…and this is a 
Another junk DNA denialist on a tirade
Category: Creationism • Molecular Biology
Posted on: January 23, 2008 11:41 AM, by PZ Myers
When I decide to take a break from the mad scramble of organizing my classes, I really shouldn't follow a whim and take a peek at Uncommon Descent. The lead article has this astonishing opening paragraph.
Remember the dark days of vestigal organs? You know, back when there was a list of 180 vestigal organs? Or remember the days of junk DNA - when repetitive DNA, large regions of non-protein-coding DNA, and all sorts of mobile DNA were assumed to be non-functional simply because the investigators had assumed Darwinism rather than design?
I'm half a century old. I remember a lot of things, but I don't remember those.
There were and are still vestigial organs, and nothing any creationist has ever said has refuted that. They constantly confuse "vestigial" with "non-functional" — the appendix, for instance, is a functional section of epithelium with many of the specialization we associate with other regions of gut epithelium, but it has lost the utility of acting as a fermentation chamber that we see in other mammals, and is greatly reduced in size…therefore, it is a vestigial cecum. The coccyx is a set of fused bones that still has muscles attaching to it, a blood supply, and sensory innervation, but it is a greatly diminished relic of the prominent post-anal tail of other vertebrates…therefore, it is vestigial. I really don't understand what's so hard to comprehend about all that; if you want to argue that your coccyx is not a vestigial tail, then please do show me how you can swat flies with it, or extend it caudally to assist in your balance, or attract mates in front of you with its display.
I remember the days when cell biologists were describing satellite DNA and all those other interesting repetitive sequences (OK, actually, it was a little before my time, but the questions were still rumbling about). I remember Arthur Whitely telling us about this stuff and scratching his head and wondering what it did — there was initially no assumption that it was non-functional, and if Darwinian preconceptions fed into the argument at all, it was to suggest that there must be an underlying utility to such ubiquitous elements of the genome. What led to the conclusion (not assumption) of non-function was observations of its nature and experimental work that showed it was highly variable, and changed and deleted without observable consequences to the organism. It also helped that comparative work showed no discernable pattern to the distribution of the stuff. Junk it was, and junk it still is.
This gibbering creationist showed right there in the beginning that he doesn't know what he's talking about, and he makes it worse a little farther down.
I'm not big into counting genes, especially as regulatory regions (you know - "Junk DNA") seem to be as important as the genes themselves.
Regulatory regions have been known since the 1950s. I know regulatory regions; developmental biologists are acutely interested in them, sometimes to the point that they forget that there are functional genes attached to them. And I assure you: regulatory regions have never been classified as junk DNA. Junk DNA and regulatory regions are not synonyms.
What has this clueless ideologue frothing at the mouth is that he has learned a tiny bit about how human DNA sequences are analyzed to find genes. What scientists do is search for sequences called open reading frames (ORFs) that meet a simple criterion: they have to begin with an initiation sequence, the three nucleotides ATG, and they extend until there is a stop codon. Any given 3-nucleotide sequence, though, will appear with a fairly high frequency in a random stretch of DNA, about once every 64 nucleotides, so just finding an ATG and announcing that there is a gene doesn't work. If every ATG marked the start of a gene, which seems to be the idiot creationist criterion, we'd probably have about 47 million "genes".
So the genomics people use other criteria. One is length: something that codes for one amino acid before coming to a halt is not likely to be a real gene, but a 300 amino acid sequence is fairly typical. Another is comparative: if an ORF has no homolog in other species, if it seems to be completely new and different from anything in any other genome, it's probably a random sequence and not a true gene at all.
Our frothing demented creationist is very upset about this criterion, because it applies evolutionary principles to sequence analysis—he says it makes "Darwinism to be the official rule book for analyzing the genome". This is actually true. Evolution has proven itself to be a very useful tool for analyzing sequences. It works! The ID approach seems to be that there should be many more genes in the genome (47 million?), therefore they want to strip away any refining technique that removes false positives, and want to accept the slackest, loosest, most undiscriminating criteria they can invent.
I will throw the poor guy a bone, though. The concluding paragraph of the press release he is citing is a mess; you can't use a set of genes filtered by comparative criteria to then declare that the mammalian genome has experienced little innovation. You have to use other information, like expression and function and developmental data that are independent of evolutionary interpretations to do that. A next step is to ask if you can find the ORF sequence in an expression library, for instance, in which you have copies of all the transcribed message RNA for a cell. Unfortunately for the creationist, we do have such information for many genes (but not all; we're a long way from completion), and that also supports the evolutionary explanation.
I think next time I get an idle moment, I'd rather read Genomicron. Ryan Gregory discusses the same issues, but unlike the poltroons of Uncommon Descent, he actually knows something about the subject.
