A Dubious "Opportunity" for IDers
by JoyEvolutionary biologist T. Ryan Gregory of the University of Guleph in Canada has offered ID supporters an 8-Fold Path to scientific legitimacy in an entry at his blog 'Genomicron', entitled -
An opportunity for ID to be scientific.
Seems T. Ryan has his nose a bit bent out of shape by recent developments in genetics which have demonstrated "Junk DNA" to actually have functions. Well, it's not so much that the discoveries have angered him, it's that ID proponents predicted that much the so-called 'junk' would turn out to have functions. While avoiding the issue of why it was that mainstream evolutionary biologists considered non-coding DNA to be useless for so long, he does invite IDers to the table at last…
…provided, of course, they can jump through his eight flaming hoops. Below the fold are all of Gregory's demands - sans commentary from me - for your amusement and analysis:
1. Specify the basis for assuming that all non-coding DNA must be functional.
2. Specify how one would go about demonstrating evidence of functions for non-coding DNA in the absence of a framework based on common descent.
3. Make specific predictions about what function(s) all non-coding DNA is likely to be fulfilling, and propose ways to test those predictions.
4. Propose functions for transposable elements that take into account their parasitic characteristics [...] but do not invoke the notion of co-option.
5. Provide a specific explanation for how the great majority of transposable elements in the human genome can be functional while showing clear signs of being inactive.
6. Provide an explanation for why the DNA sequences of non-coding regions in different species appear to correspond to degree of relatedness.
7. Propose a testable explanation for why similar species may have widely different quantities of non-coding DNA in their genomes.
8. If one does accept common descent, propose a testable explanation for how there can be significant reductions in DNA content in some lineages.
There you have it. 8 very simple requests which, once complete ID answers been provided to T. Ryan Gregory's satisfaction, will allow him to possibly think about maybe suspecting there might be something to ID after all. Or not.
[H/T: Joey Campana]
July 11th, 2007 at 10:01 pm
Well, it's not so much that the discoveries have angered him, it's that ID proponents predicted that much the so-called 'junk' would turn out to have functions. While avoiding the issue of why it was that mainstream evolutionary biologists considered non-coding DNA to be useless for so long, he does invite IDers to the table at last
I sincerely doubt that prof. Gregory is angry that IDists are able to claim functional non-coding DNA vindicates intelligent design. You're also able to claim yellow birds vindicate ID as well.
The point of his post was to invite IDists to explain why functional non-coding DNA follows from the IDist position. In other words, explain why IDists get so excited when fragments of ERVs turn out to have function.
Comment by Chris Harrison — July 11, 2007 @ 10:01 pm
July 11th, 2007 at 10:18 pm
Chris:
Chris, years ago when I voiced a suspicion that much of what was considered junk DNA then would prove to be functional the reaction was derision and skepticism to understate things. Now it is hard to find someone who derided the idea. It is as if we are supposed to forget those cliche arguments about the designer either being stupid or deceptive for designing genomes the way they were assumed to function back when. Remember how an undirected, inefficient process was expected to generate junk?
Comment by Bradford — July 11, 2007 @ 10:18 pm
July 11th, 2007 at 10:58 pm
Hi Bill,
Back when you voiced that suspicion, what was your reason for doing so?
In another of Gregory's posts, he drudges up dozens of papers from the 60s, 70s and 80s that contain evolutionary biologists predicting function for non-coding sequences. Those biologists gave sound reasons for their predictions, but what do IDists base their "it's not junk!" prediction on?
http://genomicron.blogspot.com...
Ohno coined the term "junk-DNA" in 1972, but he talking explicitly about pseudogenes, and only later did the term get used to describe anything more.
If you want to talk about "stupid" design, we can talk about processed pseudogenes. They are duplicates formed through retrotransposition, and are "dead on arrival" because they are non-functional as soon as they "arrive". In light of PPs, it's clear that undirected, inefficient processes (ie know evolutioanry mechanisms) do generate junk. Harrison et al estimated 9000 processed pseudogenes in the human genome.
http://www.ncbi.nlm.nih.gov/si...
I don't think the term "stupid design" or "incompetent designer" is worth discussing though, because it doesn't really hurt ID* if the alien designers turn out to be a little sloppy or inefficient. I'm more interested, as Gregory is, to see if IDists can ground their "not junk!" prediction in auxiliary assumptions (the ToE has common descent) that make the prediction worth a damn. As best I can tell, right now the claim from ID advocates that non-coding DNA has function no more follows from ID than the prediction that we will find more yellow birds.
* provided the ID is of the Mike Gene variety (separable from religion).
Comment by Chris Harrison — July 11, 2007 @ 10:58 pm
July 11th, 2007 at 11:00 pm
Chris Harrison:
Then Gregory has no reason to demand that ID do his job for him, does he? Maybe he gets extra in his paycheck to post throw-away nothings on a throw-away blog. That at least would explain the total waste of time and effort.
Um… nope. Requirements #1 and #3 both assert the sneaky absolute - "ALL." Even a fellow critic should have spotted that on the first skim without even trying. Absolutes tied to a misrepresentation of the views his demands seek to denigrate are very much indicative of the attitude the author seeks to portray.
Bradford:
Oh, come now, Bradford! Everybody knows that much of non-coding DNA has function! They've always known that. Just like they always knew that humans have fewer than 30,000 genes, and more than two copies of most of those. We have always been at war with Oceana. [/tongue from cheek]
Comment by Joy — July 11, 2007 @ 11:00 pm
July 11th, 2007 at 11:07 pm
I suspect the discussion is short circuited at the outset if you are determined to maintain the position that properties of an object are incapable of signaling an intelligent cause because such a position has secondary religious implications. Of course a designed process could be expected to yield results that are inconsistent with a non-design model. I gather you think the prediction that non-coding DNA has function flows from standard models or that such models predict non-function?
