FAQ4 is Open for Comment

_{Barry Arrington

April 24, 2009

Intelligent Design}

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4. ID does not make scientifically fruitful predictions.

This claim is simply false. To cite just one example, the non-functionality of “junk DNA” was predicted by Susumu Ohno (1972), Richard Dawkins (1976), Crick and Orgel (1980), Pagel and Johnstone (1992), and Ken Miller (1994), based on evolutionary presuppositions. In contrast, on teleological grounds, Michael Denton (1986, 1998), Michael Behe (1996), John West (1998), William Dembski (1998), Richard Hirsch (2000), and Jonathan Wells (2004) predicted that “junk DNA” would be found to be functional.

The Intelligent Design predictions are being confirmed and the Darwinist predictions are being falsified. For instance, ENCODE’s June 2007 results show substantial functionality across the genome in such “junk DNA” regions, including pseudogenes.

Thus, it is a matter of simple fact that scientists working in the ID paradigm carry out and publish research, and they have made significant and successful ID-based predictions.

A more general and long term prediction of ID is that the complexity of living things will be shown to be much higher than currently thought. Darwin thought the cell was a relatively simple blob of gelatinous carbon. He was wrong. We now known the cell is a high-tech information processing system, with superbly functionally integrated machinery, error-correction-and-repair systems, and much more that surpasses the most sophisticated efforts of the best human mathematicians, mechanical, electrical, chemical, and software engineers. The prediction that living systems will turn out to be vastly more complicated than previously thought (and thus much less likely to have evolved through naturalistic means) will continue to be verified in the years to come.

Comments

Mr Jerry, I agree with you that junk DNA is not enough. If ID works as a mathematical idea, there should confirmatory applications outside of historical biology. Or is it now the contention that the only 'designed' object is the human genome? Is the lack of junk DNA in another organism's genome also a prediction of ID? Does ID make a prediction about the fine tuning of the universe? Just in terms of categories, a design inference is not a prediction. If various authors in the ID camp have made predictions about junk DNA, it seems to me that they are stating a belief that the designer is conservative, efficient, parsimonious, etc.Nakashima_{April 29, 2009
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jerry [148], You ask a good question. I've been looking for updates, but haven't found anything yet. Note that the pilot project data, which were published in June 2007, involved only 1% of the genome of a single species (human). Since then, the pilot project has been expanded, according to the NIH ENCODE project site, which links to other resources: http://www.genome.gov/10005107 My hunch is that it's going to take a lot more work - and time - to more fully understand the ENCODE results. However, there are other sources of information on expression and function of non-coding DNA. Try a search for "junk DNA function" at PubMed.Adel DiBagno_{April 29, 2009
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Hi jerry,
No one has answered my question posed in #22 about ENCODE and junk DNA. At least I did not see an answer. I think it is necessary to answer it before making a big deal out of the uses of Junk DNA.
You might be interested in the blog "The RNA Underworld", maintained by RNA researcher (and occasional Panda's Thumb contributor) Art Hunt. This particular article. "Junk to the Second Power", deals with your question: http://aghunt.wordpress.com/2008/07/21/junk-to-the-second-power/ From the article:
The ID blogosphere is much agog, and has been for some time, about recent (and not so recent) results that suggest some sort of functionality in what has long considered to be nonfunctional (junk) DNA in eukaryotes. The most recent buzz centers on studies (such as ENCODE ) that indicate that large swaths of so-called junk DNA are “expressed” by RNA polymerase II. Apparently, the fact that RNA polymerase transcribes alleged junk DNA is a blow to Darwinism, and a feather in the cap of ID. Their excitement in this regard, I suspect, will wane greatly once they learn some of the true implications of these results. For the matter of “expression” in junk DNA is one wherein ID meets, and gets swallowed by, the Garbage Disposal. What follows is a discussion of a relatively recent report that rains on the ID parade. As is my habit, I’ll summarize the essay for those with short attention spans – the bottom line is that the so-called “function” that so excites the ID proponents may be little more than manifestations of quality control in gene expression, and that the supposed functional swaths of non-coding junk DNA may be nothing more than parts of the genome that encode, and lead to the production of, “junk” RNA (if I may so bold as to coin a phrase). In a nutshell, junk piled on top of junk.
Dave Wisker_{April 29, 2009
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No one has answered my question posed in #22 about ENCODE and junk DNA. At least I did not see an answer. I think it is necessary to answer it before making a big deal out of the uses of Junk DNA.jerry_{April 29, 2009
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If the view that most of the DNA was really 'junk' is so central to 'darwinist positions' how come that a number of die-hard darwinists - the heads of the human genome project - decided already in the late 80'/early 90's of the last century to sequence the complete genome including all that 'junk' and reject the alternative proposal to focus only on the protein coding regions? If anyone would have been really convinced that the 'junk' is really 'junk' and not just a very oversimplifying media and textbook catch phrase they would not have rejected the approach of only sequencing protein coding regions saving a lot of ressources since this was discussed at the time for exactly this economic reason. Thus, this bunch of 'darwinists' including jim watson and later francis collins must have been already convinced back then that they would find a lot of interesting things in that 'junk' before deciding to spend a lot of money on sequencing it. This is really not surprising since already in the early 60's jacob and monod proposed important regulatory roles for non-coding dna sequences in their operon model of gene regulation. Thus research into the function of non-coding dna sequences is mainstream molecular biology for at least four decades.rna_{April 29, 2009
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Onlookers & participants: Thanks to Internet Wayback machine [captured a lot of stuff from a lost page from ReasearchID], a trove of further facts: ________________ 1] origin: The earliest use of the term "Junk DNA" in the biological literature appears to be by Dr. Susumu Ohno in his 1972 paper titled, "So much "junk" DNA in our genome."[1] Ohno focused "mainly on the fossilized genes, called pseudo genes, that are strewn like tombstones throughout our DNA." Ohno laments that it was difficult to perceive the role repetitive DNA played, and expected much of DNA to be non-functional, due to his evolutionary presuppositions. Ohno's paper is in the collection "Evolution of Genetic Systems" (1972), part of a symposia anthology of the Brookhaven National Laboratory, Biology Department, Upton, New York. 2] Brenner's subrtlety: When challenged by someone with the argument that God would not have created us with 97 per cent of redundant or useless DNA, Brenner is said to have retorted, "I said it was 'junk' DNA, not 'trash'. Everyone knows that you throw away trash. But junk we keep in the attic until there may be some need for it." 3] Dawkins weighs in, others follow: In 1976, Richard Dawkins published his gene-centric view of evolution in a book titled The Selfish Gene.