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Evolutionary Biologist Rick Sternberg Defends Stephen Meyer, Challenges Darrel Falk

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Rick Sternberg, PhD PhD is one of the finest and most courageous evolutionary biologists on the planet. He recently has come to the defense of Stephen Meyer by Asking Darrel Falk to Pick a Number

Rick points out a peculiar claim by Darrel Falk which can be falsified:

almost certainly much, if not most, of the DNA plays no role, and in many cases can be harmful

Darrel Falk
Professor of Biology

Sternberg counters with an implicit wager after first providing some insights:

I have long questioned the assumption that most genomic DNA sequences are “nonsensical” or “junk.” And given the data that have emerged over the past seven or so years, a functionalist view of genome has robust empirical support. It is for this reason that I think many of the arguments presented by the Biologos Foundation are “wrong on many counts,” to borrow a phrase from Darrel Falk.


Here is an example. While reading the ”critique” of Steve Meyer’s book, Signature in the Cell, by Francisco Ayala, a number struck me that I know to be incorrect. The integer that I am referring to is “25,000” and it is claimed to be the known tally of genes in our chromosomes:

The human genome includes about twenty-five thousand genes and lots of other (mostly short) switch sequences…

Now, the problem with such a statement is this: While there are ~25,000 protein-coding genes in our DNA, the number of RNA-coding genes is predicted to be much higher, >450,000.1 Some of the latter range in length from being quite short—only 20 or so genetic letters—to being millions of letters long. Since 2004 we have learned that over 90% of our DNA is transcribed into RNA sequences at some developmental stage, in different cell and tissue types.2, 3, 4 (Our brain cells are unusually rich in these non-translated RNAs.) These RNAs are then processed into regulatory and structural sequences of all sizes.

It could of course be argued, as it has been, that most of these RNA transcripts are themselves junk. But a host of them are packaged into complexes with different proteins.1

So the true number of genes in our DNA is probably “450,000 + 25,000 = 475,000”. What is more, these 450,000 genes cover more than 88.5% of our 3 billion genetic letters. That’s right—most, if not close to all, of our chromosomal DNA consists of different types of genes that have only recently been discovered.

And this leads to what I characterize as a friendly gentleman’s wager:

How do these facts square with this comment made by Falk?

but this still doesn’t negate the fact that almost certainly much, if not most, of the DNA plays no role, and in many cases can be harmful.

Well, it all depends on how he is using the words “much” and “most.” I really don’t know. So I have a question for him: Exactly what fraction of the transcribed 88.5% of our DNA are you willing to say “plays no role” or can be harmful? All I am asking for is a prediction, such as “90% of these DNA letters is superfluous” (“or 79.5% of the RNAs are nonsensical”). Since he also said “almost certainly” in the above statement, he must have a figure in mind. So I say pick a number, any number…But to be a good sport, I’ll show my prediction: All of the expressed 88.5% of our DNA has diverse roles in our development.

