Evolutionists Are Losing Ground Badly: Both Pattern and Process Contradict the Aging Theory

It just doesn’t make sense that the entire biological world spontaneously arose all by itself. But the challenges to evolution go far beyond the intuition. When Charles Darwin proposed his unlikely idea in 1859 it defied much of what was known about biology in that day. Today, the situation has only become worse. If there was ever a modern-day myth this is it and science is increasingly revealing this with its empirical findings dealing with both biological patterns and processes.

If the pattern does not comply, then you must falsify

Contradictory patterns in biology include the abrupt appearance of so many forms and the diversity explosions followed by a winnowing of diversity in the fossil record. It looks more like the inverse of an evolutionary tree with bursts of new species which then die off over time. Furthermore the types of adaptive change we do observe occurring in populations does not appear to be of the form that could accumulate to the large-scale change evolution requires.

At the molecular level, DNA and protein sequences are not what was expected and evolutionists had to construct all manner of ad hoc adjustments to make sense of the data. For instance, mutations must have just happened to occur at particular locations, and they must have occurred at wildly different rates, depending on the location within the genome, the gene, the species or the era.

Equally striking are the incredible similarities we find in otherwise unrelated species. If evolution is true these species would be in distant parts of the evolutionary tree. But when we look under the hood we find profound convergence—highly detailed, specific, designs repeated in distant species. This is not an occasional or rare finding in biology as one might assume given evolutionist’s typically light treatment and downright dismissal of the evidence. This pattern is ubiquitous.

But just as common, and just as contradictory, as the incredible similarities amongst remote species are the differences amongst allied species. Again, though evolutionists have downplayed such findings, they are as striking as they are ubiquitous.

If the process does not accept, then you must reject

Patterns that contradict evolutionary theory are only part of the story. Processes are increasingly being elucidated in biology that also defy the theory. Breeders have known since Darwin’s day that the changes they could induce could only go so far and even Goethe knew there were limits. Likewise for adaptive changes observed in the field.

In fact the sheer number of hypothetical mutations that evolution would require to occur to create the millions of incredible designs is astronomical. Evolution’s only hope is that, strangely, biological designs would somehow be constructable via a long series of single mutations, none of which could be very harmful. Not surprisingly, that is exactly the opposite of what the science reveals. Even the evolution of a single protein is astronomically against all odds.

And the adaptive changes that we do observe in biology are found to be the product of incredibly sophisticated cellular and molecular mechanisms—a built-in adaptation machine, if you will.

In other words, rather than the slow incorporation of random mutations via natural selection as envisioned by evolution, populations respond rapidly to challenges with intelligent, directed adaptations. These results make no sense on evolution, but that has not stopped evolutionists from trying to force-fit them into the theory. Here is how one recent paper summarized these findings:

1. Heredity involves more than DNA. There are heritable variations that are independent of variations in DNA sequence, and they have a degree of autonomy from DNA variations. These non-DNA variations can form an additional substrate for evolutionary change and guide genetic evolution.

2. Soft inheritance, the inheritance of developmentally induced and regulated variations, exists and it is important. Soft inheritance includes both non-DNA variations and developmentally induced variations in DNA sequence.

3. Since many organisms (including humans) contain symbionts and parasites that are transferred from one generation of the “host” to the next, it may be necessary to consider such communities as targets of selection.

4. Saltational changes leading to evolution beyond the species level are common, and the mechanisms underlying them are beginning to be understood. Macroevolution may be the result of specific, stress-induced mechanisms that lead to a re-patterning of the genome - to systemic mutations.

5. The Tree Of Life pattern of divergence, which was supposed to be universal, fails to explain all the sources of similarities and differences between taxa. Sharing whole genomes (through hybridization, symbiosis and parasitism) and partial exchange of genomes (through various types of horizontal gene transfer) lead to web-like patterns of relations. These web-like patterns are particularly evident in some taxa (e.g. plants, bacteria) and for some periods of evolution (e.g. the initial stages following genome sharing or exchange).

So now those random mutations must have created life not only with DNA-based heredity, but other heredity mechanisms within the cell. The astronomically unlikely requirements for evolution just increased exponentially.

And these incredible mechanisms just happen to allow populations to undergo rapid, large-scale change in the time span of a single generation, to meet environmental challenges. Add another exponential increase to those requirements evolution must have somehow fulfilled.

And if this isn’t enough, the Tree of Life doesn’t work anymore. In the paper above the evolutionists optimistically imagine that the observed web-like patterns could have been created through various sharing and exchange of genomes. That is yet another “and then a miracle happened” explanation which makes little scientific sense. Here is just one example of many that illustrates the problem.

The notion that the entire biological world spontaneously arose all by itself defies common sense. It also defies empirical science.

Mars Space Probe Landing Animation

Darwin’s Finches: An Example of How Evidence for Evolution Works

Leading evolutionist Jerry Coyne presented Geospiza fortis as an evidence for evolution at a recent talk at Harvard in what continues to be a good example of the strong metaphysics and weak science behind evolution. Recall that the Galapagos finches provided one of Darwin’s many metaphysical arguments for his idea that the species must have arisen on their own. As Carl Zimmer explained in his book Evolution: The Triumph of an Idea:

Something, Darwin realized, was very wrong. Why should there be so many unique species on these similar islands? … Perhaps the finches had not been created in their current form. Perhaps they had evolved. [33]

It wasn’t that the evidence revealed how evolution could possibly create a finch; rather, the evidence was showing that they wouldn’t have been created. For if the finches on those different islands were different species, as Darwin anticipated in a famous notebook entry, it “would undermine the stability of species.”

