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.