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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."
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.
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.
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.
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.
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.
http://www.donarmstrong.com
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
I think that might be the crucial factor there. After all, how can we effectively measure things that we're just starting to discover?
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.
And if you thought that was boring you obviously havn't read my Journal ;-)
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.
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;}
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.
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...
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.
Real Daleks don't climb stairs - they level the building.
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.