Daggah

Has anyone here ever run into this claim, that scientists applied linguistic tests to junk DNA, using this quote from [F. Flam, Hints of a language in junk DNA, Science 266:1320, 1994.] as a reference?

The page I was directed to is <a href="http://www.psrast.org/junkdna.htm" target="_blank">here</a>.

NeilUnreal

I'm not an expert on "junk DNA" but this seems clearly incorrect. I would presume that much of junk DNA originated as DNA which was expressed at some point in the organism's ancestry. In this case, the signature of junk DNA should be similar to "live DNA."

-Neil

Daggah

Well, on further thought about this, it would seem to me that one would actually expect linguistic tests performed on nun-functional DNA to find some semblance of a language. After all, as NeilUnreal said, it's likely that at least some junk DNA was once functional DNA. And doesn't DNA itself function sort of similiar to a language? Specific codons code for specific amino acids, after all. It isn't just "random."

Source: <a href="http://www.soton.ac.uk/~gza/theorysim.html" target="_blank">http://www.soton.ac.uk/~gza/theorysim.html</a>

tgamble

At least they aren't consulting Hovind, Ham, Sarfati... That would be something to worry about!

Behe may be an ID advocate but he seems to accept more evolution than most creationists and he IS a biochemist or works at a real university.

edited to add: how the hell did that happen? I posted in the wrong place!

[ August 25, 2002: Message edited by: tgamble ]</p>

Coragyps

Flam's news article refers to a paper: E Stanley, Physical Review Letters, 5 December 1994. (No other cite given, as it wasn't on the streets yet.) I would speculate that a helluva bunch has been published on the "uses" of junk DNA in the last eight years, though - there is surely something way more concrete than two statistical tests in print now.

theyeti

"Junk" DNA tends very much to be periodic. The reason is that most of it originates from retroelements, like the Alu sequence, that are capable of self-replication. That's exactly why we have so much of it, and it's best referred to as "selfish" DNA. However, these elements themsleves get mutations until they can't reproduce, and then they are truly "junk" in any reasonable sense. Another source for "junk" DNA is tandem repeats that occur because of slippage during recombination. These consist of short, usually trinucleotide repeats. Needless to say, a series of them is highly non-random. And yet another source is pseudogenes, which either come from copies of a functional gene, or are the remnants of a functional gene whose selective pressure has been relaxed.

Anyone who expects "junk" DNA to consist of random sequences doesn't know the first thing about it. Only after a very long period of time after it first appears should a non-functional sequence tend towards randomness. Talk about a "language" that resembles human language is just plain stupid. One thing that "junk" DNA's periodicity does do however is make it more likely to code for a novel protein. Periodic sequences are more likely to produce a foldable, and potentially functional sequence than a purely random sequence will.

theyeti

NialScorva

Obviously junk DNA has simularities to language, just as god intended. Why else would god have made it out of little 'A's, 'T's, 'C's, and 'G's.

Nic Tamzek

The only mildly convincing thing that I've heard about "junk" DNA in general is that the total amount of DNA in a cell correlates with cell volume -- bigger cells, more total DNA (but not more functional DNA). This much is observed; one potential explanation is simply that bigger cells need more proteins etc. produced, which requires more chunks of DNA to be unwound and transcribed at any one time, which requires (or perhaps is controlled by) the size of the "spacers" around genes.

Obviously if this were the explanation, then variations in the amount of junk in a specific location might up- or down-regulate particular proteins, which could supply much of the merely quantitative variation (which is a huge part of evolution anyhow). So the junk would have a function (and might be increased by the action of selfish DNA and decreased by accidental deletion), but it wouldn't be sequence specific.

It sounds good to me, but I'm sure that there are criticisms of it, if anyone knows what they are I'd like to hear them.

nic

theyeti

The most plausible theory I've heard for the varying amounts of junk DNA is that it's selectively removed only in organisms for whom DNA replication/maintainance makes up a significant metabolic load. The reason why there's little or none of it in bacteria is that they're under strong selective pressure to remove it, since they replicate very fast. Single-celled eukaryotes have less presure to remove it, but carrying around too much is still detrimental -- thus they have more junk DNA than bacteria, but less than us. As you get to bigger and bigger multi-cellular organisms, the metabolic load of DNA maintainance and replication becomes insignificant. We humans use most of our energy for muscle contraction and brain function, so the metabolic load represented by our junk DNA is too small to be selected against.

I don't know if this theory can account for the sometimes large differences between some multi-cellular creatures. But I've always chalked that up to the stocastic nature of genomic expansion. Various originators of junk DNA, like an endogenous retrovirus or retrotransposon, can become active and begin enlarging the genome within a short period of time. That's why even closely related species can sometimes differ significantly in the amount of junk DNA present.

theyeti

RufusAtticus

A quasi-creationist brought up Junk DNA last week on Christian Forums. <a href="http://www.christianforums.com/showthread.php?s=&threadid=20849" target="_blank">Here</a> is the thread. My main post is below.

