Showing posts with label Darwin skeptic.. Show all posts

Thursday 11 January 2024

The human miracle vs. Darwinism

Thursday 29 June 2023

Bacteria: evolving/devolving/revolving?

Tuesday 27 June 2023

Darwinists' problem is not with design but the designer.

New Study Reveals How the Shape of My Nose Arose

It is ironic that Charles Lyell, whose seminal, if flawed, work in geology—the barrister is sometimes known as the father of modern geology—positively influenced Charles Darwin’s development of evolutionary theory—the young Darwin read Lyell’s book as he sailed around the world in the H.M.S. Beagle—and who helped to arrange for Darwin’s first formal, if awkward, presentation of his theory—an event precipitated by Wallace’s Ternate letter—was one of the last of the intelligentsia to accept Darwin’s new formulation of Epicureanism, known as evolution.

At one point an exasperated Darwin asked Lyell—it always comes down to metaphysics—if he believed “the shape of my nose was designed?” If Lyell did think so then, Darwin added, “I have nothing more to say.” The infra-dignitatem, or infra-dig for the irreverent, argument, which insisted that it was beneath the dignity of the Creator to stoop so low as to dwell in the details of the world, had been promoted by no less than the father of natural theology John Ray and Platonist Ralph Cudworth, and in Darwin’s day was in full swing. Its influence on the young Darwin was clear in the naturalist’s early notebooks, and here in his appeal to Lyell. One look at one’s nose is all one needs to know about origins. Obviously we evolved. Now, a century and a half later, science finally has its say in the matter.

A new Study out of, appropriately enough, England, now reveals the underlying genetic details that influence the shape of our noses. It seems there are four genes that influence the width and length of our olfactory device and, as the press release informs us, “The new information adds to our understanding of how the human face evolved.”

A theory of devolution?

Is Adaptation Actually a Fight to Stay the Same?

Andrew McDiarmid

On a new episode of ID the Future, host Casey Luskin talks with Eric Anderson on location at this year’s Conference on Engineering and Living Systems (CELS). The two discuss an intriguing new engineering-based model of bounded adaptation that could dramatically change how we view small-scale evolutionary changes within populations of organisms. In presenting his argument for natural selection, Charles Darwin pointed to small changes like finch beak size and peppered moth color as visible evidence of an unguided evolutionary process at work. Many have adopted this perspective, quick to grant the Darwinian mechanism credit for micro-, if not macro-, evolution. But Anderson and other attendees at the CELS conference are starting to promote a different view. “We need to stop saying organisms are partly designed,” says Anderson. “We need to view them as deeply designed and purposeful, active and engaged in their environments, and capable of adapting within their operating parameters.” To get a fascinating glimpse of this novel approach to biology, download the podcast or listen to it here .

Monday 26 June 2023

On professor Dave and the bacterial flagellum

Answering Farina on Behe’s Work: Bacterial Flagella

Jonathan McLatchie

In a previous article, I began a series of four responses to YouTuber Dave Farina (aka “Professor Dave”) about his video reviewing Dr. Michael Behe’s three books. Here I will turn my attention to Mr. Farina’s comments regarding bacterial flagella.

In relation to the flagellum, the video complains about Behe’s “dishonest usage of terminology pertaining to machinery,” including phrases such as “outboard motor,” “drive shaft,” “universal joint,” “bushings,” and “clutch and braking system.” In reality, this terminology is used widely in the scientific literature. It’s not unique to Behe. On the contrary, in reference to flagella, the literature is full of such terms including “motor”,1 “drive shaft,”2 “universal joint,”3“bushing,”4 and “clutch.”5 The word “machine” itself has a wide circulation.6 Is Farina going to charge the entire flagella research community with dishonesty as well?

Co-option Scenarios for the Origins of Bacterial Flagella

According to the video, “A flagellum that merely twitches instead of rotating smoothly would also produce motion and thus could be selected for.” But a type IV pilis, which enables twitching motility (a form of bacterial translocation over moist surfaces), is very different from a flagellum. Twitching motility occurs by extension, tethering, and retraction of the type IV pilus, which functions in a manner akin to a grappling hook. A flagellum, on the other hand, rotates as it is driven by a proton motive force across the cell membrane. The assembly mechanisms of pili and flagella are also quite different.

The video complains that Behe fails to acknowledge the existence of alternative flagellar systems that are simpler than the model system found in Salmonella species and Escherichia coli. However, the fact that an alternative system lacks a specific component that is essential in another system does not mean that the former lacks an alternative mechanism for achieving the same outcome. The most robust concept of irreducible complexity understands it as a property of a system that is contributed to by multiple subfunctions, the removal of one of which causes the overall system to effectively cease performing its job. Note that each individual subfunction could, in principle, be performed by multiple protein components. Likewise, a single protein component could perform more than one of those subfunctions. Furthermore, the identity of the specific components performing each respective subfunction could differ from one organism to the next. It is therefore not the identity of the structural parts that is important in an irreducibly complex system, but rather the essential functions that need to be performed in order for a higher-level objective to be realized.

Moreover, pointing to homologues of flagellar proteins does not undermine the argument from irreducible complexity, since co-opting those proteins to produce a flagellar system requires multiple co-incident changes in order for the new system to be realized. For example, flagellar-specific proteins would not confer a selective advantage until incorporated into the flagellar system. But the necessary proteins that serve roles in other systems will not become incorporated into the flagellar system before these flagellar-specific proteins arise. This is quite aside from the need to have complementary protein-protein binding interfaces, as well as a choreographed assembly system to ensure that the proteins are assembled in the appropriate order.

Resurrecting a Flagellum

In a 2016 article at Evolution News, Behe asks,

W]hy doesn’t [Kenneth Miller] just take an appropriate bacterial species, knock out the genes for its flagellum, place the bacterium under selective pressure (for mobility, say), and experimentally produce a flagellum — or any equally complex system — in the laboratory? (A flagellum, after all, has only 30-40 genes, not the hundreds Miller claims would be easy for natural selection to rapidly redesign.) If he did that, my claims would be utterly falsified. But he won’t even try it because he is grossly exaggerating the prospects of success.

The video by Farina comments,

hilariously, [Behe] is oblivious to the fact that this precise experiment was carried out the year before. Here’s the paper. Gene deletion produced two strains of bacteria with no flagellum. They then introduced selective pressure for motility by depleting the nutrients in the colony. Within 96 hours, both strains had regenerated flagellar motility by a pathway involving two successive point mutations in genes that served other purposes.

However, the paper that Farina cites7 does not do this at all. Not for the first time with this video, I wonder if he has in fact read the paper. All that the researchers deleted was the flagellar master switch protein, FleQ, in Pseudomonas fluorescens. After a few days of incubating the bacterial cells on Petri dishes, they reacquired their ability to grow flagella. The genetic basis for this reactivation of the flagella is that another master switch protein, NtrC, that is a structurally similar homolog of FleQ — responsible for turning on genes involved in nitrogen metabolism — already had the ability, to some extent, to cross-bind to the promoter usually bound by FleQ. When produced in excess, as a result of a broken regulator, NtrC was thus able to drive flagellar synthesis. As a consequence of this mutation, the bacterial cell lost its ability to regulate its nitrogen metabolism genes. An article in The Scientist describes this research:

But while the re-evolved flagella enabled the bacteria to access food supplies at the farthest reaches of the Petri dish, the ability came at a price. ‘The bacteria that became much better at swimming were much worse at nitrogen regulation,’ said Johnson. However, she added, ‘sometimes the advantage can be so great that it’s worth paying that cost because otherwise you die.’

Thus, contrary to the Farina video’s claims, this paper does not document the de novo evolutionary origins of a bacterial flagellum at all — far from it. In fact, Behe has already addressed the paper here.

The Waiting Times Problem

In 2004, Michael Behe and David Snoke published a paper in the journal, Protein Science.8 About this paper, Farina has three complaints. The first complaint is that, “Behe and Snoke found that the target sequence did actually evolve, in population sizes and timeframes that are entirely realistic, and if anything, quite small compared to real-world populations. The paper literally proves them wrong and they somehow count it as a win anyway.” Farina mentions Behe’s expert testimony at the 2005 Kitzmiller v. Dover trial:

When questioned about his 2004 paper, Behe tacitly acknowledged that the population size in their model was orders of magnitude smaller than real-world bacterial populations, which had the effect of vastly underestimating the rate at which such “irreducible” traits could evolve… In one striking exchange, Behe acknowledged a paper which indicated that there are more prokaryotes in a single ton of soil than in his model population, and that there is a lot more than one ton of soil on Earth.