Comment by Bradford — July 11, 2007 @ 11:07 pm
July 11th, 2007 at 11:15 pm
Joy sez:
Given Gregory's credentials as an evolutionary biologist, I had to chuckle at this comment Joy. As far as I can see, he's lending IDists a hand with that post since he's suggesting how you can make ID more respectable among biologists (spare me the list of all 400 biologists who advocate ID). He's not demanding anything, and I'm sure if he saw glimmer's of life in ID, he'd not write a book about how blind mechanisms have shaped genomes over history.
The "all"s in numbers 1 and 3 are not "sneaky" misrepresentations of some ID advocates, although you yourself may not think ever nucleotide is special.
Johnathon Wells does not qualify the following quote with "some", "many" or anything else. He says blankly:
"From an ID perspective, however, it is extremely unlikely that an organism would expend its resources on preserving and transmitting so much "junk." It is much more likely that noncoding regions have functions that we simply haven't discovered yet."
- Using Intelligent Design Theory to Guide Scientific Research, Jonathan Wells, Discovery Institute, May 10, 2004; PCID 3.1.2, Nov. 2004, p 2.
At best Gregory's inclusion of "all" does not hold for every IDist. That doesn't detract from the substance of numbers 1 and 3.
Comment by Chris Harrison — July 11, 2007 @ 11:15 pm
July 11th, 2007 at 11:52 pm
Bradford said:
That's not my position at all. I was waving my hand in the direction of whatever theological implications "incompetent design" might have for a religious person. I'm not really interested in that though. I quite realize that alien designers would not have obvious religious ties.
I assume by "standard models" you mean evolutionary theory. I do think that some functional non-coding DNA follows from the ToE, and many of the biologists Gregory cites in his post here give auxiliary reasons (ie, its highly conserved nature might indicate selection, where natural selection is the auxiliary, independent assumption) that serve to back up this "some has function" prediction.
Comment by Chris Harrison — July 11, 2007 @ 11:52 pm
July 12th, 2007 at 12:39 pm
Chris Harrison,
I agree that the situation is more complicated than, "Darwinists said it was all trash."
Two key points that can't be missed is that:
1.) Those who made predictions from the "Modern Synthesis" camp were divided among predictions of function and non-function, whereas all predictions by ID proponents were that much of the so-called "junk DNA" would have function. Auxiliary assumptions of neo-Darwinian models provided contradictory predictions, whereas ID's auxiliary assumptions provided one correct prediction.
Does this provide the definitive conclusion that life was designed? No. Does this mean that a uniform prediction of ID was validated? Yes.
2.) Now that we have found wide-spread functions in various types of junk DNA, if one is to properly deal with "standard models" of evolution by its inconsistency, it is necessary to identify the auxiliary assumptions that provided the bad prediction, and isolate those evolutionary ideas that misled many neo-Darwinists to presume non-function.
Once the misleading evolutionary assumptions are identified, it must be seriously considered whether or not to forever banish those auxiliary assumptions from the relevant parts of bioscience. (This is, of course, a decision that each researcher will have to make on their own, but if evolutionary models continue to provide conflicting predictions, it will eventually become an unavoidable choice 'for' or 'against' the assumptions.)
'Trouble for is, as far as what the particular biologists themselves said, the principle assumptions for predicting that parts of the genome are "non-functional" was that evolution has undirected and random aspects.
If I am not setting up a false dilemma here (please alert me if I have), the question then becomes:
So, what part(s) of the Modern Synthesis might have to go?
Comment by Joey Campana — July 12, 2007 @ 12:39 pm
July 13th, 2007 at 12:32 am
From Joey:
This first sentence fails to capture the "function or not?" debate in any meaningful way. Evolutionary biologists were of course divided on how much of the genome would turn out to be functional, but it was not as if there were simply two camps, one of which was saying "it's all functional", and the other saying "all those nucleotides are useless". This image is what your post seems to suggest history looks like, but it is not correct.
This is the root of our disconnect. I agree ID proponents have been saying "junk" would turn out to be functional, but what I do not agree is that there exists any independently verified auxiliary assumptions that allow ID to actually make this prediction. Sure, people that support ID have said this, but as I said, this prediction is not a prediction of ID itself, anymore than Behe/Wells/you saying "we will find more yellow birds" is a prediction of ID.
To belabor the point:
If Behe/Wells/you claimed today that we will continue to find yellow birds, and then tomorrow a new species of yellow canary was identified, do you think the ID position would be validated because Behe/Wells/you made this prediction?
Of course not. Finding yellow birds is not something that follows from the ID position. The challenge is to show why functional DNA sequences follow from ID itself, and thus why IDists' "predictions" about the functional nature of DNA are worth more than the hypothetical predictions about yellow birds.
Unfortunately again, the issue is not so black and white, because the auxiliary assumptions biologists have used in an attempt to justify their arguments for/against non-function are, as I said, independently verified. In other words, when strict adaptationists claimed "The very fact that amplified sequences have been maintained, withstanding rigours of selection, indicates some adaptive significance" (Sharma 1985), we cannot just toss out N.S. (the auxiliary assumption) simply because some non-coding DNA did turn out to be junk. The reason is that natural selection stands on it's own, even though its implication here didn't hold up.
Sharma, A.K. 1985. Chromosome architecture and additional elements. In Advances in Chromosome and Cell Genetics (eds. A.K. Sharma and A. Sharma), pp. 285-293. Oxford and IBH Publishing Co., New Delhi.
I don't think this is correct. Most likely, neutral/nearly neutral mutations, and "selfish DNA" underly the assumption that DNA is often non-functional. Kimura's work and N.S. being the independently verified, auxiliary assumptions, and this position is looking more and more correct, since as Gregory mentions, a more clear picture is emerging in genome biology, one that suggests around 5% of the human genome is functional.
Comment by Chris Harrison — July 13, 2007 @ 12:32 am
July 13th, 2007 at 9:59 am
Much? How much?
How much was predicted in each case? Which group of people went out and got the data?
Uniform? Do you mean that noncoding DNA uniformly has function?
