How OOL science can earn some respectability.

Announcing New Sewell Prize in Biological Origins Studies!
David Klinghoffer | @d_klinghoffer

Over at Uncommon Descent, mathematician Granville Sewell announces a new prize he will be administering. It sets a fascinating challenge but offers an enviable reward:

I plan to award a prize to anyone who can invent a non-trivial 3D machine which can replicate itself. The machine must be able to make copies of itself without human intervention, except possibly to supply the raw materials. Basically a 3D printer which can print a copy of itself which retains the ability to print a copy of itself, which… A page which can be photocopied does not count, because it is the photocopier which actually makes the copy, unless the photocopy machine also makes a copy of itself; a computer program which duplicates itself does not count unless the computer it runs on makes a copy of itself also.

The reward isn’t cash but something even better: 

The prize: the right to speculate about how life originated. Leave your artificial species alone and see how many generations it lasts before going extinct. If it makes accurate copies of itself for 100+ generations, then you also get to speculate about how genetic duplication errors might accumulate into major evolutionary advances.

Now go to it, you proponents of unguided abiogenesis and evolution through all sorts of brute unintelligent, and only unintelligent, natural forces. The first ever Sewell Prize in Biological Origins Studies awaits!

Blinded by fuzzy math?

Behe on Darwinism’s “Socially Inherited Dependence on Classical Yet Irrelevant Math”
David Klinghoffer | @d_klinghoffer

“Natural selection, irreducible complexity, and random mutation all reinforce each other to make Darwinian evolution very limited,” explains biochemist Michael Behe on a new ID the Future episode. That means Behe must tackle a tough question: if the limits of Darwinian evolution are so clear, as he shows in his new book Darwin Devolves, why do gifted scientists like Richard Lenski and Joseph Thornton persist in hanging on to the failed theory, against the evidence of their own experiments? 

Talking with host Andrew McDiarmid, Behe traces the errant thinking to an outdated mathematical picture taken from Ronald Fisher (1890-1962) and his 1930 book, The Genetical Theory of Natural Selection. This highly influential work was written before scientists knew what genes actually are. It’s not surprising that Fisher missed the role of broken genes in containing the creative potential of unguided evolution.

Through “a socially inherited dependence on classical yet irrelevant math,” present-day researchers are saddled with Fisher’s own “hopeful ignorance.” Download the podcast or listen to it here.

A fatwa from one of Darwinism's ayatollah's

Do Evolutionary Principles Derive from Observation, or Are They Imposed on It?
Evolution News & Views February 25, 2016 11:25 AM

Geneticist Dan Graur of the University of Houston is implacably opposed to intelligent design -- and brutally honest about his opposition, which makes for bracing clarity in what he writes. Recently he tweeted the following 12 principles of evolution, which he drafted.

You have to love Graur's principles, because they capture orthodox neo-Darwinism in its purest form:

All of Evolutionary Biology in 12 Paragraphs, 237 Words, and 1,318 Characters

Evolutionary biology is ruled by handful of logical principles, each of which has repeatedly withstood rigorous empirical and observational testing.

The rules of evolutionary biology apply to all levels of resolution, be it DNA or morphology.

New methods merely allow more rapid collection or better analysis of data; they do not affect the evolutionary principles.

The only mandatory attribute of the evolutionary processes is a change in allele frequencies.

All novelty in evolution starts as a single mutation arising in a single individual at a single time point.

Mutations create equivalence more often than improvement, and functionlessness more often than functionality.

The fate of mutations that do not affect fitness is determined by random genetic drift; that of mutations that do affect fitness by the combination of selection and random genetic drift.

Evolution occurs at the population level; individuals do not evolve. An individual can only make an evolutionary contribution by producing offspring or dying childless.

The efficacy of selection depends on the effective population size, an historical construct that is different from the census population size, which is a snapshot of the present.

Evolution cannot create something out of nothing; there is no true novelty in evolution.

Evolution does not give rise to "intelligently designed" perfection. From an engineering point of view, most products of evolution work in a manner that is suboptimal.

Homo sapiens does not occupy a privileged position in the grand evolutionary scheme.

It's fun to play around with these. Take principle 10 seriously, for instance, and taxonomically restricted genes (so-called "orphans") represent a significant puzzle to neo-Darwinian evolution. The deepest question, of course, is this: Do these principles -- in particular, numbers 4 through 12 -- derive from observations, or are they imposed on observations?

Historical parallel:

And we recall that Galileo never made use of Kepler's ellipsi, but remained to the end a true follower of Copernicus who had said "the mind shudders" at the supposition of noncircular, nonuniform celestial motion.

(Gerald Holton, Thematic Origins of Scientific Thought, Harvard University Press, p. 64)

Indeed, one could take this catechism to London in November, to the Royal Society meeting on alternatives to neo-Darwinism, as a template for where heresy may be expected to arise.

The end of innocence?

"People Are Starting to See Scientists the Way They Really Are"

David Klinghoffer 

The public used to see politicians in far more exalted terms than they do now. The same fate befell the clergy. Now it's scientists.

Dr. Ivan Oransky, MD, of Retraction Watch gets a delicious write-up from Forbes:

Among the American public, trust in professional scientists and scientific journals is declining. Yet an overwhelming majority still believes that science "remains a source for good in the world." Could the public be on to something? Medical-doctor-turned-journalist Ivan Oransky thinks so. And it's a growing problem.

