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

There's nothing about lower oxygen levels on Earth that would forbid the rise of early animals. David Klinghoffer http://www.discovery.org/p/209
Categories: Anti-Science News

Review of Darwin's Doubt: Part Two

ARN ID Update - Mon, 2014-02-24 18:12

How to build an animal

Whereas the focus in Part 1 falls on fossil evidence for an explosion of life in the Early Cambrian, we change gear in Part 2 and examine biological research relevant to the origin of animal phyla.

The starting point is the search for ways of measuring biological information representing different body plans. Shannon's theory of information (when applied to the animal genome) has the merit of mathematical rigour, but Meyer shows that this approach gives insight only into a sequence's capacity to carry information. Whether the sequence is functional is undetermined ? so discussion of biological information must extend far beyond quantitative measures. Meyer discusses the number of cell types as an indicator of complexity of embedded information. With reference to the genome, which uses digital codes, he uses the term "specified information", meaning that a genetic sequence can only be functional if the codons have a specific arrangement. Is the neo-Darwinian mechanism adequate to explain the origins of novel specified information associated with the Cambrian Explosion? Meyer describes this as a challenging question for Darwinists and claims that the necessity of "vast amounts" of specificity makes their explanations implausible.


(Source here)

To show that this argument is real, and not an argument from ignorance, Meyer devotes the next chapter to unpacking the issues surrounding specificity. In the early 1960s, Murray Eden (a professor of engineering and computer science at MIT) realised that there was a problem with neo-Darwinian theory and organised a conference to explore the issues at the Wistar Institute in Philadelphia. The theme was: "Mathematical challenges to the neo-Darwinian interpretation of evolution". The participants came from many disciplines and included Ernst Mayr (one of the architects of neo-Darwinism) and Richard Lewontin (Professor of genetics and evolutionary biology). Chairing the meeting was the Nobel laureate Sir Peter Medawar. The discussion provided by Meyer is extremely helpful in clarifying the nature of the problems and summarising some of the suggestions for resolving the dilemmas. The most favoured possible solution is explained in the quotation below, and is significant for stimulating a design-based research programme discussed in the subsequent chapter.

"The solution was this: even though the size of the combinatorial space that mutations needed to search was enormous, the ratio of functional to non-functional base or amino-acid sequence in their relevant combinatorial spaces might turn out to be much higher than Eden and others had assumed. If that ratio turned out to be high enough, then the mutation and selection mechanism would frequently stumble onto novel genes and proteins and could easily leapfrog from one functional protein island to the next, with natural selection discarding the non-functional outcomes and seizing upon the rare (but not too rare) functional sequences." (page 178)

As a research student in the late 80s, Doug Axe was not persuaded by Dawkins' rhetoric in "The Blind Watchmaker", and wanted to undertake research himself into aspects of genetic information. Reading the proceedings of the Wistar Conference stimulated many ideas for further work. This led Axe to join a protein engineering team at the University of Cambridge. Meyer's discussion of his experiments and results need to be read in full to appreciate the robustness of the empirical work undertaken. However, this is the conclusion of the first phase of Axe's research:

"Overall, therefore, he showed that despite some allowable variability, proteins (and the genes that produce them) are indeed highly specified relative to their biological functions, especially in their crucial exterior portions. Axe showed that whereas proteins will admit some variation at most sites if the rest of the protein is left unchanged, multiple as opposed to single amino-acid substitutions consistently result in rapid loss of protein function." (p.193)

In the next chapter, Meyer himself appears as part of the story-line. The year is 2004, when the Proceedings of the Biological Society of Washington carried Meyer's peer-reviewed article that made reference to Axe's work and the Cambrian Explosion dilemma. He argued that "the theory of intelligent design could help explain the origin of biological information" (p.209). In Meyer's own words, the publication of this paper created "a firestorm of controversy". Up to that time, opponents of intelligent design (ID) claimed that until ID made it into peer-reviewed literature, it could not count as science. Once they realised it had passed through, they left no stone unturned in trying to discredit the paper, the journal's editor and their peer-review process. Many months passed before anything looking like a scientific response appeared, drawing heavily on a 2003 review of thinking about the origin of new genes. Meyer devotes the rest of this chapter to analysing the arguments and showing that the research does not explain the origin of specified information and does not solve the combinatorial inflation problem identified by Murray Eden.