Sternberg labored... And brought forth a mouse: "Isochores might provide a clue to cause of the mystery signal, but the cause—whatever it may be—is outside the BioLogos box." Adel DiBagno
Nak as far as restating you position in my own words; all I have is one question; Do you or do you not believe that "errors" accumulate in alleged "junk dna" regions where they may gain functionality? If you do believe this then "my words" are actually your very own beliefs stated with an piercing honesty that you find very uncomfortable. For you to deny that this truly is so you will have to deny the premises of the question I asked you! bornagain77
further notes Nak: The Cambrian's Many Forms Excerpt: "It appears that organisms displayed “rampant” within-species variation “in the ‘warm afterglow’ of the Cambrian explosion,” Hughes said, but not later. “No one has shown this convincingly before, and that’s why this is so important.""From an evolutionary perspective, the more variable a species is, the more raw material natural selection has to operate on,"....(Yet Surprisingly)...."There's hardly any variation in the post-Cambrian," he said. "Even the presence or absence or the kind of ornamentation on the head shield varies within these Cambrian trilobites and doesn't vary in the post-Cambrian trilobites." University of Chicago paleontologist Mark Webster; article on the "surprising and unexplained" loss of variation and diversity for trilobites over the 270 million year time span that trilobites were found in the fossil record, prior to their total extinction from the fossil record about 250 million years ago. http://www.terradaily.com/reports/The_Cambrian_Many_Forms_999.html Evolution vs. Trilobites - Prof. Andy McIntosh - video http://www.metacafe.com/watch/4032589 In fact, the loss of morphological traits over time, for all organisms found in the fossil record, was so consistent that is was made into a scientific "law": Dollo's law and the death and resurrection of genes: Excerpt: "As the history of animal life was traced in the fossil record during the 19th century, it was observed that once an anatomical feature was lost in the course of evolution it never staged a return. This observation became canonized as Dollo's law, after its propounder, and is taken as a general statement that evolution is irreversible." http://www.pnas.org/content/91/25/12283.full.pdf+html A general rule of thumb for the "Deterioration/Genetic Entropy" of Dollo's Law as it applies to the fossil record is found here: Dollo's law and the death and resurrection of genes ABSTRACT: Dollo's law, the concept that evolution is not substantively reversible, implies that the degradation of genetic information is sufficiently fast that genes or developmental pathways released from selective pressure will rapidly become nonfunctional. Using empirical data to assess the rate of loss of coding information in genes for proteins with varying degrees of tolerance to mutational change, we show that, in fact, there is a significant probability over evolutionary time scales of 0.5-6 million years for successful reactivation of silenced genes or "lost" developmental programs. Conversely, the reactivation of long (>10 million years)-unexpressed genes and dormant developmental pathways is not possible unless function is maintained by other selective constraints; http://www.pnas.org/content/91/25/12283.full.pdf+html Dollo's Law was further verified to the molecular level here: Dollo’s law, the symmetry of time, and the edge of evolution - Michael Behe Excerpt: We predict that future investigations, like ours, will support a molecular version of Dollo's law: ,,, Dr. Behe comments on the finding of the study, "The old, organismal, time-asymmetric Dollo’s law supposedly blocked off just the past to Darwinian processes, for arbitrary reasons. A Dollo’s law in the molecular sense of Bridgham et al (2009), however, is time-symmetric. A time-symmetric law will substantially block both the past and the future,". http://www.evolutionnews.org/2009/10/dollos_law_the_symmetry_of_tim.html bornagain77
Nak, Well how do your "beliefs square with the facts: you stated, apparently without much thought that: "Of course, anyone arguing for the stability of genomes can’t also argue for Genetic Entropy. You do see the logical contradiction there, I hope." yet the evidence behind door # 1 is: Though it is impossible to reconstruct the DNA of these earliest bacteria fossils, scientists find in the fossil record, and compare them to their descendants of today, there are many ancient bacteria spores recovered and "revived" from salt crystals and amber crystals which have been compared to their living descendants of today. Some bacterium spores, in salt crystals, dating back as far as 250 million years have been revived, had their DNA sequenced, and compared to their offspring of today (Vreeland RH, 2000 Nature). To the disbelieving shock of many scientists, both ancient and modern bacteria were found to have the almost same exact DNA sequence. The Paradox of the "Ancient" Bacterium Which Contains "Modern" Protein-Coding Genes: “Almost without exception, bacteria isolated from ancient material have proven to closely resemble modern bacteria at both morphological and molecular