Andyjones has replied to my post with: Getting me an Education.
My first post was: Educating an Intelligent Design Creationist: Pervasive Transcription. I refuted the misconception that nobody ever investigated pervasive transcription and I explained that we know a great deal about the parts of the genome that are being transcribed, and why they are transcribed. I did not claim that this was solid evidence for junk DNA. That wasn't the point. The point was to teach andyjones that there are explanations for pervasive transcription—we don't call it junk just because we have no idea what's going on.
I also pointed out that using pervasive transcription as an argument for function (i.e. against junk) doesn't really cut it unless you don't understand basic biochemistry. Here's how andyjones responded ...
Larry thinks this (especially the situation from the 80s on) amounts to solid evidence for junk DNA, but I honestly don’t see how it does.Okay. So my attempt to explain the reality of the situation failed miserably.
Andyjones goes on to say ...
I think it’s a case of confirmation bias (something he accused us of previously). You see, those who really understand the theory, like Larry does, expect to see lots of junk for the simple reason that chance mutations are the only really creative force in this theory, and that you need to accumulate a lot of mutations to obtain significant innovations– otherwise natural selection will keep you pinned on a locally-optimal genotype (natural selection only winnows the results – in all variants of Evolutionism* including Larry’s – but in Larry’s variant chance is given a somewhat longer leash).I don't know where this is coming from. I don't recognize myself in that description; in fact, I don't recognize any evolutionary biologist.
Also, I never "expected" to see junk and I'm not the least bit surprised that most bacteria evolve quite efficiently without it.
I tried to explain that when scientists discovered pseudogenes they assumed that broken genes were, in fact, broken genes that have no function. That's why humans need vitamin C, for example. This seems like a reasonable assumption given all we know about biochemistry and molecular biology. Andyjones replied ...
So they didn’t find the function. They found some stuff you could interpret as damaged genes. Yay, that fits! (that’s the confirmation). So they told everyone its junk. But they haven’t proven that.You can never prove a negative but when you see a broken gene, what's the most logical conclusion? I think it's that we have a broken, non-functional, gene. That's a (tentative) conclusion based on facts and knowledge.
Indeed some of those pseudogenes already turned out to be functional, and with a good functional reason why they should appear similar to true genes, so now the ‘damaged gene’ hypothesis is also questionable, especially if one allows the possibility it was engineered, which every good scientist should. Oops! But since it doesn’t fit the junk story, we poopoo it and don’t tell people (that’s the bias).There are about 15,000 protein-encoding pseudogenes in the human genome. One or two might have secondarily acquired a function. Maybe even as many as ten. Is it reasonable to conclude that most of those broken genes must have a function that we can't find?
Andyjones now demonstrates that he understands the point about proving a negative. But he also demonstrates a refusal to admit that we know an awful lot more about genes than he thinks.
Now, I appreciate it is very difficult in principle to prove non-function, and so lesser evidences could be accepted. Indeed it is almost always difficult to prove a negative to those who want to believe: at the Origin of Life we have an absurdly strong appearance of a negative, and more than 50 years of experimental evidence and discoveries that compound the problem, from an ateleological point of view – but it does not seem to dissuade those who are committed to limiting science to natural (unintelligent) causes. The difference in this case is that there are already counterexamples (here’s another one – Beta Globin Pseudogene) which show that at least some pseudogenes have function and thus that pseudogenes do not always indicate non-function; clearly pseudogenes cannot simply be assumed to be junk.Broken genes are broken. They don't work. That's solid evidence for junk DNA in spite of the fact that a tiny percentage might have secondarily evolved another function over millions of years.
Could it be that many pseudogenes are functional under special conditions? Yes (same for many other classes of ‘junk’). Could it be that some are indeed genuinely broken genes, or copies of genes? Yes, even from an ID perspective that is a possibility. But in themselves, pseudogenes are simply not ‘solid evidence’ for junk DNA.
In my second post I tried to explain to andyjones that we understand how genes work. In particular, our knowledge of the fundamental principles of physics and chemistry forces us to be extremely skeptical about the postulated functionality of very rare transcripts [Educating an Intelligent Design Creationist: Rare Transcripts]. Andyjones seems to get this part.
I also explained that we have a very good explanation for rare transcripts from various parts of the genome. They are probably spurious, non-functional transcripts; a prediction that flows from our understanding of the properties of RNA polymerase and the mechanism of transcription initiation. Thus pervasive, infrequent, transcription is not an indication of function. This is not an argument based on ignorance. It's an argument based on knowledge.
