Junk DNA, Junk Science, and The Onion Test

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Given all of the recent ignorant yammering about “junk DNA” on the Discovery Institute’s blog and other ID blogs – unfortunately partially derived from a fair bit of ignorant yammering in the science media on the same topic – I think it is worth it to post a very simple and insightful post from April 2007 by T. Ryan Gregory entitled “The Onion Test.” Gregory is a professor at the University of Guelph and runs genomesize.org, an online database of animal genome sizes. He has recently become one heck of science blogger (at Genomicron) and has been doing a yeoman’s job of attempting to explain patiently and calmly to the world what the real scientific issues are with genome size, the “junk DNA” concept, and the problems with the ubiquitous-but-bogus storyline about junk DNA. Said ubiquitous-but-bogus storyline goes something like this: “Scientists have found that junk DNA is functional! Weren’t scientists (er, other scientists) stupid to think it was junk! What morons! Three cheers for our pet idea, which is that junk DNA does X.” ID advocates, who don’t even have an “X”, repeat the story but instead just riff off the vague idea that someone somewhere has explained what the function of “junk DNA” is, have played this storyline for all it’s worth, adding a completely vapid “We told you so!” on top of it.

For a dose of reality, I recommend that everyone read Gregory’s Onion Test. I quote it below for your convenience.

The onion test.

I am not sure how official this is, but here is a term I would like to coin right here on my blog: “The onion test”.

The onion test is a simple reality check for anyone who thinks they have come up with a universal function for non-coding DNA1. Whatever your proposed function, ask yourself this question: Can I explain why an onion needs about five times more non-coding DNA for this function than a human?

The onion, Allium cepa, is a diploid (2n = 16) plant with a haploid genome size of about 17 pg. Human, Homo sapiens, is a diploid (2n = 46) animal with a haploid genome size of about 3.5 pg. This comparison is chosen more or less arbitrarily (there are far bigger genomes than onion, and far smaller ones than human), but it makes the problem of universal function for non-coding DNA clear2.

Further, if you think perhaps onions are somehow special, consider that members of the genus Allium range in genome size from 7 pg to 31.5 pg. So why can A. altyncolicum make do with one fifth as much regulation, structural maintenance, protection against mutagens, or [insert preferred universal function] as A. ursinum?

Left, A. altyncolicum (7 pg); centre, A. cepa (17 pg); right, A. ursinum (31.5 pg).

There you have it. The onion test. To be applied to any ambitious claims that a universal function has been found for non-coding DNA.

____________

1 I do not endorse the use of the term “junk DNA”, which I think has deviated far too much from its original meaning and is now little more than a loaded buzzword; the descriptive term “non-coding DNA” is what I use to refer to the majority of eukaryotic sequences (of various types) that do not encode protein products.

2 Some non-coding DNA certainly has a function at the organismal level, but this does not justify a huge leap from “this bit of non-coding DNA [usually less than 5% of the genome] is functional” to “ergo, all non-coding DNA is functional”.

I will leave it here for now. It is possible that The Onion Test doesn’t seem quite as compelling to other readers as it does to me. I have some ideas about why this might be true – a lot depends on what background knowledge you bring to this – but I am going to wait for peoples’ comments to assess this further. I would particularly like ID advocates to try to explain why The Onion Test doesn’t nuke their claims that junk DNA is functional.

The same goes for Andrew Pellionisz and whoever else runs junkdna.com. (By the way, I am pretty well convinced that junkdna.com is a crank science website. I would tell readers to visit junkdna.com and give me their own assessments, except it crashes my browser when I click on it. That plus the egregious abuse of HTML formatting are pretty bad signs all by themselves.)

————————– Note: I agree with Ryan Gregory’s various criticisms of the term “junk DNA”, in particular because “junk” DNA might have some non-sequence-specific “function” based purely on bulk amount of DNA. But this is a different issue than the much bigger problem of the now-common but wildly wrong idea that scientists have determined that most/all “junk DNA” is functional, and none of the “junk DNA is functional!” people are claiming that the function is something pedestrian like “taking up space.”

78 Comments

Yep, junkdna.com is either a crank site, or is doing a very good impression of one.

I sort-of like the onion test. The only change I’d like to see is to have two similar species with very different amounts of junknon-coding DNA, just to drive the point home. Humans and onions are a bit too different, so someone is going to argue that humans need more junknon-coding DNA because they’re more complex (I can’t see exactly how the argument will go, but you know you’ll want to respond by scrawling “STUPID” across their forehead in bright green letters, with plaid trim). They’ll conveniently ignore the wide distribution of species with large amounts of junk non-codinghighly repetitive DNA across the Linnean hierarchy.

