The “All Outcomes Are Equiprobable” Argument

I Had to Write “Evolution Is True” 500 Times

I’ve been busy lately with a big landscaping job for the neighborhood evolutionist. He wanted a massive set of stones to be carefully arranged in his backyard. He wanted stones of different colors, and the careful arrangement would spell out “Evolution Is True.”

Unfortunately, the day I finished this big job there was an earthquake in the neighborhood which jumbled the stones I had carefully arranged. I had to go back to the evolutionist’s property and put the stones back in order.

To makes matters worse, the evolutionist wouldn’t pay me for the job. When I sued him he told the judge that I was lying. He said I didn’t do the job, but instead the arrangement of the stones was due to the recent earthquake.

I explained to the judge that such an event would be unlikely, but the evolutionist retorted that landscapers don’t understand probability. The evolutionist explained to the judge that all outcomes are equally probable. Every outcome, whether it spells out “Evolution Is True” or nothing at all, have a probability of one divided by the total number of possible arrangements. He said that I was committing a mistake that is common with nonscientific and uneducated people. He explained that if you toss a coin 500 times the sequence of heads and tails will be astronomically unlikely. But it happened. All such sequences, even if they spell out a message in Morse code, are equiprobable.

The judge agreed. He fined me for bringing a frivolous lawsuit against the evolutionist and made me write “Evolution Is True” 500 times.

Finally, the Details of How Proteins Evolve

A Step-By-Step Description

How did proteins evolve? It is a difficult question because, setting aside many other problems, the very starting point—the protein-coding gene—is highly complex. A large number of random mutations would seem to be required before you have a functional protein that helps the organism. Too often such problems are solved with vague accounts of “adaptations” and “selection pressure” doing the job. But this week researchers at the University of Illinois announced ground-breaking research that provides a step-by-step, detailed, description of the evolution of a new protein-coding gene and associated regulatory DNA sequences. The protein in question is a so-called “antifreeze” protein that keeps the blood of Arctic codfish from freezing, and the new research provides the specific sequence of mutations, leading to the new gene. It would be difficult to underestimate the importance of this research. It finally provides scientific details answering the age-old question of how nature’s massive complexity could have arisen. As the paper triumphantly declares, “Here, we report clear evidence and a detailed molecular mechanism for the de novo formation of the northern gadid (codfish) antifreeze glycoprotein (AFGP) gene from a minimal noncoding sequence.” Or as lead researcher, professor Christina Cheng, explained, “This paper explains how the antifreeze protein in the northern codfish evolved.” This is a monumental finding. Having the scientific details, down to the level of specific mutations, of how a new protein-coding gene evolved—not from a related gene but from non-coding DNA—is something evolutionists could only dream of only a few short years ago. There’s only one problem: it is all junk science.

The first problem is that this new “research” is, in actuality, a just-so story:

In science and philosophy, a just-so story is an unverifiable narrative explanation for a cultural practice, a biological trait, or behavior of humans or other animals. The pejorative nature of the expression is an implicit criticism that reminds the hearer of the essentially fictional and unprovable nature of such an explanation. Such tales are common in folklore and mythology.

For example, the antifreeze protein is of relatively low complexity chiefly consisting a repeating sequence of three amino acids (threonine-alanine-alanine), and the evolutionists claim that these repeating sequences “strongly suggest” that the protein-coding gene “evolved from repeated duplications of an ancestral 9-nucleotide threonine-alanine-alanine-coding element.”

Why is that true?

Why does a repeating genetic sequence “strongly suggest” that it “evolved from repeated duplications?” What experiment revealed this truth? What evidence gives us this profound principle? The answer, of course, is that there is none. Nowhere do the evolutionists justify this claim because there is no empirical justification.

There is no scientific evidence for it. Zero.

The paper continues with yet more non-empirical claims. Those nine nucleotides “likely originated within a pair of conserved 27-nucleotide” segments that flank each side of the repetitive region. And these four 27-nucleotide segments are similar to each other, “indicating they resulted from the duplication of an initial copy.” As the paper concludes, “chance duplications” of an ancestral 27-nucleotide segment “produced four tandem copies.”

But why are those claims true? Why do such similarities imply an origin via evolutionary mechanisms? The problem is, they don’t. There is no empirical evidence for any of this. This is completely evidence-free.

The evolutionists next explain that the 9-nucleotide segment duplicated a large number of times because it worked well:

We hypothesize that, upon the onset of selective pressure from cold polar marine conditions, duplications of a 9-nt ancestral element in the midst of the four GCA-rich duplicates occurred.

The above quote is an example of the non-empirical, teleology that pervades evolutionary thought. It was upon the onset of cold conditions that the needed genetic duplications occurred. This is not empirical; this is story-telling.

The paper continues with a series of one-time, contingent events crucial to their story and non-empirical claims. The genetic sequence “was appropriately delimited by an existing in-frame termination codon.”

Appropriately delimited?

The presence of a region in two of the species “indicates that it existed in the gadid ancestor before the emergence of the AFGP.” The absence of a thymine nucleotide at a location in some of the species “very likely resulted from a deletion event,” causing a fortuitous frameshift which supplied the crucial signal peptide segment, telling cellular machinery that the protein should be secreted to the bloodstream. As the paper concludes, “the emerging AFGP gene was thus endowed with the necessary secretory signal.”

Endowed with the necessary signal?

There is no empirical evidence for any of this.

Another problem with this just-so account, is the substantial level of serendipity required. The new antifreeze protein did not arise from some random DNA sequence, but rather from crucial, preexisting segments of DNA that just happened to be lying around. In other words, the fish were facing a colder environment, they needed some antifreeze in their blood, and the pieces needed for such an antifreeze gene were fortuitously available.

The authors hint at this serendipity when they conclude that their story of how this protein evolved is an example of “evolutionary ingenuity.”

Evolutionary ingenuity?

The press release is even more revealing. Cheng admits that the evolution of this gene “occurred as a result of a series of seemingly improbable, serendipitous events.” For “not just any random DNA sequence can produce a viable protein.” Furthermore, in addition to the gene itself, “several other serendipitous events occurred.”

The DNA was “edited in just the right way,” and “somehow, the gene also obtained the proper control sequence that would allow the new gene to be transcribed into RNA.”

Even the evolutionists admit to the rampant serendipity. Nonetheless they are triumphant, for “the findings offer fresh insights into how a cell can invent ‘a new, functional gene from scratch.’”

Fresh insights?

In actuality the findings arose from a series of non-empirical claims.

Religion drives science, and it matters.

Meet Jamie Jensen: What Are They Teaching at Brigham Young University?

Bacterial Resistance to Antibiotics

Rachel Gross’ recent article about evolutionist’s public outreach contains several misconceptions that are, unfortunately, all too common. Perhaps most obvious is the mythological Warfare Thesis that Gross and her evolutionary protagonists heavily rely on. Plumbing the depths of ignorance, Gross writes:

Those who research the topic call this paradigm the “conflict mode” because it pits religion and science against each other, with little room for discussion. And researchers are starting to realize that it does little to illuminate the science of evolution for those who need it most.

“Those who research the topic call this paradigm the ‘conflict mode’”?

Huh?

This is reminiscent of Judge Jones endorsement of Inherit the Wind as a primer for understanding the origins debate, for it is beyond embarrassing. Exactly who are those “who research the topic” to which Gross refers?

Gross is apparently blithely unaware that there are precisely zero such researchers. The “conflict mode” is a long-discarded, failed view of history promoted in Inherit the Wind, a two-dimensional, upside-down rewrite of the 1925 Monkey Trial.

But ever since, evolutionists have latched onto the play, and the mythological history it promotes, in an unabashed display of anti-intellectualism. As Lawrence Principe has explained:

The notion that there exists, and has always existed, a “warfare” or “conflict” between science and religion is so deeply ingrained in public thinking that it usually goes unquestioned. The idea was however largely the creation of two late nineteenth-century authors who confected it for personal and political purposes. Even though no serious historians of science acquiesce in it today, the myth remains powerful, and endlessly repeated, in wider circles

Or as Jeffrey Russell writes:

The reason for promoting both the specific lie about the sphericity of Earth and the general lie that religion and science are in natural and eternal conflict in Western society, is to defend Darwinism. The answer is really only slightly more complicated than that bald statement.

