Sunday, December 17, 2017

Evolutionists: Our Findings Suggest That Similarities in Bilateria Evolved Independently

Not Even Wrong

This week one of the top scientific journals in the world published what would seem to be a ground breaking paper. The paper claims to have found evidence for the independent evolution of nervous system similarities across the Bilateria. As the abstract explains:

Our findings … suggest that the similarities in dorsoventral patterning and trunk neuroanatomies evolved independently in Bilateria.

By the end of the manuscript the authors are even more confident:

Therefore, the expression of dorsoventral transcription factors evolved independently from the trunk neuroanatomy at least in certain bilaterian lineages

This is a monumental claim, but there is only one problem: It is blatantly false. The paper’s findings did not “suggest” the evolution, independent or otherwise, of the transcription factor expression patterns. They certainly did not demonstrate, show or find such an incredible conclusion.

It would be difficult to overstate how misleading this paper is. It provided literally zero evidence for any such evolution. Nothing. Nada.

There simply is no such scientific evidence in the paper. The claim that they found that the expression of dorsoventral transcription factors evolved independently in certain bilaterian lineages is not even wrong.

Let’s be clear about this. I am not saying their claim is weak. I am not saying their claim is faulty. I am not saying they failed to make their case conclusively. The problem is they don’t have any case at all.

We cannot criticize the science because, well, there is no science. For a paper entitled “Convergent evolution of bilaterian nerve cords,” one would have expected at least some evidence and explanation for the evolution of bilaterian nerve cords.

Unfortunately papers such as this inform journalists and science writers. They report that scientists have now discovered yet another aspect of evolution. It is yet another example of how science proves evolution.

In fact, if one is looking for a meaningful takeaway, what the study did find is that the expectations of evolution—that nervous system similarities would align with the evolutionary tree—turned out to be, like so many other of evolution’s predictions—false. But that doesn’t fit the narrative.

Religion drives science, and it matters.

Monday, November 6, 2017

Protein Mutations Are Highly Coupled

A Rugged Fitness Landscape

A new study from Michael Harms’ laboratory at the University of Oregon finds that potential amino acid substitutions in protein sequences are highly coupled. That is, if one residue mutates to a new amino acid, the swap impacts the other possible substitutions—they now have a different impact on the protein tertiary structure. As the paper explains:

Proteins exist as ensembles of similar conformations. The effect of a mutation depends on the relative probabilities of conformations in the ensemble, which in turn, depend on the exact amino acid sequence of the protein. Accumulating substitutions alter the relative probabilities of conformations, thereby changing the effects of future mutations. This manifests itself as subtle but pervasive high-order epistasis. Uncertainty in the effect of each mutation accumulates and undermines prediction. Because conformational ensembles are an inevitable feature of proteins, this is likely universal.

This coupling leads to a “profound unpredictability in evolution,” and the authors conclude that “detailed evolutionary predictions are not possible given the chemistry of macromolecules.”

This finding seems to confirm what many evolutionists have said for decades—that evolution is a contingent, not law-like, process:

These [macro]evolutionary happenings are unique, unrepeatable, and irreversible.” – Theodosius Dobzhansky, 1957.

Laws and experiments are inappropriate techniques” for explaining evolutionary events and processes. – Ernst Mayr

What science needs are “plausible scenarios for a fully material universe, even if those scenarios cannot be currently tested.” – Victor Stenger, 2004

any replay of the tape would lead evolution down a pathway radically different from the road actually taken. – Stephen Jay Gould

All of this is in direct contradiction to the science, which reveals undeniable patterns in biology that have been repeated over and over. From the pervasive instances of convergence, recurrence, and all kinds of other “ence’s”, to the non adaptive patterns discussed by Michael Denton, the biological is anything but haphazard or random. Clearly, the same solution, for whatever reason, is used repeatedly across a wide range of species, in various patterns.

This is a clear falsification of an evolutionary expectation expressed across many years, and widely held by a consensus of experts.

But there is another problem with these protein findings. In addition to confirming the complexity and coupling of protein folding, the findings also seem to corroborate what theoretical and experimental studies have shown for years, that the fitness landscape of macromolecules in general, and proteins in particular, is rugged.

The problem of evolving a protein is difficult for several reasons. First, protein function drops off rapidly with only a few mutations. Very quickly a protein loses its function as you move away from the native sequence.

Second, random or starting sequences are stuck in a flat and rugged fitness landscape. There is little sign of a the kind of smooth and gradually increasing fitness landscape that would aid evolution’s enormous task of figuring out how proteins could evolve.

These problems are just getting worse, and this new finding a good example of that trend.

Religion drives science, and it matters.

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.