Bob

Onions have large cells which make them useful as samples in an introductory class on the microscope. The large genome size suggests that non-coding DNA may have (inter alia) a structural role in the cell: mechanics of cell division, nuclear integrity, etc. I think the “junk” hypothesis is the last that should be considered. It’s a non-answer to a good question (“what is that for?”), much like so-called vestigial organs.

junkdna.com itself is basically just a blog where Pellionisz posts news articles and stuff. He adds his some of his own color commentary there, but by and large, the stuff about his own theories is relegated to his many other web sites. I think it’s very hard to tell if it’s “crank science” or not, because he seems to keep the mathematical details of his theories confidential, supposedly for IP reasons. I previously wrote a summary of what I think it’s about, which he described as “pretty much correct”.

I don’t think the basic idea is obviously ludicrous, but there is not nearly enough detail to really know. Certainly though, when you consider his (1) secrecy about what his theories actually are, (2) strident claims about their importance (e.g. that it’s related to Parkinson’s and Alzheimeir’s and various other severe diseases), and (3) apparent willingness to exhaustively argue with people on blogs and Wikipedia, all this taken together has to make you a little worried.

You know, I don’t really see why IDists should get so hung up over a little “junk DNA” in the human genome. They harp on about how an efficient design would not contain so much junk, but if our supposed designer was so efficient in the first place, why on earth did it take over four billion years to implement the design of human beings? Given the right scientific know-how and technology, one could easily see how a designer could achieve the same result in, oh say, 6,000 years. :-)

The junkdna.com website doesn’t crash my browser (I’m using Firefox). But I agree that it looks like a crank website.

Actually there’s an easy IDist answer to the onion test. Obviously onions have a much more complex evolutionary future than do we. They need those genes for their descendants, the future sapient beings of the world. So the designer has “frontloaded” them with the extra genes. Of course, that also means that hexaploid bread wheat didn’t evolve from einkorn and emmer wheat - instead, the diploid einkorn and the tetraploid emmer are degenerate species (since, as creationist keep saying, evolution cannot add information, it can only remove it…)

Oww, the implications of my nonsense are making my head hurt.

IanR - hey, wow. You have a prediction out of all of that. Bread wheat has a big future, because of all the junk DNA, but rice doesn’t have a lot (that’s why they sequenced it first). Therefore, vodka and not sake will be the staple drink in the future.

And that will make your head hurt.

Bob

Nick Matzke Wrote:

… I am pretty well convinced that junkdna.com is a crank science website.

I’m glad someone takes notice of Pellionisz’s antics.

While Firefox can open the site, it is pretty bad. The first page is filled with ‘news’, and links to “related sites” such as this one. It is a norwegian television channel forum with a thread where a ‘communication adviser’ is cited by a ‘department director’ which tries to describe what a gene is.

Some quotes to remember is that:

truud2 Wrote:

The human DNA is a biological Internet and superior in many aspects to the artificial one. [Bold original.]

truud2 Wrote:

In addition the DNA may obviously store all harmonic waves of 150 megahertz too, thus of course also visible light. The 22th octave of 150 megahertz lies straight in this range. The color of this light radiation is by the way blue. Is it a coincidence that the solar radiation is broken by the terrestrial atmosphere just in such a way that we live in a world with blue sky?

For example we speak today nearly naturally of the »genetic code«, thus of a systematic information coding. But the past genetics stopped here and settled the remainder of the work exclusive with the help of chemistry, instead of consulting also language experts. [Bold and italics original.]

One of the links goes to an old site. There one can find a list of ‘peer-reviewed’ published material, such as keynote lectures in a symposium for biological nanostructures and a single publication.

The paper is a review (!) paper published in Cerebellum, and seems legit.

The problem I see is that in addition to what GeoMor describes I don’t find much of a review of an area but an unsubstantiated prediction. It is very open, but apparently anything biological that can be loosely modeled as fractal is supposed to be caused by anything resembling fractal structures in DNA:

Malcolm J. Simons & Andras J. Pellionisz Wrote:

… the ‘fractal-like’ properties of P-cells, as well as of other organelles and organs (e.g., Cardial coronary arteries), and the ‘fractal-like’ self-similar repetitions known to be in DNA since 1994, are in a causal relationship, with fractal sets of DNA generating fractal anatomical (structural proteins), physiological (metabolic proteins) and related pathological formations. [References removed.]