levels.” Heather Maughan*, C. William Birky Jr., Wayne L. Nicholson, William D. Rosenzweig§ and Russell H. Vreeland ; http://mbe.oxfordjournals.org/cgi/content/full/19/9/1637 and this: Revival and identification of bacterial spores in 25- to 40-million-year-old Dominican amber Dr. Cano and his former graduate student Dr. Monica K. Borucki said that they had found slight but significant differences between the DNA of the ancient, 25-40 million year old amber-sealed Bacillus sphaericus and that of its modern counterpart,(thus ruling out that it is a modern contaminant, yet at the same time confounding materialists, since the change is not nearly as great as evolution's "genetic drift" theory requires.) http://www.sciencemag.org/cgi/content/abstract/268/5213/1060 30-Million-Year Sleep: Germ Is Declared Alive http://query.nytimes.com/gst/fullpage.html?res=990CEFD61439F93AA25756C0A963958260&sec=&spon=&pagewanted=2 In reply to a personal e-mail from myself, Dr. Cano commented on the "Fitness Test" I had asked him about: Dr. Cano stated: "We performed such a test, a long time ago, using a panel of substrates (the old gram positive biolog panel) on B. sphaericus. From the results we surmised that the putative "ancient" B. sphaericus isolate was capable of utilizing a broader scope of substrates. Additionally, we looked at the fatty acid profile and here, again, the profiles were similar but more diverse in the amber isolate.": Fitness test which compared the 30 million year old ancient bacteria to its modern day descendants, RJ Cano and MK Borucki Thus, the most solid evidence available for the most ancient DNA scientists are able to find does not support evolution happening on the molecular level of bacteria. In fact, according to the fitness test of Dr. Cano, the change witnessed in bacteria conforms to the exact opposite, Genetic Entropy; a loss of functional information/complexity, since fewer substrates and fatty acids are utilized by the modern strains. Considering the intricate level of protein machinery it takes to utilize individual molecules within a substrate, we are talking an impressive loss of protein complexity, and thus loss of functional information, from the ancient amber sealed bacteria. Ancient Fossils That Have Not Changed For Millions Of Years - video http://www.metacafe.com/watch/4113820 THE FOSSILS IN THE CREATION MUSEUM - 1000's of pictures of ancient "living" fossils that have not changed for millions of years: http://www.fossil-museum.com/fossils/?page=0&limit=30 bornagain77
Mr BA^77, When it is pointed out to you that these errors are shown to always be detrimental to functionality when they are truly errors, and not just changes of directed adaptations that arise from higher levels of information in the genome, you say that these rare detrimental errors, that slip through, accumulate in some unsubstantiated “Junk” part of the genome, and then, magically, as if by the will of the mad-hatter, they suddenly become functional so as to someday be incorporated into higher base levels of functionality within the genome, even through some genomes have demonstrated stability for millions of years. (Cano, Vreeland) I respect your attempt to restate my position in your own words. It was a pathetic failure, but you tried, and I respect that. My position on variation doesn't include the neat choice of categories "truly error" OR "directed adaptation". If you feel that those are the only choices, state that as your own opinion, not mine. If you need to use a modifier such as "truly", it should be an alert that your position is poorly supported. See No True Scotsman. See Weasel Word. Since the average lifetime of a species is ten million years, saying that some genomes have demonstrated stability for millions of years is really not saying much. Of course, anyone arguing for the stability of genomes can't also argue for Genetic Entropy. You do see the logical contradiction there, I hope. Nakashima
Nak, the master of rationalization and denialism. You should get a award for your ability to go in the completely wrong direction as logic dictates. Let's see how you work this one out. Darwinism requires a fairly beneficial rate of change to the genome to work on paper, even though Genetic Reductionism is shown to be completely false, yet even though you are working from a falsified foundational basis of reason in the first place, you say that the multiple layers of error correction are of no concern to you because somewhere in your "alice in wonderland" world of science a "error" is able to slip through ever once in a great while. When it is pointed out to you that these errors are shown to always be detrimental to functionality when they are truly errors, and not just changes of directed adaptations that arise from higher levels of information in the genome, you say that these rare detrimental errors, that slip through, accumulate in some unsubstantiated "Junk" part of the genome, and then, magically, as if by the will of the mad-hatter, they suddenly become functional so as to someday be incorporated into higher base levels of functionality within the genome, even through some genomes have demonstrated stability for millions of years. (Cano, Vreeland) I guess you just cant beat logic like that Nak, how could I have ever missed the obviousness of your position,,, by the way have you seen the new Alice in Wonderland yet? bornagain77