"Overall, what evolutionary biologists have in mind is something like trying to produce a new book by copying the pages of an existing book (gene duplication, lateral gene transfer, and transfer of mobile genetic elements), rearranging blocks of text on each page (exon shuffling, retropositioning, and gene fusion), making random spelling changes to words in each block of text (point mutations), and then randomly rearranging the new pages. Clearly, such random rearrangements and changes will have no realistic chance of generating a literary masterpiece, let alone a coherent read. That is to say, these processes will not likely generate specificity of arrangement and sequence and, therefore, do not solve the combinatorial search problem. In any case, all such scenarios also beg the question. There is a big difference between shuffling and slightly altering pre-existing sequence-specific modules of functional information and explaining how those modules came to possess information-rich sequences in the first place." (p.219)

Neo-Darwinians are remarkably satisfied with natural selection and their hypothetical models of gene evolution, so that platitudes often replace science. Meyer gives an example from an evolutionary text-book: "One need not go into the details of the evolution of the bird's wing, the giraffe's neck, the vertebrate eye, [. . .] Even a slight advantage or disadvantage in a particular genetic change provides a sufficient differential for the operation of natural selection." (quoted on p.234). Anyone who wants to grapple with the details soon meets problems that cast doubt on the adequacy of Darwinian mechanisms. Meyer introduces us to Tom Frazzetta, whose specialism is functional biomechanics. He found great difficulty defending the concept of gradual change because all the intermediate forms he could envisage would not have been viable. The interdependence of biomechanical systems meant that design changes could not be incremental and many would have to occur concurrently. Frazzetta came to the conclusion that "Phenotypic alteration of integrated systems requires an improbable coincidence of genetic (and hence hereditable phenotypic) modifications of a tightly specified kind." (quoted on p.233). This brings us to the work of Michael Behe and David Snoke, and their 2004 paper in Protein Science. They recognised that some inferred evolutionary changes require coordinated mutations, and they used the principles of population genetics to assess the likelihood of such coordinated changes occurring. The calculated probabilities are so low as to cast doubt on this being a widespread phenomenon in the history of life. Behe was to return to this theme later in his book: The Edge of Evolution (2007).

"In a real sense, therefore, the neo-Darwinian math is itself showing that the neo-Darwinian mechanism cannot build complex adaptations - including the new information-rich genes and proteins that would have been necessary to build the Cambrian animals." (p.254)

At this point, the focus of interest shifts from molecules to body plans; from population genetics to developmental biology. Paul Nelson (philosopher of biology) is introduced when commenting on the "great Darwinian paradox". This is the observation that mutations affecting early stage development are not beneficial, yet these are the very mutations needed if there is to be any change in the body plan. In Nelson's words:

"Such early-acting mutations of global effect on animal development, however, are those least likely to be tolerated by the embryo and, in fact, never have been tolerated in any animals that developmental biologists have studied." (p.262).

Early stage development appears to be overseen and coordinated by developmental gene regulatory networks, a concept pioneered by Eric Davidson. It is not a coincidence that developmental biologists like him have been pressing for a new evolutionary synthesis to emerge, because they are acutely aware that neo-Darwinism cannot be the way forward. The tightly integrated gene regulatory networks cannot be mutated incrementally so as to produce new body plans:

"contrary to classical evolution theory, the processes that drive small changes observed as species diverge cannot be taken as models for the evolution of the body plans of animals." (words of Davidson, quoted on p.269).

