The Fruitfulness of ID Research

Today (Monday, November 30, 2009), on his 'Recursivity' blog, Shallit states that one paper includes: "a case of inappropriate citation".

His full paragraph:

"10. Fernando Castro-Chávez, "Hepatology Microarrays, antiobesity and the liver", Annals of Hepatology 3 (4) (Oct-Dec 2004), 137-145. Full paper here. A case of inappropriate citation. The only citation to Meyer comes in the final paragraph, which reads "... to better describe the identity and function of genes and genomes, composers of a natural, complex, and precise biological software that as a genetic program, contributes to the healthy programming and the pathological reprogramming of life." The author appears to be an intelligent design advocate. I predict that inappropriate citation -- the bogus insertion of citations to pro-ID papers in irrelevant contexts -- will become more popular in the future, as creationists attempt to bolster their case that ID is scientific."

Here, I want to emphasize that at the end of the Hepatology paper we read: "...a natural, complex, and precise biological software that as a genetic program, contributes to the healthy programming..." (reference 114 *).

Such statement complements the writing at the beginning of the paper, where we read: "The mRNA abundance and its mechanisms of assembly are two complementary areas. Using Intelligent Design models, we can use the analogy of the nucleic acids (DNA and RNA) as being the Software for the building up of proteins, and the proteins as being the Hardware, with the special feature that here, the Software builds up the Hardware and the Hardware plays and modulates the Software. In the case of metabolic pathways, the proteins are sufficiently flexible to become part of the regulatory Software, in a stairway of self-contained types of Hardware: organelles, cells, tissues, organs, organisms, etc."

* Reference 114 is:

Meyer SC. The origin of biological information and the higher taxonomic categories. Proc Biol Soc Washington, 2004; 117(2): 213-239.

Here is a sampler of ten excerpts of Meyer's paper pertinent to the Hepatology paper's context on biological programming:

1 -
"...arises only if the programmer of the model system “tunes” it in..."

2 -
"...this necessary tuning involves an intelligent programmer selecting certain parameters and excluding others--that is, inputting information."

3 -
"A system of interconnected lights governed by pre-programmed rules may well settle into a small number of patterns within a much larger space of possibilities."

4 -
"...agents previously programming the system..."

5 -
"A computer user who traces the information on a screen back to its source invariably comes to a mind--that of a software engineer or programmer."

6 -
"Genetic algorithms are programs..."

7 -
"Dawkins and Kuppers, for example, have developed computer programs..."

8 -
"...these programs only succeed by the illicit expedient of providing the computer with a “target sequence” and then treating relatively greater proximity to future function (i.e., the target sequence), not actual present function, as a selection criterion."

9 -
"...Gilbert et al. (1996) argued that changes in morphogenetic fields might produce large-scale changes in the developmental programs and, ultimately, body plans of organisms. Yet they offered no evidence that such fields--if indeed they exist--can be altered to produce advantageous variations in body plan, though this is a necessary condition of any successful causal theory of macroevolution."

10 -
"Thus, it might be argued that such differences show that early developmental programs can in fact be mutated to produce new forms. Nevertheless, there are two problems with this claim. First, there is no direct evidence that existing differences in sea urchin development arose by mutation. Second, the observed differences in the developmental programs of different species of sea urchins do not result in new body plans, but instead in highly conserved structures."

At the start and at the end of the "Microarrays, Antiobesity and the Liver" paper we read about information in health and disease. Meyer’s paper is focused on molecular information; so, the citation of Meyer's paper as reference number 114 is appropriate.

For Intelligent Design to be more fruitful as a research paradigm, grants need to be awarded to it, even in disregard of ID being the target of a Darwinian "witch hunt", as the equivocal statement of Shallit clearly demonstrates.

Update on Wednesday, December 30, 2009:

Another 'bold' Darwinian, like the one that posted a first comment in this post, wrote on Shallit's post:

"Anonymous said... In case we haven't figured it out, Fernando Castro-Chávez is a creationist. I'm sure he'd say an IDist, but I've seen his website. Also, wasting time on Joe G is just that, wasting time. Best to just ignore him."

