Slashdot Mirror
New Class of Genes Discovered
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."
And yet there are people prepared to unleash modified genes on the world saying that they **know** there is no risk.
And if you thought that was boring you obviously havn't read my Journal ;-)
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...
"Provided by the management for your protection."
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.
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?
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.
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.
Stressed? Me? Of course not. Stress is what a rubber band feels before it breaks, silly.
Much more information can be found in this article taken from pubmed.
Stealth regulation: biological circuits with small RNA switches
Does this mean DNA has parity bits for error correction?
Coincidentally, I just finished reading Greg Bear's 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.
-- jchenx
If you visit the story at The Scientist, they have a much better article and a link to the PubMed, full text article.
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.
11*43+456^2
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.
So the moral is, we have a lot to learn about DNA.
Nature is a pack rat. Get used to it...
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.
Those who do study history are doomed to stand helplessly by while everyone else repeats it.
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).
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?
Service guarantees Citizenship! Questions Guarantee GITMO.... Amerika Uber Alles!
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?
There are no trails. There are no trees out here.
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.
:O)
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 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 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?
It's easier to be a result of the past, but more fun to be a cause of the future! http://www.spacefinancegroup.com/
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.
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.
int main(void) {while(1) fork(); return 0;}
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...
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
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.