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
We do not have to assume minimal function. It only appears to be a preferable option as it would better mimick historic models. An actual minimally genome is a legitimate object of study and should be empirically determinable.
The IC analogy is misleading. Behe's examples assume an already fully functional organism replete with all needed functions. It is a huge and unnecessary concession to ID critics but the easy examples used are perhaps required to sell popular books. Even so the pathways of critics are conceptual for the most part.
I'm in no hurry to jump to conclusions. This is an interesting field of study about which more data will be forthcoming. However, what you are demonstrating are avenues of research that could yield fruit from an ID perspective.
I'm quite certain it has not been done at the level contemplated or to address the question raised. Nature has her own gene knockout experiments which illustrate the consequences of even partially disabled genomic repair systems. Xeroderma pigmentosum is a hideous disease caused by mutations to genes coding for UV specific excinucleases. An accumulation of thymine dimers results which have devastating consequences for diseased victims who yet retain other fully functional repair mechanisms. A side benefit to related experiments would be a spillover to the health care field.
Comment by Bradford — July 14, 2007 @ 2:28 pm
July 14th, 2007 at 4:05 pm
I presume you forgot to add: not that anyone in mainstream science would ever dream of doing such a thing [conflating ID with the ID movement].
Why would I need to add it? It's done far more often by those within the ID movement.
Comment by JAM — July 14, 2007 @ 4:05 pm
July 14th, 2007 at 4:19 pm
Then don't be shy, define the level and specific genes that you are contemplating!
What have you done to make yourself "quite certain"
XP is the name of a large group of diseases, ranging in severity from mild to lethal. I don't think the mild forms can be described as "hideous," given that some are very difficult to even identify in the absence of a large pedigree.
Even when we get into the moderate forms, is XP nearly as hideous in animals covered with fur (the knockout mice that have been made) or in humans with a lot of skin pigmentation, relative to the hideousness of its presentation in white people who live in sunny places?
Comment by JAM — July 14, 2007 @ 4:19 pm
July 14th, 2007 at 6:34 pm
I saw the face of a child afflicted with the condition. I'll stick with the hideous adjective.
Comment by Bradford — July 14, 2007 @ 6:34 pm
July 14th, 2007 at 11:46 pm
Chris:
But the amount of functional DNA – by whatever measure one cares to use for the prediction – isn't the same thing as yellow birds. You keep saying it is, but that doesn't make it so. NDS of course didn't (and can't) predict anything about genes, genomes or variation, because it has insisted by fiat for 80 years that it's all random. That's not a "weakness" in the theory, it's built-in on-purpose automatic falsification by virtue of brick wall around cause.
ID, on the other hand, is all about cause. It's not science yet, but as it continues to develop with conceptions of front-loading and endogenous adaptive mutagenesis – boosted by incoming research by biologists armed with new technological tools on the no-longer forbidden subject of causation, and encouraged by developing theoretics of consciousness from a well-funded and star-studded multidisciplinary quest – it's still a real threat to the NDS status quo because it not only CAN make predictions related to causation, it DOES.
First you don't see a problem with the prediction, then turn right around and tell me I can't make it from an ID framework. Even though I told you twice that's precisely what I did do! I outlined a model for for telic design of biological evolution and made a very specific prediction from it. A prediction for which confirmation or disconfirmation should be coming in well within this decade without me personally having to do the work.
Biologists will do it, because that's what they do. And Neodarwinian 'Orthodoxy' no longer holds enough sway over the incoming upstarts to keep that brick wall around cause from being demolished. All I have to do is wait and watch, hope I'm around long enough to see the confirmation myself. But at the end of all things, that's not really necessary.
NDS didn't make this prediction and CAN'T make this prediction because it's about cause. I made the prediction. From an ID framework, because ID is about cause. This may itself cause a great hue and cry among the 'orthodoxen', but that's their problem, not mine. You can't change the rules (or the history) at this late stage. Prediction was demanded. Predictions have been made.
Ho, hum. Statistics generated upon probability distributions are nothing new, and can be applied to anything science cannot predict with any real degree of specificity. I can do the same "respectable job" from a framework of economics or sociology or even political science. Not very impressive biology.
Another yawner. I know y'all will sue the hell out of any school board that dares. As well you should, since I don't want my grandchildren taught Creation Science by the state either. If you didn't sue 'em, I might. That's just the same old same old same juggling of sociological interests in the political world. It has always been thus. Meanwhile, the textbooks have already been re-written without the excess NDS metaphysical baggage that so polluted them in the past. Open questions of causation are now open, as they should have been all along.
How do you know research is not being done? Are you really, really sure you've sterilized academia? What if you missed a few?
Then why are you here?
Comment by Joy — July 14, 2007 @ 11:46 pm
July 15th, 2007 at 1:06 am
Joy,
The yellow birds/prediction analogy holds until ID can build a coherent theoretical framework that is grounded in auxiliary assumptions. You cannot meaningfully predict anything without these independently verified assumptions.
This framework does not exist, despite your claims that everything will be unfolding within the next decade. The "predictions" by IDists that most/all non-coding DNA will turn out to be functional is completely detached from intelligent design itself, and current genomics tells us this is not the case anyway.
That is all so completely ridiculous and categorically false that I had to read it twice just to make sure you weren't being sarcastic. The principles born out of population genetics (ie neo-Darwinism) are pretty much the acid test through which any theory of genome evolution must pass. (This is where you start whining about orthodoxy again.) The above paragraph says a lot out about your grasp of evolutionary genetics.
We've already been over this, and I was always more a fan of cross country than track. I think this discussion has run its course.
Theoretical inertia only lasts so long, unfortunately nothing is coming out of the ID tent either. What's left? An expansion and refinement of current evolutionary theory. (I know, I know, in 10 years I'll be eating my words etc. etc.)
Probably because I'm privy to what's coming out of peer-reviewed science journals (not a word about ID), and also the fact that ID's pretend journal is (has been) defunct.
It was interesting for a while, but since Joey doesn't appear to be returning to vindicate IDists "predictions", I can't say I'll be continuing this discussion. Besides, summer's drawing to a close, pretty soon I'll be back at my university, studying under the banner of evil, dogmatic neo-Darwinian biology professors. I've got a metaphysical wall to keep in tact, remember?
Bye Joy. The final comment is yours.
Comment by Chris Harrison — July 15, 2007 @ 1:06 am
July 15th, 2007 at 3:02 am
Bradford, it should be clear that I'm not challenging the notion that severe forms are hideous. If you'll reread what I wrote, I'm challenging the notion that XP is a single condition, which is very relevant to your position on repair mechanisms.
So which form of XP did the child have? Is that particular form of XP nearly as hideous in animals covered with fur (the knockout mice that have been made) or in humans with a lot of skin pigmentation, relative to the hideousness of its presentation in white people who live in sunny places?
And if you'll take the rhetorical cheap shot of pretending that someone pointing out that not all XP is hideous constitutes a claim that no cases of XP are hideous, I have to doubt your claim, "I'm quite certain it [knocking out of repair mechanisms] has not been done at the level contemplated or to address the question raised."
What level are you contemplating to address the question? Please be specific.
Comment by JAM — July 15, 2007 @ 3:02 am
July 15th, 2007 at 10:45 am
I'm not asserting that XP is a single condition. My position on repair mechanisms is relevant to their evolution from a precellular starting point. Any theory explaining a trend toward ever increasing genomic information needs to explain why factors engendering genomic decay would not abort an incremental process. Although causes of genomic decay would exist at any point in earth's history, mechanisms that neutralize them would not exist at the outset when initial nucleic acids arose and acquired a replicating capacity. The question my position addresses is not simply how an encoding system came about in the first place. More to the point what would have prevented natural tendencies toward disorder of the very sequence specific configurations needed (and presumably generated through a replication process) to construct genetic novelties?
Comment by Bradford — July 15, 2007 @ 10:45 am
July 15th, 2007 at 12:47 pm
Chris:
Why should challenge to unverified assumptions require verification? These assumptions are always found in the metaphysical philosophy underlying an approach to evidence, and metaphysical philosophies are not empirical in the first place – they cannot be independently verified. Though they can be independently falsified. THAT is the situation at present in the matter of NDS' metaphysical brick wall around causation. It does not serve the purposes of the science anymore. Randomness isn't useful – it cannot be quantified for the practical purposes of control. Science's job description.
I did not say "everything" will be unfolding within the next decade. Science doesn't work that way. What I predict WILL unravel in the next decade is the NDS insistence that only a tiny portion of DNA in the human genome has any purpose. You've insisted that if it goes to 20-25% it will present a serious challenge to the NDS. I predict the result will be more than twice your high figure.
The 'result' will take longer than the falsification of NDS (which should come in much sooner). I further predict that the 'orthodoxen' will simply move their goalpost and pretend it was in the new place all along. We've seen it before.
I keep telling you that the prediction is NOT divorced from ID proper. Your resistance to that idea is more about your discomfort that the prediction may be verified than anything else. Both NDS and ID are approaches to evidence, informed by baseline assumptions that are in this case orthogonal to each other. The ID assumptions lead directly to the prediction that a majority of DNA in the genome will serve functions of the organism. The NDS assumptions lead directly to the long-held belief that DNA is mostly randomly accumulated 'junk' with no purpose. There can be no clearer point-counterpoint derived from theoretical fundamentals.
What "current genomics" tells us is entirely irrelevant to the predictions except as the baseline the predictions stand in contrast to.
Charlie Darwin was not the first human to understand that healthier organisms reproduce better than unhealthy ones, or that inherited traits can be magnified or reduced by selective breeding. Or that if organisms die before they reproduce, they don't have any offspring. Or that there's a range of relative 'fitness' among members of the same species and even the members of the same litter. Humans have been working with these obvious facts for thousands of years. That's how we came to have such critters as poodles, thoroughbreds and Holstein cows.
Folk wisdom can certainly be verified by science, but it's not itself science. If this is the greatest 'scientific' success Darwinism/NDS can claim after 150 years, it's less a science than an ag extension service pamphlet written in ancient Sumerian.
I agree, and suspect that the NDS desperation tactic of using civil law to enforce theoretical hegemony is going to become an albatross around science's neck it will take decades to overcome on the reputational level. Physics (that 'Chief of Sciences') has suffered its share of ugly turf wars through the generations too, but they generally don't last so long and aren't usually played out in public. It usually tends to work out in the end.
Science ultimately decides what qualifies as science. And it must follow the evidence wherever it leads or it makes itself useless to humanity (who pays the bills). Thus science itself will change its evolutionary tune when it can no longer support the metaphysical corruption that now rules that roost. And no matter how EAM-ish the next paradigm looks, science will never call it "Intelligent Design."
That's okay with me. It's even okay with me if they pretend they've always promoted an EAM-ish model. Only those few paying close attention will smile ruefully to themselves at the Orwellian thrust, and they'll all die off eventually too. Another generation or two down the road no one will remember it was ever any different. Such is the way of things.
The struggle right now in these generations is just something to do with our time and energy because we've some time and energy to spend. Everyone picks their challenges in life. And when they're gone hardly anyone remembers there ever was a struggle. That's okay too.
Bye, Chris. Thanks for the discussion. It's been real! §;o)
Comment by Joy — July 15, 2007 @ 12:47 pm
July 15th, 2007 at 1:36 pm
"I saw the face of a child afflicted with the condition."
Yes, but not as relevant as my question about what the same mutant XP alleles do in organisms with fur or darker skin is to your claim that you are "quite certain it [knocking out of repair mechanisms] has not been done at the level contemplated or to address the question raised."
That's why I have twice asked you a very pointed question that anyone who is quite certain about what has or hasn't been done should easily be able to answer, yet you have refused to answer both times.
Bradford, that's just insulting. No one's positions can never address a question. Only an answer, based on the data, can address a question.
The questions you are refusing to answer have absolutely nothing to do with how such a system came about, so I don't understand why you arent answering them.
What have you done to make yourself "quite certain"
Is XP nearly as hideous in animals covered with fur (the knockout mice that have been made) or in humans with a lot of skin pigmentation, relative to the hideousness of its presentation in white people who live in sunny places?
These are easy questions for anyone who is quite certain of what has/hasn't been done to answer.
Comment by JAM — July 15, 2007 @ 1:36 pm
July 15th, 2007 at 1:57 pm
"I saw the face of a child afflicted with the condition."
Substitute genetic disorder for condition. Why are you being pedantic about this?
My position on repair mechanisms is relevant to their evolution from a precellular starting point.
Am I mistaken in believing that an all encompassing knock out of repair mechanisms for experimental purposes has taken place? If so simply cite the reference.
Repair mechanisms extend beyond nucleotide excision repair mechanisms relevant to UV damage so why are you getting worked up over this?
What is the point of your question?
And your point is?
Comment by Bradford — July 15, 2007 @ 1:57 pm
July 15th, 2007 at 7:54 pm
JAM,
Thank you for the stimulating discussion.
I said:
You said:
You repeated that I said:
You said:
My earlier comment to Chris Harrison clears up the confusion. My intention was not to provide an all-encompassing list of black-and-white options, into which I would fit all biologists. I was specifying those biologists who made predictions were the ones I was talking about.
You said:
I think we are talking about two different things now. I'm talking about the people who have done junk DNA research that has shown that junk DNA has function. The researchers involved in the preliminary studies of the function of junk DNA (and the requisite DNA mapping projects) are the individuals that had enough money and resources to do so. Which hypothesis are you talking about?
You asked:
I said:
You said:
The percentage of functional DNA is climbing. When will this trend hit the ceiling? I have no idea, but I don't think it will be soon.
You said:
I work in a job not related to junk DNA, I happily spend time with my family, I have friends to catch up with, I have hobbies and other commitments, and I am furthering my academic career in biotechnology. I appreciate the link to the ENCODE database, I'm sure that as the data expands it will come in handy later in my career, but for now my focus is on other things.
You said:
I didn't say they did or didn't, the information in the summaries of the researchers working on the ENCODE project said they have function.
You said:
I don't know an exact number of tests, no. I would be more than happy to hear your data.
You said:
No human has enough time to read all primary and referenced sources for all possible scientific research applications. This is one topic that I do not know everything about, and I do not have time to read all of the primary and secondary literature.