As editor and publisher of Retraction Watch, a closely followed industry blog that tracks peer-reviewed journal articles withdrawn from publication, Oransky is raising awareness of the impact that competition for grants and career advancement is having on the quality of the science being produced. Far from being above the fray and immune to corrupting influences, "Scientists are just as human as anyone else," says Oransky. And increasingly, "People are starting to see scientists the way they really are."

This is especially relevant to our concerns here:

Another major problem is that many study results cannot be reliable reproduced. Oransky cites a famous paper by Dr. John Iaonnidis, "Why most published research findings are false," that shows the inherent biases and the flawed statistical analyses built into most "hypothesis driven" research, resulting in publications that largely represent "accurate measures of the prevailing bias."

Scientific pronouncements as an "accurate measure of the prevailing bias" -- those are words to commit to memory. When we say things like that, they say we're "anti-science." No, just pro-realism about scientists.

Also quoted, Dr. Thomas Stossel of Harvard Medical School:

"I realized how fundamentally honest business people are compared to my academic colleagues, who'd run their grandmothers over for recognition."

As for non-scientists who have not yet been disabused of their childlike faith, one can only say: Growing up is hard to do.

On the echo chamber called settled science.

How Consensus Can Blind Science
Evolution News & Views 

The ruins of Mayan civilization impress anyone who visits. For Harvard astronomer Avi Loeb, they spoke to him about the philosophy of science then and now. Recounting his experience for  Nature, he describes the questions that came to his mind:

This summer, I visited the Mayan city of Chichén Itzá in the Yucatán Peninsula, Mexico. It has an ancient observatory where priest-astronomers made detailed astronomical observations around AD 600-1200. The ruins -- stepped pyramids, temples, columned arcades and other stone structures -- reveal that astronomy was at the heart of this sophisticated society.
The Mayans accurately tracked changes in the positions and relative brightness of the Sun, Moon, planets and stars. They documented their astronomical data in folding books called codices, with many more quantitative details than other civilizations at the time. The priest-astronomers used observations and advanced mathematical calculations to predict eclipses, and devised a 365-day solar calendar that was off by just one month every 100 years.

So why, I wondered, didn't the Mayans go further and infer aspects of our modern understanding of astronomy? They determined the orbital periods of Venus, Mars and Mercury around the Sun, but Earth was at the centre of their Universe.

Dr. Loeb knows he is a leading figure in today's consensus views in astronomy and cosmology. But unlike some others in his profession, he did not merely dismiss the Mayan achievements as works of a backward people lost in religious superstition. Turning his contemplations inward, he asked, "Have we learned our lesson, or is today's science similarly trapped by cultural and societal forces?"

Loeb pondered how the Mayans' detailed calculations were used to support a civilization that engaged in human sacrifice and planned warfare by the stars. "I came to appreciate how limiting prevailing world views can be," he says. In their day, Mayan astronomers were held in high social esteem. So are today's astronomers. Loeb thought about how "Cosmologists today collect vast amounts of exquisite data in surveys of large parts of the sky, costing billions of dollars." But Good data are not enough, he realized.

What might have helped the Mayans break out of the box of their prevailing world view? He hit upon a solution that should be of great interest to the intelligent design community.

The consequences of a closed scientific culture are wasted resources and misguided 'progress' -- witness the dead end that was Soviet evolutionary biology. To truly move forward, free thought must be encouraged outside the mainstream. Multiple interpretations of existing data and alternative motivations for collecting new data must be supported.
We hasten to clarify that so far as we know, Dr. Loeb is not an advocate of intelligent design, even though he has proposed a design inference for SETI . His advice, though, harks back to Darwin's own admonition: "A fair result can be obtained only by fully stating and balancing the facts and arguments on both sides of each question." The question in Darwin's day was design v. naturalism, as it is today. When it comes to origins, there aren't any other options. Either the universe is designed, or it is not. Would it not be limiting to the prevailing world view to assert that naturalism is the only side of the question?

Loeb gives a brief catalog of massive projects being funded by NASA and ESA. But then he gives a Kuhnian view of these efforts. Today's astronomers and cosmologists work within a paradigm as members of a guild who cannot see outside their project. Anomalies do not alarm them, as they should. Instead, they focus their attention of puzzle-solving to establish the paradigm -- not to overthrow it.

Such projects have a narrow aim -- pinning down the parameters of one theoretical model. The model comprises an expanding Universe composed of dark matter, dark energy and normal matter (from which stars, planets and people are made), with initial conditions dictated by an early phase of rapid expansion called cosmic inflation. The data are reduced to a few numbers. Surprises in the rest are tossed away.
I noticed this bias recently while assessing a PhD thesis. The student was asked to test whether a data set from a large cosmological survey was in line with the standard cosmological model. But when a discrepancy was found, the student's goal shifted to explaining why the data set was incomplete. In such a culture, the current model can never be ruled out, even though everyone knows that its major constituents (dark matter, dark energy and inflation) are not understood at a fundamental level.

He's absolutely right; in recent news reports, dark matter remains as mysterious as ever. Astronomers have leapfrogged from WIMPs to MACHOs to axions, finding no evidence for any of them, despite expensive searches with super-sensitive detectors. Perhaps a candidate particle will turn up some day, but without empirical evidence, have physicists improved on Mayan divination? Dark energy is even more mysterious. Nobody has any idea what that is. And there's more darkness:

How each culture views the Universe is guided by its beliefs in, for example, mathematical beauty or the structure of reality. If these ideas are deeply rooted, people tend to interpret all data as supportive of them -- adding parameters or performing mathematical gymnastics to force the fit. Recall how the belief that the Sun moves around Earth led to the mathematically beautiful (and incorrect) theory of epicycles advocated by the ancient Greek philosopher Ptolemy.
Similarly, modern cosmology is augmented by unsubstantiated, mathematically sophisticated ideas -- of the multiverse, anthropic reasoning and string theory. The multiverse idea postulates the existence of numerous other regions of space-time, to which we have no access and in which the cosmological parameters have different values.