Politics
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Comments
This discussion reminds me of one of my arguments against ID. As a guy who has dealt with a lot of bit-packed data records that need to be stored efficiently, we would NEVER design a system like this. A single three-nucleotide sequence to designate start-of-record? Good raw data sequences always encode the length of the record in the header, not just a marker that says 'start of record'; it allows for easy error checking.
Ok, so this isn't a digital system, not really, but still: where's the error correction?
Just musing.
Posted by: Nathaniel | January 23, 2008 11:53 AM
PZ you are stepping on ATBC toes. You are hammering Dembksi's clown troupe regularly now. Leave some tard for the rest of us.
Posted by: Erasmus, FCD | January 23, 2008 11:57 AM
The fact that he doesn't know how to spell "vestigial" does not help his case.
Posted by: Richard | January 23, 2008 11:57 AM
The coccyx is still used to attract mates, witness, the popularity of tattoos just above it.
Posted by: Russell | January 23, 2008 12:02 PM
Just not from IN FRONT.
Posted by: Jit | January 23, 2008 12:07 PM
Sweet!
One so seldom gets an opportunity to use the word "poltroons" in mixed company these days.
Posted by: Gingerbaker | January 23, 2008 12:11 PM
"...he says it makes 'Darwinism to be the official rule book for analyzing the genome'. This is actually true."
Can any statement referring to "Darwinism" be true? Can we stop responding to the substance of any argument made about "Darwinism". There is no such beast. Science isn't about "isms".
This is a deliberately pejorative term, the use of which shouldn't be left unchallenged. (In fact, I think its use should trigger a tirade about the principles of science, every time, until these idiots either learn something or at least are trained in a Pavlovian way not to use it.)
Them's by two-cents, anyway.
Chris
Posted by: Xopher | January 23, 2008 12:30 PM
Why do these people believe they have a right to pour scorn on the careful work of trained scientists without rebuke?
Still, at least give them a biscuit for realising that knockout experiments might answer the question one way or another. Quite how they can accept the tools and techniques of molecular genetics, but not the concepts and conclusions, I don't know. Well, actually, I do know, but it is a level of intellectual dishonesty or delusion which still baffles me.
Further evidence of their cluelessness about the scientific method is that they assume that this paper has necessarily been accepted, without testing and review, into the mainstream consensus on genetics, and that any proposed "rules" contained therein will be considered comprehensive and inflexible by geneticists. I can only assume that they project their own dogmatic acceptance of received wisdom onto the rest of us.
Posted by: Bernard Bumner | January 23, 2008 12:31 PM
PZ, if you thought that was bad, read this from the same poster on the same thread:
http://www.uncommondescent.com/intelligent-design/neo-darwinism-impeding-research-again/#comment-165353
You have to either laugh or wince. I, too, wanted to give him the benefit of the doubt for being merely ignorant. Then, he started talking about intelligent genomes designing new genes to demand without natural selection.
Pure crank science. It's beautiful.
Posted by: Dan | January 23, 2008 12:41 PM
"I'm not big into counting genes, especially as regulatory regions (you know - "Junk DNA") seem to be as important as the genes themselves."
I'm sorry - any reasonable definition of a gene will be inclusive of those sequences that control their expression.
Also, for all their alleged penchant for math, ID antievolutionists sure seem to be confused, equating as they do the few percent of a eukaryotic genome that includes regulatory regions, small RNAs, and the like with the 50-70% of a typical eukaryotic genome that consists of highly-repetitive junk.
2=70 - your basic lesson in ID arithmetic for the day.
Posted by: Art | January 23, 2008 1:03 PM
Not really. That's the signal for the point where translation should start. Transcription has different, and longer, starting signals. But you are right that the length is nowhere encoded -- nor is there a way the repair machinery could measure it, as far as I can imagine.
BTW, the whole thing is digital. It just has 4 states (ACGT) instead of 2 (01).
Posted by: David Marjanović, OM | January 23, 2008 1:04 PM
I once used my coccyx to attract my mate, from in front. After I'd fallen on my laptop brick and the bloody thing was sending interestingly electric bolts of pain up my spine, I yelled, "Honey, can you bring me a baggie full of snow for my broken tailbone?"
Okay, so I used it indirectly...
Posted by: Interrobang | January 23, 2008 1:06 PM
Just an off subject question here, can anyone indicate a link to some research which discusses more specifically about the statistical analysis of the ditribution of mutations.
I'm just an interested lay person here, not biologist but mathematical Physicist from education, so I'm more interested with the mathematical aspects.
I've been trying to find something off the internet, but I'm probably not using the right terminology, and all I've found discussing errors in the copying mechanism of nucleotides is really non analytical.
