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New Class of Genes Discovered

michael posted more than 10 years ago | from the put-your-new-genes-on dept.

Biotech 106

HarryGenes writes "Reuters is reporting that Scientists Find New Type of Gene in Junk DNA. The research from Harvard Medical School describes a discovery in the Yeast Genome of a new class of gene that regulates the neighboring gene through the production of its RNA product. This has much broader implications than the article lets on to. Assuming these same type of genes exist in Humans and other organisms, the whole science behind gene expression and gene mapping will be changed dramatically. This type of mechanism can explain a lot of the 'unexplainable'. This is really exciting. I have been working in gene mapping for years and always felt that the 'junk' was there for a reason."

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The more you know....... (3, Interesting)

MrIrwin (761231) | more than 10 years ago | (#9326940)

.....the more you know how little you know.

And yet there are people prepared to unleash modified genes on the world saying that they **know** there is no risk.

Re:The more you know....... (2, Interesting)

Elwood P Dowd (16933) | more than 10 years ago | (#9327184)

No kidding.

As /. user Colin Smith said [slashdot.org] :

Who would have thought that evolution would be developing it's own roundup resistance [cropchoice.com] . Damn that Charles Darwin.

Maybe the Monsanto executives are creationists.

We are not breeding tougher species (1)

leonbrooks (8043) | more than 10 years ago | (#9331025)

We are, hah, weeding out those not resistant to Roundup, of which there will always be some. The Roundup resistance comes with a price: some loss of genetic complexity - or to put it another way, some loss of flexibility. It might be that the resistant weeds survive in a narrower temperature, acidity, humidity or other band, or a specific new weakness might not have an obvious manifestation.

What this means is that if you throw enough nasty chemicals at the weeds, you will eventually wind up with weeds which are too weak or inflexible to survive.

Unfortunately, you might also wind up with crops which are too weak or inflexible to survive. And of course, weaker crops are more susceptible to other kinds of pests and failures - insects, a dry season, whatever.

Either way, you are not witnessing the development of new species, you are seeing the exposure of existing species through the decimation of their closest competitors.

The original article title brings us to another key point: why was it called "junk DNA" in the first place? The difference between a flower and a weed is a judgement:

A weed is just a flower growing

where it isn't supposed to be.
And a flower is just a weed with sense,
To grow in a flower bed you see!

(Thank you, Andy Kazukenus [aol.com] )



The people who named "junk DNA" expected to see junk, or to put it another way, needed to see junk in support of their pet theory of the day. Because of this, research into this vast area of DNA has been effectively held up for years, probably a decade or two. Such is the fruit of an aconational philosophy, which operates to constantly hobble science.

Re:We are not breeding tougher species (2, Insightful)

Elwood P Dowd (16933) | more than 10 years ago | (#9331228)

Either way, you are not witnessing the development of new species

Who said anything about new species? It used to be that very few weeds were roundup resistant. Now that the roundup susceptible weeds are dead, there are more roundup resistant weeds.

What the hell are you talking about?

Re:We are not breeding tougher species (1)

leonbrooks (8043) | more than 10 years ago | (#9331719)

Who said anything about new species?

You originally said...

Who would have thought that evolution would be developing it's own roundup resistance.

It's not developing roundup resistance. The roundup resistance was there before the roundup.

Developing roundup resistance would imply a feature which was not previously there.

Such a feature would in many circumstances be enough to differentiate a species. The touchstone there used to be interbreeding ability, but since many beasties long regarded as separate species can in practice interbreed, science as a corpus has fallen back on distinguishing features. What Monsanto are bringing about by wiping out a subset of the available weeds is not a new, distinguishing feature.

Are you always so cheerful?

Re:We are not breeding tougher species (1)

Elwood P Dowd (16933) | more than 10 years ago | (#9332151)

Such a feature would in many circumstances be enough to differentiate a species.

Then they'd already be different species, wouldn't they?

Whatever.

Re:We are not breeding tougher species (1)

leonbrooks (8043) | more than 10 years ago | (#9332220)

Yes, they would. But they aren't. Go figure. (-:

For a moment... (1)

Cyclopedian (163375) | more than 10 years ago | (#9328356)

I thought you were from NBC.

-Cyc

Re:The more you know....... (5, Insightful)

Anonymous Coward | more than 10 years ago | (#9328373)

And yet there are people prepared to unleash modified genes on the world saying that they **know** there is no risk.

Every time somebody has a child they "unleash modified genes on the world". When people say that there is no risk, they mean there's no risk above and beyond normal behaviour.

context. (2, Informative)

gregorsamsa11 (758287) | more than 10 years ago | (#9330156)

I agree. Of course there is some inherent risk in foods modified using modern recombinant DNA technologies, but no more than with conventional breeding, in my opinion.

Many food producing species have been crossed with outside species (usually closely related, but not always). Crossing with outside species introduces a host of unknown factors, combining genes in a totally unique, unpredictable way. However, this was never a matter of heated public debate. Now if you want to add a single gene culled from some other organism, there is an outcry.

Seedless fruit varieties are generally the result of an uneven cross, where the offspring ends up with an uneven number of chromosome sets, and is thus sterile. These lineages are perpetuated by vegetative cloning (cutting).

Genetic manipulation of food producing plants has been around for some time. Now we have the technology to modify organisms in a more careful, precise way (although the outcomes are still unpredictable), but there is resistance. I think this stems mostly from sensationalist coverage of the new technology. Without the proper background information, people are shocked.

Of course this is a public health issue, and new food products should only be introduced to the public after careful testing. What irks me is the hyteria (not that the parent is hysteric).

Re:The more you know....... (1, Insightful)

Anonymous Coward | more than 10 years ago | (#9334257)

Every time somebody has a child they "unleash modified genes on the world". When people say that there is no risk, they mean there's no risk above and beyond normal behaviour.

When someone has a child in the traditional way, they are unleashing the result of a cross between a human and a human on the world. Several million years of history have shown that the risks involved are relatively low.

When someone splices a jellyfish gene into a mouse, they are unleashing the result of a cross between a mouse and a jellyfish on the world. There is no historical precedent for this. That is why the concept bothers people.

Re:The more you know....... (1)

ZiggyM (238243) | more than 10 years ago | (#9339670)

Parent should be modded UP. Grandparent tries to make the point that there are already cases in nature where humans cross different species. However, such point is not valid, because the type of plant-crossing that humans have been doing for thousands of years is 1) proven to be OK through time, and 2) The species are closely related, or at least both are plants. Now we can mix anything with anything.

Im not against investigating our new abilities to mix DNA and produce new species, in fact I think it will save us in the future. However, it is still too early to unleash these experiments on the general population. It is clear that we do not yet know enough about it.

Re:The more you know....... (0)

Anonymous Coward | more than 10 years ago | (#9347570)

There is no historical precedent for this.

have you heard of horizontal gene transfer?

Re:The more you know....... (1)

ebassi (591699) | more than 10 years ago | (#9350592)

Several million years of history have shown that the risks involved are relatively low.

Indeed, several thousands of History have shown that the risks involved in multiplicating humans are relatively high (for both humans themselves and for the other species as well).

Re:The more you know....... (1)

Mr. Slippery (47854) | more than 10 years ago | (#9335219)

Every time somebody has a child they "unleash modified genes on the world".

Barring mutation (which would explain a lot...), each of my genes can be found in one of my parents. They're shuffled, not modified.

Re:The more you know....... (0)

Anonymous Coward | more than 10 years ago | (#9336456)

Provided your child secretes BHT and glows in the dark, of course.

Falaciuos argument (1)

gacp (601462) | more than 10 years ago | (#9341476)

This is just a nonsensical argument.

The whole point of fertilization, also known as gametic fusion or (imprecisely) as "sexual reproduction", is for species to make sure there is nothing really novel, nothing unusual, in its genes, hence the need for 2 genomes of independent sources, which need not be identical but they do need to be *compatible*. Otherwise, there is no embryo. How many species of metacellulars do you know that do not practice gametic fusion? I thought so. Even partenogenic species are very rare, and probably last a sort time (in evol timescales). Gametic fusion also 'reshuffles' the genomes in a population, homogenizing the population's gene pool and minimising genetic variability (or, more precisely, minimizing intra-lineage divergence).

