Research on Intelligent Design

To put together scientific advances from the perspective of Intelligent Design.

Thursday, December 15, 2005

The Origin of Biological Information and the Higher Taxonomic Categories

Stephen C. Meyer. The Origin of Biological Information and the Higher Taxonomic Categories. Proceedings of the Biological Society of Washington (volume 117, no. 2, pp. 213-239).
Edited by Dr. Richard M. v. Sternberg

Excerpts from the Full Text:

"...neo-Darwinism affirms that new functional sections of the genome arise by trial and error process of mutation and subsequent selection. For this reason, historically many neo-Darwinists expected or predicted that the large non-coding regions of the genome--so-called “junk DNA”--would lack function altogether (Orgel, L. E., & F. H. Crick. 1980. Selfish DNA: the ultimate parasite. Nature 284:604-607.). On this line of thinking, the nonfunctional sections of the genome represent nature's failed experiments that remain in the genome as a kind of artifact of the past activity of the mutation and selection process. Advocates of the design hypotheses on the other hand, would have predicted that non-coding regions of the genome might well reveal hidden functions, not only because design theorists do not think that new genetic information arises by a trial and error process of mutation and selection, but also because designed systems are often functionally polyvalent."

" meaningful sentences or lines of computer code, genes and proteins are also specified with respect to function. Just as the meaning of a sentence depends upon the specific arrangement of the letters in a sentence, so too does the function of a gene sequence depend upon the specific arrangement of the nucleotide bases in a gene. Thus, molecular biologists beginning with Crick equated information not only with complexity but also with “specificity,” where “specificity” or “specified” has meant “necessary to function [As Crick put it, “information means here the precise determination of sequence, either of bases in the nucleic acid or on amino acid residues in the protein”: Crick, F. 1958. On protein synthesis.--Symposium for the Society of Experimental Biology. 12(1958):138-163 (p. 144 & 153); Sarkar, S. 1996. Biological information: a skeptical look at some central dogmas of molecular biology. Pp. 187-233 in S. Sarkar, ed., The philosophy and history of molecular biology: new perspectives. Kluwer Academic Publishers, Dordrecht (p. 191)]"

"...if one understands organismal form as resulting from constraints on the possible arrangements of matter at many levels in the biological hierarchy--from genes and proteins to cell types and tissues to organs and body plans--then clearly biological organisms exhibit many levels of information-rich structure."

" increase in the number of cell types implies (at a minimum) a considerable increase in the amount of specified genetic information."

"...alterations in sequencing would likely result in loss of protein function before fundamentally new function could arise (Eden, M. 1967. The inadequacies of neo-Darwinian evolution as a scientific theory. Pp. 5-12 in P. S. Morehead and M. M. Kaplan, eds., Mathematical challenges to the Darwinian interpretation of evolution. Wistar Institute Symposium Monograph, Allen R. Liss, New York; Denton, M. 1986. Evolution: a theory in crisis. Adler & Adler, London, United Kingdom). Nevertheless, neither the extent to which genes and proteins are sensitive to functional loss as a result of sequence change, nor the extent to which functional proteins are isolated within sequence space, has been fully known"

"Dawkins R. (1996. Climbing Mount Improbable. W. W. Norton & Company, New York.), for example, likens an organism to a high mountain peak. He compares climbing the sheer precipice up the front side of the mountain to building a new organism by chance. He acknowledges that his approach up “Mount Improbable” will not succeed."