You said:
I'm not complaining. What gave you the impression I was complaining? I think our conversation so far has been us talking past each other, and you trying to read my mind. Your nick-picking and your loaded questions (about specifics that I cannot know) makes me think you are attempting to have a confrontational battle with someone besides me. If I say something that is not clear, just ask. There's no need to assume. I will be happy to clarify for the sake of a gracious conversation.
Additionally, I'm not willing to wager, but I think Dr. Andras Pellionisz would be in a better position to make a bet like this. I can put you in contact with him if you would like.
You said:
I'm sure you can, but are you suggesting that you know better how to spend people's money and time than they do? I think that's a bit presumptuous, but this is a matter of opinion, and you are certainly entitled to yours.
You said:
Maybe the ID scholars knew about the huge national and international projects that are funded by megalithic governments, agencies, and universities (like ENCODE), and so they thought other interesting projects would be a better use of their time, like evolutionary informatics and mutagenesis.
Comment by Joey Campana — July 15, 2007 @ 7:54 pm
July 15th, 2007 at 7:56 pm
Chris Harrison,
Thank you for the stimulating discussion.
You said:
You're right, I mistyped the actual statement, "nothing more" is what he said and I ended up typing "nothing but." Regardless, "˜nothing more' is still an absolute, which at least implies that he meant "all."
Comment by Joey Campana — July 15, 2007 @ 7:56 pm
July 15th, 2007 at 8:09 pm
JAM,
Thank you for continuing this interesting discussion.
You said:
I don't think researchers have to make any predictions, per se. However, to design experiments, they must hypothesize, and this requires inferring what might or might not be true.
By saying that it's free, are you saying that you can predict what DNA is functional by a simple reading of the sequences that are freely available online? If you can, you need to call ENCODE and tell them that you can save them billions of dollars and millions of man-hours.
I said:
You reply:
Is it incumbent on me to do so? I don't know if I will ever have a hard number. If the researchers doing the study are unwilling to venture such an exact number, it's probably not wise for someone not doing said research to offer a precise prediction.
I said:
You said:
"˜10% SD' was an adjective modifying the noun "˜link.' Are you getting cranky, JAM?
You said:
LOL! You are very entertaining, in a middle school kind of way. Like I said before, I'm not in the research, so I'll leave it to those who are actually finding functionality in the junk to render exact predictions.
Comment by Joey Campana — July 15, 2007 @ 8:09 pm
July 15th, 2007 at 8:54 pm
Joey to JAM:
I'm not "in the research" either, Joey. But I don't think the prediction of "most" (>50%) is all that outlandish, even though it can as easily be wrong as was Gregory's source of 5%. It costs us nothing to extrapolate on a trend, and the trend is that function for previously considered 'junk' DNA is being established right and left.
Something to remember when offering cheap extrapolations is that the market for this type of research is not nearly as exclusive to academia as JAM would like to believe. Much of the new gene-function technology hitting the technology-hungry gene market right now is proprietary and specifically peripheral TO that technology-hungry market. There are billions in R&D funding right there in-house (venture capital, dedicated corporate R&D, etc., only a small percentage of it coming from public funding sources), which keeps the potential trillions in profit fully in-house as well.
There are restrictions on public funding – some projects are verboten, such as those using non-approved stem cell lines – as well as an ever-limited pool that must be spread widely to hundreds of public institutions. The potential in evolutionary biology for highly lucrative patents and future profits is unlimited. And while quite a bit of what is discovered exclusively in corporate gigacorp basement labs will remain proprietary for 50 years or more, if ANY public funding is involved the findings (if not the specific applications) will be published for general consumption.
Think of the applications… not only treatments for conditions and diseases and general purpose prescription-onlies they can market direct to the public using television as a drug dealer's wet dream, but diagnostic testing as well, means of personalizing treatment options based on genetic profiles, etc. Microarray technology is proving spectacularly useful in discovering epigenetic expression suites with incredible powers. Why, it's now possible to entertain the idea that we might someday have "Spontaneous Remission in a Bottle" – for all the gnarliest cancers that physicians talk about in hushed tones in the lounge amongst each other. Those "Miracles" that nobody can explain but that do in fact happen.
All that is more than enough reason for biological specialists to actively seek possible functions for every tiny bit of our genome. Including all that is transcribed but which we can't name a function for right now. Why would any dedicated scientist public or private want to dismiss ANY of it in this day and age? Surely they have no desire to become dinosaurs while they're still alive!
Anyway, this is why I predict function will exceed 25% within just a few years (if not sooner), and will go over 50% within a decade. It's a small, tight-knit community. Proprieties will be respected but real secrets are hard to keep. Since I am not beholden to either academia or to corporate gigacorps, I have the luxury of watching all this from the outside. Since I have experience with both academia and corporate gigacorps, I have the freedom to weigh their relative interests when analyzing what's really happening.
It's exciting, if you care about such things. It's also happening much faster than any invested turf-warrior wants to publicly acknowledge.
Comment by Joy — July 15, 2007 @ 8:54 pm
July 15th, 2007 at 9:18 pm
Good points. The attitude one brings to the table is predictive of one's predictions. Why would a non-teleological approach be expected to predict function? Why would a teleological approach not be expected to predict it?
Comment by Bradford — July 15, 2007 @ 9:18 pm
July 15th, 2007 at 9:47 pm
Bradford:
Hi, Bradford. Don't know if this was rhetorical or whether you're asking real questions. In case it's the latter, here ya go…
NDS (the non-teleology) wouldn't predict function because it relies on randomness as causation. Since functional elements are so improbable, most of the genome has to be more probable 'junk'.
ID (teleology) would predict function because life's processes are far more complex – and expensive – than those "bags of goo" descriptions ever wanted to acknowledge. It all works together on a number of levels to maintain vitality on the very razor's edge between total chaos and complete stability. There's just no room in the system for the amount of wasteful 'junk' NDS insists must be there, and no energy to spare maintaining it (some of it's in the "Ultra-Conserved" category, meaning it's been written in DNA stone unchanged for half a billion years at least).
If there's a telic impetus to life, there's a reason for most of it. What there's not a good reason for is probably detrimental.
How do you answer your questions?
Comment by Joy — July 15, 2007 @ 9:47 pm
July 15th, 2007 at 10:18 pm
Hi Joy. From a non-teleological perspective one would discern purpose as apparent and pegged to selection for reproductive fitness. That passageway can be narrow. Inefficiency would be expected of this paradigm.
OTOH, I always found it odd that long conserved non-functional sequences would remain virtually intact over geologic time frames. Undiscovered functions better explain these mysteries. What non-teleological evolutionist could honestly say he or she was not surprised by alternative splicing? A front loaded perspective will eventually win the day and we will look in vain for non-teleologists.
Comment by Bradford — July 15, 2007 @ 10:18 pm
July 16th, 2007 at 12:29 am
::hiccup::
…pardon me.
Comment by Joey Campana — July 16, 2007 @ 12:29 am
July 16th, 2007 at 11:56 am
Joey:
Thanks for the link! I try to keep track of ScienceDaily because interesting tidbits like this seem to come in almost daily, and occasional items of interest in other directions aren't rare.
It's a little befuddling to me how even the hardest core turf warriors for NDS can manage to ignore so much incoming research that belies their absolutist assertions. Or why they'd expect any telic thinkers to be ignorant of that incoming research. It looks like biological science itself has moved on with its mission of following the evidence wherever it leads, which means not even the much-maligned "Neodarwinian Orthodoxy" can keep a lid on the science anymore.
Comment by Joy — July 16, 2007 @ 11:56 am
July 16th, 2007 at 3:14 pm
What a ridiculous statement. Their job is making and testing predictions!
You are missing the idea by a mile. Real scientists use inference to construct scientifically-useful hypotheses. Any useful hypothesis makes predictions. The whole point of doing research is to make the prediction first, to overcome the human tendency of reluctance to admit error (which you exhibit in spades, Joey).
That being said, you missed my point, which is that the use of these databases is in no way limited to researchers. YOU (Joey Campana) can use them to explore the data, as well as constructing and testing hypotheses.
Yet you choose to run away. Why?
No, I'm saying that YOU can use the analytical tools (no one is simply reading the sequences) to construct hypotheses. I haven't used ENCODE, but I have used VISTA to compare/contrast mouse vs. human sequences to identify hypothetical places in which to place loxP sites for "knock-in" constructs, for example.
Why, of course it is, if you are claiming that the eeevil Darwinists are wrong and the "ID scholars" (at least you didn't fudge and call them "researchers") are uniformly claiming that most-to-all of what is currently classified as junk is functional.
Are you saying you don't agree with the ID scholars?
A soft number will do. Do you see a problem with your fear of prediction?
Where did I ask for an exact number, Joey? Do you see any contrast between your confident claims that every result showing that SOME DNA, no matter how tiny, has been moved from the junk to the functional category affirms these alleged predictions by ID scholars, with your reluctance to make a single prediction about anything?
It's incumbent upon anyone with a strong scientific opinion to offer predictions, period. The "precise" demand is an evasive excuse you generated. I simply asked you where you fell between 5% and 100%.
No, I'm having fun. In fact, you fudged "as much as 10%" to the more precise "10%" while falsely claiming that I was demanding precision. Amazing!
That seems to be the only level on which you can be reached. Tell me something, Joey: is "junk DNA" predicted by Darwinian evolution?
Like I said before, you don't have to be in the research to use the free tools available. Are you afraid of actually learning something?
Uh, Joy…I was pointing out the polar opposite of that to Joey. Anyone can use these tools. They are free. As for the use of such information in commercial applications, it is very valuable–so valuable, in fact, that if anyone actually believed the ID spin on junk DNA, they would be setting up ID-based biotech companies.
I continue to be amazed at the ability of ID proponents to run away from faith in ID as soon as it involves actual effort or risking money.
Comment by JAM — July 16, 2007 @ 3:14 pm
July 16th, 2007 at 4:43 pm
How about naming 5 of them?
But were those people testing junk DNA hypotheses? If not, how can you label it as "junk DNA research"
Let's take the Lunyak et al. paper, the one from the press release. What hypothesis were they testing?
The ID hypothesis, remember? According to you, ID scholars UNIFORMLY predict that most-to-all of what is currently categorized as "junk" will turn out to be functional.
Was the goal of the Lunyak et al. study the function of junk DNA?
Sorry, Joey, but neither of those facts represents a rational excuse for not knowing the answer. You are claiming that only one side has the money, so it's up to you to back it up or retract it, not ask me what I think.
But despite all that money, they have yet to fund any real research, correct? Don't you find that sorta odd, if ID is science, and you're claiming that there's a grand hypothesis to be tested?
Yes, but that's not due to any effort from ID scholars or money from the DI.
Joey, your fear of making predictions is palpable. The thing you need to predict is how much, not when.
Common sense predicts that sequences will move from the junk to functional categories simply because the junk category is a negative, provisional one, and we won't know everything there is to know about the genome for a long, long time.
So what? You founded this massive Web site about ID, you've written this hilarious page titled "Empirical ID Research," from which it is clear that those in the ID movement are afraid to do empirical ID research (testing an evolutionary hypothesis is not "ID research," btw), and your hobby is slumming on blogs, so your job is simply irrelevant.
ResearchID.org and slumming on blogs takes away from those, too, and you still do them.
Like writing post after post claiming how ENCODE supports ID without ever looking at it.
Where? They are transcribed; that doesn't mean they necessarily have function.
Hello, Joey?
Answering my second question is ridiculous if you are afraid to answer my first question. What's your retrodiction? If you are so gullible to believe that the presence of transcripts is sufficient to assume function, the prediction is obvious–just as obviously, your reticence screams that you don't really believe ID.
Um, where did you get the idea that I was demanding that you read all of anything? Why can't you simply acknowledge that I am pointing out that reading primary sources is better than reading press releases? Is it because you agree with me?
If you know very little about a topic, it's good to read SOME of the primary and secondary literature INSTEAD of press releases.
Your braying about this Science paper is a perfect example, too!
Which proportion of the genome does the "junk DNA" for which a function has been found in this press release represent?
1) 0.0012 (0.12%)
2) 0.000012 (0.0012%)
3) 0.00000012 (0.000012%)
Where did I claim that you were complaining?
You're the one putting words in my mouth, Joey. How did you interpret my advice that press releases often lead you astray as a demand that you read ALL primary and secondary literature?
Joey, this is about your reluctance to make predictions. In science, we make predictions about things we don't know all the time. We don't make inferences and quit.
Why not? Do you not agree with the ID scholars, or do you simply have no confidence in their predictions?
I don't know of any huge project dedicated to testing the hypothesis that everything currently categorized as junk will turn out to have a function. Do you?
Who in the ID movement is doing mutagenesis?
Comment by JAM — July 16, 2007 @ 4:43 pm
July 16th, 2007 at 5:07 pm
JAM:
Uh, Smokey… that's completely irrelevant. I can get a free download of Windows for Mac too. What I can't get is a word processor from Microsoft that makes any sense at all. By the way, do you know what those biotech companies are doing down there in the basement?
Who's running away? I made my predictions, both general and specific. I am confident they will be borne out, sooner rather than later even though I allowed a decade. What more do you want? Do you just seek to silence my voice out here in cyberspace? Ain't gonna happen.
If you're so sure the predictions are wrong, demonstrate that to the biologists and geneticists and computational genomics researchers currently funded and fully engaged in seeking real answers to these open questions. Tell THEM they're wasting their time and money. See if you can enforce your orthodoxy on them at this point in history, when your orthodoxy counts for less than zip within its own branch of science. It counts for way less than that around here.
If you can pull that off I might be impressed. Simply insulting non-biologists on internet message boards isn't impressive at all. Threatening them with your non-existent pseudonymous non-authority is a total yawner.
Put up or shut up.
Comment by Joy — July 16, 2007 @ 5:07 pm
July 16th, 2007 at 10:10 pm
In the link provided by Chris in his earlier comment, William Dembski seems to concede that ID does not yield predictions. But if this is the end of the story about his view on ID's predictive power, it is strange that he stated 3 years earlier that, "If, on the other hand, organisms are designed, we expect DNA, as much as possible, to exhibit function." I think this apparent contradiction can be cleared up by making a distinction between two different conceptions of the term "˜prediction'.
