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Thursday, May 09, 2013

On My Failure to Educate an Intelligent Design Creationist

A few weeks ago I decided to give Intelligent Design Creationist andyjones the benefit of the doubt and assumed that he really wanted to understand enough biology to have a credible opinion about genomes and junk DNA. I published a series of posts on Educating an Intelligent Design Creationist: Introduction.

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.

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.
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.

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.

Andyjones replies,
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.

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.
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?

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 God the intelligent designer took advantage of this accidental binding to convert the sites to real functional sites. The fact that we can't detect a function is just because we don't understand genes and genomes well enough.

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 God the intelligent designer. The possibility that it may not be designed at all is not on his radar in spite of my attempt to educate him. That's kind of sad, isn't it?

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.


Jeffrey Shallit said...

My experience, in arguing with creationists more than 30 years, is that the honest creationist with an open mind and a genuine desire to learn is about as rare as confirmed sightings of Bigfoot.

Larry Moran said...

Yeah, but I keep hoping .... silly me.

Mikkel Rumraket Rasmussen said...

In the end it seems Andy's entire case boiled down to the argument from ad-hoc rationalization and post-facto hypothesizing.

The intelligent designer could have meant to use spurious transcription as a way of doing x.
The intelligent designer could have intended multiple copies to serve function Y.
The lack of detection of an effect from megabase deletions could be because the mice weren't in specific situation Z.

And on it goes, it's effectively Carl Sagan's garage dragon over again. Every observation and test proposed as evidence for junk(empirically testing for dragon) is dismissed with ad-hoc reasoning. The fire is heatless, the dragon is invisible, it's body is immaterial etc. etc.

Andy is simly dismissing the simplest explanation before his very eyes with this kind of after-the-fact making up of excuses.

Why NOT simply accept the simplest explanation here? What looks like mutated sequences for broken protein-coding genes, ARE mutated and broken protein coding genes?
That spurious transcriptional noise, really IS just noise? That deletions of large amounts of apparently functionless junk, simply WAS functionless junk?

No. It has to be the product of divine foresight and supernaturally incredible engineering. Never mind what the evidence tells us (tens of thousands of broken genes for every one or two having been SHOWN to be functional), those few demonstrated cases of function apparently burns with the brightness of a blue supergiant in the mind of Andy. Talk about unquenchable faith. The numbers aren't in proportion, by three or four orders of magnitude, and yet to Andy (and presumably the average ID proponent) this is enough for him to feel confident in continuing this kind of ad-hoc reasoning and thinking he's on the side of "the evidence" and the science.

These people don't want to understand it. I'm with Shallit on this one, I don't even remember any committed creationists changing their minds other than Glenn Morton of Morton's Demon fame.

Claudiu Bandea said...

On the functions of the so called ‘junk DNA’ (jDNA)

Here is Ford Doolittle’s conclusion on jDNA in his recent article about ENCODE published in Proceedings of the National Academy of Sciences (1):

“I submit that, up until now, junk has been used to denote DNA whose presence cannot reasonably be explained by natural selection at the level of the organism for encoded informational roles. There remain good reasons to believe that much of the DNA of many species fits this definition. Nevertheless, while still insisting on SE functionality, we might want to come up with new definitions of function and junk by (i) abandoning the distinction between informational and nucleoskeletal or nucleotypic roles for DNA, (ii) admitting that there may be strong selection for C-value as a determinant of many cell biological features, (iii) fully embracing hierarchical selection theory and acknowledging that different genomic features may have legitimate functions defined and in play at different levels, and (iv) expanding the SE definition of function to include traits that arise neutrally but are preserved by purifying selection (12). Much that we now call junk could then become functional” (emphasis mine).

Well, there are several well supported hypotheses about the function of the so called ‘junk DNA”, including the ‘nucleo-skeletal hypothesis’ proposed by Thomas Cavalier-Smith (2), and the ‘nucleotypic hypothesis’ proposed by Michael Bennett and developed by Ryan Gregory (3).