Please define "wide-spread" quantitatively.
Who found the functions again? What did you do to justify your use of the first-person pronoun "we"
Comment by JAM — July 13, 2007 @ 9:59 am
July 13th, 2007 at 12:42 pm
Chris Harrison,
Thank you for your reply.
Don't worry, I wasn't trying to provide a meaningful summary of the debate in one sentence. I was merely trying to point out that some people made predictions of function, while others predicted non-function. I thought I could assume the benefit of the doubt in order to equivocate for the sake of saving space, but I guess I don't get the benefit of the doubt. Why would you think I would try to do something as foolish as provide a meaningful one-sentence summary of a scientific debate going on for 30+ years?
There are more camps in the debate, you forgot to mention that some geneticists (perhaps prudently) didn't say anything at all, and waited for the data to come in. Posting on a blog about ID and teleology, on a post about junk DNA in the context of ID vs. blind evolution, I'm talking here about the relevance of Junk DNA to ID and blind evolution. The individuals that were using junk DNA to argue against ID basically said "all those nucleotides are useless."
For example, Richard Dawkins in 1998 said:
Kenneth R. Miller in 1994 said:
So, according to ID critics who are working biologists and an endowed Professor of the Public Understanding of Science, the genome is littered with 98% wasted hard-drive space, and junk DNA is failed experiments in a random process. Litter=useless. Failed experiment=useless. This sounds like they are saying, "all those nucleotides are useless," to me.
I will address your point about ID's auxiliary assumptions in a separate comment, after I finish responding to your and JAM's questions and comments directed to me.
Natural selection wouldn't be tossed out. Based on what I have read, those Darwinists that were predicting function for agenic DNA were using NS as the auxiliary assumption to predict function. To wit, the rationale went like this: "If agenic DNA is being preserved against mutation over many thousands of generations, NS would be preserving the agenic DNA because the agenic DNA serves a selectable function." So I agree that natural selection stays.
Right, those random and undirected mechanisms that were used to predict that 98% of the human genome is non-functional. Those are the ones that each researcher will have to carefully scrutinize in further predictive exploration.
The ENCODE consortium discovered that the majority of DNA in the human genome is transcribed into functional RNA molecules. I will be interested to read where Gregory gets his 5% numbers. Can you provide a link and page location, I am too terribly busy to seek out this 5% rationale, but would like to continue discussing with you as my time permits.
Comment by Joey Campana — July 13, 2007 @ 12:42 pm
July 13th, 2007 at 12:52 pm
JAM,
Thank you for your reply.
ID scholars gave predictions that were as vague and as specific as those who were using the "junk DNA" idea to argue against ID.
The people with enough money.
I should have clarified. I mean every single ID scholar uniformly predicted such. Meaning that all ID scholars that did offer a prediction about if we will find functions among agenic DNA uniformly said we would find that much or perhaps all of it would be functional.
The ENCODE consortium discovered some interesting facts! I can only be as specific as they are, and from the portions I have read they didn't get too specific in terms of spread:
In my understanding, only 1% of the human genome has been annotated, so we are dealing with projected numbers, and it seems too early to quantitatively 'define'.
Again, the people with enough money and resources. Shouldn't this be obvious?
I should have clarified. We humans. If you interpreted my statement as saying "we geneticists in the lab discovering function in agenic DNA," then you interpreted incorrectly.
Comment by Joey Campana — July 13, 2007 @ 12:52 pm
July 13th, 2007 at 1:35 pm
I don't think Miller's quote there is explicit/detailed enough for us to conclude that he think all non-coding DNA is useless, but Dawkins' quote seems to land him in that camp. Given this, Dawkins is wrong there (though he might have changed his views in the last 9 years), because we know that some non-coding DNA has function. Also, Miller's words there seem fine to me.
Great, because it would be hard to toss out something that has been so repeatedly verified. : )
I don't have a problem with subjecting neutral mutations and retrotransposition to further inquiry, but I sincerely doubt their validity will take any kind of hit. Synonymous substitutions are real, and reverse transcription happens all the time.
The ENCODE consortium was neat, but keep in mind they only looked at 1% of the genome. As to Gregory's 5% figure, here's a (partial) email interview between himself and a writer at Scientific American who drew up a piece about the ENCODE consortium:
I think you'd be interested to read the entire thing:
http://genomicron.blogspot.com...
Comment by Chris Harrison — July 13, 2007 @ 1:35 pm
July 13th, 2007 at 1:55 pm
Hi Chris. Last night I was reading a paper about error correction mechanisms and the related importance of redundancy strategies. These strategies are easily illustrated in human coding systems but not as easily with reference to genomes. I do not have a comprehensive idea worked out but I think it is worth noting that seemingly non-functional, non-coding regions may actually be error absorbing sponges, e.g introns, whose origins and mechanisms are still unclear. So why is this not explained by NS and ToE? Maybe it is but the closer one gets to the begining of the trail the less obvious are the usual answers. An ID perspective might yet offer explanations that have eluded us so far.
Comment by Bradford — July 13, 2007 @ 1:55 pm
July 13th, 2007 at 2:19 pm
Bradford, it would be helpful if you could tell me what paper you were reading so I could understand what the authors were talking about. I don't mean to suggest that your relay here is inaccurate, but I'd like to go to the source.
If I understand your "idea" here, it is in line with previous predictions of Comings 1972; Patrushev and Minkevich 2006, who suggested non-coding regions buffer against mutations.
Comings, D.E. 1972. The structure and function of chromatin. Advances in Human Genetics 3: 237-431.
Patrushev, L.I. and I.G. Minkevich. 2006. Eukaryotic noncoding DNA sequences provide genes with an additional protection against chemical mutagens. Russian Journal of Bioorganic Chemistry 32: 1068-1620.
Unless the IDist's explanations always end up being scooped by biologists from 30 years ago.
