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

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Larry’s ‘reply’ (to my first post) appears to have replicated and evolved into a real reply (to my second post) with some real information. Well, a little information. When I say information, I don’t just mean grammatically correct and unambiguous English text, I mean things that offered ‘surprisal’ and improved my ability to understand the world and to function better in this debate. I learnt three things: firstly, some people have known since the mid 70s that most DNA is transcribed into RNA, but sat on it because apparently they didn’t realise its significance; secondly, where DNA is transcribed but a function is not known, it is generally transcribed only relatively rarely; and thirdly, that RNA polymerase (RNAP) binds at sites other than recognised promoters.

Now, to my mind the first point only underlines my original point about the cult of Darwinism (word defined according to the old-school, traditional and popular usage); that it can get in the way of the practice and dissemination of science, a dysteleological worldview which stagnates interest in trying to find function, something which has only recently been picked up again by ENCODE, and only then, Larry claims, because they don’t understand evolution.

The second point is interesting, but I have to ask the question: given the fact that we don’t know everything about the genome, isn’t it precisely those parts that are rarely transcribed that would give most difficulty when it comes to determining their functions?

The third point is also interesting. I don’t know much about this, but if RNAP is observed to bind other sites, then shouldn’t we be cautious against assuming that this is mere accident? What if (almost) everything was meant to be transcribed; ‘promoters’ merely promoting the parts that need to be heavily transcribed, without implying that they are the only things that should be transcribed? After all, the crucial thing isn’t really the nature of RNAP binding site, but what does the resulting transcript do, if anything.

Also, I think I need to explain why ID is compatible with junk DNA in principle. The thing is, almost no-one disputes the fact that evolution can create junk, and no-one disputes that some degree of evolution occurs. Even if it were true that 90% of the genome were junk, it is logically possible that the original genome was designed, and then accumulated junk over time. The reason IDists pursue this is not defensiveness, but because they smell blood; they believe that a high proportion of function is (a) increasingly supported by evidence, and (b) problematic for the best theories of Darwinism (again apologies for using the term in the popular way), because the canniest Darwinians know that their theory needs junk DNA for raw material – a place for the ‘creativity’ of chaos to escape the conservative effects of purifying selection. Either way, whether the observable genome is 10% functional or 90% functional, those functional parts still need to be explained. By contrast function is exactly what Intelligent Designers (engineers) like to do.

Actually there is that fourth thing I have learned: Larry does not like being called a Darwinist, or his theory Darwinian. The problem is, though, that without any Darwinian natural selection, neutral evolution would have no shape at all, so it would be rather disingenuous for a neutral evolutionist, for example, to pretend to disavow it altogether. For that reason, I think it is most truthful to continue using the term ‘Darwinist’ inclusively to describe those people. ‘Darwinist’ is an handy label, not an epithet.

Now for some blockquoting …

In case you missed it, the interesting thing about ENCODE is the discovery that 80% of the human genome is transcribed.

That was somewhat “interesting” in 2007 when the ENCODE pilot project was published but it wasn’t the least bit interesting last September. Scientists have known since the mid-1970s that a large fraction of our genome is complementary to RNA in the cell. We’ve known for almost as long that most “pervasive” transcription is very likely useless transcription or accidental transcription. This is consistent with a lot of papers showing that RNA polymerase binds at many sites besides functional promoters. It’s in most of the textbooks. This explanation became more widely known following publication of the pilot study in 2007. Unfortunately, it’s not only the IDiots who ignore it but also many of the ENCODE workers.

I love the way ‘known’ is juxtaposed against ‘very likely’. ‘Very likely’ indicates to me that this was and is a guess. And how do we know that RNA polymerase is meant to bind only promoters? Is it safe to assume that when RNA polymerase binds to other sites, this must be accidental or unintentional? Could it be that these other sites are meant to be transcribed only rarely? I don’t know, but I would like to know. Why don’t we encourage scientists to take a deeper look? Oh great, that’s what ENCODE are doing.

…transcription is strongly indicative of function. Thus ENCODE’s headline is on target.

Yes, it’s true that most—but not all—functional regions are transcribed and it’s true that transcription can be indicative of function, especially if the transcripts are abundant.

On the other hand, regions of the genome that are transcribed very rarely do not turn out to be reliable indicators of function because we have a better explanation. Most of pervasive transcription falls into this very rare category.

The idea that (almost) everything gets transcribed sometimes but only by accident, is an explanation, but it is one that requires no investigation, and inspires no investigation. It is much more convincing to an already-convinced Darwinist than to anyone else. A Darwinist says, nah, there’s nothing here to be understood, stop looking. But to others, that would be a presumptuous ‘evolution-of-the-gaps’. Anyone who has reason to suspect teleology (meaning: engineering intent) is going to look just that little bit harder, and is going to see the importance of pervasive transcription just that little bit earlier. I wonder if we should not be a little angry that this was not popularised in the 70s! My fiancee, who has a recent biology degree, is now annoyed that this fact was kept from her … The Darwinian establishment seem to have buried it, exactly the kind of thing I wanted to warn against.