Rachel Gross is, unfortunately, promoting the “general lie” that historians have long since been warning of. Her article is utter nonsense. The worst of junk news.

But it gets worse.

Gross next approvingly quotes Brigham Young University associate professor Jamie Jensen whose goal is to inculcate her students with Epicureanism. “Acceptance is my goal,” says Jensen, referring to her teaching of spontaneous origins in her Biology 101 class at the Mormon institution.

As we have explained many times, this is how evolutionists think. Explaining their anti-scientific, religious beliefs is not enough. You must believe. As Jensen explains:

By the end of Biology 101, they can answer all the questions really well, but they don’t believe a word I say. If they don’t accept it as being real, then they’re not willing to make important decisions based on evolution — like whether or not to vaccinate their child or give them antibiotics.

Whether or not to give their child antibiotics?

As we have discussed many times before, the equating of “evolution” with bacterial resistance to antibiotics is an equivocation and bait-and-switch.

The notion that one must believe in evolution to understand bacterial resistance to antibiotics is beyond absurd.

It not only makes no sense; it masks the monumental empirical contradictions that bacterial antibiotic resistance presents to evolution. As a university life science professor, Jensen is of course well aware of these basic facts of biology.

And she gets paid to teach people’s children?

Religion drives science, and it matters.

Leyden and Teixeira: Political “Civil War” Coming Because of Global Warming

The Politicization of Science

Twitter CEO Jack Dorsey recently tweeted that Peter Leyden’s and Ruy Teixeira’s article, “The Great Lesson of California in America’s New Civil War,” is a “Great read.” The article both urges and forecasts a blue-state takeover of America where our current political divide gives way to a Democrat dominion. This new “Civil War” is to begin this year and, like the last one will have an economic cause. Unfortunately, the thinking of Leyden and Teixeira is steeped in scientific ignorance which drives their thesis.

According to Leyden and Teixeira both the last, and now upcoming, Civil Wars are about fundamentally different economic systems that cannot coexist. In the mid nineteenth century it was an agrarian economy dependent on slaves versus a capitalist manufacturing economy dependent on free labor. Today, the conflict is between (i) the red states which are dependent on carbon-based energy systems like coal and oil, and (ii) the blue states that are shifting to clean energy and weaning themselves off of carbon. Granting this dubious thesis, why are these two economies so irreconcilable? Because of global warming and the terrible natural disasters it brings:

In the era of climate change, with the mounting pressure of increased natural disasters, something must give.

You read that right. Leyden’s and Teixeira’s thesis is driven by anthropogenic global warming, or AGW, which they sprinkle throughout the article. Red states are bad because they deny it, blue states are good because they face the truth and reckon with it with progressive policies. After all, it is “the scientific consensus that climate change is happening, that human activity is the main cause, and that it is a serious threat.”

It must be nice to go through life with such certainty. Ignorance, as they say, is bliss.

We can begin with the most obvious mistake. While it certainly revs people up to hear that global warming is “a serious threat,” we have little evidence for this. Even those “consensus” scientists agree that we are not justified in claiming the sky is falling. And, no, in spite of what you may have heard, the recent hurricanes were probably not products of global warming.

But what about that scientific consensus that Leyden and Teixeira speak of? Doesn’t that make their case?

Unfortunately, Leyden and Teixeira are the latest example of how historians have utterly failed. In spite of their best efforts, historians, and especially historians of science, have not been able to disabuse people of the myths of science.

In science, as in politics, majorities are majorities until they aren’t. A scientific consensus can occur both for theories that end up enshrined in museums and for theories that end up dumped in the trash bin.

Once upon a time the scientific consensus held the Earth was the center of the universe. Only later did the scientific consensus shift to the Sun as the center of the universe.

Both were wrong.

What Mr. Nelson taught you in seventh grade history class was right after all: If you don’t understand history you will repeat its mistakes. And Leyden and Teixeira are today’s poster children of such naiveté.

A scientific consensus for a theory means just one thing: That the majority of scientists accept the theory. Nothing more, nothing less. The problem with science, as Del Ratzsch once explained, is that it is done by people.

What we do know about AGW is that the data have been massaged, predictions have failed, publications have been manipulated, enormous pressure to conform has been applied, and ever since Lynn White’s 1966 AAAS talk the science has been thoroughly politicized.

None of this means that AGW is false, but the theories that end up in textbooks and museums don’t usually need enormous social and career pressures for sustenance.

As it stands scientists have been walking back the hype (it’s climate change, not global warming anymore), and trying to explain the lack of a hockey stick temperature rise (the ocean is temporarily absorbing the heat); insiders are backing out (see here and here), and new papers are showing current temperatures have not been so out of the ordinary (e.g., here).

AGW is certainly an important theory to study. And perhaps it is true. But its track record of prediction is far more important than the number of people voting for it.

The idea that AGW is the driver behind a new Civil War in America to start, err, later this year is simply absurd. I’m less concerned about Leyden’s and Teixeira’s political desires as I am about the mythologies they are built on.

Religion drives science, and it matters.

Brochosome Proteins Encoded By Orphan Genes

A Pattern Problem

A few years ago Paul Nelson debated Joel Velasco on the topic of design and evolution. Nelson masterfully demonstrated design in nature. For his part Velasco also provided an excellent defense of evolution. But the Epicurean claim that the world arose via random chance is not easy to defend, and Velasco’s task would be challenging. Consider, for example, the orphans which Nelson explained are a good example of taxonomically-restricted designs. Such designs make no sense on evolution, and though Velasco responded with many rebuttals, none were very convincing. Since that debate the orphan problem has become worse, as highlighted by a new study of brochosomes.

Background

The term orphan refers to a DNA open reading frame, or ORF, without any known similar sequence in other species or lineages, and hence ORFan or “orphan.” Since orphans are unique to a particular species or lineage, they contradict common ancestry’s much celebrated nested hierarchy model.

The Nelson-Valasco Debate

Velasco addressed the orphan problem with several arguments. First, Velasco reassured the audience that there isn’t much to be concerned with here because “Every other puzzle we’ve ever encountered in the last 150 years has made us even more certain of a fact that we already knew, that we’re all related.”

Second, Velasco argued that the whole orphan problem is contrived, as it is nothing more than a semantic misunderstanding—a confusion of terms. These are nothing more than open reading frames without significant similarity to any known sequence.

Third, Velasco argued that many of the orphans are so categorized merely because the search for similar sequence is done only in “very distantly related” species.

Furthermore, and fourth, Velasco argued that orphans are really nothing more than a gap in our knowledge. For the more we know about a species, the more the orphan problem goes away. And which species do we know the most about? Ourselves of course. And we have no orphans: “Well what about humans, we know a lot about humans. How many orphan genes are in humans? What do you think? Zero.”

In fact, and fifth, Velasco argued that while new orphans are discovered with each new genome that is decoded, the trend is slowing and is suggestive that in the long run relatives for these orphans will be found: “In fact if you trend the absolute number going up, as opposed to the percentage of orphan genes in organisms, that number is going down.”

So to summarize Velasco’s position, the orphan problem will be solved so don’t worry about, but actually orphans are not a problem at all but rather a semantic misunderstanding, but on the other hand the orphan problem is a consequence of incomplete genomic data, but actually on the other hand the problem is a consequence of insufficient knowledge about the species, and in any case even though the number of known orphans keeps on rising, they will eventually go away because the orphans, as a percentage of the overall genomic data (which has been exploding exponentially) is going down.

This string of evolution arguments reminds us of the classic dog-owner’s defense: He’s not my dog, he didn’t bite you, and besides you hit the dog first anyway. Not surprisingly, each of Velasco’s arguments fails, as I explained here.

In fact, there are many orphans, and while function can be difficult to identify, it has been found for many orphans. As science writer Helen Pilcher explained:

In corals, jellyfish and polyps, orphan genes guide the development of explosive stinging cells, sophisticated structures that launch toxin-filled capsules to stun prey. In the freshwater polyp Hydra, orphans guide the development of feeding tentacles around the organism’s mouth. And the polar cod’s orphan antifreeze gene enables it to survive life in the icy Arctic.

Up to a third of genomes have been found have been found to be unique, as this review explains:

Comparative genome analyses indicate that every taxonomic group so far studied contains 10–20% of genes that lack recognizable homologs in other species. Do such ‘orphan’ or ‘taxonomically-restricted’ genes comprise spurious, non-functional ORFs, or does their presence reflect important evolutionary processes? Recent studies in basal metazoans such as Nematostella, Acropora and Hydra have shed light on the function of these genes, and now indicate that they are involved in important species-specific adaptive processes. 