1. Doolittle WF. Is junk DNA bunk? A critique of ENCODE. Proc Natl Acad Sci U S A 2013 Apr 2;110:5294-300 (

2. Cavalier-Smith T. Skeletal DNA and the evolution of genome size. Annu Rev Biophys Bioeng 1982;11:273-302 (

3. Gregory TR. Coincidence, coevolution, or causation? DNA content, cell size, and the C-value enigma. Biol Rev Camb Philos Soc 2001; 76:65-101(

steve oberski said...

I think that a "creationist with an open mind and a genuine desire to learn" soon becomes a former creationist.

This selection process leaves behind a dedicated core immune to reason and evidence.

It's too bad that Andy Jones did not profit from Larry's excellent and informative series of posts on genomes and junk DNA but I'm sure that some "honest creationists" did.

And as always it was a great learning experience for interested lay people like me.

Anonymous said...

"However, such a philosophically informed theoretical expansion is not what ENCODE, or at least those authors stressing the demise of junk, so far seem to have in mind"

Claudiu, the sentence you bolded was not the most important. Forgetting the whole context of the article, and such things as the following sentence was not good either. Read the whole article instead. In terms of logic, just looking at what you quoted: that a whole lot of junk would be deemed "functional" by changing definitions (theoretical expansion) does not take away that a huge lot of human DNA is truly just junk. Don't mistake "Much that we now call junk could then become functional" with "There is no junk."

See ya.

Claudiu Bandea said...

@Negative Entropy

As indicated in quote you posted, indeed Ford Doolittle dismisses that ENCODE data supports the conclusion that 80% of the human genome is functional.

However, he concludes that by building an informed theoretical framework on genome evolution, including “(i) abandoning the distinction between informational and nucleoskeletal or nucleotypic roles for DNA, (ii) admitting that there may be strong selection for C-value as a determinant of many cell biological features”, much that we now call junk could then become functional.

As pointed out by Ford Doolittle, this informed theoretical framework on genome evolution should cover the nucleoskeletal or nucleotypic roles of genomic DNA (which included all jDNA, as in the theories proposed by Thomas Cavalier-Smith, Michael Bennett and Ryan Gregory), and that there might be strong selection for C-value (which also includes all jDNA) as a determinant of biological features.

Diogenes said...

Fred Sigworth of Yale, I believe, asked to have his name taken off the "Scientific Dissent from Darwinism" list.

Kurt Wise and Todd C. Wood are honest. Wood is not stupid.

Diogenes said...

Andyjones writes: "Might there be a design reason for having ‘jumping genes’? it possible that there are genes that are designed to jump between cells?"

Why sure, genius, and is it possible that there are genes that can accelerate faster than the speed of light and go backward in time and kill Lee Harvey Oswald? Fuck, anything is possible, but sane people are supposed to prioritize their possibilities.

The Discovery Institute gets about $4-5 million dollars per year. If you really believe a Middle Eastern war deity magically created genes that can jump from one eukaryotic cell to another, then spend let's say half of that on going and finding them.

Spend less money on LOBBYING RIGHT-WING dumbfuck POLITICIANS to write laws mandating "God did it" theory, and spend half your $$ millions DISCOVERING SOMETHING you stupid fuck!

"Is it possible that pathological viruses evolved from something designed and endogenous...?"

You're a computer scientists. You may have heard, there are things, look like boxes, with a lighted rectangle in front, called computers. GO USE A COMPUTER TO TEST YOUR HYPOTHESIS you stupid fuck.

Genomic databases are available ONLINE. Sequence search tools and alignment software are available ONLINE. USE THEM you stupid fuck. Jesus tapdancing Christ you witch doctors are LAZY.

"Of course that’s crazy talk – to an Evolutionist"

NO-- it's not crazy, it's just LAZY, because you're a computer scientist who won't use a computer to align even two sequences, you stupid, lazy fuck. LAZY is worse than crazy.

Unknown said...

Exactly ^^^^

Anonymous said...