"...recent protein studies (often using mutagenesis experiments) have shown that functional requirements place significant constraints on sequencing even at non-active site positions (Bowie, J., & R. Sauer. 1989. Identifying determinants of folding and activity for a protein of unknown sequences: tolerance to amino acid substitution.--Proceedings of the National Academy of Sciences, U.S.A. 86:2152-2156; Reidhaar-Olson, J., & R. Sauer. 1990. Functionally acceptable solutions in two alpha-helical regions of lambda repressor.--Proteins, Structure, Function, and Genetics, 7:306-316; Chothia, C., I. Gelfland, & A. Kister. 1998. Structural determinants in the sequences of immunoglobulin variable domain.--Journal of Molecular Biology 278:457-479; Axe, D. D. 2000. Extreme functional sensitivity to conservative amino acid changes on enzyme exteriors.--Journal of Molecular Biology 301(3):585-596; Taylor, S. V., K. U. Walter, P. Kast, & D. Hilvert. 2001. Searching sequence space for protein catalysts.--Proceedings of the National Academy of Sciences, U.S.A. 98:10596-10601)."

"In particular, Axe (2000) has shown that multiple as opposed to single position amino acid substitutions inevitably result in loss of protein function, even when these changes occur at sites that allow variation when altered in isolation. Cumulatively, these constraints imply that proteins are highly sensitive to functional loss as a result of alterations in sequencing, and that functional proteins represent highly isolated and improbable arrangements of amino acids -arrangements that are far more improbable, in fact, than would be likely to arise by chance alone in the time available (Reidhaar-Olson & Sauer 1990; Behe, M. 1992. Experimental support for regarding functional classes of proteins to be highly isolated from each other. Pp. 60-71 in J. Buell and V. Hearn, eds., Darwinism: science or philosophy? Foundation for Thought and Ethics, Richardson, Texas; Kauffman, S. 1995. At home in the universe. Oxford University Press, Oxford, United Kingdom (p. 44); Dembski, W. A. 1998. The design inference. Cambridge University Press, Cambridge, United Kingdom (175-223); Axe 2000, Axe D.D. Estimating the prevalence of protein sequences adopting functional enzyme folds. J Mol Biol. 2004 Aug 27;341(5):1295-315)."

"...mutagenesis experiments cast doubt on each of the two scenarios by which neo-Darwinists envisioned new information arising from the mutation/selection mechanism (for review, see Lonnig, W. E. 2001. Natural selection. Pp. 1008-1016 in W. E. Craighead and C. B. Nemeroff, eds., The Corsini encyclopedia of psychology and behavioral sciences, 3rd edition, vol. 3. John Wiley & Sons, New York.) For neo-Darwinism, new functional genes either arise from non-coding sections in the genome or from preexisting genes. Both scenarios are problematic."

" turn one protein into another with a completely novel structure and function requires specified changes at many sites. Indeed, the number of changes necessary to produce a new protein greatly exceeds the number of changes that will typically produce functional losses. Given this, the probability of escaping total functional loss during a random search for the changes needed to produce a new function is extremely small--and this probability diminishes exponentially with each additional requisite change (Axe 2000)."

"...lethal disadvantage: any process of random mutation or rearrangement in the genome would in all probability generate nonfunctional intermediate sequences before fundamentally new functional genes or proteins would arise"

"If an engineer modifies the length of the piston rods in an internal combustion engine without modifying the crankshaft accordingly, the engine won't start. Similarly, processes of development are tightly integrated spatially and temporally such that changes early in development will require a host of other coordinated changes in separate but functionally interrelated developmental processes downstream."

"This problem has led to what McDonald (McDonald, J. F. 1983. The molecular basis of adaptation: a critical review of relevant ideas and observations.--Annual Review of Ecology and Systematics 14:77-102) has called “a great Darwinian paradox” (p. 93). McDonald notes that genes that are observed to vary within natural populations do not lead to major adaptive changes, while genes that could cause major changes--the very stuff of macroevolution--apparently do not vary. In other words, mutations of the kind that macroevolution doesn't need (namely, viable genetic mutations in DNA expressed late in development) do occur, but those that it does need (namely, beneficial body plan mutations expressed early in development) apparently don't occur."