Thanks for the help.
Posted by: negentropyeater | January 23, 2008 1:14 PM
For a second there I thought that Tony Pagano from talk.origins had found his way to UD. That supposed list from the Scopes trial was one of his many idees fixe. But looking at the post, it is not nearly pompous enough to be Tony.
Tony's endless rants and declarations of victory would, if possible, make UD an even deeper sinkhole of stupid. Hmmm ... I wonder if we can point him in that direction ...
Posted by: John Pieret | January 23, 2008 1:14 PM
Of course they need millions of genes:
47 million genes x impossible small factor of chance = irreducible complex
QED
Posted by: Mu | January 23, 2008 1:27 PM
and you, sir, are no regulatory region!
(Sorry.)
Posted by: Blake Stacey | January 23, 2008 1:28 PM
That was gold, Blake, pure gold!
Posted by: Brownian, OM | January 23, 2008 1:31 PM
Ben Stein has actually repeated the same thing about "intelligent cells" and "intelligent DNA" in some of his interviews for Expelled. I'm beginning to wonder where this stuff is coming from, and who's been pushing this idea. It sounds like a really elaborate misread of Lynn Margulis, though perhaps not without her sharing some of the blame (she's flirted with these ideas from time to time). I wonder if she's interviewed in Expelled?
Posted by: Bad | January 23, 2008 1:38 PM
Bob
Posted by: Bob O'H | January 23, 2008 1:39 PM
another "enlightening" comment on UD:
So ID is a "theory" that makes no assumptions? Seems to me that a set of assumptions about how something works is the definition of a theory. So the first line defines ID as not a theory at all.
Next, "it just goes where the data leads". So ID is purely an ad hoc collection of observations that are never proposed to fit into some kind of coherent whole (i.e. a theory)?
Third, science is "foolish" to assume a purely naturalistic explanation for observation? Wow, just wow. This person clearly has no concept of what science is or does. Yes, you are supposed to assume that your theory "works" and that the data you collect will fit into that theory. What else, make up a theory for each observation independant of every other observation? Now that is true foolishness.
Posted by: SteveM | January 23, 2008 1:41 PM
Is Uncommon Descent a vestigial collective of humanity's ignorance?
Posted by: Caucasian Jesus | January 23, 2008 1:54 PM
Hell no, #21. It's a vestigal collective of ignorance.
Posted by: Tom | January 23, 2008 1:59 PM
Those familiar with the Hayes modem command set will recognize that ATG is a modem command. It starts like all commands, with AT (for "attention"), followed by a single letter (here G for "gene"), followed by up to six zillion characters of gene data, then the stop codon (or carriage return).
For more details see your Hayes GeneModem Programmer's Reference.
Posted by: Norris Lurker | January 23, 2008 2:07 PM
SteveM:
Yes! Is it not obvious?
For example, it is foolish to assume a purely naturalistic explanation for bad weather and failed crops. It is folly to arrogantly dismiss or discount the importance of Demeter's favor in determining the causes of those natural events which fall within her purview.
Posted by: Kseniya | January 23, 2008 2:15 PM
Xopher - the use of the demonstrative "Darwinism" is a pet peeve of mine also. It's just an attempt to pigeon-hole evolution into the pile of "evil-isms"; notably communism, fascism, Stalinism, etc. The ID/creation puppets simply want the public to believe that evolution is nothing more than ideology and "Darwinism" is just another marketing ploy on their part to wedge this idea into the public consciousness.
I'm all for the creationists getting some of their own medicine. Unfortunately, "creationism," while commonly used, doesn't seem to have as much of a negative connotation within the public arena. Since creationists seem to enjoy dragging Darwin's name through the mud I think turnabout is fair play. We certainly have a long list of potential candidates we could use: Beheism? Or Wellsianism? Perhaps Demskism? Maybe we need a contest.
Whatever label they get the "evil-ism" suffix as a means of signifying creation ideology would, in this case, be true.
Posted by: Todd | January 23, 2008 2:20 PM
I am 98% certain that I read very recently a creationist newsletter which was purporting that humans couldn't have evolved from apes because apes only have a vestigial Achilles' tendon. I believe "vestigial" was the word they used.
I am not certain if they made the mistake of saying that all apes have vestigial Achilles' tendons, or if they claimed that the great apes (or is it just chimps and gorillas?) which have the greatly reduced tendons. Gibbons do have fairly good Achilles' tendons, in fact.
