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[P]
Junk DNA - of mice and men

By imrdkl in News
Tue May 07, 2002 at 03:39:21 PM EST
Tags: Science (all tags)
Science

The sequencing of the mouse gene has recently been completed, and the gene-sequence database along with plenty of other information is available for free (as in speech and beer) from the Mouse Genome Server. The effort has been yet another impressive collaboration among US and European research institutes, to increase and disperse genetics knowledge. Their PDF announcement is filled with references and summary information.

The project has yielded interesting results. Some of the results were expected, but at least one big surprise was found. It turns out that so-called Junk DNA in mice is quite similar to that found in humans. Why does this matter? Read on to find out.


While Junk DNA is interesting and controversial, the mouse gene-map will likely also be a win for humanity, in terms of its potential to further the study of diseases which have known (as opposed to junk) DNA characteristics. With the mouse gene-map in hand, it's hoped that genetic contributors to these illnesses can be more quickly identified. Another interesting result to come out of this research is that approximately 75% of the mouse genes identified have a firm counterpart in the human genome. This fact will make genetic inference from mice to humans easier, and more "believable". Improved tests and treatments for diseases will also hopefully follow.

Reuters has an article about this news, including excerpts from an interview with the head of the National Human Genome Research Institute, Dr. Francis Collins. The article goes on to state that it's clear that

"Junk DNA is not unique to humans, and it is important enough to have lasted through the millions of years of evolution that separate mice and people".
But what is Junk DNA, anyway?

Junk DNA has long been a mysterious lurker in the study of genetics. The study of DNA has yielded a lot of information about a very small percentage of the DNA in the human genome. The rest, as much as 97% of the total, has been given the Junk modifier, because scientists were unable to ascribe any particular function to it, and it did not code any specific proteins. During the late 90s, there were some interesting discoveries about Junk DNA, which have begun to give a hint about its true nature. Prevailing opinions now seem to concur - there's just too much structure and organization in the sequences of Junk DNA for it to be just "molecular garbage".

There is speculation now that Junk DNA may contribute to the regulation of cellular processes, and may even hold answers to runaway cell processes like cancer. Google will help you find lots more discussion on the subject, including articles which which put forth theories that junk DNA might be something like a hidden language or a secret message with its "striking resemblance" to human language. Others have claimed, and countered, that Junk DNA is proof of evolution, since it argues against intelligent design. Junk DNA is certainly a controversial topic. It's hoped that the surprising similarities which have been verified between mouse Junk DNA and human Junk DNA will open new possibilities for research to resolve some of the controversies, and gain practical information from what was formerly called junk.

Whether you're interested in Junk DNA, or the well-known variety, the mouse gene server (also linked above) provides extensive searching capabilities based on sequence-id, markers, expressed sequence tags (EST), and single nucleotide polymorphisms (SNP). Even if you know little or nothing about genetics, it's worth a look - if only to see the colorful maps, PDF announcements and documentation.

The mouse gene-mapping effort was jointly undertaken by a number of distinguished research institutes, and other interested parties, including government organizations. The credits are impressive. As mentioned, the information produced by this effort is 100% free. This includes the mouse gene-map, as well as the human, zebrafish, fly, and mosquito gene maps. The free availability, however, may be considered a blow to Celera Genomics Inc., which is attempting to sell the same information for profit.

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Poll
Junk DNA - what is it?
o secret message 33%
o hidden language 6%
o random gobbledigook 16%
o something else (pray, tell) 42%

Votes: 59
Results | Other Polls

Related Links
o Google
o Mouse Genome Server
o PDF announcement
o article
o National Human Genome Research Institute
o 97% of the total
o discussion
o hidden language
o secret message
o proof of evolution
o gene server
o credits
o Celera Genomics Inc.
o Also by imrdkl


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Junk DNA - of mice and men | 92 comments (74 topical, 18 editorial, 0 hidden)
I make no claim to be an expert, (4.00 / 2) (#1)
by FredBloggs on Tue May 07, 2002 at 12:34:03 PM EST

but surely the approach `we dont understand it, so its probably just junk` (regarding junk DNA) was never likely to be helpful or true?


it was a little more than that (5.00 / 3) (#7)
by mongoose on Tue May 07, 2002 at 12:52:19 PM EST

It wasn't just that we didn't understand it- Junk DNA sequences appear to not encode proteins, which in the classical Moecular Biology paradigm (DNA->RNA->Protein) makes them nonfunctional.

You are correct, however, that the idea that these bits are 'just' junk is a little, um, agressively simplistic, and many researchers have believed for some time that they are somehow important. However, it was always possible that while these sequences were needed as 'spacers' or whatnot, they themselves had no active role in anything (sort of like how from the point of view of using a door under normal circumstances it doesn't matter whether it's oak or pine). The sequence composition may not have mattered, as long as x amount of junk was there.

Data like that discussed in this article, however, gives real support to the idea that jDNA plays a sequence-dependent role in cellular processes. If those sequences are maintained in disparate species, that might mean that loss of the specific sequences yields an inviable organism.

-m

[ Parent ]

junk (4.66 / 3) (#8)
by ucblockhead on Tue May 07, 2002 at 12:59:29 PM EST

The idea that it might just be random crap isn't as unrealistic as it may sound as evolution by natural selection has no way of getting rid of anything that is not harmful. Anything that is simply pointless will get passed on randomly. That's the "classic" reasoning as to why junk DNA exists. It has no negative effect, so it just sort of hangs around.

The thing about Evolutionary Theory is that it doesn't require that everything you find in a creature have definite positive impact. It only says that things that have negative impact will fade away over time.

I'm not saying that this is the case with junk DNA, merely that this is a reasonable thing to think.
-----------------------
This is k5. We're all tools - duxup
[ Parent ]

Yep. (4.50 / 2) (#9)
by ambrosen on Tue May 07, 2002 at 01:03:00 PM EST

But I'd have thought there'd be a pretty noticable overhead to creating all this "useless" DNA, so that would be something which made it at least slightly actively harmful. I couldn't begin to calculate how much effort generating it may actually cause, though.

--
Procrastination does not make you cool. Being cool makes you procrastinate. DesiredUsername.
[ Parent ]
true (4.66 / 3) (#13)
by ucblockhead on Tue May 07, 2002 at 01:15:56 PM EST

But one might make the argument that by "spacing out" the real genes, junk DNA makes it less likely that some biochemical burble will take out multiple genes at once, making lethal mutations less likely.
-----------------------
This is k5. We're all tools - duxup
[ Parent ]
well... (4.50 / 2) (#14)
by mongoose on Tue May 07, 2002 at 01:16:23 PM EST

Mostly true, except that with that much sequence one should be able to compare the expected baseline genetic drift through random mutation with the actual mutation rate in the junk DNA.

DNA sequences do change over time for 'no apparent reason','Natural Selection-wise (because NS is acting on the products of naturally-occurring divergence, not the other way around).

Even within protein-encoding sequences that 'matter' there is substantial variation from species to species, presumably due to spontaneous mutations induced by the environment. These sequences, in the absence of selective pressure, should change at a fairly constant rate from species to species; if they don't, it might mean that the exact sequence is important.

-m

[ Parent ]

Way too much speculation:) (5.00 / 2) (#22)
by trhurler on Tue May 07, 2002 at 02:07:13 PM EST

The exact sequence may not matter, but characteristics of it which happen to be fairly rare in combination may matter. For instance, length and shape. Yes, DNA is a double helix, but it isn't as simple as the structure people see in textbooks; it does bend around depending on its exact composition, and there's precisely zero proof that this bending around never matters. It is a structure in three dimensions, and maybe that structure is important in and of itself. Or, maybe the sequences are markers. We use our own markers to determine where things are, but the assumption that our landmarks are THE landmarks is pretty silly. Maybe the answer is something none of us can guess, or maybe it really is junk. Maybe the sequence matters because of a chemical process we haven't yet observed; the notion people have that microbiologists have looked into cells and observed every single thing they do is rather silly. The fact that we haven't found an "active" use for it yet hardly means it has no use; there's just too much we don't know. (In that sense, calling it "junk" is really silly; the idea that a molecule as complex as DNA only has one use(ie, RNA synthesis,) while it COULD be true, is certainly not an obvious matter of fact.)

Attaching the label "we have no fucking idea" to this one isn't what I'd call "unwarranted," regardless of any claims someone or other might have made in a book or a paper or whatever.