Accidental transcription of RNA is sufficient as a hypothesis to explain away these relatively low levels of abundance of most sequences. [hmm, yes, but functional, intentional transcription would also be sufficient, so where is the evidence that it is junk? all transcription has an element of random timing. that is not the same as accidental.]No, andyjones, the idea that most of those rare tanscripts are functional is not a reasonable explanation given what we know about gene function and expression. You are engaging in wishful thinking based on ignorance.
This argument reveals a materialist way of looking at things; measuring RNA’s importance by mass. However, there is no reason why all the DNA should be transcribed at anything like the same level. Take my own physics simulation computer code. I estimate 90% of it is used for a total of less than 1% of the time, while say 5% of it uses up 90% of the processing resources. That does not mean the 90% is junk.Does he really think we are that stupid?
Personally, I would expect a large fraction of the genome to be relevant only to embryos. In computer speak this would be the ‘initialisation process’ of an organism. Once initialised, the organism is not likely to use that part of the program again. The genome of a higher organism has to do a huge number of advanced things that no human code has yet attempted, but why should the basic principles be different?We understand differential gene expression and we understand that some genes are transcribed in some tissues and not in others. That's not what we're talking about. We're talking about transcripts that only appear in one copy per ten or a hundred cells in one tissue out of over one hundred that were examined.
I also gave andyjones the scientific evidence that most intron sequences have no function. They are transcribed and rapidly degraded. I explained that introns have a function, but that the essential part is only a small percentage of the total. This is based on extensive knowledge of what's in an intron sequence and on the comparisons of orthologous introns in different species.
Andyjones then proceeds to demonstrate that he didn't understand any of this.
That brings us to a second point, about introns and other pieces of RNA that are degraded rapidly. Are introns really non-functional? Is it possible that they affect alternative splicing, or regulation in some other way? Yes, of course it’s possible. Think of transient flashes of light down glass cables that degrade almost instantly. Materially they are almost not there. So it may be with much of the genome – we have pieces of information being carried and processed on a very short-lived medium. Perhaps protein-coding mRNA has a slightly longer lifetime because it has to leave the nucleus. Let us please not measure function by relative mass of RNA or protein.Let me repeat the obvious. All biologists agree that introns have a function and that specific intron sequences are absolutely essential for splicing. That does not mean that all of an intron is required for function. The scientific facts suggest that most intron sequences in large genomes are junk and could easily be eliminated.
I did not succeed in educating andyjones about introns.
The next post was about the biochemistry of DNA binding proteins [Educating an Intelligent Design Creationist: The Specificity of DNA Binding Proteins]. I wanted to teach andyjones (and other Intelligent Design Creationists) that spurious, non-functional binding to DNA is a required property of all specific DNA binding proteins. We should not be surprised when we see a DNA binding protein (e.g. a transcription factor or RNA polymerase) sitting on a non-functional part of the genome. It's what we expect.
This time I made a little progress .... but not much.
Larry explains in detail how promoters work, and why there is variation in binding strengths, and thus a continuum of levels of gene-promoting going on. It was very interesting, and I am not objecting to any issues of fact here.So, when we purify E. coli RNA polymerase in our student lab and use it in a transcription assay with calf thymus DNA, this is evidence that the intelligent designer anticipated that bacterial RNA polymerase would transcribe cow DNA and produce a functional RNA?
But it all misses the point. I already acknowledged that RNA is transcribed at different levels, and that RNAP binds at non-promoter sites. Although I just learnt a whole lot more, everything Larry describes is consistent with my earlier suggestion that promoters mean ‘bind here more often’ rather than ‘bind here only’. All I am saying is that an intelligent designer could take into account the subtleties and limitations of the underlying operating system, and use the fact that everything is transcribed occasionally, and make almost every DNA sequence functional.
When we detect RNA polymerase molecules sitting at non-promoter sites in the E. coli genome the conclusion, based on our knowledge of biochemistry, is that these are spurious binding sites. Andyjones wants us to believe that they are actually functional sites because
This looks like an argument from ignorance, but it this case it's an argument from ignorance that immediately follows a description of what we do know about the subject so it can't be based on lack of knowledge. That makes it an argument from arrogance.
Over the course of twenty years I have tried to convince the IDiots that there is active debate within the scientific community about the mechanisms of evolution. They should stop calling all evolutionary biologists "Darwinists" and start recognizing that many evolutionary explanations rely on non-adaptive mechanisms. It will help them understand evolution so their critiques become more credible.