Of course it's all such a stupid "argument," since the whole point of vestigial organs is that they still exist, and could usually redevelop into their former functions if selectional pressures to do so arose. Theses particular creationists have undergone a 180 deg. flip over their usual demand that transitional fossils be completely incapable of living, due to their intermediate nature, and now they're demanding that bipedalism be as efficient as it is now at its very beginning (as a side note, I have not yet been able to get one of these IDiots to address the fact that the transitionals that are known in fact fit non-teleological evolution and its predictions very well, as they are not nearly as well-adapted to their niche (think archaeopteryx) as their descendents are).
Plus, do they not realize that vestigial means that previously the organs did work? There is no certainty that human Achilles tendons even had to redevelop out of vestigial tendons, since the apes have been evolving ever since we diverged from them. These people never have a complete view of evolution, however, only a concept distorted by their own inability to conceive of biology as an integrated (via evolution, and other concepts) whole.
And of course they totally failed to address the issue of vestigial Achilles tendons existing in chimps and gorillas at all, for these are as good as platypus juvenile teeth, and a host of "broken" human genes, in indicating that evolution has indeed occurred, and not with any designer's efficiency directing it.
I'll have to find the article again when I get back to the library that has the relevant newsletter. It barely registered at the time, since I merely glanced through it and noted that it was same old same old, but PZ's post jolted my memory of the willingness of these cretinists to notice the existence of vestigial Achilles tendons in apes the moment that they thought they could use them to deny human evolution (resulting in the usual stupid failure, of course).
Glen D
http://tinyurl.com/2kxyc7
Posted by: Glen Davidson | January 23, 2008 2:21 PM
I'm with you, Todd - I've already used "Dembskiism" at least a couple of times here on Pharyngula when confronted with dogmatic assertions about "specified complexity" and the statistical virtual impossibility of the universe existing as it does exists.
Have at it.
Posted by: Kseniya | January 23, 2008 2:28 PM
I like "OrWellsian" myself. So many levels that one.
Posted by: Todd | January 23, 2008 2:36 PM
I didn't think it was possible for the level of stupid to get higher at Uncommon Descent, but in the last few months, what with O'Leary's blather and articles like these, it has doubled.
Posted by: Ric | January 23, 2008 2:39 PM
Todd (#25):
This isn't using a personal name as the basis, but how about cargo-cultism (since it mimics actual science in only the most superficial ways). Or maybe psuedo-scientific theo-delusionism. (Sounds like something that should be an APA-classified mental illness.)
Now I'm going to spend the rest of the day involuntarily trying to come up with silly names for their crap...
Chris
Posted by: Xopher | January 23, 2008 2:47 PM
The obvious counterpart to "Darwinist" is "Paleyist".
Or, really, "creationist".
Posted by: Owlmirror | January 23, 2008 2:54 PM
Further to the "better data storage format" theme in post #1:
A lot of interesting comparisons can be made with potential designs for Von-Neumann Probes (self replicating spacecraft which explore the galaxy by reproducing at each new star system, and sending the copies off in all directions). The obvious danger of such probes is that they will eventually convert every suitable object in the universe into copies of themselves.
Therefore, the probes would have to programmed with very strict rules as to where and when they were allowed to reproduce. Unfortunately, a random "mutation" in a probe's programming could affect these protections, making it more prone to reproduce. Further mutations would result in a process of evolution to more and more dangerous states. One potential way of avoiding this problem is to encrypt the programming such that flipping a single bit would completely scramble the code, thus "killing" the probe.
I don't know why "the designer" didn't hit on such a solution when designing proto-oncogenes (i.e. genes that can cause cancer when damaged). For example, he could have paired each proto-oncogene with the gene for some vitally important metabolic function, and then bound them together such that damage to one would damage the other (thus killing the cell). Therefore, an otherwise cancer-causing mutation would do no more than kill a single cell.
If there is a designer, he's an incompetent fucking twat.
Posted by: hyperdeath | January 23, 2008 2:57 PM
Just to nitpick... 94 million ORFs. Those ATGs can appear on either strand. It would be interesting to know how many ORFs are less than 100 bp... I'd do the statistics right now on random stuff, but I have to run...
Posted by: Eric | January 23, 2008 2:59 PM
So, lemme guess: Admitting that large chunks of our DNA don't actually transmit anything is verboten for the ID crowd, because that would mean admitting that DNA didn't have to be designed by some Charlton Heston lookalike in the sky, but in fact evolved on its own?
Posted by: Phoenix Woman | January 23, 2008 3:07 PM
Xopher, the advantage to basing it on a key player's name is that it counters (and balances, and mocks) the whole Cult of Personality the evolution deniers have been trying to build around Darwin since... well, since Origin was published. Darwin beats puppies, ergo evolution is an evil ideology, et cetera ad cordovaeum.