If considering all statements of ID scholars concerning functions of junk DNA, one gets the distinct impression that ID theorists are not presenting a specific prediction of one precise fact. I think that ID's prediction of function in junk DNA is a "˜heuristic prediction', or a guidance prediction, in the sense that ID suggested a fruitful direction for research. This is in contrast with the typical conception of an "˜exacting prediction,' which usually involves a prior calculation from an ongoing process that provides a proposed event, or the finding of a specific fact. These "˜exacting predictions' are typically arrived at by extending confirmed knowledge about an ongoing process into a possible single, future event.
For someone interested in ideas that led one group of scholars to make the same heuristic prediction, this is an inherently interesting case and worthy of further consideration. For someone interested in short-circuiting discussion of an interesting case, this is a great opportunity to present some non-sequitor's, impossible questions, and childish challenges in order to sidetrack the conversation.
In a bit I'll present what I think is the auxiliary proposition that led all ID scholars to offer the same heuristic prediction. But first, a question for Joy. . .
Comment by Joey Campana — July 16, 2007 @ 10:10 pm
July 16th, 2007 at 10:21 pm
Joy — Why do you predict >50%, and not >30%, or >70%? Are there any specific facts that suggest your number?
Comment by Joey Campana — July 16, 2007 @ 10:21 pm
July 16th, 2007 at 10:43 pm
Joey:
I predict >50% because I honestly don't think most of it's random junk. That might be 51%, it might be 99%. This doesn't mean all of it serves Level I or even Level II functions, it just means most of it isn't junk. There are capabilities in our genomes and epigenomes we've not even begun to notice or tap. What's junk is the stuff that causes systematic disease.
I 'suffered' a spontaneous remission of acute leukemia when I was seven. That was back in the days when atmospheric bomb testing left mud puddles (from way hot rain) reading 10R/hour in wide swaths of the countryside and "cancer clusters" that wiped out entire families and neighborhoods were so common hardly anybody noticed. There were no treatments of any kind. You got it, you died.
…unless you didn't. I didn't. No one ever bothered to ask me why, though they followed me for a decade pulling blood out of my veins as if I had it to spare (or wanted to give it to them). They never figured it out.
I use more of my genome than most people do. Thus I know that more of genomes are useful than other people (particularly NDS'ers) want to admit. Not everybody uses everything useful, but that doesn't make what they don't use non-functional.
Comment by Joy — July 16, 2007 @ 10:43 pm
July 16th, 2007 at 11:23 pm
Joey,
I might jump back in here after all.
Comment by Chris Harrison — July 16, 2007 @ 11:23 pm
July 17th, 2007 at 2:01 am
As we move along in this discussion, keep in mind the words of Robert Eisenberg, who recently wrote to Nature saying: "productive research is catalysed by assuming that most biological systems are devices. Thinking today of your biological preparation as a device tells you what experiments to do tomorrow." Why in the world would he say such a thing? Why does Eisenberg think that comparing biology to technology will be of any help? We'll answer this question in a later comment. But first . . .
Some critics of ID argued against ID by saying that an intelligent designer would not put 98% meaningless code into a functional informational system. I think that, in general, this "no designer worth his salt" proposition (as E. Sober calls it) is self-explanatory and requires no elucidation on my part. The proposition appeals to our uniform sensory experience regarding what intelligent causes do when they design a high-tech, code-based invention. The proposition as employed against ID is a functional extension of the dysteleology argument against teleological views. Sober also said that, "Many biologists take the fact that adaptations are often imperfect to provide a decisive objection to creationism and to mini-ID." Presumably, imperfect genetic adaptations would be included in this idea that "many biologists" used against ID.
When the data was telling us that only 2% of the human genome had known function, I intuitively understood why a critic saw Junk DNA as a slam dunk against ID, but I still disagreed with the critic. Now the trend is changing, and more functions are being found in the junk DNA, and so the sting of Junk DNA on ID is certainly losing its effect.
One might think it ironic, yet ID critics and ID theorists agreed on the use of this "no designer worth his salt" proposition. Predictions from ID scholars that junk DNA would have functions were based on the same logic that ID critics were using against ID.
If this "no designer worth his salt" assumption was indeed the only basis of the relevant predictions about function in junk DNA, I think it was a little bit hasty. Even though it turned out to be correct that more than 2% of the genome had function, it was (and still is) a bit too ad hoc for my palette. For me, something more substantial and, ahem, physical, needs to be presented in order to corroborate the "no designer worth his salt" proposition.
I'll work through my explanation by first giving a brief outline of a more substantial supporting concept that might corroborate the ID prediction of function. Second, a brief discussion of the human form and it's relation to the stronger supporting concept. Third, I use a quote from an ID scholar to explain how the supporting concept was used with reference to predicting function in junk DNA.
I think the ID prediction can be independently supported from a more substantial supporting concept that I call 'design isomorphism.' Design isomorphism is when a technological invention/design is later found to exist in living things. LED's, rotors, bushings, flight technologies, parallel navigation, circuitry, logic gates, and network configuration regimes are but a few examples of design isomorphisms. As it turns out, the physical structure of design isomorphisms are very similar in form and function, or exactly the same in design and purpose. Given the similarity in structure, the information needed to specify the design structure is basically the same in both cases when including the semantic information in the tally. This signifies a thought provoking connection between human engineers and the (real or apparent) design of living organisms. As it turns out, the link between biology and technology is much stronger than Descartes and Gassendi could have imagined, and this link is confirmed by physical designs existing in life and in machines.
ID suggests that both biology and technology are intelligently designed, resulting in a conceptual link between the two. This conceptual link from ID premises suggests that we should find some type of conceptual similarities. This link is supported by the independently verified similarities of "˜design isomorphisms'. The independently supported link between biology and technology suggests that certain aspects of life will have specific conditions, and these are better studied a certain way.
In my next comment, we'll look at ourselves in relation to design isomorphisms . . .
Comment by Joey Campana — July 17, 2007 @ 2:01 am
July 17th, 2007 at 6:50 am
Casey Luskin posted a blog entry on the plausibility of the idea that mice and humans share non-functional pseudogenes.
Comment by Bradford — July 17, 2007 @ 6:50 am
July 17th, 2007 at 11:01 am
To see how we might extrapolate design isomorphism into some tractable knowledge that could direct research, let's take a look at the genotype and phenotype of a human for a moment, since we have a good deal of knowledge concerning them.
The biologists that were proposing that junk DNA was "failed experiments of a random process" were suggesting that only about 2% of the genome was the genetic contribution to the formation and functioning of a human body. On its face, the 2 or so percent of the human genome contributing to the human product does not seem enough to ID scholars. Why does this figure sound too low for ID scholars?
How many bits of information are required to construct a human? A human is physically constituted with self-replicating, self-assembling, self-repairing, interdependent, cooperative cells that have within them intricate and efficient machines, which are made by production assembly regimes and coded-program control systems, utilizing (on many different levels) elaborate network functionalities, cross-domain semantic information, spatial-temporal deployment processes, and modulating inter-cellular components, all of which contribute to form a mobile bipedal organism that runs distances much farther than any other living land dweller, and also allows for self-awareness, abstraction, complex thought, which in turn allows for educational, scientific, and technological advancement.
In this short summary above, I have barely scratched the surface of the magnitude of the human body's complexity. The point is that a great deal of information is needed to specify one functional human body.
I think the auxiliary proposition of design isomorphism suggested that more functional information is needed. Taking into consideration knowledge from technological disciplines such as engineering, software development, bioinformatics, nanotechnology, computer engineering, biotechnology, general design principles, production engineering, information theory, and other such fields, 2% of our genome will not suffice to make the physical structure of a living human being. Not enough 411. Based on what we know about how things are constructed, it is blunt common sense that several hundred megabytes of information is not enough to specify the material constitution of a human person. 2% of the genome is barely enough information bits to specify a collection of quality digital 2-dimensional photos of a human, much less the 4-dimentional function and growth of an actual human body. Again, this is an understatement.
The isomorphic inference that there is not enough information in 2% of the genome to specify the physical human form has the direct consequence that there must be more functional information in the human genome. Thus, ID-based premises insisted that we continue looking for function, though the evolutionary views of Dawkins and other ID critics did not.
(As an aside, it is interesting that Dawkins was not anticipating function in the ultra-conserved junk DNA. His views were in stark contradiction with others in selectionist camps, of which he is considered a member.)
I think that most ID scholars understand design isomorphism, but employ this concept in a tacit way. I would hope that they do not present a full explanation for their prediction because they are not afforded enough airtime, or word length, to do it justice. But this is a wild guess on my part.
In my next comment, we'll take a look at one of the earlier function predictions from an ID theorist to see if ID's suggested biological-technological link is present, and if a design isomorphic proposition was used . . .
Comment by Joey Campana — July 17, 2007 @ 11:01 am
July 17th, 2007 at 7:17 pm
Joey said:
Eisenberg's suggestions in that article seem much in line with other physiologists (like Scott Turner). His reasoning is quite sound from a physiological standpoint, but not so much from a genetic standpoint.
You'll notice in the following quote that Eisenberg's treatment of DNA only extends (implicitly) to coding regions.
At the gross phenotypic level, and even at the biochemical level, function is prevalent. It makes perfect sense to investigate a metabolic pathway or an organ system from a (reverse) engineering standpoint.
There are not (m)any dead-end metabolic pathways or redundant organs. There are tons of genetic elements that are not indicative of function, and that are simply redundant (e.g. gene duplicates and the genetic code itself) or broken (e.g. pseudogenes). The research perspective of a physiologist does not perfectly overlap with one of a genomicist because the (forgive me for jumping ahead a bit in your response) "design isomorphisms" that are so obvious at the phenotypic level do not show up at the genomic level. Consider a post from PZ Myers that seems eerily well-fit to demonstrate my point here.
The genetic level often betrays the conceptual link (which often holds at the biochemical/morphological level) between biology and technology. Given that we're here to talk about DNA specifically, this point is of the utmost importance.
But as Sober goes on to say after that quotation (and with which I agree), the argument that ID is somehow refuted by the existence of "junk" is unsound. It concedes that ID is testable and subject to falsification. I (and ostensibly Sober) argue that this concession is unwarranted and that ID is ultimately powerless to predict whether or not DNA will be functional. It may seem intuitive [based on the existence of design isomorphism (DI)] that a designer will not intentionally clutter genomes with useless crap, but this intuition is simply the result of our observation that humans tend to design technology in an efficient way. Yet no one is arguing that humans are actually the designers. You are thus forced to assume that the intelligence of the designer is similar to what humans exhibit.
However, every expendable nucleotide might be the careful reasoning of a designer who wants to seem intuitively retarded. Such is the problem of a prediction based on an ID inference.
Dembski's words are again relevant:
"We cannot predict what an inventor would do short of becoming that inventor."
Yet, IDists will (implicitly) claim that the intelligent designer is human-like (given the existence of DI) in an attempt to justify the prediction of function (since humans tend not to make most of their invention useless). This is the "human-like" design inference, gleaned from the observation of "design isomorphisms (DIs)". This is still problematic with respect to non-coding DNA and putative function, given that DI does not seem to hold at the genetic level.
This is a bit of an aside, but it's still relevant. It is generally accepted among evolutionary biologists that most phenotypic evolution is adaptive (ie, functional), yet the stochastic nature of mutation, combined with the redundancy of the genetic code allow for things like genetic drift. Presumably this (among other reasons) is why DIs hold from a physiological perspective but not from a genetic one.
Ultimately though, if our genome is mostly junk, then the IDist position will of course not be refuted, the tune will just change into something like "the intelligence is not human-like after all". ID remains unfalsifiable on the whole. More relevant to our discussion however, is that the auxiliary assumption of "design isomorphism" is not valid in the case of DNA, which, given that evolutionary change results from modifications in DNA, causes ID's prediction of functional nucleotides to unravel. Perhaps ID will have better luck predicting function at the morphological level.
Having said all of that, let's consider another point.
Suppose we lend credence to your view that ID has an independently verified auxiliary assumption that allows it to predict DNA is functional (I don't actually concede this, see above), and also let's assume that most (all?) non-coding DNA has function.
Would it then be correct to take a point from evolution and give it to ID here?
Strict adaptationists have predicted a whole lot of function long before ID was around. See Gregory's post again here .
Again assuming that most non-coding DNA is functional, which prediction (ID's or adaptationism's) is validated? Who do we give the point to?
It is clear as well as ironic that if we are to concede ID's ability to predict (based on DIs), ID's prediction coincides with strict adaptationism. There is an important difference between the two however, and it concerns mechanisms (and lack thereof). Natural selection has been directly and repeatedly observed to actually mold the genetic composition of a species following mutation. Irrespective of how prevalent "design isomorphisms" may be, a (non-human) intelligently designed mechanism has never been observed to alter the genome of any organism.
ID proponents have a lot of work to do before ID becomes anything more than inference.
Comment by Chris Harrison — July 17, 2007 @ 7:17 pm
July 17th, 2007 at 9:39 pm
Chris,
I absolutely agree that this is a linchpin issue. I will definitely address it in subsequent comments.
Comment by Joey Campana — July 17, 2007 @ 9:39 pm
July 17th, 2007 at 11:03 pm
Let's take a look at one ID scholar's prediction of junk DNA function, and see if you see what I see with the use of "design isomorphism." Forrest Mims III said in 1994 that:
Mims' use of design isomorphic logic is clear. He is talking about the fact that what appears to be junk in biological code doesn't appear so useless to one who knows a good deal about technological codes.
Note also that Mims offers guidance, a "˜heuristic prediction,' not an exact prediction. (Although, an interesting design isomorph between NOP time delays and genetic regulation here: [paper] [press] [blog])
More than a decade after Mims made this prediction, Miller, Dawkins, and other critics were still chiding ID theorists for thinking junk DNA had function, and there were people on both sides of the ID issue that clung tightly to the "no designer worth his salt" proposition.
As it turns out, Mims was right on two points. 1) Junk DNA was more than useless failed experiments of a random process, based on his use of ID's link between technology and biology, and design isomorphisms between coding languages. 2) Like Mims suggested, IBM employees, bioinformationists, and other computer scientists made a huge difference in junking the idea that junk DNA was all useless refuse of a random process. This was done by interfacing biology and technology in new and innovative ways that only computer engineers and biologists, together, could formulate and implement.