We can become "blinded by beauty" that keeps us attracted to our own beliefs. Loeb mentions some paradoxes in cosmology that hint the consensus is on the wrong track. Modern cosmology is not knowledge, he says; it is organized ignorance! Only openness to other approaches can help reveal the extent of it.

Cultivating other approaches avoids stalling progress by investing only in chasing what might turn out to be 'epicycles'. After all, the standard model of cosmology is merely a precise account of our ignorance: we do not understand the nature of inflation, dark matter or dark energy. The model has difficulties accounting for the luminous gas and stars that we can see in galaxies, while leaving invisible what we can easily calculate (dark matter and dark energy). This state of affairs is clearly unsatisfactory.
The only way to work out whether we are on the wrong path is to encourage competing interpretations of the known data.

ID proponents might take advantage of Loeb's appeal in a way Paul Nelson relates in the new film Origin:

Often, when I'm reading the origin-of-life literature, considering some proposal for the formation, let's say, of RNA or proteins -- and even the author admits it's chemically implausible -- and I ask myself, How did he get himself into this jam?...
And at that impasse I want to say to the author, Look you know it's implausible, I know it's implausible, the reason that you ended up here standing at the edge of this cliff staring at implausibility is because way back down the road you decided that only a materialist explanation would work.

Dr. Timothy Standish adds:

How many different explanations that fail within the materialistic box do we have to have before we decide, maybe we need to move outside of that box. Maybe we need another kind of explanation.
When it comes to cosmology, Dr. Loeb is painfully aware of implausibilities in the naturalistic box: dark matter, dark energy, inflation, the multiverse, and the Anthropic Principle. But he is not just standing at the cliff, staring at implausibility; he is welcoming new thinking outside the box. It's an opportunity for a meaningful discussion of alternatives. And it was published in Nature, the world's leading science journal.

A healthy dialogue between different points of view should be fostered through multidisciplinary conferences that discuss conceptual issues, not just experimental results and phenomenology. A diversity of views fosters healthy progress and prevents stagnation. In September, I had the privilege of founding an interdisciplinary centre, the Black Hole Initiative at Harvard University in Cambridge, Massachusetts, which brings together astronomers, physicists, mathematicians and philosophers. Our experience is that a mix of scholars with different vocabularies and comfort zones can cultivate innovation and research outside the box. Already the centre has prompted exciting insights on the reality of naked singularities in space-time, the prospects for imaging black-hole silhouettes and the information paradox.
The "information paradox" refers to the conservation of information in the case of black holes. Think about what ID has to offer the admittedly stagnant field of consensus cosmology:

Theory of information: its source and conservation

A cause to explain the fine-tuning of the universe (e.g., see New Scientist) without the "cop-out" of the Anthropic Principle (New Scientist)

Mathematics, as seen in Origin's probability calculations for the origin of life, the Universal Probability Bound, and the "No Free Lunch" theorems

Philosophy of science unlimited by naturalism

A different vocabulary and comfort zone

Research outside the box

Loeb concludes, "Such simple, off-the-shelf remedies [i.e., multidisciplinary conferences] could help us to avoid the scientific fate of the otherwise admirable Mayan civilization." Would he extend his hand far enough to consider design? Perhaps not. But while the rise and fall of Mayan civilization is on his mind, leading him to ponder modern cosmology's potential for worldview blindness, the time seems right to engage the discussion.

Toward a theory of devolution VI

Testing Behe’s Principle that Darwin Devolves
Evolution News | @DiscoveryCSC

As Michael Behe has explained in these pages and in ID the Future podcasts, natural selection can appear to produce benefits to an organism, but at a cost. Most often, organisms carry on by breaking existing genes and proteins. This is the overriding message of his new book, Darwin Devolves. The tendency for existing complex functions to degrade in order to allow an organism to survive swamps any beneficial mutations that might arise de novo. 

Occasionally, excited headline writers proclaim that scientists are watching evolution happen in real time. Let’s scrutinize some of these claims to see what really happened. Did a new, innovative function arise by a beneficial mutation? Or did something break that provided a benefit in special circumstances?

News from the University of Wisconsin-Madison announces, “Radiation-resistant E. coli evolved in the lab give view into DNA repair.” Accompanied by a photo of undergrads (above, with postdoc Steven Bruckbauer) who “are watching evolution happen in real time,” the story appears ready to challenge Behe’s principle.

In a recent study published online in the Journal of Bacteriology, biochemistry professor Michael Cox and his team describe blasting E. coli bacteria with ionizing radiation once a week, causing the bacteria to become radiation resistant. In doing so, they have uncovered genetic mutations and mechanisms underlying this resistance.

Needless to say, high-energy ionizing radiation is not life’s friend. It’s a serious hazard for living things, including astronauts in the space station. If a microbe found a way to resist it, that’s something! First, though, the article calls this another case of “directed evolution” (aka intelligent design), not Darwinian evolution.