"DNA alone does not determine how individual proteins assemble themselves into larger systems of proteins; still less does it solely determine how cell types, tissue types, and organs arrange themselves into body plans (Harold, F. M. 1995. From morphogenes to morphogenesis.--Microbiology 141:2765-2778 (p. 2774); Moss, L. 2004. What genes can't do. The M.I.T. Press, Cambridge, Massachusetts). Instead, other factors--such as the three-dimensional structure and organization of the cell membrane and cytoskeleton and the spatial architecture of the fertilized egg--play important roles in determining body plan formation during embryogenesis."

" is not possible to predict the structure of the cytoskeleton of the cell from the characteristics of the protein constituents that form that structure (Harold, F. M. 2001. The way of the cell: molecules, organisms, and the order of life. Oxford University Press, New York (p. 125)."

"Two analogies may help further clarify the point. At a building site, builders will make use of many materials: lumber, wires, nails, drywall, piping, and windows. Yet building materials do not determine the floor plan of the house, or the arrangement of houses in a neighborhood. Similarly, electronic circuits are composed of many components, such as resistors, capacitors, and transistors. But such lower-level components do not determine their own arrangement in an integrated circuit."

"Biological symptoms also depend on hierarchical arrangements of parts. Genes and proteins are made from simple building blocks--nucleotide bases and amino acids--arranged in specific ways. Cell types are made of, among other things, systems of specialized proteins. Organs are made of specialized arrangements of cell types and tissues. And body plans comprise specific arrangements of specialized organs. Yet, clearly, the properties of individual proteins (or, indeed, the lower-level parts in the hierarchy generally) do not fully determine the organization of the higher-level structures and organizational patterns (Harold 2001:125). It follows that the genetic information that codes for proteins does not determine these higher-level structures either."

"...the mechanism of natural selection acting on random mutations in DNA cannot in principle generate novel body plans".

"...centrosome structure and membrane patterns as a whole convey three-dimensional structural information that helps determine the structure of the cytoskeleton and the location of its subunits [McNiven, M. A. & K. R. Porter. 1992. The centrosome: contributions to cell form. Pp. 313-329 in V. I. Kalnins, ed., The centrosome. Academic Press, San Diego (p. 313-329)]."

"In ciliates, microsurgery on cell membranes can produce heritable changes in membrane patterns, even though the DNA of the ciliates has not been altered [Sonneborn, T. M. 1970. Determination, development, and inheritance of the structure of the cell cortex. In Symposia of the International Society for Cell Biology 9:1-13; Frankel, J. 1980. Propagation of cortical differences in tetrahymena.--Genetics 94:607-623; Nanney, D. L. 1983. The ciliates and the cytoplasm.--Journal of Heredity, 74:163-170]. This suggests that membrane patterns (as opposed to membrane constituents) are impressed directly on daughter cells. In both cases, form is transmitted from parent three-dimensional structures to daughter three-dimensional structures directly and is not wholly contained in constituent proteins or genetic information (Moss, L. 2004. What genes can't do. The M.I.T. Press, Cambridge, Massachusetts.)"

"Cellular structures are built from proteins, but proteins find their way to correct locations in part because of preexisting three-dimensional patterns and organization inherent in cellular structures."

"...this necessary tuning involves an intelligent programmer selecting certain parameters and excluding others--that is, inputting information"

"[Kauffman] concludes that body plans, once established, will not change"

"...the fossil record does show a curious (from a neo-Darwinian point of view) top-down pattern of appearance, in which higher taxa (and the body plans they represent) appear first, only later to be followed by the multiplication of lower taxa representing variations within those original body designs [Erwin, D. H. & J. J. Sepkoski. 1987. A comparative study of diversification events: the early Paleozoic versus the Mesozoic.--Evolution 41:1177-1186; Lewin, R. 1988. A lopsided look at evolution.--Science 241:292; Valentine, J. W. & D. Jablonski. 2003. Morphological and developmental macroevolution: a paleontological perspective.--International Journal of Developmental Biology 47:517-522 (p. 518)]. Further, as Kauffman expects, body plans appear suddenly and persist without significant modification over time."