--
'God dammit, your posts make me hard.' --LilDebbie

[ Parent ]
yeah but the dude left out mobile elements (2.00 / 1) (#15)
by Subtillus on Tue May 07, 2002 at 01:23:14 PM EST

of every kind, and viral retros at least have some evolutionary significance.

I love seeing anything bio related on K5 but i'm going to give it a -1 for technical oversights and difficulties.

[ Parent ]

wow I'm a tool (none / 0) (#17)
by Subtillus on Tue May 07, 2002 at 01:33:40 PM EST

nm about the -1 thingy I just realized this was an edit queue, more below.

[ Parent ]
IMHO, yours is a wrong level to analyse evolution (4.00 / 1) (#46)
by nusuth on Tue May 07, 2002 at 06:41:48 PM EST

The thing about Evolutionary Theory is that it doesn't require that everything you find in a creature have definite positive impact. It only says that things that have negative impact will fade away over time.

Actually "creature" is not even central to the theory. If a specific form of a self replicating molecule has higher probability of being replicated, that form is replicated more often (and this is a tautology if I've ever seen one.) The obvious way is that this "form" is a sequence as part of protein encoding DNA (or RNA) and that encoded protein gives the being higher chance of reproduction, leading to higher probability of persistence of sequence over time. But this is not the only way, the sequence just might be more stable for some reason, hence transferred without change more often; it may be near to really useful sequences, hence rarely split from them; it may have a higher chance of inter-replication without devastating consequences, hence found more often... These effects may also be combined to complicate things such as higher mutation stability and slightly worse (in survival/reproduction terms) protein encoding may make a sequence vanish or prosper; it is impossible to tell which just by looking at the sequence and protein it encodes. Individual or species levels are too high levels for analysing evolution.

[ Parent ]

"junk" DNA always thought to be importan (none / 0) (#89)
by lukesl on Fri May 10, 2002 at 03:09:36 PM EST

As far as I know, no biologist has ever thought that "junk" DNA was useless, nor have I ever heard any biologist ever use the term "junk DNA." I'm not sure who invented it. I'm a biochemistry/biophysics/neuroscience grad student, BTW. But it's been known for a very, very long time that regulation of gene expression (controlling how much RNA is made from a particular piece of DNA) is controlled in large part by proteins that bind to non-coding regions of DNA. Work on non-coding regions is important because we don't know how they work or exactly what they do. But I've never ever heard anyone claim that these regions were "junk" or that they had no purpose. As far as I can tell, this is purely pop science fabrication. I should also point out that gene regulation is the most obvious example of functions of non-coding regions, but there are likely many others, and it's only now that we've finished sequencing the human genome and have lots of computer power on hand that we'll be able to answer these questions. As sequencing techniques become cheaper and faster, we'll also be able to sequence a large number of humans' genomes, as well as the genome of a number of every animal from mice up to humans. Then we'll start to figure some stuff out.

[ Parent ]
Darwin's Radio (3.00 / 2) (#3)
by Jman1 on Tue May 07, 2002 at 12:40:14 PM EST

by Greg Bear, is a scifi book I'm reading now in which posits an unrealistic but very entertaining purpose (and a cause) for the junk DNA.  I first wrote what it was, but then I realized it will spoil some of the book.

Re: Darwin's Radio (4.00 / 2) (#43)
by arthurpsmith on Tue May 07, 2002 at 05:34:31 PM EST

Yeah, I read that book too. Definitely unrealistic, but thought provoking... It reminded me somewhat of the fact that astrophysicists know that 90% of the universe is not made out of ordinary matter, and yet we think we know most of what there is to know. Similarly, biologists think they know everything, and yet 90% of our DNA (or whatever the number is) seems to have no purpose... does make you wonder...

Energy - our most critical problem; the solution may be in space.


[ Parent ]
What, no Canadian scientists?? ;) (4.25 / 4) (#5)
by pb on Tue May 07, 2002 at 12:42:26 PM EST

Seeing as how humans are <related to | descended from | share a common ancestor with> mice (according to evolution, of course), I would expect the Junk DNA to be rather similar.

If it is, indeed, Junk, then it might serve as something of a historical record, like fossils buried in the Earth's crust.  In that case, I'd expect the differences between the two to be something like the differences between how mice evolved and how humans evolved.  A "CHANGELOG", if you will.

Or, maybe it's something completely different.  :)
---
"See what the drooling, ravening, flesh-eating hordes^W^W^W^WKuro5hin.org readers have to say."
-- pwhysall

They do do that (4.66 / 3) (#11)
by ucblockhead on Tue May 07, 2002 at 01:06:32 PM EST

I believe they already do do this. They do it with normal genes as well.

On thing that is a bit misleading is that often when they say a gene is "the same" in mice and humans, it doesn't mean "identical". For example, mice probably have a gene for eye color that codes for a protein very similar to the human protein for eye color. The different human eye-color genes will have slight differences from the mice analog, though. They tend to refer to them as "the same" gene because the genes have similar structure, code for proteins with similar structures, and have a similar function.

You can use these gene analogues to estimate how related to species are, because the rates at which mutations happen, and therefore genes change, is very roughly constant over time. So, for example, you can say things like "humans are closer to cats than dogs" because for genes in which humans, cats and dogs all have analogues, the human version is more similar to the cat version than the dog version.

I know that they've recently used techniques one the primate family tree, determining that humans are more closely related to chimps than gorillas, and more closely related to bonobo ("pygmy") chimps than other chimps.
-----------------------
This is k5. We're all tools - duxup
[ Parent ]

right (3.00 / 1) (#19)
by pb on Tue May 07, 2002 at 01:54:30 PM EST

I know they do that for regular genes, but has anyone analyzed junk DNA like this?

It shouldn't be surprising that the genes for mouse eyes and human eyes are different, since our eyes are different.  And since we also know what differences the finished product is, it stands to reason that we could correlate the differences between the genes with the differences between the finished product.

(And then, we can make supermen, with eyes as sharp as mice, and a strange fascination for cheese and dark corners!  MUHUHAHAHAH!)
---
"See what the drooling, ravening, flesh-eating hordes^W^W^W^WKuro5hin.org readers have to say."
-- pwhysall
[ Parent ]

I always wanted to make a christmas mouse (4.66 / 3) (#29)
by Subtillus on Tue May 07, 2002 at 02:26:05 PM EST

think of a chocolate brown mouse with mini antlers, give him a little red felt coat and you could sell them for a hundred bucks a head.

[ Parent ]
Have you tried *staples*? [nt] (4.50 / 2) (#30)
by pb on Tue May 07, 2002 at 02:29:23 PM EST


---
"See what the drooling, ravening, flesh-eating hordes^W^W^W^WKuro5hin.org readers have to say."
-- pwhysall
[ Parent ]
Yes, but the mouse didn't like it very much. [nt] (none / 0) (#42)
by molo on Tue May 07, 2002 at 05:18:34 PM EST



--
Whenever you walk by a computer and see someone using pico, be kind. Pause for a second and remind yourself that: "There, but for the grace of God, go I." -- Harley Hahn
[ Parent ]
if you're interested (4.50 / 2) (#16)
by Subtillus on Tue May 07, 2002 at 01:29:57 PM EST

they already do this, I think it's called molecular phylogenetics.

[ Parent ]
Clearly a secret message! (2.70 / 10) (#31)
by Mr. Piccolo on Tue May 07, 2002 at 02:44:41 PM EST

And I know what it says!

It says:  "I buried Paul.  It was Colonel Mustard in the kitchen with the candlestick.  The other gunman was Bob Dole.  The spaceships you have seen are battle crusiers from the *#&$HD"RE{"F:LF#@E" race of the star you call Sirius.  All your base are belong to us."

The BBC would like to apologise for the following comment.


I officially opensource my DNA code! (4.50 / 2) (#35)
by r00t on Tue May 07, 2002 at 04:00:15 PM EST

I hope that information like this is always free (as in speech and beer). I've seen what corporate america does with computer code, I shudder at the thought of what they may do with DNA code.

-It's not so much what you have to learn if you accept weird theories, it's what you have to unlearn. - Isaac Asimov

Not a mistery at all (4.00 / 2) (#36)
by JAM on Tue May 07, 2002 at 04:22:08 PM EST

Here is the secret.
-- Sorry for my engRish (TM)
I have decoded the junk DNA in the human genome! (3.60 / 10) (#37)
by fortytwo on Tue May 07, 2002 at 04:24:42 PM EST

By converting 4-nucleotide groups into binary, then ascii, I was able to identify one message in the junk dna, repeated 42 times:

"WE ARE SORRY FOR THE INCONVENIENCE"

What does this mean?

