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.
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.
PZ you are stepping on ATBC toes. You are hammering Dembksi’s clown troupe regularly now. Leave some tard for the rest of us.
The fact that he doesn’t know how to spell “vestigial” does not help his case.
The coccyx is still used to attract mates, witness, the popularity of tattoos just above it.
Just not from IN FRONT.
Sweet!
One so seldom gets an opportunity to use the word “poltroons” in mixed company these days.
“…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
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.
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.
“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.
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).
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).
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…
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.
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 …
Of course they need millions of genes:
47 million genes x impossible small factor of chance = irreducible complex
QED
and you, sir, are no regulatory region!
(Sorry.)
That was gold, Blake, pure gold!
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?
You should post that over at UD. You too can be told you would make a good research biologist by someone with no credentials in that area.
Bob
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.
Is Uncommon Descent a vestigial collective of humanity’s ignorance?
Hell no, #21. It’s a vestigal collective of ignorance.
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.
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.
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.
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
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.
I like “OrWellsian” myself. So many levels that one.
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.
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
The obvious counterpart to “Darwinist” is “Paleyist”.
Or, really, “creationist”.
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.
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…
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?
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.
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.
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.
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.
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!
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
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.
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
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
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.
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*
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
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
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.
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.
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
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
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.
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.
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?
Hmm. I did that and called him a big fat liar and a dumbass as well. My conscience is satisfied.
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!
#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.!
“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.
But, johnnyb (Jonathan Bartlett) is a creationist computer programmer! Doesn’t that mean he is right about everything?
Jeez with the straight-lines!
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.
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 http://www.nature.com item suggests that much of what’s transcribed gets wasted:
http://tinyurl.com/32tx6b
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.)
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.
@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.
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.
Makes you want to watch “Dr. Strangelove” again….
and poor Julenissen is only one guy.
Yes, but like the Borg, relentless I am.
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?
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?
Indeed it was. My apologies. My reading comprehension must have fallen well below the level necessary here. Sorry. I’ll just potter off now …
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.
@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, which granted was a bit unneccessarily rude.
I thought that was what we were doing, but I haven’t been to work since yesterday so the agenda might have changed.
@Sili
Close, but not correct. Julenissen = Santa.
#72,
Just goes to show that I shouldn’t try to understand Norwegian …
In Danish I’d never say Julenissen=Julemanden. ‘Separated by a common language’, indeed.
Sorry.
@71 :
A standard ID ‘kick to the crotch’ attack is : “This data does not conform to what my oversimplified version of evolution predicts; therefore, DesignerDIDIT !!!!”; julenissen is chambering his foot for the kick, and Ian blocked before the attack was launched, AFAICT.
It’s a clever rhetorical trick, actually : by only complaining about how OTHER people defend evolution, you never have to state what you think (or even know anything at all about it). It can fool the less attentive into believing that you actually KNOW something about the subject. Standard follow-up at this point is complaining about the personalities of the posters here, make people guess what his views are (and tell them they are wrong, no matter what they guess), etc.
That the genome is a big network of complex interactions has been KNOWN for decades – ever hear of developmental and molecular biology ?
Ever hear of ‘cryptic promoters’ or ‘promiscuous transcription’ ? RNA polymerase can weakly recognize many sequences as a ‘start here’ signal.
Just because the DNA is transcribed does NOT mean it isn’t scrap – retroviruses transcribe their own genomes into RNA, which is reverse transcribed into DNA and inserted back into the host’s genome. How this is of much relevance to the host is up to you to back up. After all, the host genome could function just as well WITHOUT these transposons traipsing about hither an yon.
Other transposons transcribe mRNA to make proteins to move the transposon – how this is of much relevance to the host genome is up to you to back up. After all, the host genome could function just as well WITHOUT these transposons traipsing about hither an yon.
Fugu (IIRC) has the same number of genes as humans, yet its genome is a mere fraction the size. What is missing is lots and lots of repeated DNA, parasitic sequences, etc.
So, if 0.1% of transposons and repeated DNA sequences are transcribed (even if nothing more is done with the RNA), this somehow means the other 99.9% of it may sort of have a useful function of some sort ?
But what if 99.9% of it IS repetitive, parasitic, and non-conserved ?
What if it has been SHOWN to be parasitic or disposable ?
With regards to Julenissen:
You may be right, but unless you have some prior experience with him I would suggest people are maybe a bit too eager to launch their pre-emptive attacks. I certainly did not read anything resembling ID in any of his comments. As a side note: a Norwegian alias is a very strong prior against him being a creationist. They are not numerous.
To address your major points:
Repetitive:
Repetitive sequence have been shown to be both TFBSs and TSSs and can and are used in promoters for various genes. Furthermore repeats have been shown to be an essential part of for instance the silencing properties of Xist. Certainly not all repeats are important, but at least some of them are and some may have more implicit functions such as being involved in spacing or nucleosome regulation.
