Continued Uncommon Junk Talk

| 65 Comments

On Uncommon Descent, defender of ID against creationist nonsense, Davescot makes the following comment about a posting by Paul Nelson about the fascinating complexity of the genome:

DaveScot Wrote:

I still fail to see how ID predicts no junk DNA. Random mutation definitely happens and if it’s good at *anything* it’s good at producing unorganized, non-functional crappola. It can produce crap out of nothing and it’s even better at making crap out of stuff that wasn’t crap to begin with.

Of course, Davescot has failed to follow the ID game play which includes the fallacious argument that ID predicted Junk DNA to have function. A poster name BFast is quick to remind DaveScot of his technical foul.

Bfast Wrote:

Bottom line, significant IDers have said for a long time “there’s value in that junk” and the darwinists have said the opposite, that “there cannot be value in that junk because there would be too many mutations per generation to be managed by RM+NS.”

The IDers said it, it proved to be true, it’s a confirmed prediction.

BFast is Right, Wrong and Wrong. Not too shabby for an ID defender.

Right in that ID proponents have argued that based on theistic considerations, Junk DNA could not possibly be junk. He is wrong that this is a prediction of ID which cannot state more than “design is that which we do not fully understand” and he is wrong as to how Darwinists have seen Junk DNA.

And the myth continues…

Which shows once again that despite the valiant efforts of DaveScot, ID is still scientifically vacuous.

65 Comments

Maybe the reason IDists are so intent on retaining the “all junk DNA has function” idea is because so much of it is common across humanity, and even across species. If they say it has no function, they risk destroying their “big tent” by alienating YECs. YECs *have* to believe God created each species with it’s “junk DNA” 6,000 years ago, and He “must’ve had a reason”.

It is really an important issue for you people. The people that controll the editorial content of this forum continue to edit out my comments. The concepts that are embodied in my comments are NOT TRIVIAL AND NEED TO BE ADDRESSED BY ANY LEGITIMATE SCIENTIFIC POSITIONS BEING PUT FORTH IN ANY KIND OF MEANINGFUL ARENA OF SERIOUS DISCUSSION REGARDING SUCH MATTERS. Who are these people? Why don’t you as (apparently intelligent individuals who at the very least need to open mindedly consider all perpectives that viably have some legitimate statements to make regarding the topics at hand in order to even self-consider your status as a “real” scientist let alone put yourself out to the public as such.) YOu who are being paid by the public trust funds, should require yourselves to look beyond your philosophical yearnings and respect the individuals who are funding your endeavors to the point where you consider the vast array of unanswered questions remaining in respect to the (what is best described at this point) philosophical assertions put forth by the macro-evolutionary “priests”. Thank you very much.

Ka-ching…$$ .. $$ Neal you are a gem…

Tinyfrog.…

are you saying that the lack of Junk DNA is a prediction of YEC that has been confirmed?

Alan:

Tinyfrog.…

are you saying that the lack of Junk DNA is a prediction of YEC that has been confirmed?

It’s a prediction based on unfounded assumptions as to what a designer would or would not do. It’s a theological argument more than a scientific one.

PvM

Right in that ID proponents have argued that based on theistic considerations, Junk DNA could not possibly be junk

1. Was the claim that the “junk DNA” is not “junk” at all done by ID scientists based on theological considerations?

2. Even if it was based on theistic assumptions, the truth is that they got it right, while Darwinists got it wrong.

Tinyfrog:

YECs *have* to believe God created each species with it’s “junk DNA” 6,000 years ago, and He “must’ve had a reason”.

YECers do not believe that God created “each species with it’s junk DNA 6,000 years ago”.

Biologists have been very quick to call any DNA they don’t understand junk. Maybe because MET predicts lots of junk. But anyone who questions MET, and its underlying philosophy, is more likely to think the “junk” has unknown functions.

The more that is learned about DNA, the less understandable it seems. It’s similar to the situation in physics – when they figured out how to split the atom everyone thought it would be a short while before the ultimate components of matter were discovered and understood. Instead, physics is now lost in the wilderness of matrix theory and string theory, etc.