Monday, October 23, 2017

World’s Oldest Tree is World’s Most Complex Tree

Makes Perfect Sense

We have often discussed the problem of “early complexity,” and how as we peer back in time—whether in the geographic strata or by phylogenetic reconstruct—things don’t get simpler. This makes no sense on evolution and this week’s news of a fossil specimen in northwest China, revealing and ancient, and highly complex, tree, just makes it worse. As one of the authors admitted:

This raises a provoking question: why are the very oldest trees the most complicated?

Fortunately evolution is a fact.

Thursday, October 12, 2017

Welcome to Alt-Science

Expelled

Sometimes it’s obvious, as in the case of the scientific research paper that was rejected after it was accepted. While the paper was well accepted and given positive comments from peer reviewers, certain members of the editorial board of a seemingly scientific journal noticed that the results had negative implications for evolution. And so months after the editor had told the authors he was happy “to proceed with publication,” the paper suddenly was, “on further reflection and discussion,” summarily rejected.

And what exactly was the “discussion” about? That “the unspoken implication of the article is that, probabilistically, random undirected evolution is impossible.”

And that, dear scientists, is not allowed.

Random undirected evolution is, by definition, a fact. Break that ground rule, and pay the price. This isn’t about science or truth. This is the alt-science that seeks to control everything from publications and textbooks to careers and funding.

Religion drives science, and it matters.

Monday, October 2, 2017

But, But, But, … The Origin Of Life Was All But Solved!

“The origin of life is among the greatest open problems in science”

With everyone from the National Academy of Sciences to science writers such as Carl Zimmer proclaiming that the origin of life problem has essentially been solved, we wonder why we continue to find researchers, this time Yehuda Zeiri at Ben-Gurion University, admitting that:

Despite decades of research, how life began on Earth remains one of the most challenging scientific conundrums facing modern science.

and Sara Walker resorting to hope and luck:

The origins of life stands among the great open scientific questions of our time. While a number of proposals exist for possible starting points in the pathway from non-living to living matter, these have so far not achieved states of complexity that are anywhere near that of even the simplest living systems. A key challenge is identifying the properties of living matter that might distinguish living and non-living physical systems such that we might build new life in the lab. This review is geared towards covering major viewpoints on the origin of life for those new to the origin of life field, with a forward look towards considering what it might take for a physical theory that universally explains the phenomenon of life to arise from the seemingly disconnected array of ideas proposed thus far. The hope is that a theory akin to our other theories in fundamental physics might one day emerge to explain the phenomenon of life, and in turn finally permit solving its origins. […] If we are so lucky as to stumble on new fundamental understanding of life that allows us to solve our origins, it could be such a radical departure from what we know now that it might be left to the next generation of physicists to reconcile the unification of life with other domains of physics, as we are now struggling to accomplish with unifying general relativity and quantum theory a century after those theories were first developed.

But “hope” is not a good science strategy.

One sign of this problem is the proliferation of hypotheses, indicating, as we have pointed out many times, the lack of any good solution. Or as Alex Berezow a bit more bluntly puts it:

The origin of life is a profound mystery. Once life arose, natural selection and evolution took over, but the question of how a mixture of various gases created life-giving molecules that arranged into structures capable of reproducing themselves remains unanswered. Many theories have been proposed, some of which are popular (e.g., RNA World), and some of which are a far-fetched (e.g., aliens). Unlike politics, more ideas are not necessarily better; in science, a diversity of theories tends to betray the reality that scientists have no idea what's going on.

No idea what’s going on? It must be time for Jeremy England to find another Ilya Prigogine idea.

Wednesday, September 13, 2017

Your Own Evidence For Evolution

The Nature of Evidence



Charles Darwin would approve of this video showing evidence for evolution found in the human body.

Sunday, September 10, 2017

What Does Abortion Portend For Evolution?

An Unsolved Puzzle

While much has been said about the link between evolution and abortion, and how the former sanctions the latter, little has been said about the reverse. If evolution supports abortion, what does abortion say about evolution?

To appreciate fully what we can learn about evolution from abortion, we first need to understand the evolution of behavior. In the past half century evolutionists have elucidated how complex behaviors, such as altruism, evolved. A key concept is kin selection, and much of the early theoretical work was done by William Hamilton in the early 1960s.

For our purposes here, what is important is that studies in the evolution of behavior have been forced to resort to enormous levels of complexity, nuance and precision. Somehow unguided genetic modifications must have resulted in genes for a wide range of attitudes and behaviors. The list is staggering. There are of course the obvious behaviors such as love, hate, guilt, retribution, social tendencies and habits, friendship, empathy, gratitude, trustworthiness, a sense of fulfillment at giving aid and guilt at not giving aid, high and low self-esteem, competition, and so forth.

These behaviors are supposed to have evolved according to the kin selection criteria, along with many more nuanced behaviors. For instance, love not only evolved, but in varying degrees depending on the degree of shared genes. It is weaker within the extended family than within the family. Low self-esteem behavior not only evolved, but the art of not hiding it can be advantageous and so also evolved. Sibling rivalries evolved, but only to a limited degree. In wealthy families, it is more advantageous for siblings to favor sisters while in poor families siblings ought to favor brothers. So those behaviors evolved. Mothers in poor physical condition ought to treat daughters as more valuable than sons. Likewise, socially or materially disadvantaged parents ought to treat daughters as more valuable than sons.