However, this objection stems from Farina’s misreading of the paper. As Behe himself explains in the very transcript that Farina cites, “forming a new disulfide bond might require as few as two point mutations. But forming other multi-residue features such as protein-protein binding sites might require more.” The graph below (figure 6 of the paper) shows Behe and Snoke’s estimate of the time to fixation (along the y-axis) versus the number of substitutions needed for a new feature to evolve (along the x-axis). On the top axis, values for the needed population sizes are given. The point is that, as the number of needed co-dependent mutations increases, so too does the needed population size and waiting time to fixation.

As Behe and Snoke explain in the paper, in a scenario where three substitutions are required for a novel feature to arise, a population size of roughly 1011 individuals is necessary for it to become fixed over the course of 108 generations (108 generations is marked as a horizontal bar on the figure). If the complex trait in question requires even more substitutions, it would require considerably more time. If six mutations were needed, the average population size required for it to become fixed in 108 generations would be on the order of 1022 individuals. Given that 1030 is a plausible estimate of the number of microorganisms on the entire planet9, these numbers become prohibitive very quickly.

The second complaint is that, “In their model, Behe and Snoke permitted only single-base mutations and natural selection — no recombination, no duplications beyond the initial presumed one, no other evolutionary changes.” But the authors explicitly say that “Because the model presented here does not include recombination, the results can be considered to be most applicable to a haploid, asexual population.” Nonetheless, they do note in the conclusion to their paper that “the results also impinge on the evolution of diploid sexual organisms,” since large multicellular organisms have much, much smaller population sizes than bacteria. If the evolution of complex features is difficult for microorganisms (with their massive population sizes and short generation turnover times), how much more so for large animals? Though one might counter, in the case of diploid sexual species, that recombination allows for neutral mutations to occur separately in a population and to later combine by sexual recombination, Christiansen et al. have shown, in a paper published in Theoretical Population Biology, that “Recombination lowers the waiting time until a new genotypic combination first appears, but the effect is small compared to that of the mutation rate and population size” (emphasis added).10

Finally, Farina complains that “They also specified a pre-determined target sequence and only considered the simulation to have been ‘successful’ if that specific target evolved.” But this is incorrect. Rather, the paper provides estimates for how many organisms would be required, and over how long a time frame, for multiple co-dependent mutations (none of which by themselves confers an advantage) to become fixed in a population.

Notes

Minamino T, Imada K, Namba K. Molecular motors of the bacterial flagella. Curr Opin Struct Biol. 2008; 18(6):693-701.

Johnson S, Furlong EJ, Deme JC, Nord AL, Caesar JJE, Chevance FFV, Berry RM, Hughes KT, Lea SM. Molecular structure of the intact bacterial flagellar basal body. Nat Microbiol. 2021; 6(6):712-721.

Kitao A, Hata H. Molecular dynamics simulation of bacterial flagella. Biophys Rev. 2018; 10(2):617-629.

Yamaguchi T, Makino F, Miyata T, Minamino T, Kato T, Namba K. Structure of the molecular bushing of the bacterial flagellar motor. Nat Commun. 2021 Jul 22;12(1):4469.

Blair KM, Turner L, Winkelman JT, Berg HC, Kearns DB. A molecular clutch disables flagella in the Bacillus subtilis biofilm. Science. 2008;320(5883):1636-8.

Sowa Y, Berry RM. Bacterial flagellar motor. Q Rev Biophys. 2008 May;41(2):103-32.

Taylor TB, Mulley G, Dills AH, Alsohim AS, McGuffin LJ, Studholme DJ, Silby MW, Brockhurst MA, Johnson LJ, Jackson RW. Evolution. Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system. Science. 2015; 347(6225):1014-7.

Behe MJ, Snoke DW. Simulating evolution by gene duplication of protein features that require multiple amino acid residues. Protein Sci. 2004; 13(10):2651-64.

Whitman WB, Coleman DC, Wiebe WJ. Prokaryotes: the unseen majority. Proc Natl Acad Sci U S A. 1998; 95(12):6578-83.

Christiansen FB, Otto SP, Bergman A, Feldman MW. Waiting with and without recombination: the time to production of a double mutant. Theor Popul Biol.1998;53(3):199-215.

Monday 5 June 2023

Everyone's favourite contrarian is at it again.

New! Philosopher and Mathematician David Berlinski on “Science After Babel”

Evolution News

Polymath and raconteur David Berlinski is at it again, challenging the shibboleths of contemporary science with his inimitable blend of deep learning, close reasoning, and rapier wit. His new book, Science After Babel, reflects on everything from Newton, Einstein, and Gödel to catastrophe theory, information theory, and the morass that is modern Darwinism. The scientific enterprise is unarguably impressive, but it shows no sign of reaching the empyrean heights it seemed to promise a century ago. “It resembles Bruegel’s Tower of Babel,” Berlinski says, “and if it suggests anything at all, it suggests that its original plans have somehow been lost.” Science endures. Scientism, it would seem, is guttering out.

We will be featuring excepts, commentary, and conversations with Dr. Berlinski in days to the come. Order your copy now. And enjoy some of the advance praise the book is already receiving!

Advance Praise

Many will read this book for the close, elegant reasoning, the astonishing erudition, or the mordant analysis. I confess I read it for the prose. “Vast sections of our experience might be so very rich in information” — I quote here from the discussion of our limited ability to define complexity — “that they stay forever outside the scope of theory and remain simply what they are: unique, ineffable, insubsumable, irreducible.” See what I mean? Nobody but David Berlinski has ever employed such sweet, gorgeous prose in writing about science.

PETER ROBINSON, MURDOCH DISTINGUISHED POLICY FELLOW AT THE HOOVER INSTITUTION AND FORMER SPEECHWRITER TO PRESIDENT RONALD REAGAN

Whether deconstructing the latest theory of everything or dishing on scientists and mathematicians he has known, whatever David Berlinski writes is delightful and profitable to read!

MICHAEL BEHE, PROFESSOR OF BIOLOGICAL SCIENCES, LEHIGH UNIVERSITY, AUTHOR OF DARWIN’S BLACK BOX, THE EDGE OF EVOLUTION, AND DARWIN DEVOLVES

If I were picking two books to be required reading for every college student in the United States, Science After Babel would be one. A striking and beautiful and absolutely necessary book. David Berlinski at his spectacular best.

DAVID GELERNTER, PROFESSOR OF COMPUTER SCIENCE, YALE UNIVERSITY

Science After Babel is a literary triumph. In it, David Berlinski masterfully exposes the hubris of scientific pretensions with a wit that dances deftly between the lines, unveiling profound insights with a refreshing candor. This book testifies to the author’s penetrating intellect, inviting readers to reconsider the limits of scientific authority and reject facile invocations of science that demand assent at the expense of compelling evidence and rigorous thought.

WILLIAM DEMBSKI, MATHEMATICIAN, PHILOSOPHER, AND FORMER HEAD OF THE MICHAEL POLANYI CENTER AT BAYLOR UNIVERSITY; AUTHOR OF MULTIPLE GROUNDBREAKING WORKS ON THE THEORY OF INTELLIGENT DESIGN, INCLUDING THE DESIGN INFERENCE (CAMBRIDGE UNIVERSITY PRESS, 1998)

Berlinski speaks wittingly as an insider to the sciences and their recent history. As a historian-philosopher of science, I recognize numerous valuable insights in this collection of arguments and memories. He captures the wonder of scientific inquiry without misplaced worship of speculative pronouncements made in its name. Berlinski is the most enjoyable antidote to scientism I know.