Parasitic:
A lot of transposons has been “recruited” by the genome and forms fully functional alternative promoters for various genes. The majority of them probably doesn’t, but I would argue that collectively calling them junk is wrong.
Non-conserved:
Lack of conservation does not in any way imply lack of function. True, conservation is a good indicator of function but lack of conservation is not a good indication of anything. TSS and TFBS turnover for instance are well known phenomenons.
Minor points:
What part of “genes that get used later” was unclear? And please stop lecturing me, I am familiar with the field.
The transcriptional complexity of the genome has not been known for decades. This is something that has emerged with the relatively recent rise of sequence technologies. It is vastly more complex than we had reason to believe earlier.
If you could please direct me to an experiment showing that 99.9% is disposable I will be very impressed. Stop pulling numbers out of thin air. If it has been shown to be disposable, then of course it is, but this is not a particularly easy task. A definitive conclusion could only be reached by performing experiments on all tissues under all reasonable conditions. No mean feat. Of course showing that it is likely not to have a function is comparatively easy and has been done on many repeats.
Personally, I honestly don’t know how big a portion of these sequences can be considered junk, but I know it is wrong to assume that all of them are (or 99.9% for that matter).
PZ Meyers:
Where in the world did you get the idea that IDers think the whole genome is full of genes (“47 million”?)?
Using the analogy of an architect, you have basic building blocks, i.e., a materials list (=genes), and you have a blueprint which tells you how to use these materials. Ergo, by analogy, one would expect to find regulatory mechanisms in what was thought of (by Darwinists) as ‘junk-DNA’. And so it turns out to be. Is this why this assault is being conducted?
As to vestigial organs, here’s what Cornelius Hunter wrote in “Darwin’s Proof”:
“The very use of the term vestigialbegs the question, for vestigial structures serve as evidence for evolution only if they are indeed vestigial. But we cannot know they are vestigial without first presupposing evolution, because we cannot directly measure their contribution to the organism’s fitness. Therefore, when evolutionists identify a structure as vestigial , it seems that it is the theory of evolution that is justifying the claim, rather than the claim justifying the theory of evolution. As J.B. Meyer cogently observed ten years after Darwin first published his theory, Darwinism is not so much a hypothesis porposed to explain facts as an invention of facts for the support of a hypothesis.”
@Testytestacci:
So by your analogy the architect would doodle a lot of unrelated nonsense not in any way connected to the design on his blueprint because? It is fun? To confuse us?
Really? By analogy? How dense are you?
A designer would presumably be a bit intelligent and not plant a lot of garbage in the genome. Ergo by analogy (I love that phrase) there would not be garbage in a designed genome and all pseudogenes and ORFs would serve some purpose. Which they don’t. Ergo by analogy: you are wrong.
OlsenBranden:
Tell me, what is the scientific method you employ? Is it truth seeking through the use of mockery?
Good luck!
Ergo by analogy (I love that phrase) there would not be garbage in a designed genome and all pseudogenes and ORFs would serve some purpose.
Tell me, do your musings have they same truth-value as actual known facts?
Darwinists were wrong about a great many so-called ‘vestigial organs’ not having function. They’ve since been found. They were dramatically wrong about so-called ‘junk-DNA’, and now, apparently, your argument is that this ‘junk’ is really ‘junk’—just ask me, I know for certain—ergo, this couldn’t have been designed. (Do darwinists ever tire of being wrong?) This is an argument from ignorance. I’m sorry, it won’t work.
I only mock people who are too lazy to learn or have strong opinions despite lack of knowledge. The scientific method applies to performing experiments, not lecturing ignorant people.
Ah. Are we discussing “facts”? So sorry, I was thrown of by your initial “analogy” post. I’m sure I can give you some facts or references. What exactly do you consider controversial in my statements?
Regarding “vestigal organs” that is not my field and unlike others I prefer to actually know something about subjects I express an opinion about. I’m sure some other “Darwinists” might have something to say about it though. So what should I refer to you as? A “Beheist” or a “Dumbskiist”?
Is that my argument? I thought my argument was that there exists disposable elements in the genome. True, we are discovering functions that we didn’t know about earlier, but there are still sequences shown to be disposable. Something which seems an odd choice for a designer, wouldn’t you say?
Regarding “wrong”: I think you should reread PZ post, the one linked to about the history of “junk DNA” and maybe some of the literature as well. Of course, some of the historical hypotheses formed about so called “junk DNA” will turn out to be wrong, but this is a matter of “Darwinists” proving “Darwinists” wrong and science progressing. I fail to see the relevance of your religion.
Amusing :-) Given that that was what I was saying it would be an argument from “authority”, not “ignorance”. You don’t have to take my word for it though. There is something called “scientific journals” were we publish the results of experiments.
Olsen:
Since what you write is simple badgering, with no substance, there’s nothing to respond to. Next.
@Testytestacci:
Sorry if I’m being a tad bit rude, but what did you expect? See it from my perspective:
Imagine that you have been doing science for some years, meticulously gathering data and performing experiments to figure out things. Forming hypotheses and doing your best to falsify them, and gradually contributing to the collective knowledge of the human race.