We’ll stop here but the list of incredibly detailed, subtle behaviors that evolution must have precisely crafted goes on and on. Evolution must have an incredible ability to produce finely tuned and highly specific behaviors.

With that understanding, we are now ready to consider abortion. The question is: how and why did evolution produce such a behavior? What fitness calculation is satisfied by terminating the life of your own child?

I can just imagine evolutionist’s contriving just-so stories to justify such an absurdity. Killing your own child would, after all, allow one to avoid the costly physical and emotional investment of raising a child. One would be better off, and so better prepared to … To do what?

To have another child.

The whole point of “fitness,” in an evolutionary context, is reproduction. One has higher “fitness” if one can have more offspring. Fitness does not refer to physical fitness in the colloquial sense. It does not refer to financial fitness. It refers to having babies. Lots of babies.

That’s what evolutionary theory is based on. Reproductive advantage. Not physical, spiritual, emotional, or financial advantage, but reproductive advantage.

Abortion as a behavior is a flat contradiction and falsification of evolutionary expectations. It makes no sense.

If I can't run very fast for some reason, then that indirectly reduces my fitness as it may impact my survivability or otherwise my reproductive abilities (or it may not). But if I kill my child, that directly deducts from my evolutionary fitness. Abortion is a much bigger, more direct, fitness penalty.

Indeed, abortion is the ultimate fitness penalty. All the positive fitness attributes I may have are instantly and completely wiped out if I engage in abortion. Selection would weed it out immediately.

Under evolution abortion would be rapidly eliminated. Remember, in the past half century evolutionists have insisted that evolution must have crafted our many nuanced behaviors with incredible precision and specificity. Abortion would not have accidentally evolved.

Religion drives science, and it matters.

Creationists Demolish Evolutionists in Annual Football Game

Don’t Know What They’re Doing

Saturday, September 9, 2017

Galileo and a New Climate Study

A Durable Myth

Science writer Katherine Ellen Foley has another article on anthropogenic global warming, or AGW, in Quartz this past week. The AGW theory states that civilization’s production of green-house gases, such as carbon dioxide, is causing a hockey-stick like rise in the Earth’s temperatures. This has led to a range of dire environmental warnings in recent decades, some of which have already failed. Nonetheless AGW is the consensus theory amongst virtually all climate scientists. How much of this consensus is formed by non empirical factors—more common in science than is often understood—is an open question. Leaked emails have revealed strong-arm tactics—including pressure on publishers—used to squash dissent. Of course none of this means AGW is necessarily anything less than completely true. But it does compromise unsupported claims that AGW is a strong, empirical theory. Press conferences claiming a case closed won’t cut it—that kind of trust and legitimacy was lost years ago. The guiding light here must be the raw science.

All of this means that AGW appears to be another fascinating example of how science, for better or for worse, works. What I find particularly interesting are high truth claims for ideas that are politically or metaphysically charged and not obviously empirically supported. The problem with science, as Del Ratzsch has pointed out, is that it is done by people. Non empirical influences are, gasp, sometimes at work and we simply must understand the underlying science rather than blindly accept authoritarian pronouncements.

I am not arguing for or against AGW, but I am arguing for a depth of understanding that too often is missing from partisan accounts. This, unfortunately, characterizes Foley’s Quartz article, which asks the question: What about the research papers questioning AGW? While the vast majority of the literature falls squarely within the AGW-is-true paradigm, there is nonetheless a tiny sliver of papers questioning the theory.

To be sure those papers aren’t having much influence, but according to Foley AGW critics often invoke Galileo as a comparison. Just as Galileo met stiff opposition, so do these AGW dissenters. The implication is that, like Galileo, these researchers will prevail in the end.

Foley explains this is all wrong, both because it is a false analogy and because those papers are scientifically flawed. Specifically, Foley explains that Galileo’s “fellow scientists mostly agreed with his conclusions—it was church leaders who tried to suppress them.” And furthermore, a study of those dissenting papers found them to be biased and faulty.

Foley’s article hit the mark. It has instantly been reposted and retold across the Internet, on blogs, forums, and even videos, such as this one by Jeff Waldorf. Unfortunately Foley’s article is little more than AGW cheerleading, and Waldorf and the others are only too quick to pile on, assigning nefarious motives to anyone who would doubt the consensus theory. It is precisely this kind of hostile, social atmosphere which can be so stifling to science.

Foley’s article is largely a copy and paste job from other sources, and she employs the usual rhetorical devices, such as labelling her targets as “climate-change-denying papers.” Of course they are no such thing. The papers are questioning AGW, not “denying” climate change.  This sort of rhetoric, targeted at reasonable skepticism, is a sign of fake news.