Mr BA^77, How in the world do explain evolution now that multiple layers of error correction are found that prevent any undirected changes in proteins as well as in the genome? Having multiple layers of error correction is an admission that errors are still getting through all the previous layers! Do some research and find out the actual error rates, even in the presence of all these systems. And yet, humans know how to build secure error detection and correction information processing systems with much lower error rates. Why is there no checksum in DNA? If DNA is designed, it is designed to change. Nakashima
What I don't understand Nak, is why you would even have the audacity to declare 42% of the genome junk when the complexity that man has been able to decipher in the genome so far, which is clearly just the tip of the iceberg of the complexity being dealt with in the genome, far exceeds the complexity of any computer program or algorithm written by man. Basically you are saying,,, "Yeah 42% is fantastically complex compared to man's ability, but the other 58%, since we don't really have a handle on what its doing yet, is junk. Why? well ba77, because I just have to believe Darwinism is true no matter what the evidence says because to do otherwise may make me accountable to the God whom I have chosen not have to deal?" Is that a little to honest as to how it really is Nak? bornagain77
I'm in such a state of suspense, waiting for Dr Sternberg to explain isochores and why SINE distribution supports ID! Golly!! Nakashima
I forgot to ask you yesterday Nak,,, How in the world do explain evolution now that multiple layers of error correction are found that prevent any undirected changes in proteins as well as in the genome? Don't you find that a even a bit disconcerting for the love affair you have for all things Darwin? Oh I forgot, your love for Darwinism forgives all transgressions no matter how egregious the violations of logic. bornagain77
So Nak, What percent of the genome do you think is functional now? 43% instead of the 42%? lol,,, bornagain77
Thanks for the link Nak; bornagain77
And for all you ENCODE, epigenetics, rapid sequencing fans - an article on non-coding DNA influencing phenotypes. Nakashima
Hey Nak and Sal, Dr. Sternberg has another post up at ENV on "junk" DNA: Discovering Signs in the Genome by Thinking Outside the BioLogos Box http://www.evolutionnews.org/2010/03/signs_in_the_genome_part_2.html bornagain77
Nak, Cluttering? Interesting choice of adjective. Of course you wouldn't be personally biased in all this would you?,,to the point of ignoring evidence would you? Dr. Sternberg's paper yesterday,,, Ayala and Falk Miss the Signs in the Genome http://www.evolutionnews.org/2010/03/ayala_and_falk_miss_the_signs.html states,,,, And since I want to focus on the global functions of such Short Interspersed Nuclear Elements (SINEs) as human Alus and their mouse and rat counterparts, their far-from-random placement cannot be elided. In fact, I will argue that it is a critical part of the genome story that the folks at Biologos aren’t telling you. To prepare for the mysterious genomic signal, though, I want to draw your attention to this figure: http://www.evolutionnews.org/SINE%20post%201.JPG What you are seeing are the relative densities of Long Interspersed Nuclear Element (LINE) L1s and SINEs along 110,000,000 DNA letters of rat chromosome 10.1 (From Fig. 9d of reference 1.) The x-axis represents the sequence of letters in DNA and the blue line indicates where SINEs occur—what Ayala calls “obnoxious sequences” that are supposedly due to “degenerative biological processes that are not the result of ID.” The red line indicates where LINE sequences occur. Both LINEs and SINEs are types of mobile DNA, namely, retrotransposons, and together they can comprise around half of the mammalian genome. As should be clear from the figure, LINEs tend to peak in abundance where SINEs taper off and vice versa (see the blue boxes). We have known about this pattern since the late 1980s, so it is no surprise to someone who has been following the subject. What should be surprising to anyone, however, is that the same machinery is responsible for the movement of both types of retrotransposon. A complete L1 element encodes the proteins necessary to “reverse transcribe” an RNA copy of itself back into DNA, and to insert the generated duplicate into some chromosomal site. SINEs, by way of contrast, rely on the L1-specified proteins for all their copying and pasting routines. This compartmentalization of LINEs and SINEs along the mammalian chromosome can also be detected by using molecular probes for L1 or Alu(-like) sequences2: Image: http://www.evolutionnews.org/SINE%20post%202.JPG For junkety-junk elements that can make up fifty percent of a mammal’s mostly junkety-junk genome, the rule seems to be: Location, location, location. Interestingly, this higher-order pattern cannot be detected when small sections of DNA are examined. It only becomes evident when stretches that are millions of nucleotides long are studied. This banding pattern has been known for decades—but for some reason it is rarely (if ever) discussed by “junk DNA” advocates. The bands on the chromosome arms fall into two general categories: So Nak, since it is clear that function is a warranted inference to SINE's and LINE's due to the "complexity" being dealt with, a complexity you so non-chalantly scoff at, why would you be so resistant to fully investigating these elements for function and to so quickly call them "clutter"? Should you not take a much more humble approach in your investigation until more is known of their functionality? Why ar you so dogmatic so as to be unreasonable in your inquiry? Or as Dr. Hunter would ask, Why do you let your "religion" drive your science? bornagain77