[22] In this book, Dawkins presented a view of evolution that was divergent from most other thinkers of the time, and Dawkins' book became a common reference for papers seeking to explain repetitive DNA as parasitical, including Crick and Orgel (1980). In 1992, Pagel and Johnstone reiterated these evolutionary predictions of junk-DNA having no function 4] The consequent general triumph of the "junk" thesis: "These regions have traditionally been regarded as useless accumulations of material from millions of years of evolution." - Yam, 1995[25] ". . . scientists generally accept the notion that most of this [non-coding] DNA is junk." "Although the high content of "junk DNA" was initially surprising when it was discovered, our current understanding of the mechanisms of genome expansion (duplication and insertion) and the apparent lack of significant selective pressure to minimize genome size combine to make the accumulation of useless sequences in our DNA seem inevitable." - Edward Max, 2003[26] "They are the remains of nature's experiments which failed. The earth is strewn with fossil remains of extinct species; is it a wonder that our genome too is filled with the remains of extinct genes?" - Susumu Ohno, 1972[27] "Most Darwinists erroneously predicted that 98.7% of the DNA was devoid of function (“junk”), while the ID/ET theory correctly predicted some yet to be decoded function of junk DNA." - Andras Pellionisz "The simplest way to explain the surplus DNA is to suppose that it is a parasite or at best a harmless but useless passenger, hitching a ride in the survival machines created by the other DNA." - Christian de Duve, 1996[31] "The excess DNA in our genomes is junk, and it is there because it is harmless, as well as being useless, and because the molecular processes generating extra DNA outpace those getting rid of it." - Sydney Brenner, 1998 --> Notice, there is always room for the exceptional persons who say no, but we must recognise that there was a movement that had a strong reason to swim against a very strong tide. --> that is why citing odd cites to suggest that oh, there were folks who said much the same thing long ago has very little weight. [On MOST scientific topics of note, there is a pattern of minority or even fringe alternatives and oppositions.) --> We are dealing with the main weight of opinion here; what by the 1990's was the "traditional" view, propped up by the observation that 97 - 98+% of say the human genome was "junk". [Recall how that was being used rhetorically by Mr Dawkins as late as 2003 - 4 as already cited] --> By contrast, the design thinkers said no, this is wrong, and for a reason: how observed designers [the family resemblance standard against which we seek to recognise other cases of design] act, in a purposeful fashion that tends not to have great excess of that which is useless in key functional elements. --> For, you may have reserve capacity, safety margins, room for robustness etc, but as a rule, you do not load up that which is intended to function with that which has no function. 5] Design theorists and friends ResearchID summarises: >>Michael Denton in 1986 discussed "functional" and "junk" DNA sequences, in Evolution: A Theory in Crisis[36] He found that major classes of animals appear to be equidistant, not the expected evolutionary tree pattern. i.e., he posited that "junk" DNA had function. In Nature's Destiny, Denton again summarized the two positions:[37] "If it is true that a vast amount of DNA in higher organisms is in fact junk, then this would indeed pose a very serous challenge to the idea of directed evolution or any teleological model of evolution. Junk DNA and directed evolution are in the end incompatible concepts. Only if the junk DNA contained information specifying for future evolutionary events, when it would not in a strict sense be junk in any case, could the finding be reconciled with a teleological model of evolution. Indeed, if it were true that the genomes of higher organisms contained vast quantities of junk, then the whole argument of this book would collapse. On any teleological model of evolution, most, perhaps all, the DNA in the genomes of higher organisms should have some functions." In 1994, pro-ID scientist and Discovery Institute fellow Forrest Mims III warned against assuming that 'junk' DNA was 'useless.'" Science [a leading general journal, second to Nature] refused to print Mims' letter in 1994 and again in 2003.[38] . . . . In 1996, Michael Behe, in Darwin's Black Box, countered Kenneth Miller's 1994 "junk and scribbles" arguments. e.g., Behe posited possible functionality of pseudogene regions:[39] "A couple of potential uses that spring to mind as I sit here at my desk include bonding to active hemoglobin genes during DNA replication in order to stabilize the DNA; guiding DNA recombination events; and aligning protein factors relative to active genes." In 1998, John G. West, associate director of the Discovery Institute predicted: “an ID theorist, reckoning that an intelligent designer would not fill animals' genomes with DNA that had no use, predicted that much of the "junk" DNA in animals' genomes -- long seen as the detritus of evolutionary processes -- will someday be found to have a function.” [40] William A. Dembski predicted in 1998: [41] "But design is not a science stopper. Indeed, design can foster inquiry where traditional evolutionary approaches obstruct it. Consider the term "junk DNA." Implicit in this term is the view that because the genome of an organism has been cobbled together through along, undirected evolutionary process, the genome is a patchwork of which only limited portions are essential to the organism. Thus on an evolutionary view we expect a lot of useless DNA. If, on the other hand, organisms are designed, we expect DNA, as much as possible, to exhibit function. And indeed, the most recent findings suggest that designating DNA as "junk" merely cloaks our current lack of knowledge about function. For instance, in a recent issue of the Journal of Theoretical Biology, John Bodnar describes how "non-coding DNA in eukaryotic genomes encodes a language which programs organismal growth and development." Design encourages scientists to look for function where evolution discourages it." [Observe how, years later, the Darwinist mainstream was still standing by the junk estimation and was surprised by the ENCODE results etc. Notice the high street press reports on that as excerpted above in 122. paradigms are ways of seeing and simultaneously ways of NOT seeing.] Subsequent ID theorists repeated this ID prediction that functionality would be found in agenic or "Junk" DNA. Roland Hirsch in 2000 observed: "2. The complexity of the genome-proteome-phenotype relationship. Research in biochemistry and molecular biology is revealing increasing complexity in this relationship, beyond the capacity of 'natural selection' and Darwinian theory to deal with. For example, segments of DNA that are not part of any gene nevertheless appear to have critical functional roles in all living organisms; they are not 'junk DNA'."