As for the last sentence, it took me a while to understand how ‘most of something’ can fit into a category which is ‘very rare’. For clarification I think by ‘very rare’ Larry means ‘very rare transcription’ not ‘very rare regions of the genome’. So, Larry thinks that rare transcription (which he believes is due to RNAP binding sites that are not recognised promoters) indicates accidental transcription. That is his argument. Ironically, Larry is using a design heuristic here (assuming that promoter means ‘bind only here’). All I am suggesting (not claiming to know for sure) is that perhaps the correct design heuristic should be that a promoter really means ‘bind more often here’? If so, there would be no reason to assume non-function.

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.

Scientists have accumulated plenty of evidence that most of our genome is not functional in any meaningful sense of the word. It’s unlikely that this evidence will be overturned or discredited in the near future and it’s unlikely that we will find functions for any significant portion of our genome. There are some very good scientists who have been looking for decades.

The fact that some very good scientists have not found functions for all of the genome does not negate the many functions they have found so far, for many classes of genetic element, including those commonly classed as ‘junk’. And they are still working. Part of the problem is this: if a layperson were to take apart a microchip, would he be able to discern the function of all the parts at the first attempt? Probably not. The problem is not lack of intelligence, but an early lack of understanding of the principles by which the thing is built. As soon as he understands a particular design principle, suddenly huge areas of the chip will be comprehensible to him. I humbly suggest that we have a number of such minor revolutions ahead of us in molecular biology. We are making great strides, but we do not yet understand all the principles of the transcriptome never mind the whole interactome. Perhaps we there is more to learn about binding sites for RNAP? Or take pseudogenes: they have already been found to function in some cases as regulators, through their RNA transcripts interacting with real gene RNA transcripts. Then, alternative splicing is only partly understood. Who knows what other mechanisms operate at the RNA level? If you can’t imagine the function yet, it can be pretty hard to find it. But if one asserts there is no function (for example for rare transcripts) like Larry does, it will be even harder to find it.

Aside: approaching biology with design heuristics in this way is a whole lot more interesting than approaching it from the Darwinian (I insist on using that term the normal way) point of view (especially the neutralists who assume pointlessness) which focusses so much on sequence comparison often without reference to function or functional constraints.

Darwinian theories did not predict this.

That’s correct. Darwinian theory is focused on natural selection as the most important mechanism of evolution. Strict Darwinists predicted that there would be very little junk in our genome. Most of them still stand by that prediction and that’s why there are so many ENCODE workers who are opposed to junk DNA. (The IDiots know this because I’ve recently been assured that they understand the difference between Darwinism and modern evolutionary theory.)

By ‘Strict Darwinist’ who is ‘opposed to junk DNA’, I presume Larry means one of those naïve folks who believe in extremely high selection coefficients [tut tut and feel sorry for them]. To normal people however, ‘Darwinist’ includes anyone who believes in a strictly naturalistic, ateleological yet somehow creative evolution. That’s the core assumption of Darwin in the Origin of Species, and that is the one thing that hasn’t changed since, and is the thing that Intelligent Design takes issue with. As I pointed out above, ‘neutralists’ need Darwin’s mechanism too. Claims by Larry Moran and others that they are not Darwinists, seem a little bit pedantic and silly from where I am standing. Just saying (again).

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.

It’s true that Uncommon Descent has been a bit obsessive about the issue. It almost looks like discrediting junk DNA is a big deal for the IDiots in spite of what andyjones says above. If we add up all of the functional regions of the human genome that have appeared on the blog—or in Jonathan Wells’ book— they probably amount to about 0.1% of the genome … and that’s being generous. …
At the rate they’re going (0.1% in ten years) it’s going to take about 9000 years to find new functions for the 90% of the genome we think is junk.

0.1% of the genome is actually quite a lot for a single blog. And therefore, it would be more to the point to add up all the classes represented by the examples that have appeared on UD – those would include a much more significant proportion of the genome. Not such bad going really.