And this is yet another failed prediction of evolution, as this paper explains:

The frequency of de novo creation of proteins has been debated. Early it was assumed that de novo creation should be extremely rare and that the vast majority of all protein coding genes were created in early history of life. However, the early genomics era lead to the insight that protein coding genes do appear to be lineage-specific. Today, with thousands of completely sequenced genomes, this impression remains.

Why then was Velasco so confident and almost nonchalant in his argumentation? Why was he so assured that, one way or another, the orphan problem was not a problem? And why did he believe there are zero orphans in humans, and so it merely is a matter of studying biology, and the orphans will go away?

Lander Orphan Study

It could be due to a significant 2007 study from Eric Lander’s group which rejected most of the large number (several thousands) of orphans that had been tentatively identified in the human genome. The study confidently concluded that “the vast majority” of the orphans were “spurious”:

The analysis here addresses an important challenge in genomics— determining whether an ORF truly encodes a protein. We show that the vast majority of ORFs without cross-species counterparts [i.e., orphans] are simply random occurrences. The exceptions appear to represent a sufficiently small fraction that the best course is would be [sic] consider such ORFs as noncoding in the absence of direct experimental evidence.

The authors went on to propose that “it is time to undertake a thorough revision of the
human gene catalogs by applying this principle to filter the entries.”

That peer-reviewed paper, in a leading journal, was well received (e.g., Larry Moran called it an “excellent study”) and it certainly appeared to be authoritative. So it is not surprising that Velasco would be confident about orphans. For all appearances, they really were no problem for evolution.

There was just one problem. This was all wrong.

There was no scientific evidence that those human sequences, identified as orphans, were “spurious.” The methods used in the Lander study were full of evolutionary assumptions. The results entirely hinged on evolution. Although the paper did not explicitly state this, without the assumption of evolution no such conclusions could have been made.

This is what philosophers refer to as theory-ladenness. Although the paper authoritatively concluded the vast majority of the orphans in the human genome were spurious, this was not an empirical observation or inference, as it might seem to some readers. Their data (and proposed revisions to human gene catalogs), methods, and conclusions were all laden, at their foundation, with the theory of evolution.

So Velasco’s argument was circular. To defend evolution he claimed there were zero orphans in the human genome, but that “fact” was a consequence of assuming evolution is true in the first place. If the assumption of evolution is dropped, then there is no evidence for that conclusion.

Brochosomes

Since the Nelson-Velasco debate the orphan problem has just gotten worse. Consider, for example, brochosomes which are intricate, symmetric, secretory granules forming super-oily coatings on the integuments of leafhoppers. Brochosomes develop in glandular segments of the leafhopper’s Malpighian tubules.

The main component of brochosomes, as shown in a recent paper, is proteins. And these constituent proteins, as well as brochosome-associated proteins, are mostly encoded by orphan genes.

As the paper explains, most of these proteins “appear to be restricted to the superfamily Membracoidea, adding to the growing list of cases where taxonomically restricted genes, also called orphans, encode important taxon-specific traits.”

And how did all these orphan genes arise so rapidly? The paper hypothesizes that “It is possible that secreta exported from the organism may evolve especially rapidly because they are not strongly constrained by interactions with other traits.”

That evolutionists can so easily reach for just-so stories, such as this, is yet another example of how false predictions have no consequence for evolutionary theory. Ever since Darwin evolutionists have proclaimed how important it is that the species fall into the common descent pattern. This has especially been celebrated at the molecular level.

But of course the species fall into no such pattern, and when obvious examples present themselves, such as the brochosome proteins, evolutionists do not miss a step.

There is no empirical content to this theory. Predictions hailed as great successes and confirmations of the truth of evolution suddenly mean nothing and have no consequence when the falsification becomes unavoidable.

Religion drives science, and it matters.

h/t: El Hombre

Warren Allmon on the Argument from Homology

An Enormous Concession

I once debated two evolutionists on the campus of Cornell University. In that debate I raised several fundamental problems with evolutionary theory. The problems that I pointed out fell into two broad categories: process and pattern. In the latter category, I pointed out that the keystone argument for evolution from homology had badly failed. Unfortunately, that failure was waved off and went unaddressed by the evolution professors. That may not have been the case had Warren Allmon been able to participate. Allmon, Director of the Cornell University-affiliated Paleontological Research Institution (PRI), has thought more deeply about the homology argument than most evolutionists. Now in 2018, he has published, along with adjunct professor Robert Ross, a new paper containing a very important concession.

As is typical, the new Allmon/Ross paper makes several serious scientific errors, either through ignorance, denial, confirmation bias, or whatever. The paper also relies heavily religious claims and arguments, which again is typical.

I have covered this religiously-driven phony science here many times. And in future posts I will address the specifics in the Allmon/Ross paper.

But most importantly, the paper does accomplish something new. The paper takes several turns, but in the end Allmon and Ross do recognize, at least somewhat, the presence of religion in evolutionary thought. To remedy this, they downsize the argument from homology.

In its canonical form, this keystone argument proves evolution by the process of elimination. That is, it refutes design and independent creation, leaving naturalistic evolution, in one form or another, as the only solution. God wouldn’t have created these lousy designs, according to evolutionists, so the designs must have arisen naturalistically. As usual, it is the religion that provides the certainty.

This isn’t science.

Rather than deny this obvious fact (see here for examples of such denial), Allmon and Ross ultimately admit to it (after appealing to it repeatedly), and seek to reformulate the argument from homology without the religion. They do this as follows.

Rather than claiming God would not have created non optimal homologies (such as vestigial structures), Allmon and Ross walk back the claim to say merely that God did not have to create such homologies. Under independent, divine, creation, God could have done it differently. Allmon and Ross then contrast this with descent with modification which, they say, necessarily would have resulted in such homologies.

So you have Theory A (design) which can accommodate Observation X or ~X (not X). And you have Theory B (evolution) which requires Observation X, and cannot accommodate ~X. Our observation of X, therefore, makes Theory B more probable.

Readers here will know there are enormous problems with this argument. It fails badly, right out of the gate. And I will discuss these failures in the future. But before we get to that, it is important to understand the implications of the argument, even without its problems.

In their attempt to save the theory, what Allmon and Ross have done is to provide an enormous concession. What traditionally has been an iron-clad, unquestionable, textbook proof of evolution, now becomes a minor Bayesian term, slightly improving the probability of evolution.

This is a monumental concession, neutering the keystone argument for evolution. Why should anyone believe in the heroic claim that the biological world arose by itself if the strongest argument merely increases its probability by some unspecified amount?

Blindness in Cave Fish is Due to Epigenetics

Evolutionists Say “We See”

A recent paper out of Brant Weinstein’s and William Jeffery’s laboratories on eye development, or the lack thereof, in blind cave fish has important implications for evolutionary theory (paper discussed here). The study finds that the loss of eyes in fish living in dark Mexican caves is not due to genetic mutations, as evolutionists have vigorously argued for many years, but due to genetic regulation. Specifically, methylation of key development genes represses their expression and with it eye development in this venerable icon of evolution. But the finding is causing yet more problems for evolutionary theory.

Darwin appealed to the blind cave fish in his one long argument for evolution. It is a curious argument in many ways, and the first sign of problems was in Darwin’s presentation where he flipped between two different explanations. At one point he explained the loss of vision in the cave fish as an example of evolutionary change not due to his key mechanism, natural selection. Instead, the Sage of Kent resorted to using the Lamarckian mechanism or law of “use and disuse.” Privately Darwin despised and harshly criticized Lamarck, but when needed he occasionally employed his French forerunner’s ideas.

Elsewhere Darwin hit upon a natural selection-based mechanism for the blind cave fish, explaining that elimination of the costly and unneeded vision system would surely raise the fitness of the hapless creatures.

This latter explanation would become a staple amongst latter day evolutionary apologists, convinced that it mandates the fact of evolution. Anyone who has discussed or debated evolutionary theory with today’s Epicureans has likely encountered this curious argument that because blind cave fish lost their eyes, therefore the world must have arisen by itself.

Huh?

