The One Thousand Genes You Could Live Without 111
sciencehabit writes Today researchers unveiled the largest ever set of full genomes from a single population: Iceland. The massive project, carried out by a private company in the country, deCODE genetics, has yielded new disease risk genes, insights into human evolution, and a list of more than 1000 genes that people can apparently live without. The project also serves as a model for other countries' efforts to sequence their people's DNA for research on personalized medical care, says study leader Kári Stefánsson, deCODE's CEO. For example, the United States is planning to sequence the genomes of 1 million Americans over the next few years and use the data to devise individualized treatments.
Absence of evidence... (Score:5, Insightful)
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Presumably you can live without them because there are people who live without them and are fine for it.
Re:Absence of evidence... (Score:5, Funny)
Yes, but other people are are largely stupid and completely insane.
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DNA is a complex language that we are barely beginning to understand. Unlike CRISPr, this kind of thing actually is "hacking the genome" in a clueless fashion. I think this is an area where clearly some corrolary of the Hypocratic Oath should be in effect.
If it's not broken, then don't try to fix it. Leave it alone. The best thing to do (barring any indications to the contrary) is nothing.
I suspect that we are still at the "don't know how much we don't know" stage of genetics at this point.
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The thing about genetic variation is that there's a minimum set you need to live and extras which make it easier to survive if conditions change (as well as others which may well be negative, such as ones which predispose the carrier to nasty cancers after the reproductive period ends)
Just because you can live without them _now_ is not evidence they may not be useful later.
viral rootkit (Score:5, Funny)
careful my dear replicant, those are kernel extensions injected into your DNA by the Sony reverse transciptase root kit. Evidently you are a replicant. Look for the Sony Copyright and your model number to see if you have a null pre-programmed life expectancy.
floppy disk (Score:3)
What I find staggering to comprehend is that your genome will easily fit on a CD. Even if you allow for all the midochondrial DNA, and epigenetic information it still would fit on a CD. If not all of it's needed maybe there's a Damn Small Linux version of your DNA that would fit on a floppy.
#PRAGMA (Score:2)
Does that include everything needed to build the DNA-to-meat compiler, or is there some bootstrapping that must happen too?
You are quite correct that you have to bootstrap the compiler.
I tried to account for that partially by noting that there's plenty of room on the CD to store the epigenetic information. You can think of this epigenetic information as the #PRAGMA compiler directives and differences between non-ANSI compilers. So once we take those into account one could map the source code to the needs of any possible compiler. Thus in principle at least one could build a human using a compiler adapted from another somewha
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There's more to people than their genes. We're also a bunch of ecosystems: skin and gut, especially.
Is there room on that CD for the genomes of our bacteria and fungi and such, and the bootstrapping process for each?
Oh, and where to put them? You probably don't want the colon bacteria on your eyelashes, etc.
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Where do you get that? Wikipedia says that the human genome is 3,23473 billion base pairs. I mean, you could compress that to fit on a CD, but it won't fit at one byte per BP. Won't even fit at 2 bits per BP.
And if we want to think of a BP like a letter in a piece of code, with an average programming code line length of say 15 non-whitespace characters, that corresponds to a program 216 million lines long. That'd be no little program...
Of course, only a tiny fraction of our DNA codes for what we would consi
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I mean, you could compress that to fit on a CD, but it won't fit at one byte per BP.
Speaking of compression, in a certain sense, a person only needs to know their differences from one of the standard reference sequences. But there's a subtle point: there are still parts of the human genome where we don't know the sequence (e.g. highly repetitive regions near the centromeres). For the well behaved (unique/non-repetitive) parts of the human genome, a person might have somewhere around one difference from the reference every hundred base pairs. So we're talking about very roughly tens of mill
Math (Score:4, Interesting)
3 billion base pairs.
Each base pair is 2 bits (AGC or T). A byte is 8 bits or 4 base pairs. so
3E9 / 4 = 750 MegaBytes.
A CD holds up to 900MB of data. No need to even compress the data, and it would be highly(!) compressible
Q.E.D.
Your math is off by factor of 1000 (Score:2)
there are 3 billion (US definition of Billion not british) base pairs not 3 trillion.
base pair = 2 bits (AGC or T).
3billion bases = 6 billion bits = 750 megaBytes.
A CD holds up to 900MB.
So plenty of room even uncompressed.
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> Of course, only a tiny fraction of our DNA codes for what we would consider to be the "interesting stuff".
The hard part is tellling what's "junk" and what's useful data embedded in it. It's a bit like having a ROM dump and trying to work backwards from it without actually knowing what the CPU is. We know what some genes do, but not all of them, nor do we entirely know if they refer to offsets within the code as this changes when DNA is folded up as it is under normal operating conditions.