[42] Jonathan Wells in 2004:[43] "Since non-coding regions do not produce proteins, Darwinian biologists have been dismissing them for decades as random evolutionary noise or "junk DNA." From an ID perspective, however, it is extremely unlikely that an organism would expend its resources on preserving and transmitting so much "junk." It is much more likely that noncoding regions have functions that we simply haven't discovered yet." . . . . Dr. Richard Sternberg in 2002 reviewed extensive evidence of functionality of certain types of junk-DNA. He concluded that:[64] "neo-Darwinian 'narratives' have been the primary obstacle to elucidating the effects of these enigmatic components of chromosomes.". . . "the selfish DNA narrative and allied frameworks must join the other ‘icons’ of neo-Darwinian evolutionary theory that, despite their variance with empirical evidence, nevertheless persist in the literature.” >> 6] The data rolls in . . . >> Recent research indicates that active transposable elements (which make the largest part of the "junk") actually have a strong mutagenic power. They are preferably activated under stress (i.e. situations where rapid evolution is required). Thus, one evolutionary function of transposable elements is to provide genomic rearrangements (i.e. genomic turnover) that accelerates genome evolution and provides genomic "raw material" from which new variation can arise. Recently, researchers have begun operating on the premise that there is functionality in agenic DNA (the 98% non-coding portion of the genome) and that it is not "Junk DNA". For example Rosetta Genomics began exploring this region. Rosetta subsequently discovered about half the microRNA genes known. Further functionality is being discovered in "Junk DNA." e.g., in the following research: * Y-chromosome control functions * Junk DNA diseases * Association with Alzheimer's disease * Antifreeze-protein gene has evolved from Junk DNA * Two-Step Recruitment of RNA-Directed DNA Methylation to Tandem Repeats * An essential role for the DXPas34 tandem repeat and Tsix transcription in the counting process of X chromosome inactivation In 2007, the ENCyclopedia Of DNA Elements (ENCODE) project, organized by the National Human Genome Research Institute of the National Institutes of Health (NHGRI, of NIH), reported on its exhaustive, four-year effort studying 1% of the human genome for a parts list of biologically functional elements. The ENCODE consortium discovered that: 1. the majority of DNA in the human genome is transcribed into functional RNA molecules 2. these RNA transcripts extensively overlap one another. This broad transcription pattern challenges the "junk DNA" perspective that the vast majority of the genome has no biological function, with only a small active set of discrete genes. The consortium concluded: 'However, we have also encountered a remarkable excess of experimentally identified functional elements lacking evolutionary constraint, and these cannot be dismissed for technical reasons . . . >> 7] Backing away . . . >> The term “junk DNA” is slowly disappearing from research findings in the biological literature, and many occurrences of the expression appear as pejorative slurs against the concept. "I don't think people take the term very seriously anymore." - Eric Green, researcher involved with the mapping of chromosome 7 (NHGRI). 1998[70] "The fact that we don't know something has a function doesn't mean that in reality it does nothing." - Carl Schmid, Ph.D., chemist, UC Davis, 1998[71] "I think this will come to be a classic story of orthodoxy derailing objective analysis of the facts, in this case for a quarter of a century. ... The failure to recognize the full implications of this--particularly the possibility that the intervening noncoding sequences may be transmitting parallel information in the form of RNA molecules may well go down as one of the biggest mistakes in the history of molecular biology." - John S. Mattick, Director, Institute for Molecular Bioscience, Univ. Queensland, Brisbane, Australia, 2003.[72: The Gems of "Junk" DNA, W. Wayt Gibbs, Scientific American, November, 2003.] "...a certain amount of hubris was required for anyone to call any part of the genome 'junk'." - Francis Collins (2006)[73] >> __________________ GEM of TKIkairosfocus_{April 29, 2009
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derwood:
I mentioned before that the basic mechanisms for evolutionary change are empirically verifiable and thus assuming that they exiost is warranted.
The problem is you appear to conflate "evolution" with the blind watchmaker. Read "Not By Chance" By Dr Lee Spetner and then you will (maybe) understand the telic position. Hint- not all mutations are random.Joseph_{April 28, 2009
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derwood, 1- Evolution is not being debated 2- It appears that two specified mutations are about all your scenario can handle- That is from evolutionists trying to refute Dr Behe in a peer-reviewed journal- “Waiting for Two Mutations: With Applications to Regulatory Sequence Evolution and the Limits of Darwinian Evolution” (Durrett, R & Schmidt, D. 2008. Genetics 180: 1501-1509) You can read Behe's responses here, here, here, here, and here 3- As for DNA being the information:
“Yet by the late 1980s it was becoming obvious to most genetic researchers, including myself, since my own main research interest in the ‘80s and ‘90s was human genetics, that the heroic effort to find the information specifying life’s order in the genes had failed. There was no longer the slightest justification for believing that there exists anything in the genome remotely resembling a program capable of specifying in detail all the complex order of the phenotype. The emerging picture made it increasingly difficult to see genes in Weismann’s “unambiguous bearers of information” or to view them as the sole source of the durability and stability of organic form. It is true that genes influence every aspect of development, but influencing something is not the same as determining it. Only a very small fraction of all known genes, such as developmental fate switching genes, can be imputed to have any sort of directing or controlling influence on form generation. From being “isolated directors” of a one-way game of life, genes are now considered to be interactive players in a dynamic two-way dance of almost unfathomable complexity, as described by Keller in The Century of The Gene.” Michael John Denton page 172 of Uncommon Dissent
It just isn't so. 4- By observing human and other designers AND also observing what nature, operating freely can do, we can then take that KNOWLEDGE and apply it to cases in which we are investigating and don't know the cause. So if we observe something and we then infer design all one has to do is step up and demonstrate that no designer is required to produce it. 5- The anti-ID position is that living organisms are reducible to matter, energy, chance and necessity. The ToE says that the bacterial flagellum is too. Yet to date not one scientist has been able to test that premise. 6- If all bacteria required a flagellum then there wouldn't be any bacteria without at least one 7- Mike Gene thinks that if the genes are similar and the all exist- even if in different bacteria, then it is possible that all the "correct" genes to end up in one. However that doesn't even start to address the issues- assembly being one of them. Some derived molecules require chaperones to take them to the correct place to avoid cross-reactions. And most derived products are required in high quantities. So with new genes you need new binding sites, promoters, enhancers, repressors and THEN you need to slide all of that in to the existing combinatorial logic. There just isn't enough time unless it was designed to evolve. 8- What do you think the design hypothesis was for Stonehenge?Joseph_{April 28, 2009
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Hoki, Point taken- Yes those random effects on the original design that led to what we observe today could lead to real "junk" DNA. Let me soak on that while I respond to derwood...Joseph_{April 28, 2009
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Joseph:
Ya see Darwinists STILL think that most of the genomes are “junk”.
And Johnson-Dembskiists still insist that it was designed by an anthropomorphic superbeing. The difference is, there is at least evidence that some junk DNA is indeed 'junk'. I'm not sure what the policy on linking to blogs is, so I will just say search for Sandwalk and JunkDNA.
Who cares about computer programs, genomes operate somewhat differently. They are both codes- one for a computer and one genetic.
And yet beyond so basic and simplistic an analogy, they are quite different. Being conversant with softare does not, in fact, give one an upper hand when discussing genetics.
You are clue-less. Mutations are allowed to accumulate via selection- many types of selection.
Yes, I know, which is essentially what I wrote. And clueless does not have a hyphen.
