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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

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...

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...

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...

NCSE is pleased to announce the next of a new series of on-line workshops aimed at broadening and deepening the networks that make our work possible. The next workshop focuses on media outreach: the panelists will discuss their own experiences, and share advice and resources to help citizens like you plan for media outreach and be effective spokespeople for science.

 

Eugenie C. Scott

NCSE's Eugenie C. Scott received a Lifetime Achievement Award from the Center for Inquiry and Committee for Skeptical Inquiry in October 2013.

Louisiana's Senate Bill 70 (PDF) would, if enacted, repeal the state's Balanced Treatment for Creation-Science and Evolution-Science Act, which was enacted in 1981 and declared to be unconstitutional by the United States Supreme Court in Edwards v. Aguillard in 1987.

NCSE is pleased to offer a free preview (PDF) of New Trends in Earth-Science Outreach and Engagement (Springer 2013), edited by Jeanette L. Drake, Yekaterina Y. Kontar, and Gwynne S. Rife. The excerpt consists of the entirety of "Infusing Climate and Energy Throughout the Curriculum: Challenges and Opportunities," by NCSE's Minda Berbeco and Mark McCaffrey.

Public opinion about climate change was reviewed in the National Science Board's Science and Engineering Indicators (PDF) 2014.

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

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

"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

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

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

Post by midwifetoad
This is kind of slow, but here's a few Barry quotemines and their discussion at talkorigins:

[blockquote]No wonder paleontologists shied away from

evolution for so long. It seems never to happen.

http://www.talkorigins.org/faqs....3.html[

blockquote]

[blockquote]I wish in no way to impugn the potential

validity of gradualism . . . I wish only to point out

that it was never ‘seen’ in the rocks.

http://www.talkorigins.org/faqs....3.html[

blockquote]


[blockquote]The fossil record with its abrupt

transitions offers no support for gradual change

http://www.talkorigins.org/faqs....3.html[

blockquote]

[blockquote]At the higher level of evolutionary

transition between basic morphological designs,

gradualism has always been in trouble

http://www.talkorigins.org/faqs....3.html[

blockquote]


[blockquote]The absence of fossil evidence for

intermediary stages between major transitions in organic

design, indeed our inability, even in our imagination,

to construct functional intermediates in many cases, has

been a persistent and nagging problem for gradualistic

accounts of evolution

http://www.talkorigins.org/faqs....-3.html

[/blockquote]

[blockquote]With the benefit of hindsight, it is amazing

that paleontologists could have accepted gradual

evolution as a universal pattern on the basis of a

handful of supposedly well-documented lineages

http://www.talkorigins.org/faqs....-4.html

[/blockquote]


[blockquote]The main problem with such phyletic

gradualism is that the fossil record provides so little

evidence for it.

http://www.talkorigins.org/faqs....-1.html

[/blockquote]

[blockquote]f we examine the fossil record in detail,

whether at the level of orders or of species, we find –

over and over again – not gradual evolution

http://www.talkorigins.org/faqs....-4.html

[/blockquote]

[blockquote]yet to preserve our favored account of

evolution by natural selection we view our data as so

bad that we almost never see the very process we profess

to study

http://www.talkorigins.org/faqs....3.html[

blockquote]



[blockquote]The overwhelming prevalence of stasis became

an embarrassing feature of the fossil record, best left

ignored

http://www.talkorigins.org/faqs....-2.html

[/blockquote]

[blockquote]The main impetus for expanding the view that

species are discrete at any one point in time, to

embrace their entire history, comes from the fossil

record.

http://www.talkorigins.org/faqs....-2.html

[/blockquote]



[blockquote]The record certainly did not reveal gradual

transformations of structure in the course of time.

http://www.talkorigins.org/faqs....-2.html

[/blockquote]




[blockquote]Many species remain virtually unchanged for

millions of years, then suddenly disappear to be

replaced by a quite different, but related, form.

http://www.talkorigins.org/faqs....-2.html

[/blockquote]

[blockquote]When we do see the introduction of

evolutionary novelty, it usually shows up with a bang

http://www.talkorigins.org/faqs....3.html[

blockquote]

[blockquote]if you do collect a series of fossils up

through a sequence of sedimentary rock, and if you don’t

see much evidence of anatomical change through that

series, that is indeed evidence that substantial gradual

evolutionary change has not occurred

http://www.talkorigins.org/faqs....-2.html

[/blockquote]

Post by N.Wells
Quote N.Wells was talking like this is a theory dreamed up at church on a whim after watching a Discovery Institute video
You're the one talking up religion and offering proud support to creationist/IDist positions:
Quote To be religiously real (without going out of bounds of science) I made an illustration with famous artwork as a pointer: .....

From the “citizen” level the controversy is being quietly ended with the Theory of Intelligent Design winning, but not over Creationism or Creation Science that the above illustration is most properly for, which was a problem that got the Discovery Institute in what has been called a “turf-war” that made it unpopular with Creationists who need an honorable Adam and Eve established in science and Genesis friendliness.......  