To understand the evolutionary logic, or lack thereof, one must understand the history of ideas, and in particular the idea of fixity, or immutability, of species. According to evolutionists, species are either absolutely fixed in their designs, or otherwise there are no limits to their evolutionary changes and the biological world, and everything else for that matter, spontaneously originated.

Any evidence, for any kind of change, no matter how minor, is immediately yet another proof text for evolution, in all that the word implies.

Of course, from a scientific perspective, the evidence provides precisely zero evidence for evolution. Evolution requires the spontaneous (i.e., by natural processes without external input) creation of an unending parade of profound designs. The cave fish evidence shows the removal, not creation, of such a design.

The celebration of such evidence and argument by Darwin and his disciples reveals more about evolutionists than evolution. That they would find this argument persuasive reveals their underlying metaphysics and the heavy lifting it performs. It is all about religion.

We are reminded of all this with the news of Weinstein’s new study. But we also see something new: The insertion, yet again, of Lamarck into the story. The irony is that the epigenetics, now revealed as the cause of repressed eye development in the cave fish, hearkens back to Lamarck.

Darwin despised Lamarck and later evolutionists made him the third rail in biology. Likewise they have pushed back hard against the scientific findings of epigenetics and their implications.

The environment must not drive biological change.

False.

Well such biological change must not be transgenerational.

False.

Well such inheritance must not be long lasting, or otherwise robust.

False again.

This last failure is revealed yet again in the new blind cave fish findings.

False predictions count. A theory that is repeatedly wrong, over and over, in all of its fundamental expectations, will eventually be seen for what it is.

The rise of epigenetics is yet another such major failure. Evolutionists pushed back against it because it makes no sense on the theory, and that means it cannot now be easily accommodated.

One problem is that epigenetics is complex. The levels of coordination and intricacy of mechanism are far beyond evolution’s meager resources.

It’s not going to happen.

Another problem is the implied serendipity. For instance, one epigenetic mechanism involves the molecular tags places on the tails of the DNA packing proteins called histones. While barcoding often seems to be an apt metaphor for epigenetics, the tagging of histone tails can influence the histone three dimensional structures. It is not merely an information-bearing barcode. Like the tiny rudder causing the huge ship to change course, the tiny molecular tag can cause the much larger packing proteins to undergo conformational change, resulting in important changes in gene accessibility and expression.

This is all possible because of the special, peculiar, structure and properties of the histone protein and its interaction with DNA. With evolution we must believe this just happened to evolve for no reason, and thus fortuitously enabled the rise of epigenetics.

Another problem with epigenetics is that it is worthless, in evolutionary terms that is. The various mechanisms that sense environmental shifts and challenges, attach or remove one of the many different molecular tags to one of the many different DNA or histone locations, propagate these messages across generations, and so forth, do not produce the much needed fitness gain upon which natural selection operates.

The incredible epigenetics mechanisms are helpful only at some yet to be announced future epoch when the associated environmental challenge presents itself. In the meantime, selection is powerless and according to evolution the incredible system of epigenetics, that somehow just happened to arise from a long, long series or random mutations, would wither away with evolution none the wiser.

These are the general problems with epigenetics. In the case of the blind cave fish, however, there is possible explanation. It is a longshot, but since this case specifically involves the loss of a stage of the embryonic development, evolutionists can say that genetic mutations caused changes in the methylating proteins, causing them to be overactive.

This explanation relies on the preexistence of the various epigenetic mechanisms, so does not help to resolve the question of how they could have evolved. What the explanation does provide is a way for evolutionists to dodge the bullet presented by the specter of the cave fish intelligently responding to an environmental shift.

Such teleology in the natural world is not allowed.

So the evolutionary prediction is that these proteins will be found to have particular random changes causing an increase in their methylation function, in particular at key locations in key genes (i.e., the genes associated eye development).

That’s a long shot, and an incredible violation of Occam’s Razor.

My predictions are that (i) this evolutionary prediction will fail just as the hundreds that came before, and (ii) as with those earlier failures, this failure will do nothing to open the evolutionist’s eyes.

Religion drives science, and it matters.

The Philosophy of Naturalism

Why Evolution is Confirmed

Last time we saw that by wholeheartedly embracing and promoting Theodosius Dobzhansky’s famous phrase, “Nothing in Biology Makes Sense Except in the Light of Evolution,” evolutionists have backed themselves into a corner from which they cannot escape. As we saw, there is much to say about this evolutionary rallying cry, but at the top of the list is that it is false. Unequivocally false. This is not an opinion or a pushback. I’m not trying to pick a debate—because there is no debate. We may as well debate whether bachelors are male. Dobzhansky’s phrase, with all due respect, is “not even wrong,” as physicists like to say. It is silly, and yet there it is—all over the literature. The phrase is approvingly recited even in peer-reviewed technical journal papers. It is the mantra that evolutionists will not stop repeating, all the while revealing that this isn’t about science. Evolutionists will never repeal and recant, because there simply is too much at stake here. As we discussed, this isn’t like admitting that a particular prediction went wrong. Dobzhansky’s phrase was not merely a prediction, it was meta-prediction—the aphorism of an entire world view—and walking it back would be to reveal the man behind the curtain. Suddenly all those epistemological claims, such as that evolution is as much a fact as is gravity, heliocentrism and the round shape of the earth, would be left hanging, open to scrutiny and with a long, long way to fall. But Dobzhansky’s famous phrase is not the only way evolutionists have self-destructed. They have made other nonnegotiable and important claims that are equally corrosive. One is that evolution is both confirmed and required.

The National Association of Biology Teachers’ official position statement on the teaching of evolution states that evolution is (i) confirmed by the scientific evidence and (ii) a necessary going in position in order for science to function properly. Here is what the NABT says about the confirmation of evolution:

Scientists who have carefully evaluated the evidence overwhelmingly support the conclusion that both the principle of evolution itself and its mechanisms best explain what has caused the variety of organisms alive now and in the past. … The patterns of similarity and diversity in extant and fossil organisms, combined with evidence and explanations provided by molecular biology, developmental biology, systematics, and geology provide extensive examples of and powerful support for evolution.

And here is what the NABT says about the necessity of evolution:

Evolutionary biology rests on the same scientific methodologies the rest of science uses, appealing only to natural events and processes to describe and explain phenomena in the natural world. Science teachers must reject calls to account for the diversity of life or describe the mechanisms of evolution by invoking non-naturalistic or supernatural notions … Ideas such as these are outside the scope of science and should not be presented as part of the science curriculum. These notions do not adhere to the shared scientific standards of evidence gathering and interpretation.

There you have it, evolutionary theory is both confirmed and required. And the National Association of Biology Teachers is by no means alone here. The dual epistemological and philosophical claims, respectively, are broadly held by evolutionists and go back centuries.

Do you see the problem?

This philosophical position that evolutionists have staked themselves to is circular. To understand this, imagine for a moment that you witness a miracle, involving “non-naturalistic or supernatural” causes. According to evolutionists, such an event is “outside the scope of science.”

Does that imply the event was necessarily not real?

No, the fact that something falls outside of one’s definition of science does not rule it out of existence. The event does not automatically become necessarily impossible. Something can be not amenable to scientific investigation yet real.

The standard claim of evolutionists that evolution is necessary for proper science reflects a particular philosophy of science called naturalism. They present it as though it were a fact, but that is false. There are many philosophies of science, and none are facts. They are rules of the road for those who declare them to follow.

That’s it.

So evolutionists have committed themselves to yet another false statement. But that’s not the main problem. The main problem is that if one insists and is committed to naturalism, then naturalistic, evolutionary, explanations is what they will find.

So of course evolution is confirmed by the science. It has to be. For evolutionists, the question is not whether evolution is confirmed by the science, the only question is what are the particulars.

This explains why evolutionists interpret the evidence the way they do. It explains how contradictory evidence can be sustained over and over and over. It also explains why, so long as you stick to naturalism, anything and everything is allowed. Natural selection, gradualism, mutations, common descent, drift, saltationism, and all the rest are up for grabs. They all may be forfeited. Any kind of theory, not matter how at odds with the empirical data, can be contemplated.

What cannot be contemplated in evolutionary science is creationism. There must be no miracles.

This means that evidence will be interpreted, filtered, analyzed, and processed according to the rules. Non cooperative evidence will be set aside and viewed as “grounds for further research.” Or it will be ground up and recast until it can be made to work right.

Cooperative evidence, on the other hand, will be viewed a normative, and ready for incorporation into proper scientific theories.