The same thing is happening in genetics. Most DNA is non-coding, and scientists are beginning to realize that does not mean it does nothing. In fact, the so-called junk may turn out to be much more important than the small percent that is now considered non-junk.

In Darwin’s time, cells were thought to be simple. As soon as genetics was discovered, everything clicked into place. Or so they thought.

DNA will turn out to be at least as baffling and strange as the subatomic world has turned out to be.

For me, that is not a cause for despair. I expect nature to be infinitely more intelligent than ourselves. It doesn’t mean science is worthless, it just means we will never be god-like and able to completely understand and control nature.

When some of the “junk” DNA is found to have a purpose, that doesn’t prove ID or disprove MET. It isn’t that simple. But the more complex and intelligent DNA turns out to be, the less plausible the current MET will seem.

Neal, where can I get some of that “public trust fund” money?

Mats: “ID scientists”?

There aren’t any.

Oh, wow!

Neal, Mats and realpc all posting in the same thread. This is gonna take a while.

Neal Wrote:

It is really an important issue for you people. The people that controll the editorial content of this forum continue to edit out my comments.

Well, except this one. But if your accusation was true, wouldn’t they edit this comment too?

Anyhoo, Neal, IIUC, comments are edited if they are (1) wildly off-topic, or (2) offensive. This should make it easy to adopt a couple of rules of thumb that would ensure that most of your comments don’t get edited out.

The concepts that are embodied in my comments are NOT TRIVIAL AND NEED TO BE ADDRESSED BY ANY LEGITIMATE SCIENTIFIC POSITIONS BEING PUT FORTH IN ANY KIND OF MEANINGFUL ARENA OF SERIOUS DISCUSSION REGARDING SUCH MATTERS.

That depends, actually. If you are challenging what is accepted as mainstream science, the correct place to make that challenge is the scientific literature, and the tools to make that challenge are hard data and logical deductions from the data. Essentially, it is not up to the editors / moderators of a weblog to answer your challenges against widely-accepted science.

However, you are fortunate, because this particular blog is visited by several scientists who are prepared to answer any relevant question you pose, as long as you do so politely.

Who are these people?

Well, I don’t think any of the main PT contributors make any attempt to hide their identity. Just follow some of the links from the navigation options, and you should be able to find out.

Why don’t you as (apparently intelligent individuals who at the very least need to open mindedly consider all perpectives that viably have some legitimate statements to make regarding the topics at hand in order to even self-consider your status as a “real” scientist let alone put yourself out to the public as such.)

Eh?

YOu who are being paid by the public trust funds, should require yourselves to look beyond your philosophical yearnings and respect the individuals who are funding your endeavors to the point where you consider the vast array of unanswered questions remaining in respect to the (what is best described at this point) philosophical assertions put forth by the macro-evolutionary “priests”. Thank you very much.

I’m not aware of any unanswered questions in relation to evolution. Perhaps you are not aware of where the answers are published.

Try this link: http://www.talkorigins.org/indexcc/ where most of the published claims of creationist authors are answered.

If this does not answer your questions, perhaps you could pose them one at a time (where they are relevant to the topic of the blog entry) to allow commenters to answer them?

At least here they have an opportunity to contradict DaveScot without the risk of being banned.

Realpc evidently hasn’t heard of the onion test, Neal needs to publish his science (whenever he finds any) in the nearest refereed journal if his need for attention is so acute, and Mats needs to read Douglas Theobald’s article in the talk.origins archive.

Mats Wrote:

1. Was the claim that the “junk DNA” is not “junk” at all done by ID scientists based on theological considerations?

Well, it certainly wasn’t based on science. It is apparently based on good design principles, i.e. what is all that DNA for if it doesn’t code for anything? It must have a purpose, therefore it isn’t junk.

OTOH, MET is quite happy with it being a relic of old genes or with having a function. IIRC, about 5% of non-coding DNA is strongly conserved and so is suspected (by scientists) of having a function. So it actually looks like the non-coding DNA contains both functional elements and evolutionary leftovers.

2. Even if it was based on theistic assumptions, the truth is that they got it right, while Darwinists got it wrong.

Well, not really, because no scientist ever actually claimed that none of it served a purpose. The term “junk DNA” was coined as a joke, not a technical term.