The next problem is with her retelling of the Galileo Affair which is all Warfare Thesis. No it wasn’t science versus religion—that is the myth that Foley is propagating. Galileo did not heroically lead a scientific consensus with powerful and unambiguous empirical evidence against ecclesiastical resistance. Church leaders did not “tr[y] to suppress them.”

Nonetheless this gets picked up and amplified by Waldorf and the others, and historians now have yet another round of Galileo mythology to reckon with. The Galileo myth serves as yet another non empirical mandate for ideas like AGW and evolution, and that is why it is so resistant and durable.

As if to support her Galileo claims, Foley links to a 2011 phony New York Times article by Henry Fountain who provides this absurd retelling of the myth:

Galileo, whose astronomical observations confirmed the Copernican theory that the Earth revolved around the Sun, was basing his assertions on empirical knowledge and faced opposition from the Roman Catholic Church, which supported the Ptolemaic view of an Earth-centered universe.

Of course Galileo’s observations did not “confirm the Copernican theory.” Nor were his “assertions based on empirical knowledge.” Galileo flatly ignored Kepler’s finding that ellipses perfectly described the planetary orbits (as opposed to the lousy circles Galileo advocated which required epicycles). And the lack of stellar parallax observed in the seventeenth century flatly refuted Galileo’s heliocentrism. Furthermore Galileo studiously avoided mentioning Tycho Brahe’s hybrid model which competed well against heliocentrism. Galileo carefully framed the debate as strictly heliocentrism versus geocentrism.

Nor did Galileo face any kind of unified opposition from the Roman Catholic Church. That is another myth. There were many in the church who had no problem with Galileo pursuing his ideas, and the Pope had been a benefactor of Galileo before, that is, Galileo turned on him.

The Galileo Affair is far more complex and nuanced than these pathetic retellings would have it. As one historian put it, it was Galileo’s religion versus the Church’s science. But that, of course, would not service Foley’s message.

Next Foley appeals to a 2015 paper—passed off as something of recent importance—arguing that research papers skeptical of AGW are all flawed.

That’s curious.

Why does Foley now resurrect a 2015 review of even older AGW skepticism? Foley generously draws upon a 2015 Guardian article to fill in her story.

Could this retelling of an old story have anything to do with more recent research posing serious challenges to AGW? Could this be an attempt to forestall emerging skepticism, and delegitimize research that points to AGW’s on-going problems?

Consider a new study by John Abbot and Jennifer Marohasy that is suggesting a rather fundamental failure of AGW. The study shows that pre industrial climate data robustly models twentieth century temperatures.

That should not be the case if AGW is true.

If later nineteenth and twentieth century greenhouse gas emissions are causing a hockey stick temperature rise, it should not be consistent with the older data. AGW says that the climate has changed.

Now perhaps Abbot’s and Marohasy’s new research is flawed. Perhaps they have made a mistake, and so AGW is unharmed by their work.

But doesn’t that make for a more interesting article in 2017 than rehashing old myths?

Saturday, September 2, 2017

Kneecaps: “Ultimately, there might not be a simple pattern”

We can only say that so it is

Why do ostriches have four, rather than two, kneecaps? A new study has found several possible biomechanical advantages. Perhaps they allow the ostrich to straighten its leg more quickly, helping the animal to run quickly. Perhaps the lower kneecap protects the joined tendons crossing the front of the knee. One reason that does not help to explain the ostriches four kneecaps is evolution. That is because this unique design is not predicted, and makes no sense, on the theory. As one article admits: “Bizarrely, many of the ostrich’s closest relatives don’t have kneecaps at all.” Similarities across the species were a strong argument for evolution, but in fact biology is full of unique designs, particular to one or a few species. Such one-off, “lineage specific,” designs are “bizarre” for evolutionists. So while there are design reasons for the ostriches four kneecaps, on the ordinary view of the evolution of each being, we can only say that so it is.

Wednesday, August 9, 2017

Rob Stadler and the NABT

The Scientific Approach to Evolution

It’s no secret that the origins debate is highly polarized. Many people have their minds made up and too often there is no place for a reasoned evaluation of the science. That’s tragic because that is where things become interesting. I once spoke to a roomful of high school science teachers, explaining that they could accurately teach how the science bears on the theory of evolution—both positively and negatively. The response I got was that this would confuse the students who needed to be given a simple, unambiguous message. One teacher was concerned that anything other than an obvious, “evolution is true,” message would be detrimental to the learning. To be sure there can be a tension between detail and clarity in classroom settings. High school students learn introductory history lessons out of necessity. They simply are not ready for research-level topics. Clarity sometimes comes at the cost of less detail. But there is a difference between simplifying a lesson and biasing a lesson. I was again reminded of all this when I heard about how the National Association of Biology Teachers responded to Dr. Robert Stadler’s new book, The Scientific Approach to Evolution.