When evolutionists insist that science must be strictly naturalistic they show their hand. The flip side of their claim, that evolution is confirmed, is not a theory-neutral, objective finding. It is driven by the philosophy. It is circular—the conclusion was assumed in the first place. If your going-in position is that naturalism is required, then your results will adhere to naturalism.

Evolution is not a scientific finding, it is a philosophical mandate.

Religion drives science, and it matters.

Controversy Over the P-value Value

Rearranging Deck Chairs on the Titanic

There is much to agree with in Steven Novella’s article from this past week on the P-value. The latest news regarding the beleaguered statistical parameter used in hypothesis testing is the call to reduce its associated threshold for statistical significance by an order of magnitude from its venerable value of 0.05 to 0.005. This is a modest proposal compared the outright banning the use of P-values in recent years. But in any case, while a move to 0.005 would likely help to reduce problems, what is more desperately needed is the underlying training and peer review to ensure proper statistical testing, period, regardless of the value selected threshold for the P-value. This is because the problems discussed by Novella are dwarfed by hypothesis testing fallacies, such as false dichotomies, that routinely appear in the literature. Those problems, unfortunately, are routinely ignored.

New Study: Transgenerational Epigenetics Can Have a Profound Impact

The Third Rail of Evolution

In the spring of 2006 I gave a talk on the campus of Cornell University and afterwards was joined by then Cornell professors Richard Harrison and Kern Reeve for a sort of panel discussion or debate about biological evidences and origins. I presented a dozen or so interesting and important evidences that I felt needed to be recognized in any discussion of origins. The evidences falsified key predictions of evolution and so needed to be acknowledged and reckoned with, one way or another. One of the items on my list was the so-called directed adaptation mechanisms which, broadly construed, can include everything from non random, directed, mutations to transgenerational epigenetic inheritance. But I was in for a big surprise when Harrison and Reeve gave their response.

Directed adaptation is reminiscent of Lamarckism. Rather than natural selection acting over long time periods on biological variation which is random with respect to need, directed adaptation mechanisms provide rapid biological change in response to environmental challenges. Like physiological responses, directed adaptation can help an organism adjust to shifts in the environment. But those adaptations can then be inherited by later generations. Stresses which your grandparents were subjected to may be playing out in your own cells.

In the twentieth century evolutionists had strongly rejected any such capability. Lamarckism was the third rail in evolutionary circles. And for good reason, for it would falsify evolutionary theory. But empirical evidence had long since pointed toward the unthinkable, and by the twenty first century the evidence was rapidly mounting.

While there was of course still much to learn in 2006 about directed adaptation (as there still is today for that matter), it could no longer be denied, and needed to be addressed. At least, that is what I thought.

I was shocked when Harrison and Reeve flatly denied the whole story. Rick waved it off as nothing more than some overblown and essentially discredited work done by Barry Hall and John Cairns, back in the 1970s and 80s (for example here).

But there was a body of work that had gone far beyond the work of Hall and Cairns. Incredulously I responded that entire books had been written on the subject. Rick was quick to respond that “entire books are written about all kinds of discredited things.”

True enough. It was me versus two professors on their home turf with a sympathetic audience, and there was no way that I was going to disabuse them of what they were convinced of.

Confirmation testing and theory-laden evidence are not merely philosophical notions. They are very real problems. I’m reminded of all this every time a new study adds yet more confirmation to the directed adaptation story, such as the recent paper out of Nicola Iovino’s lab on transgenerational epigenetic inheritance in house flies, which states:

Gametes carry parental genetic material to the next generation. Stress-induced epigenetic changes in the germ line can be inherited and can have a profound impact on offspring development.

The press release gives little indication of the controversy as it admits that these findings were once considered impossible:

It has long been thought that these epigenetic modifications never cross the border of generations. Scientists assumed that epigenetic memory accumulated throughout life is entirely cleared during the development of sperms and egg cells.

It is hard enough to see how organisms can respond intra-lifetime to environmental challenges, but how can it be inherited as well? For epigenetic changes that occur in somatic cells, that information must also enter into the germ line as well. Somehow it must be incorporated into the sperm and/or egg cells.

It is an enormous problem to explain how such capabilities evolved. Not only are a large number of mutations required to make this capability work, it would not be selected for until the particular environmental condition occurred. That means that, under evolution, it would be not preserved, even if it could somehow arise by chance.

New Paper From Gareth Fraser’s Group Confirms Common Ancestry

If P Implies Q, Then Q Implies P, Right?

A new paper out of Gareth Fraser’s laboratory explains that vertebrate epithelial appendages, such as feathers, hair, scales, and teeth, “have evolved to facilitate wide-ranging aspects of survival and reproduction.” Readers will note the infinitive form (“to facilitate”), which reveals the usual Aristotelianism / teleology under-girding evolutionary thought, but how do the evolutionists know that these structures “have evolved” in the first place? A hint comes in the next paragraph, which informs us that:

Recent research has revealed shared ancestry among amniote epithelial appendages, based on the observation that reptilian scales, avian feathers and mammalian hair share a common foundation during early development: the anatomical placode.

This is a good example of what passes as confirmation of common ancestry for evolutionists. These various vertebrate epithelial appendages “share a common foundation during early development,” so therefore they share a common ancestor.

Simply put, similarity proves evolution.

This, of course, is false. Similarity does not prove evolution. This is the age-old fallacy of affirming the consequent. If P implies Q, then Q implies P, right?

Wrong.

Nor is this example of fallacious reasoning a rare exception to otherwise air-tight, rigorous, thinking on the part of evolutionists.

Such fallacious reasoning is ubiquitous in evolutionary thought. It is everywhere. Not only does this example blatant fallacy appear right up front in peer-reviewed paper in a leading evolutionary journal, like a nasty virus it is literally rampant throughout the evolutionary literature.

Indeed, this example cites a 2016 paper with the same fallacy appearing in the very title:

Di-Poï N, Milinkovitch MC. The anatomical placode in reptile scale morphogenesis indicates shared ancestry among skin appendages in amniotes. Sci Adv. 2016;2:1–8.

Science, if anything, is logical. Philosophers never thought to deploy logic as a demarcation criterion because, frankly, they never in their wildest imagination could believe that people would seriously set forth fallacious reasoning, with a straight face, as legitimate science.

Think again.

New Book: New Proteins Evolve Very Easily

No Free Lunch

We have seen that a new evolution book co-authored by evolutionist Dennis Venema and Scot McKnight is influenced by the mythical Warfare Thesis (here and here) and makes erroneous arguments that the fossils, echolocation, and pseudogenes support evolution (here,  here and here). We now move on to another topic: protein evolution. Proteins are composed of a linear string of amino acids, often hundreds in length, and perform all sorts of important tasks in the cell. They could not have evolved by any stretch of the imagination, and so pose a rather difficult problem for evolutionists. Our new book on evolution attempts to resolve this problem with a claim that has long since been understood to be false. In fact, the claim, properly understood, provides yet more scientific evidence against evolution.

The problem of protein evolution

For evolution to work biology must be chocked full of structures that can arise via long, gradual evolutionary pathways. Mutations must be able to slowly accumulate, gradually improving the structure. In other words, the “fitness landscape” must be smooth and gradual, not rugged or precipitous.

That evolutionary expectation has been found to be false many times, and proteins are no exception. It is now clear that for a given protein, only a few changes to its amino acid sequence can be sustained before the protein function is all but eliminated. Here is how one paper explained it:

The accepted paradigm that proteins can tolerate nearly any amino acid substitution has been replaced by the view that the deleterious effects of mutations, and especially their tendency to undermine the thermodynamic and kinetic stability of protein, is a major constraint on protein evolvability—the ability of proteins to acquire changes in sequence and function.

In other words, protein function precipitously drops off with only a tiny fraction of its amino acids altered. It is not a gradual fitness landscape. Another paper described the protein fitness landscape as rugged.

Therefore it is not surprising that various studies on evolving proteins have failed to show a viable mechanism. One study concluded that 10^63 attempts would be required to evolve a relatively short protein. And a similar result (10^65 attempts required) was obtained by comparing protein sequences. Another study found that 10^64 to 10^77 attempts are required, and another study concluded that 10^70 attempts would be required.

So something like 10^70 attempts are required yet evolutionists estimate that only 10^43 attempts are possible. In other words, there is a shortfall of 27 orders of magnitude.