Mr BA^77, How many proteins are Junk nak? I'd guess not many,but we aren't talking about proteins. So Nak please do tell me exactly why in the world you would be so audacious as to claim that the majority of the DNA is junk when faced with such staggering complexity? Because complexity does not imply function, or design. There's nothing "complex" about thousands of SINEs and LINEs cluttering the genome. Nakashima
Nak, You request a Youtube??? Light and Quantum Entanglement Proves That God Does Indeed Exist - video http://www.metacafe.com/watch/4102182/light_quantum_mechanics_reflect_gods_characteristics/ bornagain77
Nak, 42% of the genome is functional? and thus 58% is junk? You wouldn't be saying this because of personal bias, and in spite of evidence, would you? Concluding statement of the ENCODE study: "we have also encountered a remarkable excess of experimentally identified functional elements lacking evolutionary constraint, and these cannot be dismissed for technical reasons. This is perhaps the biggest surprise of the pilot phase of the ENCODE Project, and suggests that we take a more 'neutral' view of many of the functions conferred by the genome." http://www.genome.gov/Pages/Research/ENCODE/nature05874.pdf "There is abundant evidence that most DNA sequences are poly-functional, and therefore are poly-constrained. This fact has been extensively demonstrated by Trifonov (1989). For example, most human coding sequences encode for two different RNAs, read in opposite directions i.e. Both DNA strands are transcribed ( Yelin et al., 2003). Some sequences encode for different proteins depending on where translation is initiated and where the reading frame begins (i.e. read-through proteins). Some sequences encode for different proteins based upon alternate mRNA splicing. Some sequences serve simultaneously for protein-encoding and also serve as internal transcriptional promoters. Some sequences encode for both a protein coding, and a protein-binding region. Alu elements and origins-of-replication can be found within functional promoters and within exons. Basically all DNA sequences are constrained by isochore requirements (regional GC content), “word” content (species-specific profiles of di-, tri-, and tetra-nucleotide frequencies), and nucleosome binding sites (i.e. All DNA must condense). Selective condensation is clearly implicated in gene regulation, and selective nucleosome binding is controlled by specific DNA sequence patterns - which must permeate the entire genome. Lastly, probably all sequences do what they do, even as they also affect general spacing and DNA-folding/architecture - which is clearly sequence dependent. To explain the incredible amount of information which must somehow be packed into the genome (given that extreme complexity of life), we really have to assume that there are even higher levels of organization and information encrypted within the genome. For example, there is another whole level of organization at the epigenetic level (Gibbs 2003). There also appears to be extensive sequence dependent three-dimensional organization within chromosomes and the whole nucleus (Manuelides, 1990; Gardiner, 1995; Flam, 1994). Trifonov (1989), has shown that probably all DNA sequences in the genome encrypt multiple “codes” (up to 12 codes). (Dr. John Sanford; Genetic Entropy 2005) Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome - Oct. - 2009 Excerpt: We identified an additional level of genome organization that is characterized by the spatial segregation of open and closed chromatin to form two genome-wide compartments. At the megabase scale, the chromatin conformation is consistent with a fractal globule, a knot-free, polymer conformation that enables maximally dense packing while preserving the ability to easily fold and unfold any genomic locus. http://www.sciencemag.org/cgi/content/abstract/326/5950/289 The human genome, according to Bill Gates the founder of Microsoft, far, far surpasses, in complexity, any computer program ever written by man. The data compression (multiple meanings) of some stretches of human DNA is estimated to be up to 12 codes thick! (Trifonov, 1989) No line of computer code ever written by man approaches that level of data compression (poly-functional complexity). There are about three-billion letters of code on the six feet of DNA curled up in each human cell. If you were to read the code aloud, at a rate of three letters per second for twenty-four hours per day (about one-hundred-million letters a year), it would take you over thirty years to read it. The