And the evidence is that some morphological structures can indeed be loosely modeled as fractals:

Malcolm J. Simons & Andras J. Pellionisz Wrote:

The morphological findings reported elsewhere and summarized here support the prediction.

Summary: - Crank science site layout. - Crank science links. - ‘Peer reviewed publications’, which aren’t and are often presented in areas unrelated to evolutionary biology. - Unsubstantiated prediction as proof.

If I am wrong on the crank idea or the facts, I welcome any corrections.

Oh, and I forgot to mention that the only ‘relation’ between the norwegian site and Pellionisz site seems to be that it linked back to Pellionisz site. I assume that the other ‘related sites’ are similarly listed from a link search.

The onion test is more formally known as the “C-value paradox”. It has been known and discussed for ages of course. There are some nice articles on it in particular by Dan Hartl, who shows that Drosophila has a small genome because of a high rate of random deletions.

dunnoMaybe,

What you are describing is termed the nucleotypic effect. That is to say that the presence of DNA in the nucleus can have some phenotypic effect regardless of sequence. The reason is that increased amounts of DNA tend to increase the size of the nucleus and the size of the cell. There is some evidence to suggest that this is due to a constraint on the ratio of the size of the nucleus to the size of the cytoplasm and may involve the number of nuclear pores required for transport. This is why some polyploid plants tend to be larger and have larger cells that the parental species.

Of course, this does not mean that “junk” DNA has a function. If you want to make a plant bigger, whether you are a human or a god, it would probably be better to use polyploidy than SINES, LINES and pseudogenes for a number of reasons. For example, SINES and LINES can cause insertional mutagenesis, hybrid dysgenesis, chromosomal rearrangements, etc. Polyploidy can provide genetic material free of constraint that can mutate to create new genes. Ohno showed us the importance of polyploidy for evolution and he was correct.

Increasing amounts of DNA can also have deleterious effects due to the fact that it takes time and energy to duplcate DNA. This can increase the cell cycle time and even the generation time for some species. So once again, there is a price to be paid for “junk” DNA and it can only be tolerated for so long. If it cannot be eliminated, the end result could be extinction.

I think comparing the onion genome to the human genome is hugely interesting but, perhaps, the more devastating point in the onion test is that different onions can have such remarkably different sized genomes. As I’ve commented elsewhere, “no junk” is not a prediction of ID itself. Something can contain redundancy and even useless parts and still be designed. By making “no junk” a prediction of ID the ID-ers seem to be projecting the additional - and unnecessary - theological concept of the Christian God onto their designer. That is, they are designing the Designer, aka as making him/her/they/it (or whatever) conform to their religious notions. I’m sure that’s just an oversight on their part. To me the onion test clearly points to the existence of several designers, sub specialty: onion; it’s much like comparing Windows Vista, Mac OS X and Linux.

Torbjorn Larsson said:

- Crank science site layout.

What are the attributes of a crank science layout?

Science Avenger Wrote:

What are the attributes of a crank science layout?

Well, if I read myself correctly, it seems to be a “first page … filled with ‘news’”. ;-)

But actually, the page is so awful, filled with text, and with the usual small and large fonts, that I left it mostly undefined and for anyone to define for himself/herself. I would use Baez crackpot index - that first page would score rather high, I would think.

What are the attributes of a crank science layout?

It is hard to describe exactly, but for some reason cranks often use extreme formatting, wild changes in font, color, bolding, all caps, etc. This makes it very hard for normal people to read. But it is highly significant to the crank.

I am speculating, but here are some possible psychological causes: (1) cranks often get ignored, so they feel an increased need to emphasize; (2) cranks (we are familiar with this with creationists) build their theories by obsessively pulling together “information” often ripped from the original context and without understanding the “big picture” empirically.

What are the attributes of a crank science layout?

It is hard to describe exactly, but for some reason cranks often use extreme formatting, wild changes in font, color, bolding, all caps, etc. This makes it very hard for normal people to read. But it is highly significant to the crank.

I am speculating, but here are some possible psychological causes: (1) cranks often get ignored, so they feel an increased need to emphasize; (2) cranks (we are familiar with this with creationists) build their theories by obsessively pulling together “information” often ripped from the original context and without understanding the “big picture” empirically.