...

No no no (none / 0) (#45)
by marimba on Tue May 07, 2002 at 06:20:32 PM EST

it was "Thanks for all the fish." You missed a transposition.

[ Parent ]
Scientists never really thought it was junk (4.90 / 10) (#38)
by eyespots on Tue May 07, 2002 at 04:40:31 PM EST

This was merely a layman's description of the non-coding DNA that got out of hand. Now the press has refered to it as junk for so many years that the name stuck.

Most of the junk is repetitive elements such as LINEs, SINEs, and retroviral remnants. LINEs and SINEs are small pieces of DNA that copy themselves into many places of the genome (a sort of DNA parasite). Likely when genomes evolved to combat the spread of such elements, it allowed genes to be regulated in different methods (Histone deacetylation, methylation, etc...).

In some cases these repetitive elements themselves are important for proper gene regulation- such as in the beta-globin locus.

Hence, never really junk- but definitely a mess.

a good link on repetitive elements (none / 0) (#39)
by eyespots on Tue May 07, 2002 at 04:43:02 PM EST

is here.

[ Parent ]
true dat, yo (5.00 / 1) (#57)
by Subtillus on Wed May 08, 2002 at 12:01:22 AM EST

mildly opinionated, but the opinion agrees with my own so I'll let it by.

what about VNTRs and all that satelite stuff? I think this also serves a purpose most of the time, I posted an editorial about it higher up for the non-bio people.

[ Parent ]

microsatellites (none / 0) (#65)
by eyespots on Wed May 08, 2002 at 08:48:52 AM EST

are pretty interesting, though I didn't mention them since they constitute a smaller percentage of the genome (3%) than repetitive elements (35% or so). I bet that 3% serves particular functions (crossover events? transcriptional regulation? Unfortunately I don't know as much about that), though what I don't know. They are definitely great for genotyping- lots of companies use them to try to find genes involved in complex diseases like diabetes and scizophrenia.

Overall I think the genome's a mess- the end product of 3.8 billion years of evolution. But that's because all that was selected for was a working genome- not an organized one. That's why the regulation of human genes is so enomorously complicated.

I find it interesting that alot of this "junk" dna was prob. originally detrimental to the cell, but that it found ways to use it to its advantage.

[ Parent ]

well eventually (5.00 / 1) (#68)
by Subtillus on Wed May 08, 2002 at 10:57:34 AM EST

any wrench you throw into the gears of a working biological system will find a way tomake itself useful sooner or later; that's what's so amazingly cool about it all!

[ Parent ]
No, It's REALLY REALLY Intelligent Design (3.00 / 6) (#40)
by thelizman on Tue May 07, 2002 at 04:56:08 PM EST

Others have claimed, and countered, that Junk DNA is proof of evolution, since it argues against intelligent design.
Only if you buy into the "evolution is always at odds with creationism" mindset. It could just as easily be argued that God's ultimate genius was in leaving enough extra room in the container for even more highly evolved features to be built into our basic blue print. Software developers will take modularity over any other design any day because it allows you to extend and increase the capability of your software. So too, the Big-G designed our genome so that we could develop capacities in our organic form that can be carried on in our progeny.
--

"Our language is sufficiently clumsy enough to allow us to believe foolish things." - George Orwell
Not, it really ISN'T intelligent design (4.00 / 2) (#52)
by Darwin on Tue May 07, 2002 at 09:25:48 PM EST

Evolution IS always at odds with creationism. Evolutionary theory relies on the scientific method; creationism (even ID creationism) relies on myth and superstition. ID proponents always use the tired technique of taking one step "beyond" science as it continuously encroaches on "sacred" territory. Simply redefining what you mean by "creationism" every time science reveals a serious flaw in your explanation can hardly be considered an argument.

[ Parent ]
match point, evolution! (4.00 / 1) (#58)
by Subtillus on Wed May 08, 2002 at 12:04:40 AM EST

but, but, ummm ID made you say that! so there!

[ Parent ]
What? another holier than thou scientheoligist? (1.50 / 2) (#62)
by On Lawn on Wed May 08, 2002 at 03:19:15 AM EST

Evolution IS always at odds with creationism.

That may be true, but as defined mechanisms of change they are not. Lets take your arguement and see how it applies to evolution.

Simply redefining what you mean by "evolution" every time science reveals a serious flaw in your explanation can hardly be considered an argument.

It could be an easy to counter your arguement to point out that redefinition applies to any science. However, the changing definition of evolution over time has some interesting fodder for this discussion.

As defined, the one part of evolution that used to conflict with creationism has since been changed.

Evolution of a Definition

by Glen W. Wolfrom, Ph.D.

[Note: This information was taken from various sources, including Religion News Service stories and an Internet special report from the NCSE.]

The National Association of Biology Teachers (NABT) issued in 1995 their official "Statement on the Teaching of Evolution." Not surprisingly, it is blatantly anti-creation and pro-evolution in its message. One of the tenets was the following statement:

"The diversity of life on earth is the outcome of evolution: an unsupervised, impersonal, unpredictable and natural process of temporal descent with genetic modification that is affected by natural selection, chance, historical contingencies and changing environments."

This definition of evolution in terms of an "unsupervised" and "impersonal" process has been seized upon by creationists as further evidence that evolution is purely naturalistic and materialistic (i.e., it is godless). UC-Berkely law professor Phillip E. Johnson has been particularly effective in the last few years (with major books published in 1991, 1995, and 1997) in documenting this fact.

This brings us to the NABT annual meeting held October 8-11 in Minneapolis. At the board of directors meeting on October 8, a letter was presented from two "scholars" (a Notre Dame philosophy professor and a Syracuse University religion professor) who argued against inclusion of the words "unsupervised" and "impersonal." They maintained that:

"Science presumably doesn't address such theological questions ... How could an empirical inquiry possibly show that God was not directing evolution?"

These theistic evolutionists were obviously not arguing against evolution; rather, they suggested that using these two words "gives aid and comfort to extremists in the religious right for whom it provides a legitimate target." Further, they said that eliminating these two words would "help defuse tensions which, as things stand, are causing problems in our collective life."

However, after a nine-hour meeting the board voted against altering the statement. The executive director noted that changing the statement would give the creationists just the aid and comfort the scholars had argued against. However, the story does not end here.

NABT member Eugenie Scott (who is also executive director of the National Center for Science Education, NCSE, a watchdog group of anti-creationists) apparently urged the directors to reconsider, saying in a later interview that the change in wording was "a matter of staying religiously neutral." Just before the annual meeting was adjourned on October 11, the board reconvened and reversed its earlier vote.

Ms. Scott admitted that "it's no more proper to present naturalistic philosophy as valid science than it is to present religiously based arguments."...

A god slayer evolution isn't, nor should be.

[ Parent ]
Well.. (5.00 / 2) (#76)
by kitten on Wed May 08, 2002 at 11:30:01 PM EST

The crux of the creationist argument in that diatribe is:
"Science presumably doesn't address such theological questions ... How could an empirical inquiry possibly show that God was not directing evolution?"
Well, I don't know. It can't, really - God by definition must be 'supernatural', and therefore somehow above or beyond the natural and knowable.

However, the notion that God is "directing" evolution - or anything else - has been largely discarded by most theologists. Many moons ago, it was thought that God actually and literally directed everything. A flower could not open in the morning without God saying "Hey, flower, open," and a raindrop would not fall without God saying "Hey, raindrop, fall." Today, few of even the most fundamental of fundamentalists would take this position; why God would be actively "directing" evolution or anything else is beyond me.

If God were actively directing the evolutionary process, he's got an awful lot of explaining to do for the poor job he's done of it. Biological systems work, obviously, but they aren't all that robust, and some of them smack of such laughable design (I use the word "desgin" metaphorically, of course) that if an engineer were to make the same mistakes, he'd be fired on the spot. Take the human eye as a quick example - all the rods and cones (light-sensitive cells) are facing the wrong way. I'd expect a God to do a better job than that.

Most importantly, the question posed by these creationists is merely mindless rhetoric. They have no more evidence that God is involved in the process than they do unicorns, magic elves, pixies, fairies, or even Satan for that matter.
Furthermore their argument amounts to "You can't prove us wrong, so therefore we're right," which is exceedingly childish.

Evolution is most certainly a "god killer" in the traditional sense of "God". Evolution operates on natural, knowable laws (they may not be all known at present, but they are knowable) and natural causality. If a supernatural being were involved, this would not be so.