It would be difficult to find someone more qualified than Stadler to analyze how the scientific evidence bears on the theory of evolution. His academic background is in Biomedical Engineering, with degrees from the top universities in the nation (Case Western Reserve University, MIT, and Harvard). And he has twenty years of experience in the field, with more than 100 patents to his name.

Stadler’s interest in evolution skips over the usual culture wars arguments and focuses on the science. Stadler provides an approach that is sorely needed. While there are plenty of texts and popular books that review the scientific evidence for evolution, they invariably fail to provide any kind of accounting of the strength of the evidence. The field outside my window is flat and so is evidence that the Earth is flat. But of course that evidence is weak.

On the other hand, there is plenty of academic work dealing with methods of rigorous, quantitative, theory evaluation, such as Bayesian approaches. But they invariably fail to engage the real-world evidences for evolution, in any kind of comprehensive way.

For all the talk, there is too often a lack of actual practice of analyzing the evidence. Enter Rob Stadler and his thoroughly accessible approach to laying out how the evidence bears on the theory of evolution. Importantly, Stadler explains not just the evidences, but the strengths and weaknesses of those evidences.

Because Stadler’s approach is accessible, it is an excellent classroom resource. Indeed, regardless of what one believes about a scientific theory such as evolution, the learning is greatly enhanced when one is allowed to explore the evidence, think critically about it, form opinions, and defend them in discourse. Rather than rehearse the carefully selected subset of evidences routinely presented in textbooks, the science should be allowed to speak for itself.

Unfortunately those science teachers I spoke to are not the only ones uncomfortable with allowing science such freedoms. Earlier this year Stadler worked with an agency to place an advertisement for his new book with the National Association of Biology Teachers. The contract was signed, funds were paid, and beginning in May the ad was to appear on the NABT website.

But strangely enough, on May 1 the advertisement failed to appear. It was through the ad agency that Stadler learned that the NABT had no intention of running the ad. The agency informed Stadler that the NABT had “concerns” over the content of the book.

And what exactly was the problem? The Scientific Approach to Evolution allows the evidence to speak for itself. According to Stadler’s book, there could be negative evidences, as well as positive evidences.

And that was not acceptable.

The NABT was concerned that “Dr. Sadler’s attempts to address ‘strengths and weaknesses’ in order to establish a climate of controversy in the scientific community regarding evolution  where there is none.”

Ironically, the NABT was also concerned that Dr. Sadler underappreciates that “theories are open to revision and refinement as new data becomes available.” That’s ironic because Sadler’s book does precisely that. Sadler appeals to new data to refine and revise our understanding of evolution.

Indeed, if Sadler’s theory-neutral appeal to the scientific evidence makes him guilty of attempting to “establish a climate of controversy” where there is none, then how can theories such as evolution ever be revised?

The fact is, the NABT’s ground rules are a form of theory protectionism. They won’t even run an advertisement for a book that dares question evolution on scientific grounds.

And rather than address the evidence that Sadler brings forth, the NABT contrives nefarious motives. According to the NABT, Sadler is guilty of dishonest pedagogy, and seeking “to establish a climate of controversy.” In the name of scientific integrity the theory must be protected. Darwin’s supporter TH Huxley called for a very different approach. We must, Darwin’s bulldog explained:

Sit down before fact as a little child, be prepared to give up every preconceived notion, follow humbly wherever and to whatever abysses nature leads, or you shall learn nothing. I have only begun to learn content and peace of mind since I have resolved at all risks to do this.

Huxley insisted that we cast aside our preconceived notions, and follow the evidence to wherever it leads. Otherwise “you shall learn nothing.” Unfortunately Huxley would not recognize today’s classroom. The NABT would do well to heed the warning of Darwin’s most vocal advocate.

Tuesday, August 8, 2017

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.

Monday, August 7, 2017

The National Association of Biology Teachers Versus the Ribosome

A Fascinating Dissonance

Theodosius Dobzhansky famously wrote in 1973 that “Nothing in Biology Makes Sense Except in the Light of Evolution.” That phrase has since become a staple amongst evolutionists. It appears throughout the literature, from popular works to journal papers, and it motivates the view that evolution is fundamental. Students must learn biology through the lens of evolution. Researchers must formulate experiments from a Darwinian perspective. Medical students must understand the human body as the result of evolution, and so forth. As the National Association of Biology Teachers explains:

The frequently-quoted declaration of Theodosius Dobzhansky that “Nothing in biology makes sense except in the light of evolution” accurately reflects the central, unifying role of evolution in the science of biology. … Just as nothing in biology makes sense except in the light of evolution, nothing in biology education makes sense without reference to and thorough coverage of the principle and mechanisms provided by the science of evolution. Therefore, teaching biology in an effective, detailed, and scientifically and pedagogically honest manner requires that evolution be a major theme throughout the life science curriculum both in classroom discussions and in laboratory investigations. … Biology educators at all levels must work to encourage the development of and support for standards, curricula, textbooks, and other instructional frameworks that prominently include evolution and its mechanisms

Clearly the NABT thinks highly of Dobzhansky’s phrase and it draws some fairly important conclusions from it. But there is one slight problem: Dobzhansky’s phrase is unequivocally false.