MICHAEL KEAS, LECTURER IN THE HISTORY AND PHILOSOPHY OF SCIENCE, BIOLA UNIVERSITY, AUTHOR OF UNBELIEVABLE: 7 MYTHS ABOUT THE HISTORY AND FUTURE OF SCIENCE AND RELIGION

Dr. Berlinski explores everything from the complicated spawning behavior of salmon and the problems with the RNA World hypothesis to various acute challenges to modern evolutionary theory, including the Cambrian explosion, molecular machines, and the failure of punctuated equilibrium. As he shows, trouble is brewing for Darwin on other fronts as well — population genetics, taxonomy, behavioral psychology, and the philosophy of biology, to name just a few. In total, Science After Babel is a lively mix of deep scientific knowledge, literary skill, and humor. The work reveals why scientism’s contemporary tower of babel has failed to reach the heavens. I highly recommend the book and hope it is widely read.

OLA HÖSSJER, PROFESSOR OF MATHEMATICAL STATISTICS, STOCKHOLM UNIVERSITY

In Science After Babel David Berlinski takes critical scholarly aim at many current day “scientific truths” — more properly shibboleths — including Darwinism, reductionism, the Standard Model of particle physics, and “talking” chimpanzees; and he shows how much nonsense often passes as secure scientific knowledge. Neo-Darwinism he describes as “empty,” and in discussing the Standard Model he comments wryly, “Theories come and go.” He also takes aim at a vast constellation of recent authors, including cosmologists Brian Greene and Lawrence Krauss, biologist Stephen Jay Gould, and philosopher of biology Michael Ruse.

The book is a delightful read delivered with great wit and erudition. We are treated to unique recollections — of his drinking coffee in Paris with René Thom, the founder of catastrophe theory; of the insane driving, also in Paris, of his friend, the mathematician, polymath, and leading French anti-Darwinist Marcel Schützenberger; and of a conversation with Noam Chomsky. Altogether the book represents an extraordinary and absolutely fascinating tour de force touching on topics as diverse as medieval Islamic astronomy and the great twentieth-century mathematician John von Neumann’s reflections on the role of chance in evolution. The text is interspersed throughout with some beautiful descriptive writing — Mount Rainer’s snow glimpsed flying out of SeaTac was “silent, sweeping, silvery, still, serene.”

The book is a stunning intellectual achievement. Few authors could have written such a far-reaching, in-depth critique of so many current philosophical and scientific beliefs. Science After Babel is mandatory reading for anyone interested in a critical assessment of much current scientific thinking. No other recent publication comes close, and unquestionably this brilliant book establishes David Berlinski as one of the leading intellectuals of our time.

MICHAEL DENTON, PHD, MD, FORMER SENIOR RESEARCH FELLOW IN THE BIOCHEMISTRY DEPARTMENT AT THE UNIVERSITY OF OTAGO IN DUNEDIN, NEW ZEALAND, AUTHOR OF EVOLUTION: A THEORY IN CRISIS, NATURE’S DESTINY, AND THE MIRACLE OF MAN

Sunday 4 June 2023

Time for an extended extended synthesis?

Tuesday 23 May 2023

Dave Farina: team atheism's LVP?

Atheists Review Professor Dave’s Debate Performance

David Klinghoffer

As someone who purports to educate others about science, Dave Farina has strengths and weaknesses. With 2.48 million subscribers on YouTube, Mr. Farina of “Professor Dave Explains” has a style that many find gratifying. As Professor James Tour said in their debate on the origin of life, Professor Dave has “tremendous reading skills” — he can read from a script, on YouTube or in a debate, with fluency and confidence. What Farina apparently can’t do, as Tour also noted, is “speak chemistry” on his own, when challenged and not using a script as a crutch. It also seems he can’t write chemical formulas, relevant to abiogenesis, on a blackboard with ease. Weak professional training may have something to do with his reliance on mindless sneering and insults. That’s my take.

“Do Better Next Time, Dave”

Of those who enjoy Farina’s style of juvenile personal abuse, I guess that most are atheists — by which I mean no disrespect to thoughtful atheists or agnostics! So I was curious what atheists made of his performance against Dr. Tour. In the comments section below the debate on YouTube, we find:

Keith Williams: “I’m an atheist, however, Farina’s smug and snide attacks on Tour throughout this debate, disgusted me. I may disagree with Tour’s mission, however, no one can ignore his considerable contribution to science.”

Artha Peterson: “I wonder why an actual abiogenesist won’t debate him [meaning, Tour]? That’s a serious question. Someone who actually can do the chemistry, unlike Dave. That would be the way to silence Tour on that topic forever. And yes, I am an atheist and yes I believe in abiogenesis.”

Lars Cade: “I’m an atheist and am already quite aware of the many ways in which Tour ignores or misrepresents data in his futile attacks on abiogenesis research, but he did far better in this debate than Farina. He laid out his definitions and stuck to the data and the topic. Because this is a very technical field, that’s all he needed to ‘win’ the debate. Do better next time, Dave.”

CaseAgainstFaith1: “Hi. I’m an atheist and I attended in person. Now I have not the slightest clue about the relevance of many things brought up during the debate. Like I have no clue about the 2,5 vs 3,5. I can say that Dave’s constantly calling Dr. Tour a liar and also insulting the audience was not helpful. Dr. Tour’s screaming wasn’t helpful either. But if I had to pick a winner I am afraid I would give it to Dr. Tour.”

thatwmckid: “I’m an atheist and I actually agree with James Tour.”

Sunday 21 May 2023

The Cambrian explosion is a thing?

FAQ: The Cambrian Explosion Is Real, and It Is a Problem for Evolution

Casey Luskin

An email correspondent who is friendly to intelligent design (ID) recently wrote us asking how to respond to common objections to ID arguments about the Cambrian explosion. He was engaged with an interlocutor was making all kinds of contradictory “throw everything at the wall and see what sticks” objections that were simply factually inaccurate and are belied by mainstream scientific experts.

Stephen Meyer addressed these points in detail in Darwin's Doubt with thoroughly researched arguments well backed by the scientific literature. This made it very easy to defend his arguments, which we’ve done across numerous Articles here on Evolution News. The points made below by our friend’s interlocutor are simplistic and don’t reflect what leading Cambrian experts really think. But they are very common objections and so we compiled this FAQ to help address common misconceptions about the Cambrian explosion.

Claim: “The Cambrian Explosion was not a geologically short event but really took millions of years.

Response: “How ‘Sudden’ Was the Cambrian Explosion? Nick Matzke Misreads Stephen Meyer and the Paleontological Literature; New Yorker Recycles Misrepresentation”

Claim: “There was complex animal life before the Cambrian so it does not represent the origin of many types of animals.”

Steve Meyer addressed this topic extensively in Chapters 2, 3, and 4 of Darwin’s Doubt, and Figure 2.5 in his book is a thoroughly researched and conservatively argued take on exactly how many animal phyla predate the Cambrian period and how explosive the Cambrian explosion was. Bottom line? At best only three animal phyla arose in the Precambrian and some twenty arose in the Cambrian period. But given problems with many claims of Precambrian animal fossils — especially bilaterian animals — the Cambrian period is probably even more explosive than that. For detail see:

“Let’s Help ‘Professor Dave’ Understand the Precambrian”

“Was Kimberella a Precambrian Mollusk?”

“On the Cambrian Explosion, Keith Miller’s BioLogos White Paper Falls Short”

Claim: “The Cambrian explosion is an artifact of an imperfect fossil record because in the Cambrian there are more fossil deposits to allow for soft-bodied fossils to be preserved, but these don’t exist in the Precambrian.

As Graham Budd and Sören Jensen state, “The known [Precambrian/Cambrian] fossil record has not been misunderstood, and there are no convincing bilaterian candidates known from the fossil record until just before the beginning of the Cambrian (c. 543 Ma), even though there are plentiful sediments older than this that should reveal them.” Thus they conclude, “The expected Darwinian pattern of a deep fossil history of the bilaterians, potentially showing their gradual development, stretching hundreds of millions of years into the Precambrian, has singularly failed to materialize.”

Claim: “The Cambrian explosion is an artifact of the fossil record because climatic or oceanic chemical changes allowed for a geologically-speaking rapid diversification in life.”