Evolutionary metaphysics run deep and drive the science to where it shouldn’t go. This brings us back to those finches which not only provide powerful metaphysical arguments but also rather silly scientific arguments.

What is fascinating is that evolutionists believe they have found yet more powerful evidence for their idea. It is another example of how theology drives the science in evolutionary thought.

The story is that in 1977 a drought in the Galapagos Islands left a severe shortage of small seeds that G. fortis fed on. The majority of the population died off leaving only the larger birds with larger beaks which could feed off of larger seeds.

Naturally subsequent generations of G. fortis had larger beaks. As the years passed the population returned toward its pre drought state with more of the smaller beaks, but for a few generations the drought had caused a significant change in the population.

Amazingly evolutionists advertise this as powerful evidence of evolution by natural selection occurring before our very eyes. As Coyne concludes in his book Why Evolution is True:

This is a staggering rate of evolutionary change—far larger than anything we see in the fossil record. … Everything we require of evolution by natural selection was amply documented by the Grants in other studies: individuals in the original population varied in beak depth, a large proportion of that variation was genetic, and individuals with different beaks left different numbers of off-spring in the predicted direction. [134]

Everything we require? A drought occurred and the majority of a bird population died off leaving only the larger birds which could access different food sources. And that’s powerful evidence of evolution? You’re joking right? This reasoning is absurd.

The variation was already present in the finch population before the drought occurred. That’s why the change could happen so fast. The average beak size increased, as evolutionists continue to point out, because the vast majority of the smaller birds died off, not because any new design was created. As usual, natural selection merely killed off the unfit designs.

Over the years evolutionists have presented a great many evidences for their theory. But while the metaphysics make for a powerful and compelling argument, the science is inevitably weak or flawed. Darwin’s finches are no different.

Dennis Venema Begs the Question and Warns the Church That it Must Come to Terms With Human-Chimp Common Ancestry

In spite of the crystal clear message from science that evolution is not a good hypothesis evolutionists continue to add confusion and uncertainty to promote their mythology. One tactic evolutionists use is to interpret evidence in terms of evolution and then claim the result as evidence for evolution. That is not only bad science, it is fallacious. Conclusions cannot also be premises. Yesterday’s installment from evolutionist Dennis Venema is yet another example of this never ending display of petitio principia.

Venema reviews a recent paper by other evolutionists who say they have found evidence of natural selection acting on random mutations to help change a population of small primates into humans. Venema tells us that such findings are “elegant and powerful” and that they “powerfully support the common ancestry of humans with other forms of life, such as chimpanzees and other great apes.”

So did the study that Venema reviews really find such evidence of random mutations and natural selection miraculously bringing about such incredibly unlikely changes? The paper mentions “selection” 56 times, over and over claiming to have found signs of positive selection. One could be excused for having the impression that this is a solid scientific finding.

And the paper’s explanation for how it made such an amazing discovery is fairly technical and not accessible to the non specialist. This is where Venema, a specialist writing for a broad audience, could have helped. Instead he further obfuscated the implications of the study.

Very simply put, while there are many ways evolutionists test for positive selection, they all take evolution as a given. It is not possible simply to measure objectively the selection in DNA as one would, for instance, measure the voltage or current in a circuit using a multimeter.

For example, one strategy evolutionists use to test for selection is to (i) compare the DNA sequences from several species including humans, (ii) derive the corresponding DNA sequence of the common ancestor of those species, (iii) find the changes in the human DNA compared to the common ancestor, (iv) conclude that those human DNA regions with relatively large change are under positive selection and that those regions with relatively little change are under negative, or purifying, selection.

Notice that the second step implicitly assumes there is a common ancestor. And likewise the third step assumes the species evolved from that common ancestor. And so consequently the fourth step concludes that DNA regions with greater differences probably underwent positive selection. The conclusion is based on the presupposition that evolution occurred.

Venema, as a specialist, knows all this. He knows the entire project presupposes evolution. Yet he tells us that the results powerfully support common ancestry and that the church must come to terms with such findings. The irony is that the presupposition of evolution originally came from theological convictions. Venema is simply promoting a centuries old religious mandate which science has repeatedly contradicted. Now evolutionists such as Venema cast themselves as scientists informing the church of new, important findings. Religion drives science and it matters.

Whole-Cell Computer Modeling: How Evolution Fits In

The Markus Covert group’s Cell paper from last week represents a tremendous achievement toward a more systematic understanding of how biological cells work. For decades much of molecular and cellular biology has focused on single genes and single pathways. This was partly out of necessity given the cell’s astronomical complexity. And it was also due to evolutionary dogma which viewed the biological world as so many organic contraptions strapped together one way or another. The result was a rather limited perspective of cellular biology. As Bruce Alberts explained in 1998:

We have always underestimated cells. Undoubtedly we still do today. But at least we are no longer as naive as we were when I was a graduate student in the 1960s. Then, most of us viewed cells as containing a giant set of second-order reactions: molecules A and B were thought to diffuse freely, randomly colliding with each other to produce molecule AB—and likewise for the many other molecules that interact with each other inside a cell. This seemed reasonable because, as we had learned from studying physical chemistry, motions at the scale of molecules are incredibly rapid. … But, as it turns out, we can walk and we can talk because the chemistry that makes life possible is much more elaborate and sophisticated than anything we students had ever considered.

Covert’s work is another step on the way toward not underestimating cells. Science, rather than dogma, has a way of doing that. As Alexis Madrigal at The Atlantic put it, “the depth and breadth of cellular complexity has turned out to be nearly unbelievable, and difficult to manage, even given Moore's Law.”