Posted by: Kseniya | January 23, 2008 3:08 PM
PZ, I fear there may be some miscommunication going on here:
The creationists care about vestiges because if an organ (or trait) is of no use, that would support evolution, and falsify creationism, since "why would God give us an organ of no use?" Therefore, when we communicate with these people, we should give examples of vestigial organs that have no current use. If the vestige has a (new) use, then the creationists can just claim that God created it with the that use in mind (e.g. the appendix).
In other words, for arguments sake, vestiges can be split into two subcategories: 1) those that have acquired a new function, and 2) those that have no function (yet). When communicating with creationists, we should take care to think of the latter only.
Posted by: Bjørn Østman | January 23, 2008 3:13 PM
If there is a designer, he's an incompetent fucking twat.
Yeah, but he created bananas with peelable rinds that make holding them convenient.
Isn't a world full of cancer a fair trade-off for one piece of fruit that doesn't require a napkin afterwards?
Man, I am so overcome at the thought of god's love for us.
Posted by: Brownian, OM | January 23, 2008 3:20 PM
Geez, it's bad enough that you guys came up with this evolution crap in the first place, but now you're actually applying it? Bastards!
Posted by: Stephen | January 23, 2008 3:26 PM
But the problem, as I see it, Kseniya, is that it wouldn't be parody.
They make ad hominem attacks against the person, Charles Darwin while also labeling a scientific theory as Darwinism - thus tarring the theory with all of their ad hominem attack BS.
So, they remake evolution as a projection of their outlook of the world (religious and based on personal authority, not empirical evidence). If we project that back onto them, using the name of one of their heroes (e.g. Hovindism), it would be a reflection of reality and I don't think they'd see it as a pejorative.
I suppose that third parties who haven't completely lost their sense of reason might pick up on the point though.
How about Dembskian Pretentionism?
Chris
Posted by: Xopher | January 23, 2008 3:27 PM
Bjørn, I do understand your point. The problem with focusing on non-functional vestiges is that it may reinforce IDers confusion of the word "vestigial" with the meaning, "non-functional." The problem with this, of course, is that every time they find a structure referred to as "vestigial", then learn that (GASP) it does have a function, well, Darwinists have lied again. To further their evil plot. By suppressing all the evidence that evilution is falling apart.
I think your idea would make a lot of sense, coming after an explanation that there are functioning vestigial structures as well as non-functioning ones.
Posted by: kmarissa | January 23, 2008 3:37 PM
OT, but let's hope this is true:
everyoneelsebutjoel.blogspot.com/2008/01/conference-call-with-ben-stine.html
As you can see below, the quote above is taken from a standard collection of rubbish. I don't actually wish him to get "hate mail," but I'm assuming, given the lies he's told thus far, that telling him that he's an ignorant git who is against everything that is good about democracy happens to be "hate mail," no matter how true it is (and despite the fact that the ignorant old coot can't back up anything he's said).
I do like the claim that he's lost opportunities for being a shill for a few con-men. Of course it's "persecution," just like anything that dares to call lies by their right name, "lies". He deserves no opportunities from anyone who cares about the 1st Amendment. Anyway, here's the entire post from which the snippet above was taken:
Glen D
http://tinyurl.com/2kxyc7
Posted by: Glen Davidson | January 23, 2008 3:45 PM
I think you misspoke your def of ORF; an AUG is not part of the def, otherwise all the exons after the one with the AUG might not have ORFs!
the computers just look for the space between stop codons, in all 6 frames, and use some minimum number of codons in a row (60 to 100) to define possible protein coding ORFs.
Right, all those short exons, out the door....
-d
Posted by: don kane | January 23, 2008 4:57 PM
Junk it was, and junk it still is.
"The ENCODE consortium's major findings include the discovery that the majority of DNA in the human genome is transcribed into functional molecules, called RNA, and that these transcripts extensively overlap one another. This broad pattern of transcription challenges the long-standing view that the human genome consists of a relatively small set of discrete genes, along with a vast amount of so-called junk DNA that is not biologically active.
The new data indicate the genome contains very little unused sequences and, in fact, is a complex, interwoven network. In this network, genes are just one of many types of DNA sequences that have a functional impact. "Our perspective of transcription and genes may have to evolve," the researchers state in their Naturepaper, noting the network model of the genome "poses some interesting mechanistic questions" that have yet to be answered.
http://www.genome.gov/25521554
Do try and keep up or else keep your mouth shut.
You're not doing any one any favors by spouting obsolete information.
Posted by: Julenissen | January 23, 2008 5:04 PM
I've done hate posts at Ben Stein on my blog - do they count? Would email do, or does it have to be actual made-out-of-paper, delivered-by-a-gun-toting-psycho-in-waiting mail?
