Pleas visit:

http://newtonsbinomium.blogspo.....urdum.html

Do Centrioles Generate a Polar Ejection Force
N and P elements in V(D)J recombination have the purpose of structurally and functionally stabilizing proteins made from bags of pieces (last abstract in the proceedings, titled Metaprogramming and Genomics).

I don’t know if the former has a grant, and I know personally that the second one does not, ID is making predictions.

Now, out of curiosity, if you apply your same reasoning to evolution, does the same thing happen? Do you have questions which say “the evolutionary prediction is X and the non-evolutionary prediction is Y”? I’m talking about _before_ the experiment is run, not afterwards.

“I’d appriciate any links people can give me where the relationship between evolution, biology and information theory is explianed.”

It’s a large subject, but I would start with the following papers:

Biological Function and the Genetic Code are Interdependent
Chance and Necessity Do Not Explain the Origin of Life
The Origin of Life on Earth and Shannon’s Theory of Communication (I haven’t read it, but I’ve also heard good things about Information Theory, Evolution, and The Origin of Life)
Three subsets of sequence complexity and their relevance to biopolymeric information
Searching Large Spaces
Evolutionary Computation: A Perpetual Motion Machine for Design Information? (lay article)
Darwinism vs. Teleology in Genomic Change (my own lay article — the part you are probably interested in starts with “The Nature of Computational Systems and Programs”)

“Preferably not one where people calculate the probability of entire proteins forming spontaneously out of random combinations of amino acids etc. Im particularly interested in how things like changes in regulation are covered, and how small changes in the genotype that cause large changes in genotype are treated in the context of information. Also something that deals with natural selections branching/pruning would be very interesting.”

While I don’t _remember_ those articles using spontaneous protein generation as the explicit model to refute, I know they all at least have other interesting focuses. The small changes in genotype causing large changes in phenotype are covered in my lay article, which I may try to publish some papers on parts of it. As far as branching/pruning, I would just say that it’s not hugely relevant.

In light of Dembski’s “Searching Large Spaces”, you should read Chance Favors the Prepared Genome, especially this: “A genome’s ability to grow and to explore new organizational structures would be severely constrained, if its options were limited to simple point mutation…most organisms tolerate only relatively low levels of point mutation in a gneeration. Instead they have evolved mechanisms that generate multiple sequence changes in a single step, allowing them to bypass unselected neutral, and negatively selected, sequences that may lie on point mutation pathways between the current sequence and a more optimal sequence. Indeed, where genomic sequences have been available to provide a window into the evolution of a new gene, the series of steps revealed has been complex.”

Also less relevant, but still somewhat on topic, see my own discussion of irreducible complexity.

Not really I read most of Darwin’s Black Box and a lot of Discovery Institue articles before I’d even heard of the NCSE etc. My problem is similar to David Heddle’s, he says:

“I will accept ID as science when I read something like this:
A scientist at (some respected research university) has been awarded a grant to do experiment X. ID predicts the result of the experiment will be Y. Non-ID predicts the result will be Z.
And don’t tell me this cannot happen because the secular scientific community would never allow it. I was a practicing scientist before I was a believer, and we never had any secret meetings where we discussed our true agenda of destroying Christianity in the guise of science.

Predictions such as We will never discover an evolutionary pathway for (whatever) or We will never detect a parallel universe are interesting and important, but they are not examples of predictability arising from a full-fledged scientific theory.”

“Such a thing is the equivalent of a propetual motion machine for information.”

I’d appriciate any links people can give me where the relationship between evolution, biology and information theory is explianed. Preferably not one where people calculate the probability of entire proteins forming spontaneously out of random combinations of amino acids etc. Im particularly interested in how things like changes in regulation are covered, and how small changes in the genotype that cause large changes in genotype are treated in the context of information. Also something that deals with natural selections branching/pruning would be very interesting.

“The view of the genome that you are espousing (and what is being taught in schools) is both 15 years out-of-date and was based on arguments from ignorance when they originated.”