From the 128 computers running in parallel to the 500 megabytes of state data generated for a single cell cycle, Covert’s simulation of Mycoplasma genitalium—the smallest known free-living organism of a mere 525 genes—is immensely complex.

But nonetheless the simulation is not particularly detailed. It is a so-called mesoscale simulation, meaning it takes a grander view at the cost of omitting the fine-grain details. Consider a mesoscale simulation of an automobile, for instance.

It might model the engine by accounting for the rate at which fuel is burned and the level of torque that is produced. That would omit the stresses and strains of the engine block, the temperature of the metal, the action of the valves allowing oxygen to enter the cylinder, the electrical signal that ignites the spark plug, and a million other details.

The high-level engine model, accounting only for the fuel burn and torque, would be worthless to anyone interested in designing engines. But it is appropriate for, say, the problem of modeling the economics of surface transportation.

So it is with Covert’s simulation. A tremendous wealth of data are omitted, mostly out of necessity. The data are either unavailable, would drive the simulation compute resources through the roof to include, or is beyond current modeling and simulation technology.

And while omitting these data is appropriate for mesoscale cell simulations, there is a large gray area. Exactly which details are needed and which can safely be ignored in a mesoscale cell simulation?

The automobile simulation could ignore the details of the engine operation because there is a decoupling between phenomena at different time scales. Sub millisecond dynamics, for example, wash out and are irrelevant when studying annual trends.

This decoupling is well understood in machines that we build. It is less well understood in biology. In fact the lack of such decoupling can be important in molecular simulations, where phenomena on different time scales can interact.

Exploring such issues will be one of many scientific uses of whole-cell simulations. But don’t expect results too soon. It is a big problem and even simulating the standard E. coli bacteria, with 10 times more genes, is far beyond today’s state of the art.

This is to say nothing of populations of unicellular organisms, or the more complex multicellular organisms. If Covert’s simulation needs half a gigabyte of data for a single cycle of M. genitalium then imagine where the compute requirements go with, for instance, structures with millions of the vastly more complex mammalian cells.

Of course the high-and-going-higher compute requirements imply something about the ever-increasing evolutionary requirements as well.

Both the simulation state data and perhaps more importantly the models that input and output those data, all must have been created by random mutations and the like. Unlikely events must have conspired to design and assemble everything represented in Covert’s simulation, and much more. Care to explore the simulation’s Kolmogorov complexity (the code is available here)?

The more we learn, the more unlikely the “fact” of evolution becomes.

Bacterial Protein Acetylation: The Dawning of a New Age

Molecular biology is not only a story of complex molecules, machines and processes but also of massive information flow via a variety of molecular messages. And while information flow is often associated with the DNA macromolecule, there are less celebrated but ubiquitous armies of molecular machines that are busy attaching, modifying and removing small chemical tags to and from both DNA and proteins. It is a massive information network and these chemical tags—such as methyl, hydroxyl and phosphate groups—act as a sort of molecular modifier or barcode regulating a diverse array of cellular functions. Another molecular barcode is the acetyl group, long thought to be mainly at work in eukaryotes, has now found to be important in bacteria as well. It is, as one evolutionist put it, the “dawning of a new age.” (click above)

According to evolutionists, life began simple and gradually increased in complexity. Therefore early life should be simpler life. And so evolutionists have continually been surprised to find high complexity throughout the living world. As the research paper concluded:

Bacteria have long been considered simple relatives of eukaryotes. Obviously, this misperception must be modified. From the presence of a cytoskeleton to the packaging of DNA to the existence of multiple post-translational modifications, bacteria clearly implement highly sophisticated mechanisms to regulate diverse cellular processes precisely.

With evolution we now must believe that even protein acetylation miraculously appeared very early in the history of life. This would require (i) the enzymes to attach and remove the acetyl groups, (ii) the capability to attach those groups at the right place and under the right conditions, and (iii) of course right influence such that the presence of the acetyl groups produced the needed functional modification.

And all of this must have occurred spontaneously. As per evolutionary theory, the changes must have occurred at random. In other words, the need at hand could not have influenced the changes. Those astronomically unlikely, incredibly complex, changes must have arisen to create the phenomenal protein acetylation functionality, so that it then could be selected for. There is no scientific evidence for a long, gradual series of designs leading to this capability. Even for a single protein this evidence is lacking.  It is yet another example of dashed expectations even in this New Age.

It’s Much Ado About Nothing at the Something From Nothing Club in Tempe

Forget about Second City, Tempe’s new Something From Nothing comedy club is rocking with this hilarious spoof on evolutionary thought featuring Lawrence Krauss as the neurotic Rick Moranis and Richard Dawkins as the pompous Dave Thomas. It’s Sophism gone-wild as the Woody Allen and Bob Hope characters trade one fallacy after another over an ironically-placed stack of great books, all in front of the huge neon sign looming above assuring that it is all “Something From Nothing.” Meanwhile a sort of inverse teleprompter is recording their every precious word. The only thing missing was chapter and verse citations.

The skit begins with the usual adoration of biology’s version of the perpetual motion machine where the entire organic world appears spontaneously. But this is old news and the new news is that it is not just the biological world that happened to happen, but the whole world. And it is not just the universe that we can see, but the laws of physics and even empty space itself. It all just happens. In this all-too-real spoof, the all-knowing wise men assure the commoners that everything could have literally come from nothing.

There is the usual value-laden themes running throughout the skit. Skepticism of their lunacy is found to be pathetic and the discovery that something can come from nothing is “immensely exciting,” “stunningly exciting,” and “worth celebrating.”