Genetic engineering, and especially the trans-specific kind that is also *unstable*, is another thing altogether, quite. It is done by arrogant, irresponsible people who are simply ignorant of how life work, and is a veritable Pandora box.

BTW: this 'new' kind of genes is nothing new; it has been predicted decades ago. It's just that mainstream (pseudo)biology flatly refuses to face the evidence, because it would mean *progress* and that's something the High Priests of Science, Inc. just won't have. No sir. No stinkin' falsation of pet theories, thank you so much, I'm quite confortable in my chair. So we are still stuck with things like the stupid myth of Darwinism, and we still cannot cure cancer or have any clue how ecosystems work. And we play with truly dangerous things we cannot understand...

[But don't you worry, they get paid for it.]

New kinds of genes? Guess what? There are even more kinds! Many more! You'll see. They are predicted by (modern, non-traditional) theory---it will be a good test for it.

--

Re:The more you know....... (0)

Anonymous Coward | more than 10 years ago | (#9348795)

Indeed! And in fact those children people unleash have done far more harm than any other GMOs out there!

Re:The more you know....... (5, Insightful)

Shihar (153932) | more than 10 years ago | (#9328415)

I don't **know** that the meat I am eating is free of mad cow disease. I don't really care though because I live with one a few billion odds.

There is certainly a risk involved with genetically modified things. Hell, we know this for a fact because we have been doing it for hundreds of years through more primitive means, and we have screwed up in the past. That said, there comes a point when you need to go over your fear and dive in. We will never know anything for sure, and pretty sure is good enough most of the time. I am pretty sure I am not going to die in a car accident on the way to work each morning and that is good enough for me.

Now, there are plenty of reasons to be weary of modified plants and animals, but all of them are patenting and legal issues. As to the raw science of it though, such concerns are negligible with enough foresight. I don't know about you, but I would merrily risk two or three people in an entire population dying because genetically modified super corn gives them an allergic reaction then watch a few hundred thousand people die because their refuse to grow in the barren land that they live.

People need to put a careful eye to potential risks and rewards. Humans are horribly crafty bastards. Sure, we screw up for time to time, but we are not all that bad at dealing with the consequences. If you need any proof that we fix things more then we break them, you need only look at the average human life expectancy has changed over time.

Re:The more you know....... (3, Informative)

FlyingOrca (747207) | more than 10 years ago | (#9329123)

Man, I don't know. Animals are one thing, but plants are quite another. Ever check out plant genetics?

I'm more of an animal guy, but my ex was into plant biology, and her take on the whole plant genetics thing is nothing less than... very worrisome. Plants swap and adopt chromosomes, hybridize, etc. much more freely than animals.

The problem therefore is not that the actions of a gene in one species aren't known (though I'm not convinced they're know well enough); it's that the gene can get into other species far too easily. There are bigger nightmares in that scenario than a few allergic reactions.

I'll be the first to admit I'm no expert in plant genetics - but a fair number of people who ARE experts are concerned. I'm inclined toward caution. I'd suggest that the best thing to do is to clearly label products containing material from GMOs and let the consumers decide, but the shee^H^H^H^Hconsumers are the same folks with unpatched Windoze boxen. Cheers!

Re:The more you know....... (2, Funny)

JWW (79176) | more than 10 years ago | (#9329740)

After reading your post, all that I can think of is

"Feed me Seymore!!"

Feed me all night long (0, Offtopic)

FlyingOrca (747207) | more than 10 years ago | (#9330151)

That was a truly great flick. I went to see it with a couple of women who were die-hard, I mean "dress-up-'n'-shout-alternate-dialogue" Rocky Horror fans, and all three of us walked out of Little Shop of Horrors thinking it was the best horror musical ever. Thanks for the memories!

Re:The more you know....... (3, Interesting)

Canar (46407) | more than 10 years ago | (#9332214)

You think plants are crazy? Check out bacteria. They swap so many genes its unbelievable. And if the genes kill that bacteria, well, it's been selected against. That won't prevent them from picking up genes elsewhere.

A shovel-full of dirt contains a regular frenzy of bacteria swapping genes not unlike getting fish, birds, reptiles, mammals, and earthworms together for a big bisexual orgy. The only difference is that with the bacteria, it actually works from time-to-time because they haven't specialized as much.

Plants are a lot of fun though 'coz they're multi-cellular and we can actually see what's going on. With bacteria, we just have staining, which is a piss-poor substitute for watching that little green mass of cells differentiate over several days.

Re:The more you know....... (0)

Anonymous Coward | more than 10 years ago | (#9333970)

A shovel-full of dirt contains a regular frenzy of bacteria swapping genes not unlike getting fish, birds, reptiles, mammals, and earthworms together for a big bisexual orgy.

That has to be the most frightening and yet intruging mental images I've ever experienced in my life.

Re:The more you know....... (1)

Schwarzchild (225794) | more than 10 years ago | (#9343207)

You think plants are crazy? Check out humans. They swap so much bacteria its unbelievable. And if the bacteria kills that human, well, it's been selected against. That won't prevent them from picking up bacteria elsewhere.

Re:The more you know....... (1)

JavaLord (680960) | more than 10 years ago | (#9335155)

There are bigger nightmares in that scenario than a few allergic reactions.

Hah, like the super plants growing out of control and killing everyone? Sounds crazy right? There is a good write up about it here [xs4all.nl] Interesting stuff.

Makes sense (1)

phorm (591458) | more than 10 years ago | (#9345651)

If you think of it this way... you can't breed a dog and a cat, or a human and chimpanzee (although the intelligence of some of the locals here suggests it may have happened), but you can graft or crossbreed a lot of different trees.

Oranges, Apples, most fruits... and they've managed to crossbreed with nicotine plants. Granted that many of these plants are still fairly related... but I've heard of some very interesting crosses in the world of flora. Fauna is a bit behind on that, I think.

Re:The more you know....... (2, Interesting)

Jtheletter (686279) | more than 10 years ago | (#9330367)

If you need any proof that we fix things more then we break them, you need only look at the average human life expectancy has changed over time.

Humans master fire:
+ life expectancy goes up.
- Number of people being killed (broken) by fire increases dramatically
- Number of forests destroyed(broken) by fire goes up

Humans master agriculture:
+ life expectancy goes up.
- millions of acres of forest are clearcut(broken) for farming land and buildings for farming villages
- genetic diversity of agricultural plants stagnates(broken) as farmers regrow seed year to year

Humans master building materials:
+ life expectancy goes up.
- millions of acres of land turned into cities(broken) and towns
- More land clearcut(broken) to make room for enlerging populations
- thousands of species go extinct(broken) as their environments are developed and polluted

Etc Etc Etc

The point here is that we've broken way the hell more than we've fixed just to increase our life expectancy such as we have. Entropy is the nature of the universe. It is very nearly impossible to create without destroying, and humans have proven to be very sloppy up to this point.

Re:The more you know....... (1)

Shihar (153932) | more than 10 years ago | (#9338664)

Everything you point out is certainly true - if you are a plant or animal. If you are a non-human animal or tree, having humans around sucks. Lucky for us, we are all human here. I care about the environment exactly as much as it has some sort of impact on humans.

So yes, agriculture has completely changed the face of the world and wiped out many pieces of the environment, but I give agriculture a big thumbs up. Agriculture means that I don't have to go get my own food, and that gives me plenty of time to be an engineer, doctors work on extending my life, and scientists to unlock new technologies.

Simply put, humans have a very consistent track record of improving their situation. They fuck up from time to time to be sure. We would be gods if we could avoid every mistake, and obviously we are not gods. That said, the general trend is clear. When humans sit down to work a problem they come up with solutions better then they had before. We as a species live longer and healthier lives now then we did in the past. The world is by no means perfect, and it has more then its fair share of problems, but clearly things are always getting better. A clear and obvious indication of this is the fact that human life expectancy continues to climb without faltering. Even through all of our mistakes we get enough right to leave our children with longer lives then we have, and so I thumb my nose to arguments that decry we shouldn't touch something simply because we might make a mistake. Of course we might make a mistake, but we also might make a great achievement. Relentlessly moving forward is all apart of being human. It would be unwise to forget that the darkest moments in our history are when we forget this.

