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Sewing The Seeds Of Biology’s Post-‘Shannon Information’ Era

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Synopsis Of The Fourth Chapter Of Signature In The Cell by Stephen Meyer
ISBN: 9780061894206; ISBN10: 0061894206; Imprint: HarperOne

When talking about ‘information’ and its relevance to biological design, Intelligent Design theorists have a particular definition in mind. Indeed they see information as “the attribute inherent in and communicated by alternative sequences or arrangements of something that produce specific effects” (p.86). When the twentieth century American mathematician Claude Shannon laid down his own theory for quantifying information he drew attention to a mathematical relationship that on its surface appeared intuitive. Information as Shannon noted was inversely proportional to uncertainty. That is, the more information we had about our world the less uncertainty there was over the outcome of future events. Shannon also proposed that the more improbable an event the more information such an event would impart once it actually took place (say, throwing a six on a role of dice).

Nevertheless Shannon’s theory was deficient in at least one crucial aspect- it made no distinction between meaningful and meaningless information-rich strings. While equally long sequences of alphabetical characters did not always elicit tangible (meaningful) outcomes, they nevertheless always displayed the same level of Shannon-style uncertainty. And yet language in itself was more than a random assortment of letters even though Shannon’s theory ascribed the same degree of information content to such an assortment as it did to an equally long but meaningful series of sentences.

What was missing in Shannon’s synthesis was a term that accounted for the so-called ‘specificity’, that is the “precise arrangement or sequence” of letters in, say, human language (p. 100). Therein lay a biological connection. After all, the swinging 50s brought with it a host of scientific breakthroughs, notably those of X-ray crystallographers Fred Sanger and John Kendrew who were instrumental in unveiling the ‘twisted, turning, tangled chain’ nature of proteins. In so doing they sewed the seeds for a process of discovery that would eventually culminate in an unexpected realization- proteins contained a high degree of structural and sequence specificity. That is, if proteins were to fulfill their hugely diverse repertoire of functions in the cell both their structural organization and amino acid sequence had to fit within a very narrow subset of all possible arrangements. Just like human language that only takes on meaning when letters and words are set out in universally recognizable and interpretable sequences, proteins could be considered as being rich in specified information.

In 1958 Francis Crick’s Sequence Hypothesis formalized the idea that protein amino acid sequences were inextricably linked to the base sequences of DNA. Years earlier, geneticists George Beadle and Edward Tatum had supplied evidence that strongly suggested a link between genes and proteins. The elucidation of the DNA genetic code in the 1960s, defining the base triplets that coded for each amino acid, revolutionized the molecular biology arena. Most significant of all was the revelation that both DNA and proteins bore the same ‘specificity’ fingerprint as human systems of code. In short, the cellular world appeared to be intelligently designed.

In the fourth chapter of Signature In The Cell, Stephen Meyer displays an enviable clarity in his exposition of biology’s post-‘Shannon information’ era. In so doing he masterfully dispels any concern that the intelligent design inference does not carry with it a sound scientific foundation.

Comments
"Probably because the vitalism and anti-reductionism of this approach have not resulted in any application, any results beyond French witticisms." Nakashima can always be counted on for meaningless observations. *Note to biologists wishing to advance a rationale: Beware of French witticisms.Upright BiPed
August 14, 2009
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GEM, that was a gem! "Now, why do you think that is?" Because "Darwinians have too simple a conception of biology, rather like a locksmith improbably convinced that his handful of keys will open any lock." I remember as a child discovering that our car key worked on my uncle's car. Darwinists point to periodic "beneficial mutations". IDers cannot say that beneficial mutations can never happen, periodically the handful of keys will open a lock, but not nearly often enough to assume that the locksmith's chain is enough to qualify him to universally pick locks.bFast
August 13, 2009
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KF-san, Probably because the vitalism and anti-reductionism of this approach have not resulted in any application, any results beyond French witticisms.Nakashima
August 13, 2009
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bFast: It might interest you to see Schutzenberger's discussion, which seems to trace back to Wistar, 1966; here. Here's a little slice of the cake:
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: 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.
And, that's not just blog commenters at UD speaking . . . the issue has been on the table at he very highest levels for over forty years, but has been largely ignored, for decades. Now, why do you think that is? GEM of TKIkairosfocus
August 13, 2009
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ROb, I understand your frustration. This is why some of us are attracted to the concept of FSCI, function specifying complex information. If what is specified is something that functions, that can perform a specific task, then the nature and parameters of specificity become much clearer.bFast
August 13, 2009
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"I have yet to find a closed definition" A good dictionary might help or common sense use of the term. From the American Heritage Dictionary of the English Language "To determine or bring about (a specific result): a gene that specifies the synthesis of a single protein." I am sure you will find other helpful definitions in other dictionaries.jerry
August 13, 2009
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I have yet to find a closed definition, much less a closed operational definition, of specificity. Is there a fixed set of criteria outside of which everything is non-specified, or at least not verifiably specified? Specificity seems a key concept in ID, but it also seems quite malleable. For instance, Robert Deyes equates specificity with semantic content, but Dembski says that specified information is not the same as semantic information. Without a fixed, preferably operational, definition, it's too easy to come up with ad hoc reasons for saying that something is or is not specified.R0b
August 13, 2009
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In this sense I hit upon an interesting opinion that DNA belongs actually to phenotype and not genotype. It is information which is important. DNA is only phenotypic expression of given information. In this sense the same genes in population are actually redundant and have no additional meaning. http://cadra.wordpress.com/VMartin
August 13, 2009
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