Of course the metaphysics does not stop there. For the world is full of “bad design features” that “any decent engineer would send back to the shop.”

There is no one so metaphysical as those who deny metaphysics and the skit is topped off with a hilarious exchange which finds that skeptics are the ones who are guilty of cognitive dissonance. Woody Allen wonders aloud “It’s interesting to me, at the same time, how people can hold beliefs which are incompatible with other beliefs they have” [24:36] and Bob Hope reassures the younger sophist that “It demonstrates, clearly, intellectual deficiency. And, in fact, scholarly deficiency … they’re hypocrites.” [27:01]

The not-too-subtle play on SCTV to spoof evolutionary mythology is as ingenuous as are the performances of Krauss and Dawkins. We trust a good time was had by all.

Carl Zimmer Doubles Down on Chromosome Two Lies and Misdemeanors

For several years now evolutionists have presented the human chromosome number two as an excellent example of how science supports and confirms evolution and this week science writer Carl Zimmer continued the celebration in his Discover magazine blog. What Zimmer and the evolutionists fail to comprehend, however, is that their argument from the human chromosome number two is an excellent example of the religion and rationalism at the heart of evolutionary thought.

You can read the details of how evolutionists have presented the human chromosome number two evidence here. Simply put, the idea is that after the human and chimpanzee lineages split from their common ancestor about six million years ago, the human lineage experienced a chromosome fusion event where two chromosomes fused together to become one, thus reducing the count from 24 to 23. Since our chromosomes come in pairs, the total number reduced from 48 to 46.

That story is reasonable enough, but in the hands of evolutionists it quickly becomes a sordid tale of lies and misdemeanors. There’s something here for everyone as evolutionists cycle through several of their typical fallacies and hypocrisies including shifting the burden of proof, naïve falsificationism, affirming the consequent, theological naturalism, abuse of science and circular reasoning.

Shifting the burden of proof

Ever since Darwin called for skeptics to prove his speculative ideas wrong this strategy of shifting the burden of proof has been a favorite of evolutionists. Darwin wrote:

If it could be demonstrated that any complex organ existed, which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down. But I can find out no such case.

But this was hardly a concession. Darwin may sound generous here, allowing that his theory would “absolutely break down,” but his requirement for such a failure is no less than impossible. For no one can show that an organ “could not possibly” have been formed in such a way. So in short order Darwin reduced what seemed to be a dilemma for his theory into a logical truism. Evolution was protected from criticism and all that was needed to explain complexity was a clever thought experiment. Darwin so lowered the requirements that anyone with a pen and a vivid imagination can now claim to have solved the problem of complexity.

Zimmer used this same strategy this week when he demanded that skeptics of the chromosome two argument show why the evolutionary fusion hypothesis is not possible:

Why is it so hard to answer one question? What is the evidence claimed by members of the Discovery Institute that human chromosome could [not] have evolved through fusion six million years ago? Why do I have to engage in a drawn-out debate about an entire book to get an answer to this one question? [Note: Zimmer’s point is nonsensical because he accidentally omitted the word “not”]

Of course no such claim was made. It is the evolutionists strategy to shift the burden of proof so that evolution enjoys the position of being true by default. Everything evolved from nothing unless you can prove otherwise to the evolutionist’s satisfaction.

Naïve falsificationism

Evolutionists argue that the chromosome two fusion event is important because evolution successfully passes a test of falsification. Zimmer approvingly cites a Ken Miller talk (click above) where Miller makes this argument and concludes:

But there’s something that’s really interesting, and has the potential, if it were true, to contradict evolutionary common ancestry. [0.47]

Evolution has survived so many false expectations with creative conjecture that claims that “this time it’s different” have long since lost credibility. When predictions turn out to be false we are told they were soft and not binding. Evolutionists reassure us that it is all a part of science following the data as the theory is contorted yet again. But when predictions turn out to be true we are told they were hard and binding. An evolutionist once told me that evolution certainly would be falsified by the finding of functionally unconstrained yet conserved DNA sequences. That was before the finding of functionally unconstrained yet conserved DNA sequences.

Beyond this problem of after-the-fact evaluation of predictions, there is the problem that even the success of a hard prediction, by itself, carries only limited information. For instance, science is full of theories that are considered to be false yet enjoy any number of confirmed predictions.

Affirming the consequent

Another problem with successful predictions is that evolutionists view them as not only providing a hard falsification test, but as also providing a sort of confirmation of evolution. At its worst this amounts to the logical fallacy of affirming the consequent. At its best it is a failure to reckon with the meaning of a successful prediction. For instance, Miller triumphantly concludes:

It confirms the prediction of evolution. [3:46]

So what? Science is, again, full of theories considered to be false which make all kinds of successful predictions. This example is particularly awkward since the chromosomal fusion event would have occurred exclusive of any evolutionary speciation event. In other words, perhaps evolution needs it, but it doesn’t need evolution.

Theological naturalism

Theological arguments for evolution’s strictly naturalistic account are crucial. They are evolution’s raison d'être and no less so in this chromosome two argument. As pointed out above, as a falsification test and as a successful prediction, the case of the chromosome two fusion is, from a scientific perspective, of limited importance. The key, as always, is the religious interpretation.