"Kauffman acknowledges that mutations that occur early in development are almost inevitably deleterious."

"...the kind of form that physical laws produce is not analogous to biological form--at least not when compared from the standpoint of (algorithmic) complexity."

"Further, physical laws lack the information content to specify biology systems. As Polyanyi (Polanyi, M. 1967. Life transcending physics and chemistry.--Chemical and Engineering News, 45(35):54-66; 1968. Polanyi, M. Life's irreducible structure.--Science 160:1308-1312, especially p. 1309) and Yockey [Yockey, H. P. 1992. Information theory and molecular biology, Cambridge University Press, Cambridge, United Kingdom (p. 290)] have shown, the laws of physics and chemistry allow, but do not determine, distinctively biological modes of organization. In other words, living systems are consistent with, but not deducible, from physical-chemical laws (Yockey 1992:290)."

"...distinctively biological regularities depend upon preexisting biological information. Thus, appeals to higher-level biological laws presuppose, but do not explain, the origination of the information necessary to morphogenesis."

"Budd and Jensen (Cladism) do not explain what causes the origination of biological form and information", because they simply concluded: "the alleged phenomenon of the phyla appearing early and remaining morphologically static is not seen to require particular explanation” [Budd, G. E. & S. E. Jensen. 2000. A critical reappraisal of the fossil record of the bilaterial phyla.--Biological Reviews of the Cambridge Philosophical Society 75:253-295 (p. 253)].

Conway Morris himself intimates that all of this has been “underpinned by a purpose” [Conway Morris, S. 2000. Evolution: bringing molecules into the fold.--Cell 100:1-11 (p. 8); Conway Morris, S. 2003b. Cambrian “explosion” of metazoans and molecular biology: would Darwin be satisfied?--International Journal of Developmental Biology 47(7-8):505-515 (p. 511)]"

"Could the notion of purposive design help provide a more adequate explanation for the origin of organismal form generally? Are there reasons to consider design as an explanation for the origin of the biological information necessary to produce the higher taxa and their corresponding morphological novelty?"

"...scientists and philosophers of science have considered teleological explanations for the origin of form and information despite strong methodological prohibitions against design as a scientific hypothesis [Gillespie, N. C. 1979. Charles Darwin and the problem of creation. University of Chicago Press, Chicago; Lenior, T. 1982. The strategy of life. University of Chicago Press, Chicago (p. 4)]"

"Neo-Darwinists such as Ayala [Ayala, F. 1994. Darwin's revolution. Pp. 1-17 in J. Campbell and J. Schopf, eds., Creative evolution?! Jones and Bartlett Publishers, Boston, Massachusetts (p. 5)], Dawkins [Dawkins, R. 1986. The blind watchmaker. Penguin Books, London, United Kingdom (p. 1)], Mayr [Mayr, E. 1982. Foreword. Pp. xi-xii in M. Ruse, Darwinism defended. Pearson Addison Wesley, Boston, Massachusetts (pp. xi-xii)] and Lewontin (Lewontin, R. 1978. Adaptation. Pp. 113-125 in Evolution: a Scientific American book. W. H. Freeman & Company, San Francisco) have long acknowledged that organisms appear to have been designed. Of course, neo-Darwinists assert that what Ayala (1994:5) calls the “obvious design” of living things is only apparent since the selection/mutation mechanism can explain the origin of complex form and organization in living systems without an appeal to a designing agent. Indeed, neo-Darwinists affirm that mutation and selection--and perhaps other similarly undirected mechanisms--are fully sufficient to explain the appearance of design in biology. Self-organizational theorists and punctuationalists modify this claim, but affirm its essential tenet. Self-organization theorists argue that natural selection acting on self organizing order can explain the complexity of living things--again, without any appeal to design. Punctuationalists similarly envision natural selection acting on newly arising species with no actual design involved"

"...this review has argued that neo-Darwinism does not adequately account for the origin of all appearances of design, especially if one considers animal body plans, and the information necessary to construct them, as especially striking examples of the appearance of design in living systems. Indeed, Dawkins [Dawkins, R. 1995. River out of Eden. Basic Books, New York (p. 11)] and Gates [Gates, B. 1996. The road ahead. Blue Penguin, Boulder, Colorado (p. 228)] have noted that genetic information bears an uncanny resemblance to computer software or machine code."