As I have said before what is taught in school is always out of date and it is certainly a state of affairs that needs remedying. Im not sure what it has to do with ID though, it certainly isn’t a scheme to stop people questioning evolution, as if what scientists know now somehow weakens the theory. Personally I would have loved to have learned about evodevo, plasticity, epigenetics etc, but it will probably be a long time before these things are taught in high school, which is a shame.

Predictions such as We will never discover an evolutionary pathway for (whatever) or We will never detect a parallel universe are interesting and important, but they are not examples of predictability arising from a full-fledged scientific theory.”

Bull! The classic prediction of Darwinian evolution that would falsify it is finding human and dinosaur fossils together in the same strata. In fact it was the basis of a famous hoax where some scientists carefully staged just such a fossil discovery to tease the YECs. -ds

“Notwithstanding an average evolutionary increase of genome size in the higher plants due to activity of transposable elements, threatened plant species (those that are now on the brink of extinction) are shown here to have on average larger genomes than their more secure relatives, which indicates that redundant DNA in the plant genome might increase the likelihood of extinction. The effect is (at least partially) independent of the duration of the plant’s life cycle. Polyploidy is found not to be associated with the increased risk of extinction. These data agree with the hypothesis of ‘selfish’ DNA and indicate an antagonism between different selection levels, thereby supporting the concept of hierarchical selection.”

The “selfish” DNA hypothesis is a nice story, but like most such stories, simply isn’t consistent with the facts. Transposable elements are used by the genome for many purposes, including function modulation and whole-genome resstructuring.

A good paper against the “selfish” DNA hypothesis:

On the Roles of Repetitive DNA Elements in the Context of a Unified Genomic–Epigenetic System

A good paper on how transposable elements are used by cells in very beneficial ways:

Transposable elements as the key to a 21st century view of evolution

Basically, transposable elements are tied to the circuitry of the cell’s genetic engineering system, and are used to help in the manufacture of novel genetic variation.

Transposons are often activated in times of stress, and help the genome re-engineer itself to recover from the stress. Transposons contained entire packets of function that can be quickly mobilized and distributed to the locations in the genome where it is needed.

The view of the genome that you are espousing (and what is being taught in schools) is both 15 years out-of-date and was based on arguments from ignorance when they originated. In fact, the modern view of transposons as “controlling elements” was that which was expressed by the scientist who found them, Barbara McClintock. IIRC they wouldn’t even let her publish her findings because they were so at odds with the view of biology at the time. Finally, after her work was finally recognized, they were relabelled “selfish DNA” to avoid the obviously telic implications of a functionally structured genome. And this label unfortunately persists despite mounds of evidence to the contrary.

Quite a bit of junk DNA will of course turn out to be functional too (it’s a one-way street), but roughly 50% of human DNA supposedly consists of the remnants of transposible elements (TEs), “selfish” DNA (see Mung’s comment) that spreads by inserting copies of itself all over the genome. Quite functional (i.e. NS) from the viewpoint of the TE itself, but bad for the organism. That stuff is worse than junk from the individual point of view, but of course not from the TE’s point of view.

The presence of functionless DNA in the genome is no longer regarded as a puzzle. Dawkins’ (1976) selfish-gene theory predicts it, and elaborations on the idea of “selfish DNA” were simultaneously developed by Doolittle and Sapienza (1980) and Orgel and Crick (1980) (see Dawkins 1982, ch. 9, for details).

Raevmo: Can anyone give an example of truly (i.e. identical) redundant systems in nature?

Brains.

Salvador: DNA is classified as junk simply because scientist are ignorant of it’s possible function.

It’s my understanding that DNA is classified as junk for theoretical reasons, not observational reasons. Can anyone else comment on this?

According to some estimates, 95 percent of the human DNA is “junk.”

Does anyone know the source for Mayr’s figures? Who made these estimates, and what were they based upon?