capacity of a DNA molecule to store information is so efficient all the information needed to specify an organism as complex as man weighs less than a few thousand-millionths of a gram. The information needed to specify the design of all species of organisms which have ever existed (a number estimated to be one billion) could easily fit into a teaspoon with plenty of room left over for every book ever written on the face of the earth. For comparison sake, if mere man were to write out the proper locations of all the protein molecules in just one human body, in the limited mathematical language he now uses, it would take a bundle of CD-ROM disks greater than the size of the moon, or a billion-trillion computer hard drives, and that’s just the proper locations for the protein molecules in one human body, that billion-trillion computer hard-drives would not contain a single word of instruction telling those protein molecules how to self assemble themselves into a body. (The Bit and the Pendulum - Tom Siegfried - Samuel Braunstein) First-Ever Blueprint of 'Minimal Cell' Is More Complex Than Expected - Nov. 2009 Excerpt: A network of research groups,, approached the bacterium at three different levels. One team of scientists described M. pneumoniae's transcriptome, identifying all the RNA molecules, or transcripts, produced from its DNA, under various environmental conditions. Another defined all the metabolic reactions that occurred in it, collectively known as its metabolome, under the same conditions. A third team identified every multi-protein complex the bacterium produced, thus characterising its proteome organisation. "At all three levels, we found M. pneumoniae was more complex than we expected," http://www.sciencedaily.com/releases/2009/11/091126173027.htm "To the skeptic, the proposition that the genetic programmes of higher organisms, consisting of something close to a thousand million bits of information, equivalent to the sequence of letters in a small library of 1,000 volumes, containing in encoded form countless thousands of intricate algorithms controlling, specifying, and ordering the growth and development of billions and billions of cells into the form of a complex organism, were composed by a purely random process is simply an affront to reason. But to the Darwinist, the idea is accepted without a ripple of doubt - the paradigm takes precedence!" - Michael Denton How many proteins are Junk nak? The Ribosome: Perfectionist Protein-maker Trashes Errors Excerpt: The enzyme machine that translates a cell's DNA code into the proteins of life is nothing if not an editorial perfectionist...the ribosome exerts far tighter quality control than anyone ever suspected over its precious protein products... To their further surprise, the ribosome lets go of error-laden proteins 10,000 times faster than it would normally release error-free proteins, a rate of destruction that Green says is "shocking" and reveals just how much of a stickler the ribosome is about high-fidelity protein synthesis. http://www.sciencedaily.com/releases/2009/01/090107134529.htm So Nak please do tell me exactly why in the world you would be so audacious as to claim that the majority of the DNA is junk when faced with such staggering complexity? bornagain77
scordova, If selection doesn’t see it, it’s dubious that selection can account for it’s functionality. You do remember that selection doesn't create function, don't you? Your friends over here in NDE-land agree that redundant genes are under less selection pressure. That is what lets one of them change and be modified to a new function. Duplication, exaptation - thanks for showing how it works! Nakashima
Mr BA^77, Nak, as Dr. Sternberg asked Falk; Pick a number any number. 42 is obviously the correct number! ;) But seriously, I'd rather wait for the expermentalists to tell me the number. I'll stick with 42% if you want me to, I don't share Dr von Sternberg's conviction that ALUs etc are functional, unless "causes cancer" is a function. Nakashima
Mr BA^77, ,,, by the way do you know that the basis of gravity is not a material basis? Dude, you're on a roll. Don't ruin it. I see that ,,, and I know a YouTube video can't be far behind. Nakashima
Mr BA^77, DNA contains the instructions for the building blocks of the body but not for the overall blueprint of how the body is built. I don't know if you were reading UD last December, but there was a long discussion on this. It ended with the evidence from hybrid rabbit/human stem cells, in which human DNA was implanted into enucleated (no DNA, etc) rabbit cells. The results grew up as human cells. That result says the body plan information and the building block information is in the nucleus. More to the point of this discussion, it is physical. Nakashima
Nak, as Dr. Sternberg asked Falk; Pick a number any number. bornagain77
Mr Joseph, The point being removing DNA from an organism really doesn’t tell us very much- we could have removed a redundant system. Yes, or we could be scraping the rust off the bottom of the chassis. We are in violent agreement that some DNA isn't functional, though Dr von Sternberg is predicting that a lot is functional. Nakashima
Ayala and Falk vs. Meyer and Sternberg,,, Now THAT would be a cool debate!!! bornagain77