The challenge to the neo-Darwinian synthesis is even more formidable than this. The mindset of Darwinists is that life is digital. Everything is reduced to bits in the genome sequence. However, what happens to the adequacy of their theory if they are dealing with only part of the information story? What happens is some information is located in the cell independent of the genome? At very least, if this is true, the textbook orthodoxy can only claim to be a partial account of origins. But it also needs to be considered whether neo-Darwinism is a diversion to the real issues affecting life's diversity. These matters are discussed in Meyer's chapter dealing with the epigenetic revolution.

"Many biologists no longer believe that DNA directs virtually everything happening within the cell. Developmental biologists, in particular, are now discovering more and more ways that crucial information for building body plans is imparted by the form and structure of embryonic cells, including information from both the unfertilized and fertilized egg." (p.275)

Much of this chapter draws on the work of Jonathan Wells, whose analysis of the inadequacy of neo-Darwinian theory incorporates the growing evidence that epigenetic influences on development are substantial. (See also here.)

"Yet both-body plan formation during embryological development and major morphological innovation during the history of life depend upon a specificity of arrangement at a much higher level of the organizational hierarchy, a level that DNA alone does not determine. If DNA isn?t wholly responsible for the way an embryo develops - for body-plan morphogenesis - then DNA sequences can mutate indefinitely and still not produce a new body plan, regardless of the amount of time and the number of mutational trials available to the evolutionary process. Genetic mutations are simply the wrong tool for the job at hand." (p.281)

A particularly useful aspect of these chapters is that ID-related research is presented in a way that demonstrates the coherence and value of the design paradigm. Researchers operating within a design framework are addressing issues that are of central importance, publishing their work in peer-reviewed papers and other scholarly forums, and engaging in a constructive discourse with scientists working within the naturalistic evolutionary paradigm. Many will be aware of the work of individual scientists mentioned above, but Meyer's account shows how they contribute to the bigger picture and complement one another. This approach to science is exemplary and one hopes it will inspire young scientists to emulate their endeavours.

Where does this lead us? For the answer to that question, we must turn to Part 3 of Meyer's book.

"[T]he Cambrian explosion now looks less like the minor anomaly that Darwin perceived it to be, and more like a profound enigma, one that exemplifies a fundamental and as yet unsolved problem - the origination of animal form." (p.287)

To be continued.

Darwin's Doubt: The Explosive Origin of Animal Life and the Case for Intelligent Design
by Stephen C. Meyer
HarperOne (HarperCollins), New York, 2013. 520 pp. ISBN 9780062071477.

Darwin's Doubt Website

Categories: Anti-Science News

CS Lewis (1898-1963) honoured at Westminster Abbey

ARN ID Update - Mon, 2014-02-24 03:23

Readers of Uncommon Descent will recall that mid-20th century Christian apologist C.S. Lewis's views on Darwinism and scientism have attracted considerable interest of late. And some misrepresentation as well, as some zealous followers of Darwin have tried to claim him as one of their own.

More...

Categories: Anti-Science News

For His Substance-Free Contribution to the Debate with Stephen Meyer, American Spectator Readers Pummel John Derbyshire

ARN ID Update - Mon, 2014-02-24 03:15

As reported in ENV...Congratulations to The American Spectator for having such sensible readers. Sometimes it's gratifying to find that the people who should know better actually do.

In January, the conservative magazine featured paired articles by Stephen Meyer and John Derbyshire arguing respectively for and against intelligent design. Derbyshire "argued" only in the limited sense of tossing off snide insults and trying to paint ID absurdly with the brush of "Occasionalism," a medieval theological concept.

More...

Categories: Anti-Science News

ID Proponent Schools Theistic Evolutionist Theologians on Intelligent Design

ARN ID Update - Mon, 2014-02-24 03:00

Christian Post contributor Anugrah Kumar writes that Casey Luskin, a proponent of Intelligence Design, says that most theistic evolutionists appear to be unfamiliar with what ID theorists say, and they wrongly maintain that it's a "God of the gaps" argument.

More...

