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(More) Function, the evolution-free gospel of ENCODE

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I need a picture of a small, hot-blooded mammal taunting an irritable dinosaur. An animation would be even better: the dinosaur would have a tic which makes him roar ‘IDiot’ constantly. Maybe make that several small mammals, becoming dozens and then hundreds. Singing something witty to the hamster dance. Or maybe not that last bit.

Larry Moran has sort-of replied to my previous blogpost but disappoints with only one substantive point. And even that one point is wrong: ID is not committed to the idea that individual genomes be well-designed; that is just an expectation some of us derive based on belief in a designer which is established on other evidence. ID would still be true if only globular proteins were designed (lookup Axe), or even if only the flagellum was designed (lookup Behe), or even if only the first life form was designed (lookup Meyer – and please read their actual work, not cheap reviews, because reviewers often dont pick up on the salient points – more below). I just say this lest readers get the impression that this is ID’s strongest point, or in any sense a weak point. It is neither. But it would be very damaging to the Darwinian narrative. Hence the strong fire-fighting reaction from their side.

In case you missed it, the interesting thing about ENCODE is the discovery that 80% of the human genome is transcribed. Darwinian theories did not predict this. For anyone who does not have a strong upstream thought-filter*, and has not been brain-washed by the cult, transcription is strongly indicative of function. Thus ENCODE’s headline is on target. It is quite reasonable now to expect that details of actual function will subsequently be found for much of the genome. Therefore we should keep looking for that function. This site (UncommonDescent) has many articles on elements of DNA, previously thought junk, that turned out to be of importance. For examples, pseudogene transcripts regulate those of real genes, and ERV-elements turn out to be important in developing embryos. As I said, quite reasonably I think, ‘Time will tell’ for all the rest as well.

But one of the commenters below Larry’s post (here it is again) thinks that time has told already. By this I presume he means: ‘there is no need to continue doing science looking for actual function because Darwinian theory has already given us the answer that there is no function’. The danger of this is that Darwinian-theory ends up artificially filling what are actually only gaps of ignorance in our knowledge about genome function. By doing so, Darwinian theory (mis)directs researchers away from assuming a design heuristic and thus from genuine experiment-driven discovery of new functions. This is ‘Darwin-of-the-Gaps’. I wish Larry had quoted the whole of my (short) article rather than piecemeal. Clearly that commenter had not read it. Perhaps I was not clear enough. 🙁

Secondly, I also observe that Darwinists are good wrigglers. Depending on who you listen to, 90% is still non-functional, or ~80% is potentially functional but we call most of it junk anyway because we believe we can infer neutral evolution rather than natural selection (what about design?!) and these are just bits and pieces of flotsam that happen occasionally to serve some useful purpose or contribute vaguely to the general schmoo that is our messy genome (I paraphrase). Yeah, well if I interpreted our ignorance of the genome in the way that you do, I would also be as pessimistic about finding function. But it seems to me that Darwinists add a hundred extra suppositions to every bit of data they look at, through the language they use. They are not objective. We should be using terms that are less narrative-driven, and more data-driven, for example more heuristically useful for understanding in the first place the ding an sich before us rather than its unobserved origin. For that reason, I have some sympathy for those who object to ENCODE announcing ‘Function’, because not all the function is known, but I guess ‘transcription strongly suggesting function’ was not snappy enough. Some suggested definitions:

Functional: that which performs a known function.

Transcribed: that which is copied out from the DNA (and thus is quite possibly functional where it was previously presumed inert).

Garbage: DNA that is known to be non-functional or of functionally-deleterious** effect.