Re:The more you know....... (2, Insightful)

MrIrwin (761231) | more than 10 years ago | (#9330602)

"I don't know about you, but I would merrily risk two or three people in an entire population dying because genetically modified super corn gives them an allergic reaction then watch a few hundred thousand people die because their refuse to grow in the barren land that they live."

Ahem, are we saying that GMC's are being used as a solution to world famine? I am no expert, but I know in Europe the EU commision has problems curbing production levels because they are too high. So is there any logic introducing GMC on a production scale?

I agree with using genetics were otherwise loss of life or extreme hardship would be the alternative.

I agree with scientific research and small scale controlled research projects.

I do not agree with with genetics that are not particularly necessary, and I am not alone in this. Hence the claim, to make it more palatable, that there is no risk.

Given that there is an awful lot to learn about genetics and that consequences may only be clear after many years, that would seem to be a very un scientific claim.

Complexity = unintended consequences (2, Informative)

garyebickford (222422) | more than 10 years ago | (#9332251)

Patent and legal issues are the easiest. Foresight is essentially impossible in any practical sense. Identifying potential interactions of genetic modifications is many orders of magnitude more complex than, for example, nuclear waste management. The state space for the interactions between genes has dimensionality (IIRC) 2^2^log(n) for n genes, and each dimension has variance 2^n. For as few as 20 genes, you have a space too large to search for significant interactions.

Now, expand that space to account for the 98% of the DNA once thought to be junk that has now been shown to have unidentified and mysterious interaction with the "proper" genes.

To make matters worse, you are working with a dynamically stable ecosystem, within which a minor change in a single gene in a single plant can cause transformation or collapse of an entire ecosystem - usually not, but it has happened. The recent debacle [nerage.org] of Monsanto's Round-up resistant seed crops is instructive, as it shows that the genetics is just one small part of the puzzle. The relationships between all the other parts of the system are altered, like dropping a bowling ball on a multidimensional trampoline. Ecosystems adapt, usually in ways that are not convenient for anyone trying to force them into a particular pattern. This article [web-dictionary.org] is worth reading and well-linked to related facts and definitions.

Also, as someone who regularly suffers allergic reactions to foods that are improperly labelled, Inote that statistics mean something entirely different to statisticians than to victims. Does this mean you're volunteering to be one of those two or three? :O)

Re:The more you know....... (2, Interesting)

Mr. Slippery (47854) | more than 10 years ago | (#9334764)

As to the raw science of it though, such concerns are negligible with enough foresight

Like the foresight we used when we put lead in gasoline? Or put CFCs in aerosol cans? Or started using fission for electrical power generation without a plan for storing nuclear waste? When profits enter the picture, foresight is a rare commodity.

I don't know about you, but I would merrily risk two or three people in an entire population dying because genetically modified super corn gives them an allergic reaction then watch a few hundred thousand people die because their refuse to grow in the barren land that they live.

First, how about letting us make own own decisions about the risks we want to assume, and labeling GM foods?

Second, there's a huge problem with a socioeconomic system that has people growing modified corn in an area where corn doesn't naturally grow, rather than growing the native crops that can thrive there. (Cf. "golden rice".)

Third, the big risk is not allergic reaction, it's the ecological risks: crop monculture, horizontal gene transfer, increased use of pesticides (think what "Roundup Ready" means), et cetera.

Re:The more you know....... (1)

ebassi (591699) | more than 10 years ago | (#9350655)

but I would merrily risk two or three people in an entire population dying because genetically modified super corn gives them an allergic reaction then watch a few hundred thousand people die because their refuse to grow in the barren land that they live.

Sorry to burst your bubble, but I Call For Bullshit(R) here

The agricoltural assets are just about enough to feed every living person on this planet, given a fair redistribution of those assets (in fact, in the EU, the goverments pay the farmers not to go in "full production mode"). The "GMO will feed the hungry" BS has been spread essentially by the same industries that create Genetically Modified Organisms in the first place.

GMO are indeed useful in reducing the needed chemical anti-cryptogamic compounds used for boosting the output; or to enrich a plant with minerals or vitamins needed for a balanced diet (see Golden Rice in China).

Re:The more you know....... (1)

Coos (580883) | more than 10 years ago | (#9333323)

And yet there are people prepared to unleash modified genes on the world saying that they **know** there is no risk.

Genetic engineering consists of moving DNA for a reason - i.e. its done with the sequences that we know well how they work. No-one is creating commercial GMOs out of 'junk' DNA today - but now our understanding is growing, some of that junk isnt junk any more, and when it *is* understood, it probably will feature in future biotechnological innovation.

It's only in Nature that you see huge chunks of DNA crossing species barriers in the absence of intent or control

Re:The more you know....... (1)

nine-times (778537) | more than 10 years ago | (#9334262)

there are people prepared to unleash modified genes on the world

It's so scary. After all, genes have gone unmodified since the beginning of time, no one knows what could happen if you change them from their original, perfect form.

I mean, if anyone had different genes, they're libel to become zombies or something. Hasn't TV taught us anything?

OK, ok. I was tempted to stop here, and have a nice little troll, but some of what we hear about as "genetic engineering" really is little more than the selective breeding that people have been doing for thousands of years. That's why we have plump pigs, juicy chickens, carrier pigeons, and helpful dogs.

Sure, we want to be careful, as we want to be careful with any scientific endeavor. You think there aren't dangers in working with particle accelerators? If we ever successfully create an AI, we'd have to worry about it becoming a real-life SKY-Net. Should we not be working on AI? New medications can have side effects that aren't obvious or don't manifest for years. Should we halt all testing?

As with any technological or scientific advancement, we should be careful to create ethical applications after careful and thorough testing. But we shouldn't run and hide because it sounds like a good premise for a horror movie.

Lord knows, I love my dog.... (0)

Anonymous Coward | more than 10 years ago | (#9353618)

but the way she's been bred, she'd last about ten minutes without humans around. (She seems to think squirrels are her friends, and want to play. Dumb (although cute) bitch.)

Yeah, But (3, Interesting)

4of12 (97621) | more than 10 years ago | (#9327124)


I have been working in gene mapping for years and always felt that the 'junk' was there for a reason.

Sometimes, too, the gene may have moved into the junkyard for a good reason.

Just imagine reactivating some junk human genes to see what happens:

Human females have a more pronounced season of going into and out of heat.

Get an extra furrowed forehead to better protect vision during rainstorms and intense heat on veldt.

Get large hairy ears to better pick up on approaching predators like lions.

Given the current rate of change in human environment due to social and cultural changes, I'd venture to guess we have a lot more junk DNA that needs to exit (eg, propensity to develop diabetes if not on a hunter/gatherer diet) than we have need to reactivate old junk DNA.

If we could engineer useful new DNA, probably creating a visual transmitter capable of expressing information more quickly than voice or hand movement would be high on the list. I would call this the Teletubby gene...

Mmm, sexy. (5, Funny)

mopslik (688435) | more than 10 years ago | (#9327222)

Human females have a more pronounced season of going into and out of heat.
Get an extra furrowed forehead... [and] large hairy ears

Well, those two should help cancel each other out, no?

Re:Yeah, But (1)

shaitand (626655) | more than 10 years ago | (#9327514)

Actually all of these would be good things if you ask me:

Knowning when the ladies are in heat... that can't be bad at all. Evolution took this out because we don't need it to survive.. what we need and what we want aren't always the same thing.

Extra furrowed forehead which gives better vision, better vision sounds good. The cosmetic affect after all is irrelevant, when everyone has this it won't "look bad" anymore.

Improved hearing, this is bad?

Re:Yeah, But (3, Funny)

Patrik_AKA_RedX (624423) | more than 10 years ago | (#9327701)

Improved hearing, this is bad?
If you live in a flat with thin walls, I say it is.

Re:Yeah, But (0)

Anonymous Coward | more than 10 years ago | (#9331496)

I wouldn't, but then again, I know what my next door neighbours look like (lesbian couple), and they aren't quiet. And I don't mind.

Re:Yeah, But (1)

jc42 (318812) | more than 10 years ago | (#9329984)

Knowning when the ladies are in heat... Evolution took this out because we don't need it to survive.

Actually, "Evolution" probably took it out for a positive reason, not just because we didn't need it.

There are a number of other species in which the female estrus is weak or nonexistent and females are sexually active much of the time. These species have a number of characteristics that they share with us humans: They are mostly social species in which the males contribute a great deal to the raising of the young. Female sexual availability is a pretty good way to encourage males stick around and contribute to the welfare of the social group.