Returning to Eisenberg's biological-device proposal, the biology-technology connection was offering encouragement for researchers to seek functions in junk DNA. Andrew Reynolds points out another interesting historical thread in bioscience:
Is design isomorphism an independently verified auxiliary proposal? Yes, design isomorphisms are confirmed and their physical existence cannot be doubted. And their existence strengthens the theoretical connection between technology and biology, and this connection has yielded entire fields of study, including bioinformatics and systems biology.
So, what is the independently verified auxiliary proposition that informs ID's prediction of functionality in junk DNA? I think it is design isomorphism.
Comment by Joey Campana — July 17, 2007 @ 11:03 pm
July 17th, 2007 at 11:11 pm
I think it possible that major trends in design isomorphs, biological convergences, and TRIZ, all analyzed in a meta-comparison (perhaps in network configurations like systems biologists render), may one day hold the key to some very important predictions. Based on our current rate of scientific progress, this type of isomorphic comparison may be centuries or millennia away.
Comment by Joey Campana — July 17, 2007 @ 11:11 pm
July 17th, 2007 at 11:27 pm
"Junk DNA" was used as an argument against ID.
"Junk DNA" is confirmed by data to be more than failed experiments of a random process.
"Junk DNA" can no longer be used effectively as an argument against ID.
Also on the agenda, what is to be done with those auxiliary propositions that led to the false prediction that junk DNA was "nothing more than failed experiments in a random process"
There is much more to say, but I will let the discussion proceed from here.
Comment by Joey Campana — July 17, 2007 @ 11:27 pm
July 18th, 2007 at 12:13 am
The tie is still exceedingly tenuous at the genetic level, and the cobbled together nature of most gene networks are clearly not something we would expect from a human or human-like intelligence. This is not to mention the vast redundancy found in genomes (and the genetic code itself), nor pseudogenes, the latter of which completely confound intelligent explanation (especially processed ones).
It is expected that regulatory networks will be well-timed, given the spatio-temporal aspects of gene expression. There is no other way for expression to work if it isn't controlled by regulatory DNA. That's a few percent of the genome. You've got a lot more to account for.
Good find about the NO OPeration instructions though, these do seem to be analogous to, well, at least to the regulation of SRC-3/AIB1.
The ID prediction of a lot of function is still indistinguishable from strict adaptationism. Essentially they are the same. ID works from a intelligent design inference that must assume a human-like intelligence, while adaptationism bases its prediction off a (blind) design mechanism.
Which ID researchers are working on uncovering an ID mechanism? Without one, the prediction of "lots of function" is best taken as vindication of adaptationism.
Comment by Chris Harrison — July 18, 2007 @ 12:13 am
July 18th, 2007 at 12:19 am
Chris, why would the genetic code not be something expected of a human-like intelligence?
Comment by Bradford — July 18, 2007 @ 12:19 am
July 18th, 2007 at 12:21 am
No. Using the term correctly, as when Ohno first explicitly defined it in 1972 (as pseudogenes), junk DNA is a failed evolutionary experiment. As you seem to use "junk-DNA" as a synonym of "non-coding DNA", your comment is still not entirely correct. Some non-coding DNA has confirmed function. This is not news.
It never was. ID remains unfalsifiable.
Also on the agenda, what is to be done with those auxiliary propositions that led to the false prediction that junk DNA was "nothing more than failed experiments in a random process"
Random genetic drift, relaxed selective pressures, retrotransposition etc. aren't going anywhere. We've yet to find function for the majority of the genome. Don't get ahead of yourself.
Here's something:
http://www.pnas.org/cgi/conten...
Here's another: ID remains an inference, unsubstantiated by positive evidence, and lacking a demonstrable mechanism.
Comment by Chris Harrison — July 18, 2007 @ 12:21 am
July 18th, 2007 at 12:27 am
William:
The "design isomorphisms" are based on the observation that when humans design things they are sometimes analogous to what we find in biology. Humans tend to strive for efficiency (to predict functional DNA, ID's human-like design inference must assume this). Redundant codes are not efficient.
Comment by Chris Harrison — July 18, 2007 @ 12:27 am
July 18th, 2007 at 12:38 am
I'm not sure of that. The redundancy can protect against genetic errors. I'm doubtful that one could align a non-redundant code without also tampering with properties of basic cellular components. Do you have something in mind?
Comment by Bradford — July 18, 2007 @ 12:38 am
July 18th, 2007 at 12:40 am
Not so. Show the means by which cells would arise. Evolution would presumably take over from there. No need for intelligent input right?
Comment by Bradford — July 18, 2007 @ 12:40 am
July 18th, 2007 at 12:43 am
What do we need to worry about genetic errors for if they're all designed in the first place?
Comment by Chris Harrison — July 18, 2007 @ 12:43 am
July 18th, 2007 at 12:47 am
Love me some argument from ignorance.
A hypothesis is not falsified via the proof another one unless they are mutually incompatible. Are you saying that evolution is incompatible with ID?
Comment by Chris Harrison — July 18, 2007 @ 12:47 am
July 18th, 2007 at 12:48 am
This type of question basically asks if a designer could design perfectly why would perfection not be observed? It's a good question but invokes an answer focused on intent. That is beyond biology.
Comment by Bradford — July 18, 2007 @ 12:48 am
July 18th, 2007 at 12:52 am
No, but if you can specify conditions under which cells would arise, strictly as a consequence of unguided natural forces, you would narrow ID possibilities to alien seeding IMO. Let me just add that one could still envision a teleological process resulting from laws themselves but that would depend on some unknown factors.
Comment by Bradford — July 18, 2007 @ 12:52 am
July 18th, 2007 at 12:55 am
Then the assumption of human-like design falls apart. Either design isomorphisms are a valid assumption or they are not. Humans design with intention.
Comment by Chris Harrison — July 18, 2007 @ 12:55 am
July 18th, 2007 at 12:56 am
Agreed. The question is whether intent is discernible not whether it exists.
Comment by Bradford — July 18, 2007 @ 12:56 am
July 18th, 2007 at 12:57 am
The mind boggles.
First you say ID is falsifiable, but now you say it isn't, coz we can't rule out the aliens.
Comment by Chris Harrison — July 18, 2007 @ 12:57 am
July 18th, 2007 at 12:59 am
A resolution of the question of the aliens' origin could settle the matter. Time for bed. You have the last word tonight.
Comment by Bradford — July 18, 2007 @ 12:59 am
July 18th, 2007 at 12:59 am
With respect to the evolution of life, the question is most definitely whether it was designed with intent. This is the crux of ID, is it not?
Comment by Chris Harrison — July 18, 2007 @ 12:59 am
July 18th, 2007 at 1:12 am
Going back to one of Joey's posts that I somehow missed:
OK
If the ID inference of functional DNA is based on a positive correlation between organismal complexity and the amount of functional DNA, then the findings coming from genome size research throw a hell of a wrench into your spokes.
This is Gregory's 7th point from the original post:
From his "onion test":
The idea that an increase in the amount of DNA is proportional to an increase in complexity is entirely inconsistent with the known variability of genome size among closely related eukaryotes.
Comment by Chris Harrison — July 18, 2007 @ 1:12 am
July 18th, 2007 at 1:29 am
Chris Harrison:
This is an exemplary argument from ignorance.
Still, if you're saying, "If I Were The Intelligent Designer I Wouldn't Have Done It This Way", then feel free to create life in accordance with your superior design. We'll all watch with interest as to how it turns out.
Comment by stunney — July 18, 2007 @ 1:29 am
July 18th, 2007 at 1:41 am
How is that an argument from ignorance? Gregory was not saying that someone's inability to explain why an onion need 5x more non-coding DNA that humans proves that it's all non-functional.
No, that's not what I'm saying at all.
Comment by Chris Harrison — July 18, 2007 @ 1:41 am
July 18th, 2007 at 4:15 pm
Chris,
Let's clear this muddled thinking out of the way ASAP. I don't think playing tit-for-tat like this is helpful. In fact, I think it is unhelpful in key ways:
– ID and evolution are not mutually exclusive.
– It serves as a very effective distraction from productive discussion of the topic at hand.
From your other comments, I take it you don't subscribe to tit-for-tat either?
Comment by Joey Campana — July 18, 2007 @ 4:15 pm
July 18th, 2007 at 4:24 pm
Chris,
I am very much enjoying this discussion, thank you for your civility and desire to dialog.
I can appreciate the fact that you still think it is tenuous. Let's address that. What's the line of relevance for you? What if we found three isomorphs at the genetic level? Would the biological-technological connection then be tenable?
Most of the conceptual tools of science are unfalsifiable. That ID may or may not be falsifiable is not as much of a concern to me as finding helpful conceptual tools.
I'm interested in finding out why it is that ALL ID scholars made a correct heuristic prediction, whereas scholars pursuing views of blind evolution were divided among various degrees of right and wrong. I want to know if there is anything here that might be helpful to a working biologist.
Not all selectionists and adaptationists thought searching for function was a helpful avenue of research. Based on what he said, Dawkins certainly did not give me the impression that he thought that searching for function was a helpful avenue of research.
What would constitute positive evidence for ID, and the use of the idea of a "mechanism" by ID, are extremely complicated issues that go far beyond this discussion. They are intriguing questions, and I can understand why these issues may make someone throw in the towel on ID.
In most online forums, the questions you bring up derail helpful discussion. For my part, I will be sticking to the present discussion about Junk DNA and ID's auxiliary proposition, and I value your input and would prefer that you continue with us on our present topic.
Unless the code is intended as a robust foundation for an adaptive, modulating program that controls the assembly of functional products. In that case, redundant code could be used to provide stability where necessary, and provide wiggle-room for changes in the regulatory code.
We worry about them because they might kill us, but that's just my opinion. Getting back to our topic, when writing an evolving code, a backup can be used by an error-correction mechanism to fix a terminating error, and allow functionality to continue.
Comment by Joey Campana — July 18, 2007 @ 4:24 pm
July 18th, 2007 at 4:29 pm
Bradford said:
Then Chris said:
If life was designed, it was designed to function, i.e. live and reproduce. Precise statements about intent are difficult, but I think the desire of function and reproduction is a safe inference.
Comment by Joey Campana — July 18, 2007 @ 4:29 pm
July 18th, 2007 at 4:32 pm
I'm listening very carefully.
I'm not pretending like I have a testable explanation yet. A *possible* explanation is that non-coding DNA was designed to allow modulation.
A (one) universal function for non-coding DNA? Who thinks that? I'm going to give Gregory the benefit of the doubt here and assume he's saying, "The onion test is a simple reality check for anyone who thinks 'all non-coding DNA has function(s)'." I do not know a single person that is proposing that all DNA is currently functioning. Who might Gregory be speaking about?
The problem of the non-correlation between genome size and relative complexity is a wrench in everyone's spokes. No spokes are immune at the moment. Why do some species have a remarkably higher amount of non-coding DNA than other species of similar complexity? Aren't these problems for all perspectives on biology? I would think that anyone saying they have a correct answer, is actually offering a post hoc explanation at best. Do you know something I don't that solves this?
I think that stunney might be interpreting your presentation of the "˜onion test' as:
If you don't know why an onion has five times more non-coding DNA for this function than a human, then you've got a wrench in your spokes, and so your proposal is wrong.
If this was Chris' intended use of the onion test, then this certainly looks like an argument from ignorance to me.
stunney, did I get you right?
Chris, what is your point with the "˜onion test'? Were you just giving us notice of an issue to be dealt with down the road?
Comment by Joey Campana — July 18, 2007 @ 4:32 pm
July 18th, 2007 at 7:04 pm
Joey's statement might appear imprecise at first glance but is it any more imprecise than attributing selective value to a function that confers enhanced reproductive fitness?
Comment by Bradford — July 18, 2007 @ 7:04 pm
July 18th, 2007 at 9:32 pm
Joey,
I don't quite follow your use of "tit-for-tat" here.
My point about "giving a point to ID" or "taking one from evolution" was in reference to the fact that adaptationists have predicted a lot of function a long time before ID had its genesis. If we are to concede that ID can in fact predict "lots of function", do we give points to both ID and adaptationism if this turns out correct?
Comment by Chris Harrison — July 18, 2007 @ 9:32 pm
July 18th, 2007 at 10:03 pm
Joey,
You're welcome. Thank you for being a reasonable debater as well. I should admit that I've a difficult time reading most ID proponents (e.g. Luskin) for more than 30 seconds without rolling my eyes or laughing out loud. This discussion has been fun (still not an ID proponent though). ; )
[quote]I can appreciate the fact that you still think it is tenuous. Let's address that. What's the line of relevance for you? What if we found three isomorphs at the genetic level? Would the biological-technological connection then be tenable?[/quote]
Three specific examples? Like, what regulates the SRC-3 coactivator, plus two other ones? No, this would be rather unimpressive still. There are a lot of nucleotides out there to account for.
I should have bit more to say about design isomorphism's ability to serve as an auxiliary assumption for ID in a bit. Things are still blinking around in my head right now though.
Hmm. It seems quite plausible to me that (you're going to love this), since the ID movement was initiated by a handful of Christian apologists, the IDists that predicted a high amount of function saw an obvious clash between "junk" and the Christian deity. In any case, it is not clear that there was a uniform reason why IDists have claimed most non-coding DNA is functional.
That's quite fine. Dawkins doesn't do research in genome biology anyway. There are thousands of evolutionary biologists who actively scan genomes for function. Their findings are published all the time.
.
Positive evidence for intelligent design would be just that. We would observe the design process, just as we consistently observe the evolutionary process. Why are we unable to detect this process? And yes, this is definitely the main reason ID is not accepted by the myself or the vast majority of evolutionary biologists. No one would accept evolution if it wasn't for the fact that, well, it just happens. IDists need ID to happen.
I should be posting more on this as I said. Perhaps not tonight, though.
Yes but under the IDist position, whether or not an organism is changed is a decision left up to an intelligent agent. If we are to allow the designer the ability to modify genomes at whim, there is no reason to think a redundant code is necessary for this to happen. You don't need to allow buffering against mutations when the mutations themselves are specifically designed.
Good. But when humans write an "evolving code", they are not directing the mutations, only the selective pressures (presumably). ID claims that yes, the IDer directs mutation.