Their experiment in “directed” evolution is simple. Lead author and postdoctoral researcher Steven Bruckbauer split a population of E. coli into four groups. Once a week, he and a team of undergraduate researchers use equipment in the Department of Medical Physics to hit each population with ionizing radiation until 99 percent of the cells are dead. They then grow the survivors — the one percent that best resisted the radiation — in culture. Most of the new bacteria that grow from these carry beneficial mutations for radiation resistance.

Maybe it bears looking closer at what actually happened in this case. Lo and behold, the genes for resistance were already present in all the bacteria. 

While the overall mechanisms, such as enhanced DNA repair, are the same as in naturally resistant bacteria, many of the mutations that caused those changes have never been seen before. Bruckbauer adds that beyond DNA repair and changes to RNA polymerase, there are entirely new ways of being resistant that could arise.

Actual new functions were found! — but only in the imagination:

“These mechanisms for conferring resistance are just the ones we’ve seen,” he says. “It’s exciting to think about the novel possibilities we haven’t identified or that haven’t even evolved yet. There are some other mechanisms seen in nature that we expect to pop up eventually but then new ones might start evolving.”

The team celebrated after 125 rounds of zapping the bacteria, but then admitted that they only uncovered a previously existing “latent ability to become highly radiation resistant with modifications to a few existing DNA repair proteins.” It means that a stressful environment brought out something that was already present. Most likely, the “modifications to a few existing DNA repair proteins” broke regulatory controls on the repair system so that it became unleashed under this specific barrage of radiation. In any case, the bacteria survived, but nothing new evolved.

Gut Feelings

The human gut microbiome is a good place to test for innovative functions undergoing selection. Mutations happen so frequently, the microbiome could be evolving within our lifetimes. Isabel Gordo in PLOS Biology analyzes theoretical and experimental work on what kind of evolution is going on in those dark passageways. No surprise; it’s Darwinism by devolution:

The observed patterns of between-host polymorphism reject the predictions of a simple neutral model of molecular evolution for several human gut bacteria. Synonymous site polymorphism (i.e., that does not lead to changes in the protein sequence) exhibits a variance clearly inconsistent with a model, in which neutral mutations arise in each host and a single lineage transmits between hosts. However, the pattern of polymorphism at synonymous and nonsynonymous sites is consistent with the slightly deleterious theory of molecular evolution, in which widespread purifying selection may keep a microbial ecosystem functional, at long time scales, for all hosts. Much of the variation observed can be explained by postulating the recurrence of a high fraction (90%) of mutations whose effects decrease fitness by a very modest amount (approximately 0.01%) but still strong enough to be purified in the long run.

Staying Afloat

A study reported by Stanford University says that “Species evolve ways to backup life’s machinery.” Essentially, “A new analysis of biological data reveals that every species from bacteria to primates has developed ways to bypass breakdowns in the networks of proteins vital to sustaining life.” As Behe would put it, are organisms removing car doors to improve gas mileage? Are they tossing cargo overboard to keep from sinking?

The scientists studied 1,840 species — from bacteria to primates — to understand how evolution built life forms that could survive in the face of natural adversities. What they discovered was profound yet intuitive: Every species has evolved backup plans that allow its protein machinery to find bypasses and workarounds when nature tries to gum up the works. No previous study has ever surveyed such a broad swath of species to find a survival strategy common to all life: Develop a versatile and robust molecular machinery.

The “interactome” of life — the set of gene regulatory networks and protein interactions — must survive perturbations to keep organisms alive. Mutations do not construct new complex machines. This study says that they “gum up the works.” Unless species “from bacteria to primates” had pre-existing strategies to backup and survive degradation by mutations, life would quickly devolve to extinction.

Short Stories

Briefly, here are some other tests of Darwinism’s ability to innovate:

• A paper in PNAS by Milner et al. shows that fungi can gain new functions! Yes, but the method is by horizontal gene transfer (HGT) — i.e., by borrowing existing genes. Scientists found that fungi can gain transporter-encoded genes by HGT, giving them a “distinct competitive advantage in a given environment,” they say. “This has wide implications for understanding how acquisition of single genes by HGT can drastically influence the environments fungi can colonize.” How many other claimed instances of gain-of-function mutations are really cases of HGT?
• Darwin is devolving in beehives. Here is the honeybee version of the children’s story, “The Town Mouse and the Country Mouse.” Phys.org says that the “waggle dance” method of communication is disappearing in urban settings. “One possible reason may be human-induced habitat change,” which led to the loss of this complex, informative behavior.
• Another Phys.org article says that antibiotic resistance genes “spread faster than so far thought.” The reason? It’s not the emergence of novel genes by mutation. Instead, “resistance genes hop around the genome.” Methods of gene sharing include viruses, phages, and transposons. An international team was surprised to find that “mobile genetic elements induce a fast distribution of resistance genes among genomes of different organisms.” One said, “The finding that resistance is also extensively transferred between bacteria without the involvement of plasmids is really quite surprising.”
• Scientists found a plant genome with “among the most GC-biased genomes observed to date.” The parasitic plant uses only six amino acids, and is 95 percent composed of AT base pairs. “Darwin help us!” exclaims the exasperated author David Roy Smith in Current Biology. Apparently these two parasitic plants have forsaken richer genomes because they are able to get by with less.
• Let’s all evolve like the birds evolve. How do birds adapt their songs? With “preexisting genetic variation.” Lai et al., writing in PNAS, seemed to want to hear their favorite Darwin tune, but found that parrotbills in Taiwan select “standing genetic variation” instead of de novo mutations. They found that “the evolutionary potential of a population depends significantly on its preexistinggenetic diversity.” Selection of existing genetic variation is likely to swamp new beneficial mutations, because “a high level of standing variation may allow a faster response to environmental changes than waiting for appropriate mutations to arise.” Understandably so.
• Are humans evolving new beneficial mutations? Analysis of the human genome at the University of Barcelona identified 2,859 genes that apparently have been under selective pressure. Further reading shows that some of these result from “hybridisation of the human species with the Neanderthals and other hominid species,” which implies sharing of existing genetic information. Other genetic changes aiding survival in certain environments, such as for lactose tolerance or ability to endure high altitudes (hypoxia), may result from relaxation or breaking of controls of existing genes. Overall, the research is revealing “how the introgression of archaic genomes have modelled our current genomes.”