Darwinists should probably stop using the word ‘Junk’ altogether as the previous clarity of its meaning appears to have been compromised. 😉

Thirdly, it appears from the comments that these guys do not know the strength of the ID case at the origin of life. If they would actually read Meyer’s Signature in the Cell for themselves, they would know that the big problem is not the origin of the simple monomer molecules. It is a continuing niggle, but they are right to say its not such a big deal. The real problem has long been how to put monomers together into a self-replicating yet evolvable object. The problem is not just the empirical fact that physics and chemistry do not do it, no matter how much we try to set up favourable conditions (this has been verified by countless imaginative experiments). Nor is the problem just that idealised models such as Kauffman’s show that metabolism does not just self-organise.
The problem is that these things require and imply a large amount of information to constrain nature (physics and chemistry) to do the things that are intelligently meaningful. Once it is realised that the problem is all about functional information, not only does that point to intelligence in itself, the error catastrophe problem kills (or ought to kill) any idea of self-organisation at a theoretical level. The even bigger problem is that even intelligent humanity can’t solve the engineering problem yet***. Yet many of us, including most Darwinists I hope, believe that we will one day be able to do it, when our technological intelligence has increased. The implication is that this problem requires intelligence greater than our own.

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* Function would be indicative of design, and too much of it causes problems for Darwinian theories. Design plus problems for Darwinism will as a Darwinist cause me humiliation and pain, plus indirectly but altogether too closely the possibility of a God that I dont like (blinding feelings of a religious nature) therefore as a anti-theist Darwinist I filter it out before it gets anywhere near there. In the comments under Larry’s piece a ‘Sam Harris’ accuses us of ‘projection’ in these matters. Well, the feelings are more than mutual. Let’s leave that stuff aside and focus on the science and philosophy.

** It helps to distinguish ‘deleterious’ in terms of function from ‘deleterious’ in terms of fitness because (a) most successful microevolutionary mutations are deleterious to the biochemical subsystem they code for, even though this benefits the organism in certain special situations (read for example Behe’s Edge of Evolution if you dont already know), and (b) this totally pulls the rug from under those who claim that function can be defined by fitness, as was attempted in the original article.

*** Splicing two preprepared halves of itself is really not replication for a long RNA molecule, to those who are honest, nor does this ‘function’ evolve. If you know what I am talking about, great. If not, you’re not missing much.