Comment by Chris Harrison — July 13, 2007 @ 2:19 pm
July 13th, 2007 at 2:20 pm
Chris Harrison:
I don't know how other ID supporters rationalize the prediction according to their models. EAM postulates that evolutionarily pertinent adaptive genomic rearrangements, functional organization and expression suites arise endogenously in response to selective stresses from the environment or opportunities offered by the environment. This would include gene duplications, even those whose expression is de-activated (and which accumulate random or less-than random mutations over time, may later become new genes or alter proteins/enzymes within a class to serve new functions, be reassigned to new expression suites responsive to different triggers, etc., and/or provide what we now know to comprise most of the genetic differences between individuals and groups.
Serious stress can also generate whole genome duplications. Not everything that's not active is 'junk' - a lot of it is a work in progress. This helps to explain why some critters and plants display radical anomalies in number of chromosomes - some of those between males and females of the same species. Species of voles can't be identified without a chromosome count, yet they all look alike. Donkeys display a rather wide range of chromosome counts. Some plants in the same family have two or three times the chromosomes as their next-of-kin. And we already know human-designed transgenes are promiscuous as hell. Anyone can grab those, as they come complete with attached promoters intelligently designed to cross major boundaries. Life is chock full of both designers and conspicuous consumers of "gene inventions." Genomes are their rented storage units for all that stuff…
This also explains why so much of the so-called 'junk' is highly conserved despite serving no apparent real-time function. Sort of a "reserve toolkit" and/or new capacities in-progress. Genomes do apparently have the ability to file whole sections of 'apparently useless' DNA in conserved regions, or file them where they're likely to accumulate substitution mutations, or excise them completely and toss them out with the trash. Heck, they even have the ancient papyrus room in the basement (somewhere) that allows them to correct creative 'mistakes' if they don't work out so well. Transposable elements appear to be part of this filing system too, likely as mechanism.
IOW, EAM sees genomes as life's Grand Research Library. Historical records, real-time developmental and operating programs, emergency relief services and savings account for the future. Life as owner, designer and operator of the library (and all database maintenance, creative expression organization and read-write functions) of DNA, as opposed to NDS's view of life as the hapless victim of egotistical genes and random accidents.
Which is not to say accidents don't happen (they do), or that individual organisms don't vary a good deal in their ability to use the machinery, or that choices made by individual systems under stress aren't fallible. EAM thus further predicts that the provisional solutions to stress are often less than ideal, and that random accidents of replication or genome damage leave a genomic legacy of disease causing maladaptions that can infect the gene pool if they aren't fatal early on. This would make the randomness of NDS's mechanisms the cause of genetic disease and genomic decay rather than of adaptive evolution. The varied, less than perfect endogenous design elements generated under stress account for most significant (non-recombinant) in-species variation, while manipulation of major tool-box genes and expression details accounts biodiversity and major evolution.
Anyway, that's the EAM explanation. It's no more fanciful and no more an Anazi Tale than anything mainstream evolutionary biology ever offered. I think it's a lot more reasonable, and explains far more of the mysteries than magical poofs do, from either the goddidit or the random accident crowds. Very little of what is retained in successful genomes will turn out to be 'junk'. What junk there is is very likely well on the way to excision. Per the EAM view.
Only 5%? Hmmm… Why do you suppose the department of computational genomics at Cornell reported just yesterday that as much as 10% of the human genome displays evidence of recent selection (thereby accounting for genomic differences within and among major human groups)? Were they just trying to tweak Kimura's snotty nose?
Comment by Joy — July 13, 2007 @ 2:20 pm
July 13th, 2007 at 3:04 pm
Eastern Academy of Management? Electric Accounting Machine?
Electric Aero Modeling?
It's very difficult to follow your post given that I have no idea what EAM refers to.
Can someone tell me what EAM is, before I respond to Joy's post?
Comment by Chris Harrison — July 13, 2007 @ 3:04 pm
July 13th, 2007 at 3:45 pm
Endogenous Adaptive Mutagenesis.
Comment by Joy — July 13, 2007 @ 3:45 pm
July 13th, 2007 at 4:01 pm
Chris Harrison,
Thank you for your reply.
The "nothing but" part, which is an absolute statement, is what makes me think he is saying "all."
Their existence is very difficult to doubt. But I'm not talking about their existence. I'm talking about their impact on predictive exploration. When researchers are making predictions, they will have to carefully consider how "random" and "unguided" mechanisms may have misguided other researchers in the past. (No pun intended)
Thank you for the link to Gregory's page where he talks about the 5%. I checked into his post and the email. I have no problems with much of his rationale, but I expect that there will be more than 5% functionality in the human genome. I think Joy's 10% SD link is one piece of the Junk DNA puzzle that tells us it will be more than 5%. When I comment about the auxiliary axiom of ID that led to a function prediction I will explain my reasoning a bit more.
Comment by Joey Campana — July 13, 2007 @ 4:01 pm
July 13th, 2007 at 4:04 pm
It concerned algorithms involving number sequences used with modems but there are concepts likely applicable to the storage and transmission of information stored in DNA.
Whether 30 years ago or today how much are biologists actually able to account for?
Comment by Bradford — July 13, 2007 @ 4:04 pm
July 13th, 2007 at 4:12 pm
And thank you for yours.
Are you sure? Because above, you wrote that
That seems very black/white and all/nothing to me. Is a binary nature what you intended to convey?
So how did they get money to test such a vague hypothesis? What is the size of the DI budget relative to the average NSF grant in evolutionary biology?
OK, good. Even though you are fudging "junk" to "agenic," at least you have the entire ID camp in the "much-to-all" category.
So my question for you is, do any data from the last 30 years or so even suggest that much-to-all of "junk DNA" has function?
But why limit yourself to reading, Joey? Why not look at the data and use it to test hypotheses for yourself?
OK, but how can you judge those data to be sufficient to conclude that those transcripts must have function?
Before you answer, try some retrodiction: if a mouse gene is expressed throughout the embryo at 7.5 dpc (2 weeks before birth), you can hypothesize that those transcripts are functional.