Evolutionists believe that this chromosomal arrangement would never have been designed or created. The key word here is “believe.” It is a religious argument and it is here that evolution has all its strength. Again, Miller makes it clear:

How would intelligent design explain this? Only one way. By shrugging and saying “That’s the way the designer made it.” No reason, no rhyme. Presumably there’s a designer who designed human chromosome number two to make it look “as if” it was formed by the fusion from a primate ancestor. I’m a Roman Catholic, I’m a theist in the broadest sense I would say I believe in a designer, but you know what, I don’t believe in a deceptive one. I don’t believe in one who would do this to try to fool us. And therefore I think this is authentic and it tells us something about our ancestry. [3:48]

There you have it. If one doesn’t believe the chromosomal arrangement is possible under design or creation then, yes, evolution is left as the “None of the above” answer. It must be true, one way or another. As usual evolutionists are quite clear about the metaphysics that motivates and underwrites their theory. This is the power of evolutionary thought.

Abuse of science

The idea that the universe came from nothing and that the biological world arose spontaneously is, of course, not scientifically motivated and not scientifically expected. It is another case of religion driving bad science. The chromosome two case is not nearly the abuse of science that much of evolutionary theory is, but it does have its problems. The site of the fusion event on human chromosome number two does not provide an obvious picture of a past fusion event. There certainly are suggestions of such an event, but it is far from obvious as evolutionists claim.

Furthermore such an event, if it could survive, would have to take over the pre human population. In other words, the existing 48 chromosome population would have to die off. This is certainly not impossible, but there is no obvious reason why that would occur.

There are problems with the evidence. Perhaps the fusion event occurred, but the evidence carries nowhere near the certainty that evolutionists insist it does. It is not so much that the evidence is conclusive against the event but that it is not conclusive for the event as evolutionists claim. Their interpretation is driven by their theory, and this leads us to the final fallacy.

Circular reasoning

If you believe evolution is true to begin with, then you would conclude that the human chromosome number two is the result of a fusion of two ancestral chromosomes. There would be no question about it for several reasons. It would reconcile the different chromosome counts in humans and chimpanzees. And there are a great many similarities between the human chromosome number two and the two corresponding chimp chromosomes.

But if evolution is not taken as an a priori, then these evidences are far less compelling. From this theory-neutral perspective, what is important is not reconciling chromosome counts or chimp-human chromosome similarities (after all, those are found throughout the respective genomes). What is important is the more direct evidence of a fusion event, such as in the region where the two chromosomes would fuse, and other tell-tale signs in the chromosome two.

Here the evidence is mixed. Certainly it is far less compelling than evolutionists ever tell their audiences. This need not be controversial. But it is.

Why? Because evolutionists are essentially incapable of such a dispassionate analysis where presuppositions and evidences are clearly laid out. Their analysis is deeply influenced by their dogmatic assertion that evolution is a fact. For evolutionists it is a metaphysical certainty and they simply are unable to evaluate the evidence from a theory-neutral perspective.

All of this results in a stubborn type of circular reasoning where evolution is presupposed, evidence is interpreted accordingly, and the results then service evolutionary apologetics as though they were obtained from objective science.

In this case, from the evolutionary perspective the chromosomal fusion event is beyond any reasonable doubt. And that event is then used as powerful evidence for evolution. It is all circular.

This is a subtle yet influential motif in evolutionary thought that often underlies discussions and debates while escaping detection.

The human chromosome number two is a concise illustration of evolutionary thought. There is, of course, much more to evolutionary thought than can be packed into this tight vignette, but it does capture the subtleties and intricacies that inevitably weave their way through any defense of evolution.

Ken Miller and Chromosome Fusion

[Ed: This post, from October 12, 2010, is worth a second look in light of Carl Zimmer’s recent piece on human chromosome fusion]

In the 2005 Kitzmiller v. Dover Area School District court case, federal judge John Jones was heavily influenced by the first expert witness, evolutionist Ken Miller. As Jones later recalled, he “was taken to school.” Unfortunately what Miller “taught” Jones was a series of scientific misrepresentations. Miller focused on two examples from molecular biology: a pseudogene and a fused chromosome. In both cases Miller gave Jones many facts but the lessons were carefully tailored to misrepresent both the science and evolutionary theory.

As I explained here, Miller’s pseudogene example included four key misrepresentations: that the pseudogene has no function and is broken, that the pseudogene DNA sequence has “errors” or “mistakes,” that there is no reason for broken genes aside from common descent, and that the evolutionary interpretation of such pseudogenes is objective science.

As was well known and documented when Miller and the ACLU lawyers devised Miller’s testimony, pseudogenes that had been investigated often exhibited functional roles, such as gene expression, gene regulation and generation of genetic diversity. Pseudogenes were found to be involved in gene conversion or recombination with functional genes. Pseudogenes sequences were found to be conserved with reduced nucleotide variability, excess synonymous over nonsynonymous nucleotide polymorphism, and other features that are expected in genes that have functional roles.

Any expert witness testifying on such a narrow topic would have been well aware of these well known results which were published by leading researchers in top tier scientific journals. And yet Miller gave no such perspective to the Dover court, and instead unequivocally represented his pseudogene example as non functional and broken. That was the evolutionary interpretation of pseudogenes, not what the scientific evidence was indicating.

And even if Miller’s selected pseudogene was truly broken, that would not mandate an evolutionary explanation as Miller unequivocally stated to the court. Miller told judge Jones that a pseudogene found in different cousin species, with common mutations, “must mean that these two organisms are descended with modification from another organism” and “leads us to just one conclusion,” which is evolution’s common descent. But this too was a lie, as any expert witness on this topic would know of the many instances of pseudogenes with mutations common to multiple species that do not fit the evolutionary pattern. In these cases even evolutionists must admit that common descent does not explain the mutations.

Perhaps most importantly, Miller’s pseudogene testimony misrepresented the evolutionary argument as objective science whereas Miller and the evolutionists, when not in federal court, make one religious argument after another. The religious foundation of evolution goes back to 18th century Enlightenment and before, and would automatically expel evolution from our public schools.