Not that all social species do this, of course. But in those that do, it's probably not just loss of unused genes; it's more likely a direct adaptation to a social lifestyle.

Re:Yeah, But (2, Interesting)

s0l0m0n (224000) | more than 10 years ago | (#9330244)

Knowning when the ladies are in heat... Evolution took this out because we don't need it to survive.

Actually, "Evolution" probably took it out for a positive reason, not just because we didn't need it.


I don't think that it's gone. Your lady may want to have sex with you on a regular basis, but she is most fertile on certain days of her cycle. The natural planning method of birth control would work, except for the fact that sperm are able to live for quite some time whilst looking for an egg to fertilize.

If you really pay attention to your woman, you might notice that she does still have cycles, and that she's way hornier at certain times of the month. ;) It's about the only thing that makes up for the fact that they bleed for a week straight. :D

I think that the original function of the fertility cycle probably has to do with the timing of which offspring are born. Animals are ruled by the weather.. If the offspring are born at the wrong time (say, during the middle of winter), they may well not survive. Humans have largely mastered the effects of weather, thus eliminating the need for a cycle that prevents us from bearing children in the winter.

Re:Yeah, But (2, Interesting)

shaitand (626655) | more than 10 years ago | (#9330299)

Females are sometimes in heat and sometimes not NOW. Being in heat being more pronounced won't make them want sex any less or less often, our species mates for recreation as well as breeding.

The only difference would be that you'd have women walking up to you at various times and rubbing their bodies against yours.

Actually however, our social structure isn't really a superior way to propogate the species. The males sticking around is really a bad thing.

The purpose of a species of course is perpetuate, in many senses sex is the answer to that silly question some people ask "what is my purpose in life?" duh, your purpose is procreate and advance the human species however you can... that's it.

A species in which females are sexually active (in heat) most all the time, and which engages in sex for recreation. But in which the females care for the young and the males move to the next available females means MUCH more procreation (and happier males).

Personally I think lions are an example we should look to for enlightenment. Genetic advances could allow us to increase the ratio of female to male children and a couple generations down the road we'd have a greatly improved world.

Re:Yeah, But (1)

MrWim (760798) | more than 10 years ago | (#9330870)

A species in which females are sexually active (in heat) most all the time, and which engages in sex for recreation. But in which the females care for the young and the males move to the next available females means MUCH more procreation (and happier males).

It wouldn't mean more procreation, it is in such a way that just the right amount of procreation occurs and this polygamous system would adapt to this meaning that some males have multiple mates and some have none. It would probably be a much more violent society also because there would be more competition for mates

Re:Yeah, But (1)

shaitand (626655) | more than 10 years ago | (#9331513)

ok, you must have missed the part about leaving the old females behind ;) Just because I'm with two or three tonight doesn't mean they won't be there for someone else tomorrow.

Re:Yeah, But (1)

MrWim (760798) | more than 10 years ago | (#9341486)

Not at all, in a promiscuous species it is benificial for the males to try to mate with as many females as possible, whereas it is still only benificial for the females to mate witht he same regularity as before (actually less as in a promiscuous species males become much more fertile -a chimp has testicles 4x the size of human testicles compared to body size). So the females have more choice to choose from so are more picky and it becomes much less likely for a female to consent to mating with a male.

So, net result, females need less sex because of increased male fertility, so overall males get less, but because of the competitive environment they want more and are more aggressive. Females want less because they have more choice and it pays to be picky.

Less sex and more aggression doesn't sound like the kind of environment I'd like to live in personally, would you?

Re:Yeah, But (2, Interesting)

isotope23 (210590) | more than 10 years ago | (#9329873)

"I'd venture to guess we have a lot more junk DNA that needs to exit (eg, propensity to develop diabetes if not on a hunter/gatherer diet) than we have need to reactivate old junk DNA."

I was struck by this as it is connected with something I have been thinking about for awhile.
Namely the impact of Race and DNA on diet.

We know that issues such as lactose intolerance are regional :

http://www.gnxp.com/MT2/archives/001681.html

I would suspect that tolerance of other foods are as well, given the differing availabilty of food around the world. With the above, it surprises me that instead of things like Atkins, there is not a more racial approach to diet. I.E. A "northern european" diet heavier on dairy, an asian diet heavier on fish etc.

Re:Yeah, But (2, Interesting)

4of12 (97621) | more than 10 years ago | (#9330100)


With the above, it surprises me that instead of things like Atkins, there is not a more racial approach to diet. I.E. A "northern european" diet heavier on dairy, an asian diet heavier on fish etc.

Actually, there is.

A while back people started coming out with the notion that the ideal diet (and, for that matter, entire lifestyle including exercise regimen) depended on blood type [about.com] , which roughly characterizes some racial features.

Blood type (2, Interesting)

isotope23 (210590) | more than 10 years ago | (#9330869)

Interesting idea, but from looking at blood type distribution it does not seem to closely related to differing areas of the world. The blood types seem to be rather evenly spread.

My thinking is that the prehistoric people regardless of blood type would have all had to survive on the available local foods. I would think that the lack of choice, i.e. "rabbit or nothing" would have killed off those in the region incapable or less well suited to digesting most of the local quisine.

The question for me is are there other genetic predispositions like lactose tolerance (although to a lesser degree) which would allow some to make better use of certain types of food than others?

Re:Yeah, But (1)

hplasm (576983) | more than 10 years ago | (#9332984)

females have a more pronounced season of going into and out of heat. Get an extra furrowed forehead to better protect vision during rainstorms and intense heat on veldt. Get large hairy ears to better pick up on approaching predators..... I would call this the Teletubby gene...

I would call it the Ferengi gene...

bad article (5, Insightful)

merdark (550117) | more than 10 years ago | (#9327212)

As usual, the quality of a mainstream news outlet reporting on science news is bad. This really has nothing to do with 'junk DNA' from what I can tell. Also, the term 'junk DNA' is terrible.
There are repeats (sometimes referred to as 'junk DNA') and there are introns and intergenic regions with no *known* function (also referred to as 'junk DNA').

So while it is technically true that the gene was found in 'junk DNA', it's also true that EVERY new gene is found in junk DNA. That is not what is interesting here at all.

Basically, they found a gene that turns another gene on or off via it's RNA product. This is what the intereseting news is.

Good article (5, Informative)

cariaso1 (674515) | more than 10 years ago | (#9327532)

Until this article was published, 'junk dna' would be considered the correct term for this region. Broadly speaking, the term suggests that there is no known function for the region. We don't know much beyon "is a region is a coding region?" and "is a region regulatory?". Now this region can be classified as regulatory, but it uses a mechanism never before observed. That is news.

Much more information can be found in this article taken from pubmed.

Stealth regulation: biological circuits with small RNA switches [genesdev.org]

Re:Good article (2, Insightful)

merdark (550117) | more than 10 years ago | (#9327665)

Sorry, but I still think it's a bad article. What do they mean by 'junk DNA'? Is it a repeat (turns out no), intergenic, intron? Junk DNA is a terrible term to use. As I said in my previous post, every new gene or regulatory region is found in so called 'junk DNA'. This is nothing new.

The important part of the article is that this is a new never before seen *type* of gene. That's the news here, not this sillyness about junk DNA. That part should have been completely left out IMO.

Re:Good article (0)

Anonymous Coward | more than 10 years ago | (#9328038)

Perhaps your trying to say junk DNA is a bad term, because it implies the DNA has no use at all, infact is in the way. While in reality a fair amount of it is just simply not really researched yet. Orhas some kind of really minor use where it doesn't furrther matter much what's in it, as long as it makes sure to be of a certain minimal length.

Quickshot

Re:Good article (1)

martinX (672498) | more than 10 years ago | (#9342952)

Junk DNA is a terrible term and should be phased out. It would be analogous to calling unexplored parts of the earth "garbage dumps" simply because we haven't explored them yet and don't know what's there.

I hereby propose DUFF - DNA of Unknown Form and Function.

Re:Good article (1)

RevAaron (125240) | more than 10 years ago | (#9332867)

I am with you on this one, cariaso.

While my specific area of interest is not genetics or molecular biology- it is mathematical and computational ecology- I do have the basic knowlege of genetics required of anyone in a college biology program.