Is it really true that nothing in biology makes sense except with evolution? No it is not as I have discussed many times (here, here, here, here, here, here, here, here, and here). Dobzhansky’s phrase is equivalent to: “Everything in biology only makes sense in light of evolution,” or “If-and-only-if evolution is true, then will we find what we find in biology.” In its logical form, Dobzhansky’s phrase is clearly not even scientific. Indeed, the phrase comes from the title of a paper which appeared in the American Biology Teacher, the official journal of the National Association of Biology Teachers, and in that paper Dobzhansky gave a litany of theological arguments that mandated evolution.

But it gets worse. Not only is this famous phrase a theological claim, it also fails the test of comparative anatomy. For example, consider the various types of echolocation found in different species of bats. As I have discussed (here, here, and here), the echolocation designs do not fit the expected evolutionary pattern. In other words, here we have something in biology that does not make sense with evolution. Evolution does not help to explain what we observe, instead with evolution we must resort to ad hoc stories. As one paper concluded:

the animal’s habitat is often more important in shaping its [echolocation] call design than is its evolutionary history

If you want to understand a bat’s echolocation design, look to its habitat, not its supposed evolutionary history. The scientific evidence makes no sense on the theory of evolution.

Or again, consider how glycan molecules compare across the different species. Again, it isn’t according to the evolutionary model (see here). As one paper explained, glycans show “remarkably discontinuous distribution across evolutionary lineages,” for they “occur in a discontinuous and puzzling distribution across evolutionary lineages.” This dizzying array of glycans can be (i) specific to a particular lineage, (i) similar in very distant lineages, (iii) and conspicuously absent from very restricted taxa only. The patterns contradict what evolution expected. As another paper admitted:

There is also no clear explanation for the extreme complexity and diversity of glycans that can be found on a given glycoconjugate or cell type. Based on the limited information available about the scope and distribution of this diversity among taxonomic groups, it is difficult to see clear trends or patterns consistent with different evolutionary lineages.

In other words, the glycans make no sense on evolution.

Echolocation and the glycans are but two examples. There are many, many more examples where they came from. The biological world is full of patterns of comparative anatomy across different species which make no sense on evolution.

But it gets worse.

It is not just comparative anatomy where the evidence fails to make sense on evolution. In design after design, what we observe in biology does not reflect contingency, as Darwin and later evolutionists predicted, but functional need. In fact, the designs we find are highly efficient and optimal in various ways. To cite just one example of a great many, consider the work of William Bialek.

Bialek discusses compound eyes of insects such as the fly. These compound eyes have a large number of small lenses packed into an array. A large number of small lenses gives high resolution, just as does a digital camera with a large number of pixels.

But when the lens becomes too small its optics become distorted due to diffraction. So in determining the best lens size there is a tradeoff between resolution and diffraction. In the optimum solution the lens size is roughly proportional to the square root of the radius of the head. And indeed, Bialek shows an old paper surveying the compound eye designs in more than two dozen different insects. That paper shows that for the different size insects, the lens size is proportional, as predicted, to the square root of the head size.

This is one of Bialek’s half a dozen or so examples showing the optimization of biological designs and, as Bialek assures us that there are many, many more. Here is how one science writer explained it:

Yet for all these apparent flaws, the basic building blocks of human eyesight turn out to be practically perfect. Scientists have learned that the fundamental units of vision, the photoreceptor cells that carpet the retinal tissue of the eye and respond to light, are not just good or great or fabulous at their job. They are not merely exceptionally impressive by the standards of biology, with whatever slop and wiggle room the animate category implies. Photoreceptors operate at the outermost boundary allowed by the laws of physics, which means they are as good as they can be, period. Each one is designed to detect and respond to single photons of light — the smallest possible packages in which light comes wrapped.

And where did those “apparent flaws” come from? Evolutionists of course. From an evolutionary perspective, vision systems were full of “flaws.” But in fact those systems were optimized—we just had to stop looking at biology in terms of evolution.

This brings us to the protein synthesis machine—the ribosome. A paper from last month out of Johan Paulsson’s laboratory elaborates on several of the ribosome’s highly efficient, or optimal, design features. Ribosomes are comprised of both protein and RNA molecules, and their proteins make up a sizable fraction of the total protein content of many cells. Cells contain many ribosomes, and naturally in order for the cell to duplicate, the ribosomes must be duplicated. This means a lot of protein synthesis must take place, in order to create all the proteins in all the ribosomes.