But it gets worse. The estimate that 10^43 attempts are possible is utterly unrealistic. For it assumes billions of years are available, and that for that entire time the Earth is covered with bacteria, constantly churning out mutations and new protein experiments. Aside from the fact that these assumptions are entirely unrealistic, the estimate also suffers from the rather inconvenient fact that those bacteria are, err, full of proteins. In other word, for evolution to evolve proteins, they must already exist in the first place.

This is absurd. And yet, even with these overly optimistic assumptions, evolution falls short by 27 orders of magnitude.

The numbers don’t add up. Proteins reveal scientific problems for evolution. What is interesting is how evolutionists react to these problems.

The “solution” to protein evolution

A common solution cited by evolutionists for the problem of protein evolution is the case of nylonases—enzymes that rapidly arose in bacteria, in the last century, and are able to breakdown byproducts of the nylon manufacturing process. The idea here is that these byproducts of the nylon manufacturing process were present in the bacteria’s environment for the first time. The bacteria had never been exposed to such chemicals, and yet in an evolutionary blink of an eye, were able to produce proteins to metabolize the new chemicals. Does this not demonstrate that the chance origin of a protein-coding genes is not a problem? Proteins could have evolved with no problem, after all, we just witnessed it occur with the origin of nylonases. As the new book explains, protein evolution “appears to be trivial for evolution to achieve.” [86]

Unfortunately this icon of evolution is an enormous misrepresentation of the science.

The science

The evolutionary claim that the nylonases demonstrate how easy protein evolution is non scientific for several reasons. Indicators of this include that fact that the nylonases evolved so rapidly—in an entirely unrealistic time frame under evolution, and that they arose in bacteria with thousands of preexisting proteins. Again, this evolutionary claim of how proteins evolve is circular, it requires the preexistence of proteins.

None of this is feasible given the problems of protein evolution discussed above. The scientific inference would be that the bacteria developed the nylonases because those chemicals they metabolize were present in the environment. In other words, directed adaptation.

Indeed, this is precisely what researchers in the field have concluded. They hypothesize that the new metabolism capability is a stress response, an adaptation to a challenging environment. In other words, the environment influenced the adaptation. This is not a case of evolutionary change. The nylonase enzymes did not arise from a random search over sequence space until the right enzymes were luckily found and could be selected for. That would have required eons of time, and is far beyond evolution’s capability, as we have seen. Instead, cellular structures rapidly formed new enzymes, due to the environmental change.

Indeed, such adaptation to nylon manufacture byproducts has been repeated in laboratory experiments. In a matter of months bacteria acquire the ability to digest the unforeseen chemical. Researchers speculate that mechanisms responding to environmental stress are involved in inducing adaptive mutations.

This does not demonstrate protein evolution. In fact it refutes evolution. Evolution does not have the resources to have created directed adaptation mechanisms. And even if it did, such mechanisms would not have been selected for because they provide no immediate fitness improvement.

This is not evidence that protein-coding genes can evolve by chance. A new gene, arising within a modern cell responding to an environmental challenge, is not analogous to chance origin. Unfortunately evolutionists have a long history of inappropriately claiming otherwise (for example, see here and here).

We have seen that this new evolution book makes erroneous arguments that the fossils, echolocation, and pseudogenes support evolution. We now see another erroneous argument for protein evolution.

All these arguments and evidences are typical. They are icons of evolution, and it is astonishing how durable they are in the evolution literature given their complete failure.

If evolution was indicated by the science I would be the first to sign up. But in fact it is an age-old religious idea that makes no sense on the science. And likewise this new book is an utter disaster. The confection immediately crumbles under even a little probing.

Religion drives science, and it matters.

New Book: Olfactory Receptor Genes Prove Common Descent

The “Shared Error” Argument

We have seen that a new evolution book co-authored by evolutionist Dennis Venema and Scot McKnight is influenced by the mythical Warfare Thesis (here and here) and makes erroneous arguments that the fossils and echolocation support evolution (here and here). We now move on to another topic: broken genes, or pseudogenes. This is a popular argument amongst evolutionists and Venema uses as his example the olfactory receptor genes. The idea here is that, in different species (such as the human and chimpanzee), the same damaging mutation can be found in the same pseudogenes. When we find the same strange spelling mistake in the homework of different students we conclude that plagiarism occurred. It is more likely that the mistake had one source, rather than occurred twice, independently. Likewise, the same mutation in different species points to a single source in a common ancestor—common descent. Furthermore, we don’t see mutations that violate the expected pattern. Clearly common descent is the obvious, most parsimonious explanation. As Venema concludes, common descent is “overwhelmingly supported.” [36] This is a powerful argument for evolution that has influenced many people. There’s only one problem: It fails historically, philosophically, and scientifically.

First, the olfactory system is profoundly complex. Odors entering the nose interact with finely-tuned receptor proteins (created from the olfactory receptor genes), setting off an incredible cascade of events in the cell, resulting in an electrical signal sent to the brain. Studies have found that each cell expresses only a single olfactory receptor gene, and so is sensitive to a particular odor. At the brain, the signals are grouped and organized by odor. In other words, for all the cells in the nose expressing the same olfactory receptor gene (and thus sensitive to the same odor), their signals spatially converge as they feed into the brain area.

And of course, as with all the senses, These incoming signals are providing mere electrical information. There is no odor, or light, or sound entering the brain via these nerve cells. Instead, a bunch of electrical signals are entering the brain via these nerve cells. The brain, by itself, has no way of knowing what these electrical signals mean. It must somehow be given the source and meaning of these incoming signals. It then processes and interprets these signals and the end result is that we are conscious of images reported by our eyes, sounds reported by our ears, smells reported by our nose, and so forth. All of this defies evolution, and should give us pause.

Second, the evolutionist’s contention that common descent is needed to explain those shared mutations in different species contradicts the most basic biology. Simply put, similarities across species which cannot be explained by common descent, are rampant in biology. The olfactory system is no exception. Its several fundamental components, if evolution is true, must have evolved several times independently. The level of independent origin which evolutionists must admit to (variously referred to as convergent evolution, parallel evolution, recurrent evolution, cascades of convergence, and so forth depending on the pattern) is staggering and dwarfs the levels of similarities in the olfactory receptor genes. To cast those relatively few similarities as mandates for common descent, while ignoring the volumes of similarities that violate common descent constitutes the mother of all confirmation biases.

Third, the strength of this evolution argument is lack of function, but that renders it fallacious. As lawyers know, if you can’t convict the defendant on the facts, you decry how horrifying the crime is. In this case, the entire argument hinges on the utter uselessness of the broken genes. As Venema explains, they are “damaged,” “defective,” “mess[ed] up,” “wrong,” and “ruin[ed].” Clearly, according to Venema, these genes are useless—that’s why they are called pseudogenes. This is crucial because, for evolutionists, this means they would only arise by chance (what designer would implement useless designs?).

All of this means that evolutionists have a very simple formulation: Either those crippling mutations arose once in a common ancestor, or they just happened to arise by chance, coincidentally, multiple times. Clearly the former is much more likely, and this points to common descent. It is, as Venema concludes, “overwhelmingly supported.” [36]

But this powerful argument comes at a cost. There is no free lunch.

The conclusion that common descent is “overwhelmingly supported” utterly depends on our knowing the pseudogenes are useless. Disutility underwrites the assumption of chance as the only alternative to common descent. And chance as the only alternative is crucial. It is why the argument is so powerful, because the chance hypothesis is so unlikely.

Restricting the problem to a contest between evolution and chance makes evolution the obvious winner, but amidst the celebration we forget the weak link. We forget that the entire edifice resides on our certainty of disutility. This, it turns out, is a very weak link.

The history of evolutionary thought, going back to the Epicureans, is full of predictions of disutility gone wrong. It is, quite literally, a theory of gaps. When gaps in our scientific knowledge leave us with ignorance about function, evolutionists routinely assume there is no function. After all, if the world arose by chance, it should be a claptrap, full of aimless, useless designs, if they could even be called that.

But as those gaps close with the inexorable march of scientific progress, it seems we inevitably learn of function. Evolutionists are consistently claiming disutility at brand new findings, only to be proved wrong, again and again. Look no further than the seemingly endless parade of “We thought it was junk, but now …” stories.