Ahem. Sorry. Adjectivitis. *coughs weakly*
Posted by: Mike the Englishman | January 23, 2008 5:14 PM
I suspect that telling him that he's wrong, in any context, would be just about good enough.
They're rather "liberal" when it comes to evidence, truth, and honesty.
Glen D
http://tinyurl.com/2kxyc7
Posted by: Glen Davidson | January 23, 2008 5:26 PM
I had to laugh at this:
Here's some of the most dishonest people who are able to cobble together a shitty piece of propaganda, comparing us to Nazis, and with Stein writing this:
And don't you know, they just want to be our friends, to have open and intelligent dialog with us. Other than the fact that we'd need some intelligence on the other side for an intelligent dialog, somehow we're not interested in discussing the value of the vile lies that they've told against us. And btw, dumbasses, there are numerous forums which would love to have you come by and "dialog," no matter how brazenly stupid and dishonest you all are. But you're simply lying about this as well, since only you fascists censor your forums, preventing dialog from taking place--such as when you prevented me from responding to Javascript's lies and quotemines on your very own blog.
Yes, there are would-be fascist dictators about, and they're putting out a movie with as much dishonesty as possible, including the attempt to pay to fill seats to skew peoples' perceptions about how popular a rant against honesty and freedom of religion is.
Glen D
http://tinyurl.com/2kxyc7
Posted by: Glen Davidson | January 23, 2008 5:51 PM
PZ said "Junk it was, and junk it still is."
Julenissen responded "The ENCODE consortium's major findings include the discovery that the majority of DNA in the human genome is transcribed into functional molecules, called RNA, and that these transcripts extensively overlap one another. This broad pattern of transcription challenges the long-standing view that the human genome consists of a relatively small set of discrete genes, along with a vast amount of so-called junk DNA that is not biologically active.
The new data indicate the genome contains very little unused sequences and, in fact, is a complex, interwoven network. In this network, genes are just one of many types of DNA sequences that have a functional impact. "Our perspective of transcription and genes may have to evolve," the researchers state in their Naturepaper, noting the network model of the genome "poses some interesting mechanistic questions" that have yet to be answered.
http://www.genome.gov/25521554
Do try and keep up or else keep your mouth shut.
You're not doing any one any favors by spouting obsolete information."
You should be skeptical of revolutionary pronouncements from the same people who are the revolutionaries. Just because RNA transcripts are produced does not make the DNA or the RNA functional. If the transcripts are extensively overlapping, it sounds as if the ribosome is having trouble keeping straight where to begin and where to end.
Posted by: Tracy P. Hamilton | January 23, 2008 5:54 PM
Still, at least give them a biscuit for realising that knockout experiments might answer the question one way or another.
They've done junk knockout experiments with mice, with no ill effects on the progeny, though it's possible that these sequences confer some weak advantage that only becomes apparent after many generations.
Some of this stuff may be "functional" in the sense that you need a gap of a certain length between two other sequences. In which case, a knockout might be harmful, but one sequence is as good as another. This is the opposite of the sort of specificity that creos claim as an indication of design.
To claim that there's no junk whatsoever is to claim that retroviruses and selfish elements don't exist.
Posted by: ngong | January 23, 2008 5:56 PM
WRT #26, I looked up the article to which I was referring there, and can now quote exactly part of what they wrote:
OK, they didn't use the term "vestigial," but it's all the same thing, even if they use quote marks. The great apes have only a "small vestige" of an Achilles heel, which raises no thoughts in their minds except the notion that it raises a problem for our evolution, not that it is one of many evidences for ape evolution.
Here's how they confuse the issue of selection wrt the Achilles tendon:
Note the shift at the end, to suggest that bipedalism itself would be impossible if our ancestors had a vestigial Achilles tendon (which does not appear to be certain, I repeat), when the main issue is efficient running.
Of course any time when our ancestors shifted between bipedalism and quadrupedalism, selection for more efficient bipedal running would be expected, especially as quadrupedalism became more difficult. Until then, we likely ran quadrupedally when we really wanted to go fast--one notable fact is that bipedalism certainly didn't evolve for speed.
Anyway, I rather like the fact that the problem of great apes having only "small vestiges" of the Achilles tendon becomes acceptable whenever some half-assed creationist "argument" occurs to one of these dolts.
Glen D
http://tinyurl.com/2kxyc7
Posted by: Glen Davidson | January 23, 2008 6:36 PM
Julenissen responded "The ENCODE consortium's major findings include the discovery that the majority of DNA in the human genome is transcribed into functional molecules, called RNA"
problem is: what's the function? Are these overlapping transcripts translated? diced? regulatory? are they a structural part of heterochromatin? Just because they exist (says 1 study, and potentially at really really low levels) they have function? And is this function dependent on their sequence? Or is it a case of junk begets junk? Or junk begets RNA important to silence junk? Who knows, but its premature to call these transcripts 'functional' because they are there...