Powerful stuff BA77. I may post separately on Sternberg's takedown of Ayala. Their best (ayala and falk) are no match for our best (meyer and sternberg). scordova
Dr. Sternberg has a new article up at ENV: Ayala and Falk Miss the Signs in the Genome Excerpt: In my last blog, I showed that the vast majority of the genome is transcribed, either into protein-coding genes or into regulatory RNAs. The technical literature—some of which I cited in that blog—reports that the genome is an RNA-coding machine. Clearly, most DNA really does have function. In this and subsequent posts, I will provide other sorts of evidence that so-called “junk DNA” is not junk at all, but functional. http://www.evolutionnews.org/2010/03/ayala_and_falk_miss_the_signs.html bornagain77
Megabase deletions of gene deserts result in viable mice
Futhermore, if the base pairs are found to be functional in a redundant way, this is evidence selection doesn't see it. If selection doesn't see it, it's dubious that selection can account for it's functionality. Thus we have physical evidence of a Darwin breaker:
If it could be demonstrated that any complex organ existed, which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down. But I can find out no such case.
Examples of Darwin breakers: 1. Irreducible complexity 2. Redundant systems scordova
Megabase deletions of gene deserts result in viable mice
Megabase deletions are a horrible way to gauge functionality in complex systems. See: Airplane Magnetos Contingency Designs and Reasons ID Will Prevail for the full treatment of that misunderstanding. Hopefully it will that discussion will help cure Darwinist perversions of reality. We see this Darwinist misperception played out in a small way:
Minimal genome should be twice the size, study shows “Previous attempts to work out the minimal genome have relied on deleting individual genes in order to infer which genes are essential for maintaining life,” said Professor Laurence Hurst from the Department of Biology and Biochemistry at the University of Bath. “This knock out approach misses the fact that there are alternative genetic routes, or pathways, to the production of the same cellular product. When you knock out one gene, the genome can compensate by using an alternative gene. But when you repeat the knock out experiment by deleting the alternative, the genome can revert to the original gene instead. Using the knock-out approach you could infer that both genes are expendable from the genome because there appears to be no deleterious effect in both experiments.”
That's the problem with Darwinism. It defines functionality in terms of reproductive success. BAD idea. Andreas Wagner points out tis better to define in functionality in terms of integrated well-matched parts. Hmms sounds more like Behe! scordova
Nak, there is zero demonstrated direct DNA linkage to novel morphogenesis of Body Plans, and much evidence for the overall architectural information of Body Plans to reside outside the DNA. i.e. DNA contains the instructions for the building blocks of the body but not for the overall blueprint of how the body is built. A fact to which you admit, in a kind of sitting on the fence way. You can hypothesize all you want about where this "ontogenetic" information may reside, but the take home point is that neither you, nor any other evolutionist, has a real clue as to where the "blueprint" for body plans resides. Because the blueprint, wherever it is, and the building blocks must have intricate communication, the level of integrated complexity actually being dealt with just shot up exponentially. But none-the-less, despite this very critical gap in human knowledge of where the information for body plans resides, a gap that invalidates over 50 years of evolutionary research based on "DNA reductionism", evolutionists are adamant that evolution is "a fact as well established as gravity",,, by the way do you know that the basis of gravity is not a material basis? bornagain77
Gee, Nakashima-san, I can take the doors off of my car and it still drives just fine. I can remove all the glass and it would drive just fine. The point being removing DNA from an organism really doesn't tell us very much- we could have removed a redundant system. Joseph
Mr BA^77, No worries. :) The issue for a sutdy like this is that Sternberg has predicted "all", so even one tenth of one percent is going to force him to rework or nuance his position away from how it is stated here. It seems from this megabase deletion research that there are some stretches of ncDNA (what they call a 'gene desert') which can be deleted and some which can't. That in turn suggests that some of the RNA is functional and some isn't. Sternberg has staked out an extreme position by predicting all of it will be functional. Another fallback objection by Sternberg could be - oh, that might be true for mice, I'm only making a prediction about humans. To your points on morphology and gentic reductionism - It isn't my position, or a standard 'Neo-Darwinian' position that every change to DNA should cause a change to the phenotype. That is, if anything, Sternberg's position. Remember that Neo-Darwinians have lots of places in the process of phenotype building to point and say, "See, a change back there isn't going to make a difference after this point." 