Then there are those who claim that God set up the mechanism of evolution and then let it take it's course without further intervention, but this smacks too close to the cold and - gasp! - impersonal god of Deism for most people's comfort.
mirrorshades radio - darkwave, synthpop, industrial, futurepop.
[ Parent ]
Directing vs. Guiding (4.50 / 2) (#78)
by thelizman on Thu May 09, 2002 at 12:09:37 AM EST

There's a vast difference in this argument depending on whether you think God actively controls, or if you accept that he merely guides. Most Christians accept the concept of free will (if not in practice, but that's another story). God gave us free will, because then our acceptance and worship of Him is for no other reason than love (see Job). We can accept or reject him wholesale, because ultimately the choice is ours. But at the same time, God is not above actively intervening to prevent the individual fall of a human being (unless you're related to him, then you're pretty well fucked).
--

"Our language is sufficiently clumsy enough to allow us to believe foolish things." - George Orwell
[ Parent ]
What? (4.00 / 1) (#79)
by kitten on Thu May 09, 2002 at 12:53:38 AM EST

There's a vast difference in this argument depending on whether you think God actively controls, or if you accept that he merely guides. Most Christians accept the concept of free will

Human free will has absolutely nothing to do with what we were discussing - namely, God's direction or guidance of natural events such as evolution, rainfall, or whatever else.

Furthermore, the notion that God is omniscient pretty much destroys the concept of free will. If God knows everything, then our fates are predestined. He knows exactly what we'll do - with 100% certainty. If God knows everything, then we only have the illusion of free will.. I may think I'm deciding to do this or that, but God already knew I was going to do it. I may decide to think this or that, but God already knew I would think that.

Thus far, no theologist has been able to make a satisfactory reconciliation between an omniscent, omnipotent God, and human free will. It's difficult to argue that we have free will while also arguing that everything we do and the outcome of our every move is already known.
mirrorshades radio - darkwave, synthpop, industrial, futurepop.
[ Parent ]
Back At Ya (4.50 / 2) (#83)
by thelizman on Thu May 09, 2002 at 02:22:44 PM EST

Human free will has absolutely nothing to do with what we were discussing - namely, God's direction or guidance of natural events such as evolution, rainfall, or whatever else.
It has *everything* to do with what we are discussing. We are as much a part of nature as evolution and rainfall.
Furthermore, the notion that God is omniscient pretty much destroys the concept of free will. If God knows everything, then our fates are predestined.
In an ironic twist, you go on to equate two things which are unrelated. Omniscience has nothing to do with, let alone justifies predestiny. Just because we have the choice, and just because He knows in advance that we will make a given choice, does not mean that we do not have free will to make those choices. I know you will argue with me on this point; Does that suddenly mean you lack free will?
--

"Our language is sufficiently clumsy enough to allow us to believe foolish things." - George Orwell
[ Parent ]
Red-Herring... (2.00 / 1) (#85)
by On Lawn on Thu May 09, 2002 at 03:42:45 PM EST

If God knows everything , then we only have the illusion of free will.. I may think I'm deciding to do this or that, but God already knew I was going to do it. I may decide to think this or that, but God already knew I would think that.

Even in your hyperbole the logical breakdown is obvious. What does prior knowledge have to do with choice? For example, if I knew that you were going to make such a fallocious arguement, does that mean I made you do it?

Thus far, no theologist has been able to make a satisfactory reconciliation between an omniscent, omnipotent God, and human free will.

This has the look and feel of a red-herring, but I'll bite anyway. No philosopher has ever satisfactorily argued there is a contradiction. All of the tries I've seen their is flaw in the logic that produces the contradiction. The most populer seems to be to create an omniscient being that really isn't omnicient by limiting knowledge to only determined outcomes.

You watch, and every time it gets to the point of logic where you define what the omniscient being knows it looks something like this.

Omniscient being knows what your going to do (yada)

Therefore, you'll do it and don't have a choice.(yada) Bam, all of a sudden omniscience is limited to just the knowledge of the outcome, not possible outcomes and so are is the person being observed. So this works only if the being of omniscience does not know something, and knows everything which is a contradiction (flaw in logic). Want to try the Rock and God contradiction next? That one has a very simple and patent answer also.

[ Parent ]

Strawman.... (2.00 / 1) (#84)
by On Lawn on Thu May 09, 2002 at 03:04:39 PM EST

The crux of the creationist argument in that diatribe is: "Science presumably doesn't address such theological questions ... How could an empirical inquiry possibly show that God was not directing evolution?"

Interesting, but the crux of the diatribe is the statement I put in bold, which was for all intensive purposes the deciding argument for removing that language.

Lets look at it again...

Ms. Scott admitted that "it's no more proper to present naturalistic philosophy as valid science than it is to present religiously based arguments."...
However, the notion that God is "directing" evolution - or anything else - has been largely discarded by most theologists.

I find what theologist think about evolution to be as interesting as listening to a movie star talk about presidential politics.

What people think science says about God is probably just as silly. I think Scientheologist is a good word for them, although scientist probably identify with Ms Scotts use of "Naturalist Philosphy".

I'm remided of Robert Millikan's quote, "To me it is unthinkable that a real atheist could be a scientist" which I've made my slashdot sig for the next little while.

To Millikan, Pasteur, Newton, Einstein (and yes I've very prepared to enter into a debate on whether he was atheist or not), and other giants in the realm of science, they don't find it a God slayer. You may find a more complete list here.

At the end of the day, this is about what a scientific community thinks of Evolution. Namely that Evolution is no God killer any more than God is an Evolution killer. The NABT (as pointed out in the diatribe) even realized that as worded the definition of evolution was reaching much farther than the evidence at hand could support.

Forgive me if I do not comment specifically on your other arguements. I find the strawman they build is neither interesting or useful.

[ Parent ]

Nope (4.00 / 1) (#77)
by thelizman on Wed May 08, 2002 at 11:53:57 PM EST

Evolution IS always at odds with creationism
No, it isn't. Only shortsighted close minded morons are willing to accept this. Even the catholic church has ruled that evolution is not incompatible with the concept that God created all life. Serious students of theology never question that the growth of the human race allows that we were not always how we are now, and even the Moody Bible Institute (scarey) has discussed that evolution represents the hand of God in guiding our growth.
--

"Our language is sufficiently clumsy enough to allow us to believe foolish things." - George Orwell
[ Parent ]
Well, if the Catholic Church says so... (none / 0) (#86)
by Darwin on Thu May 09, 2002 at 10:33:53 PM EST

Only shortsighted close minded morons are willing to accept this.
Grow up. You can't call people close-minded because they don't buy into the same religious dogma that you do.

Even the catholic church has ruled that evolution is not incompatible with the concept that God created all life.
What's this? Could it be a perfect example of a Christian religious organization conceding to science? Whatever happened to "the world is flat," "the world is 10,000 years old," "the Earth is the center of the universe," and "god created the human race with Adam and Eve?" Curious how every time science steps in and provides a logical explanation (along with the requisite amount of empirical evidence) for phenomena that had previously been the domain of religion, the general populace prefers the scientific explanation and it is religion that is forced to "clarify" its beliefs so people don't roll their eyes at those great aristocratic spiritual leaders who once-upon-a-time guided social change.

Retreat, religion, retreat! The steady march of human progress makes your safety ephemeral at best.

[ Parent ]

non-coding DNA is direct evidence for evolution (5.00 / 1) (#88)
by lukesl on Fri May 10, 2002 at 12:57:57 AM EST

Evolution is always at odds with intelligent design. I think the issue here is that ID and creationism aren't necessarily the same thing. ID is at odds with evolution, by its very definition. Creationism is not necessarily, since it's possible that God used evolution to do the creating. But ID (at least the manifestations I'm familiar with) actually makes falsifiable claims about what processes were used in the creation of life on earth, and these claims are at odds with evolutionary theory.

In any case, I thought that in case anyone was interested, I'd repost a post I made on /. a while ago describing a study comparing the mouse and human genomes. This study provides what I think is pretty much undeniable evidence of evolution of humans from lower life forms. It's not that it can directly demonstrate evolution as opposed to ID. It's that evolutionary theory would predict a bizarre non-random arrangement of the genes and pseudogenes that is so highly improbable it could never happen by chance. And this arrangement is EXACTLY what's observed. This doesn't rule out ID, but it does demonstrate that if there is a God, s/he has put a lot of work into tricking us.