I have always heard the term "junk DNA" refer to sequences of genetic code that appear to have no use, oftentimes appearing just to be big repeating patterns of nonsense and outside of a coding region.

What interests me especially about this article is that since I first heard of so-possed "junk DNA" I have had a gut feeling that it was not all just junk. At least some of it had to have some use, and I was quite excited indeed to see this article pop up. If I had to confine myself to genetics research for one reason or another, looking in to this would be it. :)

Re:bad article (2, Insightful)

HarryGenes (772322) | more than 10 years ago | (#9328782)

This is novel and interesting for the fact that the gene was found in 'intergenic space' and does not have all the normal features and functions of a gene. You are taking the reference of Junk DNA far to personally. It is not to say the DNA has no purpose. If it is there for nothing else, it minimizes the odds of mutating important genes. If the genome was just one gene stacked end to end, then every time a mutation occurred, it would be in a gene. Since 95% of the material has no known function, at the very least it reduces the chances of harmful mutation. We have been inside a box for years thinking that genes have a specific structure, specific role. We find that it is not that simple. I wonder now, in light of this, if introns might have a more important role than previously thought...

Re:bad article (1)

merdark (550117) | more than 10 years ago | (#9328942)

But most new genes are found in 'intergenic space'. That it has a different structure is interesting for sure, but I just don't see the focus of being found in 'intergenic space' to be all that important.

The article almost makes it sound like this is about junk DNA. It's not though, it's about this new type of gene. That's why I feel it's a bad article. And it would have been nice if they at least provided a reference to the lab or paper.

Precedent for "junk DNA" (2, Interesting)

jc42 (318812) | more than 10 years ago | (#9330135)

There is a fair amount of precedent in science and math for this sort of terminology.

For example, a few centuries ago some mathematicians started studying the funny numbers like the diagonal of a unit square, and proved that they weren't the ratio of two integers. The idea that there were such numbers was widely ridiculed. The mathematicians' reaction was to say "We need a name for these new numbers. People are calling us irrational for talking about them. Why don't we just call them `irrational' numbers?" And so it was.

Some time later, in the 1800's, some mathematicians started talking about numbers whose squares were negative. Others criticised this as saying that there were no such numbers. Again, a name for these new numbers was needed, and someone suggested adopting the critics' terminology and calling them `imaginary'. And again mathematicians liked the sound of this, and adopted the term, with `real' the name for the numbers that their critics believed in.

Part of the education of a mathematician or scientist is learning to take a disconnected, "objective" view on such terminological quibbles. Adopting your critics taunts is a good way to get across the idea that "it's just a word" with no connotations other than the technical definition.

In the computer field, we have the term `hacker' that originated as an insult, and is still used as such by outsiders. But to us, it's a useful technical term with no negative connotations.

Just as `irrational' and `imaginary' are considered simply descriptive terms by mathematicians, with no value judgement implied, we can expect that biologists will use `junk DNA' as a technical term for specific kinds of DNA long after they fully understand the function of the `junk'. You'll find it precisely defined in textbooks, and people will use the term without thinking that it's derogatory.

Re:Precedent for "junk DNA" (2, Informative)

GeoGreg (631708) | more than 10 years ago | (#9330852)

For example, a few centuries ago some mathematicians started studying the funny numbers like the diagonal of a unit square, and proved that they weren't the ratio of two integers. The idea that there were such numbers was widely ridiculed. The mathematicians' reaction was to say "We need a name for these new numbers. People are calling us irrational for talking about them. Why don't we just call them `irrational' numbers?" And so it was.

Actually, irrational numbers are so named because they can't be formed from the ratio of two integers. It so happens that in Latin, ratio can mean either "reason" or "computation". Thus the name describes a mathematical property, not any perceived faulty reasoning.

Re:Precedent for "junk DNA" (1)

sartin (238198) | more than 10 years ago | (#9336675)

For example, a few centuries ago some...irrational....

This is some weird combination of revisionist history (the ancient Greeks knew about irrational numbers) and just plain making shit up (irrational means it can't be expressed as a ratio of integers). See Mathworld's definition of irrational number [wolfram.com] for one more credible, and more researched, version.

Some time later, in the 1800's... imaginary....

Imaginary numbers under a variety of names were discussed at least as early the 16th and 17th centuries and credible sources [princeton.edu] claim references back to the ancient Egyptians; this reference also says the term "imaginary" was in common use at the time of Descartes (though makes no reference in the online material as to who coined the term). Many less credible [pballew.net] online sources [fortunecity.com] place the name as coming from Descartes and claim it to be dergatory, but many of those sites [campusprogram.com] appear to be copying [thefreedictionary.com] from some common source of unknown origin. So, the guess that imaginary was derogatory may be correct.

I suppose one of four (calling the fact of the name and date of discovery each as guesses at the truth)possibly correct speculations isn't bad for just spewing stuff that sounds credible

Re:bad article (1)

abiggerhammer (753022) | more than 10 years ago | (#9331576)

I don't quite follow why that's even so interesting, though. RNA inhibition is a pretty hot topic; we've known about antisense RNA [rcn.com] (which is produced by DNA to complement mRNA and inhibit translation) for about 30 years now, RNAi [sirna.com] for about five, and microRNA for probably two (the latter two, again, regulate gene expression by interfering with mRNA, though RNAi cleaves the mRNA in the process and microRNA doesn't).

Of course, most people reading a Reuters article probably don't even know what RNA is, much less RNA inhibition. But it seems odd that the article would make such a big deal about it, unless it's some new kind of interference that we haven't seen before.

There is real naivete (4, Interesting)

JGski (537049) | more than 10 years ago | (#9327225)

Irrational enthusiasm expressed by too many biotech execs (I used to be in the business - my sister and brother-in-law are "wheels" in the business) is concerning.

This article is about is genomics knowledge which is one of the best understood areas of biotechnology and molecular biology, yet it's always bugged me that PhDs in biology would simply dismiss what didn't fit into their neat little model as "junk DNA". That "junk DNA" was conserved gave serious doubts about it being junk. That it has to be a "control system" component has pretty obvious.

Until recently though, math and systems theory have not been strengths of biologists in general - when I was in school, biology was what people took to be able to do science without a lot of math. Ask a biologist about Laplace, Linvill or Liapunov and you'll get a blank stare - which is truly scary if they're mucking around with living feedback systems being spread into the broader environment. There's still a generation that probably needs to be purged before the profession can be deemed "systems theory aware".

What's scarier: the whole knowledge-base of proteomics and enzyme/metabolic circuitry is far more primitive that genomics, yet this area represents far more of the biology activity in cells than genomics. Which makes plunging head-long into rolling out things like Monsanto safflower extremely dubious and dangerous.

That said, I'd be the last to advocate ceasing this type of genetic research and technology development - only it is different from most every potentially dangerous technology humanity has developed, so considerable caution and process safe-guards are needed.

Re:There is real naivete (0)

Anonymous Coward | more than 10 years ago | (#9328192)

The biologists your describing there sounds more like psychologists, I incidentally didn't get those terms you named there in my maths in biology, but then I didn't hear then in my physics maths either. Maybe it's just the difference in language. Alternatively it's due to you not understanding that not all fields of biology need great knowledge in maths. Most don't actually. However, for certain types of research, and even more so for reengineering you definitly would need to use amths to beter understand consequences.

Anycase, biology already was purged for great extent of non scientific thinkers. Atleast I havn't noticed them where I am. Anycase, I'm not quite sure what you mean with system theory aware. Are you referring to how all the sperate objects are relating with each other? As you can see in ecosystems etc.

As for junk DNA, the point of this article. I've always thought that most of it was there for a reason. We already know that some sections are for sure waste, and we already knew sections of it had regulation uses. So I can't really say it comes as a great surprise that yet more of the unkown portions get figured out for either true junk, or has a reason, or function.

Quickshot

PS, biotech exec exuberance is likely one of those hype kind of things, some people will just never learn, though you'd think the internet bubble aught to have done it. That being said, there are some very good biotech ideas out there though.