Miller’s pseudogene argument was just another example of a centuries-long history of religious mandates for evolution. Miller had been making such religious arguments for many years before Dover. He argued that life revealed features “that no engineer would stand for” so they must have evolved. That may be true, but such knowledge cannot come from objective science.

As Miller informed the Dover court, his pseudogene example was “just a mess.” That’s one of his favorite ways of making evolution’s religious argument. As he wrote more than 10 years before Kitzmiller:

In short, this sixth gene [the same pseudogene Miller testified of in the Dover court] is a mess, a nonfunctional stretch of useless DNA. From a design point of view, pseudogenes are indeed mistakes. So why are they there? Intelligent design cannot explain the presence of a nonfunctional pseudogene, unless it is willing to allow that the designer made serious errors, wasting millions of bases of DNA on a blueprint full of junk and scribbles.

It is a powerful argument, but it is not scientific. Miller routinely makes these religious arguments in his books and presentations, but they were carefully edited out for his testimony to the Dover court.

The ACLU lawyers and evolutionists argued that Intelligent Design is a religious theory because there was religious intent. They carefully traced this in early documents. But in evolutionary theory no such careful tracing is needed. The religious claims are boldly pronounced by evolutionists all through their literature. Darwin’s book was chocked full of religious claims, and today’s evolutionists are no different.

This hypocrisy of evolutionary thinking was equally evident in the second of the two examples Miller presented to the Dover court. In that example, Miller showed evidence that two of our chromosomes have been fused together and claimed it was powerful evidence for evolution: “the closer that we can get to looking at the details of the human genome, the more powerful the evidence has become.”

But from a scientific perspective, the fusion event occurred in, and spread through, the human population. There is no evolutionary relationship revealed. Even if evolution is true, this fusion event would give us no evidence for it. The fused chromosome did not arise from another species, it was not inherited from a human-chimp common ancestor, or any other purported common ancestor.

The reason why evolutionists find this argument to be so powerful is, once again, from a religious perspective. According to evolutionists, the evidence mandates evolution because it disproves creation and design. As evolutionist Barry Starr explains:

An alternative explanation is that the designers fused the two chromosomes together when they created humans. ...

The difficulty with this idea is that there is no obvious advantage to having 46 chromosomes instead of 48. ...

And even if there were, a designer who can easily put in the 60 million or so differences between humans and chimpanzees should be able to accomplish whatever results a chromosome fusion gives more elegantly than sticking two ape chromosomes together.

The power of the argument is not that evolution is confirmed, but rather than design is falsified. As Denis Alexander elaborates in his book Creation or Evolution, the fused chromosome “reveals our shared ancestry with the apes.” [211] Of course the chromosome reveals no such thing. It provides no more evidence for evolution than any other similarity. Starr, Alexander and the evolutionists may as well be discussing similarities we share with the apes in our bones or our biochemistry. But the evolutionists focus on cases such as the fused chromosome because these cases provide far more powerful religious evidence. As Alexander explains:

The suggestion that God has planted misleading ‘molecular fossils’ in our bodies is parallel to the suggestion that God planted misleading physical fossils in the rocks to test the faith of the believer. The obvious and profound theological problem with such a suggestion, as we considered in Chapter Six, is that it makes God into a deceiver on a grand scale. It would mean believing in a God who deliberately confuses people, making it look certain that we had shared common ancestry with the apes, when really this was not the case. [213]

And likewise Miller, when not deceiving federal judges, makes this same argument about the very evidence he presented in the Dover court:

So all we have to do is to look at our own genome, look at our own DNA, and see, do we have a chromosome that fits these features?

We do. It's human chromosome number 2, and the evidence is unmistakable. We have two centromeres, we have telomere DNA near the center, and the genes even line up corresponding to primate chromosome numbers 12 and 13.

Is there any way that intelligent design or special creation could explain why we have a chromosome like this? The only way that I can think of is if you're willing to say that the intelligent designer rigged chromosome number 2 to fool us into thinking that we had evolved. The closer we look at our own DNA, the more detailed a glimpse we get of our own genome, the more powerful the evidence becomes for our common ancestry with other species.

In his testimony, Miller told the Dover court that:

the closer that we can get to looking at the details of the human genome, the more powerful the evidence has become.

And when out of court, he makes the same statement:

The closer we look at our own DNA, the more detailed a glimpse we get of our own genome, the more powerful the evidence becomes for our common ancestry with other species.

The difference is he carefully omits the religion when in court. Nor did Miller reveal to the court that evolution is in no way required to explain the chromosome fusion evidence.

Miller also omitted several other inconvenient truths. Judge Jones said he received the equivalent of a degree in the expert testimony, but that degree didn’t include the fact that, beyond speculation, evolution has no explanation for how chromosomes evolved in the first place. And Miller did not explain the great number (more than a thousand) genes unique to the human genome. Again, beyond speculation evolution does not explain the rapid appearance of these novel genes. Indeed, as one evolutionist admitted, the secret to evolving a human from a chimp is to make fast changes in just the right places:

The way to evolve a human from a chimp-human ancestor is not to speed the ticking of the molecular clock as a whole. Rather the secret is to have rapid change occur in sites where those changes make an important difference in an organism’s functioning.

Finally, Miller presented the chromosome fusion evidence as a “beautiful” confirmation of an evolutionary prediction. What he didn’t explain to the court is that science is full of theories known to be false which yet make all kinds of confirmed predictions.

The Kitzmiller trial was one long series of misrepresentations. Yes judge Jones was schooled, but he didn’t learn the truth.