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And when I put it in a CD player, it plays Mozart. True story....
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3.3 Billion base pairs (nibbles) is not quite that small in terms of raw data. It will fit onto a DVD though.
Re:Absence of evidence... (Score:4, Insightful)
Yar, something as complex and time-tested as the human genome can surely be understood and manipulated by us with no unforeseen consequences.
Keyword "apparently" (Score:4, Insightful)
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"Well they looked at DNA extracted from the blood, I'm not sure how they know (or why they think they know) those sequences are representative of those in each tissue."
You are not sure how they know because you didn't pay attention to your high school biology classes.
They think they know because they did pay attention to their high school biology classes.
*All* nucleated cells in a body share the same DNA load (barring local mutations -which are really minimal, and with obvious exception of the germinative
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In fairness to the GP, high school biology is pretty much the worst fucking class ever.
We had to dissect a fucking shark. It was awful. I can still smell it. The poor souls at the bench next to us had a frozen cat in a bag whose face looked like Scratchy got a rear end stuffed full of cocaine.
I'll take my D+ and be on my merry way, thank you.
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"*All* nucleated cells in a body share the same DNA load (barring local mutations -which are really minimal, and with obvious exception of the germinative line)."
Except, chimeras?
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Except chimeras, yes.
Are you going to claim they appear in any significant number in mammals? (and I know about prions) ...on a thread about somebody ignoring the very basic fact that multicellular organisms own just one genotype?
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Well, not exactly. [wikipedia.org] The answer to the question of how the immune system can defeat a foe that is mutating and evolving so quickly is "it also is mutating and evolving quickly". Immunoglobulin genes in B cells mutate very rapidly. Those whose antigen binds best with an invader are stimulated to reproduce (and evolve more), ultimately differentiating into plasma B cells (whose job it is to mass produce antibodies) and memory B cells (which stay alive for long periods of time, allowing the body to "remember" h
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You are right. I forgot about B cells, and I've should mentioned them since I did it about the germinative line exception.
Now: do you think talking about B cells makes any difference for the base answer to the original question, "I'm not sure how they know (or why they think they know) those sequences are representative of those in each tissue."?
Boo, you fad killer! (Score:5, Insightful)
Today's fad is to try and come up with the "perfect" human. Always happy, 200 IQ, and the personality of a turnip as to not be offensive to anyone at any time. Of course they must be orange skinned, no hair, and no gender features (I hope you saw the South Park episode) because if anything visible marked one of them as "different" the project would be a failure. Perfect is quoted, because this perfection is severely subjective and the person who's ideal you are going to meet probably does not match your own.
As you point out, there is no way to know what these apparently unused genes do until we start making modifications. These are pretty dangerous times we live in for many reasons. People believing they are smarter than billions of years of evolution gives me no assurance that these people have a clue, let alone care about modifying people.
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Re:Boo, you fad killer! (Score:5, Insightful)
"there is no way to know what these apparently unused genes do until we start making modifications."
No way? sure?
What if, for instance, you find a person that simply lacks a gene and still is perfectly functional?
Now, go read the article.
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What if, for instance, that gene is only required when you've been exposed to some common element or set of circumstances that the "perfectly functional" person just happened to avoid, by chance?
What if, for instance, that "perfectly functional" individual isn't, in fact, perfectly functional? What if, for instance, any complications simply haven
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Re:Boo, you fad killer! (Score:5, Interesting)
People believing they are smarter than billions of years of evolution gives me no assurance that these people have a clue, let alone care about modifying people.
Putting evolution on a pedestal isn't much smarter. It's not some godlike entity which designed humans with a goal in mind, it's a very long, very sinuous process which often gives locally optimal but globally suboptimal results. There is no reason to think that humans, for some reason, can't do better.
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I'll avoid the troll because you would lose that debate in a fair platform but alas, Slashdot is not such a platform... I will however address your insinuation that we know enough to be superior to nature. Science today is run by profits, not by philosophical standards. Ethics and Morality are not being questioned, only the outcome which yields the best profits receives funding and publication.
Long time anti-GMO scientist Bill Nye is a great example, who after spending a month with Monsanto suddenly says
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Humans can do it better. It's a fact proven by a few thousand years of doing it better and so much faster.
I've lost too much faith in average intelligence to spend time in trying futilely to further explain to you why you're an imbecile.
Ok, that's enough slashdot for today. I'm tired of this shit.
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The funny thing is that humans are "so good at it" that they don't really need the new fangled approaches with the higher risks. We have been doing "conventional" genetic manipulation for thousands of years. Compared to that, our relatively short experience with direct genetic manipulation really doesn't hold up.
The "conventional" approach just takes longer and confers no monopoly benefits to any herbicide mongers.
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That humans don't always do it better doesn't mean that humans can''t do it better.