Re:There is real naivete (2, Insightful)

dondelelcaro (81997) | more than 10 years ago | (#9328672)

Until recently though, math and systems theory have not been strengths of biologists in general - when I was in school, biology was what people took to be able to do science without a lot of math. Ask a biologist about Laplace, Linvill or Liapunov and you'll get a blank stare - which is truly scary if they're mucking around with living feedback systems being spread into the broader environment. There's still a generation that probably needs to be purged before the profession can be deemed "systems theory aware".
Oh please. You're conflating your high school biology teacher with serious research biologists, biochemists, genetisists, and biophysicists. Worse, you're using an ill-informed mainstream article to do your misdirection without even bothering to read the original article in question. [nature.com]

Clearly there is room for improvement in our understanding of all of these fields, which is why people doing biological research have been teaming up with computer scientists, mathematicians, physicists, and statisticians. I personally straddle a few of these fields every time I hoist a test tube and then analyze the data that comes back from it.

Re:There is real naivete (1)

mike3411 (558976) | more than 10 years ago | (#9330004)

Good reply, but those of us without Nature subscriptions can't view the actual article. What does the actual research say? The original Reuters article doesnt really supply enough information to understand.

Re:There is real naivete (1)

dondelelcaro (81997) | more than 10 years ago | (#9330115)

Transcription by RNA polymerase II in Saccharomyces cerevisiae and in humans is widespread, even in genomic regions that do not encode proteins. The purpose of such intergenic transcription is largely unknown, although it can be regulatory. We have discovered a role for one case of intergenic transcription by studying the S. cerevisiae SER3 gene. Our previous results demonstrated that transcription of SER3 is tightly repressed during growth in rich medium. We now show that the regulatory region of this gene is highly transcribed under these conditions and produces a non-protein-coding RNA (SRG1). Expression of the SRG1 RNA is required for repression of SER3. Additional experiments have demonstrated that repression occurs by a transcription-interference mechanism in which SRG1 transcription across the SER3 promoter interferes with the binding of activators. This work identifies a previously unknown class of transcriptional regulatory genes. [From the abstract]
Not being an expert in S. cerivisiae myself, I'm not totally sure exactly what SER3 does, but it looks like they've located a novel regulation form in the upstream regulatory element at -583 (SRG1) which produces an RNA which competes with transcription factors necessary for transcription of SER3 . [In effect, yet another rather interesting mode of genetic repression in yeast.]

Re:There is real naivete (1, Flamebait)

JGski (537049) | more than 10 years ago | (#9331032)

Sorry, No. When I said "school", I meant college, undergrad and graduate. High school is about as distant as kindergarten from my point of view. A few graduate degrees will do that. Perhaps you see the past differently.

My biology-majoring school (I mean, university) friends, both in undergrad and graduate school did, in point of their own words, pick biology because of the minimal math. Those people are now runnng biotech and pharma companies today. Statistically significant? - well, a dozen data points. Even my own sister, who is a PhD in biology and director of operations at a major biotech firm, has told me the same - she picked biology over engineering or physics, in part because of the milder math requirement. She is quite good at math I should note and probably could have easily done physics or EE.

I am thankful that bioinformatics curricula are becoming so prominent. It's a step in the right direction vis-a-vis the true complexity of the biological system. I think the profession is trending to greater mathematic sophistication but technical knowledge and expectations are always generational. I'm still involved in a number of proteomics and metabolic circuit projects so I see it first-hand. Unfortunately nothing in these will be used by the biotech industry for a good 5-10 years. Academic lab projects != commercial R&D projects.

I have read the original article, thank you. My comment was specifically with regard to my actual conversations with actual PhD's in biology running actual top-ten (earnings, reputation, your pick) biotechnology and pharma companies. This type of origianl journal article's discovery, from what I've seen personally, actually surprises folks who I would have thought/hoped knew better, but clearly don't, despite their PhDs (my sister excepted, of course). Admittedly even PhDs can become PHBs when they become VPs.

The profit motive causes as much corner-cutting in biotech as any other commercial field. Further, the opinions of those without the "gold standard" degree (in biotech that would be a PhD in biology) are discounted as much as they are in other industries, which leads to naive strategies and decisions despite the availability of other voices (sounds like Iraq). Similar things happen elsewhere: try getting promoted at Agilent above group manager without an EE degree - it will never happen! It causes the same blindspot problem.

Re:There is real naivete (2, Insightful)

mz2 (770412) | more than 10 years ago | (#9333384)

What I hate the most in scientific debates are those people whose arguments are both heated and unknowledgeable. Junk DNA is something of a junk word if you ask from a real geneticist, as many examples of regulatory and other types of function have been attributed to the non-protein-coding regions of the genome.

This is because your personal DNA sequence is not just the blueprints for all your components, it also works as a script to trigger synthesis of these components at a right place and time -- as a response to extra- and intracellular signals. And some of the non-protein-encoding regions are very well known to function in the required regulation. And also, some of the other "non-functional" (already a misleading term) part of the genome can be categorised to quite a few different origins and functions, e.g. the spacer DNA which is thought to be there for causing correct folding of the chromosome for certain regulatory proteins to bind and thus cause or inhibit transcription of a gene/genes. In fact, it's these highly complex and far-reaching regulatory areas of the genome that make e.g. higher animals such a lot more complex and "advanced", not the evolution of the gene products.

And how about the maths? Have you ever heard of the algorithms developed for DNA/RNA/protein sequence analysis? Or the whole field of systems biology, that tries to understand and predict cellular mechanisms purely with mathematical models? Which is certainly not the easiest applications of mathematics... Besides, for some parts of biology/biochemistry/genetics it is quite true that mathematical knownledge of a researcher doesn't have to be top-knotch (it does have to be decent for any scientist, though!), because of the quite evident experimental side of things. If you look at biology as opposed to e.g. particle physics, as biologists we're still rather in the data-gathering, catergorising phase of the science instead of predicting and synthesizing phase. Which means that we also need those for which the microscope is a more applicable tool than knowledge of mathematical models.

Very ironic (2, Interesting)

hung_himself (774451) | more than 10 years ago | (#9335879)

I think you are looking at the wrong sample. You could probably say the analogous things about computer execs. The real algorithmic research of course happens at the universities and similarly that's were the real biology research is happening - not at the biotechs.

You are correct that nowadays biology and mathematics are intertwined, attracting more quantitative people. Where you are mistaken is your implicit assumption that the naivete is on the biologists side. There is a lot of knowledge that needs to be accumulated before the biological literature can be adequately digested. Your post is point in proof - had you been more experienced in genetics you would have realized that no geneticist really believes in junk DNA - it is really a term that laymen have found useful.

As someone who does both, I would also argue that it is much easier to pick up the mathematics than the biology. If you are a quantitative person it is very easy to learn what a Laplacian is, and to apply it to your biological problem. While it may be just as easy to look up junk DNA - it is very difficult to get to the point where you realize that is what should be questioned. The problem I see is not so much biologists who waste time because their projects are mathematically unsound, but more so, mathematically trained people spinning wheels on research which is not relevant or based on dubious biological tenets. However, I do think it is a transition thing as specialists in both fields learn (the hard way) about the pitfalls.

Multi-dimensional (1)

UnknownSoldier (67820) | more than 10 years ago | (#9327236)

Boy, I can't wait till they find out that genes are multi-dimensional, the same way a fugue is. :)

--
The fallacy of government is that it assumes everyone needs to be told how to live, but the fact remains it is unconstituational to homogenize community by its own standards. When it passes more laws until it makes everyone a criminal it has made the mistake of placing the intent on the "Letter of the Law" over the "Spirit of the Law."
"The more corrupt the republic, the more numerious the laws" -- Tacitus, A.D. 55
ALL civilizations eventualy collapse. Are you that ignorant and arrogant to assume that yours won't?

Re:Multi-dimensional (3, Informative)

Coos (580883) | more than 10 years ago | (#9333339)

Boy, I can't wait till they find out that genes are multi-dimensional, the same way a fugue is.

Sorry, but they already are!

A single gene can contain up to three overlapping reading frames, and some virii and bacteria can generate three completely different and functional proteins from the same gene sequence by this method. Add to that that certain gene products may be broken into subunits at different points along their sequence, and a highly-evolved (or carefully designed) gene could encode >10 proteins.

Re:Multi-dimensional (1)

UnknownSoldier (67820) | more than 10 years ago | (#9345663)

> A single gene can contain up to three overlapping reading frames, a

Now that's cool.

Got any links or references so I can show others this?