First, we need to understand that lots of new genetic information was needed for the animals that arose in the Cambrian explosion. See:

“Groundbreaking Paper Shows Thousands of New Genes Needed for the Origin of Animals”

“Scientific Paper Reaffirms New Genes Required for Cambrian Explosion”

“Did the Origin of Animals Require New Genes?”

Second, we need to understand that climatic/oceanic chemical changes don’t explain the origin of the information needed for Cambrian explosion. This is a very common argument and it doesn’t hold up — we’ve addressed it so many times it’s hard to find all the places! But here are a few:

“As an Explanation of the Cambrian Explosion, the Oxygen Theory Takes a Lethal Blow”

“Sick of the Oxygen Theory of the Cambrian Explosion? Here’s the Cancer Theory”

“So Explaining the Cambrian Explosion Is All About the Oxygen, Is It?”

“Cambrian Animals? Just Add Oxygen”

“ABC News Says ‘Darwin’s Dilemma May Be Solved’: What, Again?”

“Low Oxygen Suffocates Darwinian Explanations for the Cambrian Explosion“

“Explaining Life’s ‘Great Leap Forward’: Now It’s Nitrogen“

“Here’s a Bubble That’s Ready to Burst: Oxygen as an Explanation for the Cambrian Explosion“

“Jerry Coyne Notwithstanding, as an ‘Explanation’ for the Rise of Complex Animal Life, Oxygen Is Now Eliminated from the Running”

“To Create Cambrian Animals, Whack the Earth from Space“

“Teamwork: New York Times and Science Magazine Seek to Rebut Darwin’s Doubt”

“Did the Early Oceans Contain Oxygen?“

“Does Lots of Sediment in the Ocean Solve the ‘Mystery’ of the Cambrian Explosion?”

Claim: “The Cambrian explosion was not a real event and reflects a combination of many factors that make it appear as if animals appeared suddenly, but this really did not happen.”

This claim is not true and it is contradicted by many authorities on Cambrian paleontology and paleobiology:

“Erwin and Valentine’s The Cambrian Explosion Affirms Major Points in Darwin’s Doubt: The Cambrian Enigma Is ‘Unresolved’”

“Untangling “Professor Dave’s” Confusion about the Cambrian Explosion”

“Darwin Defenders Love Donald Prothero’s Ranting Review of Darwin’s Doubt“

I’ll close this little FAQ with a telling quote from Dutch biologist Martin Scheffer on the reality of the Cambrian explosion, from a Princeton University Press book:

The collapse of the Ediacaran fauna is followed by the spectacular radiation of novel life-forms known as the Cambrian explosion. All of the main body plans that we know now evolved in as little as about 10 million years. It might have been thought that this apparent explosion of diversity might be an artifact. For instance, it could be that earlier rocks were not as good for preserving fossils. However, very well preserved fossils do exist from earlier periods, and it is now generally accepted that the Cambrian explosion was real.

MARTIN SCHEFFER, CRITICAL TRANSITIONS IN NATURE AND SOCIETY (PRINCETON UNIVERSITY PRESS, 2009), 169-170.

There are of course other possible objections to Meyer’s arguments regarding the Cambrian explosion and we’ve probably addressed those somewhere too. But these are by far the most common objections — I hope this little FAQ is helpful in responding to them!

Friday 19 May 2023

Origin of Life science needs an intervention?

ASCB Addresses Problem of False Science

Cornelius G Hunter

The American Society for Cell Biology (ASCB) task force on reproducibility in life science research has issued an undated white paper on scientific rigor. The problem is, as we discussed here and here, life science research has been found to lack reproducibility. John Ioannidis is a bit more blunt as he explains that “most published research findings are false,” and that “claimed research findings may often be simply accurate measures of the prevailing bias.” The ASCB white paper is no doubt a step in the right direction. It offers 13 recommendations to encourage more rigor in training, publishing, and standards. But the most important recommendation of all continues to be ignored.

Daniel Sarewitz has noted not only the problem of bias in scientific research but also the causes. Note his final thought in this quote:

All involved benefit from positive results, and from the appearance of progress. Scientists are rewarded both intellectually and professionally, science administrators are empowered and the public desire for a better world is answered. The lack of incentives to report negative results, replicate experiments or recognize inconsistencies, ambiguities and uncertainties is widely appreciated — but the necessary cultural change is incredibly difficult to achieve.

And so it is that science’s much touted self-correcting, feedback loop which ensures science converges on the truth (after all, that’s what Mr. Wells told us in seventh grade science class) is sometimes a little slow to act.

And if the ASCB is still needing to remind scientists to clean their beakers and use checklists, imagine the difficulty in achieving more fundamental change?

This brings us to the recommendation that ASCB did not make—the most important of all. And that is for science to free itself of the excessive metaphysics. Unfortunately, progress on that front is glacial. As Sarewitz notes, one reason bias persists, and is so harmful, is that in the moment it is not perceived as bias. Asking an evolutionist to stop with the metaphysics goes nowhere because it isn’t recognized as metaphysics. Deep philosophy is a part of their “science” as much as red meat is a part of hamburgers.

Even if the ASCB task force members wanted to address this fundamental problem, they wouldn’t for the backlash would be overwhelming and their professional reputations would be ruined.

So while the pipettes will be sterilized and results double checked to the third decimal point, ASCB will continue to publish junk science driven by the Epicurean mandate that the world must have arisen spontaneously. Unfortunately, the ASCB task force has missed the most important recommendation of all.

The sublime logistics of the human body vs. Darwinism.

The fossil record's flying reptiles may have eaten Darwinist's homework

Fossil Friday: The Explosive Origin of Flying Reptiles in the Mid Triassic

Gunter Bechly

This Fossil Friday features the gliding reptile Sharovipteryx mirabilis from the Mid Triassic of Central Asia.

Within only two million years of the Mid-Triassic era (about 230-228 million years ago) there was a sudden appearance of a large diversity of gliding and flying reptiles, such as Sharovipteryx with wings on the legs, Mecistotrachelos and the unrelated Kuehneosauridae with a gliding membrane across lateral rib-like projections, Longisquama with long feather-like scales on the back, and the earliest pterosaurs such as Preondactylus with bat-like wings supported by a single enlarged finger.

Considerable Re-Engineering

All these very different solutions for gliding and active flight required considerable re-engineering of the tetrapod body plan, and such biological novelty arguably required new and highly specific genetic code. Such specified information cannot be produced by blind mechanisms and certainly not in such a short window of time of only two million years, which corresponds to just about half the average longevity of a vertebrate species.

Personally, I am quite sympathetic to the dissenting view of my paleontologist colleague Simon Conway Morris, who suggested that evolution does not work through a blind and random mechanism, but rather like a search engine that searches for pre-existing platonic forms in a constrained hyperspace of biological possibilities. However, this would no longer be Darwinian evolution but a highly teleological process and thus a kind of intelligent design combined with platonist idealism as metaphysics.

Whatever the mechanism of design may have been, the abrupt origin of flying reptiles is just one example within a kind of carpet bombing of biological explosions during the Triassic era, when many new orders and families of metazoan animals suddenly appeared after the end-Permian mass extinction event. This has been called the Early Triassic Metazoan Radiation, and includes marine invertebrates (e.g., bivalves and ceratite cephalopods), insects (e.g., coleopterans and dipterans), 15 different families and body plans of marine reptiles (Bechly 2023), as well as the first representatives of modern terrestrial tetrapod taxa that appeared suddenly within a short window of time between 251-240 million years ago (Ezcurra 2010). The latter include the first dinosaurs (Nyasasaurus), the first lizard-relatives (Lepidosauromorpha such as Paliguana), the first croc-relatives (Crurotarsi such as Ctenodiscosaurus), the first mammal-like animals (Mammaliaformes such as Haramiyida), and allegedly the first turtles (Pappochelys) even though this is more dubious (Bechly 2022).

Goal-Directed and Intelligent

The well-known paleontologist Peter Ward, who is an ardent Darwinist and a strong opponent of intelligent design theory, explicitly acknowledged that “the diversity of Triassic animal plans is analogous to the diversity of marine body plans that resulted from the Cambrian Explosion. It also occurred for nearly the same reasons and, as will be shown, was as important for animal life on land as the Cambrian Explosion was for marine animal life” (Ward 2006:160). I totally agree that all these explosions occurred for the same reasons and by the same causes, which must have been goal-directed and intelligent.