Of course, you can test the hypothesis by looking at the phenotype of a homozygous null mutant for that gene. What's your retrodiction? We can simplify by limiting ourselves to lethals if you'd like.
Do you realize how many times such hypotheses have been tested?
This is why it's not smart to go by press releases.
But it's never too early to predict!
I have a wager for you: let's find a noncoding region of the human genome with at least 50 tandem repeats. Since you complained about vague hypotheses, let's bet on a specific one; that the single repeat in the middle of this array has a function.
Shall we?
Yes, but you haven't identified them. I can point to people with money and resources on both sides of the question.
So my final question is, if you are correct that ID scholars uniformly predicted that most-to-all of "junk" DNA (which should never be conflated with "agenic" DNA or "noncoding" DNA by anyone striving to inform) would be functional, why didn't they put together the experiments themselves using money from the DI or some rich evangelical donor?
Comment by JAM — July 13, 2007 @ 4:12 pm
July 13th, 2007 at 4:13 pm
From Joey:
I don't see a "nothing but" in the quote from Miller that you provided.
Okie dokie.
William said:
How much of what are biologists able to account for?
Comment by Chris Harrison — July 13, 2007 @ 4:13 pm
July 13th, 2007 at 4:43 pm
From Joy:
This is reminiscent of Lamarkism, if I understand you correctly. You are saying that mutations suddenly appear when an opportunity is opened that allow them to become adaptive, and that the processed pseudogenizations, tandem repeats and polyploidy events are all "good stuff waiting to happen".
I don't have much to say about this, other than I see no possible way to test or falsify this idea. Also, selection cannot preserve what is "waiting in the wings", so you'll need a mechanism that allows your reservoir to hang around without accumulating a bunch of deletions and stop codons.
Is the human genome a successful one? If so, then I think EAM's prediction will turn out wrong, and the paper you cite seems to support me.
Williamson et al's paper is a good one, but 10% functionality doesn't appear to be in line with EAM. I wonder what they are missing?
Comment by Chris Harrison — July 13, 2007 @ 4:43 pm
July 13th, 2007 at 5:11 pm
I guess I was wrong when I asked a "final question" above.
When you write like this, what I don't get is the notion that researchers have to make predictions and do predictive exploration when it comes to sequence evidence. Anyone can do it, and it's free!
How much more? You characterized ID scholars as uniformly predicting most-to-all (>50%) would be functional. Where do you fall in that huge space between 5% and 100%?
But how much more? Didn't Joy say "as much as 10%"
I'll show you my prediction if you show me yours…
Comment by JAM — July 13, 2007 @ 5:11 pm
July 13th, 2007 at 7:08 pm
Chris:
There's a neo-Lamarckian aspect to EAM, as some genomic mutations occur in direct response to stress. There's also recognition of a permeable germline 'barrier'. There is also recognition of lateral transfer, as well as the possibility of 'borrowing' pieces of invading genomes for the purpose of engineering resistance or immunities. None of these phenomena are unknown to biology or applications research (like gene therapy, for instance).
"Good stuff waiting to happen" seems a pretty dismissive assessment - especially since in the next breath you tell me you don't have much to say about it - but if you want to insert absolutes despite the fact that I didn't assert any, I don't mind.
While I think it odd that you require of me an explanatory framework NDS has never bothered to offer, it's nice that you acknowledge the 'mystery' inherent in the known existence of wide swaths of genomes that is highly conserved by evolution in spite of it having no apparent vital function. EAM would postulate that 'selection' has nothing to do with the maintenance of this DNA. NDS has no explanation at all.
How so? Weren't you previously asserting the 5% figure? The Cornell paper doubles that, yet you say it supports that assertion. How convenient for you. As for what you think about EAM's predictive power, that's entirely irrelevant. What will be will be, though it's possible that everybody's wrong.
Having yet again mentioned the possibility of error, where is your admission of fallibility? Or am I to presume that you do not hold the NDS provisional?
The other 90% if basic arithmetic still holds. If that has changed recently, do let me know.
Comment by Joy — July 13, 2007 @ 7:08 pm
July 13th, 2007 at 7:38 pm
Joy,
Wide swaths? Perhaps you can cite research that shows all this highly conserved non-functional DNA.
Irrespective of EAM's postulations, the evidence that selection cannot maintain what is not in use is all around us. Our olfactory receptor genes, hemoglobin genes in antarctic Nototheniods etc.
Whether or not the figure is 5 or 10%, this is far cry from what EAM postulates(>50%), according to you.
Everyone is prone to error, and all science is provisional. The obviousness here seems not worth mentioning. I wonder why you bring it up.
Sarcasm doesn't fill in for your inability to answer. The paper suggests up to 10% of the human genome has seen recent adaptive evolution–arguably suggestive of function. This is at odds with EAM's prediction. As far as I can tell, this paper's empirical evidence refutes ID's prediction that most of our genome is functional, unless you can point out what they missed.
Comment by Chris Harrison — July 13, 2007 @ 7:38 pm
July 13th, 2007 at 7:54 pm
What figure would be inconsistent with ToE? If at some future point the percentage of known function doubles from what it is today then what? ToE would simply be adjusted right? So what identifiable forces inducing genomic changes shed real light on the issue?
Comment by Bradford — July 13, 2007 @ 7:54 pm
July 13th, 2007 at 8:05 pm
William,
I don't think we can say for sure, but I guess that if the figure rises above 20% is functional, you're going to get a lot of confused genomicists. I'd say, given my knowledge of evolutionary biology, if the figure rose above 25% functionality, we'd have a significant disconnect between theory and data. This is just what I'm tossing out here, and I don't expect you to think an undergraduate's opinion here is worth much.
If you want an overview of the mechanisms that govern genome evolution, as well as the relevance and implications of these mechanisms with respect to the ToE, I suggest you pick up Gregory's The Evolution of the Genome. : )
Comment by Chris Harrison — July 13, 2007 @ 8:05 pm
July 13th, 2007 at 8:06 pm
I should proof my posts more. 20-25% sounds about right.