Hell, we've got major cytosolic organelles ('Vaults') that are conserved in Eukaryotes, that appear critical for.....nothing much.....
http://en.wikipedia.org/wiki/Vault_cytoplasmic_ribonucleoprotein
http://cancerres.aacrjournals.org/cgi/content/abstract/62/24/7298
Posted by: RobertC | January 23, 2008 6:44 PM
WRT RobertC's response to Julenissen...there's also "leaky transcription". Folks want to cleanly divide DNA into transcribed and non-transcribed regions, but there's probably plenty of gray area too.
Posted by: ngong | January 23, 2008 7:34 PM
I use my coccyx to attract my mate with displays from the front and the back. I don't know where YOUR gluteus maximus inserts, but mine inserts to my gluteal tuberosity in the rear and my iliotibial tract alongside, and although its principal job is to extend and rotate the thigh laterally, without it I certainly couldn't wiggle my hips very well - and if it didn't originate at my coccyx as well as all the upper hip-bits, my wiggle wouldn't be nearly as interesting.
And that doesn't even bring up all the interesting bits anchored to the *interior* of my coccyx and sacrum. As the song says, I enjoy being a girl - and that goes for my highly functional yet vestigial bits, too.
However, I want to know how the ID folks explain the fact our knees last about half the current human lifespan. Cancer's comparatively rare but I guarantee you that nearly everyone who lives past 40 has knee pain, and most experience at least some loss of mobility.
Posted by: jen_m | January 23, 2008 8:11 PM
God don't make no junk DNA. That seems to be the basic idea here.
Really, though, what would be an ID-based explanation for DNA that doesn't seem to be doing anything--God thinks it's pretty?
Posted by: Sensitive Poet | January 23, 2008 9:15 PM
Posted by: Mike the Englishman | January 24, 2008 4:47 AM
Ah, old Johnny B - Jonathan Bartlett.
He is - are you ready? - a computer programmer and YECist who is now attending Seminary.
He has a couple of creationist blogs here and here.
I've exchanged comments with him and written about his nonsensical claims a few times.
He thinks humans and dinosaurs lived together, that ReMine's dilemma is a big problem for evolution, etc.
Typical "I know everything because I am a creationist computer geek" doofus.
Yes, he is clueless, but boy is he CONFIDENT!
Posted by: slpage | January 24, 2008 8:15 AM
#26, it's not that the creationists don't realize that vestigial organs had a use, it's that they've convinced themselves that vestigial organs are not vestigial: they do have use, which is the use they were designed for.
For example they insist that the appendix isn't vestigial since it was designed to serve an immune system function. The coccyx has a use in assisting bowel movements! So, they maintain, these organs aren't vestigial at all and never were.
And #25, as far as the -isms are concerned, why restrict ourselves? We should fragment ID into a multitude of -isms reflecting the fact that there is no single creation "theory" or model, neither is there a single ID model.
Just as there isn't one faith, there's a separate faith for every believer, there's also a creation/ID model for every creationist/ID proponent. When we're talking about bad design inference, we're talking Dembskiism. When we're talking clueless IC, we're talking Beheism. When we're talking just plain clueless, we're talking Wellsism, etc.!
Posted by: Ian | January 24, 2008 8:17 AM
"It is folly to arrogantly dismiss or discount the importance of Demeter's favor in determining the causes of those natural events which fall within her purview."
Exactly right! That's why we need the intecession of the Vestigal Virgins.
Posted by: Adam | January 24, 2008 10:46 AM
But, johnnyb (Jonathan Bartlett) is a creationist computer programmer! Doesn't that mean he is right about everything?
Posted by: slpage | January 24, 2008 12:41 PM
Posted by: Sven DiMilo | January 24, 2008 2:16 PM
Boy, are these people all mixed up. Evolution is a farce. They talk about complexity and believe it is real. Yet, at the same time they ignore the fact that complexity does NOT come from chaos. Evolutionists, make us a cell, from scratch. That is from the chemicals that one might find in the rocks of the earth. The honest evolutionists will admit it is impossible,and will remain impossible for a great while if not forever. It is simply illogical to believe that even the simplest cells could have come from the random motion of mud in a puddle, being occasionally struck by a bolt of lightning.
Evolutionists, make us a cell the above way and we will reevaluate your point.
Posted by: James Collins | January 24, 2008 2:17 PM
I wonder if it's commenter 43 who really needs to "keep up or else keep [his] mouth shut"?
45% of our genome is transposons, 20% is pseudogenes. Can he demonstrate that this is transcribed into RNA?