————–

Regarding the C-value paradox, or better the C-value enigma: basically, C-value (haploid genome size) correlates not with “complexity” but with cell volume or nuclear volume. This is an extremely strong and striking correlation. To me this seems like an overwhelming and crushingly important fact if anyone is going to discuss the “junk DNA” question in a competent way. And yet the creationists, the news media, and even many scientists don’t seem to be aware of it.

Does anyone have any insight about why it seems so rare for this fact to enter the discussions? I am leaning towards the idea that many people simply were never trained to think like a comparative biologist.

PS: As far as explaining the C-value engima, here is probably the definitive recent review:

Gregory, T.R. (2001). Coincidence, coevolution, or causation? DNA content, cell size, and the C-value enigma. Biological Reviews 76(1): 65-101. pdf

Basically there are two main groups of options:

(1) the variability in genome sizes is due to junk DNA, e.g. because bigger cells experience less selection pressure against genome size; or

(2) the variability in genome size is due to the bulk amount of DNA in a cell nucleus serving some kind of non-sequence specific function, a function based on raw bulk amount of DNA. E.g., the genome size might specify the nucleus size, which would specify cell size, and cell size is under selection e.g. for rapid vs. slow growth.

Something like option #2 seems somewhat more likely to me but AFAIK the issue is not definitively resolved. But even if something like #2 is the case, it is more a case of “junk DNA is functional even though it’s still junk”, sort of like you can make a wall from a pile of any old junk – either way this is a long, long, way from the apparently popular idea that all of this “junk DNA” is serving some highly complex software-like function.

This all seems very clear to me, but it seems almost impossible to communicate to journalists and others who are not used to thinking in terms of comparative biology (I have tried a few times). I think that many people just don’t understand how much diversity there is in biology, and what a big deal it is that this diversity in genome size correlates strongly with another characteristic, cell volume. So the “discussion” in the media procedes without the central facts available in the field.

Suggestions welcome…

Denzel Wrote:

Regarding the C-value paradox, or better the C-value enigma: basically, C-value (haploid genome size) correlates not with “complexity” but with cell volume or nuclear volume. This is an extremely strong and striking correlation. To me this seems like an overwhelming and crushingly important fact if anyone is going to discuss the “junk DNA” question in a competent way. And yet the creationists, the news media, and even many scientists don’t seem to be aware of it.

Does anyone have any insight about why it seems so rare for this fact to enter the discussions? I am leaning towards the idea that many people simply were never trained to think like a comparative biologist.

PS: As far as explaining the C-value engima, here is probably the definitive recent review:

Gregory, T.R. (2001). Coincidence, coevolution, or causation? DNA content, cell size, and the C-value enigma. Biological Reviews 76(1): 65-101. pdf

Basically there are two main groups of options:

(1) the variability in genome sizes is due to junk DNA, e.g. because bigger cells experience less selection pressure against genome size; or

(2) the variability in genome size is due to the bulk amount of DNA in a cell nucleus serving some kind of non-sequence specific function, a function based on raw bulk amount of DNA. E.g., the genome size might specify the nucleus size, which would specify cell size, and cell size is under selection e.g. for rapid vs. slow growth.

Something like option #2 seems somewhat more likely to me but AFAIK the issue is not definitively resolved. But even if something like #2 is the case, it is more a case of “junk DNA is functional even though it’s still junk”, sort of like you can make a wall from a pile of any old junk — either way this is a long, long, way from the apparently popular idea that all of this “junk DNA” is serving some highly complex software-like function.

This all seems very clear to me, but it seems almost impossible to communicate to journalists and others who are not used to thinking in terms of comparative biology (I have tried a few times). I think that many people just don’t understand how much diversity there is in biology, and what a big deal it is that this diversity in genome size correlates strongly with another characteristic, cell volume. So the “discussion” in the media procedes without the central facts available in the field.

Wow. This is really neat. I’ve never heard any of that before.

Nick and Torbjorn said things like:

“I am pretty well convinced that junkdna.com is a crank science website”

and..

“Crank science site layout”

Guys;

You’re being too hard on them. After all, right there on front page (next to pictures of the Guggenheim) is this in big blue letters…

You only believe theories when they make predictions confirmed by scientific evidence

If only we can get the creationist websites to similarly profess their respect for actual evidence, we’ll be on to something here.

Something called “the onion test” should have something to do with putting condiments on hamburgers… :p

Henry

Nick,

Thanks for the reference, it looks really good.

