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.