Even if he can, can he then show that all of the RNA actually is put to some use after transcription instead of being deleted? This www.nature.com item suggests that much of what's transcribed gets wasted:
http://tinyurl.com/32tx6b
Posted by: Ian | January 24, 2008 2:26 PM
James, you're arguing against something the theory of evolution does not claim or predict. The "mud puddle struck by lightning" argument? Oh, please. You can do better than that. (Or so I presume.)
Posted by: Kseniya | January 24, 2008 3:08 PM
This is just one of those baseless assertions that crackpots like to throw around, wishful thinking rather than fact. There are plenty of examples of complexity coming from chaos. Weather patterns are complex, and also chaotic. The same goes for asteroid orbital dynamics.
Posted by: trrll | January 24, 2008 3:59 PM
@Ian:
We have demonstrated that a majority of the genome is transcribed. How big portions of this is pseudogenes/repeats I do not know, but probably a big chunk.
Probably not, but this is hardly a mature field and poor Julenissen is only one guy. Aside from the large number of ncRNA with demonstrable function like miRNAs, snoRNAs, Air, Xist etc. there are phenomenons such as antisense that can probably account for many. Furthermore transcripts can be indirectly functional in the sense that the transcription itself leads to nucleosome rearrangements or epigenetic effects. It's not necessarily junk just because the exact DNA sequence is unspecific.
I fail to see the relevance of this article. It is about translational control of genes presumably known to be functional.
Posted by: OlsenBanden | January 24, 2008 4:19 PM
I wonder if it's commenter 43 who really needs to "keep up or else keep [his] mouth shut"?
I think not...
You missed the whole point. The evidence suggests that the genome is a "complex, interwoven network" that is highly organized and constructed of multiple processes and structures all working together to produce function.
Deletion or de-activation of intermediary components is likely to be routine and only demonstrates more cleary the dynamic nature of the living genome rather than its previously perceived static nature.
"Oh, but you who philosophize disgrace and criticize all fears, Bury the rag deep in your face
For now's the time for your tears.
http://youtube.com/watch?v=wC5P9PmXM5U
Makes you want to watch "Dr. Strangelove" again....
Posted by: Julenissen | January 24, 2008 4:44 PM
and poor Julenissen is only one guy.
Yes, but like the Borg, relentless I am.
Posted by: Julenissen | January 24, 2008 4:54 PM
Yes, but like the Borg, relentless I am.
Aha! I knew there was something fishy about you. No one produces that many toys and delivers them all in one day without time travel technology and some serious ulterior motives. So is there a cube at the north pole or is it hidden elsewhere?
Posted by: OlsenBanden | January 24, 2008 5:11 PM
For those who've forgotten their Danish/Norwegian (Danwegian?) - not that there'll be many on a Minnesotan blog as Ksenia, OM kindly informed me a while ago - "Julenissen" is "Santa's Elf". Presumably he's an adherent of "External Delivery".
Hmmm ... is it too early to call sockpuppet on #63?
Posted by: Sili | January 24, 2008 7:53 PM
Indeed it was. My apologies. My reading comprehension must have fallen well below the level necessary here. Sorry. I'll just potter off now ...
Posted by: Sili | January 24, 2008 7:56 PM
Julenissen wrote: "I think not" and for the first time i find myself in agreement, because whilst you can publicise all the design interpretations of the genome you wish, you cannot escape some simple facts of science:
1. Significant portions of the genome are broken
2. Significant portions of the genome aren't conserved
3. Not everything that's translated is used
4. There are huge differences in genome size even amongst closely-related species.
When these issues are addressed scientifically rather than with religious fervor, I'll consider buying into it.
Posted by: Ian | January 25, 2008 8:09 AM
@Ian:
I didn't see any design interpretations in Julenissen's comments, could you please direct me to them. Or have I interrupted some historical feud between the two of you? Anyway, the ENCODE paper certainly did not argue for any form of design, it just pointed out that there's a lot more going on than we know. and that the genome is a big network of complex interactions rather than the (semi) discrete gene units that we previously envisioned.
Returning to PZ's comment that originally initiated this: "Junk it was and Junk it still is" refering to repetitive sequences is what I took issue with. This is in many cases demonstrably false. There exists examples of both of repeats and transposons acting as start sites for transcription and therfore performs a function (yes, also for downstream genes that get used later). Anyway, I can't speak for Julenissen but I'm certainly not arguing that all the bases in the genome are somehow relevant/functional or indispensible. The main message is that PZs statement is wrong in the general case and that you shouldn't be so quick to dismiss everything just because it is repetitive, seemingly parasitic or non-conserved. That was also what I read into Julenissens initial response, w