Categories: Anti-Science News

For His Substance-Free Contribution to the Debate with Stephen Meyer, American Spectator Readers Pummel John Derbyshire

Sometimes it's gratifying to find that the people who should know better actually do. David Klinghoffer http://www.discovery.org/p/209
Categories: Anti-Science News

Watching Tommy: Yes, Whether Scientific or Otherwise, a Culture Can Pull Back from the Brink

In the controversy over scientific materialism, animalism, Darwinism, whose fallout is documented in The War on Humans, it often seems like our culture stands at a precipice. David Klinghoffer http://www.discovery.org/p/209
Categories: Anti-Science News

Dean Koontz on Wesley J. Smith's The War on Humans

"An irrational and misanthropic ideology has metastasized that in its fanaticism is as dangerous as the fascist and communist crusades of the past century." Evolution News & Views
Categories: Anti-Science News

Online Premiere: To Understand What's Really at Stake in the Evolution Debate, Watch The War on Humans Now

If the attitude of animalism carried the day in our culture, the reign of bestiality -- what else to call it? -- would mean the end of our culture. David Klinghoffer http://www.discovery.org/p/209
Categories: Anti-Science News

Can All the Numbers for Life's Origin Just Happen to Fall into Place?

We are told that theories in science should be beautiful, and chance does offer a sort of bleak, existential grandeur. Denyse O'Leary
Categories: Anti-Science News

The War on Humans, pt. 1

ID the Future - Sun, 2014-02-16 21:33
Listen Now. On this episode of ID the Future, hear from bioethicist Wesley J. Smith as he talks about his new book The War on Humans, also adapted as a documentary film. In this first podcast of the series,...
Categories: Anti-Science News

What Gives? In Exchanging Falsehood for Truth, Wikipedia's Editors are Slowing Down

When it comes to putting a Darwinist spin on anything to do with intelligent design, they have previously been more vigilant. David Klinghoffer http://www.discovery.org/p/209
Categories: Anti-Science News

Does Intelligent Design Picture a Living Creature as a "Machine"? Short Answer: No

Speaking of owls as being "engineered," thoughtful reader Donald sends along this clip from the 1988 film Clash of the Titans that we somehow missed. Evolution News & Views
Categories: Anti-Science News

Suddenly, It's OK to Say that Owls Are Engineered

A mechanical engineer at Michael Behe's university thinks owls are "engineered for stealth and silence." Evolution News & Views
Categories: Anti-Science News

For Darwin Day, Discovery Institute Names University of Chicago Biologist Jerry Coyne as "Censor of the Year"

ID the Future - Fri, 2014-02-14 06:09
Listen Now. On this episode of ID the Future, David Klinghoffer announces Discovery Institute's 2013 Censor of the Year award. Listen in as Klinghoffer explains why we've chosen to recognize University of Chicago biologist Jerry Coyne, out of several...
Categories: Anti-Science News

Dr. Michael Egnor: How Science is Censored

ID the Future - Fri, 2014-02-14 06:09
Listen Now. On this episode of ID the Future, Dr. Michael Egnor is on the show again to talk more about his recent debates with atheist evolutionary biologist Dr. Jerry Coyne. Listen in as Egnor and Research Coordinator Casey...
Categories: Anti-Science News

In Love With Death: Belgium Passes Child-Euthanasia Law

Targeting the youngest and most vulnerable, in the name of principles that sound high-minded, may hold a sadistic allure for a certain personality. David Klinghoffer http://www.discovery.org/p/209
Categories: Anti-Science News

Suggestion to Our Readers: Edit Wikipedia and Correct the Lincoln/Darwin Myth

I'll then set my stopwatch and see what happens. David Klinghoffer http://www.discovery.org/p/209
Categories: Anti-Science News

Wikipedia Invents a Mythical Account of Lincoln and Darwin

Wikipedia makes up a fanciful story about Abraham Lincoln reading and being deeply moved by Charles Darwin's On the Origin of Species. John G. West http://www.discovery.org/p/18
Categories: Anti-Science News

Help Us Educate the Next Generation of Scientists and Scholars!

World Magazine interviewed (anonymously in some case) students who participated in last year's Summer Seminar. Evolution News & Views
Categories: Anti-Science News
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