retina

But Darwin didn’t have the best argument of all. What Darwin did not know was that our eye’s retina is a kluge—it is backwards. Over and over, as evolutionists such as Ernst Mayr and Elliott Sober have pointed out, Darwin argued that nature’s absurdities mandate evolution. The backward retina would have been a gem for Darwin. Needless to say when the inverted design was found, it became yet another metaphysical mandate for evolution. As Richard Dawkins has explained:

Like any nerve, the optic nerve is a trunk cable, a bundle of separate “insulated” wires, in this case about three million of them. Each of the three million wires leads from one cell in the retina to the brain. You can think of them as the wires leading from a bank of three million photocells (actually three million relay stations gathering information from an even larger number of photocells) to the computer that is to process the information in the brain. They are gathered together from all over the retina into a single bundle, which is the optic nerve for the eye.

Any engineer would naturally assume that the photocells would point towards the light, with their wires leading backwards towards the brain. He would laugh at any suggestion that the photocells might point away from the light, with their wires departing on the side nearest the light. Yet this is exactly what happens in all vertebrate retinas. Each photocell is, in effect, wired in backwards, with its write sticking out on the side nearest the light. The wire has to travel over the surface of the retina, to a point where it dives through a hole in the retina (the so-called “blind spot”) to join the optic nerve. This means that the light , instead of being granted an unrestricted passage to the photocells, has to pass through a forest of connecting wires, presumably suffering at least some attenuation and distortion (actually probably not much but, still, it is the principle of the thing that would offend any tidy-minded engineer!).

This much celebrated inverted design has served as a canonical example of why design is false, and evolution true. It isn’t that the design is not complex (indeed it is). It is that the design is not right. No designer would have done it that way. Dawkins must admit that the attenuation and distortion may not be significant, but so what? It is “the principle of the thing.” The retina obviously is not intelligently designed. This is evolutionary metaphysics.

Not junk after all

Now that evolution has been safely established, new research is showing that this icon of dysteleology actually improves vision. As one report explained:

in 2007 researchers analyzing the retinas of guinea pigs reported that the glial cells which nourish and physically support the bed of neurons also act as optical fibers for the rods and cones. These Müller cells are funnel-shaped, with wide tops that cover the surface of the retina and a long slender body that guides light to the receptors below. … findings suggest that sending light via the Müller cells offers several advantages. ... This suggests the cells act as light filters, keeping images clear. … The researchers also found that light that had leaked out of one Müller cell was unlikely to be taken up by a neighbor, because the surrounding nerve cells help disperse it. What’s more, the intrinsic optical properties of Müller cells seemed to be tuned to visible light, leaking wavelengths outside and on the edges of the visible spectrum to a greater extent.

The cells also seem to help keep colors in focus. Just as light separates in a prism, the lenses in our eyes separate different colors, causing some frequencies to be out of focus at the retina. The simulations showed that Müller cells’ wide tops allow them to “collect” any separated colors and refocus them onto the same cone cell, ensuring that all the colors from an image are in focus.

“It suggests that light-coupling by Müller cells is a crucial event that contributes to vision as we know it,” says Kristian Franze, a neurophysicist at the University of Cambridge and co-author of the 2007 study.

Optical fibers, light filters, autofocus, light-coupling? Is the evolution of such design not in question? Is this another just-so story? Is this not absurd in the highest degree?

It isn’t right

Of course not. It may have a fancy function, but the design still isn’t right. It must have evolved. There remain the blind spot and the wires going off in the wrong direction. Whatever enhancements we discover to the retina are just that, enhancements. It surely could have been done better.

As evolutionist Ken Miller cautions, none of this means that the backwards retina itself helps us to see. Rather, it emphasizes the extent to which evolution has fixed the problem:

The shape, orientation and structure of the Müller cells help the retina to overcome one of the principal shortcomings of its inside-out wiring.

This is evolution. A genre rich in metaphysical pronouncements that otherwise are enshrined in scientific terminology. Miller isn't making any new claims. He is simply being consistent with the traditions of evolutionary thought to which he subscribes. Religion drives science and it matters.