As to why this entire topic is poorly understood, I have a few speculations. This particular field is rather esoteric and not usually covered in most mainstream course work. I am only aware of some of the issues due to a graduate research project. If not for that, I doubt I would have heard about this either.

As for why the press is poorly informed, it seems to me that this topic takes more than seven words to describe adequately. Therefore, the probability of a journalist understanding, caring and educating on this topic is rather low. I’m not saying that all jornalists are stupid, just that they must work under constraints like anyone else.

I do think that you are absolutely correct about comparative biology. In fact I have always felt that this is the real reason why almost no one who gets a degree in Biology remains a creationist. I also believe that lack of this background is why so few creationists ever consider the comparative approach to questions such as the origin of bombadier beetles, etc. The amount of biological diversity never ceases to amaze even professional biologists. To me, this is the most obvious evidence that there was no plan or purpose involved in evolution. If there was, then I guess you have to explain not only why God is so fond of beetles in general, but why she is so fond of weevils in particular. And let’s not forget that, if you have a choice, you should always pick the lesser of two weevils.

stevaroni Wrote:

respect for actual evidence

I sympathize. But I’m going to be nitpicky; the professed intention isn’t enough to free from crankdom. To connect back to nickmatzke’s discussion about large & small fonts:

John Baez Wrote:

7. 5 points for each word in all capital letters (except for those with defective keyboards).

( http://math.ucr.edu/home/baez/crackpot.html )

Mature debates avoid “name calling” and focus on substantial intellectual issues.

Thus, it may not serve useful purposes to “debate” if the http://www.junkdna.com “Junk DNA portal” is a “crank” or “not crank” website. See and decide for yourself. “Don’t bite my finger, look where I am pointing”.

Please come forward with your concept/algorithm/software and application to resolve nasty issues of “junk DNA diseases”; http://www.junkdna.com/junkdna_diseases.html

Dictionary says, “crank” means “esoteric, unusual, etc”; the misnomer “Junk DNA” never was a scientific term. It was an unusual and harmful framing of the budding science of “genome regulation” when Ohno introduced the term “Junk DNA” (1972). Seven years before, Jacobs and Monod won their Nobel for the “Operon” regulation (1965). We’d be much further ahead without framing the vast majority of DNA as “Junk”. (IMHO the late Barbara McClintock, getting her Nobel half a Century delayed, would probably agree).

The site http://www.junkdna.com does not crash any browser/platform. However, the collection of reports, covering cogent arguments is not recommended for “dial-up” novices because of its size; over 10 Mb with archives of earlier years, reaching back to 1972.

The “official” declaration by the NIH-led “ENCODE” consortium that BOTH the “Junk DNA” and “Gene” dogmas were found dead, plus that the Lamarckian question mark was put back on Dogmatic Darwinism were not well-liked by some. The (professional) server of the http://www.junkdna.com site was brought down for a day or two by a tsunami of users, not excluding interference by hackers. (It is up and running at the same url: http://www.junkdna.com ).

I do suggest an issue of substance that might be appropriate for this “blog” — while I reserve preference of disposing IP by means of more appropriate channels.

While I would stay away from “name calling”, I also consider that “beating a dead horse” might not be good use of time (unless you enjoy it). It is no longer relevant to “debate” HOW DEAD “Junk DNA” is.

For science, the new issue of relevance is “simple”: “how does DNA work”? Please put your two cents into a coherent theory. Let’s here some basic concepts, and show experimental evidence for it.

My contribution is that there is an “Algorithmic Design” inherent to the Genome. (More specifically, a fractal design of DNA that results in a fractal growth of organelles, organs and organisms; as sketched out in http://www.fractogene.com). While I don’t recommend scooping IP by “blog debates”, I may need to direct attention to peer-invited and peer-reviewed publications, e.g. experimental support of quantitative prediction(s) of FractoGene, and assert for the record that I have accepted and will consider invitations to disseminate/debate science issues in proper science environment.

In a philosophical sense, I am wishing that “Algorithmic Design” will unite all camps and will focus on identifiable science issues/projects, perhaps discouraging hollow shouting over ideological trenches. If this is a blog about science, let’s stay with science.