Brain Development Is Guided by Junk DNA That Isn't Really Junk - Apr. 15, 2013 Excerpt: Specific DNA once dismissed as junk plays an important role in brain development and might be involved in several devastating neurological diseases, UC San Francisco scientists have found.,,, While researchers have been busy exploring the roles of proteins encoded by the genes identified in various genome projects, most DNA is not in genes. This so-called junk DNA has largely been pushed aside and neglected in the wake of genomic gene discoveries, the UCSF scientists said. In their own research, the UCSF team studies molecules called long noncoding RNA (lncRNA, often pronounced as "link" RNA), which are made from DNA templates in the same way as RNA from genes. "The function of these mysterious RNA molecules in the brain is only beginning to be discovered,",, Unlike messenger RNA, which is transcribed from the DNA in genes and guides the production of proteins, lncRNA molecules do not carry the blueprints for proteins. Because of this fact, they were long thought to not influence a cell's fate or actions. Nonetheless, lncRNAs also are transcribed from DNA in the same way as messenger RNA, and they, too, consist of unique sequences of nucleic acid building blocks. Evidence indicates that lncRNAs can tether structural proteins to the DNA-containing chromosomes, and in so doing indirectly affect gene activation and cellular physiology without altering the genetic code. In other words, within the cell, lncRNA molecules act "epigenetically" -- beyond genes -- not through changes in DNA.,,, Ramos combined several advanced techniques,, to identify lncRNAs,,, The research revealed roughly 2,000 such molecules that had not previously been described, out of about 9,000 thought to exist in mammals ranging from mice to humans. In fact, the researchers generated far too much data to explore on their own.,,, "There's enough here for several labs to work on," said Ramos, http://www.sciencedaily.com/releases/2013/04/130415172010.htm bornagain77
Transposable Elements Are Key to Genome Regulation by Jeffrey Tomkins, Ph.D. - March 2013 Excerpt: Evolutionists once thought that transposable DNA elements, originally labeled 'jumping genes,' were merely the ancestral vestiges of viruses that, ages long ago, infested and bloated genomes. Much to the chagrin of evolutionists, the past decade of research has clearly shown that transposable elements play vital and purposeful roles in regulating how genes and the genome function. Moreover, they specifically play key roles related to the type of context in which a cell is located (i.e., tissue type).1, 2, 3 In fact, a high-profile research paper titled "Transposable Elements Re-Wire and Fine-Tune the Transcriptome" was just published in the journal PLoS Genetics.4 The transcriptome refers to the sum total of the protein coding and regulatory RNAs that are copied from various genes across the genome when they are activated in the cell. One of the most interesting facets of how transposable elements are key to life is the fact that they are now implicated as critical regulatory features in mammalian embryo development. http://www.icr.org/article/7388/ bornagain77
OT: The Simple Cell? - Chuck Missler Darwin's Natural Selection vs God's Intelligent Design. You judge! - video http://www.youtube.com/watch?v=n8Qo3SuhtaY bornagain77
The third point is also interesting. I don’t know much about this, but if RNAP is observed to bind other sites, then shouldn’t we be cautious against assuming that this is mere accident? Well, accidental binding and spurious transcription are inevitable. That's because we're dealing with chemistry, not engineering. Simple (well, that's what the professors all say) thermodynamics dictate that there must be accidental binding and transcription. For cells, it is energetically prohibitive for enzymes to be perfect. For RNAP, this means that spurious transcription is unavoidable. It also pays to keep in mind that a great deal of the low-level, genome-wide transcription that is seen leads to RNA that is immediately (perhaps co-transcriptionally) degraded. Thrown away. Tossed out in the trash. Garbage. Junk. These are but two of the reasons why Larry intimates that the assignment of parts of the genome as junk is not a matter of ignorance, but rather of knowledge and understanding of the chemistry, and of the fates of the products of spurious transcription. It's what we know that leads us to this conclusion, not what we don't. Arthur Hunt
OT: One of the best timelapse films I've ever seen: New Zealand Landscapes Timelapse Volume Two - video https://vimeo.com/62980495 "I believe in Christianity as I believe that the sun has risen. Not only because I see it, but because by it I see everything else." - C.S. Lewis The Biggest Stars in the Universe - video http://www.youtube.com/watch?v=2LUQVzerseI You could fit 262 trillion earths inside (the star of) Betelgeuse. If the Earth were a golfball that would be enough to fill up the Superdome (football stadium) with golfballs,,, 3000 times!!! When I heard that as a teenager that stumped me right there because most of my praying had been advising God, correcting God, suggesting things to God, drawing diagrams for God, reviewing things with God, counseling God. - Louie Giglio bornagain77
Semi related: The Multi-dimensional Genome--impossible for Darwinism to account for-- by Dr Robert Carter - video http://www.youtube.com/watch?v=K3faN5fU6_Y&feature=player_detailpage#t=690s bornagain77
And why would Dr. Moran presuppose 'neutrality'?
"Moreover, there is strong theoretical reasons for believing there is no truly neutral nucleotide positions. By its very existence, a nucleotide position takes up space, affects spacing between other sites, and affects such things as regional nucleotide composition, DNA folding, and nucleosome building. If a nucleotide carries absolutely no (useful) information, it is, by definition, slightly deleterious, as it slows cell replication and wastes energy.,, Therefore, there is no way to change any given site without some biological effect, no matter how subtle." - John Sanford - Genetic Entropy and The Mystery of The Genome - pg. 21 - Inventor of the 'Gene Gun'
This was very interesting. I realize they've been saying for years that 90% of the genome is junk, but how is having 80% of the genome transcribed a problem for Darwinists? Doesn't that still give them 20% for evolution to act upon? onething

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