============================================

Okay I read the Beaton & Cavalier-Smith paper over lunch and here are some brief comments.

The paper does not find a function in junk DNA. It is refered to as functional because the amount of DNA (primary plus secondary) has selectable effects on the phenotype of the cell. It isn’t some found function of secondary DNA, but rather a function for DNA period. Beaton & Cavlier-Smith (1999) is attempting to identify the selection pressures that lead to genome expansion. Thus anyone attempting to use this paper as evidence against evolution has a flawed argument. Basically, they are ignoring, either by deception or ignorance, the conclusions of the authors, which deal with the evolutionary aspects of genome size. This is readily apparent to just about anyone reading this paper. If anyone here, (s0uljah, npetreley, etc.) wants to contest my understanding of this paper, I invite you to get a copy and read it yourself. The paper is available free from the following link.

<a href="http://matilde.catchword.com/vl=7091841/cl=22/nw=1/rpsv/cgi-bin/cgi?body=linker&ini=nlm&reqidx=issn=0962-8452vl=266is=1433yr=1999mn=Octpg=2053" target="_blank">Beaton & Simth (1999)</a>

This paper uses a class of related organisms that have two sets of DNA: one in the nucleus and the other in the “nucleomorph.” This is because these organisms are the result of a symbiotic fusion of a red alga with a biflagellate host, several hundred million years ago. The nucleus of the biflagellate host has been maintained, whereas the red alga has lost most of its DNA and nucleus. The nucleomorph is all that remains of the red alga’s nucleus. The morphology of these organism is a good argument against intelligent/common design, since the chloroplasts are inefficiently placed inside an extra membrane. Plants and algae don’t have this odd organelle-within-an-organelle configuration. If these creatures are the result of scient design, then it is not a very good one with respect to organization. Furthermore, the differences in chloroplast placement imply that the same scient designer is not responsible for plants/algae and cryptomonads, since there isn’t a common design there.

More info on cryptomonads:
<a href="http://www.wikipedia.com/wiki/Cryptomonads" target="_blank">http://www.wikipedia.com/wiki/Cryptomonads</A>
<a href="http://www.talkorigins.org/faqs/evolution-research.html#endosymbiosis" target="_blank">http://www.talkorigins.org/faqs/evolution-research.html#endosymbiosis</A>

Now back to the paper. Here is a section of the paper with discusses various attributes of secondary DNA. It is good background information for those who don’t want to read the paper.

Let’s look at the interpretation offered by the website in s0uljah’s post:

What is interesting after I read this paper is that the above interpretation is found no where in the paper and is not supported by it. It takes a rather far stretch to justify the above interpretation using the actual study. In fact the paper has nothing to do with design, pro or con. It is only testing between three evolutionary theories, finding two insufficient to explain the observations. It confirmed that the third evolutionary explanation is the only one that explains the data. Since it shows that there is an explanation from evolutionary theory that stands up with all the data, it is amazing how the webpage can even claim that evolution has been discredited here. In no way has this paper supported any concept of design or anti-evolution beliefs.

The quote that the website offers up to support its claims is from the abstract of Beaton & Cavalier-Smith (1999).

To a person who hasn’t read the paper carefully or even at all, the quote looks like it is saying that the authors have shown that there is no such thing as selfish or junk DNA. However, this is not this case, and the above quote is actually referring to the two hypotheses of why secondary DNA accumulates, not hypotheses of whether it does something or not.

Here are the three hypotheses:
<ol type="1">[*]Secondary DNA accumulates because it is junk and there is no strong selection pressure against it: the ‘junk’ hypothesis.[*]Secondary DNA accumulates because it is parasitic: the ‘selfish’ hypothesis.[*]Secondary DNA accumulates because the mass of DNA directly determines nuclear volume and the nuclear volume is under selection: the ‘skeletal’ hypothesis.[/list=a]

Using cryptomonads, the authors looked at ratios of cell volume to the size of the nuclear genome and the nucleomorph genome. What they found is that the size of the nuclear genome scaled up with the volume of the cell, but the size of the nuclemorph genome stayed relatively constant. If in these organisms DNA accumulated because of the first or second hypotheses, then the nucleomorph’s genome should be affected just like the nucleus’s genome. Because this doesn’t happen, the authors argue (probably correctly) that the first and second hypotheses cannot account for the observations. The authors then showed how the third hypothesis accounted for both the scaling of the nuclear genome and the non-scaling of the nucleomorph genome. (Read the paper for more information.)

What the authors didn’t do is show that there is no such thing as selfish or junk DNA, only that selfish or junk attributes of secondary DNA aren’t enough to explain why it accumulates. Because the webpage posted by s0uljah is claiming that they did the former, it is fundamentally flawed by depending on an erroneous interpretation.

But you don’t have to take my word for it; the paper is freely available online for you to read. If you have problems understanding the more technical aspects of the paper, I’ll be glad to discuss it. Please read the primary literature for yourself and post your comments in this thread.