And, who was it that discovered that non-coding DNA has a function? Was it IDists? Nope, it was scientists. How did they discover it? By sequence comparisons, which are only meaningful in the context of MET. If you deny common descent, you deny the ability of science to detect regions of non-coding DNA that are conserved.

Mats Wrote:

YECers do not believe that God created “each species with it’s junk DNA 6,000 years ago”.

I notice that you underlined the words “each species”. I guess you meant to indicate that YECs tend not to claim that a “kind” is the same thing as a species.

However, you seem to have missed the point. Each kind of organism (whether you take “kind” to mean genus, species, sub-species, breed, variety or family) has much non-coding DNA. If the non-coding DNA serves no purpose, this is a problem for YEC, because it indicates seriously sub-optimal design. In fact, even if only a few portions of it serve no purpose, it is a problem for YEC.

I tried to suggest the absolute minimum that ID would need to do in order to be viewed as scientific on this topic. I was not even expecting *data*, so this is less than is demanded of scientists who work on this subject. No responses yet, except some sarcasm on an ID blog.

An opportunity for ID to be scientific

realpc Wrote:

Biologists have been very quick to call any DNA they don’t understand junk.

On the contrary. “Junk DNA” is not used as a technical term, only a casual one. The technical term is “non-coding DNA”, and it remains that even if some parts of non-coding DNA are found to have a function. We are able to assign this appellation because any coding region must contain (or be a part of) an open reading frame (ORF). ORFs are easy to identify with modern analytical tools. Anything that isn’t an ORF is either a regulatory region or unknown. The DNA outside ORFs is termed non-coding DNA.

And, just to get a little picky here: scientists understand DNA. What we don’t know is what some of it does. There is a difference, albeit a subtle one.

Maybe because MET predicts lots of junk. But anyone who questions MET, and its underlying philosophy,

The underlying philosophy is this: starting from “we don’t know”, examine the evidence, then make logical deductions from the evidence.

is more likely to think the “junk” has unknown functions.

It’s fortunate for us, then, that “junk DNA” is not a term used in any technical sense by biologists and molecular biologists, isn’t it? Large sections of non-coding DNA have no known function.

A scientist can acquire kudos (and hence further funding) by identifying functions that were previously unknown. Plus, they are driven by the same insatiable curiosity that made them become scientists in the first place.

The more that is learned about DNA, the less understandable it seems.

Well, maybe that means you need to work harder at the fundamentals, hmm?

Our understanding of the function of DNA and its interactions with other parts of the cell and of the organism as a whole continues to deepen.

It’s similar to the situation in physics – when they figured out how to split the atom everyone thought it would be a short while before the ultimate components of matter were discovered and understood. Instead, physics is now lost in the wilderness of matrix theory and string theory, etc.

Matrix theory? I shall assume you mean brane theory. It is true that, at the start of the 20th century, there was, in some quarters, an unjustifiable optimism about physics. However, such unjustifiable optimism has never been seen in biology.

It is true that intracellular signalling systems are more complex than was first imagined, and it may be true that the regulation of gene expression is also more complex than was initially imagined, but this does not imply that biology is getting harder to understand. What it implies is that our understanding is getting closer to reality.

The same thing is happening in genetics. Most DNA is non-coding, and scientists are beginning to realize that does not mean it does nothing.

I am sure that most scientists have always accepted that non-coding DNA may have a function. I dimly recall attending a lecture in the late 1980s in which the lecturer expressed his personal feeling that non-coding DNA served some kind of purpose.

In fact, the so-called junk may turn out to be much more important than the small percent that is now considered non-junk.

Except that none of it is considered to be “junk” by biologists, so I’m not sure what you mean here. Of the non-coding DNA in our genome, it is suggested that about 5% has a function; this figure arises from sequence comparisons that indicate strongly conserved stretches of non-coding DNA. This 5% could have a very important function. However, the other 95% of non-coding DNA may genuinely have no function at all. Or it may have a function that is less important and is less likely to give rise to conserved sequences.

In Darwin’s time, cells were thought to be simple.

Yes, and he went to great lengths in TOOS to emphasize our ignorance about so many details of biology.