1 - Trimming exons. 2 - Genetic code. A base change might still code for the same amino acid. 3 - Protein folding - even a different AA might get buried inside the protein, or have the same polarity as the previous AA before the base change, and therefore affect protein shape and function very little. 4 - Developmental issues - even a changed protein might only be expressed in a few cell types, or during one phase of development. 5 - The existence of another version of the original gene elsewhere in the genome. If there are multiple genes for the same protein, then the other copy could take up the slack. Any of the above would be a reason to NOT expect a direct DNA-morphology linkage. Do I hold to some kind of Genetic Reductionism? Yes, I think that heredity is a matter of copying physical, material objects by some imperfect physical, material process. Those material objects could be (and mostly are) bases of DNA, but they are not only bases of DNA. We know about histone changes being heritable. We know about maternal mitochondria, and prions or bacteria living inside egg cell cytoplasm. So to me, evolution's "heritable variation" is a case of imperfect copying of physical objects, but not a belief that all variation is mutation of DNA. Nakashima
Nak. Thanks for being objective. I'm surprised that you would admit to the weakness of your evidence, bornagain77
Mr BA^77, A good response, especially as it contained your own thoughts and no links. A better response would be that while one million bases sounds like a lot, the mouse genome is almost as big as ours - 2.7 gigabases. Chopping a million bases out of it is less than one tenth of one percent. Nakashima
Nak, Looked at another way you can say that particular experiment is one more nail in the coffin for the Neo-Darwinian view of morphological novelty being related to DNA variability, since no "loss of" morphological novelty was witnessed. Don't you hold to the falsified Neo-Darwinian view of Genetic Reductionism? Furthermore, in that particular experiment, the author was clear that the experiment did not mean the DNA was functionless i.e. Junk, as you want it to mean. As well, the testing did not include testing for reproductive variability with control group, nor disease stress. bornagain77
scordova, Sternberg should easily account for this result, then: Megabase deletions of gene deserts result in viable mice The functional importance of the roughly 98% of mammalian genomes not corresponding to protein coding sequences remains largely undetermined. Here we show that some large-scale deletions of the non-coding DNA referred to as gene deserts can be well tolerated by an organism. Nature 431, 988-993 (21 October 2004) | doi:10.1038/nature03022; Nakashima
Sal, I think I read a while back that Dr. Sternberg has a book on "Junk" DNA in the works. Since many Top evolutionists seem to think this one point of evidence of "Junk" DNA, derived from their severely prejudiced reading of the evidence and their ignoring of the mountain of evidence in favor of ID, is the final word on the case for evolution, the book should be a severe thorn in the side for top evolutionists, since they will no longer have their major rhetorical device to work with. bornagain77
BA77, I've looked through the UD archives and I don't see a specific post in the aftermath of Sternberg and Meyer buldozing over Shermer and Prothero. Think I should post links to the audio and solicit comments? Here is one characterization of the debate and how Rick Sternberg rolled over the Darwinists:
Some of the best points came later in the debate, when Sternberg slammed Prothero with factual put down after factual put down, citing the current literature time and again. His command of the subject matter — from population genetics to junk DNA — was so far and above beyond Shermer and Prothero's knowledge, so far above their pay grade, that it was almost painful to watch him school them point after point. As I said before, shortly you'll be able to watch the debate for yourself. But be warned, it isn't pretty.
You're the best Rick! scordova
BornAgain77, YOU DA MAN!!!!! Thanks. Sternberg hits the issue of ERV's and pseudo genes out of the park!!!!! WHOA! WHOA!!!! Ken Miller (Dover's star witness) was wrong. Behe prevails. No surprise. Nice to hear the applause at the end. So much good info. So little time. Score another point against the judicial bozo presiding over Kitzmiller vs. Dover scordova
This is an excerpt from the debate - Meyer-Sternberg vs Shermer-Prothero at the 2:30 mark Sternberg addresses pseudogenes: Refutation Of Endogenous Retrovirus - Richard Sternberg PhD. - video http://www.metacafe.com/watch/4094119/refutation_of_endogenous_retrovirus_richard_sternberg_phd/ bornagain77
One technical question which I don't have an answer for, but would be appreciative if some one in the know could clairfy. Would the DNA sternberg refers to include pseudo genes? Ken Miller has used the pseudo-gene argument against Behe. If Sternberg's hypothesis covers pseudo genes, then Ken Miller's claims have been potentially falsified as well. Thanks in advance to those with info. scordova

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