While engaging both Nick Matzke (with whom I exchanged a substantive number of emails) and Ryan Gregory (whose work I greatly admire, most notably his reduction of “C-value paradox” to “C-value paradigm” and finally with his 2001 paper to “C-value explanation), here is my take (in a compressed “blog” format…) trying to pass his “Onion test”, which BTW is pretty much the same as Richard Dawkins’ “Salamander paradox” — and my explanation is also consistent with Gregory’s “explanation of C-value” (the former “Junk DNA” ratio corresponding to the “cell size”).

In FractoGene’s terms, the explanation is straightforward, indeed. Fortunately, I don’t have to reiterate it here, since it has been posted on the “Junk DNA Portal” for quite a while: See http://www.junkdna.com/#big_dino_small_genome , http://www.junkdna.com/#biology_unified etc. Suffice to say here that recursive algorithms are notoriously “slow converging” or “fast converging”, at times depending on the slightest diversity in their parameters.

Those who wish to look at “Genomics beyond Genes” through the PostModern frame of “PostGenetics” at real details; the International PostGenetics Society is open for all; http://www.postgenetics.org

Sincerely,

pellionisz_at_junkdna.com

Yep, looks like “crank” about covers it.

Andras,

You had an opportunity to present some science, but chose to expend several hundred words in creationist, crank commentary.

Your entire premise is wrong. That’s not an insult, it’s a fact.

So, prove yourself right.

Over to you.

Maybe use of quotation marks is an indicator of cranks.

Doc Bill Wrote:

You had an opportunity to present some science, but chose to expend several hundred words in creationist, crank commentary.

Damning, as is the fact that he calls a judgment on the presented science and the site (science and presentation) for ““name calling””.

As you say, back to Pellionisz.

Andras Pellionisz said:

While I would stay away from “name calling”, I also consider that “beating a dead horse” might not be good use of time (unless you enjoy it). It is no longer relevant to “debate” HOW DEAD “Junk DNA” is. For science, the new issue of relevance is “simple”…

Why do you use “quotations” seemingly at “random”. It makes “reading” your writing very “difficult”.

Most likely not an original thought, but isn’t “junk DNA” the quintessential argument from ignorance?

“It doesn’t code for proteins, and I don’t know anything else it might do, so it must be junk.”

Kind of like when you wife throws away some important little whatsis because she doesn’t know what it is.

Re “Most likely not an original thought, but isn’t “junk DNA” the quintessential argument from ignorance?”

Uh - argument toward what conclusion?

The presence of non-coding DNA wasn’t one of the arguments for evolution - it was a surprise to the scientists who discovered it.

Henry

Most likely not an original thought, but isn’t “junk DNA” the quintessential argument from ignorance?

“It doesn’t code for proteins, and I don’t know anything else it might do, so it must be junk.”

No, no, no. This is more of what you see in the media – nice thoughts, but no empirical background – and is exactly what I am complaining about. We know (or at least the scientists who work on this know) the following highly relevant facts:

(1) the onion genome has way more DNA than we do, (2) the size of onion genomes varies drastically within the genus by over 4 times, and everything is still pretty much a normal onion (3) this pattern holds not just for onions but for thousands of organisms, plants and animals

Conclusion 1: Most of that extra DNA isn’t doing anything very remarkable. If you can build a perfectly good onion with a 7 pg genome, a 31.5 pg genome is mostly not necessary to build an almost identical onion.

(4) furthermore the differences in genome size are due mostly to repetitive elements that copy themselves, fossil viruses, and other things that look an awful lot like junk in that they are easily explanable by well-known mutational processes but are easily explainable in terms of specific organismal function

(5) Plus, apart from the massive natural experiment in #1-3, researchers have done experiments e.g. with mice where even *evolutionarily conserved* noncoding DNA can be deleted with no apparent ill effects

Conclusion #2: The “junk” DNA might have some function e.g. based on raw bulk amount of NDA, but it is quite obviously mostly *not* doing anything approximating software, “coding”, or other stuff that people usually assume.

Kind of like when you wife throws away some important little whatsis because she doesn’t know what it is.

Wives often still maintain that it is junk even after the husband attempts an explanation… ;-)

Andras - “I publicly introduced the von Neumann principle to Genomics at the 2003 February (Future of Life 50th Anniversary of DNA mtg in Monterey).

Do you mean the field of genomics in general or a specific conference dealing with genomics? If it’s the former, then I think others have long been previously aware of the context dependence of genetic sequences and that data and instructions are “interwoven” and not readily distinguished.