Comment by Chris Harrison — July 18, 2007 @ 10:03 pm
July 18th, 2007 at 10:36 pm
Joey,
Recall your words here:
I understand this to say that the complexity of an organism is correlated with an increase in genome size. So using Gregory's onions, the genome of Allium altyncolicum is 7 pg (about twice as much as the human genome). According to your words above, Allium altyncolicum should be roughly twice as complex as humans.
I think we both agree this is not the case.
Now, an onion closely related to A. altyncolicum (in the same genus), Allium ursinum, has a genome that is 31.5 pg, or 30,807,000,000 (that's almost 31 billion) base pairs, compared to the other onion's 6,846,000,000 basepairs, and our measily 3,423,000,000 baepairs.
Looking at just the two onions, is Allium ursinum 5 times more complex than Allium altyncolicum?
Allium altyncolicum is on the left here, with Allium ursinum on the right.
I'll repeat myself here:
The idea that an increase in the amount of DNA is proportional to an increase in complexity is entirely inconsistent with the known variability of genome size among closely related eukaryotes.
My point was the paragraph that directly precedes what I'm quoting from you here. This (the decoupling of C-values from complexity) is perhaps very relevant to the putative reason ID predicts "lots of function". More to say about this later.
I didn't mean to say the variability in genome size, and its detachment from organismal complexity was explained by any one model. They don't call it the C-value enigma for nothin'.
You should definitly read some of Gregory's publications, because he researches the variability and evolution of genome size. Also, I just finished his book, and I highly recommend it to anyone interested in genome biology.
You might have "got stunney right", but stunney didn't get me! I brought up Gregory's onion test as a response to your bit about how the complexity of humans suggest more function. I think this should be clear by the time you get to this part of my comment however.
Comment by Chris Harrison — July 18, 2007 @ 10:36 pm
July 19th, 2007 at 2:18 pm
In a discussion of ID and evolution, I don't think it is the case that a point for one is a point against the other. I do not subscribe to this line of reasoning w/ ID and evolution, except in a very few cases that extremely narrow and well-defined.
Yes, on my scoresheet ID gets a point for offering a valid heuristic prediction. Does adaptationism get a point? Adaptationism gets a point on my scoresheet after we figure out why an adaptationist like Richard Dawkins did not think that conservation meant there might be function. Saying that Dawkins doesn't do research in genome biology does not moot my challenge. His book, The Selfish Gene, was cited by geneticists, including Crick and Orgel. Even if he is not a geneticist, geneticists saw his ideas as relevant and took them serious enough to cite him in the relevant peer-reviewed literature and expound on his ideas.
Comment by Joey Campana — July 19, 2007 @ 2:18 pm
July 19th, 2007 at 2:20 pm
You're welcome. But just so you know, I don't see this as a debate; I see this as a productive and friendly discussion among reasonable individuals.
Is there a line of relevance for you? 1, 3, 4, 8, 10 . . .?
Comment by Joey Campana — July 19, 2007 @ 2:20 pm
July 19th, 2007 at 2:26 pm
You are aware that there is a diverse variety of IDist positions, right? Some allow the designer the ability to modify genomes at whim, some do not. In my understanding of the concept, front-loading would not allow for the idea that the designer can modify genes at whim, but allows for a genome that might buffer against specific mutations for a future purpose.
Comment by Joey Campana — July 19, 2007 @ 2:26 pm
July 19th, 2007 at 2:35 pm
My proposal regarding the human body and design isomorphism is entirely detachable from the C-value enigma, polyploidy, etc. I'm talking about the human form, and someone like Dawkins saying that 60 million functional bases are enough to constitute the human body. I'm not talking about onions, or anything else. My proposal is not dependant on the idea that the complexity of an organism is correlated with an increase in genome size.
Please allow me to break down my proposal a bit more, so that I can make clear that C-value is detachable.
I'm talking about requisite information. There is no comparison between organisms going on here. My proposal touches on the amount of information necessary for the human form to have the following functions:
1. Specify the structure of objects (i.e. proteins, tissues, organs)
2. Construct objects
3. Troubleshoot and Repair objects
4. Replicate objects
General knowledge concerning the amount of information required to specify, construct, repair, and replicate objects is from fields such as computer science, information theory and industrial engineering. Computer automation of production processes brought to the forefront a new understanding of the sheer volumes of information that is necessary for automated construction of an object. The fact that cells are self-replicating increases the amount of necessary information.
Calculating the amount of information necessary to have self-repairing objects is currently beyond our abilities, but systems biology, epigenetics, and biosemiotics is breaching that ground.
My proposal is dependent on the idea that about 60 million base pairs (3 billion X 2%) are not even close to the amount of information needed to specify, construct, repair, and replicate all of the features of human function and development at the levels of subcellular, cellular, tissue, organ, and organ systems. This is a quantitative claim, not a comparative claim. Comparing relative genome sizes is unnecessary to make this proposal. Inferring from what we know about automated construction processes, 6 x 10^7 base pairs is not enough information to account for functions 1, 2, 3, & 4 above. With reference to my proposal, C-value enigma neither adds nor detracts, neither procedes nor precedes, neither negates nor supports.
How does the C-value enigma impinge on the idea that 60 million base pairs is not enough information to specify, construct, repair, and replicate the intersystemic complexity of the human body? Please help me see. Perhaps you are clearly stating, but I am not understanding.
Comment by Joey Campana — July 19, 2007 @ 2:35 pm
July 19th, 2007 at 4:38 pm
Joey,
This is interesting. We can disregard the fact that many adaptationists have predicted "not really junk" because Dawkins alone didn't jump on that bandwagon? So if I can find one ID proponent who is OK with "junk", then ID doesn't get that point after all?
That is silly. As I've been saying this entire thread, it does not matter that people are able to predict function/nonfunction. The focus is on whether or not this prediction is tenable under a given assumption. I can't say why Dawkins says what he says, but adaptationists are able to predict function given the observed nature of selection.
Of much relevance though, is this article, which claims that "junk-DNA" follows from the ID perspective that draws analogies to human software design. This ID article takes the perspective that design isomorphisms in fact suggest that "junk" should exist. This is, obviously, the exact opposite of what you suggest DIs tell us about non-coding DNA.
The Panda's Thumb has more.
I need to better familiarize myself with the concept of design isomorphism, as well as take a much closer look at specific examples. I'll try to get something up in the next couple of days.
My understanding of front-loading is that it does not necessarily preclude additional modifications, only that it provides the meat of what will be needed. I've not researched it much though.
Comment by Chris Harrison — July 19, 2007 @ 4:38 pm
July 19th, 2007 at 6:11 pm
Chris, there is no absolute, black and white position that demarcates the differences between IDists and their critics. At best we can look for predictions that relate to percentage ranges.
I can't help wondering where all the conventional thinking types went who thought that significant percentages of non-junk were absurd.
Comment by Bradford — July 19, 2007 @ 6:11 pm
July 19th, 2007 at 6:19 pm
I did not state it explicitly because I assumed that you would recognize it, but the claim that the complexity of an organism requires a certain number of functional nucleotides is tied to both to C-values, and ID's claim that most non-coding DNA is functional. I have a hard time believing that you're not seeing this connection. (I'll address your points about "what's needed to get a human" after this.)
Your proposal that you've outlined above, that there must be a certain amount of functional DNA to satisfy the informational complexity of an organism is a given. You're not going to get a human with a few thousand basepairs. The more interesting thing is how your proposal relates to C-values and to your previous claim that most non-coding DNA is functional. Something doesn't add up between them. Let me explain with the onions.
The genome of Allium altyncolicum contains 6,846,000,000 basepairs, which, irrespective of the actual percent of functional DNA therein, must be enough to make this plant do what it does. Let's say that every single one of those nucleotides is functional, and absolutely critical to the plant. This is of course ridiculous, but given this ridiculous assumption, consider the closely related Allium ursinum, with its 30,807,000,000 basepairs — roughly five times as many.
Working from an ID (or a strict adaptationist) position that the majority of non-coding DNA is functional, Allium ursinum should require roughly five times more DNA than Allium altyncolicum. The other option is that no, these onions only need about the same amount of functional information; the one with the larger genome contains a huge amount of non-functional DNA that is not required by the plant.
As the "larger" onion is definitely not 5 times more complex than its "cousin", the IDist (and strict adaptationist) positions are untenable.
As you admit this is a quantitative question, forgive me for not being persuaded here without any quantitative evidence. I do not concede that 60, 100, 1000 million nucleotides is not enough to get a human.
Also, there are relevant genomic processes that we must consider when trying to say "we need at least X many nucleotides to get a human".
Alternative splicing is a big one, as it allows one specific mRNA to be spliced into a variety of forms by leaving out certain exons or by recognizing alternative splice sites. Citing Gregory's book (and references therein), recent research suggests somewhere around 60% of human genes involve alternative splicing, with an average of 2-3 transcripts per gene.
Comment by Chris Harrison — July 19, 2007 @ 6:19 pm
July 19th, 2007 at 6:27 pm
William,
The problem is that IDists are able to draw two conclusions from design isomorphisms, both of which seem valid. One is that non-coding DNA should be functional, and the other is that it shouldn't, and that we should expect design to result in junk. This makes DI heuristically empty.
Comment by Chris Harrison — July 19, 2007 @ 6:27 pm
July 19th, 2007 at 7:49 pm
Both design and non-design approaches can be heuristically ambiguous with respect to function. A design approach entails a somewhat broader perspective though. Non-design is limited by present conceptual perspectives about natural processes. A teleological approach incorporates an added element. It may be superfluous to results attained but on occasion may yield otherwise unforthcoming insight.
Comment by Bradford — July 19, 2007 @ 7:49 pm
July 20th, 2007 at 3:02 am
Chris,
Dawkins was not alone. Neo-Darwinian Ken Miller was also hangin' tough against the prediction of more functional DNA.
Besides, Dawkins is not some nobody in the adaptationist camp. The man's mind is completely conformed to the adaptationist view. I remember Larry Moran once took Dawkins to task for how Dawkins so flippantly dismisses the random aspects of evolution. I'm sure you've read some of Dawkins' books where he chronicles his reverence for natural selection. I saw a video where he further explicates his veneration of natural selection into a veritable Hallelujah chorus of praise. His emails to ID scholars that have been posted on the internet are especially revealing of his adulation of natural selection. Dawkins clings to Natural selection as tightly as any religious adherent to their holy writ. No, Richard Dawkins is not an insignificant outlier in the adaptationist camp. Before I give a point to the adaptationist camp, I want to know why Oxford's Simonyi Professor of the Public Understanding of Science misunderstood the science of natural selection, and why the virtual champion of Natural Selection broke ranks.
If it was found that an ID scholar said that 98% of the human genome was wasted space, and no further function would be found, then I would give up ID's point. I would then find out why the ID scholar made that prediction, and in what way their view diverged from other ID theorists. And I would not pick the point up and give it back to ID unless it was found that the ID loner used reasoning that was radically different from other ID theorists who were saying that 98% of the human genome wasn't wasted space. If this happened, the ID loner who predicted 98% wasted space would be in his own category, and no point awarded to the solo shot.
You are entitled to your opinion. I find it sillier that you think that a group of scholars invoked their deity and got a uniformly correct heuristic prediction.
I disagree with you here. I think it does matter.
It's only the exact opposite if one is purposefully trying to misunderstand what isomorphic logic might lead us to think.
Used or unused extensible stubs are the reason I have made no exact predictions with design isomorphic logic. As I understand it, right now isomorphic reasoning can only lead us to think that we should continue looking for function.
Comment by Joey Campana — July 20, 2007 @ 3:02 am
July 20th, 2007 at 3:08 am
Chris,
Maybe this is why your connection is eluding me:
I think I'm going to hold out for now on how the C-value enigma might impinge on isomorphic reasoning. When we know more, I'll proceed with caution.
I can't find where I claimed such and I don't remember making this claim. JAM was incessantly taking me to task for not making a claim you said I made:
Where did I say that most non-coding DNA is functional?
I'm not working from that assumption, are you? Since I don't think you are, let's put that baby to rest.
No, no. Please forgive me for not providing quantitative data and estimates concerning the complexity of all known specification, construction, troubleshooting, repair, and replication processes in humans among the intersystemic levels of cells, tissues, organs, and organ systems. I was hoping you could extrapolate due to my lack of NSF and NASA funding to bankroll my megalab to crunch these numbers for you.[/sarcasm]
I think you know what I'm getting at here with my isomorphism argument. In order to have a productive conversation in a forum like this, I think some benefit of the doubt has to be given. If you don't want to work with me on this point, we can move on to another.
If you choose the first option in your list, I think you will be wrong. Didn't ENCODE already show that more than 60 million nucleotides are functional?
The problem with your logic is that ID scholars don't agree, and they offered good heuristic guidance despite your apparent confusion.
Yes, the design isomorphism of signal amplification by alternative splicing cannot be forgotten. Another reason I have not offered an exact prediction.
Comment by Joey Campana — July 20, 2007 @ 3:08 am
July 20th, 2007 at 3:13 am
Chris,
So let's get on with it, shall we?
Let us come directly to a key point with design isomorphism and genetics: What are the conceptual resources that can allow us to continue the progress of bioscience? What current knowledge can help us conceptualize potential knowledge? What can we use to hypothesize about the still unknown inner workings of life?
To answer this, we must first ask: What group of entities are 1) understand, and 2) works in ways similar to the ways that life does?
In discussing these questions, I'll use DNA replication as our discussion point, since we are talking about genetics here.
On a non-derivative level, we have the conceptual resources of chance and necessity. Although these factors are necessary to understand life's inner workings, they are not sufficient to conceptualize a model of a biochemical process. The inner workings of DNA replication do not work like the events of rolling a dice or flipping a coin, etc. The inner workings of DNA replication are not like how gravity or friction operates.
How about physico-chemical properties? Again, these factors are necessary to understand life's inner workings, but cannot conceptualize a model of a biochemical process. The inner workings of DNA replication do not work like the events of electron sharing, and understanding the mass of a neutron does not help us conceptualize a biological process so that we can design an experiment to test our hypothetical process. Hubert Yockey puts it like this:
How about astrophysical processes? Not helping in the genetics lab.
How about geological processes? The inner workings of biochemical processes are not similar enough to the hydrologic cycle, etc to be useful in the manner needed.
How about mental abstractions like mathematics and logic? Also necessary for bioscience, and helpful for honing and validating proposals, but these abstractions are not actually directly producing models for us.