Next you would be testing YOUR sode’s claims by figuring out how far something can be reduced.
At which point you would just declare that at THAT point ID occurred. And so on.
It is YOUR position that says living organisms and their parts can be reduced to matter, energy, chance and necessity.
I don't recall ever reading anyone on 'my side' ever mentioning such things.
That you can’t even understand that simple fact demonstrates you are well beyond reasoniung with.
I suppose so, but being a former research scientist and zoology/marine biology student, it seems that you could explain it all to me. After you divulge where you engaged in this study and what research you have done.
So, what is the ID hypothesis for the appearance of the bacterial flagellum? That if it was designed it would not be reducible to matter, energy, chance and necessity.
That is not an hypothesis as to why or how it was designed.
What does the ToE say?
I don't know - I already explained that I do not know enough about it specifically to comment. But OK - the Designer is constrained to Designing bacterial locomotive parts and some intracellular molecules. When it is discovered that such Designer action is not necessary (I have little doubt that such a thing will eventually be discovered - 'naturalism' has a pretty good track record in finding things out and thus minimizing the role for magical tinkerers), what then? Will IDists and creationists claim that individual monomers are the product of Design? Allow me to answer that - Yes. I have already been told this by an IDist on another forum. There is no way that ID advocates will allow that their position is built on sand.
What is the ID explanation for as to why there is more than one kind of flagellum in bacteria? Why does ID have to explain that?
Doesn't ID present itself as a viable alternative to evolution? As such, does it not have to be at least AS good as evolution, if not better? If not, what is the impetus for abandoning evolution?
The ToE doesn’t.
Perhaps not specifically (as I said, I don't know much about bacterial flagella), but it would seem to me that since it appears that one type of flagellum arose via modification of related structures, that other types of similar structures could similarly be coopted. ReMine wrote in his latest entry that life is set up to look like it was designed by a single designer. Why would a single designer but different flagella in organisms that are essentially the same?
What is the ID explanation for as to why not all bacteria have flagella? Not all bacteria require one.
How do you know what bacteria require?
Your turn: How can we test the premise tat the bacterial flagellum arose from a population that never had one via an acumulation of genetic accidents?
We can analyze the genomes/proteomes of bacteria in a phylogenetic framework and infer the homologies and polarity of changes occurring through time as indicated by genetic changes. This has been done, and the analyses caused your own Mike Gene to all but acknowledge that the flagellum likely arose via evolution: "But in a far more important and global sense, it does indeed look like Matzke's hypothesis is correct and that the TTSS machinery is homologous to the F-ATPase. In The Design Matrix, I explore how the concept of IC interfaces with cooption and intelligent design and offer the following as part of my approach: [...] Multiple points of homology between the components of the F-ATPase and flagellum/TTSS would clearly qualify as "various parts of the machine" having "homologs that are in turn part of a system that is more ancient than the machine."" Hadn't you heard?
derwood_{April 28, 2009
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Experience and observation of human intelligent designers in action is just that: experience/ observation of intelligent designers in action.
Actually, observing human intelligent designers is observing humanintelligent designers. Transferring human activity to an unknown entity or entities is at best unwarranted.
Are you in a position to argue that humans exhaust the possible set of designers? Or, that non-human designers will never manifest such diagnostic signs?
Are you in a position to argue the contrary? If we can identify 'design' in nature, can we also identify 'poor' design? If not why not?
Or, can you show where signs such as IC and FSCI are known — observed — to be the result of spontaneous, undirected chance + necessity?
Is there a way,other than via post hoc rationalizations and contrived 'filters' - to demonstrate that such properties even exist in nature?
But design is not a science stopper. Indeed, design can foster inquiry where traditional evolutionary approaches obstruct it. Consider the term “junk DNA.” Implicit in this term is the view that because the genome of an organism has been cobbled together through along, undirected evolutionary process, the genome is a patchwork of which only limited portions are essential to the organism. Thus on an evolutionary view we expect a lot of useless DNA. If, on the other hand, organisms are designed, we expect DNA, as much as possible, to exhibit function. And indeed, the most recent findings suggest that designating DNA as “junk” merely cloaks our current lack of knowledge about function.
I may be new here and all, but it would be nice if ID advocates could slow down and read something an opponant writes for a change, instead of churning out knee-jerk, pre-fabricated expositions. For had anyone done so, they might have read some facts that contradict these prevailing - and quite false - notions that evolutionists declared all 'junk DNA' totally useless, etc. You might have seen that, in fact, it was evolutionists who not only speculated on and predicted, but actually FOUND function in some junk DNA decades before ID creationists claimed to have "predicted" it. ***************** It seems to me that in order for someone to make a prediction, they cannot or should not already know that what they are predicting has already been discovered. That is, in order for ID advocates to take credit for “predicting” function in junkDNA, that such function should not already have been discovered, otherwise, they are not really making predictions. So I have to wonder what the status of papers like: Cell. 1975 Feb;4(2):107-11. The general affinity of lac repressor for E. coli DNA: implications for gene regulation in procaryotes and eucaryotes. In which a function for junkDNA was predicted, or maybe this one: A general function of noncoding polynucleotide sequences 1981 Zuckerkandl. wherein it is proposed that junk DNA acts as transcription factor binding sites and such (which it does). Or any of the papers cited here. What do ALL of these papers have in common? 1. They were researched and written by run of the mill evolutionists. 2. They pre-date the supposed ID predictions by decades. It is not fair to claim that ID advocates ‘predicted’ something after the fact. Wells’ supposed 2004 ‘prediction’ is especially suspect.derwood_{April 28, 2009
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First you have to remeber what we are observing today is NOT what was originally designed. It is the result of numerous generations with random effects.
And this can be differentiated from evolution how?
And you are (wrongly) assuming the sequence is the information. It isn’t any more than the disk is the compuetr information.
And yet if you wipe a disc of it's information, the disc remains intact. Wiping a chromosome of it's "information" would require altering the DNA sequence or destroying it. So clearly, in a genome, the 'information' IS the DNA (or is on it or however you wish to phrase it). It is inherent in the sequence of nucleotides. Which is why I am unhappy with the use of the term 'accidents' when referring to mutations, for accidents implies a negative outcome. And I know 'evos' use the term, and I wish they would stop.derwood_{April 28, 2009
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Wrong!!!! Ya se it is very safe to make assumptions as long as those assumptions have some basis. Scientists do that every day. Then we test those assumptions.