As Dr. Jonathan Wells has pointed out in his book 'The Myth of Junk DNA", "Junk" DNA is found to have functionality by a few more methods than merely transcription:
Unexpectedly small effects of mutations in bacteria bring new perspectives - November 2010 Excerpt:,,, using extremely sensitive growth measurements, doctoral candidate Peter Lind showed that most mutations reduced the rate of growth of bacteria by only 0.500 percent. No mutations completely disabled the function of the proteins, and very few had no impact at all. Even more surprising was the fact that mutations that do not change the protein sequence had negative effects similar to those of mutations that led to substitution of amino acids. A possible explanation is that most mutations may have their negative effect by altering mRNA structure, not proteins, as is commonly assumed. http://www.physorg.com/news/2010-11-unexpectedly-small-effects-mutations-bacteria.html Testing Evolution in the Lab With Biologic Institute's Ann Gauger - podcast with link to peer-reviewed paper Excerpt: Dr. Gauger experimentally tested two-step adaptive paths that should have been within easy reach for bacterial populations. Listen in and learn what Dr. Gauger was surprised to find as she discusses the implications of these experiments for Darwinian evolution. Dr. Gauger's paper, "Reductive Evolution Can Prevent Populations from Taking Simple Adaptive Paths to High Fitness,". http://intelligentdesign.podomatic.com/entry/2010-05-10T15_24_13-07_00 Response from Ralph Seelke to David Hillis Regarding Testimony on Bacterial Evolution Before Texas State Board of Education, January 21, 2009 Excerpt: He has done excellent work showing the capabilities of evolution when it can take one step at a time. I have used a different approach to show the difficulties that evolution encounters when it must take two steps at a time. So while similar, our work has important differences, and Dr. Bull’s research has not contradicted or refuted my own. http://www.discovery.org/a/9951 Jonathan Wells on Darwinism, Science, and Junk DNA - November 2011 Excerpt: Mice without “junk” DNA. In 2004, Edward Rubin?] and a team of scientists at Lawrence Berkeley Laboratory in California reported that they had engineered mice missing over a million base pairs of non-protein-coding (“junk”) DNA—about 1% of the mouse genome—and that they could “see no effect in them.” But molecular biologist Barbara Knowles (who reported the same month that other regions of non-protein-coding mouse DNA were functional) cautioned that the Lawrence Berkeley study didn’t prove that non-protein-coding DNA has no function. “Those mice were alive, that’s what we know about them,” she said. “We don’t know if they have abnormalities that we don’t test for.”And University of California biomolecular engineer David Haussler? said that the deleted non-protein-coding DNA could have effects that the study missed. “Survival in the laboratory for a generation or two is not the same as successful competition in the wild for millions of years,” he argued. In 2010, Rubin was part of another team of scientists that engineered mice missing a 58,000-base stretch of so-called “junk” DNA. The team found that the DNA-deficient mice appeared normal until they (along with a control group of normal mice) were fed a high-fat, high-cholesterol diet for 20 weeks. By the end of the study, a substantially higher proportion of the DNA-deficient mice had died from heart disease. Clearly, removing so-called “junk” DNA can have effects that appear only later or under other circumstances. https://uncommondesc.wpengine.com/intelligent-design/jonathan-wells-on-darwinism-science-and-junk-dna/ Demolishing Junk DNA as an icon of evolution - July 2011 Excerpt: "The genome is hierarchical, and it functions at three levels: the DNA molecule itself; the DNA-RNA-protein complex that makes up chromatin; and the three-dimensional arrangement of chromosomes in the nucleus. At all three of these levels, DNA can function in ways that are independent of its exact nucleotide sequence." (p.93) [. . .] "At the third level, the position of the chromosome inside the nucleus is important for gene regulation. In most cells, the gene-rich portions of chromosomes tend to be concentrated near the center of the nucleus, and a gene can be inactivated by artificially moving it to the periphery. In some cases, however, the pattern is inverted: rod cells in the retinas of nocturnal mammals contain nuclei in which the non-protein-coding parts of chromosomes are concentrated near the center of the nucleus, where they form a liquid crystal that serves to focus dim rays of light." (p.94-5) (The Myth of Junk DNA) http://www.arn.org/blogs/index.php/literature/2011/07/15/demolishing_junk_dna_as_an_icon_of_evolu Shoddy Engineering or Intelligent Design? Case of the Mouse's Eye - April 2009 Excerpt: -- The (entire) nuclear genome is thus transformed into an optical device that is designed to assist in the capturing of photons. This chromatin-based convex (focusing) lens is so well constructed that it still works when lattices of rod cells are made to be disordered. Normal cell nuclei actually scatter light. -- So the next time someone tells you that it “strains credulity” to think that more than a few pieces of “junk DNA” could be functional in the cell - remind them of the rod cell nuclei of the humble mouse. http://www.evolutionnews.org/2009/04/shoddy_engineering_or_intellig.html Scientists' 3-D View of Genes-at-Work Is Paradigm Shift in Genetics - Dec. 2009 Excerpt: Highly coordinated chromosomal choreography leads genes and the sequences controlling them, which are often positioned huge distances apart on chromosomes, to these 'hot spots'. Once close together within the same transcription factory, genes get switched on (a process called transcription) at an appropriate level at the right time in a specific cell type. This is the first demonstration that genes encoding proteins with related physiological role visit the same factory. http://www.sciencedaily.com/releases/2009/12/091215160649.htm Not in the Genes: Embryonic Electric Fields - Jonathan Wells - December 2011 Excerpt: although the molecular components of individual sodium-potassium channels may be encoded in DNA sequences, the three-dimensional arrangement of those channels -- which determines the form of the endogenous electric field -- constitutes an independent source of information in the developing embryo. http://www.evolutionnews.org/2011/12/not_in_the_gene054071.html A look at some systemic properties of self-bioluminescent emission - 2008 Excerpt: There is an apparent consensus in the literature that emission in the deep blue and ultraviolet (150-450nm) is related to DNA / RNA processes while emission in the red and near infrared (600-1000nm) is related to mitochondria and oxidative metabolisms,,, http://adsabs.harvard.edu/abs/2008SPIE.7057E...8C

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