As soon as genetics was discovered, everything clicked into place. Or so they thought.

Can you supply a source for this statement? I’d be interested to know who it was that thought that understanding Mendelian genetics would solve all the remaining mysteries in biology.

DNA will turn out to be at least as baffling and strange as the subatomic world has turned out to be.

This is unlikely, because DNA operates on a scale of intermolecular interactions, and the laws that govern these are well understood. Subatomic physics, OTOH, had to work out a new set of laws as it went along.

For me, that is not a cause for despair. I expect nature to be infinitely more intelligent than ourselves.

Speak for yourself!

It doesn’t mean science is worthless, it just means we will never be god-like and able to completely understand and control nature.

I disagree. There is nothing fundamental that says “humans can understand so much but no more”. I believe that the universe can be understood by humans.

As to controlling nature, we already do this to a large extent. You only have to look at our domestic breeds of dog, cat, chicken, cattle and so on to see this.

When some of the “junk” DNA is found to have a purpose, that doesn’t prove ID or disprove MET.

I agree. However, MET allowed the discovery to occur - without MET we would not have been able to derive meaning from the sequence comparisons.

It isn’t that simple. But the more complex and intelligent DNA turns out to be, the less plausible the current MET will seem.

What is the basis for this claim? How can DNA be more “complex” and “intelligent”? What do these terms mean when describing a molecule that I can draw on a page to atomic detail? How are we to measure an increase in the “intelligence” or “complexity” of DNA? And how exactly would such an increase pose a problem for MET?

You tease, realpc. You have raised a potentially interesting point but failed to develop it.

realpc wrote:

“When some of the “junk” DNA is found to have a purpose, that doesn’t prove ID or disprove MET. It isn’t that simple. But the more complex and intelligent DNA turns out to be, the less plausible the current MET will seem.”

I really hate to so this, but for once I agree with realpc. In fact, some “junk” DNA has been found to have a “purpose”, (or at least a function), that has only recently been discovered. Indeed, that doesn’t prove ID or disprove MET. It merely shows that some things are not yet fully understood and that science is always making progress. It also means that current evolutionary theory will definately have to be revised and updated in order to account for the new knowledge. Of course that really isn’t a problem, since it has already happened repeatedly since Darwin published The Origin of Species.

Still, there are good theoretical reasons for provisionally assuming that the majority of “junk” DNA indeed has no function. This observation can easily be accounted for by MET. However, if YECs or IDists or anyone else wants to predict that all DNA has a function and that there really is no such thing as “junk” DNA, then the burden of proof is on them to demonstrate the function and to explain the observations better than the “junk” hypothesis. Until they do, they can whine about our lack of understanding all they want, but no one is going to take them seriously until they get into the lab and do some science.

I do have to disagree with realpc on one point however. I don’t really think that calling DNA “intelligent” is useful or meaningful, especially if you can’t define it, measure it, or test it. DNA can be selected, adapted, information-rich, complex, etc. but it cannot be “intelligent” as anyone making the claim has already demonstrated.

Neal:

Who are these people? Why don’t you as (apparently intelligent individuals who at the very least need to open mindedly consider all perpectives that viably have some legitimate statements to make regarding the topics at hand in order to even self-consider your status as a “real” scientist let alone put yourself out to the public as such.) YOu who are being paid by the public trust funds, should require yourselves to look beyond your philosophical yearnings and respect the individuals who are funding your endeavors to the point where you consider the vast array of unanswered questions remaining in respect to the (what is best described at this point) philosophical assertions put forth by the macro-evolutionary “priests”. Thank you very much.

My wife, a real scientist (i.e. a researcher and published in many solid-to-prestigious journals, including Cell, Nature, blah, blah, blah) read your comment and got a good laugh. She says that while she is paid from public funds, her job is to teach you that there are no “magical flying ponies, and” to debunk your belief that your “magical flying pony theory” is serious science.

In my terms, her job is to teach you, not keep you ignorant and kow-tow to your demented ignorance and you need to STFU and grow up.

RealPC, you need to back up your statements.

A while ago, people started hammering you about ID being an actual ‘theory’ or not. So you just waved your hands and disappeared.

I know you’re busy. We all are.