These examples show that all life, from cells to primates, do survive the onslaught of nature’s attempts to “gum up the works” with mutations. They do this, though, not by innovation of complex new functions by chance. Instead, they go to desperate extremes to stay alive in spite of mutations. They can exchange pre-existing genetic information from other sources. They can rely on built-in mechanisms to fix and work around the mutations. In short, Behe is right: Darwin devolves, yet life goes on.

Darwin just keeps on Devolving?

Behe on Joseph Thornton’s Work: “A Big Monkey Wrench that Even I Did Not Expect”
David Klinghoffer | @d_klinghoffer

In  Darwin Devolves,  Michael Behe demonstrates the limitations of unguided evolution from the work of “dyed in the wool” Darwinists themselves. We’ve focused so far on National Academy of Sciences member Richard Lenski at Michigan State, with whom Behe has had an extensive back-and-forth.

Lenski has conducted the famed Long Term Evolution Experiment on which Behe draws extensively. But another outstanding researcher, Joseph Thornton at the University of Chicago, also comes in for praise and examination in the book. Professor Behe talks with host Andrew McDiarmid about Thornton’s work, which throws “a big monkey wrench [in the strained argument for Darwinism] that even I did not expect.”

Download the podcast or listen to it here.

It was interesting to see fellow University of Chicago biologist Jerry Coyne casually shoehorn Thornton into a Washington Post review of Darwin Devolves as a supposed defeater for irreducible complexity.  As Behe noted here,  “I spent half of Chapter 8 on Thornton’s work, discussing why it shows deep and unexpected problems for Darwinian evolution. Coyne not only doesn’t summarize my argument, he doesn’t even tell readers I make one.” That is typical.

Physics vs. Darwin

Physicist David Snoke on Denton's Evolution: Still a Theory in Crisis
David Klinghoffer February 23, 2016 12:50 PM

I highly recommend reading a review, by University of Pittsburgh physicist David Snoke, of Michael Denton's Evolution: Still a Theory in Crisis. It's fascinating and wonderfully lucid. While expressing some disagreement, he concludes that the book deserves to sit on the same shelf with Stephen Jay Gould's work -- a high compliment whatever your position on evolutionary questions.

I think that Dr. Snoke's comments as a physicist are particularly helpful and illuminating. He draws a comparison to the "topological argument" well known in his profession:

We are all so programmed by the current evolutionary debate to see Darwinian evolution as the only viable materialist theory that it is hard to understand at first what Denton is proposing, if not intervention from a spirit world, and it is hard to grasp that there were evolutionists who preceded Darwin, with strong arguments against Darwin's ideas. To understand Denton's view (and Owen's) it is crucial to realize that it is first and foremost an empirical theory. Science has a long tradition of empirical theories which simply state the facts in unifying language without proposing any mechanism at all to explain them. Thus, for example, Newton famously proposed that gravity force could act at a distance, without proposing any explanation why. We are all so used to Newton's laws now that we forget how empirically driven it was. The same empirical approach was used to build the Periodic Table of chemistry, long before quantum mechanics explained why it has the form it does. In the same way, Denton, following Owen, draws us to look at a glaring and obvious fact of nature: that living organisms do not exist in a continuum of small differences with gradual transitions between them; rather, they exist in highly distinct types and forms, with specific identities and unique features for each type. Thus, for example, mammals all have four limbs, five digits per limb, two eyes, mammary glands in pairs, etc. These patterns persist over hundreds of millions of years despite all manner of selective pressure in different directions.

Darwinian evolutionists are familiar with these properties, of course, and have a standard explanation that they are leftover vestiges from archetypal ancestors. Against this, Denton has two main arguments. First, the record strongly supports the view that new Forms appear suddenly, without precursors. This is known as "saltation" -- the sudden appearance of a fully formed new structure. In all of the cases we know, the "transitional forms" between one type of organism and another do not consist of creatures with half-novelties, but rather, creatures with whole and complete novelties. Their transitional nature is identified because they have a subset of a larger set of several wholly novel features belonging to later descendants. But in each step that we see along the way, that which is new is whole and complete. The problem this creates for Darwinian evolution is similar to what is called a "topological argument" in physics. There are some things that can be continuously transformed into other things, while some things cannot. In the canonical example, a coffee cup can be transformed continuously into a doughnut, but not into a saucer. In the same way, all feathers are tubular, which requires a follicle with circular form, while reptile scales are flat sheets. Topologically, a flat sheet cannot be continuously transformed into a tube. (It was fascinating to me to hear that the dinosaurs-acquiring-feathers story actually creates new problems for Darwinism.) There are also more generalized topological arguments. Some molecular cycles in the cell are circular -- the so-called "chicken-and-egg problems" in which element A is required to create element B, and B is required to create C, but C is required to create A. These loops therefore have the same toplogical problem of lack of continuous generation from a prior process.