"...could the emergence of novel information-rich genes, proteins, cell types and body plans have resulted from actual design, rather than a purposeless process that merely mimics the powers of a designing intelligence?"

"This review, and much of the literature it has surveyed, suggests that four of the most prominent models for explaining the origin of biological form fail to provide adequate causal explanations for the discontinuous increases of CSI (“complex specified information”) that are required to produce novel morphologies. Yet, we have repeated experience of rational and conscious agents--in particular ourselves--generating or causing increases in complex specified information, both in the form of sequence-specific lines of code and in the form of hierarchically arranged systems of parts."

"A computer user who traces the information on a screen back to its source invariably comes to a mind--that of a software engineer or programmer. The information in a book or inscriptions ultimately derives from a writer or scribe--from a mental, rather than a strictly material, cause. Our experience-based knowledge of information-flow confirms that systems with large amounts of specified complexity (especially codes and languages) invariably originate from an intelligent source from a mind or personal agent."

"...the highly specified hierarchical arrangements of parts in animal body plans also suggest design, again because of our experience of the kinds of features and systems that designers can and do produce. At every level of the biological hierarchy, organisms require specified and highly improbable arrangements of lower-level constituents in order to maintain their form and function"

"Genes require specified arrangements of nucleotide bases; proteins require specified arrangements of amino acids; new cell types require specified arrangements of systems of proteins; body plans require specialized arrangements of cell types and organs. Organisms not only contain information-rich components (such as proteins and genes), but they comprise information-rich arrangements of those components and the systems that comprise them."

"As Berlinski (Berlinski, D. 2000. “On assessing genetic algorithms.” Public lecture. Conference: Science and evidence of design in the universe. Yale University, November 4, 2000) has argued, genetic algorithms need something akin to a “forward looking memory” in order to succeed." "

"...we know, based on our present experience of cause and effect relationships, that design engineers--possessing purposive intelligence and rationality--have the ability to produce information-rich hierarchies in which both individual modules and the arrangements of those modules exhibit complexity and specificity--information so defined. Individual transistors, resistors, and capacitors exhibit considerable complexity and specificity of design; at a higher level of organization, their specific arrangement within an integrated circuit represents additional information and reflects further design."

"Conscious and rational agents have, as part of their powers of purposive intelligence, the capacity to design information-rich parts and to organize those parts into functional information-rich systems and hierarchies."

"Clearly, we have good reason to doubt that mutation and selection, self-organizational processes or laws of nature, can produce the information-rich components, systems, and body plans necessary to explain the origination of morphological novelty"

"What natural selection lacks, intelligent selection--purposive or goal-directed design--provides."

"...the construction of complex technological objects and products, such as bridges, circuit boards, engines and software, result from the application of goal-directed constraints (Polanyi 1967, 1968). Indeed, in all functionally integrated complex systems where the cause is known by experience or observation, design engineers or other intelligent agents applied boundary constraints to limit possibilities in order to produce improbable forms, sequences or structures."

"Analysis of the problem of the origin of biological information, therefore, exposes a deficiency in the causal powers of natural selection that corresponds precisely to powers that agents are uniquely known to possess. Intelligent agents have foresight. Such agents can select functional goals before they exist. They can devise or select material means to accomplish those ends from among an array of possibilities and then actualize those goals in accord with a preconceived design plan or set of functional requirements. Rational agents can constrain combinatorial space with distant outcomes in mind. The causal powers that natural selection lacks--almost by definition--are associated with the attributes of consciousness and rationality--with purposive intelligence. Thus, by invoking design to explain the origin of new biological information, contemporary design theorists are not positing an arbitrary explanatory element unmotivated by a consideration of the evidence. Instead, they are positing an entity possessing precisely the attributes and causal powers that the phenomenon in question requires as a condition of its production and explanation."