Junk DNA == Slashdot Trolls (4, Funny)

RobertB-DC (622190) | more than 10 years ago | (#9327266)

Reading the article, it was fun to substitute "Junk DNA" with "-1, Troll posts". The concept is similar: troll postings serve no useful purpose, but they do modify the discussions in subtle ways. Referring to any particularly offensive link as "goat-related" is one of the obvious examples.

Since I'm bored today, I'll try my hand at rewriting the Reuters article.

Slashdotters Find New Type of Moderation in Troll Postings

LONDON (Reuters) - Troll posts may not be so useless after all.

Slashdotters coined the term to describe the textual wasteland within the Slashdot database, or book of posts, which consists of long uncharted stretches of text for which there is no known function.

But researchers from Hard Vard Medical School in Jamaica said on Wednesday that within troll postings in the Science database they have discovered a new class of post.

Unlike other posts, the new one does not produce an Insightful or Interesting comment to carry out its function. But when it is browsed at -1, it moderates a neighboring post.

"This doesn't explain all troll posting. It gives a potential use for some troll posting," Professor Red Finster, who headed the research team, said in a made-up Slashdot posting.

"I cannot think of another regulatory post such as this one," he added.

There are about 3,000,000 to 4,000,000 posts in the Slashdot database. Much of the database consists of troll postings which scientists are trying to decipher to determine the causes and potential treatments for boring, inane discussions.

The new troll called GOAT1 blocks the function of the adjacent posting in the Science database. Finster and his team, who reported their finding in the science journal UnNature-al, believe other trolls could work in the same way and in other databases including the main database.

"We found one example of a type of troll posting that hasn't been found before that might alert investigators to look for it in other offtopic discussions," Finster said.

"This type of moderation may occur in other cases throughout the message board kingdom," he added.

The new troll works by making Frustration, a cousin of Interest, which causes down-moderation or turning off the adjacent post.

"When people are looking to understand the regulation of posts from whatever database -- main, games, Apple, science -- they cannot just look for messages that are acting there. It might be that it is simply the act of moderating that is causing regulation," said Finster.

The Moderation alphabet consists of several moderations -- Flamebait and Troll to Insightful and Informative -- which carry instructions for making all databases. The sum of the moderations carries the score. Each set of moderations corresponds to a single comment score, which join up in many different combinations to make discussions.

"We want to understand the psychology behind the regulation (of the postings). It is a previously unidentified type of moderation and if we could understand how it is controlled, we will learn more about Slashdot moderation," said Finster.

Re:Junk DNA == Slashdot Trolls (1)

hcg50a (690062) | more than 10 years ago | (#9329088)

Bravo! This is one of the funniest Slashdot posts I've ever seen!

Re:Junk DNA == Slashdot Trolls (0)

Anonymous Coward | more than 10 years ago | (#9331267)

"This doesn't explain all troll posting. It gives a potential use for some troll posting," Professor Red Finster, who headed the research team, said in a made-up Slashdot posting.

Shouldn't this be Professor Firster, so that you would be quoting a made-up Firster posting?
I'm just askin'...

Bad joke (0)

Anonymous Coward | more than 10 years ago | (#9327391)

And it turns out Levi Strauss already owns the patent on them.

so let's see... (2, Interesting)

MoOsEb0y (2177) | more than 10 years ago | (#9327773)

Does this mean DNA has parity bits for error correction?

Greg Bear's Darwin series (2, Interesting)

jchenx (267053) | more than 10 years ago | (#9327874)

Coincidentally, I just finished reading Greg Bear's [wikipedia.org] Darwin's Radio and Darwin's Children novels. They use the premise that "junk DNA" is not junk at all, but is used to drive evolution.

Re:Greg Bear's Darwin series (1)

Lord Grey (463613) | more than 10 years ago | (#9339377)

Coincidentally, I just finished reading Greg Bear's [wikipedia.org] Darwin's Radio and Darwin's Children novels. They use the premise that "junk DNA" is not junk at all, but is used to drive evolution.
Just in case someone wants another opinion on this: I've read Darwin's Radio [barnesandnoble.com] but haven't picked up Darwin's Children [barnesandnoble.com] yet. I highly recommend the first book. As the parent post says, the major premise is that the so-called "junk DNA" is really a latent genetic disease that causes sudden, drastic changes in the species, which in turn cause the next major step in evolution. The first book is very well written and I'm looking forward to reading the second book.

Paper search (1)

Sgt York (591446) | more than 10 years ago | (#9327912)

OK, is anyone else having trouble finding the actual paper? Winston, in Nature, at Harvard. I went on Pubmed and searched for him, no hits. He has a faculty webpage [harvard.edu] at Harvard, but I can't find this paper through Pubmed or from Nature's website.

Anybody know where I can get this paper? I hate reading news blurbs on research. I want the meat!!!

Re:Paper search (0)

Anonymous Coward | more than 10 years ago | (#9328584)

These things are always advertisements for the current issue of Nature. Winston isn't an author. He "headed the reseach teem."
Gene regulation: A reason for reading nonsense 510 SABINE SCHMITT AND RENATO PARO The process of transcribing DNA can itself regulate gene expression in yeast: in the case concerned it is the very act of reading the DNA, not the message produced, that carries out the regulatory job.

The nature article makes a whole lot more sense than Science News.

Re:Paper search (4, Informative)

HarryGenes (772322) | more than 10 years ago | (#9328680)

If you visit the story at The Scientist, [biomedcentral.com] they have a much better article and a link to the PubMed, full text article.

Another Idea: (1)

A55M0NKEY (554964) | more than 10 years ago | (#9328105)

Maybe junk DNA is like a bucket of lego-like building blocks that are randomly cut out and reinserted elsewhere during recombination, maybe they have *evolved* to be error prone in this way. If ACTG are the letters of the DNA alphabet, maybe the stuff in the Junk DNA sections are the words in the DNA dictionary ( or even common sentences ). Maybe having Junk DNA around made up of sequences that tend to be useful when an organism needs to adapt over multiple generations via evolution is worth conserving. Maybe not.

Re:Another Idea: (1)

Cragen (697038) | more than 10 years ago | (#9330887)

Or maybe they are just the adjectives, connectives, or articles in the DNA dictionary. (OK, so I have no idea what I am talking about. This is /., isn't it?)

Computer Parallels (3, Insightful)

photon317 (208409) | more than 10 years ago | (#9328704)


The more I heard about genetic codes, the more they resemble certain thigns in the computer world to me. Probably convergent evolution of sorts. Sounds like they've been staring at an incomprehensible data-set they were examining byte by byte to understand where the data was stored in what format. They found isolated bits that matched up and identified their purpose, but large amounts of the code remained a mystery. Then with this discovery, they just realized that they're actually staring at a huge peice of mixed data and code (probably in some cases dual-purpose bits which are both data and code) - just like in the computer case. Well, not so much in a high level language's case, but remember when people used to write ultra-compact self-modifying code/data in asm? When you think about it, for any given computing problem that can be solved by some chunk of code and data, the most space-efficient hyper-optimal way to do it usually ends up being self-modifying assembler "code", which re-uses code for data and data for code where possible.

It is of course mind-bogglingly complex to write code in this fashion for any sufficiently complex software, which is why we only tend to have examples of this on very small scales (tiny little DOS programs and simple virii back then).

But.. if that's the most efficient way to pack the functionality into a small space - and if writing DNA is similar in nature to writing assembler code - then evolution would naturally gravitate towards this method of encoding, eventually becoming such a complex self-modifying code/data mess that it causes us all these problems trying to unravel it.

Re:Computer Parallels (0)

DigiShaman (671371) | more than 10 years ago | (#9332515)

Very true, I would agree. Though, I'm sure we will have computer to reverse engineer DNA code through some form of emulation software. Once we are able learn how and what DNA sequences are needed to make cells, we will be able to artificially make life.

Imagine coding a machine or chemical factory in source code. Then, compiling that source code into a DNA sequence rather then binary. From there, you can make the DNA chain synthetically and grow the product. Of course, with any tool there is a dark side. I'm sure some bastard would use this to make a weapon in the form of a virus. It could spread to everyone, but only kill the host it would recognize. Basically, a bio-bullet with your name on it spelled out by your genetics. Scary huh? Let's just hope this technology will be used to provide immortality rather then the destruction of the human race.