The transitional forms which indicate common descent also therefore create huge problems for gradual change via Darwinian selection as a mechanism. The most plain reading of the data is "descent with saltation." This occurs at every level. New organs occur suddenly, new processes occur suddenly (such as human language), and new genes occur: in every form of life there are whole genes (known as ORFans) that appear to be utterly unique to that form, with no homolog in any other type of creature. In some cases, even when genes from an ancestor are used, they are pressed into service to perform utterly new functions via the sudden appearance of a completely new set of switches and timers.

Snoke wrote his review for the Christian Scientific Society, so not surprisingly he asks about the relevance for Christians of Denton's "heavily empirical and materialist book." The "materialist" descriptor may be a little confusing, since Denton's view also "sounds a lot like neo-Platonism." Anyway, Snoke says this about anatomical features that seem to serve no purpose:

The idea of robust Forms is worth examining for the Christian. As Denton notes, much Christian thinking has been as utilitarian as Darwinist thinking. We tend to assume that everything in living systems must have a useful function. Perhaps some things, especially overall architectures, have their particular form not for function but for beauty or diversity. This leads to, for example, a helpful way of looking at the problem of male nipples. If we ask "What are male nipples for?" we are assuming a fully utilitarian view of living forms, and can get into knots trying to decide what they are good for, or if God has made a mistake. If we adopt a view of Forms, we can say that male nipples exist because the proper form for human bodies is to have nipples there.

Also, regarding the implications of Denton's thinking that run contrary to Darwinian racism:

The idea of Forms also makes a difference when think about race and racism. Darwinism has always had an ugly flirtation and sometimes open marriage with racism. If all of life is a continuum of gradual changes, then it makes sense that various subgroups of humans would be at different stages in evolutionary development, some closer to apes and others closer to the next upward step. Darwin argued in The Descent of Man that "lower" versions of humans such as Hottentots were proof of his theory of evolution. But Denton makes the case that, like other creatures, humans have had a stable single Form since they first existed, with all the basic gifts of language and culture in all geographical locations from the very beginning.

Snoke observes the irony that current evolutionary thinking is so hidebound -- "calcified," is how he puts it -- that it took Discovery Institute, leading advocate of intelligent design (not a materialist theory), to give a forum to Dr. Denton, whom Snoke sees as a sort of latter-day Gould. I think Denton's structuralism is in fact best understood as a form of ID. But the point is well taken. In today's orthodox evolutionary circles, protected from criticism behind walls of academic prestige, the spirit of intellectual exploration and discovery is largely extinguished.


Editor's note: Get your copy of Evolution: Still a Theory in Crisis now. For a limited time, you'll enjoy a 30 percent discount at  CreateSpace by using the discount code QBDHMYJH.

Published paper on nervous system's information processing does just fine minus Darwinian gloss.

Design Paper Hits a Home Run
Evolution News &Views

Baseball lovers will appreciate this glimpse into what your senses and nerves have to do to bat a homer. A news item from Oregon State:

Researchers have discovered a mechanism of intercellular communication that helps explain how biological systems and actions -- ranging from a beating heart to the ability to hit a home run -- function properly most of the time, and in some scenarios quite remarkably. [Emphasis added.]

It's a noisy world out there. The batter can't focus on irrelevant sounds from the stands. The information coming in through his senses has to be sorted and organized quickly. Simple but accurate representations must be served to the brain. Then, the brain's decision has to signal responses in the muscles, nerves and heart. All this must happen very quickly. Each cell is a player on a vast field:

In this process, a chemical stimulus called ATP functions as a signaling molecule, which, in turn, causes calcium levels in a cell to rise and decline, and tells a cell it's time to do its job -- whether that be sending a nerve impulse, seeing a bird in flight or repairing a wound. These sensing processes are fundamental to the function of life.

So how does the body pull all this together? There are trillions of cells involved, all signaling each other. The resulting "interactive chatter" among them would be overwhelming, but the body takes advantage of collective wisdom. Physicist Bo Sun at OSU explains:

"The thing is, individual cells don't always get the message right, their sensory process can be noisy, confusing, and they make mistakes," Sun said. "But there's strength in numbers, and the collective sensory ability of many cells working together usually comes up with the right answer. This collective communication is essential to life."

Cells have a way of voting a consensus:

This interactive chatter continues, and a preponderance of cells receiving one sensation persuade a lesser number of cells reporting a different sensation that they must be wrong. By working in communication and collaboration, most of the cells eventually decide what the correct sensory input is, and the signal that gets passed along is pretty accurate.

Now let's put it together in a real-life situation requiring rapid response. Watch a baseball play from the cells' perspective, as the batter sees a 93-mile-per-hour fastball coming in low:

The photoreceptor cells in the batter's eyes see the pitch coming. Some cells see it as a curve in the dirt, and some mistake it for a changeup, a slower pitch. But the majority of the cells come to the correct conclusion, it's a fastball at the knees, and they spread the word. After extensive communication between all these cells, a conclusion is reached and the correct message is sent to neurons in the brain.

Think how fast this has to happen. That's a pretty rapid committee meeting! The conclusion is barely out the eyeballs, and the fastball keeps coming at 93 mph.

The brain cells, in turn, send a strong signal through nerves to muscles all over the batter's body, the shoulders, legs, and especially arms. The signals arrive and once again a collaborative process takes place, deciding what the message is and how to react. Calcium ions in muscle cells are triggered and a brutally fast-but-accurate response is triggered, swinging the bat. This entire process, from the ball leaving the pitcher's hand to contact with the bat, takes less than half a second.

