The expression “seemingly chaotic” may be used here in the colloquial sense roughly equivalent to “random” (without underlying mathematical rules, an undeterministic “mess”).

Those familiar with informatics know that “chaotic” (and their complementary fractal) systems are completely deterministic and are ruled by strict (albeit not trivial) mathematical rules (call them “reasons” if you will).

Principle of Recursive Genome Function (peer-reviewed journal article, full text made available in full, accompanied by a press release, etc) is found at http://www.junkdna.com/pellionisz_principle

Regarding a side-question re-surfacing in blog debates “how is it that the fugu has 1/8 of the “junk” compared to e.g. the human genome”, the above Principle paper cites an earlier peer-reviewed journal giving an explanation in terms of the “fugu prediction of fractogene”.

Pellionisz_at_junkdna.com

1. “You are speculating in the face of abundant evidence that the DNA has no function”

I think there is an increasing body of evidence saying that much of this DNA has a function. Some of this documentation you can find in the links in the post, I’ll provide you with more when a respond to your list, including the “secret hidden function” of sequences in pseudogenes.

2. “They cannot accept scientific evidence suggesting that something may have evolved by chance and have no adaptive significance”

For the record I accept that all evolution is based on chance, but I also believe that the same chance events will remove most unnecessary DNA over time and consequently minimize the amount of “junk”. This, simply because minimizing junk would be advantageous….

It follows then that we should be looking for possible function rather than dismissing it, but…

3. You are assuming that I believe every single basepair has a discrete essential function. Both you and I understand very well that such a situation would have not allowed for evolution to occur. Some of this DNA clearly serves a buffering capacity. That does not however, mean it cannot have other functions as well.

You are speculating in the face of abundant evidence that the DNA has no function. You are even questioning whether pseudogenes might have a secret hidden function that has escaped our notice for three decades.

That’s exactly what adaptionists do. They cannot accept scientific evidence suggesting that something may have evolved by chance and have no adaptive significance.

The reason why I criticize those who question junk DNA is because the logic of their arguments is flawed. Not only do they ignore all the evidence in favor of the junk explanation, they exaggerate and misrepresent any “evidence” that refutes it.

If you enjoy speculation so much then speculate on this …

1. Why do pseudogenes and most of the transposon-related sequences look so much like broken genes?

2. Why is the DNA sequence in most of our DNA not conserved?

3. Why can we delete large segments of mammalian DNA with no observable effect?

4. Why is there so much variations in repetitive DNA within a species? Some people have segments that are ten times longer than segments found in other people. Are all of the nucleotides in the longer segments functional?

5. Why is the Fugu genome so much smaller than that of other fish?

6. When two similar species differ in genome size by a factor of two—probably due to an ancient polyploidization—is the majority of DNA in both species functional?

7. In the human lineage there are over one million Alu sequences. They all look like degenerate versions of 7SL RNA. Are all of these sequences functional? If so, what function could they be doing? And why do the human Alus look so different from the mouse ones?

8. Most intron sequences do not seem to have a function. Why does the size of introns in the same gene vary so much in related species and why isn’t the sequence conserved in most cases?

I have changed “assume” into “speculate” in the original post, you were right that this was an inaccurate phrasing.

I find that your comment to the Stonehenge analogy says a lot. This is not about withholding scientific data, on the contrary. You certainly are entitled to publish your opinion on “junk” being “junk” and nothing else (you already have), and that is not the issue. The issue is that you keep criticizing others for speculating that this DNA has function, – why ?? What is that about ??

There were and still are, good reasons to speculate on the origins of the Stonehenge formation, I find that there are good reasons to speculate on the function of “junk”-DNA/RNA as well (why is so much “junk” transcribed when we know that energy conservation is a major issue for all organisms ?). Speculating and asking questions like this does not make me an adaptionist, – please, please, stop calling me that…

Hindsight will tell you that if you had examined Stonehenge and found no evidence of human involvement, you would have been wrong. I believe you may come to see that you are making a similar mistake with “junk”-DNA…

Let’s say you carefully examine the pile of rocks and conclude on the basis of all evidence available to you that it has a perfectly natural origin. The piles were not made by humans.

Are you saying that you should keep that conclusion to yourself out of fear that it may inhibit further investigation?

How would that work? Does one just give up publishing any paper that reaches such a conclusion?

It would certainly have one effect that you may like. All the proponents of random genetic drift and evolution by accident would soon lose their grants and you adaptationists would have the field to yourselves.

Say you are the first to discover Stonehenge. As a scientist you can choose between two approaches: 1) dismiss the stone-formation as a pile of rocks with no significance or 2) try to understand why they are arranged in this peculiar manner. This latter approach would require hypothesis and speculation on possible explanations. Using the onion test on the other hand, you would reach the conclusion that there are bigger piles of rock with no apparent function elsewhere, thus this pile of rock is no different. Consequently, using the onion test you would have stood in the way of scientific progress.

Dismissing reasons for the obvious complexity using terms like “junk-DNA” is not going to get us anywhere.

Instead, let’s start by acknowledging that we know very little.

I will do no such thing. We know a great deal about junk DNA. We know, for example, that 50% of our genome consists of defective transposons. There are many other reasons why scientists are confident that most of our genome has no function. You can read about it at Genomes and Junk DNA.

I understand that you may not know these things but you make a big mistake in assuming that the term “junk” DNA is based on similar lack of knowledge.