Quote Respecting the past this way, makes the theory very faith-friendly and useful there.  And where the planet sizzles or has another ice-age that makes technology all gone it’s then only what religion can make sense of that easily carries on.  Not that I become a Jesus it’s actually here more from the emerging legend of Kathy Martin who to spite their religious way of seeing things prevailed, with help from a science guy who focused on the science work while explaining important connections that parallel religion that keeps the search for our Creator going for at least a few more hundred years hopefully forever.

Quote Theory can now read so much like Genesis I could go on and on about how things are for the most part working out well for what you would call "creationists".

However, my point was more nuanced: your approach to knowledge is more like a religious approach than a scientific approach, in that you make assertions based on what seems self-evident to you, and you have no interest in testing your ideas or supporting them scientifically.  You apparently just expect your audience to accept your stuff on faith, because you sure aren't making your case in ways that are scientific.



Re Anirban Bandyopadhyay:  I stick by my statement that his "organic computer" work seems potentially really important.  I agree that the paper you cited is odd in many ways, including its grammar and jargon and its somewhat problematic venue (the MPDI organization that publishes "Information" has got itself into trouble in recent years for publishing some truly crappy articles).  I also agree that this is far outside my specialty (so I could easily be wrong).  Nonetheless, Bandyopadhyay's "molecular organic computer" stuff from a few years ago (an earlier phase of this research) was published in Nature Physics, sounded very exciting, and got a lot of good press that spelled out immense potential for his line of work if he is right only on a small fraction of his ideas (e.g., http://www.gizmag.com/organic....).  

Bandyopadhyay has been part of a large group of people at prestigious places like Japan's National Institute for Materials Science, Michigan Technological University, and Japan's National Institute of Information and Communications Technology, and they've been publishing in prestigious places like http://www.nature.com/nphys....6.html, with funding from places like NSF.   Whatever the shortcomings of his most recent paper, Bandyopadhyay's stuff is at least well enough done that it's hard to dismiss it out of hand, while yours falls far short of that and is obviously crappy to anyone (except you) who reads it.  One of the commenters on the website you cited said, "Trying to figure out some extremely intricate, extremely unconventional computer architecture based on undefined words, unrelated buzz words, and insufficient detail is not worth my time, and probably is not even possible. [/quote]".  Except for "extremely intricate .... computer architure",  the other things in that complaint apply better to your crap than to Bandyopadhyay's - how come you are so blinded to your own shortcomings?

Post by JohnW
Quote (Richardthughes @ Feb. 18 2014,13:41) Quote (OgreMkV @ Feb. 18 2014,15:34)See Joe argue in support of Noah's flood: http://www.skepticink.com/tipplin....e-flood
Joe: "Nope, I have no interest in the Bible other than it is a collection of old books."

but also

Joe: "And I only hate atheists who misrepresent the Bible"

and "What Bible are you using? And why do all Bible scholars disagree with you?

“And the waters prevailed exceedingly upon the earth; and all the high hills that were under the whole heaven were covered. Fifteen cubits upward did the waters prevail; and the mountains were covered” (KJV).

High hills,not mountains.

See also- http://www.answersingenesis.org/....sis....sis.org "

and

Joe: "And yes a 6,000 year old earth is dumb and it isn't part of the Bible"

And also:

That whole page is a shrine to his Tard.
He's hit the jackpot:
Quote Talk to Walter Brown and associates
Joe, you do know that's tantamount to saying "i know absolutely fuck all about basic, middle-school-level physics", don't you?

Post by socle
Quote (Richardthughes @ Feb. 18 2014,15:41)   Quote (OgreMkV @ Feb. 18 2014,15:34)See Joe argue in support of Noah's flood: http://www.skepticink.com/tipplin....e-flood
Joe: "Nope, I have no interest in the Bible other than it is a collection of old books."

but also

Joe: "And I only hate atheists who misrepresent the Bible"

and "What Bible are you using? And why do all Bible scholars disagree with you?

“And the waters prevailed exceedingly upon the earth; and all the high hills that were under the whole heaven were covered. Fifteen cubits upward did the waters prevail; and the mountains were covered” (KJV).

High hills,not mountains.

See also- http://www.answersingenesis.org/....sis....sis.org "

and

Joe: "And yes a 6,000 year old earth is dumb and it isn't part of the Bible"

And also:

That whole page is a shrine to his Tard.
Nice to see Wally B's Hydropants Theory getting a mention by Joe in that thread.

Post by Richardthughes
Quote (OgreMkV @ Feb. 18 2014,15:34)See Joe argue in support of Noah's flood: http://www.skepticink.com/tipplin....e-flood
Joe: "Nope, I have no interest in the Bible other than it is a collection of old books."

but also

Joe: "And I only hate atheists who misrepresent the Bible"

and "What Bible are you using? And why do all Bible scholars disagree with you?

“And the waters prevailed exceedingly upon the earth; and all the high hills that were under the whole heaven were covered. Fifteen cubits upward did the waters prevail; and the mountains were covered” (KJV).

High hills,not mountains.

See also- http://www.answersingenesis.org/....sis.org "

and

Joe: "And yes a 6,000 year old earth is dumb and it isn't part of the Bible"

And also:

That whole page is a shrine to his Tard.

Post by OgreMkV
See Joe argue in support of Noah's flood: http://www.skepticink.com/tipplin....e-flood