Re:Computer Parallels (1)

thogard (43403) | more than 10 years ago | (#9332625)

I wonder how much of the Junk DNA is just part of a data segment? Most of it will never even get looked at but some tiny bit of that junk might describe how to make the inside bit of a big toe.

Many of the people I know that were involved with the early stages of the human gome project also where involved in the theoritcal computer science.

On the other hand... (3, Informative)

Indomitus (578) | more than 10 years ago | (#9328903)

New Scientist [newscientist.com] has an article about some scientists who removed pretty huge chunks of a mouse's "junk DNA" and the mouse was just fine in every way they could measure.

So the moral is, we have a lot to learn about DNA.

Re:On the other hand... (3, Insightful)

mopslik (688435) | more than 10 years ago | (#9329239)

...the mouse was just fine in every way they could measure.

I think that might be the crucial factor there. After all, how can we effectively measure things that we're just starting to discover?

Re:On the other hand... (1)

Indomitus (578) | more than 10 years ago | (#9330600)

Oh yeah, I don't think anybody's willing to start cutting out the "junk" in our DNA or anything yet. It's an interesting finding though.

One of the theories about the junk DNA is that it's there to help reduce the chances that a mutation could cause catastrophic harm to the organism. If you've got 5 times as much stuff to hit with a cosmic ray, for example, you're more likely to hit the "padding" than the useful stuff. If that's correct, you would see exactly what they're seeing with this mouse, until an important bit of the DNA gets mutated.

Re:On the other hand... (2, Insightful)

meringuoid (568297) | more than 10 years ago | (#9334012)

New Scientist has an article about some scientists who removed pretty huge chunks of a mouse's "junk DNA" and the mouse was just fine in every way they could measure.

I forget where I saw this analogy, but... imagine you're reverse-engineering a car by removing parts of it and seeing what stops working. You remove the windscreen wipers and the headlamps and hey, nothing's wrong! They're junk components.

At least, until you drive at night in the rain.

The argument was that junk DNA might contain contingency plans for conditions that simply haven't arisen during testing - and indeed might not have existed for millennia.

Re:On the other hand... (1)

smoondog (85133) | more than 10 years ago | (#9342354)

OK. Lets test that by cutting off your pinky toe.

Lots of Junk (3, Funny)

Anonymous Coward | more than 10 years ago | (#9329568)

I have been working in gene mapping for years and always felt that the 'junk' was there for a reason."

Nature is a pack rat. Get used to it...

I thought they found its purpose (1)

mcraig (757818) | more than 10 years ago | (#9333309)

I remember reading an article in New Scientist I think that talked about research that had been done on so called junk dna and they found that it worked as a repair mechanism. Essentially they found that dna can transmit electrons and what was happening was when something tried to damage an area of dna by giving it an extra electron, if it didn't need it it could pass it down the line so to speak till it reached one of these areas where it would cause no real harm. Likewise areas that were robbed of an electron could pinch one back from its nearest junk dna area. Anyone else care to confirm ?

Evolution and spaghetti (2, Insightful)

cazzazullu (645423) | more than 10 years ago | (#9333376)

I am a firm believer of Darwin's theory of evolution, and as you all know the main point of this theory is survival. This implies that in contrast to what some previous posts here mentioned, there is no need for "optimal", "efficient" or "errorchecking (-free)" coding in the neuro-bio-chemical-whatever way DNA does this coding. Just the fact that it works is enough, you will live, hopefully survive, and pass on this "working" code to your offspring (well, at least pieces of it). One scientist once said: "DNA is the most incredible spaghetti-code you can imagine, that just happens to work out in (our) real world"

Well, what if there are BS pieces of code in there? As long as they don't interfere with the simple fact that the organism "works" there is no reason at all why these chunks shouldn't be there. It is not that each organisms DNA get's carefully designed, debugged, optimized and compiled. Design happens by pure selection, debugging is automatic (if it doesn't work it dies) and optimization is unnecessary.

Another point of view I read before and sounds very plausible to me is that these junk-pieces contain sequences of code that were one time usefull during our evolution into what we are now, but are now deactivated. Look at it as containers of pieces of perfectly good code, but obsolete or unnecessary now. I.e. code to grow tails, fins, ... to produce certain chemicals found in (very old) ancestors of us but now not usefull anymore... There is of course not a evolutionary "reason" as to why these pieces of code are kept, but just looking at the mere process of mutation/reproduction and crossing pieces of these code makes it very plausible to assume this may indeed be the case.

Total Genome size (2, Insightful)

Coos (580883) | more than 10 years ago | (#9333674)

The Human Genome Project surprised us by finding far fewer genes than were theorised to be neccessary for life: perhaps if a significant amount of the regulatory function is carried out by DNA-previously-known-as-junk, a new genome annotation exercise might produce a figure closer to the estimate. It can't be long before ampaper along these lines is published...

This isn't exactly new... (3, Informative)

dnaboy (569188) | more than 10 years ago | (#9334607)

Researchers have been discovering these genes for some time now. They're generally extremely short (~21 nucleotides) and in their endogenous form are referred to as micro RNAs (miRNA).

Interestingly, the mechanism was actually understood before functional miRNAs had been discovered. Back in the 90s there was an upswelling of new biotech companies (Isis, for one) looking at antisense technology. Basically, the idea is that if you insert a complementary RNA strand to a messenger RNA (mRNA- The RNA's which code for proteins), you could block the expression of that gene into protein. The problem was that these weren't very specific (relative to what people would expect, since it was the exact complement of the gene sequence). Also, it's a bitch to get a full length RNA strand into cells reliably, short of using viruses. Generally a bad stigma.

Over time, people started realizing that these antisense targets being inserted were being cleaved into really small (~20 to 25 nucleotide) pieces by an enzyme group called the RISC complex (It's a lot more complecated than that, but whatever). This explained one thing. ~20 nucleotide chunks are much more likely to stick to another gene. There's a much better chance that the 20 bases are identical to 20 bases in another gene, than several hundred to several thousand being repeated. What it didn't answer is what was going on.

It was assumed that the complex that large antisense targets made blocked translation into protein. 20 base pieces were much less likely to do that. What people came to realize is that another enzyme called DICER was chomping up the genes where these ~20 nucleotide pieces stuck. This technique isa called RNA interference, or RNAi, and these ~20 nucleotide sequences were called short interfering RNAs or siRNAs. The sweet thing is these, relative to their much longer antisense couterparts are relatively trivial to insert into cells.

Anyway, to make a long story short, researchers didn't really know why this worked at first, and consensus was that it was either an evolutionary legacy, a mechanism to fight RNA viruses, or a fluke (which generally, very few things in biology end up being).

Anyway, this article points out what researchers all over are finding which is that these little guys appear to be present all over the human and other genomes. They are much more likely to be a mechanism for regulating gene expression. For more info, google 'micro RNA'.

Cheers

Implications to Myotonic Muscular Dystrophy (1)

RhettLivingston (544140) | more than 10 years ago | (#9335618)

This is exciting but not unexpected news to me. Two of my children have a flaw in one of these junk areas that causes dramatic effects for them. Their symptoms range from mild mental retardation to muscular effects throughout every muscle type. Its amazing, given the many known diseases that result from flaws in junk DNA, that its taken them this long to come close to admitting there is no such thing as junk DNA. So called "scientists" have a remarkable blindness to the facts that they can't explain that makes science anything but. Anyway, here is an excerpt from a site discussing congenital myotonic dystrophy.

... The unusual nature and marked genetic instability of the expanded CTG repeat in DM continues to be a source of fascination. However, the DM mutation is just as notable for its unusual position, because it is located in a part of the DMPK gene that does not code for protein. Seven years after the gene discovery, it remains unclear how a mutation that does not interrupt the DMPK protein coding sequence has a dominant effect with such severe consequences. Complex molecular mechanisms have been postulated at the DNA level, the RNA level, and the protein level (reviewed in reference 13). At the DNA level, the expanded CTG repeat may alter the structure of chromatin, raising the possibility of a "ripple effect" on the function of neighboring genes. At the RNA level, the expanded CUG repeat in the DMPK mRNA may bind to specific proteins and interfere with nuclear function. At the protein level, reduced levels of DMPK, a protein kinase, may interfere with signal transduction pathways. Evaluating each of these proposed mechanisms has proved to be a slow and difficult process.

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