Ultimately, the long history of disutility claims are informed by the theory rather than the evidence. This is a classic example of what philosophers refer to as theory-laden observations.

None of this means there are no truly useless structures in biology. There may well be plenty of them. But it has a terrible history.

Furthermore, regardless of the history, disutility is very difficult to know. As with the proverbial “proving a negative,” proving that a pseudogene, or anything else in biology for that matter, actually is useless, is a very difficult undertaking.

From introns to transposons, initial claims of uselessness have given way to a steady stream of findings of function. And, yes, the olfactory receptor “pseudo” genes are no exception. They are now being called pseudo-pseudogenes because all those evolutionary claims of uselessness are rapidly fading. As one recent paper concluded, “such ‘pseudo-pseudogenes’ could represent a widespread phenomenon.”

This is yet another example in a long history of failed disutility predictions. Clearly, the assumption that we know that olfactory receptor pseudogenes are useless is unfounded. Even the name (pseudogenes) will serve future generations of scientists as a constant reminder of this evolutionary foible. Venema’s powerful argument was demolished before the book was even published.

The story does not end here for even if something like pseudogenes could somehow be proven useless, this would not justify the evolutionary formulation of random chance origin as the only other alternative.

Evolution fails to explain how even a single gene could evolve, let alone the entire olfactory system. In fact the presence of supposedly useless structures, such as pseudogenes, is hardly a plus for evolution. As Elliott Sober has pointed out, there is nothing about this story that provides a positivistic argument for evolution.

The argument, and all its strength, hinges entirely on the refutation of the alternative. This is a proof by the process of elimination. Hence it becomes utterly crucial that the alternatives are carefully and exhaustively considered. In particular, all possible alternatives must be known, understood, evaluated, and disproved.

Do you see a pattern here?

This powerful evolutionary argument not only crucially depends on knowing that the pseudogenes are useless, it also crucially depends on knowing that a simple random chance model is the only alternative to evolution, for their origin.

Not only is this philosophically problematic (how do we know that the random chance model is the only alternative?), historically it has a terrible track record. As Kyle Stanford has shown, the history of science is full of theories that were advocated with this type of contrastive reasoning (by disproving a perceived alternative), only later to fail because the assumed alternative was wrong.

To summarize, this highly influential, popular, argument from similar structures that appear to be useless, lies in ruins. It is a disaster. It fails historically, philosophically, and scientifically. It should never have been used in the first place, for its scientific failure was entirely predictable from both the history and philosophy of science.

“When Facts Fail”: Oh The Irony

Fossils and DNA

Because when an evolutionist, such as Michael Shermer in this case, warns readers that people don’t change their minds even when presented with the facts, the irony should be savored:

Have you ever noticed that when you present people with facts that are contrary to their deepest held beliefs they always change their minds? Me neither. In fact, people seem to double down on their beliefs in the teeth of overwhelming evidence against them. The reason is related to the worldview perceived to be under threat by the conflicting data.

Yes, there certainly are conflicting data.

It gets worse:

Creationists, for example, dispute the evidence for evolution in fossils and DNA because they are concerned about secular forces encroaching on religious faith.

Evidence for evolution in DNA? What exactly would that be? Ultra conserved elements, orphans, replication, duplication, the universal DNA code, protein synthesis, protein coding genes, genetic regulation, recurrent evolution, convergence, cascades of convergence, and … well you get the idea. The evolutionist is demonstrating some of those “facts that fail” and the attendant doubling down, right before our eyes.

And what about those fossils? More “evidence for evolution”? How about those fossils that appear “as though they were planted there” as Richard Dawkins once admitted. One of those “planted” classes, the humble trilobites, had eyes that were perhaps the most complex ever produced by nature. [1] One expert called them “an all-time feat of function optimization.”

And even Shermer’s go-to source, Wikipedia, admits ancestral forms, err, “do not seem to exist”:

Early trilobites show all the features of the trilobite group as a whole; transitional or ancestral forms showing or combining the features of trilobites with other groups (e.g. early arthropods) do not seem to exist.

Likewise, even the evolutionist Niles Eldredge admitted [2] they didn’t make sense on standard evolutionary theory:

If this theory were correct, then I should have found evidence of this smooth progression in the vast numbers of Bolivian fossil trilobites I studied. I should have found species gradually changing through time, with smoothly intermediate forms connecting descendant species to their ancestors.

Instead I found most of the various kinds, including some unique and advanced ones, present in the earliest known fossil beds. Species persisted for long periods of time without change. When they were replaced by similar, related (presumably descendant) species, I saw no gradual change in the older species that would have allowed me to predict the anatomical features of its younger relative.

And it just gets worse:

The story of anatomical change through time that I read in the Devonian trilobites of Gondwana is similar to the picture emerging elsewhere in the fossil record: long periods of little or no change, followed by the appearance of anatomically modified descendants, usually with no smoothly intergradational forms in evidence.

Any more facts Mike?

1. Lisa J. Shawver, “Trilobite Eyes: An Impressive Feat of Early Evolution,” Science News, p. 72, Vol. 105, February 2, 1974.

2. Niles Eldridge, “An Extravagance of Species,” Natural History, p. 50, Vol. 89, No. 7, The American Museum of Natural History, 1980.

Evolutionist: Evolution Is Happening Faster Than We Thought

Not

The fact that we can travel at speeds of hundreds and even thousands of miles per hour does not mean we can go faster than light. We can fly to the Moon in a matter of days, but the propulsion technology that allows us to do that is not scalable to travelling faster than 186,000 miles per second. A fundamentally different technology is required. The creators of Star Trek understood that, and so they created the concept of warp drive, a faster-than-light propulsion technology, fundamentally different from today’s technology. One would have to be very ignorant to confuse the two, but this is precisely what evolutionists do when they cast biological adaptation as confirmatory evidence of evolution. Adaptation and evolution are two very different things.

Biological adaptation relies on the preexistence of populations, organisms, genetics, DNA, genes, alleles, proteins, massive molecular machines, inheritance, cellular and molecular mechanisms such as horizontal gene transfer and epigenetics, directed mutations, and so forth.

Evolution, on the other hand, is a theory that attempts to explain the origin of all those things.

Observations of the former are not evidence of the latter. That is backwards. It also would also introduce enormous serendipity. For it would mean that evolution created the very structures and mechanisms required for, drumroll, evolution.

Evolution, in other words, created itself.

And even if we were to go along with this ridiculous idea, the resulting biological adaptation is not capable of generating evolutionary change. Adaptation does small things, evolution requires big things.

Even evolutionists, in their honest moments, have understood this. Macroevolution is more than repeated rounds of microevolution. As one evolutionist admitted, “the rate of random DNA sequence mutation turns out to be too slow to explain many of the changes observed.” His point, which is not new and has been known for a long time, is not that adaptation cannot occur, but that the idea of mutations (which can fuel adaptation) adding up to result in novel, large-scale evolutionary change doesn’t work.

Adaptation and evolution are fundamentally different “technologies.”

You can’t travel faster than the speed of light by combining liquid hydrogen and liquid oxygen, and you can’t create novel, complex, biological structures via adaptation mechanisms.

This is why evolutionary biologist Menno Schilthuizen’s article from last year in the Sunday Review is of concern. The article is entitled: “Evolution Is Happening Faster Than We Thought,” and it is all about various adaptations observed in city-dwelling species. Unfortunately, Schilthuizen presents those examples of adaptation as examples of evolution, and proof that, amazingly enough, evolution happens orders of magnitude faster than we once thought:

For a long time, biologists thought evolution was a very, very slow process, too tardy to be observed in a human lifetime. But recently, we have come to understand that evolution can happen very quickly

Evolution’s deep time requirement was particularly evident when William Thomson (later Lord Kelvin), only a few years after Darwin had published his book on evolution, argued that the earth could be no older than 100 million years. Thomson later revised that figure downward to as little as 20-40 million years.

This short time window was an enormous problem for evolution. As Darwin wrote, “Thomson’s views of the recent age of the world, have been for some time one of my sorest troubles.” As Darwin’s friend Thomas Huxley explained, “Biology takes its time from Geology.”

Lord Kelvin’s estimate was eventually dropped, but this example illustrates how important deep time was, both to nineteenth and twentieth century evolutionists. And therefore, the rapid evolution that is now commonly celebrated by evolutionists such as Schilthuizen represents an enormous falsification of a major, fundamental, prediction of evolutionary theory.