Own Goal: Evolutionists Explain How Complex Structures Evolved—First They Evolved So Then They Could Evolve

Depending on the environment the roundworm Pristionchus pacificus may develop two very different types of mouth structures. If the developing worm is in a bacteria-rich environment then it develops small teeth and a narrow oral cavity. But if there is a food shortage or overpopulation of worms, then Pristionchus pacificus develops a wide mouth with strong, vicious teeth structures with which to devour other worms. So now those random mutations not only morph species to ever improved designs, they actually design construction mechanisms that switch between alternative morphologies depending on the environment. Truly remarkable.

What may be even more remarkable than evolution’s heroics is how absurdly evolutionists interpret these results. Of course there is no scientific explanation of how those random mutations could have done all this. Nonetheless, bloodied but not bowed evolutionists turn this into yet another triumphant moment. Not only does this remarkable developmental polyphenism show “how frugally evolution works,” but it also facilitates phenotypic evolution. Or in plain English:

Moreover, the existence of alternative body structures is viewed as paving the way for evolution: "In order to change the mouth structure permanently, the genetic control would only have to be decoupled from the environmental dependency," explains Ralf Sommer.

If that still is unclear, the ludicrous message is this: The way evolution constructs such elaborate designs as the worm’s killer oral cavity is first to evolve it as one of two alternatives in a complex developmental program. Then, you get rid of said program, and you’re left only with the killer oral cavity. Presto, just like that evolution evolved a fancy new design. Religion drives science, and it matters.

Evolutionists Unconscious of Their Consciousness

Research into consciousness reminds us that evolutionists not only believe that consciousness originated from random mutations and the like, but that this speculative claim is, in their minds, a fact. It is a severe indictment of evolutionary thought which, as always, evolutionists have brought upon themselves. It is not hyperbole nor exaggeration to say that evolutionists literally make false claims. For while the spontaneous origin of consciousness is obviously a bizarre and non scientific thought, it is not even debatable that the claim this is a fact is simply false.

Wrong Again: This Time it is Striated Muscle Evolution

By now this must seem tedious but there is Bayesian value in evolution’s endless stream of failed expectations. This time it is striated muscles, in bilaterians and non-bilaterian eumetazoans. They seemed to evolutionists to have a common evolutionary origin. But now the molecular differences do not support that expectation. Instead, the considerable similarity across these various species would likely have arisen independently, via those random mutations.

But evolutionists forget about this long list of false expectations. Evolution must be a fact, regardless of the evidence.

Professor Confirms Evolutionary Equivocations

If anyone doubted that evolutionists equivocate, or that such equivocation is prevalent, they need doubt no more. I recently pointed out several examples of evolutionists equivocating on evolution. When they proclaim that evolution is an obvious fact, they are referring to the origin of species by random mutation, genetic drift, natural selection and a host of other explanatory mechanisms evolutionists employ when needed. This claim goes against the scientific evidence. Evolution may or may not have occurred. That is an ontological claim that can be argued. But there is absolutely no question the origin of species by evolution is not a fact. That is an epistemological claim which is undeniably false. The claim that evolution is a fact refers to our knowledge. It refers to the facts and theories of science. We may not know what happened in the distant past, but we do know exactly what is our current knowledge of what happened in the distant past. That knowledge indicates there are substantial problems with evolution. It is not something that likely happened, according to our current knowledge. It certainly is not a fact.

And so to justify and defend their false claim, evolutionists change the meaning of the word. To prove that evolution is a fact and indeed occurs, they switch from one end of the spectrum to the other. Evolution goes from the origin of the species to the incredibly trivial changing of gene allele frequencies or virus mutation.

I pointed out one example in the book Arguing for Evolution: An Encyclopedia for Understanding Science, where the evolutionists triumphantly asserted that the evolution of the species is a fact and then used an example of an allele frequency changing from 40% to 36% in a population of rock pocket mice.

Is this and other examples that I pointed out exceptions to the rule? Are these simply uninformed evolutionists making a blunder? Unfortunately such arguments are common in both the classroom and the literature.

If these were exceptions, then we might expect other evolutionists to reject such equivocations. Instead they supported and reaffirmed the equivocations. One evolutionist suggested that the book Arguing for Evolution: An Encyclopedia for Understanding Science, was merely referring to allele frequency change when it claimed that evolution is a fact. She commented: “I'd point out that evolution by Moore and Cotner's definition is also a fact by Gould's definition.”

The book had approvingly quoted Stephen Jay Gould who argued that while we may not know how evolution occurred, we do know that it occurred, based on the usual non scientific, metaphysical, arguments. In that context the book claimed that evolution is a fact. And throughout the book evolution was portrayed, not surprisingly, as the idea of the origin of species by random mutations, natural selection, and so forth.

A professor also defended the equivocation with yet more equivocation. He commented:

The mice example is mundane, but that's the nature of great scientific theories: they describe both the mundane and the profound. Theory of gravity applies equally well to a falling apple and the Moon in its orbit. The Earth keeps the Moon in a nearly circular orbit but barely deflects a comet's path. Both are still manifestations of gravity. So it is with evolution. It views small changes in populations through the same prism as the appearance of new species.

With gravity, one can adequately explain both a falling apple and the Moon in its orbit with the same simple law. The professor draws a false parallel with evolution: “So it is with evolution.”

No, it is not that way with evolution. Changing allele frequencies are not sufficient to explain the origin of species. Not even close. In fact evolutionists do not have a scientific explanation for the large-scale change their idea requires.