This is true. So what are the assumptions for this Designer that have a basis (in fact? reality?)? I mentioned before that the basic mechanisms for evolutionary change are empirically verifiable and thus assuming that they exiost is warranted. What of thid Designer can we do the same for? And NOT rely on mere analogies to human activity?derwood_{April 28, 2009
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PPS: I probably need to remind us all that natural selection plays no creative role in the evolutionary paradigm. It is a culler that "weeds out" those entities that are non functional or inadequately functional relative to competitors, in reproducing populations in environments where -- as Malthus explored -- there is competition for scarce resources. So, it is proper to focus our attention on the required engine of variation -- one form or another of chance contingency generation. Then, we look at the issue that certain degrees of function are informationally complex [500 - 1,000 bits being a handy rule of thumb threshold], so that islands of function [recall codes are specific, and algorithms moreso, as well, and coded data and data structures too] will be deeply isolated int eh space of possible configurations. So isolated that it is maximally unlikely for chance based processes to get to shorelines of function for hill-climbing cumulative selection processes to have any hope of success. Worse, such cumulative processes per the malaria case, are credibly impotent to create the scale of novel information that would be onward required . . . (Toy scale simulations like Weasel and even its modern Genetic Algorithm descendants routinely duck the scale of complexity challenge.)kairosfocus_{April 28, 2009
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Onlookers (all up to 6,000 - 9,000 per day; and of course participants): Much of the immediately above is rather tangential to the focus of the thread, but a few notes will be helpful: 1] JM, 128: Can you show where CSI has been calculated for a biological construct such as the bacterial flagellum, taking into account known evolutionary mechanisms? Of course, first, the flagellum is usually presented as an illustration of irreducible complexity, not of complex, specified information. (And, after years of attempted dismissals, it still stands as a clear demonstration of the limits of chance + necessity. Along with many, many other cases, to which I add the case that the DNA- RNA- Ribosome- enzymes- etc system constitutes an algorithmic, flexible program digital information processing device; i.e. a computer. In point of fact the real -- and unmet -- burden of proof is that evolutionary materialists ant heir fellow travellers have a challenge to show that such entities are reasonably achievable on their premises. Much in the way of just-so stories, very little in the way of showing that the proposed prebiotic and macroevolutionary mechanisms are capable of what they claim, on the gamut of our observed universe, much less this small planet. Indeed, on this,t he latest evidence is that 2 - 3 single point mutations are a formidable threshold, per the largest single empirical test case we have seen, the malaria parasite. As to the blood clotting cascade, in the most public case of a challenge, the objector cleverly selected the portions that were not in the context of where irreducible complexity applies, i.e a strawman fallacy.) So, the first issue is that until the information is present,t he system will not work and will be selected against by natural selection. And, there has been no empiriclaly anchored presentation of a means by which already functional entities can be so co adapted all at once that we get around that. For instance the TTSS is on the evidence a derivative of teh flagellum, just the opposite of the assumption that the flagellum is an extension of it. Indeed, that leads to the complex-ification of functionality that a functional subsystem is embedded in the flagellum gene set and assembly instructions/algorithm. Also, given that the flagellum embeds several dozen specific proteins and a truly unusual self-assembly algorithm [think about chained proteins injecting themselves up a pre-assembled tube then reassembling in situ, while locking together to grow a filament, and a metric based on chain length that helps control the phases of the process . . .] the flagellum is doubtless functionally specific and complex information-based. Indeed, just taking 40 proteins times a short typical protein length of 150 AA by 3-letter codons by 2 bits per base gives 40 * 150 * 3 * 2 = 36,000. this greatly exceeds the 1,000 bit rule of thumb threshold for functionality that is beyond the reach of random search strategies on the gamut of our observed cosmos. Why so? [Simple: 1,000 bits specifies a config space of 10^301, ten times the square of the number of quantum-states of the ~10^80 atoms in the cosmos over its reasonably estimated lifespan. So, for an entity taking up just 1,000 bits of information in its functionality, we would not be able to scan as much as 1 in 10^150 of the available configs. In that context the likelihood of the chance variation part of any spontaneous mechanism -- and, per empirical observation, it is either chance variation or purposeful arrangement that one sees as possible sources of information-bearing configs [unless there is yet another bit of materialist magic -- "poof" -- to be played . . .] -- getting to the shoreline of an island of functionality is negligibly different from zero. So, it is utterly unsurprising that all observed entities that use at least that much information in their function, of which we do know the causal story, are artifacts of design.] (Onlookers, notice, not one time that this has ever been put at UD as a challenge, have evo mat advocates and their friends been able to put up a single counter example. Given that we have a whole Internet full of cases in point of the validity of the FSCI threshold, that is no great surprise.) So, on the simplest metric, for the subset of CSI we have termed FSCI, we have excellent reason to see that something is amiss with the assertions above. (And, onlookers, similar calculations have been presented in this blog many times, by myself and by others esp GP.) On a more formal metric, and as repeatedly pointed out here at UD -- it is even in the WACs -- there are 35 published protein FSC calculations, embedded in a methodology that leads to a general approach. A methodology that is a direct application of the Dembski general FCSI metric,using the incidence of observed functional families of proteins to estimate target zones in config spaces. So, the above was an exercise in improper shifting of burden of proof, and a bluff. But all of this is tangential, there is . . . 2] I would also note that you are still falling into the fallacy of the false dichotomy. It is not sufficient to tear down modern evolutionary theory. For ID to be a scientific theory, it must make positive, testable predictions which could potentially falsify ID theory. That is what the answer to this FAQ needs. Again, we are in the regime of inference to best, empirically anchored explanation across known alternatives. That is, the scientific method. (Translated: promissory notes on possible future explanations hold no cogency, so one cannot properly hold up vague logical possibilities as though this specifically discredits the best current explanation. That is selective hyperskepticism playing off improper shifting of a burden of warrant.) Second, what is being addressed in general by the design inference is a key issue: design is a known cause of complexity, one that is known to go beyond the capacity of chance variation and mechanical forces of necessity. thus, to suppress this as a possible explanation on matters where worldview level assumptions of evolutionary paradigms come into play -- a la Lewontin -- is improper. Worse, the progress of design theory is increasingly showing how design may be credibly empirically detected, extending methods well known from statistics, various applied sciences and even statistical thermodynamics and information theory. So, the idea that ID is just tearing down MET is false. A methodology is being corrected in science and evo mat censorship of scientific inference on origins is being exposed, along with the way that resulting just so stories have thus been given a free pass. As to positive, testable predictions, you have just dodged one of them: at the simplest level, FSCI will -- practically speaking -- only be seen in the context of