It also represents terribly flawed thinking. Adaptation is not evolution.

Desert Mice Fur Changes Color to Match the Terrain

An Example of Evolution in Every Detail?

About fifteen years ago researchers discovered genetic differences that probably explain the different fur coloring in desert mice populations in New Mexico and Arizona (see papers here and here). Mice populations living on light colored terrain tend to have light colored fur, and those on dark colored terrain tend to have dark colored fur. Blending in with the terrain helps to camouflage the mice, protecting them from predators. And that is, apparently, exactly what the mice did about a thousand years ago when desert lava flows produced the darkened terrain. But that is where the science is overtaken by the dogma. Evolutionists have misappropriated this research work, casting it as a textbook example of evolution, and creating a highly produced video (see above) used to indoctrinate students.

The first problem in casting the dark colored mice as an example of evolution is that their genetic differences are not known to be the result of random mutations. For evolutionists there simply is no question that the genetic differences that are thought to cause the dark fur color arose from random mutations.

Now that may be correct. But it may not be. We simply do not know.

This is not merely a technical objection—in spite of evolutionary theory which called for random mutations to be the source of change, in recent decades directed mutations have been found to be at work in an ever increasing number of cases. For many years evolutionists have ignored and even resisted these findings. Too often I have debated evolutionists who, when I point to this evidence, simply deny it.

So while the genetic differences in those dark mice may well be the result of random mutations, evolutionists do not even give this a second thought. They simply assume from the start, and inform their audience in no uncertain terms, that random mutations are the cause.

This is an example of what philosophers refer to as a “theory-laden observation.” Science can get into trouble when the measurements and observations themselves, rather than being theory-neutral and independent of the theories which explain them, are in fact intertwined with those theories.

This can become circular very quickly, and this desert mouse case is a good example of that. Evolutionists assume the genetic differences arose from random mutations, and then claim the evidence as a powerful confirmation of evolution.

The second problem in casting the dark colored mice as an example of evolution is that the dark coloration may be the result of multiple genetic changes. In one case, four mutations are identified, all of which perhaps are required to bring about the coloration change.

It very well could be that only a lone, single mutation is required. But that is not known.

And if multiple genetic changes are required, then this quickly transitions from an example of what random mutations can do to an example of what random mutations cannot do. If four mutations are required, then we’ve just found yet another hard failure of evolution. But again, the evolutionists give no hint of this interesting question. If everyone had their “burning curiosity,” (as Clarence Darrow put it) then science would have long since come to an end.

The third problem in casting the dark colored mice as an example of evolution is that the coloration is too precise. The dark colored fur appears on the top of the mice, but not their underbelly. This makes sense since the topside is mainly what is exposed to predators. But in the evolution narrative, there is no fitness advantage to such precision. Darkening the entire mouse would, apparently, work just as well.

Small scale adaptation

Everything we’ve talked about so far is an unknown. Evolutionists are proclaiming a slam dunk, case closed, example when in fact there are many unknowns. Some of them could demolish the evolution narrative altogether.

But there is one big known we haven’t yet mentioned. It is that none of this amounts to evolution in the first place. It would be a deceptive equivocation to label fur coloration change via a few mutations as “evolution” when, in fact, this is nothing more than small scale adaptation.

In their “honest moments,” as Stephen J. Gould once put it, even evolutionists admit that random mutation isn’t enough, and that adaptation mechanisms are not enough, to explain the kind of large scale change evolution requires.

Mice changing fur color does not demonstrate how metabolism, the central nervous system, bones, red blood cells, or any other biological wonder could have arisen by evolution’s random mutations coupled with natural selection.

This is an old myth evolutionists have exploited ever since Darwin. Demonstrate biological change, any biological change no matter how trivial, and claim victory. Evolutionist Steve Jones once claimed that the changes observed in viruses contain Darwin’s “entire argument.” That is a gross equivocation and misrepresentation of the science, designed to mislead audiences.

It is a pathetic canard which evolutionists continue to rely on. In the above video, Sean Carroll states that thanks to these mice, “science has an example of evolution, crystal clear, in every detail.” [6:42-48]

It would be difficult to imagine a more absurd misrepresentation. Mice changing color is not a crystal clear “example of evolution … in every detail.” Not even close. Carroll should be ashamed of himself.

Religion drives science, and it matters.

Dennis Venema, Galileo, and Protein-Protein Binding

Don’t Count on the Duchess

We have looked at Dennis Venema’s articles on evidences for common descent here, here, here, here, here, and here. In a recent discussion with Venema, he made the erroneous claim that the mammalian immune system, with its search for, and production of, antibodies, is a good example of why evolving protein-protein binding sequences is not a problem. In fact the mammalian immune system is yet another enormous problem for the theory of evolution. Furthermore, the mammalian immune system is not a good example because it is designed for this job of creating protein-protein binding sequences. It searches a well-defined design space extremely rapidly, and measures the success of its search experiments accurately and quickly. The fact that our immune system successfully designs antibodies in short order does nothing to address the problem of how random mutations occurring throughout the genome is supposed to have found myriad binding sequences, crucial for life. Venema also referred to another example which he has written about. Unfortunately this example also fails to demonstrate Venema’s claim of “evolution producing a new protein-protein binding event.”

The problem with evolving protein-protein binding is that too much gene sequence complexity is required to achieve the needed binding affinity. You could say it is an “all-or-none” type of problem.

One or two mutations will not generally do the job—you usually need more mutations before the two proteins stick together very well. And stick together they must, on a massive scale, in order to perform their necessary tasks. Even the simplest, unicellular, organisms contain massive protein machines, consisting of dozens of different proteins binding together to perform crucial life functions.

The study Venema referred to did a beautiful job in confirming this “all-or-none” character of protein-protein binding sequences. The study showed that in order for a viral protein to perform a relatively simple switch from one protein to a very similar protein required four types of mutations.

Anything less and no dice.

The twist in this study was that subsets of the four mutation types were apparently useful for a different function (strengthening the binding affinity to the original protein). So while in general the evolution of protein-protein binding sequences is astronomically difficult because too many simultaneous mutations are required, in this case the four mutation types could be accumulated, with useful benefit realized at some of the intermediate steps.

This is not a general result. It is not a revolutionary new finding that reverses our understanding of protein-protein binding sequences.

It confirms our knowledge, and adds a fascinating outlier case where the “all-or-none” character is circumvented by intermediate functions which, fortuitously “push” the design in the right direction. As the study explains:

The “all-or-none” epistasis among the four canonical phage mutations implies that it would have been unlikely for the new function to evolve on the scale of our experiments, except for the lucky fact that some of the mutations were beneficial to the phage in performing their current function, thereby pushing evolution toward the new function.

The study provides no indication that the untold thousands upon thousands of protein-protein binding problems in molecular biology would enjoy this type of setup. And if they did, oh what a most suspicious sign of design that would be.

Venema is mistaken in his failed attempt to recruit this study as a solution to the evolution of protein-protein binding sequences.

Strangely enough not only had Michael Behe provided his explanation of this study, but Venema was aware of it at the time of his writing. Venema explained that in his next article he would address Behe’s explanation, but in fact Venema simply rehashed Behe’s original explanation for why protein-protein binding is a problem for evolution.

Venema did not address Behe’s explanation but simply concluded that Behe’s original explanation must be false because, after all, this new study demonstrates the evolution of just such protein-protein binding sequences.

This is an unfortunate misrepresentation of a study that most readers will not understand. Venema completely misappropriated the study, and force-fit it into an evolutionary proof.

Additional problems

In addition to this basic problem of serendipity, this confirmation of the “all-or-none” character of protein-protein binding sequences was possible only with a very contrived, designed, laboratory experiment.

Simply put, a virus population was provided with a willing, and well fed host to live off of. In the meantime, many more host targets awaited the virus population. So a few mutations helped the virus’ infect the initial hosts, and mere single additional mutation then allowed the virus’ to infect the second group of hosts.

It was an entirely artificial, laboratory, environment, that wasn’t even intended to replicate a realistic evolutionary environment. Venema nowhere explained this.

Second, the study also discovered even more serendipity. Not only were there “luckily” intermediate fitness benefits, but the finding of the four mutations types also required certain mutations in the host genome.

Without them, no dice.

[Ed: Final section on the absence of synonymous substitutions removed, given the short timeline of the experiment.]