Anyway:

There's a paper in the latest issue of Nature Neuroscience from Stuart Firestein's group at Columbia that provides some really interesting evidence from a very different angle. Some background: mice are animals that rely heavily on olfaction, or their sense of smell. Over half their brain is dedicated to it. In "lower" mammals (or however you want to look at it), the sense of smell is also very important (dogs, cats, etc.) For humans, however, smell is not as important. We don't smell predators coming or track prey by scent; we use vision (and a huge portion of our brain is dedicated to it).

Anyway, In this article they do a rigorous analysis of the data on olfactory receptor (OR) genes from the recently acquired mouse genome compared to the data from the human genome project. I forget the exact numbers, but mice have about 1000 OR genes. Humans have about the same number, but something like 75% of ours are pseudogenized. Basically, this means they've been converted to pseudogenes, or sequences in the genome that obviously used to be functional genes but have mutated to a nonfunctional state. This much was known before. In this paper, however, they use techniques based on similarity of sequences to group the mouse OR genes into families and subfamilies. Then they group the human OR genes into the same families. To sum up what they found, if you were to take a random group of say six mouse OR genes, there will be five or six human genes that are the human counterparts of those mouse genes (over 90% of human OR genes have a mouse gene that's over 95% identical at the protein sequence level, and 77% have a mouse gene that's over 99% identical, so reliable identification is not a big issue). However, within that group of five or six human genes, all but one of them has been converted to a pseudogene. They find this over and over again. There's only one functional gene in each group. Each group, BTW, can be thought of as sensing when a certain class of feature is present on a molecule. In an analogy to vision, it would be like if mice could see different shades of six types of red, but we could see only shades of one.

Okay, here's an evolutionary explanation. A long time ago humans were monkey-like animals. Before that, dog-like animals, before that mouse-like animals, etc. Whatever animal we used to be, it was heavily dependent on a highly-developed sense of smell for survival (hence an entire 2% of our genome being dedicated to it--think about that). However, as we progressed evolutionarily, having an exquisitely sensitive and precise sense of smell became less and less important, but smelling things in general was still necessary. The genes mutated and mutated, but if the last member of a family became pseudogenized, that would compromise our ability to smell molecules with a certain class of molecular features (by analogy, if we couldn't see red at all), and those pre-humans would die. As a result, we're left with the HIGHLY nonrandom distribution of working genes. I want to point out that while this could be written off as "microevolution," consider two things: #1- all humans on earth will turn out to have >98% identical OR genes. #2- I say this because that nonrandom of a pattern with that many genes involved would take a LONG time to evolve, or at least a lot longer than humans have been on different continents. Almost certainly longer than we have been Homo sapiens.

Can anyone come up with a non-evolutionary explanation that explains 1) why so many of the genes are pseudogenized, 2) why the selection of which genes are pseudogenized is so highly nonrandom and optimized for the real world? I'm not asking for a critique of my evolutionary explanation, as the reasoning as I've presented it is not intended to be bulletproof. However, I do think that the underlying model is correct and I don't think there's any better explanation.


p.s. since this is evidence for microevolution on a macroevolutionary time scale, I would argue that this actually is direct evidence for macroevolution.

[ Parent ]
Finally, (3.90 / 10) (#41)
by derek3000 on Tue May 07, 2002 at 05:03:33 PM EST

someone covered this topic.

I've been doing a lot of layman's research into "Junk" DNA, devouring every abstract and thesises I could get my hands on, even delving into the depths of g**kdom at alt.sci.dna. I'm glad that this is finally getting some legitimacy, despite the fact that the name remains off-putting.

When you think about it, the fact that we have the same kind of junk DNA that mice have makes perfect sense, since the evolutionary process had to go along these routes. I know this was mentioned before, but I wanted to add it for posterity.

Anyways, that being said, I think that the new advances in human cloning provide a great opportunity for us too see exactly how useful this "junk" dna is. If we fuse the DNA sockets of a human egg with the DNA sockets of a mice's sperm, we may be able to tell which genomes are useful and which aren't. Some researchers may be afraid to "go for the cheese", as it were, because of the legalities, but there has to be some use for countries with horrible human rights records, no?

Anyway, regardless of the ethics involved, I'm sure that I'm not the first to suggest a splicing of human and animal genes. Well, why wait anymore? If the lifeform doesn't come to term, then no harm done, right? It's time for the human rights apologists to take a back seat to advances in science that could very well end up saving our race.

-----------
Not too political, nothing too clever!--Liars

one step at a time there buddy, this isn't a movie (3.00 / 1) (#59)
by Subtillus on Wed May 08, 2002 at 12:10:04 AM EST

The much touted human cloning, was little more than a semi botched attempt at just that. they never got it beyond what, I can't remember the exact number but 8 cells? 12? it wasn't very impressive other than the fact that they actually got out there and tried it.

as for human animal hybrids, I have no idea why one might want to create such a monstrosity but I think it would be funny to watch.
"Of Mice and Men" -> "Of Mice-Men and the Men who Enslave Them".

[ Parent ]

An alternative theory (4.71 / 7) (#44)
by cyberdruid on Tue May 07, 2002 at 05:56:01 PM EST

In genetic algorithms (the AI-method) you can plainly see that, after a while, the genome reaches a state where it rapidly increases in length until it hits the bounds (whatever those are set to be). This rapid increase in length is accomplished by the algorithm by adding introns (or "junk DNA" as you call it, meaning that they are neutral as regards the phenotype) to the genome. Now, genetic algorithms is certainly different enough from the real thing, that you can't draw any conclusions from these results. They are however similar enough to nature that they can be used for inspiration.

One use that the genome in GA can have for these introns, is to protect parts of the code that should be together. Sort of like functions in programming. If you have 97% (or whatever) introns, it can be used to divide the functional parts of the code into blocks, so that mutations gets more likely to move around entire segments of logically united code instead of just randomly splicing the genome and being likely to destroy "functions".

Natural mutations do not work quite in the same way as those in artificial GA, but it is certainly conceivable that introns could be used by the DNA in a similar manner. Providing space between logical chunks, the added information in the structure thus increases the probability of meaningful mutations.

Junk DNA (4.00 / 2) (#47)
by StephenThompson on Tue May 07, 2002 at 07:08:47 PM EST

Has anyone considered that the 'junk dna' is part of the 'search' algorithm for the family of organisms. That is to say, it is dna coding that directs or protects the 'ratcheting' mechanims of evolution so species can evolve to fit environments similar to past environments quickly.

That is to say, these are 'genes' that protect the vitality of the meta-organism and operate above the level of individual gene expression and competition.

Well it makes sense to me anyway :)

sounds great on paper, but... (none / 0) (#60)
by Subtillus on Wed May 08, 2002 at 12:26:02 AM EST

I say a big old NO to you though, I'm not an expert on evolution but, I have sat through my share of genetics.

In my experience the way that an organism is made adaptable to new environments is with the diversity that is already pre-contained within a population. On that note, a lot of mutation's are neutral and can be exapted (put into use for a purpse other than the original)later on. This is called the neutral theory of selesction, I think it's pretty fashionable now. A good example is that of feathers which were origianlly definitely not used for flight and most probably for warmth or sex appeal. They appeared on dinosaurs as little tufts or something. to reiterate, what might look funny today could look _awefully_usefull_ tommorow. This is yet another reason why eugenics and selecting for particular traits is utter nonsense.

Variance can be defined for you math and computer people as the statistical variance of a population Vt(sum of squares), minus the variance of a genetically identical population Ve as in a genetically identical population, all variance is due to environmental effects.
Vt-Ve=Vg
It gets even more complicated with some genes hiding others at certain places and times and all that...

junk DNA has a few other putatative functions that are being looked into, if you're interested I put up a link in an editorial further up the page.
; )


[ Parent ]

not sure it's too suspicious......... (4.16 / 6) (#48)
by wmclaren on Tue May 07, 2002 at 07:22:44 PM EST

There seems to me to be a few mislead assumptions being made in this debate. It seems the opinion is that if this "junk" DNA is without function then it should be a random sequence of bases. However, people are assuming that junk DNA has been with us since the dawn of time. Not so. Way back in time we descended from single-celled organisms that still exist in similar form today that contain no junk DNA - i.e. the prokaryotes.

Therefore to get between having no junk DNA (in prokaryotes) and a genome full of it (eukaryotes - us, mice, monkeys etc.) there must have been some sort of progressional evolutional process creating the junk DNA.

Much of this junk DNA consists of repetitive sequences, especially tandemly repeated DNA (e.g. ATA ATA ATA ATA, CGC GCG CGC etc.), remnants of functional parts of the genes (such as gene fragments copied possibly in error during DNA replication or exchanged during meiotic crossing over) and many other sequences who's origin can be traced if you look hard enough.