You're are still missing the point. Strong selection for C-value does not mean strong selection for a particular point. It could be selecting for a minimum value, it could be selecting for a maximum, but that does not mean that this would justify all the junk, nor that junk would become nonexistent. Still, that there "might be" does not mean that there "is." Again, you miss the point. Ford also talks about positive evidence for junk.

Read the whole thing. Make sure that you understand what it means, rather than make it mean what you prefer it to mean.

Claudiu Bandea said...

@Negative Entropy

Obviously, I can reply on the same note: “Read the whole thing. Make sure that you understand what it means, rather than make it mean what you prefer it to mean"

Anyway, what do you think about the nucleoskeletal or nucleotypic theories developed in dozens of papers and books by Cavalier-Smith, Michael Bennett and Ryan Gregory?

Diogenes said...

P.S. WHY ARE ONION GENOMES SO LARGE, and why are the differences between two onion genomes LARGER than the entire human genome?

Oops, you forgot to answer that!

Diogenes said...

The Five Laws of Creationism

1. Just because creationists can emit English sentences, does not mean they can understand English sentences.

2. Just because they can use scientific jargon, does not mean they know what it means.

3. No factoid is too large or too small, too important or too trivial, too easily verified or too obscure for creationists to lie about it.

4. Majority opinion does not determine truth, except when right-wing politicians are mandating creationism, in which case, it does determine truth.

5. When they catch ya lyin', just remember, Darwin = Hitler.

Anonymous said...

I am convinced that some DNA can act as spacers necessary given the way eukaryotic genomes organize. I doubt though that they are the exact size that would be required. I agree, for example, that some programmed alternative splicing is evolutionarily selected for, thus making alternative splicing, in those cases, necessary for a healthy organism, but that does not mean that such thing justifies the sizes and the number of introns. In other words, introns contain junk regardless of how necessary some of them might have become.

I do think that we can't paint all DNA whose specific sequence is not kept by negative selection as useless and junk. But I doubt that such things mean that therefore there's no junk. I am still convinced that there's abundant junk because evidence points to that. example, the famous onion test also proposed by Ryan Gregory. Something else I might disagree, is that there's a clear demarcation between junk and selfish DNA. Still, a huge amount would be just junk. Also, I think we should not put the cart before the horse. That some transposons might have originated promoters does not mean that transposons are thingies whose function is to produce promoters. That some pseudogenes have acquired functions does not mean that pseudogenes arise for a purpose. Evolution is a mess. Things happen because they can happen. For example, it could well be that we need lots of DNA "so that" DNA can be packed. But maybe we would not have any need to pack it if we didn't have so much DNA ...

In any event, there's tons of selfish and of junk DNA. I have had doubts one way or another, and lots of education have proven me wrong in one way or another. My view is the result of changing my views due to the evidences accumulated by lots of research since I first hear about both selfish and junk DNA, about introns, about alternative splicing, and so on. This is why I read carefully. I rather not put my meanings into what Ford wrote, for example. I pay attention. There's a reason Ford said "might be", rather than "is," et cetera, et cetera. I read the whole paper, and Ford is far from suggesting that there's no junk.

Larry Moran said...

Something else I might disagree, is that there's a clear demarcation between junk and selfish DNA.

I think there's a clear demarcation. Selfish DNA (i.e. active, functional transposons) is not junk. I don't see how anyone could think it is.

AllanMiller said...

As someone who has spent somewhat more of his working life as a computer programmer than as a biochemist, can I just say we don't all think the genome is just like one big computer program? It can be a useful analogy, in some circumstances; don't get carried away.

AllanMiller said...

I think there's a clear demarcation. Selfish DNA (i.e. active, functional transposons) is not junk. I don't see how anyone could think it is.

It must depend on perspective? Taking Ohno's condition - junk is 'that which cannot suffer a deleterious mutation', then as far as the organism is concerned, selfish DNA fits that bill. As far as the sequence itself is concerned, then of course it can, as it can be disabled, which is deleterious to the transposon. Disabled, it becomes part of the organism's junk, but it seems inconsistent to take the organism perspective only at that point. (Not that I think it matters unduly).