One way to help alleviate this production problem would be to have yet more ribosomes in the cell. But that would, in turn, create an even greater protein synthesis burden, since even more proteins would be needed for those additional ribosomes. One way to solve this conundrum is to use RNAs in ribosomes rather than proteins, where possible.

It is a fascinating problem, and the paper concludes that we can understand the solution not as the result of evolutionary contingencies, but as a solution to a functional need:

Rather than being relics of an evolutionary past, the unusual features of ribosomes may reflect an additional layer of functional optimization that acts on the collective properties of their parts.

These are but a few examples and there are many more showing that evolution is by no means required to understand biology. Indeed, evolution is usually redundant—a “multiplied entity” in the language of Ockam’s Razor.

There is no question that Dobzhansky famous phrase has failed. It simply is not true that “Nothing in Biology Makes Sense Except in the Light of Evolution.” Indeed, it would be difficult to imagine a perspective more at odds with the science of biology. But while a few rare voices, such as Massimo Pigliucci, admit that the phrase is “patently wrong,” evolutionists for the most part continue to rehearse the famous phrase in robotic fashion, revealing an underlying agenda that has strayed badly from the science.

Evolutionists are so heavily invested in Dobzhansky’s phrase they will never admit it has failed. Even Pigliucci soft-pedaled the problem, explaining that “Dobzhansky was writing for an audience of science high school teachers,” as though it is OK to misrepresent science to high school teachers. Also, Pigliucci’s admission was limited to the fact that spectacular progress has occurred in the life sciences while ignoring evolutionary theory. True enough, and that certainly demolishes Dobzhansky’s phrase, but it is only the tip of the iceberg. It is a safe criticism that avoids the more damning problems.

There simply is too much at stake here. It isn’t like admitting that a particular prediction went wrong. Dobzhansky’s phrase was not merely a prediction, it was meta-prediction—the rallying cry of the entire world view—and walking it back in any genuine way 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.

The National Association of Biology Teachers’ holding up of Dobzhansky’s phrase reveals the underlying, nonscientific dogma at work. We are seeing a fascinating dissonance and hypocrisy, for the phrase is unequivocally false and yet it cannot be abandoned.

A demonstrably false claim is feverishly held up as true. Religion drives science, and it matters.

Saturday, August 5, 2017

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.

Monday, July 31, 2017

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.

Sunday, July 30, 2017

The Astonishing Examples of Repeated Evolution

Does Similarity Imply Common Ancestry?

According to evolution the species arose as a consequence of random events, such as mutations. Yet the biological world is full of repeated designs. These so-called convergences are ubiquitous. And while a fundamental tenet of evolutionary theory is that similarity implies common ancestry, convergences are similarities found in more distant species—they cannot have arisen from a common ancestor. This falsifies the fundamental tenet that similarity implies common ancestry. This tension can be further amplified by complexity and multiplicity. Similarities in different species which are highly complex can be difficult to explain how they evolved once, let alone twice in independent lineages. Add to this similarities which are found not twice, but a multiplicity of times, and you have what the press release of a new study out of Germany on the evolution of jawed vertebrates called “astonishing examples of repeated evolution.”

Sunday, July 23, 2017

Subcellular Map of the Human Proteome Reveals “Highly Complex Architecture”

A High Degree of Regulation and Control

New research is using antibodies to map out the spatio-temporal locations of 12,003 different proteins in human cells. The results are another example of how, as Bruce Alberts put it in 1998: “We have always underestimated cells.” Alberts explained how cells were once naively viewed as something of a random affair, where molecules “were thought to diffuse freely, randomly colliding.” The new research reveals the “the highly complex architecture of the human cell” and adds more detail to the fact that the workings of the cell are far from random:

A total of 12,003 proteins targeted by 13,993 antibodies were classified into one or several of 30 cellular compartments and substructures, altogether defining the proteomes of 13 major organelles.

Although evolutionists “thought the cell was so simple,” this research is showing that the “cellular proteome is compartmentalized and spatiotemporally regulated to a high degree.” In fact “[m]ore than half of these 12,003 proteins localize in more than one compartment at the same time.” This is consistent with the fact that most proteins are capable of performing multiple functions, and is another indicator of high complexity:

Moreover, proteins that localize to more than one compartment may have context-specific functions, increasing the functionality of the proteome. The fact that proteins “moonlight” in different parts of the cell is now well accepted. … The more complex a system is, the greater the number of parts that must be sustained in their proper place, and the lesser the tolerance for errors; therefore, a high degree of regulation and control is required.

Indeed, the degree of regulation and control required for this system is not only enormous, but contrary to evolutionary expectations.

Saturday, July 22, 2017

Human Evolution: Missing Link Still Missing

The Need For Theory Evaluation

The evolution of humans is, in many ways, similar to evolutionary theory on the whole. As Colin Barras reveals in his recent article at the BBC, There are conflicting evidences, a lack of details, opposing hypotheses held with great confidence, and a wide range of explanatory mechanisms that are routinely used as needed. That much is obvious. What is a bit more subtle, and arguably even more important, is the absence of a serious evaluation of the theories at hand.