There is so much in the workings of eukaryotic cellular processes that we do not understand that there are likely even more mechanisms by which junk DNA can be created.

As to its evolutionary purpose, the argument that introns and the like break up logical coding segments of the genome seems sound to me. And although not strictly true (due to a feature of higher eukaryotic genomes known as CpG islands - too long and complicated to explain here) mutations should occur at random across the genome. The fact is that a huge percentage (just below 100%) of mutations are not evolutionarily favourable, so surely a larger genome with junk DNA would protect the important coding DNA. Not necessarily a consequence of this (I don't actually know - anyone?), prokaryotes have a much higher rate of mutation in their genomes than eukaryotes. There are other factors that can explain this - a simpler, less protected genome is one, but I'm not sure they totally cover the difference.

I am aware of the arguments against my points (I'm a Biochemistry And Genetics student), but these are my opinions.

I agree with you completely (none / 0) (#61)
by Subtillus on Wed May 08, 2002 at 12:33:17 AM EST

not too mention the relationship between something like huntington's disease and a microsatelite. not too mention TELOMERES which are a minisatelite (right?) and let's just say that active telomerase (it's not supposed to be) is present in an overwhelming majority of cancers.


[ Parent ]
modern prokaryotes are not our ancestors (4.50 / 2) (#87)
by lukesl on Fri May 10, 2002 at 12:15:16 AM EST

Way back in time we descended from single-celled organisms that still exist in similar form today that contain no junk DNA - i.e. the prokaryotes.

Strictly speaking, prokaryotes are MUCH more evolved than we are at the molecular level because they have been around a lot longer, and they reproduce and mutate much faster. We are in no way descendants of anything that resembles modern day bacteria. While it's often presented in intro classes that we're more advanced version of prokaryotes (we have RNA splicing, better post-translation modifications, etc.), prokaryotes also do things we don't (histidine kinase signaling, protein splicing, etc.). I agree with your fundamental point that non-coding regions (I can't stoop to calling them junk DNA...I don't know what journalist invented this term, but I've never heard anyone in biology use it) were probably created with a purpose, but your line of reasoning is flawed. You say that prokaryotes don't have them and we do, therefore they must have been created. However, if you've studied molecular biology you must know that it's more accurate to say that we share common prokaryotic ancestors with modern-day prokaryotes. Since prokaryotes evolve much faster than we do, it's possible (even likely) that ancient prokaryotes had lots of weird stuff in their genomes that got edited out sometime between ancient bacteria and modern bacteria. Having a streamlined genome might be a significant evolutionary advantage for a bacterium, but for us there are more important and mutually exclusive ones. Like greater chromosomal stability, so we don't get cancer every five minutes. If you took HeLa cells (cells from a tumor that killed HEnrietta LAcks in the 50's that have essentially mutated into aggressive single-celled organisms with more-or-less human genomes that are used in many labs) and gave them ten million years, you might see excision of many non-coding sequences.

I also disagree with your assertion that having more non-coding regions somehow protects coding regions from mutation. Well, I don't necessarily disagree, I just don't see why that would be the case. Could you explain?

As a last thing, I want to add one of my own opinions, which is that the fundamental distinction here should not be between prokaryote and eukaryote, but between single-cell and multicellular organism. Multicellular organisms have to do lots of things that unicellular ones don't. One of those is differentiation. All humans start out as a single cell. As that cell divides, the resulting cells start to become muscle cells, nerve cells, etc. With the exception of B and T cells and sperm/eggs (and possibly olfactory receptor neurons), all cells in the body have exactly the same DNA, yet the genes they express are completely different. This places HUGE demands on the genome in terms of transcriptional regulation that don't exist in bacteria. Large non-coding regions could play significant roles in the chromatin changes underlying cell differentiation. It's possible that ancient prokaryotes had tons of bizarre noncoding sequences too, as part of their evolutionary past, but they were able to get rid of them because they didn't need them while we did.

Another thing is that the molecular mechanisms underlying evolution in humans are fundamentally different than in bacteria. For example, in bacteria, it's advantageous to have a high rate of mutation. If 10% of bacteria mutate so much that they're all screwed up, it's still advantageous because the other 90% will still survive, and it's all the more likely they will be able to adapt to different situations. If 10% of your cells mutated like that, you would die of cancer in a week. Evolution in humans is dominated by sexual reproduction and different combinations of polymorphic regulatory (and coding, but imho mostly regulatory) sequences, which modify traits largely at the systems level. Size and organization of vessels, nerves, muscles, etc.

To make a very simple analogy, we shuffle the deck, while bacteria make new cards. Making new cards is a potentially more powerful approach, but it only works if you don't have things like cancer or organ system failure to worry about. By shuffling the deck, you know all the cards are good. Fundamentally, I agree with what you're saying, I just don't agree with what you're saying to support it.

[ Parent ]
fair enough, but..... (none / 0) (#91)
by wmclaren on Wed May 15, 2002 at 09:27:47 PM EST

I also disagree with your assertion that having more non-coding regions somehow protects coding regions from mutation. Well, I don't necessarily disagree, I just don't see why that would be the case. Could you explain?
This is only a suggestion, but maybe the way chromosomes are packed (histones etc.) could in some way protect the genome from mutagens.

I take your point about our common ancestry with prokaryotes - I think some bad phrasing on my part lead to the wrong impression being given. But are there not prokaryotes that have existed in largely unchanged forms since we diverged?

Another intersting point that i meant to raise is mitochondrial DNA. This has remained intron-less in humans, but contains large gaps and introns in yeast. I have only recently studied the ancestry of mitochondrial DNA, so i don't really have any explanations for this.

I like your points about single and multicellular organisms.

[ Parent ]
prokaryotes, etc. (none / 0) (#92)
by lukesl on Thu May 16, 2002 at 02:49:32 PM EST

This is only a suggestion, but maybe the way chromosomes are packed (histones etc.) could in some way protect the genome from mutagens.

That could be true, but I see how coding vs. non-coding regions makes a difference there. Well, I guess I could. But if one imagines that most mutations are due to either replicative errors or mutagens, the first has nothing to do with coding vs. non-coding, and the second probably has more to do with things like repair mechanisms, triggering apoptosis, or expression of p-glycoprotein, which pumps the mutagens out (hence its high expression levels in bone marrow stem cells and sperm/egg precursors). I agree that what you're saying could be possible, but I doubt that protection from unwanted mutation was a strong enough selection pressure to create or maintain those non-coding regions.

But are there not prokaryotes that have existed in largely unchanged forms since we diverged?

I don't know, but I don't see how we could know one way or the other. I do know that bacteria can do molecular tricks that we probably can not (e.g. protein splicing), and many of them also have things like virulence factors demonstrating that they have evolved to co-exist with multicellular eukaryotes.

The mitochondrial DNA thing is definitely an interesting point, and I had never heard that yeast mitochondria have introns. That's pretty interesting... I still stick by my points about complex gene regulation and different mechanisms of evolution underlying most of these effects, though. Supposedly the jump from prokaryote was a much smaller jump than from eukaryote to multicellular eukaryote in terms of how many millions or billions of years it took, so maybe proliferation of all those non-coding regions took place then, enabling differentiation of cells with identical genomes? Pure uninformed speculation...

[ Parent ]
Program vs Data? (3.40 / 5) (#49)
by Baldrson on Tue May 07, 2002 at 08:01:46 PM EST

Imagine some highly factored computer program -- so well factored that it is, in effect, compressed -- and then imagine some data upon which it operates, such as a corpus of text or similar uncompressed natural database. The corpus may be large compared to the highly factored computer program, and the compressability of the two would differ dramatically. One of the things that is nice about highly factored code is that it is useful for things like genetic algorithms where you want to snip out pieces here and there and recombine them and remain relatively confident the resulting parse tree would look like a valid program.

Well, gee whiz, lookie here at this!