"For this reason, recent scientific interest in the design hypothesis is unlikely to abate as biologists continue to wrestle with the problem of the origination of biological form and the higher taxa."

Extra Notes:
To see a video of Dr. Stephen C. Meyer:

Dr. Stephen Meyer explains the basics of intelligent design theory in an engaging interview with Tavis Smiley. We recommend this interview for those who want to understand the basics of ID in a few minutes.
The Tavis Smiley Show(PBS)
Fellow: Stephen Meyer
August 29, 2005
Windows Media (42.5MB)
Audio MP3 (3.29MB)
To see a video of Dr. Richard von Sternberg
Bill O'Reilly. Factor Follow Up Segment
August 24, 2005.
Life after "Intelligent Design"
Guest: Dr. Richard Sternberg, editor, Proceedings of the Biological Society of Washington (click here to see the video)

The theory of "intelligent design," which posits that the universe must have been created according to a plan, has become increasingly controversial. Biologist Richard Sternberg, who edited a scientific journal, published an article defending the theory. Dr. Sternberg told The Factor what happened next. "A number of outside groups demanded my ouster. Apparently there is an unstated rule that you don't accept a manuscript that counters Darwinism and I had committed the terrible sin of allowing this to be published. It's an attempt to suppress dissent, and it's politically and religiously motivated." The Factor asserted that some scientists are eager to quash unpopular opinions. "This is a concerted effort in a fascist way to punish anyone who might want to inject a 'higher power' into any scientific discussion."
Audio Files:
November 10, 2005, All Things Considered (NPR)
Audio MP3 (14.5MB)
September 11, 2005, Awake, Alive & Jewish (WTOP)
Audio MP3 (4.50MB)


Blogger analyysi said...

Richard Sternberg (October 22, 2004) on "Genomes as Complex systems"
Power Points
Video (size more than 300 MB)

Richard Sternberg (October 22, 2004) on "Reorganizing the Genome Information Generating or Information Shuffling?"
Power Points
Video (size more than 300 MB)

Friday, December 16, 2005 3:45:00 PM  
Blogger analyysi said...

Oops, silly me.

"PN2Homology.mpeg" is not Sternberg's video. It is Paul Nelson's. (Topic: "Can Intelligent Design Illuminate Homology?")

Sternberg's videos were:
"Genomes as Complex systems":
"Reorganizing the Genome information Generating or Information Shuffling?":

Saturday, December 17, 2005 4:32:00 AM  
Blogger fdocc said...

Dear Analyysi,

Congratulations for your great website, it is delightful to see Intelligent Design flying to Finland. Keep up the Good Work. More eyes than the ones we even imagine are reading us!

Älykäs suunnittelu

I reviewed the links that you submitted and I wish to repost them here, as they hold great information:

Richard Sternberg (October 22, 2004) on "Genomes as Complex systems"
Power Point:
Video (349 MB):

Richard Sternberg (October 22, 2004) on "Reorganizing the Genome Information Generating or Information Shuffling?"
Power Point:
Video (355 MB):

Another video in that same webpage is 305 MB:

While the video of Paul Nelson "Can Intelligent Design Illuminate Homology?" is 325 MB long:
Being his Power Point presentations:
PN-helsinki1.ppt (19.1 MB)
PN-Helsinki2.ppt (2.5 MB)

From the amazing:
Laboratory of Bioprocess Engineering, Department of Chemical Technology, Helsinki University of Technology.

The poster for those Lectures can be seen at:
Biology - Tackling Ultimate Complexity. A Four Lecture Seminar Series

Once more, congratulations in your work!

Monday, December 19, 2005 9:48:00 AM  

Post a Comment

<< Home