However, Joe G really brought "life" to that shallow post, writing amongst many, many other things:

"Joe G said...

Jeffrey,
Do you realize that all you have to do to refute ID is to actually start substantiating the claims of your position?
If you want to talk about fruitlessness you need to look no further than your position.
There isn't any peer-reviewed articles that demonstrate that accumulating genetic accidents can do what they are claimed to have done.
And when you say that ID is a " religio-political charade" you really expose your ignorance.
What religion?
Does ID say who to worship? No.
Does ID say anything about worship? No.
Does ID depend on religious texts? No.
Does ID require a belief in "God"? No.
Does Jeffrey Shallit think his ID ignorance is meaningful discourse? Yes."
Also:
"You don't have an argument only bald assertions.
Artificial life does not correlate to biology.
And Barbara Forrest is a known liar on an agenda.
1- Artificial life was made by man.
2- Anyone who says that ID is religious or ID is Creation is either a liar or on some agenda.
Want to know why?
Because they cannot support their claims. All Forrest can do is make bald assertions.
It appears that is all you have also.
ID does NOT say anything about worship- nothing about who, why, when, where nor how.
ID does not require a belief in "God".
ID does not require the supernatural."
"Takis,
ID is a branch of creationism only to the willfully ignorant.
All IDists are not religious.
I am an IDists and don't care about religion.
I said:
However there isn't any evidence that any amount of mutational accumulation can give rise to useful novel protein machinery and new body plans.
Jeffrey responds with:"A lie. Go read about the Italian mutation."
No new protein MACHINERY there Jeff. And definitely no new body plans.
Changing one protein does not create new protein machinery.
Heck we can't even test the premise that humans and chimps shared a common ancestor- no one knows if the transformations required are even possible.
Jeffrey:"You really have no idea how science works, do you?"
Unfortunately for you I do.
Ya see in science one needs to be able to test one's claims.
And to this day no one on this planet even knows whether or not the transformations required are even possible.
Joe says:
ID does not say anything about worship- nothiung about who, what, where, when nor how.
ID does not say anything about giving service.
ID is not based on any religious doctrine.
ID does not say anything about the supernatural.
ID does not require a belief in "God".
So Jeffrey responds with: "because any being with the causal powers to tweak the fundamental constants of nature - as ID followers claim - must be a god or have god-like powers."
Or just have advanced technology.
So the bottom line is ID is religious if and only if we change the definition of religion.
Got it.
Artificial life was made by man.
Jeffrey (wrote):"World's dumbest argument, Joe."
Why? It is true.
Man made artificial life and man doesn't know enough about biology in order to mirror it.
Jeffrey (wrote): "Every experiment we do was done by people, but that doesn't mean that every natural event studied is the result of intelligent intervention."
No but if man makes something then blind and undirected processes did not.
Jeffrey,
The designer could be "God" and that would not mean ID is religious.
IOW Jeffrey you don't seem to understand the definition of religion.

Some of the links added by Joe G:
http://intelligentreasoning.blogspot.com/2009/06/biological-evolution-what-is-being.html
http://www.newworldencyclopedia.org/entry/Intelligent_design
http://www.trueorigin.org/bacteria01.asp
http://www.chem.duke.edu/~jds/cruise_chem/Exobiology/miller.html
http://www.creationresearch.org/crsq/articles/43/43_3/baraminology.htm
http://www.answersingenesis.org/get-answers/topic/speciation
http://www.discovery.org/a/2735
http://www.discovery.org/scripts/viewDB/filesDB-download.php?id=349
http://www.discovery.org/scripts/viewDB/filesDB-download.php?command=download&id=697

Joe G also wrote:

' Other people have also weighed in on this- including John Morris, the president of the Institute for Creation Research:"...While all creationists necessarily believe in intelligent design, not all ID proponents believe in God. ID is strictly a non-Christian movement, and while ICR values and supports their work, we cannot join them." '

And from Andrew Rowell's Blog: http://idintheuk.blogspot.com/2009/12/proof-of-truth-is-in-citation-index.html