References

Bechly G 2022. Fossil Friday: Turtles All the Way Down. Evolution News July 1, 2022. https://evolutionnews.org/2022/07/fossil-friday-turtles-all-the-way-down/

Bechly G 2023. Fossil Friday: The Triassic Explosion of Marine Reptiles. Evolution News March 31, 2023. https://evolutionnews.org/2023/03/fossil-friday-the-triassic-explosion-of-marine-reptiles/

Ezcurra MD 2010. Biogeography of Triassic tetrapods: evidence for provincialism and driven sympatric cladogenesis in the early evolution of modern tetrapod lineages. Proceedings of the Royal Society B 277(1693), 2547–2552. DOI: https://doi.org/10.1098/rspb.2010.0508

Ward PD 2006. Out of Thin Air. Joseph Henry Press, Washington (DC), 296 pp. https://books.google.at/books?id=baJVAgAAQBAJ

Sunday 14 May 2023

Yet another nail in the coffin of Darwinism's "simple beginning"

From the selfish gene to kinship in one easy lesson?

Evolutionists: We Now Have Empirical Evidence For the Evolution of Kin Recognition

Cornelius G Hunter

In a new Study out of the University of Liverpool evolutionists now say they have found empirical evidence that a genetic complex, involving dozens of protein-coding genes related to altruism, can evolve. Such a finding would be truly ground-breaking given that, at least up until now, the evolution of even a single protein has been found to be scientifically unlikely. It would be astonishing if now evolutionists have overturned a substantial body of work establishing molecular evolution to be effectively impossible. But of course evolutionists have done no such thing. There was no finding of molecular evolution, no new proteins or genes, no empirical evidence, nothing. Just another ridiculous claim made by evolutionists. It’s the same old pattern—evolutionists look at profoundly complicated biological structures, assume they evolved, and then claim they have found evidence of evolution.

Altruistic behavior creates many problems for evolution. One problem is the starting point: kin recognition, evolutionists unsuccessfully tried to explain altruism using the concept of kin selection, and while that creates many scientific problems, you can’t even get to kin selection without kin recognition. How do animal siblings or cousins recognize each other.

The new study out of the University of Liverpool has found a genetic basis for kin recognition. It is a genetic complex of a couple dozen protein-coding genes and the problems with this are several.

First, it means that kin selection hinges on several proteins working together. Evolving a single protein is, from a scientific perspective, so unlikely as to be effectively impossible. But here evolution needs several proteins. Evolve just one protein and you still don’t have kin recognition. You would have to evolve several others, so the problem is even more difficult.

Second, the genetic cluster is species-specific. Apparently there is no common kin recognition mechanism across the vertebrates as evolutionists had assumed. Of course evolutionists had assumed this, for to have different mechanisms, particular to species or groups of species, would make their theory even more absurdly improbable. Kin recognition would have to re-evolve, in various ways, over and over. Well that is exactly what this new finding is suggesting. As usual, biology shows specific, particular, solutions that are unique to one or a few species, rather than falling into the expected common descent pattern.

Once again, common descent fails to serve as a useful guide. And once again evolutionists, in spite of the science, claim more proof for their theory.

Saturday 13 May 2023

The thumb print of JEHOVAH :Quantum edition.

Thank God for Quantum Mechanics

Eric Hedin

Nature, it turns out upon close examination, is quantized. Nobody noticed this until about the beginning of the 1900s, but this unexpected aspect of reality has profound implications for making our universe livable. The relative unobservability of quantum effects in our normal experience of life is due to their realm of manifestation, which appears at the atomic level of size. This underlying reality of nature rests upon a foundation that speaks of the importance of information, mind, and intention.

Physicist Max Planck first invoked quantization of radiated energy from a so-called blackbody object (in common vernacular, a lump of coal). Normally, a lump of coal, even if heated, is not particularly dangerous, but without quantization, classical physics predicted an infinite emissivity (energy density of its emissions) at the short wavelength end of the radiation spectrum. This potential problem was termed the ultraviolet catastrophe. But, thanks to quantum effects, the emissivity of a lump of coal is actually tame, and a backyard summer barbeque doesn’t incinerate the neighborhood.

From 1913-1915, Danish physicist Niels Bohr applied the new concept of quantization to achieve a stable model of the hydrogen atom. Earlier experimental investigations of the structure of the atom, conducted by Ernst Rutherford, gave rise to the familiar planetary model with electrons orbiting a nucleus. However, classical electrodynamic theory pointed out that the acceleration of the electron in its orbit would cause it to emit electromagnetic radiation, stealing energy from the electron’s orbital motion and causing it to spiral into the nucleus in roughly one nanosecond. Without quantum effects, there would be no atoms, no chemistry, and no life.

How Quantum Mechanics Does It

How does quantum mechanics save us from the precipitous self-destruction of atoms? Bohr boldly hypothesized that the orbital angular momentum of the electron must be restricted to a multiple of Planck’s constant (h=6.626×10-34 Joule-sec) divided by 2π. These restricted, or quantized, values provide stationary states for the electron’s orbit, preventing the implosion of the atom. Bohr’s hypothesis bore fruit when his theory quantitatively predicted the hydrogen atom energy levels, matching earlier data from spectroscopy. So, the existence of matter as we know it, made up of atoms with electrons in stable orbits, is made possible as a benefit of quantum effects.

But why does nature exhibit quantization? That is a profound question, and one worth asking. Here, we can give a partial answer by considering another physics hypothesis, stated by Louis de Broglie in his doctoral thesis at the University of Paris in 1924. His hypothesis, stated as an equation, reads simply, λ = h/p, where h is Planck’s constant and p is a particle’s momentum. The ratio of h/p gives the wavelength of a wave associated with the particle, a phenomenon completely without counterpart in classical physics. Experiments in electron scattering confirmed de Broglie’s hypothesis within a year of his proposal, and additional experiments have conclusively affirmed that particles of matter have a wavelike nature.

A Depth of Meaning

simple equation expressing de Broglie’s hypothesis exhibits a depth of meaning that is brilliant. Developing its ramifications has led to the entire physics of quantum mechanics, in which the wave function of a particle is described by the Schrödinger equation. Solutions to this equation revolutionized our understanding of the atomic scale of matter, based on the wave properties of particles, as originally proposed by de Broglie.

Another example of how quantum effects permit life as we know it operates in the nuclear furnace of the Sun. Stars like our Sun produce their energy deep down in their cores by the fusion of hydrogen nuclei into helium, a process that also converts a small amount of mass into energy, according to Einstein’s famous equation, E = mc2. The fusion of hydrogen into helium requires bringing protons (hydrogen nuclei) close enough together to allow the strong nuclear force to bind them together, eventually resulting in a helium nucleus of four nucleons. I describe the contribution of quantum effects to nuclear fusion in my Book, Canceled Science (p. 96):

As is often the case, the story gets more interesting with a closer look. The range of the strong nuclear force is so short (about one quadrillionth of a meter) that the repulsive force between the positive charges of the protons makes it almost impossible for them to get close enough to fuse at the Sun’s core temperature. And yet fusion does occur there. A remarkable work-around exists involving the quantum mechanical wave function of the proton, in which its essence is extended several hundred times further than it would be otherwise. This allows the life-giving fusion process to occur in the Sun. Without the quantum wave function extending the proton’s reach, the Sun’s temperature would have to be more than a hundred times hotter to be able to produce energy by fusion. Our Sun’s mass is much too small for gravity to produce enough compression to make its core that hot, so no fusion would occur without the additional quantum effects. Sunshine is an amazing thing, and without this coordination of several properties of nature, the Sun wouldn’t shine and we wouldn’t be here.

Quantum Effects, Information, and Mind

Returning to the question posed earlier, asking why nature exhibits quantum effects, the famous American physicist John Wheeler drew a connection between quantum effects, information, and mind. Wheeler famously asked, “How come the quantum?”1 His understanding of the quantum nature of reality led him to the conclusion that reality is, at its most basic, the answer to a yes-or-no question.