Yet if you are going to take the time to post an assertion, then you need to take a little more time to actually back up your statements.

Hit-and-run postings don’t cut it.

Post here by all means…but make coherent arguments. Please.

Mats said in regard to “predictions” by ID “scientists”

2. Even if it was based on theistic assumptions, the truth is that they got it right, while Darwinists got it wrong.

even a broken clock “gets it right” twice a day

and “Darwinists” (I assume he means actual scientists) never “predicted” that non coding DNA is non-functional - just that it has no known function. The absence of evidence is NOT evidence of absence

in addition you don’t get credit for making a “prediction” without proposing a testable/disprovable mechanism that shows how you made the prediction- this is why astrology and the psychic friends network are not considered scientific endeavors!

Dearly beloved we are gathered here today to praise “real” scientists.

Now all please hold hands and kneel (or you will be Nealed in your public purse by farce).

Oh Darwin we beseech you, show us a sign.

*a cricket chirps*

(couldn’t resist k.e.)

realpc wrote: “For me, that is not a cause for despair. I expect nature to be infinitely more intelligent than ourselves. It doesn’t mean science is worthless, it just means we will never be god-like and able to completely understand and control nature.”

I’m not sure what you mean by nature being more “intelligent” than ourselves. But I do believe that there will always be a scientific frontier and that mankind’s’ destiny is to continue to challenge that frontier. Some would say that our reach exceeds our grasp for a reason, I think that this property of our being pre-disposes us to be explorers, to push the edge of the envelope so to speak. Why would this be a cause for despair? it is the source of wonder!

David Stanton Wrote:

Still, there are good theoretical reasons for provisionally assuming that the majority of “junk” DNA indeed has no function. This observation can easily be accounted for by MET. However, if YECs or IDists or anyone else wants to predict that all DNA has a function and that there really is no such thing as “junk” DNA, then the burden of proof is on them to demonstrate the function and to explain the observations better than the “junk” hypothesis. Until they do, they can whine about our lack of understanding all they want, but no one is going to take them seriously until they get into the lab and do some science.

I agree. I might go a little further still. The existence of DNA that has no function would pose a challenge to any form of creationism, be it YEC, OEC, DAC or ID. While it is, of course, impossible in principle to prove that a particular stretch of DNA has no function at all, as we find functions for various bits of the non-coding DNA, the remaining non-coding DNA that has no known function will still be there. Waiting.

MET can happily accommodate non-functional DNA (in fact, pseudogenes are a confirmed prediction of MET). Any system that postulates design or any kind of teleology has to explain why there is nonfunctional stuff present at all. As we find more functions for non-coding DNA, the possibilities for what remains will diminish. One day, we may well end up facing the fact that some of our DNA has no function at all.

mats:L2. Even if it was based on theistic assumptions, the truth is that they got it right, while Darwinists got it wrong.

nope, darwinists did not get it wrong and no creationists did not make a prediction based on ID

Even before I clicked the Comments link, I predicted that realpc would post his junk arguments on a thread about “junk DNA.” And, lo and behold, my prediction proved true. I’m a scientist! WOOHOO!!

I now offer a testable hypothesis: realpc is attracted, as if my magnetism or some mindless atavistic force, to posts about “junk DNA,” and is compelled to repeat the same old discredited arguments he’s already posted innumerable times before. After experimental verification, I guess the next step would be trying to identify the specific force. (It’s probably not supernatural – I’ve never heard of any spirits that stupid.)

Possible functions for non-coded DNA:

1. Each length serves as a bridge to connect the lengths on either side. Without that length of so-called junk, the opposite ends would drift apart. Think about it.

2. They serve as repositories for nucleic acids. If a gene is short a cup of cytosines, it can borrow them from the junk pile.

3. They sequester atoms that otherwise might spontaneously combine to form toxic snake venoms.

4. They make the ‘slack’ in the chromosome. Without them, the chromosome would be far too tight and snap like a rubber band when its tied up in those ‘X’ shaped thingies.

For those interested in DNA, there are some spectacular models of DNA at the thednastore.com. Select the Models option. I particularly like the children’s DNA toy. I think we will all agree it is never to early to start learning about DNA.