PHYSICS NEWS UPDATE A digest of physics news items by Phillip F. Schewe, American Institute of Physics Number 202 November 9, 1994

SO-CALLED "JUNK" DNA, regions of genetic material (accounting for 97% of the human genome) that do not provide blueprints for proteins and therefore have no apparent purpose, have been puzzling to scientists. Now a new study shows that these non-coding sequences seem to possess structural similarities to natural languages. This suggests that these "silent" DNA regions may carry biological information, according to a statistical analysis of DNA fragments by researchers at Boston University and Harvard Medical School (contact H.E. Stanley of Boston University, 617-353-2617). Studying DNA sequences from humans, viruses, bacteria, yeast, and other organisms, the researchers performed statistically-based linguistics tests on the 37 known DNA sequences each having at least 50,000 "base pairs" or "letters" of DNA code. The researchers first performed a variation of a test known as Zipf analysis, in which the words from a text are arranged on an x-axis from most frequently occurring to least frequently occurring; plotted against their rank is the actual number of occurrences of that word in the text. For natural languages one invariably gets a straight line (on a graph using logarithmic axes) whose slope is about -1. The non-coding DNA sequences had linear slopes when base pairs were grouped into genetic "words" consisting of 3, 6, 7, or 8 base pairs. Interestingly, the slope values for non-coding sequences were closer to -1 than for coding DNA, supporting a hypothesis that protein-coding DNA may be more like a compressed computer file than a natural language. (R.N. Mantegna et al., upcoming article in Physical Review Letters.)

-------- Empty the Cities --------


One important thing to remember is that... (5.00 / 4) (#50)
by Humuhumunukunukuapuaa on Tue May 07, 2002 at 08:51:20 PM EST

...junk DNA is there because it has survived.  It has survived because it was able to get itself into the genes of its host's ancestors better than other DNA strings.  Note that in order to do this it doesn't have to provide any advantage for the host - it just has to make sure that it gets propagated differentially better than other strands.  For example the 3d structure of junk DNA might be able to skew things during meiosis to make itself more likely to appear in a succesful gamete.  There are countless other potential mechanisms and the field is wide open for research.  It only takes a slight advantage for a particular string to find itself widespread trough the population after many generations.
--
(&()*&^#@!!&_($&)!&$(*#$(!$&_(!$*&&!$@
Not useless for cell function, that's for sure. (4.50 / 6) (#51)
by xriso on Tue May 07, 2002 at 09:22:27 PM EST

First of all, useless DNA can be dealt with by natural selection (look at all the DNA in nature that is completely filled with coding DNA), so selfish or junk DNA interpretations are not too credible. And we do know of biological functions that this non-coding DNA can accomplish. For example, one study of a certain eukaryotic organism called Cryptomonad indicated that the amount of junk DNA is proportional to the size of the nucleus, which is in turn proportional to the cell size (Cryptomonads can have cell sizes very different from one another). Furthermore...

Oh, it appears that you have already linked to that site. heh.
--
*** Quits: xriso:#kuro5hin (Forever)

Most of it *is* junk, i.e. waste (4.00 / 4) (#53)
by Rainy on Tue May 07, 2002 at 10:21:12 PM EST

One good explanation I've heard is that amoebas and most flat worms have up to 35 times more genetic information than humans. It's obvious that most of their genetic info is 'junk' since they're obviously much simpler than us, and since our genetic makeup is fairly similar, it makes it very likely that the whole thing is very wasteful, from the very beginning there was perhaps 1 or 5 percent of genetic information that carried purposeful information. It's almost like our genes are pools of mud where a few pieces of mud here and there arrange themselves in fine structures, but very few of them do.

It's also interesting to see how nature's design may surprise us - we're accustomed to think of waste in percentages - if 99% of wasted, that's no good, but to nature, only the absolute number matters. If an animal is wasting a bit of resources to build 0.00001 gram worth of genetic junk data, that's okay 'cause the number is not high enough to hamper his chances of survival considerably. I guess this seems particularly odd to us 'cause when we design things, we pay the most attention to these things being easily taught to and understood by other people. Nature obviously doesn't care that somebody will want to figure it all out.
--
Rainy "Collect all zero" Day

The plant geneticists (none / 0) (#56)
by Anonymous 7324 on Tue May 07, 2002 at 11:47:15 PM EST

especially of Arabidopsis have long pointed out with much glee that their lowly weed has many more genes than even a mammal such as a human.

From what I understand, the animal geneticists, by contrast, have mostly defended themselves with things like compounding due to several types of regulation: transcriptional, translational, differential splicing, differential transcriptional start sites, differenetial translational start sites, mRNA degradation rates, DNA organzational control (euchromatin/heterochromatin), insulator and enhancer sequences, and whatnot.

Of course, I'm just a lowly biochemist, so I'm probably wrong on at least half of this. :P Although I do know for a fact that dosage compensation in Drosophila and the NF-kappa-B / I-kappa-B immune system genetics represent most of the above forms of regulation that make humans more complex, even though we have less "genes" overall.

[ Parent ]
Thanks (none / 0) (#75)
by Rainy on Wed May 08, 2002 at 10:11:23 PM EST

That's interesting, and it explains difference in size. I should really read some books on genetics..
--
Rainy "Collect all zero" Day
[ Parent ]
absense of proof is not proof of absense (none / 0) (#63)
by juju2112 on Wed May 08, 2002 at 04:17:47 AM EST

It seems to me that "Junk DNA" is a very poorly chosen name for this.

What everyone seems to be saying is, "I don't know what it does -- therefore it's junk". Just because you don't know what something does, that doesn't mean that it doesn't do anything.

Also, a larger DNA strand doesn't necessarily mean that the organism has to be complicated. The code could be poorly written and inefficient. Think of DNA as code. A 100 line program can be more efficent than a 1000 line program if the shorter program is coded more efficiently. It's all in how you organize the information.

[ Parent ]

this isn't "absense of proof" case (none / 0) (#73)
by Rainy on Wed May 08, 2002 at 10:08:26 PM EST

Why would it be so much more poorly written? Besides, there doesn't seem to be an inversed correlation, either, which you'd expect if primitive organisms had much less efficient encoding.
--
Rainy "Collect all zero" Day
[ Parent ]
The theory I had heard (4.00 / 1) (#54)
by Adam Tarr on Tue May 07, 2002 at 10:53:29 PM EST

The explanation I had heard for "junk" DNA was that it served a purpose earlier along in our evolution, but is no longer needed.  For example, a huge portion of frog DNA exists solely to regulate development from egg through tadpole; when to hatch, how to deal with late frosts, et cetera.  It seems likely that our predecessors had this same genetic programming built into their DNA, but when controlled, internal gestation evolved in mammals it became extraneous, "junk" DNA.

I'm sorry I don't have a citation on this, but I read it somewhere.  Perhaps someone more informed than me can flesh this out.

-Adam

Meaning of junk DNA. (4.00 / 2) (#64)
by bogado on Wed May 08, 2002 at 08:00:15 AM EST

I would argue that junk DNA, if it is indeed is so similar in humans and rats, is not junk at all. It must have some function that we do not yet see. Why? Simply because if it were junk it wouldn't be affected by nature selection, if I would change a bit in a code that is not runned it would not make any difference in the performance of the program. Now if it does have a function, if I changed this change would affect the final product. If this change is for the better it would stick, if not then the being would die and the rest of the population would stay with the same coding.

In this I assume that changes in the DNA are random, and there is no place in the DNA that is more likely to change. Also that this likelyhood is not probable by chance, someone else in here said that this "junk" DNA is composed mainly from repetition of some sequences, if there is some reason that this useless sequence are some what are more probable to happen, it could be possible that this would happen just by chance.


[]'s Victor bogado da Silva Lins

^[:wq

More like a messy file (4.33 / 6) (#66)
by iGrrrl on Wed May 08, 2002 at 08:49:26 AM EST

Everyone has what I call a chaos drawer. It gathers those instructions from consumer electronics, random sizes of rubber band, a three-prong socket tester, &etc. If you combine that chaos drawer with a pretty well maintained filing system, that's more like so-called junk DNA.

Some of it indeed is made up of the leftovers from gene duplication or retrovirus insertions. Much of it, however, is very important for regulatory function. Some of it is structural, in that its purpose is more for the physical structure of the chromosome itself.

In a mammal, DNA is not just a linear molecule ready to be transcribed and translated. The chromosomes are wound around histone proteins to make structures that can then form even more complex molecular architectures. These architectures have much to do with storage of information, and with availability of genes. To anthropomorphise, if you're a beta cell secreting insulin in an Islet of Langerhans, you pack away the genes important for muscle contractions. There are DNA sequences that regulate the packing.

But that's not all. There are two more important points about what non-coding DNA is doing. First, it contains promoter, repressor, and enhancer elements that allow for exquisite control of gene expression. If a gene needs to be expressed only in response to insulin binding the cell surface, there's a set of molecular switches to make sure that transcription is tightly controlled. Second, the introns allow one gene to be spliced together to make many different proteins. In many proteins, the exons are somewhat modular (Lego-ish?), and protein function by changed depending on which exons go into the final mRNA.