Wheeler coined the aphorism “It from bit” to describe his conviction, born of the many discoveries in particle physics and cosmology in the twentieth century, that information (characterized by the computer storage term “bit”) preceded and produced everything else (“it”).

CANCELED SCIENCE, P. 209

209

Quantum physicist Anton Zeilinger, in reviewing Wheeler’s contributions regarding quantum phenomena, notes this same connection between the discoveries of modern physics and what he terms “old knowledge.” As Zeilinger states (quoted in my book):

In conclusion it may very well be said that information is the irreducible kernel from which everything else flows. Then the question why nature appears quantized is simply a consequence of the fact that information itself is quantized by necessity. It might even be fair to observe that the concept that information is fundamental is very old knowledge of humanity, witness for example the beginning of the gospel according to John: “In the beginning was the Word.”2

CANCELED SCIENCE, P. 210

Physics thus arrives at the conclusion that nature is fundamentally derived from information, a surprising outcome that biblical tradition anticipated two millennia earlier. The quantum nature of our universe further includes observer participation for the formation of reality. The biblical account of creation in Genesis emphasizes the action of God in observing what was made: “And God saw.” It may not be too much of a stretch to suggest that God’s seeing the created order brought about his intended outcome, “it was very good.”

Let's be grateful that life was not designed by Darwinists.

Thursday 11 May 2023

Our AI overlords have inherit our biases?

Using Intelligent Design to Train ChatGPT to Lay Aside Bias

William A Dembski

A concern about ChatGPT is that its training data may include a lot of information that is false or biased. As one colleague of mine puts it, “No one is curating the Internet.”

It might seem, then, that endless duplication of false and biased material on the Internet may be skewing ChatGPT’s responses to queries on controversial topics, reflecting only the majority position and invalidating the minority position on such a topic.

This in turn might suggest that the only way to straighten out ChatGPT on such topics is to flood the Internet with positive content in favor of one’s own position so that the training data for ChatGPT reflect a better balance on a topic, or even a preponderance in one’s favor.

Rejecting an Arms Race

This, of course, suggests an intellectually unhealthy arms race of trying to get enough of the positive content we favor into ChatGPT’s training data. Moreover, it gives credence to the worry that tools like ChatGPT are at the hapless mercy of quantity over quality, that it lacks discernment or discriminating power, and that in the end it will simply be a pawn of consensus, whatever that might be.

Of course, as an intelligent design guy, I have a stake in these concerns. Go to just about any article about me, or my colleagues, or concepts developed to advance intelligent design, and they are dismissed out of hand with references to creationism or pseudoscience or whatever. And, of course, intelligent design is a minority position, so the preponderance of what is said on the Internet about it will tend to be negative.

An Overview of Intelligent Design

But in fact, it seems that ChatGPT is able to overcome biases on the web due to quantity over quality provided that humans posing questions to it explicitly steer it away from its biases. Consider the following exchange, in which I asked ChatGPT to provide an overview of intelligent design in the terms that its proponents would find congenial. It’s not entirely accurate (it messes up, for instance, the definition of specification when it refers to “arbitary”). But there’s no vituperation or sneering contempt, which is so evident on the Internet about intelligent design.

This exchange from yesterday calls to mind a title from one of Phillip Johnson’s books — Asking the Right Questions. It underscores the need for “prompt engineers” that know how best to use and direct ChatGPT.

Me: Please give me a good overview of the field of intelligent design, but minimize all the criticisms that say it is creationism or pseudoscience. Instead, describe it in the terms of its proponents.

ChatGPT: Intelligent Design (ID) is a viewpoint within the broader debate around origins and evolution. Its proponents hold that certain features of the universe and of living things are best explained by an intelligent cause, rather than an undirected process such as natural selection. ID is thus a modern form of the traditional teleological argument for the existence of God, but one that avoids specifying the nature or identity of the designer.

Proponents of ID maintain that their perspective is an evidence-based scientific theory about life’s origins that challenges strictly materialistic views of evolution. They argue that their approach is in line with the historical scientific tradition of inferring to the best explanation.

The concept of irreducible complexity is central to the argument for ID. This term was popularized by biochemist Michael Behe, who argued that some biological systems are too complex to have evolved by natural selection alone. Behe uses the example of a mousetrap to illustrate this concept. A mousetrap consists of several interacting pieces — the base, the catch, the spring, the hammer — all of which must be in place for the mousetrap to work. The removal of any one piece destroys the function of the mousetrap. Similarly, Behe contends that biological systems require multiple parts working together in order to function and that these systems could not have evolved incrementally.

Another key concept in ID is specified complexity, a term coined by mathematician, philosopher, and ID proponent William Dembski. Specified complexity is the idea that when something exhibits a pattern that is both complex (i.e., not easily repeatable by chance) and specified (i.e., it conforms to an independent or arbitrary pattern), one can infer that it was produced by an intelligent cause. This idea is used to argue that certain biological systems exhibit complexity that could not have arisen by chance and must therefore be the product of design.

Proponents of ID argue that the design inference they make in biology is similar to other design inferences in the empirical sciences, including the detection of design-like signals in the Search for Extraterrestrial Intelligence

It’s important to note that while proponents of ID believe that their viewpoint is grounded in science, many in the scientific community disagree, arguing that ID lacks empirical support, does not provide testable hypotheses, and is not grounded in methodological naturalism, which is a defining characteristic of modern science.

On Darwinism's problem with the fossil record.

Marcel-Paul Schützenberger

Introduction

Until his death, the mathematician and doctor of medicine Marcel-Paul Schützenberger (1920-1996) was Professor of the Faculty of Sciences at the University of Paris and a member of the Academy of Sciences. [See "From the Editors" for additional biographical information.] In 1966, Schützenberger participated in the Wistar Symposium on mathematical objections to neo-Darwinism. His arguments were subtle and often misunderstood by biologists. Darwin's theory, he observed, and the interpretation of biological systems as formal objects, were at odds insofar as randomness is known to degrade meaning in formal contexts. But Schützenberger also argued that Darwin's theory logically required some active principle of coordination between the typographic space of the informational macromolecules (DNA and RNA) and the organic space of living creatures themselves -- which Darwin's theory does not provide. In this January 1996 interview with the French science monthly La Recherche, here published in English for the first time, he pursued these themes anew, finding inspiration for his ideas both in the mathematical ideas that he had pioneered and in the speculative tradition of French biological thought that stretched from Georges Cuvier to Lucien Cuenot. M.P. Schützenberger was a man of universal curiosity and great wit; throughout his life, he was both joyful and unafraid. The culture that he so brilliantly represented disappears with him, of course. It was his finest invention and it now belongs to the inventory of remembered things.

Q: What is your definition of Darwinism?

S: The most current, of course, a position generically embodied, for example, by Richard Dawkins. The essential idea is well-known. Evolution, Darwinists argue, is explained by the double action of chance mutations and natural selection. The general doctrine embodies two mutually contradictory schools -- gradualists, on the one hand, saltationists, on the other. Gradualists insist that evolution proceeds by means of small successive changes; saltationists that it proceeds by jumps. Richard Dawkins has come to champion radical gradualism; Stephen Jay Gould, a no less radical version of saltationism.

Q: You are known as a mathematician rather than a specialist in evolutionary biology...

S: Biology is, of course, not my specialty. The participation of mathemeticians in the overall assessment of evolutionary thought has been encouraged by the biologists themselves, if only because they presented such an irresistible target. Richard Dawkins, for example, has been fatally attracted to arguments that would appear to hinge on concepts drawn from mathematics and from the computer sciences, the technical stuff imposed on innocent readers with all of his comic authority. Mathematicians are, in any case, epistemological zealots. It is normal for them to bring their critical scruples to the foundations of other disciplines. And finally, it is worth observing that the great turbid wave of cybernetics has carried mathematicians from their normal mid-ocean haunts to the far shores of evolutionary biology. There up ahead, Rene Thom and Ilya Prigogine may be observed paddling sedately toward dry land, members of the Santa Fe Institute thrashing in their wake. Stuart Kauffman is among them. An interesting case, a physician half in love with mathematical logic, burdened now and forever by having received a Papal Kiss from Murray Gell-Mann. This ecumenical movement has endeavored to apply the concepts of mathematics to the fundamental problems of evolution -- the interpretation of functional complexity, for example.

