Ken Miller may face more embarrassing facts, Behe’s DBB vindicated
| July 11, 2007 | Posted by scordova under Intelligent Design |
[slight correction and update follows]
[update: I had previously taken a second hand quotation from Paul Nessleroade of Ken Miller here (2003 Wedge Update). Below I give a quote by Miller by a better source document here: Life's Grand Design.
However, the more accurate quotation still demonstrates Miller made an embarrassing assessment about the architecture of DNA. I apologize to him for the inaccuracy, however, it was not a material inaccuracy as can be seen in the quotation from his website.
The greater burden is on Miller to retract his mistaken ideas from the public sphere. Further, he owes an apology to many in the ID movement for misrepresentations and errors of fact which he has promoted currently, over the years, and even under oath.]
the designer made serious errors, wasting millions of bases of DNA on a blueprint full of junk and scribbles.
Ken Miller, 1994
Empirical evidence 13 years later is putting some egg on Miller’s face [remember Ken Miller is the guy who made misrepresentations under oath in the Dover trial].
Encyclopedia Of DNA: New Findings Challenge Established Views On Human Genome
The new data indicate the genome contains very little unused sequences and, in fact, is a complex, interwoven network. In this network, genes are just one of many types of DNA sequences that have a functional impact. “Our perspective of transcription and genes may have to evolve,” the researchers state in their Nature paper, noting the network model of the genome “poses some interesting mechanistic questions” that have yet to be answered.
Other surprises in the ENCODE data have major implications for our understanding of the evolution of genomes, particularly mammalian genomes. Until recently, researchers had thought that most of the DNA sequences important for biological function would be in areas of the genome most subject to evolutionary constraint — that is, most likely to be conserved as species evolve. However, the ENCODE effort found about half of functional elements in the human genome do not appear to have been obviously constrained during evolution, at least when examined by current methods used by computational biologists.
According to ENCODE researchers, this lack of evolutionary constraint may indicate that many species’ genomes contain a pool of functional elements, including RNA transcripts, that provide no specific benefits in terms of survival or reproduction.
Behe 10 years ago, in Darwin’s Black Box (DBB) suggested junk DNA may not be junk after all. Behe has been vindicated by the facts, Miller refuted.
Finally, there is at least one other interesting fact in this article: “the ENCODE effort found about half of functional elements in the human genome do not appear to have been obviously constrained during evolution“. This means these designs NOT attributable to natural selection. Features in the genome have been shown not to be likely products of “slight successive modifications”. How I love science!
55 Responses to Ken Miller may face more embarrassing facts, Behe’s DBB vindicated
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DaveScot,
This is a great point and fires gaping holes in the ‘Darwinism is vital to medicine’ argument.
In one breath it is argued that we can’t test Darwinism because it takes too long (Behe’s 10^20 malarial cells just aren’t enough) and is necessarily outside of our field of observation. In the next it is argued that if you don’t agree with the historical conjecture about that which happens too slowly, too long ago and always somewhere else, then you can’t practice science or medicine.
#26
Agree. I didn’t say that this was their intention. It’s the existence of a toolkit isn’t that isn’t a speculation, while a speculation is their idea that the toolkit did evolve by RM+NS. What I mean is just that, as reasonably the toolkit couldn’t be evolved by RM+NS, front loading hypothesis is now more plausible, IN SPITE of their NDE speculations.
Hi DaveScot,
Two points. First, about that mouse genic “desert”, the original report was made before other genomes were available for comparison. Which is probably why you see the more recent and less, um, provocative stance from the author(s). If you take the time to get lost in the genome browser (for some of us, its more addictive than computer games), you will find that this region is, for all practical purposes, drifting randomly. This is apparent if you look at the nature and distribution of the mutational changes, and if you look at the conservation in other, more distantly-related genomes. There really is nothing remarkable about this region.
As far as garbage disposals, it may be easier for the crew here to think in terms of an analogy. Grant, for the moment (I can hear the snickers..) that Microsoft Word is a lean, mean package of, say, 100 MB of executable code. The concept of “junk DNA” as commonly held would translate to an interspersing of this code with some 10 GB of stuff – lines that just sit there and are ignored.