Having a model of this extraordinary molecule at hand, brings a certain reality to these discussions. Perhaps some of the ID advocates could use these models in an effort to find a theory and begin some research.

I will also note that Watson and Crick bobble head dolls, a bronze bust of Charles Darwin, and a spectacular DNA lamp are available.

While I have no affiliation, thednastore.com, is the most enjoyable webstore I have every encountered.

rog

It’s monotonously true that IDists are wholly disingenuous in pretending to predict anything at all, including “junk DNA,” because they accuse us of being unfair any time we note “poor design” or some such thing. As junk DNA happens to be “poor design” compared with any sort of optimal design (ignoring the need for evolutionary material and mechanisms, that is), and that’s how it’s largely been portrayed in these exchanges, either the IDists need to acknowledge that they do predict that there is little or no “poor design”, or acknowledge that they cannot predict anything about “junk DNA.”

OK, but that’s obvious. Almost certainly the real reason they claim to predict it, other than that they like to pretend to be doing science, is that they deny (in essence) evolution and its mechanisms. We said that there is useless DNA (typically we’re careful about not claiming that too much is useless), they said that MET doesn’t work, so when some “junk DNA” is found to be useful they think that they predicted something. We, of course, have tended to point to specific “junk DNA”, like the defunct gene in primates for manufacturing ascorbic acid. Unsurprisingly, they ignore all the details and try to claim that the fact that some “junk DNA” has functions is a triumph for ID. Well, it isn’t, because, not just the devil, but everything in science is in the details, and ID lacks the ability to deal with details at all.

The fact of the matter is almost certainly that eukaryotic evolution does depend upon non-coding DNA in order to provide some of the important material of adaptation (chromosome doubling is evidently important even in animals). In that sense, actual “junk DNA” really isn’t “poor design” in any sense (I’m writing of “junk” overall, not the parastitical and damaging DNA), rather it is important material for the very processes that IDists deny. If we were to grant that ID predicts that important evolutionary mechanisms do not occur–which it really cannot do, and which “prediction” thus couldn’t provide any evidence for ID even if they were fulfilled–in that sense we might grant that ID predicts little or no junk DNA. But of course ID has to make its own predictions if it is to ever be science, hence its sheer denial of evolutionary mechanisms yields no inherent predictions at all.

And really, the issue is not “junk DNA” at all, it is non-coding DNA, which ID cannot explain where it provides regulatory functions, where retrotransposons have inserted “junk” that either has or has not been subsequently adapted for our use, where transposons produce damage, or where the “vitamin C gene” has evidently evolved out of a functional gene. A real science would address the specifics, as MET does, while only a pseudoscience would treat all non-coding DNA as if it constituted a single category.

It is ID’s inability to explain any single thing, or any of the integrated complexities of life, that makes it such a woefully bad excuse for “science”. For, it thinks that it becomes science if it manages to find any flaws in the actual science by dint of “winner-takes-all” rules. Real science, though, explains real data, instead of mistaking science as a fight to win against the hated “atheists”, or whoever the enemy might be.

IOW, IDists continue to project that evolution exists to get rid of God, so their only goal is to defend “God”, as if any real God would need their pathetic “defense”. This is why they can’t even imagine what science is, and thus cannot imagine what it would take for ID to be science.

Glen D http://tinyurl.com/2kxyc7

Seems like that in the long run, it’s probably a bad idea to refer to a technical detail (such as proteins don’t get used to generate DNA or RNA) as a “central dogma”. It wasn’t a dogma, it was a conclusion to be tested.

Henry

But getting back to Neal….

No thanks, I’d rather not. ;)

Henry J– Yeah, Crick regretted the term later. He told the science writer, Horace Judson, “.…one has paid for this terribly, because people resented the word ‘dogma,’ you see, and if it had been ‘central hypothesis’ nobody would have turned a hair.” But, since Crick was at least an agnostic, if not an atheist, he didn’t take a religious term like dogma very seriously. He was partly telling people, though, NOT to treat it as an hypothesis to be tested, because it looked like it wouldn’t pan out. So they concentrated on how nucleic acid codes for protein instead– which turned out to be an immensely fruitful line of research. At this point, it would probably be better if the entire term ‘central dogma’ was dropped, but it seems to have taken on an entire new life as a strawman to be knocked down– more’s the pity.