design, per search space reasons. tha tis FSCI, FSC and CSI will be shown to be reliable signs of intelligent design. There are abundant confirmatory cases and ZERO disconfirmations. So, the test has been passed -- just not acknowledged. As to the WAC 4, above I have documented where per wider themes in design, it was a prediction of leading ID scientists and thinkers that junk dna so-called would turn out to have serious degrees of function. This cut across the documented expectations of the evolutionary materialism champions. And, it is the design thinkers who have been vindicated by the facts emerging across the past decade or so. On the broader theme of the complexity of life, this expectation has been vindicated across the past 50 - 100 years or so. 3] JM, 136: detection of design requires some assumptions regarding the nature of the designer Again, this inverts the empirical ladder of inference, turning it into a metaphysical assertion instead. Design detection methods make no claims to be able to infer to all instances of design, just those that are empirically evident relative to the way known -- i.e. observed -- designers work; in light of tested, empirically reliable [not logically bulletproof] signs of intelligence. (Post Godel, not even mathematics is logically bulletproof.) We have known designers, observed to create entities that exhibit IC, FSCI, FSC, CSI etc, as reliable signs of intelligence. Parallel to that, we have well-warranted knowledge that [1] necessity produces low contingency, [2] chance search is stochastic, [3] purposeful configuration is capable of outperforming chance on finding islands of function. Observed designers do this through insightfully, imaginatively and sometimes expertly harnessing the forces and materials of nature, as well as powers of reasoning etc, to create novel patterns that work towards goals. In so working, there are traces that reflect the underlying purposefulness and cleverness that are sufficiently often empirically evident to be worth the following up. So, from reliable signs per OBSERVED designers, we can infer to characteristics of cases of evident design where we do not observe the designers directly. This is of course falsifiable through counter example or analysis that shows that the capacity of chance to generate such configs is greater than is currently estimated. Which is simply to say that this is a case of science at work, producing provisional knowledge claims, as per usual. And, as per usual, since we are resign on large bases of empirical evidence, we are reasonably confident of th extensions -- so much so, that unjustifiable a priori censoring rules of imposition of materialism a la Lewontin are being inserted by evo mat advocates to try to block such from being made. Therefore, just opposite to t e assertion, we are inferring FROM the observed signs to the presence and characteristics of designers, form their evident artifacts. In this case, we have contrasting expectations that DNA molecules will store a lot of functional information vs that most of it will be junk. At the first the evidence seemed to be in favour of the junk advocates, but further investigation is proving the ones who inferred from the FSCI evident in the known aspects of DNA that there would be further functional aspects embedded in what was being written off as junk, to be right. And, such successful risky prediction in the teeth of the expectations of the dominant -- and in this case rather hostile -- school of thought is precisely a strong indicator of the power of an emerging research programme. So, the WAC is precisely correct to highlight this as a strong case in point of a successful courageous prediction now increasingly vindicated by the facts. GEM of TKI PS: BTW, interwoven multi-layer data and regulatory codes in a data storage system -- as now observed for DNA -- is a multiplication of the degree of complexity beyond the mere enumeration of bit length. I never ever even tried to do that trick in my own designs -- tough to do, very, very tough to do. And the odds of that happening by chance are so close to zero as makes no difference.kairosfocus_{April 28, 2009
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Joseph @134

First you have to remeber what we are observing today is NOT what was originally designed.
If ID theory says nothing about the designer, how do you know this?
What I said has nothing to do with the designer.
Of course it does. You are saying both that the designer is no longer interfering with natural processes and that the designer didn't design in such a way as to prevent accidental changes.
I have no reason to infer that all living organisms are as they were originally designed.
You have no reason to infer otherwise, either, and yet you are.
Things change- mutations happen. So given that my statement seems pretty elementary.
How do you know that the mutations aren't part of the designer's design? Do you see now why detection of design requires some assumptions regarding the nature of the designer? It's pretty elementary. JJJayM_{April 27, 2009
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Joseph (#134):
Things change- mutations happen.
And they couldn't have created junk DNA? You have just made the ability of ID to predict the existence of junk DNA even worse.
But anyway- again our EXPERIENCE doesn’t offer any/ many successful designers that don’t check what they are doing.
I take it you don't know much about genetic engineering?
And you are (wrongly) assuming the sequence is the information.
No I don't.Hoki_{April 27, 2009
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First you have to remeber what we are observing today is NOT what was originally designed.
If ID theory says nothing about the designer, how do you know this?-JayM
What I said has nothing to do with the designer. I have no reason to infer that all living organisms are as they were originally designed. Things change- mutations happen. So given that my statement seems pretty elementary.Joseph_{April 27, 2009
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Joseph @132
First you have to remeber what we are observing today is NOT what was originally designed.
If ID theory says nothing about the designer, how do you know this? JJJayM_{April 27, 2009
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Let’s assume that the designer(s) had imperfect techniques at the molecular level for stringing together DNA.
First you have to remeber what we are observing today is NOT what was originally designed. It is the result of numerous generations with random effects. But anyway- again our EXPERIENCE doesn't offer any/ many successful designers that don't check what they are doing. And you are (wrongly) assuming the sequence is the information. It isn't any more than the disk is the compuetr information.Joseph_{April 27, 2009
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Joseph (#127)
Ya se it is very safe to make assumptions as long as those assumptions have some basis. Scientists do that every day.
Let's run with that. Let's assume that the designer(s) had imperfect techniques at the molecular level for stringing together DNA. Like humans, we'll assume that they spliced bits and pieces together using various restriction enzymes and ligases. This can be a hit-and-miss affair. They never checked to make sure that they only got the DNA fragments they were interested in. From this we can predict that we should find lots of junk DNA. So... different assumptions, different conclusion. ID predicts both.Hoki_{April 27, 2009
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Hoki:
No…… my point was that ID says nothing about the designer what-so-ever, whether it’s human or not.
Your point is wrong. Ya see ID is NOT about the designer but that does NOT mean IDists cannot make assumptions based on our knowledge of designers. Also ID is about the detection AND study of said design. ID does NOT stop at detection.Joseph_{April 27, 2009
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Hoki:
Experience from humans, by any chance? You are making the assumption that the designer would think and act like a human would. ID doesn’t make this assumption. Neither should you.
Wrong!!!! Ya se it is very safe to make assumptions as long as those assumptions have some basis. Scientists do that every day. Then we test those assumptions.Joseph_{April 27, 2009
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kairosfocus @124
Or, can you show where signs such as IC and FSCI are known — observed — to be the result of spontaneous, undirected chance + necessity?