What the trf4 paper (and others like it) suggests is something far more bizarre. Not only would the Word code be interspersed with 100 fold more “junk”, it would actually be interrupted by or wrapped around 100 times as much executable code. Code that is running all the time, occupying 100 times more processor resources than the actual program, but producing no useful output (in fact, no output at all).
Art
There really is nothing remarkable about this region.
Bona fide researchers in this area of expertise such as Arend Sidow disagree with you. What can I say? Should I put more stock in an anonymous blog commenter or people like Arend Sidow? No disrespect meant but I’m going with Sidow’s opinion over yours. See my recent article (I wrote it with you in mind) quoting Sidow’s reaction to the experiment which you don’t think means anything.
Art
re Genomic garbage collection.
If it’s true that cells devote enormous resources to unproductive activities it’s just another nail in Natural Selection’s coffin. The cell lines you mention, like all living cell lines, have been undergoing selection for (ostensibly) billions of years. NS works to make cell lines more fit. If the huge amount of garbage collection is true that’s awfully less fit. The garbage is most efficiently dealt with by removal from the genome rather than the transcriptome after considerable resources have been devoted to transcription.
If true then it would be adverse to the veracity of both natural selection and interventionist theories of intelligent design pretty much only leaving a genome front-loaded billions of years ago as the best explanation with genetic entropy over billions of years explaining the gross inefficiency found today. That’s fine with me as I already believe front loading is the best explanation but still I’d be rather surprised if the garbage collection in the transcriptome is really garbage collection rather than some misunderstood critical process. As I said the acid test would be to artifically eliminate the suspected genomic garbage from the genome so that it never reaches the transcriptome and see if there’s any adverse effect from the knockout on the GM organism. Be sure to let me know when that’s been done otherwise I think talking about transcriptome garbage collection is little more than woolgathering.
We must bear in mind that the most modern design paradigms in engineering today do not deal with deeply deeply redundant, self-healing, self-assembling architectures that operate with high levels of internal quantum noise.
At the quantum level there is substantially much more noise to deal with then say macroscopically engineered artifacts. Today’s engineers tend to think linearly, cause effect.
In contrast, modern day nano-molecular engineering is having to confront non-linear thinking where at every step of the way something is presumed to go wrong because of quantum effects. This gives a totally different mode of how to build computational architectures.
I got a taste of this building satelite software where you actually presumed, at the end of a module exection, your software may not have executed properly due to cosmic radiation. To compensate for this, one had what looked to the uninitiated, an absolutely horrendous amount of convolution and apparently meaningless “waste”. Not so.
I think it pre-mature to call certain processes garbage. Biology may be telling us, that this sort of convoluted architecture is what works best at the nano-molecular level.
Art2 is expressing his prejudice that biology is an accident. Modem signals to the uninitiated ear sound like a accidents too….
[...] [NOTES] 1. These recent developments are in addition to the egg on Ken Miller’s face and laurels for Michael Behe. [See: Ken Miller may face more embarrassing facts, Behe’s DBB vindicated] [...]
Trying to check out Miller’s statement, as you cite it in the opening of the thread. What is “Life’s Grand Design?” A book? An article? I’m not finding it at Amazon, or anywhere else. Help!
[...] 1. Ken Miller is the guy who has taken various bruisings from scientific evidence and continues his misrepresentations and story telling as he did under oath in the Dover trial. [See: Ken Miller may face more embarrassing facts, Behe’s DBB vindicated and Ken Miller caught making factually incorrect statements under oath] [...]
Mr. Cordova, in the article I found, under the title you cite, by Kenneth Miller, he says something quite different from how you quote him. May I ask where you got the quote?
Thank’s for pointing out my error.
It was 2nd hand from Paul Nesslerode.
Cornelius Hunter gives the correct reference through Behe’s DBB page 225-226.
Ed Darrell,
The full essay was here: Life’s Grand Design
There were two version, one for PBS and one for Technology Review. You probably got the PBS version.
Nesselrode’s citation, it turns out, was correct.
Salvador
The orignal quote had some errors, but now it’s repaired. Apologies to Ken Miller for the earlier mis-quotation.
Unfortunately for him, the corrected quotation even more clearly demonstrates the gravity of his error.
This is the blow for darwinists. The DNA will continue to display complexity that astound researches as more is revealed.
To Quote The Psalmist. “I will praise You for I am fearfully and wonderfully made!”