In spite of my previous failures, I decided to try once more with andyjones when I wrote Educating an Intelligent Design Creationist: The Meaning of Darwinism. I did not succeed. Here's what andyjones thinks.
So, Larry does not want to be called a Darwinian. I hear him when he complains about conflating scientific issues with things like Social Darwinism. But that is not what I think of when I use the term, and I think his real motivation is that he wants us to call him an ‘evolutionary biologist’, emphasising his mainstream-ness. The first problem with that is that I have good friends who are evolutionary biologists, and also believe in ID, so that phrase really doesn’t capture the difference between Larry and us. The second problem is that whatever other processes evolution may include, Darwin’s mechanism is the only candidate to replace design. It is the only thing that winnows the chaff (junk) and skews probabilities in the direction of anything that would look like design (with adaptation/function standing in as a proxy for design). If Larry believes in evolution without new adaptations, then really he ought to join our club. Nearly everyone believes in neutral evolution, if I may interpret that as lots of essentially random, non-adaptive, minor changes. Neutral evolution really isn’t problematic to anyone. It’s the Darwinism that is problematic. If Larry is really innocent of the sin of Darwinism, then I am very sorry for calling him a Darwinian. For the purposes of this post I have called him an Evolutionist (capital E and –ist to denote the ideology that goes way beyond the observable facts of evolution) in the hope that he will not have a heart attack.The problem is obvious. Evolution can help explain why we have so much junk DNA. Darwinism cannot. If andyjones is committed to the idea that Darwinism is what he opposes then he will never be able to understand the scientific controversy over junk DNA. He firmly believes that our genome is designed and that the only possible explanations are design by natural selection and design by
My last post was Educating an Intelligent Design Creationist: Evidence for Junk. I was hoping to explain to andyjones that there is a lot of evidence for junk. This is important because creationists, and many secular scientists, seem to believe that the concept of junk DNA is simply a conclusion based on ignorance.
I had some success ...
Firstly, some stuff probably genuinely is junk. Evolution creates junk, there has been at least some evolution, so there must be some junk. For the mouse examples, I accept that as evidence for junk. On the other hand, it is not proof of junk: the fact that those researchers did not find an effect from deleting huge chunks of mouse genome does not necessarily mean there is no effect from those sequences. It could be those were regions that are activated or relevant only under special conditions in the wild.Let's be clear about one thing. The fact that several large regions of the mouse genome could be deleted without observable effect is powerful evidence that these regions do not contain functional sequences. The result could have been different. It is not absolute proof that the deleted regions are junk because one can always find an excuse to preserve your favorite hypothesis by making up stories. That's what andyjones is doing. Creationists are good at that sort of thing—and so are some secular scientists.
Secondly, having multiple copies of a code does not mean the code is junk, or that any of the copies are junk. Many cases of the C-value paradox can be partly explained by simple polyploidy. But apart from that, again from computer science there are reasons why one might wish to have a smaller code or a larger code that does much the same thing: Generally one wants small codes that can be stored and loaded efficiently. However, there are certain conditions where one might want a larger code: if you ‘unroll’ a loop (that means copying the code out several times so you don’t have to return to the start of the cycle quite as often). A biological equivalent might be a copied gene that speeds up the transcription and thence expression of a particular protein. It might be less efficient for cell division, but there are other advantages. Indeed, in some cases the purpose could be to slow cell division. Also, some computer codes edit themselves to adapt to particular needs. Could it be that different tissues types have different copy numbers of certain genes? Might there be a design reason for having ‘jumping genes’? Getting way off on a tangent: is it possible that there are genes that are designed to jump between cells? Is it possible that pathological viruses evolved from something designed and endogenous, for example something that locally changed the properties of some tissue (think of a wart – that’s a virus – but self-limiting and benign)? Have virus-like elements been associated with placenta-formation? Could it be that knocking out certain ERVs would prevent embryos from developing? Of course that’s crazy talk – to an Evolutionist – because its all fundamentally and originally junk.Oh dear, he forgot to give us an excuse for rejecting the genetic load argument. I'm sure it was just an oversight.
The point is obvious. Here's a computer scientist who, quite obviously, knows very little about biology. I tried to educate him but he still thinks he knows more about the subject than the experts in the field. Why is that? It's because we are stupid and biased and IDiots are able to see things that we just can't comprehend.