Pedro A B Pereira said...

There is one honest creationist I know of: Todd Charles Wood. You can check him at his blog Todd's blog. He will be the first person to tell you that there is NO problem with evolutionary theory, and he gets quite pissed at all the misinformation and lies coming from other creationists, including ID. He is quite honest and upfront about why he doesn't accept TE in the face of evidence: because his religious beliefs don't let him. That's why he turns to Baraminology...

Pedro A B Pereira said...

"Kurt Wise and Todd C. Wood are honest. Wood is not stupid"

Yep. I just commented on Todd Wood above before seeing your post. Todd knows well what he talks about. I didn't know about Kurt Wise except some mentioning. I see they both have the same stance: no problem whatsoever with the sceintific theories (at least from Todd) but no matter how sound the evidence is their fate takes precedence. That's why Todd turns to Baraminology.

Anonymous said...

Active functional transposons are selfish. I agree, but, for example, inactive transposons might be transposed by active transposon machinery, or because active transposons might fall close by and thus carry a bigger piece, et cetera. I find it hard there to decide if, for example, it is junk turned selfish, though maybe passenger-junk DNA, or hitchhicking-junk DNA, might work. :)

steve oberski said...

As someone who has spent his entire working life in the software development area I hope to god that the genome is not just like a computer program (at least the ones I've been involved in).

Claudiu Bandea said...

@Negative Entropy

I enjoyed reading your last comment, and I agree with much of what you said.

In my previous comments here and in other posts, I brought up the ‘nucleo-skeletal hypothesis’ proposed by Thomas Cavalier-Smith (2), and the ‘nucleotypic hypothesis’ proposed by Michael Bennett and Ryan Gregory, which have been discussed in dozen of papers and books. For whatever reason, you and the other bloggers discussing potential function for jDNA, here or at Gregory’s blog (, have not addressed them.

Again, what do you (and Larry and Allan) think about these hypotheses? Are they irrelevant?

Chris said...

Funny how much andyjones writes about bias, while being •utterly blind• to his own. Larry patiently explained the reasons for junk dan, and andyjones points out the would-be bias of those explanations, while responding directly from the midst of his own biases with completely contorted ad-hoc reasoning.

This was a very instructive exchange.

Chris said...

Twice the damn spell corrector changed my 'dna' to 'dan'!

nmanning said...

Come on now - no creationist would EVER engage in confirmation bias. Of course, I do wonder how it was that those mice with 3% of their genome's removed did OK when ALL of their genome was designed to be functional...

nmanning said...

Excellent points. I also love how frequently and without any realization at all the creationist employs the very things he accuses Larry of employing. Then there is the blatant Dunning-Kruger effect...

nmanning said...


"Might there... Is it not possible" are NOT arguments, they are childish cop outs. IDiots really are idiots.

nmanning said...

Funny thing about computer scientists/engineers that are creationists - they will argue exact opposite positions in order to prop up their creationist fantasies. I had one creationist computer guy, one CK Lester, insist that like genomes, computer programs can 'absorb' all sorts of 'mutations' (bad code) and still work just fine. Yet another creationist computer guy, R. David Pogge, has an essay on his website declaring that computer programs can deal with almost NO 'mutations', and since a genome is just like computer code, evolution is wrong because it relies on mutations.

And the frustrating thing is, they both insisted that they are 100% right...

Schenck said...

"AJ: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."
To which LM responds:
"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."

AJ talks alot about how darwinism is anti-teleological, and that because of this it has an inherent bias towards accepting explanatory "dead-ends", and thus is something of a 'science-stopper'.
So if ID is the opposite of that, then why aren't any IDists trying, or even realizing, that there's an obvious experiment that can be performed here. They can check to see if there's a difference in rare transcripts at different stages of early development. They could even do an experimental version of the "onion test" and see if there is a difference in rare transcripts during early development of closely related species with extremely different c-values.

But they don't, because, not surprisingly, ID 'theory' /is/ a science stopper.