Nobody bats a thousand, we know. The real wonder is that the batter connects at all.

On a perfect day -- the cellular debate over what pitch was coming was sufficiently short-lived, the timing exact, the muscle contractions just right -- the ball explodes off the bat and sails over the center field fence.
On a more realistic day -- since the best hitters in the world only succeed 3 times out of 10 -- the ball bounces weakly to the second baseman for an easy out. This in turn triggers the collective groans of 30,000 disappointed fans. But the heart has cellular communication that continues to guarantee its normal beating, and the player lives to bat another day.

Behind this colorful description is a scientific paper in the Proceedings of the National Academy of Sciences about the chemical details of cellular signaling, without the baseball references. The paper is notable for its mention of "design principles" and utter lack of Darwinian vocabulary like natural selection, phylogeny, or evolution. Enjoy this refreshing outlook, loaded with design concepts:

Decoding the cellular response to environmental perturbations, such as chemosensing, photosensing, and mechanosensing, has been of central importance in our understanding of living systems. To date, most studies of cellular sensation and response have focused on single isolated cells or population averages. An emerging picture from these studies is the set of design principles governing cellular signaling pathways: these pathways are organized into an intertwined, often redundant network with architecture that is closely related to the robustness of cellular information processing.

The Oregon State researchers had a hunch that a higher level of information processing is going on:

However, many examples suggest that collective sensing by many interacting cells may provide another dimension for the cells to process environmental cues. Examples, such as quorum sensing in bacterial colonies, olfaction in insects and mammals, glucose response in the pancreatic islet, and the visual processing of retinal ganglion cells, suggest a fundamental need to revisit cellular information processing in the context of multicellular sensation and response, because even weak cell-to-cell interaction may have strong impact on the states of multicellular network dynamics. In particular, we seek to examine how the sensory response of cells in a population differs from that of isolated cells and whether we can tune between these two extremes by controlling the degree of cell-cell communication.

They've set up an intriguing question. How does the inside of a body respond to cues from the outside? What translates sensations into chemical signals? How are those signals communicated inside cells and between cells? The OSU team describes their approach:

We study a population of fibroblast cells that responds to a chemical stimulus (ATP) and communicates by molecule exchange. Combining experiments and mathematical modeling, we find that cells exhibit calcium oscillations in response to not only the ATP stimulus but also, increased cell-cell communication. Our results show that, when cells are together, their sensory responses reflect not just the stimulus level but also, the degree of communication within the population.

And thus, with exemplary scientific techniques, they shed light on a phenomenon of great interest to us all. OSU's Dr. Sun explains why this is "remarkable":

"These processes of collective sensory communication are usually accurate, but sometimes work better than others. Mistakes are made," Sun said. "Even so, this process makes life possible. And when everything goes just right, the results can be remarkable."

We don't know if these folks at OSU will appreciate the applause, but ask any researcher anywhere: Would a Darwinian spin have added anything to this paper? Baseball games are familiar to us all, and each time a batter swings, these phenomena -- cell signaling, quorum sensing, and information processing -- really happen. The evidence for "design principles" is pretty clear every time the batter connects with the ball. Learning about how that happens makes for good scientific work; it is sufficient without a narrative gloss about how it might have "evolved."
Show us the phenomenon, describe how it works, and advance our understanding with sound laboratory practices. If the phenomenon exhibits good design principles, it's OK to say so. If all scientists followed OSU's example in this paper, and if science reporters wrote like the author of the news items cited above, then the science-consuming public would be well served.

Between education and indoctrination.

What Is Teaching Evolution All About?
Sarah Chaffee 

In Education Week, Adam Laats and Harvey Siegel offer a seemingly humane and generous compromise on teaching evolution in public schools. "Teaching Evolution Isn't About Changing Beliefs," says the headline.

Authors of a new book from the University of Chicago Press, Teaching Evolution in a Creation Nation, they argue that students should learn about evolution, but not be indoctrinated in it. Students, they say, simply need to understand the theory, but teachers should not force them to believe it.

While I agree with part of their approach, their propositions are obvious -- almost too much so. They write:

By teaching comprehensive science curricula that includes evolution and teaching students to confront subjects they may not agree with, schools are not trying to change beliefs. Understanding is enough.

On one level, this makes a lot of sense. Students do need to understand evolution. It is important that teachers educate them on the evidence for neo-Darwinism.

This approach is also a big improvement on recent National Science Foundation-supported research aimed at investigating ways to get students to accept -- not just understand -- evolution.

However, Laats and Siegel leave out some crucial information. For one thing, they seem to believe that only parents who think "the world is only 6,000 years old" would have a problem with teaching evolution as unquestionable dogma. Not so.

Many parents and educators who value critical thinking and, frankly, honesty in education advocate that students be exposed to the fascinating ambiguities of current knowledge about biological origins.

The authors, however, simply ignore that there is a major scientific debate over evolution. They say:

Evolutionary theory is a building block of our understanding of life. As the best existing scientific explanation of the way our species came to be, how evolution works is vital for all students to understand. Students should not have the right to opt out of learning about a central tenet of contemporary science. But if students have religious objections to the theory's implications, the public school has no right to insist that they believe it -- that is, to regard evolutionary theory as true.