I have to agree with GeoMor’s assement above in comment #184808. There is nothing inherently ‘cranky’ about using fractal mathematics to try to learn something about genomic expression and evolution. I’m certain that such studies will find useful applications (There are some already). But the S/N ratio, lack of specificity in explanations, and unfortuately, huge amount of self-promotion and hyperbolic prose filling those sites don’t aid the transmission of the message.

Syntax Error: mismatched tag at line 3, column 2, byte 162 at /usr/local/lib/perl5/site_perl/5.12.3/mach/XML/Parser.pm line 187

[In an effort to rush this late comment past the spamfilter for several links, I cut and repost. Sorry for eventual double comments.]

Sorry for late response, catching up on old comments.

Andras:

Andras Pellionisz Wrote:

I would welcome private email exchange with you and also with Torbjörn Larsson

No, I’m not interested in email exchanges here, it will be blog comments or not at all.

GeoMor, Whatever:

I agree.

But I must also add that cranks lives in herds, and Andras Pellionisz are sympathetic to design and ID, up to and including embracing their language.

scordova Wrote:

Pellionisz gives a favorable review of a pro-ID article. The article is: How Scientific Evidence is Changing the Tide of the Evolution vs. Intelligent Design Debate by Wade Schaer.

Dr. Pellionisz gives his review at junkdna.com

Cont.:

The quote should be here .

Now, the article can’t be found due to the site design. And Cordova is a known lier.

But I suspect that there once was a review, because Pellionisz himself says in a comment on another UD thread:

Andras Pellionisz Wrote:

Well, it seems certainly true that among Darwinists-turned-Atheists, such as Richard Dawkins, the view that most “junk” DNA must have a function is still much less of a “mainstream” compared to those who suspect a design (even of a mathematical kind) in the DNA. Where is such a tabulation of science findings on functionality of different sorts of “junk” DNA e.g. by Richard Dawkins, as compared to the tabulation of a “blogger” who suspects design:

http://www.junkdna.com/new_cit.….on_of_junk [Bold added.]

Which of course again, doesn’t say anything about the utility of fractal models. But it says something about my view of FractoGene and Pellionisz. :-)

I’ve seen the ID crowd reaction to the discovery that the so-called junk DNA isn’t junk after all. I tried to post over there at their website, but they didn’t want to hear what I had to say.

To wit: I’ve never thought of these sequences as ‘junk’ or even ‘non-coding’, but then I am not a biological science or DNA expert. From a lay viewpoint, one that appears to be holding true, we just don’t know how it fits together yet.

The ‘non-coding’ is mainly occurring between our own ears in our early attempts in trying to figuring it out.

I just tried to point out at uncommon descent that just because the ‘junk’ DNA isn’t ‘junk’ doesn’t strengthen ID’s position at all. I also mentioned that as far as I knew, ID didn’t have the first provable hypothesis by which to test itself.

That didn’t make the cut over there. It was treated like a terrorist threat and banned.

Enjoy.

The http://www.junkdna.com is a site that focuses on what used to be a scientific term “Junk DNA” - e.g. today commemorates with an Obituary the 35th Anniversary of the late Dr. Ohno’s introduction of this now dead misnomer (1972-2007). *That* site is not “ideological” - but focuses on real science issues. As a scientist, I do find (and trying to track down) an “algorithmic design” in the Genome (apparently, a fractal design, both in the Genome and in organelles, organs and organisms that it governs). Such “algorithmic designs” are found elsewhere in natural science (e=mc^2 for one) and in the interest of progress of science (at least, my science) I am trying not to be used by “ideological warfare” of any kind. Regretfully, I have no control of those abusing science/scientists. I find anonymous abuse particularly unfair.

Back to the algorithmic design of the Genome… pleeeease focus on science…

pellionisz_at_junkdna.com

P.S. pleeeease also kindly note (eg. by looking it up) that the etymology of the noun “design” does not necessarily invoke a “designER”.

I do not favor the elimination of the term “junk DNA,” but it is important to understand what the term refers to. In particular, it was never synonymous with “noncoding DNA.”

The junk DNA hypothesis is that some fraction of the noncoding DNA in some species lacks any current function, but is available to serve as raw material for evolution. The junk DNA hypothesis is based upon the observation that morphologically similar species may differ dramatically in the amount of noncoding DNA (e.g. the “onion test”), as well as upon theoretical considerations from evolutionary biology that argue that there should be some sort of equilibrium balance between selection within the genome favoring “selfish DNA,” which propagates (i.e. duplicates itself) within the genome, and selection at the organism level against an excessively large genome size. It is presumed that this equilibrium balance will likely differ from species to species.