Comment by Chris Harrison — July 13, 2007 @ 8:06 pm
July 13th, 2007 at 9:14 pm
Chris:
Well, we had quite a lively discussion here a few weeks ago about knock-out mice engineered without wide swaths of highly conserved 'junk' DNA, for the purpose of seeing what gnarly horrors would ensue. Oddly enough, they did just fine without any of it. Some were of the opinion that maybe selection hadn't caught up to all this 'junk' yet (no real explanation, given the NDS assertions about selection you've echoed here), and others cautioned that the pampered life of engineered lab mice isn't particularly relevant to real world mice and what they might need to survive. Also an unsatisfactory excuse. Thus the mystery remains.
Sorry, I do not recall what that thread was or I'd link it for you. Perhaps someone else recalls. I'm old, thus not required to keep up with such details. §;o)
In the meantime, since you appear to be interested and confident (as well as rather surprisingly ignorant of things like this), you could probably find such research for yourself without my help.
Is there an echo in here? Again, familiarize yourself with recent findings coming in from the fields - they're quite interesting. Such as the finding that primates apparently traded olfactory receptor genes for trichromatic vision. Not that I bought that conclusion (trichromatic vision is another extremely interesting poke full of NDS Anazi Tales), but it was another fine stone for the soup. Someday maybe I'll collect them up and write a children's book.
LOL!!! There is no hurry. I do not believe genomes are all that important anyway once the developmental and reproductive stages are completed (and my children's complement from my side of the family came into the world WITH me). Unless what you've got left harbors a time bomb or suffers accident or insult that ends up killing you. But then, everybody has to die of something. It doesn't matter to evolution.
Perhaps as an indication of why I lean in the directions I lean, as opposed to the direction you embrace. You asked for an ID alternative so I offered you one. You aren't required to like it.
Garbage. You asked, I answered. Again, you aren't required to like that answer. No skin off my teeth. Last I checked 10 from 100 is still 90. I presume by your response that's still true.
Well, there you go! If it mutates it suggests function. On the other hand, if it's highly conserved that also suggests function. of course, here we have the difference between mice and men, and we don't do knock-out men. At least, not legally. Then there's recent findings that gene copies (accounting for another 10% of human genomes) account for the difference between men. Which is pretty amazing if you recall the confident pronouncements of genome sequencers that there's only a 1.5 - 2% difference between chimpanzees and men! Depending on whose press releases you're reading today, that is. We could play this silly numbers game all day and never get off the merry-go-round!
As for me, I'm keeping an eye on those pesky voles. They're telling us something about genomes, even if it's not something the NDS 'orthodoxen' care to hear.
Where's the refutation? The prediction is that most non-coding DNA will turn out to have function. All this paper does is demonstrate that 10% of DNA in humans shows signs of recent selective evolution. Since genes account for only ~1.2% of the human genome, the non-coding portion of this 10% goes beyond Gregory's asserted 5%. That means MORE previously assumed to be 'junk' DNA looks to have function. Next week (or the next, or the next) they'll add to that. There's no hurry - the predictions were made long ago. What will be will be.
P.S. By the way, another 3.5% of previously 'junk' human DNA is in the "Ultra-conserved" category. This must be added to the above 10%. Add the known-to be functional genes, promoters, start-stop sequences, transcribed RNAs, etc. and we're up to nearly 20% already.
Comment by Joy — July 13, 2007 @ 9:14 pm
July 13th, 2007 at 9:46 pm
Chris Harrison wrote:
I thought mainstream science was of the opinion that ID made no testable predictions. Are you you a fringe element?
That said, does mainstream science hold that most of the human genome never had a function?
Comment by stunney — July 13, 2007 @ 9:46 pm
July 13th, 2007 at 9:56 pm
That all depends on whether you conflate ID with the ID movement. The ID movement doesn't seem to offer any testable predictions, but it's easy to make predictions from ID hypotheses.
Comment by JAM — July 13, 2007 @ 9:56 pm
July 13th, 2007 at 10:49 pm
Joy:
I presume you're talking about this paper from Nóbrega et al:
Megabase deletions of gene deserts result in viable mice.
Reading the paper, they don't say what mice they used, but glancing at this page tells me the average genome size for mice is around 3.0 pg, converting into basepairs, that's about 2934000000 basepairs. The reserachers deleted two regions that totaled to 2356000 basepairs, so they deleted around 0.080% of the mouse's genome. This doesn't really seem like a "wide swath" to me, but OK.
I've known that the evolution of full color vision in primates correlates with an increase in the percent of olfactory receptor pseudogenes.
No. You're confused. Mutations in pseudogenes do not suggest they are functional.
When you stop reading press releases, and sit down to read the real papers, perhaps you'll be better informed. The 1.5 - 2% difference between humans and chimps is still a valid number so long as you point out what it's in reference to (alignable nucleotides, ignoring indels). I'm sorry that a press release misinformed you.
If the 10% figure is indeed indicative of function, the 5% is incorrect, obviously. I'll email Gregory to see what he thinks about this paper. Your enthusiasm that a 20% figure is just around the corner is humorous, but as you say "what will be will be".
You still have the problem that ID can't actually predict anything about the functional nature of DNA, so no matter what the actual figure is (my bet's on
Comment by Chris Harrison — July 13, 2007 @ 10:49 pm
July 13th, 2007 at 10:52 pm
Stunney said:
My reference to ID's "prediction" was in jest, obviously. I've been arguing that ID cannot actually make any such prediction.
How old is the human genome? Your question doesn't really make sense, if I understand it correctly.
Comment by Chris Harrison — July 13, 2007 @ 10:52 pm
July 13th, 2007 at 10:55 pm
I dunno what happened to my post (2 above), but the end was gone..
It should finish with..