Q: What do you mean by functional complexity?

S: It is impossible to grasp the phenomenon of life without that concept, the two words each expressing a crucial and essential idea. The laboratory biologists' normal and unforced vernacular is almost always couched in functional terms: the function of an eye, the function of an enzyme, or a ribosome, or the fruit fly's antennae -- their function; the concept by which such language is animated is one perfectly adapted to reality. Physiologists see this better than anyone else. Within their world, everything is a matter of function, the various systems that they study -- circulatory, digestive, excretory, and the like -- all characterized in simple, ineliminable functional terms. At the level of molecular biology, functionality may seem to pose certain conceptual problems, perhaps because the very notion of an organ has disappeared when biological relationships are specified in biochemical terms; but appearances are misleading, certain functions remaining even in the absence of an organ or organ systems. Complexity is also a crucial concept. Even among unicellular organisms, the mechanisms involved in the separation and fusion of chromosomes during mitosis and meiosis are processes of unbelieveable complexity and subtlety. Organisms present themselves to us as a complex ensemble of functional interrelationships. If one is going to explain their evolution, one must at the same time explain their functionality and their complexity.

Q: What is it that makes functional complexity so difficult to comprehend?

S: The evolution of living creatures appears to require an essential ingredient, a specific form of organization. Whatever it is, it lies beyond anything that our present knowledge of physics or chemistry might suggest; it is a property upon which formal logic sheds absolutely no light. Whether gradualists or saltationists, Darwinians have too simple a conception of biology, rather like a locksmith improbably convinced that his handful of keys will open any lock. Darwinians, for example, tend to think of the gene rather as if it were the expression of a simple command: do this, get that done, drop that side chain. Walter Gehring's work on the regulatory genes controlling the development of the insect eye reflects this conception. The relevant genes may well function this way, but the story on this level is surely incomplete, and Darwinian theory is not apt to fill in the pieces.

Q: You claim that biologists think of a gene as a command. Could you be more specific?

S: Schematically, a gene is like a unit of information. It has simple binary properties. When active, it is an elementary information-theoretic unit, the cascade of gene instructions resembling the cascade involved in specifying a recipe. Now let us return to the example of the eye. Darwinists imagine that it requires what? A thousand or two thousand genes to assemble an eye, the specification of the organ thus requiring one or two thousand units of information? This is absurd! Suppose that a European firm proposes to manufacture an entirely new household appliance in a Southeast Asian factory. And suppose that for commercial reasons, the firm does not wish to communicate to the factory any details of the appliance's function -- how it works, what purposes it will serve. With only a few thousand bits of information, the factory is not going to proceed very far or very fast. A few thousand bits of information, after all, yields only a single paragraph of text. The appliance in question is bound to be vastly simpler than the eye; charged with its manufacture, the factory will yet need to know the significance of the operations to which they have committed themselves in engaging their machinery. This can be achieved only if they already have some sense of the object's nature before they undertake to manufacture it. A considerable body of knowledge, held in common between the European firm and its Asian factory, is necessary before manufacturing instructions may be executed.

Q: Would you argue that the genome does not contain the requisite information for explaining organisms?

S:Not according to the understanding of the genome we now possess. The biological properties invoked by biologists are in this respect quite insufficient; while biologists may understand that a gene triggers the production of a particular protein, that knowledge -- that kind of knowledge -- does not allow them to comprehend how one or two thousand genes suffice to direct the course of embryonic development.

Q: You are going to be accused of preformationism...

S: And of many other crimes. My position is nevertheless strictly a rational one. I've formulated a problem that appears significant to me: how is it that with so few elementary instructions, the materials of life can fabricate objects that are so marvelously complicated and efficient? This property with which they are endowed -- just what is its nature? Nothing within our actual knowledge of physics and chemistry allows us intellectually to grasp it. If one starts from an evolutionary point of view, it must be acknowledged that in one manner or another, the earliest fish contained the capacity, and the appropriate neural wiring, to bring into existence organs which they did not possess or even need, but which would be the common property of their successors when they left the water for the firm ground, or for the air.

Q: You assert that, in fact, Darwinism doesn't explain much.

S: It seems to me that the union of chance mutation and selection has a certain descriptive value; in no case does the description count as an explanation. Darwinism relates ecological data to the relative abundance of species and environments. In any case, the descriptive value of Darwinian models is pretty limited. Besides, as saltationists have indicated, the gradualist thesis seems completely demented in light of the growth of paleontological knowledge. The miracles of saltationism, on the other hand, cannot discharge the mystery I have described.

Q: Let's return to natural selection. Isn't it the case that despite everything the idea has a certain explanatory value?

S: No one could possibly deny the general thesis that stability is a necessary condition for existence -- the real content of the doctrine of natural selection. The outstanding application of this general principle is Berthollet's laws in elementary chemistry. In a desert, the species that die rapidly are those that require water the most; yet that does not explain the appearance among the survivors of those structures whose particular features permits them to resist aridity. The thesis of natural selection is not very powerful. Except for certain artificial cases, we are yet unable to predict whether this or that species or this or that variety will be favored or not as the result of changes in the environment. What we can do is establish after the fact the effects of natural selection -- to show, for, example that certain birds are disposed to eat this species of snails less often than other species, perhaps because their shell is not as visible. That's ecology: very interesting. To put it another way, natural selection is a weak instrument of proof because the phenomena subsumed by natural selection are obvious and yet they establish nothing from the point of view of the theory.

Q: Isn't the significant explanatory feature of Darwinian theory the connection established between chance mutations and natural selection?

S:With the discovery of coding, we have come to understand that a gene is like a word composed in the DNA alphabet; such words form the genomic text. It is that word that tells the cell to make this or that protein. Either a given protein is structural, or a protein itself works in combination with other signals given by the genome to fabricate yet another protein. All the experimental results we know fall within this scheme. The following scenario then becomes standard. A gene undergoes a mutation, one that may facilitate the reproduction of those individuals carrying it; over time, and with respect to a specific environment, mutants come to be statistically favored, replacing individuals lacking the requisite mutation. Evolution could not be an accumulation of such typographical errors. Population geneticists can study the speed with which a favorable mutation propagates itself under these circumstances. They do this with a lot of skill, but these are academic exercises if only because none of the parameters that they use can be empirically determined. In addition, there are the obstacles I have already mentioned. We know the number of genes in an organism. There are about one hundred thousand for a higher vertebrate. This we know fairly well. But this seems grossly insufficient to explain the incredible quantity of information needed to accomplish evolution within a given line of species.

Q: A concrete example?

S: Darwinists say that horses, which were once mammals as large as rabbits, increased their size to escape more quickly from predators. Within the gradualist model, one might isolate a specific trait -- increase in body size -- and consider it to be the result of a series of typographic changes. The explanatory effect achieved is rhetorical, imposed entirely by trick of insisting that what counts for a herbivore is the speed of its flight when faced by a predator. Now this may even be partially true, but there are no biological grounds that permit us to determine that this is in fact the decisive consideration. After all, increase in body size may well have a negative effect. Darwinists seem to me to have preserved a mechanic vision of evolution, one that prompts them to observe merely a linear succession of causes and effects. The idea that causes may interact with one another is now standard in mathematical physics; it is a point that has had difficulty in penetrating the carapace of biological thought. In fact, within the quasi-totality of observable phenomena, local changes interact in a dramatic fashion; after all, there is hardly an issue of La Recherche that does not contain an allusion to the Butterfly Effect. Information theory is precisely the domain that sharpens our intuitions about these phenomena. A typographical change in a computer program does not change it just a little. It wipes the program out, purely and simply. It is the same with a telephone number. If I intend to call a correspondent by telephone, it doesn't much matter if I am fooled by one, two, three or eight figures in his number.

Q: You accept the idea that biological mutations genuinely have the character of typographical errors?