Barras’ article is a good summary, from TH Huxley and Darwin up to today, of how evolutionists have viewed human evolution. What is humanity’s phylogenetic neighbor, our so-called sister species, and what is our most recent common ancestor?

Following Huxley, gorillas or chimpanzees were typically held by early evolutionists as both our sister species and representative of the common ancestor, which swung from branch to branch and rambled along on all fours. But some evolutionists held that monkey’s were our closest evolutionary neighbor.

With the rise of molecular biology came genetic comparisons and the firm conclusion that chimpanzees and bonobos are our sister species. Huxley, it seemed, was right. Students were told, in no uncertain terms, that the chimp was our sister species—after all, we shared something like 99% of our DNA in common.

But then new evidences arose, questioning this seemingly incontrovertible truth. Subtle differences between gorillas and chimps suggested independent evolution, rather than inheritance via a common ancestor, of certain traits. Furthermore, a new fossil species, Ardipithecus ramidus, as well as anatomical and behavioral comparisons, called into question the accepted human-chimp relationship.

All of this leaves evolutionists today contemplating a range of explanations for human evolution. One common theme of all the different explanations, however, is their lack of detail. The explanations do not provide any sort of detailed account of the rise of the many unique traits and capabilities in humans.

And where detailed evidence does exist, such as in the chimp, gorilla, and human DNA data, it makes little sense (see here, here, and here, for example).

The theoretical problems and lack of detail with human evolution, and evolution in general, raise the question of how good these theories are. Evolutionists repeatedly state that evolution is a fact, just as much as gravity, heliocentrism, and the roundness of the Earth are facts. There is no question about it.

But the science does not support this claim. What we need is a legitimate, serious evaluation of the theories at hand.

Monday, May 22, 2017

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-Po├» 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.

Saturday, May 20, 2017

The Real Problem With Convergence

Worse Than Lightning Striking Twice

Biology is full of convergence—repeated designs in distant species. Marsupials and placentals, for instance, are mammals with different reproductive designs (placentals have significant growth in the embryonic stage attached to the nutrient-rich placenta whereas marsupials have no placenta and experience significant development after birth) but otherwise with many similar species. The marsupial flying phalanger and placental flying squirrel, for example, have distinctive similarities, including their coats that extend from the wrist to the ankle giving them the ability to glide long distances. But evolutionists must believe that these distinctive similarities evolved separately and independently because one is a marsupial and the other is a placental, and those two groups must have divided much earlier in evolutionary history. Simply put, evolution’s random mutations must have duplicated dozens of designs in these two groups. Isn’t that kind of like lightning striking twice?

It is kind of like lightning striking twice but for evolutionists—who already have accepted the idea that squirrels, and all other species for that matter, arose by chance mutations—this is not difficult to believe. It simply happened twice rather than once (or several times, in the cases of a great many convergences).

What is often not understood however, by both evolutionists and their critics, is that convergence poses a completely different theoretical problem. Simply put, a fundamental evidence and motivation for evolution is the pattern of similarities and differences between the different species. According to evolutionary theory, the species fall into an evolutionary pattern with great precision. Species on the same branch in the evolutionary tree of life share a close relationship via common descent. Therefore they share similarities with each other much more consistently than with species on other branches.

This is a very specific pattern, and it can be used to predict differences and similarities between species given a knowledge of where they are in the evolutionary tree.

Convergence violates this pattern. Convergence reveals striking similarities across different branches. This leaves evolutionists struggling to figure out how the proverbial lightning could strike twice, as illustrated in a recent symposium:

Does convergence primarily indicate adaptation or constraint? How often should convergence be expected? Are there general principles that would allow us to predict where and when and by what mechanisms convergent evolution should occur? What role does natural history play in advancing our understanding of general evolutionary principles?

It is not a good sign that here in the twenty first century evolutionists are still befuddled by convergence, which is rampant in biology, and how it could occur. This certainly is a problem for the theory.

But a more fundamental problem, which evolutionists have not reckoned with, is that convergence violates the evolutionary pattern. Regardless of adaptation versus constraint explanations, and any other mechanisms evolutionists can or will imagine, the basic fact remains: a fundamental evidence and prediction of evolution is falsified.

The species do not fall into the expected evolutionary pattern.

The failure of fundamental predictions—and this is a hard failure—is fatal for scientific theories. It leaves evolution not as a scientific theory but as an ad hoc, story-telling, procedure. The species reveal the expected evolutionary pattern—except when they don’t. In those cases, they reveal some other pattern.

So regardless of where you position yourself in this debate, please understand that attempts to explain convergence under evolutionary theory, while important in normal science, do nothing to remedy the underlying theoretical problem, which is devastating.

Religion drives science, and it matters.

Sunday, April 23, 2017

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.

Monday, April 17, 2017

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.