You still have the problem that ID can't actually predict anything about the functional nature of DNA, so no matter what the actual figure is (my bet's on
Comment by Chris Harrison — July 13, 2007 @ 10:55 pm
July 13th, 2007 at 11:02 pm
Uh, the rest of my post hasn't shown up twice now. One more try:
You still have the problem that ID can't actually predict anything about the functional nature of DNA, so no matter what the actual figure is (my bet's on less than 15%) ID cannot be vindicated. (recall my bit about yellow birds above)
Comment by Chris Harrison — July 13, 2007 @ 11:02 pm
July 13th, 2007 at 11:26 pm
JAM wrote:
I presume you forgot to add: not that anyone in mainstream science would ever dream of doing such a thing.
Chris Harrison wrote:
Hahahahahahahahahaha. Obviously.
Are you sure you're not a fringe element?
I take it you mean not merely that it cannot as things stand, but that it's logically impossible, because you have visited every logically possible world in person and have verified that in not a single one of them was ID found actually making such a prediction.
You understand that I simply want to be absolutely certain that you are not a fringe element.
Very.
Very, very, very old. Why, it's as old as a very, very, very, very, very, very, very, very, very old thing.
But good question. You can never be too vigilant.
If you understand it, then it makes sense. Which is why your statement doesn't make, you know, sense.
But that's okay, Chris. Just as long as you're not, like, um, a fringe element. Know what I mean?:cool:
Comment by stunney — July 13, 2007 @ 11:26 pm
July 14th, 2007 at 1:20 am
Chris:
Primates Trade Smell For Sight. Don't you just love how the Anazi Tales work? I sure do. Here we have a case of "independent" evolution of the same trait in similar critters on two different continents, along with a coincidence of "independent" deterioration in olfactory prowess in all the independently evolved primates. So we get a "proposal" [a.k.a. NDS Anazi Tale] that correlation equals cause.
Once you can see red fruit, you no longer need to be able to smell that it's ripe (substitute hot sexy butts and the ability to scent estrus or some other Anazi Tale of choice here). Sounds positively neo-Lamarckian, doesn't it? So inventive!
? This particular 10% of the genome (the subject of the Cornell research I linked) showed evidence of recent selective evolution. Mutating pseudogenes aren't "selective evolution," are they? Shouldn't they be invisible to selection? You yourself said,
"…arguably suggestive of function." Are you now arguing not so?
Give me a break. I am not a biologist, so I don't need to read the papers (though I do if they're publicly available and I am interested). I, like all other non-biologists in this country, get my biology news from the science press. I can read what the researchers say and how they portray their findings as well as anybody else. If y'all can't manage to pitch your Anazi Tales to the interested and scientifically literate public well enough to get your points across, then you've already lost this so-called "culture war." Getting huffy and more insulting than usual won't impress anybody.
I wasn't 'misinformed', Chris. Did you not finish the paragraph? My comments are often tongue-in-cheek. That may be an acquired taste, but I thought the joke was delivered well enough when I called it a "silly numbers game" and a "merry-go-round." Lighten up!
Glad to see you're open to what's happening, because it's happening with or without you. There now appear to be levels of coding in DNA, some of it related to chromatin dynamics and those ever-inventive expression suites. Because of the dynamics and oscillating form of compacted chromatin (real-time DNA functioning), a good bit of it has to do with positioning of expressed genes in a suite and their various promoters and adjuncts, which lengthy nonsense repeats may be vital for accomplishing. THAT is function too, even if none of the necessary spacing filler is transcribed.
We've some nifty new tools and some exciting new approaches going for biology right now, and can expect more new technologies to keep proliferating as market potential keeps rising. That means we can expect knowledge to increase - perhaps exponentially. It's plain dumb to expect what is learned not to change the paradigm significantly.
Clinging to an antiquated evolutionary philosophy that has always been insufficiently explanatory seems counterproductive. Y'all should be floating right now, as physics has been floating ever since the Standard Model fell apart. Trying to enforce provisional theory by civil law is a transparent act of political desperation. Maybe it's time to just do the science and leave people's metaphysical beliefs to their own conscience.
I just made several predictions about the functional nature of DNA (and I'm not even a biologist), so obviously you're wrong. It remains to be seen whether ID can be vindicated, or you wouldn't be here arguing about it, would you?
Comment by Joy — July 14, 2007 @ 1:20 am
July 14th, 2007 at 2:24 am
Joy:
I'm a non-biologist, and though I do read popular science articles/blogs from science writers, I go to the source whenever I can, especially if I'm trying to make an argument for or against some scientific position.
I am of the mind that scientists should make an effort to accurately relay their research to the public, but the fact is that press tends to get things wrong. We can't place all the blame on scientists.
A google search for "anazi tales" only brings up two other TelicThought posts, so apparently you are the only person on the entire internet that knows what these are.
I think I'm right. You just a made a prediction, but ID is still powerless to predict. Even Dembski admits this:
Joey claims to have a post in the work that addresses my comments about this, but we'll have to see what he comes up with.
Comment by Chris Harrison — July 14, 2007 @ 2:24 am
July 14th, 2007 at 10:30 am
Chris: I think I'm right. You just a made a prediction, but ID is still powerless to predict. Even Dembski admits this:
Dembski is only partially correct. It is true that an intelligently designed outcome is an innovative process allowing for multiple pathways to the same result; the actual pathway chosen being a consequence of choice. However, it is equally true that an indicator of an intelligently designed end product is the incapacity to get the same outcome through unguided natural forces alone.
Comment by Bradford — July 14, 2007 @ 10:30 am
July 14th, 2007 at 10:31 am
Chris:
I actually think most scientists do a darned good job portraying their work and qualifying their conclusions from their extrapolations. While headlines can be hilarious and "department spokespersons" assigned by the university PR/journalism politicians can be incredibly dense, the science press does a pretty good job.
You just have to sometimes do your own geometry and scale-drawing to keep things in perspective. And I too have found primary sources (usually emails are included in press releases) to be largely willing to discuss their work and answer questions. I've even encountered a few who will send a copy of their paper even though it's behind a paid firewall for the public.