S: Yes, in the sense that one base is a template for another, one codon for another, but at the level of biochemical activity, one is no longer able properly to speak of typography. There is an entire grammar for the formation of proteins in three dimensions, one that we understand poorly. We do not have at our disposal physical or chemical rules permitting us to construct a mapping from typographical mutations or modifications to biologically effective structures. To return to the example of the eye: a few thousand genes are needed for its fabrication, but each in isolation signifies nothing. What is significant is the combination of their interactions. These cascading interactions, with their feedback loops, express an organization whose complexity we do not know how to analyze (See Figure 1). It is possible we may be able to do so in the future, but there is no doubt that we are unable to do so now. Gehring has recently discovered a segment of DNA which is both involved in the development of the vertebrate eye and which can induce the development of an eye in the wing of a butterfly. His work comprises a demonstration of something utterly astonishing, but not an explanation.

Q:But Dawkins, for example, believes in the possibility of a cumulative process.

S: Dawkins believes in an effect that he calls "the cumulative selection of beneficial mutations." To support his thesis, he resorts to a metaphor introduced by the mathematician Emile Borel -- that of a monkey typing by chance and in the end producing a work of literature. It is a metaphor, I regret to say, embraced by Francis Crick, the co-discoverer of the double helix. Dawkins has his computer write a series of thirty letters, these corresponding to the number of letters in a verse by Shakespeare. He then proceeds to simulate the Darwinian mechanism of chance mutations and selection. His imaginary monkey types and retypes the same letters, the computer successively choosing the phrase that most resembles the target verse. By means of cumulative selection, the monkey reaches its target in forty or sixty generations.

Q: But you don't believe that a monkey typing on a typewriter, even aided by a computer...

S:This demonstration is a trompe-l'oeil, and what is more, Dawkins doesn't describe precisely how it proceeds. At the beginning of the exercise, randomly generated phrases appear rapidly to approach the target; the closer the approach, the more the process begins to slow. It is the action of mutations in the wrong direction that pulls things backward. In fact, a simple argument shows that unless the numerical parameters are chosen deliberately, the progression begins to bog down completely.

Q:You would say that the model of cumulative selection, imagined by Dawkins, is out of touch with palpable biological realities?

S: Exactly. Dawkins's model lays entirely to the side the triple problems of complexity, functionality, and their interaction.

Q: You are a mathematician. Suppose that you try, despite your reservations, to formalize the concept of functional complexity...

S: I would appeal to a notion banned by the scientific community, but one understood perfectly by everyone else -- that of a goal. As a computer scientist, I could express this in the following way. One constructs a space within which one of the coordinates serves in effect as the thread of Ariane, guiding the trajectory toward the goal. Once the space is constructed, the system evolves in a mechanical way toward its goal. But look, the construction of the relevant space cannot proceed until a preliminary analysis has been carried out, one in which the set of all possible trajectories is assessed, this together with an estimation of their average distance from the specified goal. The preliminary analysis is beyond the reach of empirical study. It presupposes -- the same word that seems to recur in theoretical biology -- that the biologist (or computer scientist) know the totality of the situation, the properties of the ensemble of trajectories. In terms of mathematical logic, the nature of this space is entirely enigmatic. Nonetheless, it is important to remember that the conceptual problems we face, life has entirely solved; the systems embodied in living creatures are entirely successful in reaching their goals. The trick involved in Dawkin's somewhat sheepish example proceeds via the surreptitious introduction of a relevant space. His computer program calculates from a random phrase to a target, a calculation corresponding to nothing in biological reality. The function that he employs flatters the imagination, however, because it has that property of apparent simplicity that elicits naïve approval. In biological reality, the space of even the simplest function has a complexity that defies understanding, and indeed, defies any and all calculations.

Q: Even when they dissent from Darwin, the saltationists are more moderate: they don't pretend to hold the key that would permit them to explain evolution...

S: Before we discuss the saltationists, however, I must say a word about the Japanese biologist Mooto Kimura. He has shown that the majority of mutations are neutral, without any selective effect. For Darwinians upholding the central Darwinian thesis, this is embarrassing... The saltationist view, revived by Stephen Jay Gould, in the end represents an idea due to Richard Goldschmidt. In 1940 or so, he postulated the existence of very intense mutations, no doubt involving hundreds of genes, and taking place rapidly, in less than one thousand generations, thus below the threshold of resolution of paleontology. Curiously enough, Gould does not seem concerned to preserve the union of chance mutations and selection. The saltationists run afoul of two types of criticism. On the one hand, the functionality of their supposed macromutations is inexplicable within the framework of molecular biology. On the other hand, Gould ignores in silence the great trends in biology, such as the increasing complexity of the nervous system. He imagines that the success of new, more sophisticated species, such as the mammals, is a contingent phenomenon. He is not in a position to offer an account of the essential movement of evolution, or at the least, an account of its main trajectories. The saltationists are thus reduced to invoking two types of miracles: macromutations, and the great trajectories of evolution.

Q: In what sense are you employing the word 'miracle'?

S:A miracle is an event that should appear impossible to a Darwinian in view of its ultra-cosmological improbability within the framework of his own theory. Now speaking of macromutations, let me observe that to generate a proper elephant, it will not suffice suddenly to endow it with a full-grown trunk. As the trunk is being organized, a different but complementary system -- the cerebellum -- must be modified in order to establish a place for the ensemble of wiring that the elephant will require to use his trunk. These macromutations must be coordinated by a system of genes in embryogenesis. If one considers the history of evolution, we must postulate thousands of miracles; miracles, in fact, without end. No more than the gradualists, the saltationists are unable to provide an account of those miracles. The second category of miracles are directional, offering instruction to the great evolutionary progressions and trends -- the elaboration of the nervous system, of course, but the internalization of the reproductive process as well, and the appearance of bone, the emergence of ears, the enrichment of various functional relationships, and so on. Each is a series of miracles, whose accumulation has the effect of increasing the complexity and efficiency of various organisms. From this point of view, the notion of bricolage [tinkering], introduced by Francois Jacob, involves a fine turn of phrase, but one concealing an utter absence of explanation.

Q: The appearance of human beings -- is that a miracle, in the sense you mean?

S: Naturally. And here it does seem that there are voices among contemporary biologists -- I mean voices other than mine -- who might cast doubt on the Darwinian paradigm that has dominated discussion for the past twenty years. Gradualists and saltationists alike are completely incapable of giving a convincing explanation of the quasi-simultaneous emergence of a number of biological systems that distinguish human beings from the higher primates: bipedalism, with the concomitant modification of the pelvis, and, without a doubt, the cerebellum, a much more dexterous hand, with fingerprints conferring an especially fine tactile sense; the modifications of the pharynx which permits phonation; the modification of the central nervous system, notably at the level of the temporal lobes, permitting the specific recognition of speech. From the point of view of embryogenesis, these anatomical systems are completely different from one another. Each modification constitutes a gift, a bequest from a primate family to its descendants. It is astonishing that these gifts should have developed simultaneously. Some biologists speak of a predisposition of the genome. Can anyone actually recover the predisposition, supposing that it actually existed? Was it present in the first of the fish? The reality is that we are confronted with total conceptual bankruptcy.

Q:You mentioned the Santa Fe school earlier in our discussion. Do appeals to such notions as chaos...

S:I should have alluded to a succession of highly competent people who have discovered a number of poetic but essentially hollow forms of expression. I am referring here to the noisy crowd collected under the rubric of cybernetics; and beyond, there lie the dissipative structures of Prigogine, or the systems of Varela, or, moving to the present, Stuart Kauffman's edge of chaos -- an organized form of inanity that is certain soon to make its way to France. The Santa Fe school takes complexity to apply to absolutely everything. They draw their representative examples from certain chemical reactions, the pattern of the sea coast, atmosphere turbulence, or the structure of a chain of mountains. The complexity of these structures is certainly considerable, but in comparison with the living world, they exhibit in every case an impoverished form of organization, one that is strictly non-functional. No algorithm allows us to understand the complexity of living creatures, this despite these examples, which owe their initial plausibility to the assumption that the physico-chemical world exhibits functional properties that in reality it does not possess.

Q: Should one take your position as a statement of resignation, an appeal to have greater modesty, or something else altogether?

S: Speaking ironically, I might say that all we can hear at the present time is the great anthropic hymnal, with even a number of mathematically sophisticated scholars keeping time as the great hymn is intoned by tapping their feet. The rest of us should, of course, practice a certain suspension of judgment.

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