The above conceptual resources inform a proposal, and provide boundaries, but generally cannot be used directly as brainstorm templates from which we might work out proposed models for how an unexplored bioprocess works.
Chris, what conceptual resources did scientists use to generate models of DNA-related processes, when these were first being elucidated?
Comment by Joey Campana — July 20, 2007 @ 3:13 am
July 20th, 2007 at 6:49 am
I've pointed out that in exchanges a few years ago, prior to a point when function was identified for some of what was considered Junk DNA, it was not uncommon for an IDist to face ridicule flowing from deity based logic of critics. The argument being based on the comparison of perfect design to what was depicted as a biological example of a polar opposite- DNA which was almost all junk. What kind of God would do that? Fill in the blank with your favorite put-downs.
Under either a teleological or non-teleological outlook there are reasons to doubt that genomes consisting largely of non-functional DNA would remain intact over geologic time eras; there being no selection effect.
Comment by Bradford — July 20, 2007 @ 6:49 am
July 20th, 2007 at 6:58 am
Good question. As soon as it was apparent that DNA contained coding sequences of nucleotides, model logic became clear. When you have encoding sequences you need a decoding or translating mechanism. So even if you have not yet identified mechanisms related to a translation function, you have a paradigm in place guiding the search. Interestingly the paradigm is associated with an intelligent design approach; for where do we find symbolic coding systems? Generated in the minds of the same species that will discover the translation function.
Comment by Bradford — July 20, 2007 @ 6:58 am
July 20th, 2007 at 1:55 pm
Then all I need to do is find a prominent IDist who, for some good reason, has no problem with the existence of junk, and according to you, we won't give ID a point if most non-coding DNA is functional. Who wrote this?
I will repeat that this is silly, because even though Dawkins is a seen as a significant proponent of adaptationism, it is not about what one person or another says. It is about whether or not their words are backed up by natural selection/design isomorphism etc.
I've not seen you give any reference as to why Dawkins' thinks 98% of our genome is extraneous. The quote you gave previously is almost 10 years old, so I have to think the man has changed his mind since then.
Evolutionary biologists are doing that anyway. Papers are published every month that reports on function/nonfunction of non-coding DNA. Design isomorphism will need to do a little better than merely suggest "we should continue looking for function".
Joey the first paper is about the only one of relevance here, although the others are interesting. It looked only at small genomes, for which there is a roughly positive correlation with complexity. There is no "C-value paradox" in prokaryotes, for example, as their genomes are small and directly correlated with gene number. Don't forget about the two onions either.
Here's an image showing the range of genome size that covers all major groups. The C-value enigma is real, and there is a lot of research going on right now investigating it.
Indeed I am confused. First you were interested in explaining why all IDists have predicted lots of function for non-coding DNA, and you followed that up with Mills' obvious design isomphism-influenced logic, but now you are saying that IDists are not all in agreement here. And you also tell me that you are not convinced that most non-coding DNA is functional.
If the heuristic guidance put forth by design isomorphism is unable to say whether or not non-coding DNA should be functional or not, I fail to see why it is even worth talking about. We are already looking for function in non-coding DNA.
I do not know. Arguably they reverse engineered the process while assuming replication actually does something. Perhaps they put themselves in the position of "If I wanted to replicate DNA, and this is what I have to do it with, how would I do it?"
Joey I quite realize reverse engineering is applicable and helpful when investigating biology. As to how this relates to genetics specifically, I cannot say. The DNA responsible for the replication process is encoded in the 1.5% of our genome that encodes protein. We were interested in non-coding DNA. If I were to suggest avenues of research for you, I'd be hitting the books to understand the mechanisms whereby genomes acquire agenic DNA, be it processed pseudogenes, retroviral infection or intronic insertion.
William:
By a few years ago, you mean the 1970s, right?
Comment by Chris Harrison — July 20, 2007 @ 1:55 pm
July 20th, 2007 at 3:30 pm
Oh no, no, no. The 90s is more like it and I recall a research biologist as late as 2003 or 04 who argued that suppositions about junk were unlikely to substantially change.
Comment by Bradford — July 20, 2007 @ 3:30 pm
July 20th, 2007 at 7:27 pm
Chris to Joey:
I realize you're arguing against somebody else's scarecrow (straw man), but can you offer anything specific to MY arguments? I have not suggested that nucleotides themselves *must* be functional, much less that "every single one" of them must be functional. Nor have I suggested that function for non-coding DNA *must* be "absolutely critical" to the organism. You're quite right that it's ridiculous, but since I haven't asserted these things, let's just leave them out.
Here's my view of alliums, since you brought them here: First, despite being in the same family, your example of chives and bear garlic (a.k.a. ramson) are different plants inhabiting different ecologies and facing different selective pressures. It isn't the least bit surprising that different varieties of allium in differing conditions will respond to selective pressures in various ways, using pretty much every genomic trick available to them by which to deal with pest attacks, drought, excess moisture, fungal invasions, diminished sunlight, shortened season, competition, etc., etc., etc. Alliums represent ~1250 species, one of the largest plant genera known. You could not get more oppositional exemplars as the two you've offered.
While all alliums are rich in vitamins, iron, sulfur compounds (health maintenance and healing properties), the wild alliums – those are the ones with what you consider to be "too much" genome (and a great many "civilized" humans consider to have way too much flavor) – are particularly useful in traditional medicine due to a host of coincident flavonoids and increased expression of some of the alliums' most powerful sulfur compounds.
Alliums (particularly the strong, wild garlics) have been used topically as antibiotic, systematically as general tonic, as antibiotic for bacterial infections and for treatment of several types of fungal infection. Traditional medicinal uses of allium are blood purification, control of acne, reduction of blood pressure and cholesterol, reduction of inflammation, easing of rheumatism pain, and to aid in blood clotting. Tests confirm antibiotic activity against candida, cholera, staphylococcus, salmonella, dysentery and typhus. It clears phlem, thus has been useful to treat colds, bronchitis, pulmonary tuberculosis and whooping cough. Some of its compounds are currently undergoing testing for use in treating lead poisoning, some carcinomas and diabetes.
Alliums are among the oldest of culinary plants used in a wide variety of native cuisines particularly in warm climates where they are useful in controlling bacterial contamination of foods. They've been wildcrafted and carefully cultivated since before grains were domesticated. They have been bred and cross-bred, hybridized and re-hybridized into literally thousands of useful varieties of garlics, onions, chives, scallions and shallots, and preserved in tinctures, wines, liqueurs and oils as one of the oldest continually used general purpose medicines on earth.
We have recently come to understand that "most" (according to researchers) of the difference between people arises from the number of gene copies they have in their genomes – quite of few of which are indeed expressed in some way or they wouldn't count, would they? Plants will duplicate their entire genomes under stress much more readily than animals will (animals usually just duplicate genes and their associated sequences), and some of the most useful plants have genomes that have duplicated more than once. Some plant alkaloids in one variety of a plant are expressed in tens or even hundreds of times more concentrated form than close relatives (and even direct descendents) bred toward cultivation for other traits. Like poppies, for instance. Or cannabis.
Thus despite your obvious belief that my mild-mannered but pretty little purple chives growing between the rosemary and thyme and bordering the calla lilies are somehow more "genomically conservative" (like they're a "purer" breed of plant or something? Plantism?) than those precious wild ramps that carpet the bottomland marsh in early spring is in my view completely misguided. The ramps are worth their weight in silver (literally), but you can't grow them as a crop like you can ginseng (worth its weight in gold). You've got to "encourage" a habitat and harvest with care towards maintenance. And there's honestly no good way of preserving them in all their ramp-ish glory. But there are ramp festivals every spring all over these mountains, and your system just ain't ready for spring unless you've eaten all you can find.
You just won't be convincing me by quoting Brayton or Gregory's second hand arguments that the genome of those ramsons is mostly "junk" just because my bred-for flowers border chives are mild and practically flavor-free with their much smaller genomes. A lot of that multi-duplicated genome is expressed. That's what gives these wild alliums their seriously pungent, tear-causing taste and their high value as medicinals.
In order to convince me it's just "junk," you'd have to demonstrate that specific research has established this beyond shadow of doubt. Since there is in fact a large difference between border chives and wild ramsons, it sure seems to me that simple comparison of genome size doesn't establish anything other than a difference in genome size.
Comment by Joy — July 20, 2007 @ 7:27 pm
July 20th, 2007 at 8:03 pm
Chris,
Thanks for the link to the C-value illustration, this was how I imagined a spread would look like.
No. You would have to find an ID scholar that said that 98% of the human genome was wasted space, and no further function would be found.
That is my question concerning Dawkins' reasoning. I'm glad to hear we're interested in the same thing.
So you're admitting that someone can legitimately back up their words with design isomorphism?
I'm just kidding, I don't think you are convinced.
Right. I don't know his reasoning. As far as I know, Dawkins somehow drew his conclusions directly from natural selection, and his reasoning is sounder than everyone else using the natural selection view who expected more function. Are you proposing that since I don't know the argument of the Public Understander of Science, that I should give adaptationists a point? Isn't that an argument from ignorance? [/tongue in cheek]
Good grief, I hope he changed his mind. For the sake of our conversation here, I would even graciously give Dawkins the benefit of the doubt, and assume that he thinks his former mind on "wasted space" was putrid filth.
Awesome. I for one am very glad that real scientists did not pay much attention to the Simonyi Public Understander of Science.
Oh, Chris, my friend, you will see.
For the record, I said that "stubs are the reason," but I meant that stubs are a reason.
Trust me, I will not.
Your new confusion is my fault; I did not specify which subjects were connected with which predicates. Let me try again:
The problem with your [attempted use of ID-based] logic is that ID scholars don't agree [with your use], and they offered good heuristic guidance despite your apparent confusion [of what ID entails].
Please excuse my hesitation, I like to have data before I make a prediction.
I think isomorphism is worth talking about because it could yield guidance in other areas of research, and indeed it has. Hang tight, more of my suspicions will be disclosed in my next few comments.
In my understanding, all DNA is replicated. That's beside the point.
I appreciate the research suggestions. I'm more interested in epigenetics, but down the road, maybe junk DNA will become more relevant for my biological forays.
Ah, yes! Reverse engineering. You are like a magnanimous king of old who brings good gifts to others! Reverse engineering, long used to discover the inner-workings of man-made machines, was and still is used to understand the inner-workings of life.
Conceptual models are important too! Let's see what the conceptual models were . . .
Comment by Joey Campana — July 20, 2007 @ 8:03 pm
July 20th, 2007 at 8:32 pm
Chris,
Let's hear from John Maynard Smith a brief description of which conceptual models were helpful when the function of DNA was first investigated, and what was not:
Coding analogy, a design isomorphism. ID's conceptual link between technology and biology, and design isomorphism, is holding pretty tight at the genetic level, from the beginning of its investigation to today.
Yockey again helps us, by aiding our understanding that design isomorphic logic applies at the genetic level:
The genetic codes are not codes in a loosely analogous way. There is an identity. The genetic codes are codes in an isomorphic way. Is the conceptual link between biology and technology at the genetic level becoming clearer yet?
Which scholars are standing shoulder to shoulder? Biologists, computer scientists, engineers, physicists and mathematicians. Any indications of design isomorphism? Seems awfully suspicious to me.
Have design isomorphisms even bothered to show up at the genomic level?
Let's have an informal muster:
– 'Coding' in languages and computers are inseparably tied by an isomorphic conceptual link to the genetic "code"
– 'Transcription' functions are used by taking the scripted code of DNA syntax and putting it into the scripted code of RNA syntax
– 'Template modeling and functionality' is an effective means of producing many copies of the same structure, and the transcribed code that is read off the DNA is an mRNA template
– 'Template reuse and materials recycling' is an efficient way to reuse templates to make multiple products from one template, and multiple templates from the same materials; this is the manner in which mRNA templates are reused for multiple protein products, then RNases break down the templates for recycling nucleotide materials to be made into other templates
– 'Translation' functions are at work when the scripted code of RNA syntax is put into the product code of amino acid syntax
– 'Finishing rooms' complete the gene's final protein product, and this work is done inside the chaperonin
– 'Production assembly regimes' and 'coded-program control systems' are working with the information coded in DNA, and are conceptually very similar to processes in an automated factory, and in automated data-handling systems
– 'NOP time delays' working in genetic regulation
– 'Communication signals' in the genetic networks are being explored by by epigenetics and systems biology
– 'Signal amplification' by alternative splicing
– 'Intra-textual Caesar ciphers' in the genome's ARF's
– 'Transposition ciphers' are at work in the nucleosome code
– 'Data compression' is used by cells to increase efficiency and facilitate replication.
– 'Zip codes' help direct proteins to targets, including regulating gene expression, and fibroblast gene expression programs
– 'Input-output regulators' in production controllers work like 'quorum sensing' genetic production regulation in microorganisms
– 'Boolean logic' in gene regulatory regions functions much like a logic gate in computer languages
– 'Zippers' are conceptually at work in the DNA double helix, which is "unzipped" for replication and transcription
– 'Circuitry' has some interesting isomorphic features in genetic networks by the use of tandem control switches and output amplifiers. Also see "An Introduction to Systems Biology: Design Principles of Biological Circuits," by Uri Alon
– 'Network configurations' of living organisms are being mapped by methods of systems biology, which tackles the mapping of biological networks and biological circuits. E.g. "Systems Biology: Properties of Reconstructed Networks," by Bernhard O. Palsson
– 'Troubleshooting process-schemas' are at work to initiate repair mechanisms. (These could operate like checksum's, SED-DED's, and other code-based models)
– 'Repair schemas' are at work to fix errors in the DNA. (Channel coding is a possibility to be considered.)
Chris, I'm going to have to disagree with your idea that there is a loose connection for design ismorphisms at the genetic level. When I look at the data, there is no absence of isomorphism at the genetic level. I see design isomorphism as strong conceptual resources and models.
Comment by Joey Campana — July 20, 2007 @ 8:32 pm
July 20th, 2007 at 8:39 pm
Chris,
This is a crucial point: Which non-isomorphic models of error correction does Natural Selection, or neo-Darwinism, or Neutral Theory yield for geneticists exploring unknown bioprocesses? I don't think they can, not as they currently exist. RM+NS, NT, and the Modern Synthesis can do other things in the biosciences, but a major sounding board for proposing models of unknown processes is design isomorphism. (Next to raw data, perhaps the most useful conceptual models are from isomorphic resources.)