I've worked in the press for many years. Their job is different from scientists' job, so it's good to be literate in their means. Sometimes the conflict leads to great confusion, when clarity should be the goal.
Huh. I'd have thought there would be innumerous sites out there! Anazi is a spider. He's the star of African folk version of Uncle Remus-like tales of the world told to children. Anazi is equivalent to 'Trickster', has a gigantic ego and is clever enough to think up wildly complex schemes to get someone else to do his work for him. Which inevitably end up making a fool of silly Anazi, while the poor victim of his plots ends up with spots (cheetah), stripes (zebra), a ridiculously long neck (giraffe), a crazy horn on his nose (rhino) or some other outrageous trait like a nose as long as his body is tall or ears the size of a savannah pond (elephant).
My children grew up on these fables, used to enlist their friends and put on plays for the neighborhood. The analogy seems apt to me per some of the silliest evolutionary tales about how the leopard got his spots. Always entertaining, change as often as the researchers getting paid to make up stories.
But you began in this thread admitting that ID predicts most DNA will turn out to have function. Is that not what you've been attempting to dismiss? I further predicted levels of coding pertinent to 'junk' that might only be filler so the compaction dynamics work per epigenetic functions. Is that not a legitimate prediction? If not, why not?
Sometimes I think people get confused by NDS pretensions to prediction that aren't predictions at all. They're POST-dictions, just more Anazi tales. Any good storyteller can do that. PRE-dictions about what we may find as our knowledge of phenomena increases upon more evidence is in truth a more scientifically valid exercise.
Nobody needs to predict what humans will evolve into or if insects will inherit the earth. We make predictions about process and mechanism and where our knowledge may lead us. IMO, but I'm more accustomed to dealing with physical science than with biology. Perhaps that's the difference between 'hard' and 'soft' science.
Finally, I'm not one who lets Bill Dembski or Mike Behe or any of the "ID Movement" leadership define boundaries on what I can and can't do. They've got their ideas, I've got mine. Fortunately telic thinking isn't limited to anyone's metaphysical black boxes, either religious or materialist. I enjoy the freedom.
Comment by Joy — July 14, 2007 @ 10:31 am
July 14th, 2007 at 12:37 pm
William:
If that is correct, then unless humans are privy to every unguided natural force, and all the capabilities of them, ID's design inference will forever be born out of our own ignorance.
Comment by Chris Harrison — July 14, 2007 @ 12:37 pm
July 14th, 2007 at 1:01 pm
Perhaps not. Adaptation is dependent on both a capacity for genomic change and the necessity to maintain genomic integrity. In the absence of functions enabling the latter genetically essential information could be lost faster than it is generated. These functions would have to be generated very early in a natural history time frame. That suggests a test as to whether or not a minimally functional genome lacking genomic repair elements would evolve them faster than natural forces would engender the decay of such a genome. If decay outpaces the evolution of adaptive responses we would have evidence that a basic paradigm is flawed.
Comment by Bradford — July 14, 2007 @ 1:01 pm
July 14th, 2007 at 1:18 pm
Joy,
ID advocates have said they expect the majority (all?) of the genome to be functional, but this is an empty prediction that is unable to vindicate ID either way, for reasons I've outlined previously. It is no more a prediction of intelligent design than a hypothetical prediction from Behe/Wells/Luskin/you that we will find more species of yellow birds. Joey tells me he has a comment in the works that will allow ID to make this prediction, but we'll have to wait and see what he comes up with.
Neat prediction, one I don't see a problem with. However, if this "came true", it would still be a non-sequitur to attribute this to ID making accurate predictions, as far as I can see. What about ID itself suggests "levels of coding to 'junk' that might only be filler so the compaction dynamics work per epigenetic functions" What auxiliary, independently verified assumption that works off ID itself, makes this a prediction of ID, anymore than those yellow birds?
Certainly, and although standard neo-Darwinism didn't predict, nor expect many of the findings coming from genomics, it still did a respectable job in other areas (population genetics, especially). There is not some huge rift in evolutionary biology, and although there is not a perfectly uniform theoretical framework that extends from allele frequencies to macroevolutionary patterns, evolutionary biology does not look to be going anywhere. Past ideas will be tweaked in light of new research, poor hypotheses will be falsified, but overall, ID does not seemed poised to make a large dent. This has a lot to do with the fact that it such a amorphous and incoherent set of vague ideas, but also the fact that IDists seem to be more interested in sneaking their ideas straight into highschool textbooks, while attempting to dodge the peer-review process. This does not bode well for any burgeoning scientific theory, and I'll be testifying against ID books at my state's Board of Education meetings until IDists demonstrate the validity of their ideas. But then we turn around and realize that there is no novel research going on by ID advocates.
I don't have any bias against IDists, but for these reasons I can't help but think ID will continue to be irrelevant in any discussion on the diversity and continuity of life.
Quite respectable. It's still an interesting quote by Dembski. : )
Comment by Chris Harrison — July 14, 2007 @ 1:18 pm
July 14th, 2007 at 1:42 pm
Bradford:
This assumes that the functioning and architecture of any currently "minimal" genome sans DNA repair mechanisms is representative of what was in existence 3.8 billion years ago. This is the same kind of problem that Behe's IC suffers from (it appears to be IC, in fact). OK, well Behe's IC examples have more than one problem, but whatever.
As a relevant example, current techniques (ie gene knockout) suggest that 250-300 genes is the number needed for any "minimal genome". Does this suggest that evolution must have been "jump started" by a population of cells comprised of 200 genes apiece? No, this would be a spurious conclusion because this is a test of the way things currently are.
The knocking out of repair mechanisms would be a neat experiment nonetheless, and could potentially reveal a lot about how the genome operates. I wonder if this has been done before.
Comment by Chris Harrison — July 14, 2007 @ 1:42 pm
July 14th, 2007 at 2:28 pm