It is yet more equivocation, piled on top of the previous equivocation. These types of apologetic arguments are at the foundation of evolution. For if evolution were portrayed according to the science, it would lose all support.

Professor is Scandalized: Evolutionists Would Never Do That!

When I explained that evolutionists equivocate by using different definitions of the word evolution, a professor was shocked. Such allegations were “pretty despicable” and the only equivocation on evolution, she retorted, “is coming from you.” Such is the life of a messenger. Evolutionists misrepresent science in various ways, and when you point it out they put the blame on you. I once debated a biology professor and when I pointed out that evolutionists misrepresent science in their insistence that evolution is a fact, he said I didn’t understand the word “fact.” That retort might make sense if evolutionists had some nuanced meaning in mind, but they don’t. Quite the opposite, their claim is that evolution is as much a fact as is gravity or that the Earth is not flat. Not much subtlety there. But his sound bite accusation achieved the desired effect. It is standard for evolutionists to misrepresent science, and it is standard then to assign the blame on the messenger who points out the misrepresentation. In this case, the professor was scandalized when I pointed out the standard equivocation of defining evolution as mere genetic tweaking. While on the one hand claiming that it is an indisputable fact that the entire biological world arose by itself spontaneously, evolutionists on the other hand will explain evolution as the mere shifting of allele frequencies, an utterly uncontroversial observation which no one disputes. In other words, they make a dogmatic claim that is contradicted by science, and then justify it with a completely different definition of the word. It would be like claiming the Earth is flat, and then arguing strenuously that a field is flat, as though that was the basis of the dispute. However dignified the evolutionary argument is made to appear, it is ultimately nothing more than a shell game.

This equivocation is often presented with viruses. Evolutionists argue that since viruses mutate therefore nature’s millions of species originated via evolution and all of biology arose spontaneously. For example, Steve Jones, writes that the changes observed in HIV contain Darwin’s “entire argument.” [1]

Similarly professor Pamela Bjorkman states that a mutating virus is “evolution at work” and that “In the same way, people have evolved, but over a much slower time scale.” [2]

Incredibly, the equivocation is sometimes even more blatant than this, such as in this example from Randy Moore and Sehoya Cotner:

These theories, in the words of the late Stephen Jay Gould, have been “confirmed to such a degree that it would be perverse to withhold provisional assent.” Evolution is one such theory.

Definition of Evolution

Most simply, evolution is any change in a population’s genetic composition over time. There are several key features of this definition:

1. Evolution is a population-level phenomenon, rather than something that can be measured in individuals. Populations evolve; individuals do not.

2. Evolution has occurred when any genetic change—even something that seems insignificant—happens to any number of individuals in a population.

3. Evolution can be measured in generational time.

To appreciate this, consider a population of rock pocket mice living on the lava outcrop in the southwestern United States. At an initial observation, 40% of the mice possessed an allele (or genetic variant) that produces lightly colored fur when inherited from each parent. A few generations later, only 34% of the mice possessed this allele. This change in the genetic composition of the population means that evolution has occurred. For evolutionary biologists, the fact that evolution has occurred is often not as exciting as the questions that arise as the result of this observation. For example, why did evolution occur? [3]

Here Moore and Cotner argue that the origin of species via evolution is a fact and then explain it as “any change in a population’s genetic composition over time.” They give an example of a population of rock pocket mice with an allele that changes frequency which “means that evolution has occurred.” Obviously evolution must be a fact, right?

Such bait-and-switch shell games are standard fare in classrooms and the evolution literature. They are one of the many types of misrepresentations evolutionists use to promote their non scientific, religious dogma. This is not to judge evolutionists and I certainly forgive evolutionists for misleading people. Forgiveness is crucial and grace is needed all around. But to forgive a misrepresentation does not mean to accept a misrepresentation. We need to understand evolution for what it is.

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1. Steve Jones, Darwin’s Ghost, p. 15.
2. http://darwins-god.blogspot.com/2011/11/pop-quiz-who-believes-and-promotes.html
3. Randy Moore, Sehoya Cotner, Arguing for Evolution: An Encyclopedia for Understanding Science, p. 2.

The Evolutionist Speaks: Savor the Irony

People sometimes ask me if evolutionists are at all changing their minds given the overwhelming scientific evidence against their religious mandate. The answer of course is “no.” But there are some evolutionists, well one anyway, that at least acknowledges some of the evidence. That would be the one and only Lynn Margulis who illustrates just how far an evolutionist can go, but no further. In her 2011 Discover magazine interview, after stating that “All scientists agree that evolution has occurred,” the University of Massachusetts professor goes on to explain that natural selection “eliminates and maybe maintains, but it doesn’t create,” that she believed the textbook orthodoxy that random mutations lead to evolutionary change and new species “until I looked for evidence,” and that “There is no gradualism in the fossil record.” Kudos to Margulis for acknowledging the evidence. It seems strange to laud someone for stating the obvious, but that’s evolution for you. Margulis also recounts how evolutionists denigrated her for coming too close to the hypothesis of acquired characteristics—another example of how evolution has harmed science.

So why was Margulis an evolutionist? As usual it’s all about religion as Margulis unwittingly explains:

The critics, including the creationist critics, are right about their criticism. It’s just that they’ve got nothing to offer but intelligent design or “God did it.” They have no alternatives that are scientific.

Man has spoken (or woman in this case). Savor the irony. With metaphysical logic the evolutionist criticizes the others for their perceived metaphysics.

But who is the metaphysician, the one who rejects a priori certain answers or the one who follows the evidence wherever it leads?

Evolution always has been, and remains today, a religious theory, even for open-minded evolutionists such as Lynn Margulis.