This is the de.ath blow for darwinists. The Dna will continue to astound researchers as more of the complexity is revealed. Dr. Sanford quotes a preliminary study that indicates the encryption of the DNA is up to 12 CODES Thick.
To Quote the Psalmist, “I will praise you for I am fearfully and wonderfully made!”
Regarding the 12 CODES, I had an intersting exchange with PZ Myers here.
PZ complains about poly-constrained codes:
Yet this supposed “fiction” is turning out to be fact. PZ couldn’t believe Darwinism would make such structures, therefore they don’t exist.
But let me quote a greater scientist than PZ, renowned Cornell Geneticist John Sanford from the landmark ID book, Genetic Entropy:
bfast
He held that ID would fall if junk DNA proved to be junk. This is surely the PRIMARY prediction of ID.
I completely disagree. Life could have been designed billions of years ago with no intervention since then and a lot of junk could have accumulated since that time even as the planned phylogenesis was unfolding. If you drive your car long enough without cleaning the windshield you get a lot of bugs on it but that doesn’t mean the car wasn’t designed or no longer able to do what it was designed to do.
Where junk DNA doesn’t play well is in special creation in the recent past. It’s hard to reconcile a load of junk in a brand spanking new design.
I have said in the past that the existence of junk does not imply the aritifact was un-designed. I maintain that position. I have owned cars that had broken non functioning parts. I worked on spaceships that were expected to have (over the course of time due to extreme conditions in space) various systems failures in the course of its mission.
The functionality of the “junk DNA” was suspected for at least 2 reasons:
1. The creationists needed an explanation for the appearance of common descent ( formally speaking this was not an ID reason at all)
2. ID proponents who accepted universal common ancestry sensed the patterns were well designed and non-random (beginning with Michael Denton’s “Biochemical Echo of Typology” and then various other studies thereafter).
What proceeded from ID theory was the intuition to presume design at some point stated by Bill Dembski:
I personally was interested in the “broken part” interpretation of design. Because if parts are broken, this suggests they can be somehow “fixed” and this would have medical implications….
The ID proponents in general had less to lose with the junk being junk interpretation, but the creationists had quite a bit at stake in the controversy.
On the other hand, if large amounts of “junk DNA” were not junk it would make Haldane’s dilemma very accute and it would also destroy large amounts of Neutral Theory and the Molecular Clock Hypothesis.
Further, it reveals that biology is orders of magnitude more complex than what we even thought only 10 years ago. These polyconstrained architectures are complex beyond imagination.
Consider the term “junk DNA.” … Design encourages scientists to look for function where evolution discourages it.
– William Dembski, “Intelligent Science and Design,†First Things, Vol. 86:21-27 (October 1998)
Genomes are littered with nonfunctional pseudogenes, faulty duplicates of functional genes that do nothing, while their functional cousins (the word doesn’t even need scare quotes) get on with their business in a different part of the same genome. And there’s lots more DNA that doesn’t even deserve the name pseudogene. It, too, is derived by duplication, but not duplication of functional genes. It consists of multiple copies of junk, ‘tandem repeats’, and other nonsense which may be useful for forensic detectives but which doesn’t seem to be used in the body itself… Can we measure the information capacity of that portion of the genome which is actually used? We can at least estimate it. In the case of the human genome it is about 2 per cent…
– Richard Dawkins, “The Information Challenge,” The Skeptic, vol. 18, no. 4 (December 1998)
OUCH!
DaveScot, “It’s hard to reconcile a load of junk in a brand spanking new design.”
Maybe, but not impossible. Maybe the length of a particular sequence matters, but not the particular nucleotides. Like packaging “peanuts.” Or maybe the values of a particular segment are something like informational dross produced as a byproduct of cellular division because of some otherwise logistical problem in sloughing it off during the duplication. Until we fully understand the entire process, we probably won’t understand what the junk is. One thing seems obvious though- conserved sequences of junk between species with hundreds of millions of years of evolution from their alledged divergence is harder to explain with MET and ID.
“…harder to explain with MET than with ID”, I meant to write.
(I wish this forum had a way to edit a post.)
Does anyone know where in Darwin’s Black Box Behe suggests “junk DNA” functionality (what pages)? Thanks!
[...] Ken Miller, 1994 [...]
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