Can you show where CSI has been calculated for a biological construct such as the bacterial flagellum, taking into account known evolutionary mechanisms? Despite repeated requests for a reference to such a calculation, I have never seen one. With regard to irreducible complexity, there are strong suggestions that the blood clotting cascade and the various bacterial flagella are the result, at least in part, of exaptation. I have high hopes the Dr. Behe's research into the limits of known evolutionary mechanisms will result in observations that positively support ID, but those two initially promising examples of IC are probably not such evidence. I would also note that you are still falling into the fallacy of the false dichotomy. It is not sufficient to tear down modern evolutionary theory. For ID to be a scientific theory, it must make positive, testable predictions which could potentially falsify ID theory. That is what the answer to this FAQ needs. JJJayM_{April 27, 2009
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kairosfocus @124
Experience and observation of human intelligent designers in action is just that: experience/ observation of intelligent designers in action.
Not exactly. It is observation of designers with the type and level of intelligence that can be expected of humans applying that intelligence to human problems. Hoki is raising the point that I raised lo these many months ago in one of Dr. Fuller's threads: It is impossible to identify design without making some assumptions about the nature of the designer. Further, any investigation into design necessarily increases our understanding of the designer. The attempt to keep the nature of the designer off limits is doomed to failure. JJJayM_{April 27, 2009
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kairofocus (#124)
Or, that non-human designers will never manifest such diagnostic signs?
No...... my point was that ID says nothing about the designer what-so-ever, whether it's human or not. But here we have Joseph and yourself claiming that non-human intelligence would manifest such diagnostic signs.
Where such designers have known characteristic artifacts or effects that are beyond the credible reach of chance + necessity, then we are entitled to infer to ID on seeing such reliable signs of intelligence.
And this is as far as ID alledgedly goes. Given an observation that, for example, something has lots of CSI and function, the hypothesis is that something intelligent created it. I have a sneaking suspicion that some ID supporters seem to infer from this that as soon as something intelligent does something, it will always create something functional containing CSI.Hoki_{April 27, 2009
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PS: Cf the fate of junk DNA as summarised above . . . and who predicted it.kairosfocus_{April 27, 2009
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Hoki: Experience and observation of human intelligent designers in action is just that: experience/ observation of intelligent designers in action. Where such designers have known characteristic artifacts or effects that are beyond the credible reach of chance + necessity, then we are entitled to infer to ID on seeing such reliable signs of intelligence. Are you in a position to argue that humans exhaust the possible set of designers? Or, that non-human designers will never manifest such diagnostic signs? Or, can you show where signs such as IC and FSCI are known -- observed -- to be the result of spontaneous, undirected chance + necessity? If not, we are entitled to reason from signs of design to designers, even beyond where humans are implicated. GEM of TKIkairosfocus_{April 27, 2009
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Joseph (#117)
Why does ID predict little or no “junk” DNA? Experience. That is we have experience with designers that do NOT design junk into their functioning designs- especially designs that require coding. How many successful computer programs contain lines “junk” code?
Experience from humans, by any chance? You are making the assumption that the designer would think and act like a human would. ID doesn't make this assumption. Neither should you.Hoki_{April 27, 2009
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Putting a few facts into play . . . 1] Mr Dawkins, in the Devil's Chaplain, 2004: Genomes are littered with nonfunctional pseudogenes, faulty duplicates of functional genes that do nothing, while their functional cousins (the word doesn't even need scarequotes) get on with their business in a different part of the same genome. And there's lots more DNA that doesn't even deserve the name pseudogene. It too is derived by duplication, but not duplication of functional genes. it consists of multiple copies of junk, 'tandem repeats,' and other nonsense which may be useful for forensic detectives but which doesn't seem to be used in the body itself. . . . Creationists might spend some earnest time speculating on why the Creator should bother to litter genomes with untranslated pseudognes and junk tandem repeat DNA. [p. 98] 2] Donald Voet and Judith G. Voet, Biochemistry, pg. 1020 (Jon Wiley & Sons, 2006) No function has been unequivocally assigned to moderately repetitive DNA, which has therefore been termed selfish or junk DNA. This DNA apparently is a molecular parasite that, over many generations, has disseminated itself throughout the genome through transposition. The theory of natural selection predicts that the increased metabolic burden imposed by the replication of an otherwise harmless selfish DNA would eventually lead to its elimination. Yet for slowly growing eukaryotes, the relative disadvantage of replicating an additional 100 bp of selfish DNA in an 1-billion-bp genome would be so slight that its rate of elimination would be balanced by its rate of propagation. Because unexpressed sequences are subject to little selective pressure, they accumulate mutations at a greater rate than do expressed sequences. 3] Mr Dembski, in First Things on "Science and Design," oct 1, 1998: . . . Even if we have a reliable criterion for detecting design, and even if that criterion tells us that biological systems are designed, it seems that determining a biological system to be designed is akin to shrugging our shoulders and saying God did it. The fear is that admitting design as an explanation will stifle scientific inquiry, that scientists will stop investigating difficult problems because they have a sufficient explanation already. But design is not a science stopper. Indeed, design can foster inquiry where traditional evolutionary approaches obstruct it. Consider the term "junk DNA." Implicit in this term is the view that because the genome of an organism has been cobbled together through along, undirected evolutionary process, the genome is a patchwork of which only limited portions are essential to the organism. Thus on an evolutionary view we expect a lot of useless DNA. If, on the other hand, organisms are designed, we expect DNA, as much as possible, to exhibit function. And indeed, the most recent findings suggest that designating DNA as "junk" merely cloaks our current lack of knowledge about function. For instance, in a recent issue of the Journal of Theoretical Biology, John Bodnar describes how "non-coding DNA in eukaryotic genomes encodes a language which programs organismal growth and development." Design encourages scientists to look for function where evolution discourages it. --> Contrast: 2004 and 2006 vs 1998, and . . . 