Much of this is very close to correct, as far as it goes. They neglect to mention, though, that some scientists are currently questioning whether Darwinian evolution is "the best" explanation -- and therefore if it is indeed foundational to our "understanding of life."

Researchers are asking whether natural selection acting on random mutations is able to account for the complexity of life. If Darwinian theory with its proposed mechanism of change is in need of a major reevaluation, as substantial mainstream scientific opinion now concedes, that should not be concealed from young people. Not if education is about seeking the truth.

The real issue isn't "creationism" or religion versus evolution. I should add too, for the umpteenth time, it's not about intelligent design either. (See our Science Education Policy.) It's about whether students will be introduced to a fair picture of mainstream research on a vital subject of scientific inquiry.

This brings us to the second part of Laats and Siegel's argument: Teachers should require students simply to understand -- not accept -- evolution. Again, this is true. A teacher should not try to make a student internalize any theory of evolution. They can simply require that the student learn the proposition -- which should mean analyzing it intelligently not just spitting it back on command -- if they want to achieve a certain grade. But students may not be gaining an accurate understanding of evolution if they learn only the scientific strengths, and not the weaknesses, of the theory.

Laats and Siegel try to outline what teaching evolution is not about. But they do not address what it is about. The goal of scientific instruction, ultimately, is not to confirm or upend any religious teaching.


It is partly about how information is presented. But it is mostly about the information itself -- interacting with it, and drawing conclusions based on critical reasoning and examining the evidence.

Darwin is outnumbered and outgunned?

Vindicated by Behe: Devolution Is Natural, Evolution Is Not.

 Granville Sewell

 

 

I know many other mathematicians and engineers who share my low opinion of Darwinism, but most are reluctant to express their views publicly because they feel that the issue is simply outside their area of expertise and they will not be taken seriously. I also tend to defer to specialists on scientific issues outside my discipline — until those specialists try to tell me something clearly absurd, for example, that unintelligent forces alone could have reorganized the basic particles on Earth into computers and airplanes and Apple iPhones. Then I don’t hesitate to jump into the debate. I have done so, for example, in a 2000 Mathematical Intelligencer opinion piece, “A Mathematician’s View of Evolution,” and in a 2017 Physics Essays article, “On ‘Compensating’ Entropy Decreases.”

A Very Simple Principle

It is really not necessary to be a biochemist or a paleontologist to understand the main issue in the debate between Darwinism and intelligent design. That is because it is a very simple principle, as I keep emphasizing: natural (unintelligent) causes do not create order (or information). They destroy it. That is the main theme of the first half of my video “Why Evolution Is Different.”

While every other natural process tends to turn order into disorder, Darwinists have always believed that natural selection is the one unintelligent process in the universe that can create spectacular order out of disorder. So I feel vindicated by Michael Behe’s new book, Darwin Devolves, which disputes this belief, and argues that despite all the claims about the creative powers of natural selection, it has never actually been observed to produce anything new and complex, only “devolution”:

 Darwinian evolution proceeds mainly by damaging or breaking genes, which, counterintuitively, sometimes helps survival. In other words, the mechanism is powerfully devolutionary. It promotes the rapid loss of genetic information. Laboratory experiments, field research, and theoretical studies all forcefully indicate that, as a result, random mutation and natural selection make evolution self-limiting….Darwin’s mechanism works chiefly by squandering genetic information for short-term gain.

Only Devolution Occurred

As another illustration that selection and mutations can only degrade, in this interview on German TV, geneticist Wolf-Ekkehard Lönnig recounts (minutes 24:00 to 28:00, turn on English subtitles if you don’t speak German) the well-funded attempts at, among other places, his own Max Planck Institute for Plant Breeding Research, to speed up evolution in plants using radiation and advanced artificial selection techniques. Lönnig reports that only devolution occurred: the only progress observed before this effort was given up was that the genes that made some plants toxic were damaged, making these plants more useful as animal fodder.

That it seems even superficially plausible that random mutations could produce major improvements relies completely on the observed but inexplicable fact that while they are awaiting rare favorable mutations, living species are able to preserve their complex structures and pass them on to their descendants without significant degradation, generation after generation.

To appreciate how astonishing this is, imagine that it were possible (though it is far beyond our current technology) to construct a fleet of cars that contained completely automated car-building factories inside, with the ability to construct new cars — and not just normal new cars, but new cars containing automated car-building factories inside them. If we left these cars alone and let them reproduce themselves for many generations, is there any chance we would eventually see major advances arise through natural selection of the resulting duplication errors?

Of course not. We could confidently predict that the whole process would grind to a halt after a few generations without intelligent humans there to fix the mechanical problems that would inevitably arise. And we don’t need to know the details of how these cars work and reproduce to predict this, because there is a simpler principle involved here: devolution is natural, evolution is not.

The Argument Could Not Be Clearer

I am very grateful that there are biologists like Michael Behe and W.E. Lönnig who doubt Darwinism, because doubts expressed by mathematicians like me would otherwise never be taken seriously. But you really do not have to study the biochemical details to understand why the accumulation of genetic accidents cannot produce human brains and human consciousness. And you do not really need to study mutations for thirty years, as Lönnig has done, to predict that bombarding plant chromosomes with radiation would not lead to major agricultural advances.

The argument against Darwinism, or any other attempt to explain what has happened on Earth without intelligent design, could not be simpler or clearer: a few fundamental, unintelligent, forces of physics alone cannot rearrange the fundamental particles of physics into computers and airplanes and Apple iPhones. And any attempt to explain how they can must break down somewhere, because they obviously can’t