Then suddenly some guy comes along who has read something on the web about the field and based on those few paragraphs formed very strong opinions that goes against all available data and makes no sense whatsoever from a scientific point of view. Now imagine that this person, armed with these small tidbits of nonsense, instead of asking questions and trying to actually learn something has the arrogance to actually pretend or imagine himself to be knowledgeable in the field. Furthermore, setting up nonsensical arguments and demanding to be taken seriously. Do you understand now why I don’t show you any respect?
As for lack of substance I did actually address some of your arguments. Albeit, not in a polite manner.
Olsen:
Forming hypotheses and doing your best to falsify them, and gradually contributing to the collective knowledge of the human race.
If only this were true. Darwin said that if intermediate forms weren’t found in the fossil record, this would be a strong argument against it. The fossil record is almost completely known now, and there are but few intermediate forms, not the thousands that Darwin’s theory requires. The Cambrian explosion is not what Darwin expected; he expected a whole series of intermediate forms leading up gradually to what is seen in the Cambrian. But none of this seems to slow Darwinism down. Why not? Is it because Darwinism is unfalsifiable? I think so. Now, who should be mad: you, or me? I’m the one that points out that the ’emporer has not clothes’ and is belittled. So, if you’re going to think things through, then why don’t you simply acknowledge that hectoring is not what is needed–good, straightforward reasoning is what’s called for.
Try to take this in the kindest way possible: you are ignorant. And unless you’re truly beyond redemption I suspect you might at least have a slight suspicion of this yourself.
So here’s the deal: Is there anything I can say or do that will actually make you read some of the references and or literature that I can direct you to. And is there any way you can admit that you are maybe not the world’s leading authority on biology and maybe entertain the slightest possibility that you might be wrong? In that case I (and maybe others) might actually dedicate the time to at least try to have serious discussion with you. If, on the other hand, you are not willing to read the literature and evaluate opposing arguments any discussion will be a waste of time. Now, as a small test I will direct you to this site:
http://talkorigins.org
And your task is to figure out what biologists have to say about your arguments regarding the Cambrian explosion and transitional fossils. And you can tell me why you think this view is wrong accompanied by the relevant references supporting your argument. Good luck!
Wow…
You’re listening to the wrong people, Testy. Listen to the likes of Olsen instead. It’s time to get yourself some edumacation. The only alternative is to [continue to] make a complete and utter fool of yourself when discussing this topic.
This is no reflection on your character or intelligence. You simply have no frakkin clue what you’re talking about. It’s up to you to change that.
Spoiler warning for Your Inner Fish, a superb book which I am reading now on MAJeff’s and others’ recos (and not, as Mr. thalarctos slanderously suggests, because I’m procrastinating on a bunch of deadlines)….
Really, if you don’t want to hear about an important story early on in the book, you shouldn’t read this comment any further. Dr. Shubin, I hope it’s ok to retell your story from my memory here–it sent chills down my back to read it, and it’s directly on point here, I think. (Everyone else: get the book! You won’t be sorry!)
When I was a child, I read an autobiographical essay by Isaac Asimov about how he was on a ship for the first time in the service. Seeing rain fall on the ocean for the first time, he just burst into laughter at the irony of it: the rainwater falling on that other immense expanse of water. In that essay, Asimov managed to convey the sense of the immensity of Nature, and the relative puniness of the human observer.
Many years later, I had a similar moment at Kilauea, watching (from a safe distance, of course) tons of lava pour into the ocean, and knowing that one misstep on the solidified lava I was on, and I’d disappear forever–but it wouldn’t make any difference to Kilauea, who would continue to generate tons and tons of lava which would flow into the ocean, oblivious to the presence or absence of one human observer.
Finally, a story that Shubin tells in Your Inner Fish recreates that sense of immensity, while simultaneously giving the lie to Testy’s assertion above. There is a lot of explanation about what kinds of sites are promising for fossil-hunting, and a recount of a trip to Nova Scotia for an expedition. The team found a spot near enough to the water that tides could actually strand them if they didn’t pay attention, and–lots of omissions here on my part–found a jawbone from an extremely remarkable and previously-unknown transition form, a discovery that was only established when they were back home in their lab and the season was over.
With that victory, they eagerly went back the next season to continue digging–only to find that the whole site where they had found the jawbone had been washed away by the ocean over the winter! The way he told that story, I got the whole wave of immensity all over again.
So, Testy, here are my questions to you:
If
1) we know about sites like that which have been washed away before they can be thoroughly explored, and
2) we know additionally that some sites are forever inaccessible at all because of housing, malls, and other development, and
3) we can reasonably infer that over the scope of history, many sites have been washed away or otherwise lost without even one human observer to mark the passing, let alone examine what was in the site…
then:
How can you possibly assert that the fossil record is almost completely known now?
What is your basis for your statement, and how do you reconcile it with the loss of all of those sites referred to above?