As has been pointed out, "junk" is a terrible misnomer. You may need that three-prong socket tester someday.

remove obvious illegal character in email address

But .... (none / 0) (#71)
by mami on Wed May 08, 2002 at 07:24:26 PM EST

has every person its very own unique "chaos drawer" and filing system ? Could it be used for ID purposes ?

Someone asked if people would be willing to donate their DNA code to central authorities to be stored in databases to facilitate prosecutor's task to find people suspected of having committed rape crimes and such. Someone answered he would only donate his "junk DNA", because he seemed to think that the non-coding DNA could still be used for identification, but not for other kinds of medical profiling purposes. I like to know it that is a "bogus" idea.

[ Parent ]

bogus (nt) (5.00 / 1) (#81)
by iGrrrl on Thu May 09, 2002 at 10:12:15 AM EST



[ Parent ]
another issue on junk DNA (4.00 / 1) (#67)
by KiTaSuMbA on Wed May 08, 2002 at 09:28:04 AM EST

If some huge regions of DNA do not code for / regulate anything why keep carrying such "garbage" with us?
One answer could be that it *used* to be useful in our evolution course but has no sense now. Since there is no specialised "garbage man" in our cells we keep it scrambled between meaningful DNA code.
Another one is, that we keep our garbage with us for protection, however strange this sounds. We all know that point (one-base) mutations are very often and sometimes have devastating effects (e.g. generate a STOP signal inside a protein code allowing  only half the molecule to be produced). As evolution led to continuously more complex organisms the strugle against entropy was getting more important than "trying out" by chances new versions. If most of the DNA is meaningless, then the probabilities of a random mutation damaging vital code decreases in a very impressive manner.
There is no Dopaminergic Pepperoni Kabal!
Reasons for "junk" DNA (5.00 / 3) (#69)
by Stickerboy on Wed May 08, 2002 at 02:13:49 PM EST

1. It's DNA with structural or regulatory function, but doesn't code for anything.

DNA does not necessarily have to code a protein to serve a current use.  For example, steroid hormones bind do transcription factors in the cell which then activate and bind to specific regions of DNA, inhibiting or encouraging the transcription of other genes.

Another example would be 'meaningless' sequences of DNA which serve as physical transcription guides when complexed with certain proteins.  These proteins twist around the DNA to provide a template for RNA transcription that wouldn't otherwise be there.  This could mean several things: a) the protein in question is made of several highly conserved functional domains that evolved separately, but natural selection has found an advantage in lumping together, b) the protein has undergone mutation over time, and the intervening sequences are no longer useful, c)the protein belongs to a specific family of proteins that share common genetic code (yes, Nature was into object-oriented programming long before man invented computers) and the intervening sequence belongs to a different member of the protein family, and so on.

2. It really is junk DNA.  Viral leftovers that are no longer active, genes that natural selection has left for the garbage heap, etc.

3. Deactivated genes that are activated in special cases that we don't know about, have no idea what their function is, or are specific to a cell type that we haven't fully studied yet.  Almost all the cells in the human body have differentiated, specializing themselves for certain tasks and letting other functions fall by the wayside.  The DNA that is actively expressed in a neuron, for example, isn't the same DNA that is actively expressed in a macrophage or an epithelial cell.

Science's knowledge about how the human body works, while making great advances in the last 25 years, is still nowhere near complete.  There are certain bodily functions that science understands to a good degree (cellular respiration, for instance), others that we're beginning to get a handle on (endocrine signalling) and a lot of areas where what we don't know is a lot easier to point out than what we do know (long-term memory).  

True "junk" would not be highly conserve (5.00 / 4) (#70)
by jmanning on Wed May 08, 2002 at 05:04:16 PM EST

> It turns out that so-called Junk DNA in mice is quite similar to that found in humans.

This is significant. Why? Through normal evolution, many many random changes are made.
If a random change is made to a truly non-important region, no big deal. It doesn't affect the survival of the individual at all. That non-important region will become extremely varied over time. (aka not-conserved).

Now consider an important region - either a protein coding gene, or a useful segment of some sort. If it provides a needed benefit, than a change in this region is harmful, and often causes nonviable (dead) or non-reproducing organisms. This causes these regions to be highly conserved. They vary little between organisms over billions of years. Gene segments that code for DNA replication or protein binding domains exhibit this behavior.

Now, if it were truly junk, you would expect this to have significant random variation, especially in the time between when humans and mice diverged on the evolutionary tree.  Granted, this is a very short time on an evolutionary scale, but if you compare the drift of these "junk regions" to the active regions, I think you'll find them comparable. This is not what you'd expect if they were truly junk with no genetic significance.

Highly conserved between species = significant, not really junk. It must have some genetically useful function to resist random drift.

~Jon

interesting point, some considerations (4.33 / 3) (#74)
by KiTaSuMbA on Wed May 08, 2002 at 10:10:31 PM EST

What is *considered* nowdays junk DNA (a rather inefficient name too) is what we have not *found* a specific function for *yet*. Therefore, it does contain meaningful code as well as "real" junk. In my previous post I consider only the "real" junk DNA as theoritically defined "non meaningful code, either for encoding or for regulating".
The nowdays thought-to-be junk DNA could be better represented by the name of "orphan" DNA since no function is yet to be found. Considering the fact that much of the orphan DNA code does have a function we do not know of yet, this explains the preservation of code.
Now, considering the idea that "orphan" DNA is a mix of both "useful" sequences and junk, preservation rates should not be distributed homogeneously inside it, but rather delimit functioning parts. Given enough computation power, one could "track down" regions of the orphan DNA to investigate for a yet-to-know function instead of a carpet research, and if molecular genetists aren't doing so as we speak is probably because there is not enough CPU to spare!

   
There is no Dopaminergic Pepperoni Kabal!
[ Parent ]

Not junk, then what? + comparitive genomics (5.00 / 4) (#80)
by jmanning on Thu May 09, 2002 at 09:58:40 AM EST

I didn't go too much into this earlier, but you're exactly right. These conserved regions are one of several things.
  1. A previously unknown gene.
  2. Some structural element (it's been found that some sequences are required for replication, DNA folding, etc. It doesn't code for actual genes, but it's very important to hold everything together and make sure it can replicate itself)
  3. Something else entirely. We just don't know yet.
  4. Duplicate, but not functional genes. Some of these are useful because they provide variation for later change.
  5. Junk. Random leftovers. A lot of it is a frequent repeat sequence like one called ALU that inserts itself all over the human genome. ALU makes up nearly 5-10% of the human genome.
As for comparing the two and finding out, don't worry, people are working on it. One of the reasons we're working on both the Human sequence and the mouse sequence is for exactly the reason you describe - comparitive genomics. We're also sequencing the zebra fish - it has most of the same genes as mice and humans, but in a much smaller genome. They suspect this means they simply have less junk - so that should help us sift through and distinguish junk from something we just haven't discovered yet.

~J

PS - By "we", I mean the Genome Sequencing Consortium. I work for one of the instutions that make up the consortium. You might find this informative: http://www.nhgri.nih.gov/NEWS/initial_sequencePR.html

[ Parent ]

5! (5.00 / 1) (#82)
by KiTaSuMbA on Thu May 09, 2002 at 11:17:53 AM EST

for both excelent posting AND actually doing the job
 :-)
There is no Dopaminergic Pepperoni Kabal!
[ Parent ]
Ya know.... (none / 0) (#72)
by Ressev on Wed May 08, 2002 at 08:05:22 PM EST

It is always incredible how much we don't know (and fail to admit we don't know even as we 'admit' it) and yet act and speak as if we know the answers! Like vestigial organs - they are all used in human development.
"Even a wise man can learn from a fool."
"There is something fascinating about science. One gets such wholesale returns of conjecture out of such a trifling investment of fact." - Mark Twain
Possible Secret Message... (5.00 / 1) (#90)
by bobothy on Sat May 11, 2002 at 03:03:37 AM EST

GodCorp Human XP Professional.

END-USER LICENSE AGREEMENT

You may install, use, and duplicate this product in "DNA" form only. The product must not be used on more than 1 entity at a time.

Copying of the Product is not permitted, and any attempt to do so will result in corrupted data. You may install this product on a seperate entitity, providing it is combined with another licenced product of the same version.

The Licence rights granted under this EULA permit use for the first 80 years. After this, the product will begin to deactivate.

GodCorp reserves the right to terminate your use of this Product at any time without prior notification.


Junk DNA - of mice and men | 92 comments (74 topical, 18 editorial, 0 hidden)
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