One day, we may well end up facing the fact that some of our DNA has no function at all.

“One day”?

Over half of the human genome consists of rotting retrovirus corpses in various stages of decay. What good can half a transposon, with its excision sites and start codons mutated and random stop codons introduced, possibly be?

Then there’s the repetitive stuff. This is where (slight) variations in the amount are found between individuals; that’s how paternity tests work. But what else can millions of repeats of (for example) GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA be good for?

That doesn’t leave much. The most optimistic estimates say that 20 % of the human genome – as opposed to 3 or 5 – might have a function.

Then there’s the onion test…

Then there’s the experiment: if you cut out several megabases of junk out of a mouse, what happens to the mouse? Nothing. Done, published.

There does seem to be one function for genuine junk: genome size is correlated to cell size, and cell size has influence on metabolism and the like. But this is a function of the amount of junk, not a function of what the junk precisely is. Take all my junk DNA and replace it with random copies of a randomly chosen part of the junk DNA of a random amoeba – I bet nothing would happen, as long as the amount doesn’t change by more than a few tens of megabases or something.

Possible functions for non-cod[ing] DNA:

Note that none of them suggests a function for a specific sequence, only for the sheer bulk of junk:

1. Each length serves as a bridge to connect the lengths on either side. Without that length of so-called junk, the opposite ends would drift apart. Think about it.

I don’t understand that. Please explain.

2. They serve as repositories for nucleic acids. If a gene is short a cup of cytosines, it can borrow them from the junk pile.

That’s not how DNA replication works. The junk is just as faithfully repaired as the rest; the repair enzymes can’t read.

3. They sequester atoms that otherwise might spontaneously combine to form toxic snake venoms.

Snake venoms are proteins. Proteins don’t form spontaneously. To make a protein requires energy and a template – a gene. Plenty of genes for snake venoms have been sequenced.

4. They make the ‘slack’ in the chromosome. Without them, the chromosome would be far too tight and snap like a rubber band when its tied up in those ‘X’ shaped thingies.

Without junk, the chromosome wouldn’t need to be wound up like that, which is done to save space. You have it backwards. :-)

David Marjanovic Wrote:

“One day”?

Over half of the human genome consists of rotting retrovirus corpses in various stages of decay. What good can half a transposon, with its excision sites and start codons mutated and random stop codons introduced, possibly be?

Then there’s the repetitive stuff. This is where (slight) variations in the amount are found between individuals; that’s how paternity tests work. But what else can millions of repeats of (for example) GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA be good for?

That doesn’t leave much. The most optimistic estimates say that 20 % of the human genome – as opposed to 3 or 5 – might have a function.

Then there’s the onion test…

Then there’s the experiment: if you cut out several megabases of junk out of a mouse, what happens to the mouse? Nothing. Done, published.

There does seem to be one function for genuine junk: genome size is correlated to cell size, and cell size has influence on metabolism and the like. But this is a function of the amount of junk, not a function of what the junk precisely is. Take all my junk DNA and replace it with random copies of a randomly chosen part of the junk DNA of a random amoeba – I bet nothing would happen, as long as the amount doesn’t change by more than a few tens of megabases or something.

You raise a good point. I was oversimplifying. Of course we have much DNA that is known to be non-functional in terms of its original function (e.g. ERVs, pseudogenes, multiple repeats). However, I did not wish to rule out the possibility that these chunks of redundant code may actually be doing something useful now. If their new function is subtle, it may be difficult to detect and / or elucidate.

However, when we have more powerful tools for associating functions with specific stretches of DNA, then we may be able to make a reasonable and confident claim that certain chunks of DNA serve no function at all.

About this Entry

This page contains a single entry by PvM published on September 24, 2007 3:16 PM.

Fiskin’ Luskin: Anti-religious or Pro-reality was the previous entry in this blog.

Dinosaurs, Birds, Feathers, and Conodonts (Oh, My!) is the next entry in this blog.

Find recent content on the main index or look in the archives to find all content.

Categories

Archives

Author Archives

Powered by Movable Type 4.361

Site Meter