NAS member Phillip Skell helps us wrap our minds around this limitation. (The full article is available here.)
Let's return for a moment to something I said earlier:
Chris, how are we doing with design isomorphism? Please share your thoughts.
Comment by Joey Campana — July 20, 2007 @ 8:39 pm
July 20th, 2007 at 9:06 pm
Joy:
Joy the purpose of the to Alliums is not to prove that one's genome is full of junk. As I've already explained, the purpose is to show how decoupled organismal complexity is from C-values. That's nice that the wild "big genomed" onions are more flavorful/have more sulphur/etc, but these differences probably do not require a five fold increase in DNA.
Also, Gregory is not arguing that A. usinum's genome is junk, and who the hell is Brayton?
Comment by Chris Harrison — July 20, 2007 @ 9:06 pm
July 20th, 2007 at 9:19 pm
: ) OK Joey. You can have your genetic design isomorphisms.
Now what do we do with them, besides continue to discover them? What does their presence suggest? How, since they are tied purely to human design(technology), are they able to vindicate ID, which argues for non-human design?
Comment by Chris Harrison — July 20, 2007 @ 9:19 pm
July 20th, 2007 at 9:38 pm
Chris:
As to where to go from here?- I'd have to think about that. But your depiction is not precise. ID infers intelligence and purposefullness which has a broader meaning than simply non-human design. Some, if not all, the citations make a prima facia case for that.
Comment by Bradford — July 20, 2007 @ 9:38 pm
July 20th, 2007 at 10:19 pm
Reviewing the last portion of this thread, I can't help but feel like we've lost connection with intelligent design itself. It appears as though we're just drawing out analogies between human technology and biology, and I fail to see why this relevant to ID as an alternative/extension of evolutionary theory.
Comment by Chris Harrison — July 20, 2007 @ 10:19 pm
July 20th, 2007 at 10:57 pm
Chris:
Not being a biologist, I had to go look that up. And I will agree with you that C-value is an obviously erroneous means of calculating the "complexity" of any organism, junk or no junk. Since we've enough proteins from a mere ~22-25,000 genes to do just fine in this world. Most other "complex" organisms in and out of the food chain have similar or identical proteins (or building blocks thereof), which makes them quite nutritious (though some have 'extras' that prove harmful). Number of proteins obviously doesn't determine "complexity."
Apart from the protein coders and associated machinery (since number of gene copies apparently affects expression), there is nothing in this C-value to demonstrate that non-coding DNA isn't functional on some level for the organism (and/or its environmental niche, since selection does happen). It just demonstrates that C-value doesn't determine number of proteins or "complexity" of the organism.
You may have missed my point, though I did try to make one. A five-fold increase in DNA over the course of evolution for ramsons says things about ramsons that the supposedly "efficient" genome of Chinese chives (and their many hybridized varieties culinary and presentational) doesn't say about chives (or Vidalias or elephant garlic or garden leeks or red shallots or…).
There are a number of families of plants and animals telling us we don't understand genomes very well. As we learn more about them and what they do (in addition to coding for proteins and expressing those), we are likely to find that genomes do more than code and express proteins. My ID prediction is still >50%, both in chives and in ramsons. I don't think C-value has been successful in predicting anything pertinent, but biologists might have just read it wrong.
Comment by Joy — July 20, 2007 @ 10:57 pm
July 20th, 2007 at 11:02 pm
Chris:
Chris, I also cannot help but feel that you are so focused on human technology that you are unable to see the implications of the parallels. The point of the obvious parallel is its contrast to existing conventional thinking invoking exclusively ateleological, unguided processes.
Comment by Bradford — July 20, 2007 @ 11:02 pm
July 21st, 2007 at 12:13 am
Joy,
Genome size is a fairly important topic, and understanding the evolution of them has significant implications for evolutionary theory. The mechanisms whereby genomes are reduced or expanded are often not the standard "neo-Darwinian processes", ie changes in allele frequency. The post genomic era can be expected to change the structure of evolutionary theory, and it will definitely help close the gap between paleontology (macroev) and population genetics (microev). This will be an expansion of current evolutionary theory, nor a replacement.
Anyway, C-values are a very interesting topic, and the size of an organisms' genome can have implications on development rate/complexity, metabolism, cell/body size etc.
William,
We have a pretty decent grasp of how evolution works, and it really can't be helped that the observable mechanisms are blind. This outcome was not some master plan to introduce dysteleology.
Finding analogies between biology and human technology are neat, but the mechanisms of evolution are still blind, so I'm afraid teleology will continue to be excluded until an intelligently guided evolutionary process is observed.
Design isomorphism, whatever its merits as an auxiliary hypothesis, is not a mechanism that affects biology.
Comment by Chris Harrison — July 21, 2007 @ 12:13 am
July 21st, 2007 at 1:20 am
Chris Harrison wrote:
Well, at least you don't beg the question.:roll:
I'm afraid ateleology will continue to be excluded until an unintelligent, unguided evolutionary processes is observed.
Evolutionary processes have been observed. But the property of their being unintelligent and unguided hasn't.
So stop hijacking the label of science for the claim that it has. That's merely your interpretation of the data. It's not the data.
That's odd. I could have sworn the Empire State building was designed by biological specimens. Bird nests too.
Comment by stunney — July 21, 2007 @ 1:20 am
July 21st, 2007 at 4:49 am
Chris:
We do indeed have an idea as to how evolution would work as well as ideas as to how it would not work. Evolution would not be expected to stochastically generate genes containing two frames that are read in the same direction. It's not a natural selection issue. As the relevant link indicated the presence of dual coding would presume functionality. But how is it plausible that a chance process would generate the outcome in the first place? I'm not at all surprised by the statement that simulations indicate the unlikelihood of this outcome and would call that an understatement.
Unless one is into suspension of disbelief that any dysteleological evolutionary scenario could be implausible, dual coding is exactly the type of outcome that suggests front loaded causality. There is more than the evolution of multiple frames involved. There is a timing issue as well. Chances are highly likely the end products interact with multiple proteins requiring their availability as well as the coevolution of needed gene expression components and an evolutionary explanation that can be tested for probability as well.
Comment by Bradford — July 21, 2007 @ 4:49 am
July 21st, 2007 at 10:42 am
Bradford,
Being improbable is not always synonymous with being the result of intelligence. If we do not have positive evidence that explains something, then we do not just start chalking it up to the gods or intelligent designers. As to your question itself, I don't know. You yourself claim simulations indicate it's unlikely.
Given that no one has ever observed front loading, and given that the entire idea begs the question of an intelligent designer (also for which there is no positive evidence), I'll suspend my (dis)belief. I'll try to get around to listening to Mike Gene's audio interview about front loading later today.
Comment by Chris Harrison — July 21, 2007 @ 10:42 am
July 21st, 2007 at 10:59 am
Chris Harrison wrote:
Has anyone ever observed any cases of codes being spontaneously generated from non-code stuff by unintentional processes? Ever? Anywhere? At any time?
Has anyone ever observed an intelligent being designing a code by means of an intentional process?
Comment by stunney — July 21, 2007 @ 10:59 am
July 21st, 2007 at 12:38 pm
Chris:
This is a cop out that says no matter how improbable a theorized cause, it is still the default option because secondary implications of intelligent causality must be avoided at all costs.
Good point stunney. ID critics are very selective about the applicability of the "noone has ever observed" remark. For that matter noone has ever observed the evolution of dual coding genes. Belief in the process hinges on extrapolations from vastly simpler RM + NS scenarios.
Have you not heard? We are supposed to pretend that no inductive inferences can be drawn from results of human intellectual input.
Comment by Bradford — July 21, 2007 @ 12:38 pm
July 21st, 2007 at 2:24 pm
Chris:
Well, duh! Sometimes what you say displays stunning faith in someone else's uber-theoretic, while at the same time spotlighting the blindfold you're wearing. I do suppose it's unreasonable to expect you to see it – even in a mirror – since it is covering your eyes, after all.
No kidding.
What is "post-genomic" about the study of genomes, their coding and levels of operation? Are you planning to go back to projection of agency onto the weather again (good ol' Zeus makes another comeback)? I must say I find it pretty ironic that your uber-theoretic is held to 'predict' anything you might find as well as its opposite. Seems scientifically vacuous to me.
I know. It's just that biologists who interpreted C-value as a measure of "complexity" (which they cannot define) as well as a 'confirmation' of their erroneous ideas about junk-DNA need to go back to 'Go' and not collect the $200.
Consider the lowly vole. Which geneticists label bizarre. They are possibly the fastest-evolving mammal (60-100 times faster than the 'average' vertebrate), with anything from 17 to 64 chromosomes in the different species (as determined by number of chromosomes, but even that doesn't work for some of 'em)…
Obviously, the vole with 64 chromosomes is not appreciably more "complex" than a vole with 17 chromosomes, if the only way you can tell them apart is by counting chromosomes. One might be tempted to expand one's consideration of differences by looking at the environment in which the vole lives. What kind of pathogens it comes in contact with, who its predators are and what defenses the species has developed, whether its diet is restricted or broadened and in what directions, its habitat habits and behavioral specialties, even the specifics of its germline meiosis, recombination mechanics and developmental timelines. Examine interfertility and what differences (if any) in recombination that results in. Why, the dynamics of their genomes and propensities to rearrange or duplicate under stress might even lend some basic knowledge to the stew!
Not to mention the expression suite-ing that results in the physical indistinguishability of voles across such a wide range of C-values. That little exercise might even tell us something pertinent about different levels of coding affecting different abilities and propensities specific to what conditions interior or exterior the vole will face in life.
Why, we might even learn whether whole portions of genomes are simply "reserve stock" to facilitate on-the-spot behaviors the animal may need when dealing with unprecedented challenges, and how much is "ancestral memory" of challenges met in previous generations.
What we can be pretty sure we will NOT learn from examination of vole genomes is that C-value correlates with organismal "complexity" based entirely on the number of proteins are coded for.
"Change in the structure of evolutionary theory" has been overdue for a long time.
Chris to William:
Balderdash. You do NOT have "a pretty decent grasp" of how evolution works or biologists wouldn't have erred so spectacularly on that C-value interpretation. Nor do you know that the observable mechanisms are blind – this is merely a dogma of orthodoxy, an a priori assumption long past its 'sell-by' date. And yes, there was indeed a master plan to enforce dysteleology and it's still going strong.
We can't do anything with causes that were by formal, ideologically motivated edict declared "random," way back before anyone had ever even heard of nucleic acids or genes, and cells were just "little bags of goo." Science will go where the evidence leads or it will cease to be science. New technologies have opened the floodgates. THIS is as it should be. Finally.
It also explains why the die-hards have abandoned science at this point in time in order to take their ideology to a broader sociological level. They've no hope of maintaining their previous stranglehold on biology, or to reinstate biology's authority to justify seriously repressive pogroms against humans they don't like. So they've openly declared jihad against the idea of telic design instead.
Comment by Joy — July 21, 2007 @ 2:24 pm
July 21st, 2007 at 5:03 pm
Kaput.
This discussion has completely disintegrated thanks to personal attacks and the fact that we've entirely lost touch with intelligent design.
You're right Will. We do not have a model for how dual coding genes evolved, or how abiogenesis happened. Unfortunately, this has absolutely nothing to do with intelligent design. ID is not shoveled in to plug that gaps in our knowledge.
ID is in a sad state if this is how its proponents plans to advance its agenda, by just crying about orthodoxy, metaphysical walls and "jihads", all the while contenting themselves to merely point out areas of human ignorance.
Comment by Chris Harrison — July 21, 2007 @ 5:03 pm
July 21st, 2007 at 5:22 pm
I see my last post on this thread has been sent to the memory-hole. Why? I asked a very pertinent question about the correlation (or absence thereof) between C-value and chromosome number in voles. Plus I expressed some worry about Joy's medical condition, that's all. Doesn't even come close to the average level of vulgarity of, say, stunney's posts (which doesn't bother me in the least by the way).
Comment by Raevmo — July 21, 2007 @ 5:22 pm
July 21st, 2007 at 5:40 pm
Chris:
Got tired of chasing the goal posts you were moving, Chris. This thread got too long to follow anyway. Perhaps next time you'll do a little less assertion of orthodoxy (and other people's arguments), so as to require a little less backpeddling when you realize nobody's buying it.
If you're going to play an 'expert' on ID in a forum where there are actual ID proponents, it doesn't hurt to understand some things about it. Saves on the bill for scarecrow stuffing that could be better used to make compost.
Raevmo:
Alas, you choose to lob cheap insults in my thread, so your cheap insults end up in the Hole. Such is the way of things here, where I may moderate my thread as I choose. This was not your first contribution to the Hole's very long run-on thread. I doubt it'll be your last.
Perhaps you haven't noticed that stunney refrains from such descent into Tourette's while in my threads. Maybe he's smarter than you. Or just quicker on the uptake.
Comment by Joy — July 21, 2007 @ 5:40 pm
July 21st, 2007 at 5:52 pm
Joy:
Well, then I guess that calling biologists jihadists and instigators of pogroms is not resorting to cheap insults, since your post didn't end up in the hole.
But what about those c-values of voles? Do they match the variation in chromosome numbers?
Comment by Raevmo — July 21, 2007 @ 5:52 pm
July 21st, 2007 at 7:16 pm
Chris,
Apologies for my absence, life so often obstructs my hobbies.
This thread has taken a sharp turn. Please let us continue our dialog civilly and graciously.
I will answer your questions shortly.
Comment by Joey Campana — July 21, 2007 @ 7:16 pm
July 21st, 2007 at 7:35 pm
Chris:
Yeah, I know. Nothing in nature could possibly be generated as a result of intelligent input. We can automatically rule out the possibility that a teleological process is connected with abiogenesis or what occured subsequently. If a natural phenomenon does not lend itself to a non-ID explanation it is because we have not found the answers that are out there somewhere. See. I know exactly how the game is played.