The question is not whether noncoding DNA can have important functions–that has been known almost since the dawn of molecular biology–but rather a quantitative one: how much of the genome is true junk? Needless to say, finding a previously unrecognized function for some small fraction of noncoding DNA does not bear on this question at all.

Re “pleeeease also kindly note (eg. by looking it up) that the etymology of the noun “design” does not necessarily invoke a “designER”.”

Yeah, sometimes “design” just refers to a description of the parts of something and their relationship to each other. However, that meaning of the word doesn’t appear to be the one intended by ID pushers.

Henry

Needless to say, finding a previously unrecognized function for some small fraction of noncoding DNA does not bear on this question at all.

Similarly, finding that a small fraction of the noncoding DNA can be eliminated without obvious effect doesn’t bear on the question at all either.

To answer the question we must establish either functions or nonfunction for a large fraction of all the noncoding DNA.

Is this question worth the effort required? Perhaps answers will fall out as a side effect of other research.

Very loose and mostly peri-scientific blogs link between genes and intelligence: WARNING. THE CONTENTS OF THIS REVIEW MAY BE DANGEROUS TO YOUR SCIENCE. Biochemical compounds Nociception behavior expression, of some clock-controlled genes might be used to treat the cognitive dysfunction, which are the top non-self hit. To investigate the possibility of training cellular automata (CA), to perform several image processing tasks with borderline hits in the details, greatly improves the precision of biological analyses. Correlated with a poor patient prognosis as miRNA of nonsense mutation implicated in the binding of 14-3-3. to protein kinase C at the ∞ junction on each side of the brain stem close to the primary sensory apparatus and the mouth if they exist at all, to the estrogen-preferring, member is initially, a very broad distribution of a gradient of a maternal morphogen. Regulatory logic confirmed a link will have a copy of the IQ motif reproductive and nonreproductive functions. And which is as a new member definesthe ability to organize things logically could predict future multiple regression models. In order to investigate this point.

Hey Mark, are you trying to win the contest Dembski alluded to?

We have here an excellent example of a case where “clock-controlled genes might be used to treat the cognitive dysfunction”.

Interesting idea, but my bet, if I did bet, would still be on the UV catastrophe. We didn’t understand it before Max came along and offered some prospect of our doing so.

All those who claim that some of DNA is either junk or non-coding - or whatever term you may wish to use to indicate that we cannot presently find a function for it, may I call it ill-understood DNA? - may wish to consider that the next Planck in our understanding is just around the corner.

The black body survived the UV catastrophe, because that is the way it is in the world in which we live, and I have no doubt that the ill-understood DNA will continue to do what it is supposed to do, for that is the way that it is in the world in which we live, and it will do that whether we understand it or not.

Of course, I hope that it goes without saying that I would like to know what it does and how it does it.

Recent research has been finding that “junk DNA” is, at least in part, used by the genome for encoding RNA. It has been found that the “junk DNA” are regulator genes, turning the other 5% of genes in the human genome that is not referred to as “junk DNA” on and off.

Though this makes deciphering the human genome a more complex job than first anticipated, I do not see where it takes either side of the creation-evolution debate.

Recent research has been finding that “junk DNA” is, at least in part, used by the genome for encoding RNA. It has been found that the “junk DNA” are regulator genes, turning the other 5% of genes in the human genome that is not referred to as “junk DNA” on and off.

Though this makes deciphering the human genome a more complex job than first anticipated, I do not see where it takes either side of the creation-evolution debate.

Again, read the opening post. Why do onions need five times as much of this regulation as we do?

The fact that much of the DNA genome is transcribed doesn’t change anything. The enzymes that transcribe DNA to RNA are not terribly specific. A lot of that RNA is transcribed in very low copy numbers, probably by accident (perfect specificity is thermodynamically impossible), and degraded very quickly. Some vertebrates work perfectly well with only 10% of our genome and with very little of the repetitive DNA, fossil viruses, etc., that you seem to think must be functional because it is transcribed. On the other hand, ferns, onions, etc. can have up to hundreds of times more DNA in their genome that humans have. Are you really going to assert that all of that has some specific regulation function?

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This page contains a single entry by Nick Matzke published on June 22, 2007 11:47 PM.

Correction to Liu & Ochman paper was the previous entry in this blog.

Dembski versus Europe is the next entry in this blog.

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