4] BBC, May 12, 2004: "'Junk' throws up precious secret": Researchers inspecting the genetic code of rats, mice and humans were surprised to find they shared many identical chunks of apparently "junk" DNA. This implies the code is so vital that even 75 million years of evolution in these mammals could not tinker with it . . . . Before scientists began laboriously mapping several animal life-codes, they had a rather narrow opinion about which parts of the genome were important. According to the traditional viewpoint, the really crucial things were genes, which code for proteins - the "building blocks of life". A few other sections that regulate gene function were also considered useful. The rest was thought to be excess baggage - or "junk" DNA . . . . David Haussler of the University of California, Santa Cruz, US, and his team compared the genome sequences of man, mouse and rat. They found - to their astonishment - that several great stretches of DNA were identical across the three species. To guard against this happening by coincidence, they looked for sequences that were at least 200 base-pairs (the molecules that make up DNA) in length. Statistically, a sequence of this length would almost never appear in all three by chance. Not only did one sequence of this length appear in all three - 480 did . . . . The regions largely matched up with chicken, dog and fish sequences, too; but are absent from sea squirt and fruit flies. "It absolutely knocked me off my chair," said Professor Haussler. "It's extraordinarily exciting to think that there are these ultra-conserved elements that weren't noticed by the scientific community before." The really interesting thing is that many of these "ultra-conserved" regions do not appear to code for protein. If it was not for the fact that they popped up in so many different species, they might have been dismissed as useless "padding". But whatever their function is, it is clearly of great importance. We know this because ever since rodents, humans, chickens and fish shared an ancestor - about 400 million years ago - these sequences have resisted change. This strongly suggests that any alteration would have damaged the animals' ability to survive. "These initial findings tell us quite a lot of the genome was doing something important other than coding for proteins," Professor Haussler said. He thinks the most likely scenario is that they control the activity of indispensable genes and embryo development. Nearly a quarter of the sequences overlap with genes and may help slice RNA - the chemical cousin of DNA involved in protein production - into different forms, Professor Haussler believes. The conserved elements that do not actually overlap with genes tend to cluster next to genes that play a role in embryonic development. "The fact that the conserved elements are hanging around the most important development genes, suggests they have some role in regulating the process of development and differentiation," said Professor Haussler . . . . Despite all the questions that this research has raised, one thing is clear: scientists need to review their ideas about junk DNA. Professor Chris Ponting, from the UK Medical Research Council's Functional Genetics Unit, told BBC News Online: "Amazingly, there were calls from some sections to only map the bits of genome that coded for protein - mapping the rest was thought to be a waste of time. "It is very lucky that entire genomes were mapped, as this work is showing." He added: "I think other bits of 'junk' DNA will turn out not to be junk. I think this is the tip of the iceberg, and that there will be many more similar findings." 5] Colin Nickerson,"DNA unraveled A 'scientific revolution' is taking place, as researchers explore the genomic jungle," Boston Globe Staff, September 24, 2007: The science of life is undergoing changes so jolting that even its top researchers are feeling something akin to shell-shock. Just four years after scientists finished mapping the human genome - the full sequence of 3 billion DNA "letters" folded within every cell - they find themselves confronted by a biological jungle deeper, denser, and more difficult to penetrate than anyone imagined. "Science is just starting to probe the wilderness between genes," said John M. Greally, molecular biologist at New York's Albert Einstein School of Medicine. "Already we're surprised and confounded by a lot of what we're seeing." A slew of recent but unrelated studies of everything from human disease to the workings of yeast suggest that mysterious swaths of molecules - long dismissed as "junk DNA" - may be more important to health and evolution than genes themselves. Meanwhile, a tricky substance called RNA - for decades viewed as the lowly "messenger boy " for genes and proteins - turns out to be a big league player in cell function. It may even represent the cell's command and control system, according to its more vigorous proponents. In any event, lots of basic biological beliefs are going out the window these days as new discoveries come so rapid-fire that the effect is almost more disorienting than illuminating. The discoveries have one common theme: Cellular processes long assumed to be "genetic" appear quite often to be the result of highly complex interactions occurring in regions of DNA void of genes. This is roughly akin to Wall Street waking to the realization that money doesn't make the world go 'round, after all. "It's a radical concept, one that a lot of scientists aren't very happy with," said Francis S. Collins, director of the National Human Genome Research Institute. "But the scientific community is going to have to rethink what genes are, what they do and don't do, and how the genome's functional elements have evolved. "I think we're all pretty awed by what we're seeing," Collins said. "It amounts to a scientific revolution." For half a century, the core concept in biology has been that every cell carries within its nucleus a full set of DNA, including genes. Each gene, in turn, holds coded instructions for assembling a particular protein, the stuff that keeps organisms chugging along. As a result, genes were assigned an almost divine role in biological "dogma," thought to govern not only such physical characteristics as eye color or hair texture, but even much more complicated characteristics, such as behavior or psychology. Genes were assigned blame for illness. Genes were credited for robust health. Genes were said to be the source of the mutations that underlay evolution. But the picture now emerging is more complicated, one in which illness, health, and evolutionary change appear to be the work of almost fantastical coordination between genes and swaths of DNA previously written off as junk. The idea that genes possess a singular supremacy took a knock when the human genome was fully sequenced in 2003, revealing that only about 1.5 percent of our DNA consists of actual genes coding for protein. Another 3.5 percent of DNA is of gene-linked regulatory material whose function isn't well grasped, but which is recognized as vital because it has been precisely duplicated in living things for hundreds of millions of years. "That's smoking gun evidence that nature cares about this stuff," said Eric S. Lander, director of the Broad Institute, a research center affiliated with MIT and Harvard that focuses on applying genomics to medicine. As for the remaining 95 percent of the genome? "There's this weird lunar landscape of stuff we don't understand," Lander said. "No one has a handle on what matters and what doesn't." Until recently, the rest of the genome - the murky regions between individual genes - was viewed as occupied by more or less useless glop. Noncoding DNA is the polite term for junk DNA. But the glop is starting to look like gold. And genes, in a sense, are losing some of their glitter. "To our shock and consternation, we're learning how little we know about the parts of the genome that may matter most," said Dr. David M. Altshuler, associate professor of genetics and medicine at Harvard Medical School and also a top researcher at the Broad Institute. "Maybe some of it really is junk. Maybe most of it is junk," he said. "But one shouldn't bet against nature. Maybe it all serves some sort of a purpose. We really don't know." This is how science goes forward, of course. Not in a smooth march to the future, but with stumbles, back-steps, and wrong turns . . . . In June, a consortium of 80 research institutions in North America, Asia, Europe, and Australia completed the first comprehensive effort to plumb all the inner workings of the DNA molecule, not just the genetic portions. The Encode study shattered the view that genes carry out their labor in relative isolation. Instead, genes appear to overlap each other and share stretches of molecular code. Moreover, genes and nongenetic DNA appear to work in close, if mysterious, conjunction and also seem to communicate across relatively vast genomic distances in ways not understood. Scientists have long understood that small numbers of RNAs act as "dimmer knobs" that adjust the intensity of genes, thus regulating biological processes. But few had predicted the complex orchestration of genes and nongenetic DNA suggested by the Encode research. Even more sunning was the Encode finding that most "junk DNA" is transcribed, or copied, into more RNA molecules than can be accounted for by most prevailing theories. ++++++++++++++ Okay, looks like the point of fact highlighted in Weak Argument Corrective no 4 is fairly well demonstrated then. Perhaps the most telling science-stopper point is the report that there were people who did not want to bother with going after the "useless" non-coding regions. No prizes for guessing why. Almost as hard hitting is the point that ever so few sceintists predicted that non-coding regions of the chromosomes would have function. I wonder why, and I wonder just who were among those few exceptions, why. But, bottomline: once the fact cited in rebuttal is "there," the weak argument is corrected. GEM of TKIkairosfocus_{April 27, 2009
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