Comment by Bradford — July 21, 2007 @ 7:35 pm
July 21st, 2007 at 9:01 pm
Bill Bradford:
I don't think you do. You need to come up with some *positive* evidence that an Intelligent Designer did it. It's not enough to point to gaps in knowledge. See. There is positive evidence for the action of RM+NS, but not for (non-human) ID. You may legitimatly object to the extrapolation to deep time, but you need to show some positive evidence if you ever want to be taken seriously by scientists.
Comment by Raevmo — July 21, 2007 @ 9:01 pm
July 21st, 2007 at 11:02 pm
Raevmo:
I'm not going to waste time on this so let's simply point out that when positive evidence for an observed outcome is lacking (abiogenesis) the presumed gap, which is not explained by RM + NS, but is explained by a promissory note representing unknown and unspecified pathways, is nonetheless considered sufficient to exclude consideration of an ID alternative. I do know how this is played after all.
Comment by Bradford — July 21, 2007 @ 11:02 pm
July 23rd, 2007 at 11:02 am
Chris,
I must again offer apologies for my absence. I respond to your questions below.
That is very honest of you to concede the point. In my eyes, this shows me that you are a fair and courteous communicator.
Bioscientists use them to guide research by hypothesizing and discovering the mechanisms of unknown processes.
As biologists explore the unknown designs of the living world, they frequently use the conceptual resources and models of design isomorphisms in order to propose new models to aid in elucidating the functions and mechanisms of life. You look for similarities among different isomorphisms, including functional goals (teleological goals?) and propose models that can be tested to see if they match up with data.
A bioresearcher exploring an unknown aspect of the cell imagines what characteristics that unknown aspect has, usually extrapolated from related data and conceptual models (like design isomorphism). Then, the bioresearcher derives ways of taking measurements and testing whether those characters are present.
Isomorphisms will often serve as idea templates, or thought models, off of which biologists can lift helpful concepts for exploring the living world.
I think the best example of successful design isomorphic research is the elucidation of the inner workings of DNA. As John Maynard Smith pointed out, the isomorphic concept of informatic coding guided the illumination of the genetic material. The logic of symbols was and still is the modus operandi of molecular genetics and proteomics.
One great example of design isomorphic research currently underway is the work of Albert de Roos. He is using the software development concept of design-by-contract to propose models of the evolution of biomolecular interfaces.
The existence, frequency, and foundational presence of design isomorphisms suggest that there is a specific and profound link between biology and technology. Both biological designs and technological designs utilize fundamental aspects of the universe in order to manifest boundary conditions that yield the distinct informatic structures and mechanical units that form the respective biological and technological products. Isomorphic designs on the distinct bio and tech levels both utilize the characteristics of space-time, fundamental forces, elementary constants, essential qualities of matter, and features of energy, so that they allow for similarly specified functions. This link suggests that whatever caused the genetic code and protein machines, that cause has a specific conceptual link with human designers.
This means that certain aspects of life will have conditions that make them better studied as intelligently designed entities. I don't think that there is a literal "vindication" of ID from design isomorphism, but 1) a clear example of how ID-based reasoning has profoundly helped research biologists, 2) a fact-based conceptual resource that says that ID-based reasoning will continue to be a help to researchers, 3) a framework that can provide the power of heuristic prediction, 4) has a strong potential of being developed into a conceptual resource that can yield precise predictions, 5) a good reason to think that ID will one day be more fully-affirmed by human knowledge.
In one sense, I have lost a connection with the ID movement. I am interested in how ID is useful for working biologists, whereas many in the ID movement are only interested in detecting design. I am keenly interested in heuristic use of ID.
I think that it is often the case with those who are not open to ID that the introduction of an analogy becomes an impediment to continuing down the stream of thought that an ID scholar is proposing. This is most unfortunate because, in strict logical rigor, all new knowledge is extrapolated by analogy, as opposed to tautology.
We have not lost touch with ID. I think that we have lost touch with a home-spun rhetorical attack on ID. We have lost touch with what some critics think that ID should be about. Design isomorphic reasoning challenges the illusion that ID is just a bunch of religionists invoking their deities. The use of design isomorphism by biologists is a rebuke to the critics who say that ID is about getting God into the US public school science classroom.
The rhetorical attack of some critics is a terribly dishonest distraction, used by those who want to use ID for political purposes, or by those who want to bury the obvious help that design-based ideas have given to biology. I have showed you that ID-based conceptual models have brought exemplary utility to biology, by the use of design isomorphisms. We have entirely lost touch with an illusion that ID is about religion.
You are correct Chris. ID is not used to artificially plug gaps in our knowledge. The ID-based conceptual resource of design isomorphism is used to bridge current knowledge with potential knowledge, and this allows researchers to postulate, test, and elucidate the underlying logic of life.
Let's get back on topic here. Though others might want to leave this thread, I would welcome your thoughts on how design isomorphisms are an independently verified auxiliary proposition that brought ID scholars to heuristically predict that we should continue looking for function in what others considered useless genetic detritus.
Comment by Joey Campana — July 23, 2007 @ 11:02 am
July 23rd, 2007 at 7:05 pm
Joey,
You'll be glad to know that I really find no problems with your words here, and have no criticisms of biologists looking at things under the assumption of functional design. This seems quite reasonable to me, and it is obviously a useful assumption.
This is not all their is to ID though, as I'm sure you're well aware. ID advocates have attempted to reword textbooks and give "equal time" to the "alternatives", and the ID movement was initiated by a handful of Christian apologists who attempted to use it as a "wedge" for their religious beliefs. This is all old news to you, but what I'm saying is that the criticisms of ID won't go away even if everyone the understood the value of design isomorphic logic. The reason is because this is not what ID proponents have chiefly been concerned with.
Your discussion here also doesn't really address whether or not the design in nature is illusory, which is the main topic that ID has consistently attempted to address. Essentially DI based logic is just a conceptual tool that allows biologists to solve puzzles. This is an extremely neutered version of ID, and I don't mean that pejoratively.
Yes, this was what our comments were originally about.
Although independently verified, I do not see how design isomorphism is inseparably tied to (non-human) ID itself. Here's my question.
Why is the claim that "the designer deliberately attempts to stay hidden by cramming genomes full of junk to make evolution look blind and inefficient" wrong? If someone making this claim could find obvious differences between human technology and biology (design nonisomorphisms?), this would allow them to predict nonfunction in the exact same way as DI allows you to predict function. There are of course many examples where biology is in stark contrast to human technology.
The fact that ID proposes a mind means that we cannot predict what it will do.
ID, in and of itself, is just the idea that an outside intelligence influenced the biology on planet Earth. There is no claim to how this happened, when this happened, or why this happened.
The fact that we can draw analogies between biology and technology is detachable from ID itself.
Design isomorphism is not a necessary auxiliary assumption for ID.
This is what I think Dembski was getting at with his quotes. The intelligence that ID believes is responsible for biology is not predictable.
This is in contrast to evolutionary theory, which has built itself around repeatedly demonstrable mechanisms that are not assumed to be the product of a mind (ie not intelligent). In this sense, evolution is just plain easier than ID. Without knowledge of a designer's intentions, DI based logic hinges on the assumption that what the designer has previously done (the biology half of design isomorphism) allow ID to predict. This is an assumption within an assumption, because we cannot verify that any biological organism is the result of non-human intelligence.
In short, I do not think design isomorphism allows ID to predict that non-coding DNA is functional.
Comment by Chris Harrison — July 23, 2007 @ 7:05 pm
July 24th, 2007 at 10:50 am
Great! Progress is a beautiful thing.
Yes, this is all lamentable, but it must not hinder the exploration of useful ideas by those interested in advancing scientific exploration.
You're right. Nothing will satisfy most critics. They can't be satisfied. They will spin the rhetoric as long as there is any traction, and rhetoric usually has a very, very, very long shelf-life. Especially pathos and ad hominems.
This is an interest shift in goal posts, but I'm game. As Hume made clear, the truth value of a statement cannot be absolutely proven empty by the scientific method, especially because science utilizes inductive reasoning. This is why ideas investigated by science often come and go . . . and come back. Strictly speaking, ID could be true, as a mere possibility. So, starting from a mere possibility, is there anything in nature that might lead someone to suspect there is real design in nature? Yes, there is. The pervasive presence of design isomorphisms. And I don't think the "value of design isomorphic logic" (your words) should be set aside because it is not the whole enchilada, or because some individuals tried to use it as a political tool.
Because the designer does not attempt to conceal all evidence of design. I have found that there are design isomorphisms at the foundation of life and at most all of the levels above it. This includes the genetic CODE, and multi-layered SYMBOLIC LOGIC, and BOOLEAN LOGIC GATES, and protein MACHINES, and biological CIRCUITS, and regulatory NETWORKS that fulfill GOALS, LED SEMICONDUCTOR DEVICES, and living things have an innate desire to fulfill the intrinsic PURPOSE of PROCREATING.
This is an amazingly bold argument from ignorance, considering it is coming from a skeptic of ID. No, that would mean they were not engaging the data concerning design isomorphisms that do exist, and they were not realizing that predicting non-function would be folly based on isomorphic reasoning. I could explicate this if you like.
I think design isomorphic reasoning can overcome this limitation. But when critics keep telling others that they can't do it, can't do it, can't do it, it's not science, not science, not science, then people start to believe the words of the critics, even though the critics could be wrong. I think the words of the critics are wrong.
What about design isomorphs? Hello? Have I feverishly typed in vain?
Darwinism would have been still-born if Darwin shared your approach to scientific reasoning. Darwin had not even one single, tiny, itsy-bitsy inkling of the shadow of a sneeze of a clue how two NECESSARY components of his theory actually happened. I'm speaking here about inheritance and variation. Darwin did not how these happened, when these happened, or why these happened. After reading the Origin, Charles Lyell wrote to Darwin and told him that he might want to, "here and there insert an actual case." Based on your reasoning, none of Darwin's ideas were legitimate when he proposed them.
I cannot accept your reasoning.
If you understood what it means to have independently verified correlates, the key word being independent, as this relates to the philosophy of science, Duhem's proposals, the history of science, and simultaneously took the past successes of isomorphic reasoning seriously, you would understand why this separability is a strength, not a weakness.
So because blind evolution is simple, and ID is complicated, then ID is wrong, and blind evolution is right. Chris, please tell me you can see how this is flawed reasoning? Darwinian ideas had to be built, remember? Where did it start from? It certainly wasn't finished when it was started. It certainly is not finished now.
I must profoundly disagree. The presence of design isomorphisms tells us that we should axiomatically assume general functionity until we understand the part in question, and after elucidating all processes related to the part in question. You obviously do not understand the implications of isomorphic reasoning. This has to be my fault, I am sorry I have failed you thus far. I can expound on this functionality point more if you would like. You also are not very familiar with the history and philosophy of science, but that may not be your fault either. I have no idea how old you are or what grade/year you are in.
Imre Lakatos noted, "All scientific theories are born refuted, and die refuted." Anyone who knows the history of science understands that this is true, and there are no exceptions. Should I toss away these interesting (and useful) isomorphic facts, and insights as they relate to ID, because all of the other evidence that you want is not already in my hand? Can you see that this is a very, very small-minded approach?
Had your reasoning been part of the mindset of the conceivers of scientific methods, your reasoning would have aborted the scientific enterprise in toto. Why, it would not have even been an abortion! Science would have been contracepted by your reasoning, before the idea of science could even be conceived! (pun intended) Science would have never gotten off the ground in the first place if your approach was embraced by the fathers of science. Aristotle, Albertus Magnus, Roger Bacon, Von Helmont, Descartes, Bacon, Kepler, Laplace, and Newton would have all stuck to their other philosophical interests if they subscribed to your line of reasoning.
Science is about pursuing lines of evidence and figuring out how unknown aspects of nature work. Science is not about knowing everything before one begins an investigation. No scientific progress was ever made by a scientist always trying to cover their backside. They have to pursue the strength of an argument, and sure up the leaky spots as the investigation proceeds.
But ID critics would prefer we never begin in the first place. And the critics are making sure ID gets contracepted. They're working double-time to stifle exploration by playing good-cop-bad-cop, denying tenure, rolling heads, refusing funds, rejecting continued enrollment, threatening to flunk students open to ID, more threats to deny degrees, silencing ideas, haranguing ID scholars at every opportunity, getting the press to tell cute little fibs or larger outright lies, ousting institutes, protecting scientific dogmas/hegemonies/orthodoxies by legal fiat, big $ legal threats from the ACLU, telling school boards they cannot ever never ever never ever never critique or disparage or sneer at Darwinism not in any way not ever so never, and generally wreaking havoc on the educational and professional lives of anyone who even sniffs in the general direction of ID.
That's not impressing those of us who are interested in helpful ideas.
Design isomorphisms are damn interesting lines of evidence. If there were another new concept out there that had some valuable, useful, interesting, independently verified correlates like ID has isomorphisms, scientists would be dimwitted fools to abandon it. Some incredibly successful ideas in the history of science have had almost no evidence at all, others had no evidence and hardly any interesting correlates whatsoever, and for some ideas the evidence at-hand was all opposed. What overcame all of these hurdles were people committed to developing the idea. I'm in this for the long-haul.
As far as I can tell most critics are only in this for the cheap potshots and the petty thrills of tipping over someone else's bowl of useful ideas. It's shameful.
I cannot accept the nay-saying and boohooing about not having this part finished, or that part to propose, or anything else that may not be successfully completed. If the past is any indication, I already have more than is necessary for a fruitful scientific concept in my hand. Only time and hard work will tell if the proposals and successes are forthcoming.
I grow weary of laboring the point. Either design isomorphism is worth pursuing as an idea, or it is not. That is a determination that each scientist and thinker is going to have to make. Given the fact that we know design isomorphisms exist, I am going to ignore your flawed reasoning and I'm going to pursue this fact-based concept.
I'm going to continue finding more isomorphs, continue to find connections and patterns between biology and technology, to investigate how isomorphism relates to other ID-based concepts, to explore how ID-based reasoning has profoundly helped research biologists, continue to seek how isomorphisms help science as conceptual resources, to figure out how I can more effectively use this fact-based conceptual resource that tells us that design-theoretic reasoning will continue to be a help to researchers, to give a good hard attempt at producing a theoretical framework that can yield more heuristic predictions and even precise predictions, and to survey how design isomorphism might be a good reason to think that ID will one day be more fully-affirmed by human knowledge.
Comment by Joey Campana — July 24, 2007 @ 10:50 am