There are three available possibilities. People can fund science the harms them - why would they do that? People can fund science that has no effect on them - why would they do that? People can fund science that benefits them - a rational activity. People claiming that there's something wrong with the third alternative either aren't deep
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Your troll was this comment "It's not some godlike entity which designed humans with a goal in mind", though you probably know it and are just denying. Nuh uh in this post does not address or argue any of my points, which clearly demonstrate that it's not an issue of my ability or desire to debate. The issue is yours.
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These are pretty dangerous times we live in for many reasons. People believing they are smarter than billions of years of evolution gives me no assurance that these people have a clue ...
And CERN? Doesn't it make sense that every black hole in the universe at one time was a really tiny black hole? Is it a good idea to just start making a bunch of those?
Re: Boo, you fad killer! (Score:2)
A black hole isn't a purse where you stuff things and are lost forever. They are energetic balloons that feast and starve, and eventually disappear in a pop. I wouldn't be surprised if collapsed super massive black holes would look like the Big Bang.
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1. Evolution is not smart.
2. Evolution just picks for reproduction.
Basicly you can drop dead after you reproduce a few kids and you are success by the standards of evolution.
Re:Keyword "apparently" (Score:5, Informative)
1) 60% of the DNA is _definitely_ junk, as they consist of known repeated elements (LINEs, SINEs and others) and defunct genes. This is not an 'absence of evidence', we know exactly how this DNA has happened.
2) Around 10% of DNA is structural. While this is technically not 'junk', this DNA does not encode anything useful.
3) Around 5% are coding sections and regulatory elements.
4) Another 5% of DNA appear to be stable under mutation pressure. So it might have some function.
4) And finally we have around 20% of DNA whose purpose is not known, but we know that random mutations in it do not visibly affect the phenotype.
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How do we know that those repetitions are not needed to accelerate (by parallel processing) some important process which, with a single expression, would otherwise be too slow to survive?
We don't fully understand how the phenotype is developed from the genotype, and it very well might depend on statistical
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How do we know that those repetitions are not needed to accelerate (by parallel processing) some important process which, with a single expression, would otherwise be too slow to survive?
You absolutely do NOT want them to be expressed. In fact, your genome tries really hard to suppress them - all they do is replicating themselves. That's the reason so much of your genome consists of them.
Dependency on statistical properties is doubtful - organisms have more than 100x natural variance in genome sizes within fairly closely related species (just look at plants) without much outward difference. Even in animals, some species have a small and compact genomes (pufferfish) without much junk.
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They said the same thing about "junk" DNA [wikipedia.org]. 10-15 years from now, it may no longer be apparent that you can do without them.
I don't think that's likely. There is a subtle nuance here about what they are claiming. The is a very distinct difference between "genes you can live without" versus something like "these gene are junk and have no function". The claim that you can live without a certain gene is easily proven; find people who have lived to adulthood and are carrying two copies of deletions/disruptions in the same gene (so they have no functional copies of that gene). This is actually not that surprising as your body ha
The thousand genes we don't know if are needed. (Score:2, Troll)
If they have not yet done deletion experiments they can't say that we could "apparently" live without those genes.
Re:The thousand genes we don't know if are needed. (Score:4, Informative)
Re:The thousand genes we don't know if are needed. (Score:5, Insightful)
Any of those genes could encode a protein whose function can be done by another protein that other people may or not express. Obviously the people identified did not need "that" specific protein to do its work but it may be completely possible that a majority of people do not have the compensating gene.
Until experimentation is done to evaluate the need of those genes you can say that those "may" not be indispensable, but saying that apparently they are not needed is too strong a conclusion for the work done.
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The point is to more easily identify causative mutations in rare genetic disorders by eliminating these non-essential genes from consideration.
Or in the case of Iceland, finding out which of your third cousins it is safe to date.
With a small population that has been relatively isolated for a long time it can be tricky to avoid relatives and this leads to an extra interest in genetics.
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Because having a copy of a gene is only one possibility of compensation, in processes like innate immune response it is common to have more than one pathway of activation, and to a certain point the presence of one protein can compensate the lack of another even if they are not structurally similar. A blast search can't be used in that case to rule out the need of that specific gene in other people. I am simply saying that proving that some people can survive without some genes without really having studied
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Re:The thousand genes we don't know if are needed. (Score:5, Funny)
This explains republicans....
(ducks)
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What is this about marking people down as 'troll' or similar for expressing a slight note of doubt? This is petty, at best - either reply with something intelligent or ignore it.
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What is this about marking people down as 'troll' or similar for expressing a slight note of doubt? This is petty, at best - either reply with something intelligent or ignore it.
We need a -1 "Didn't RTFA" mod.
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We need a -1 "Didn't RTFA" mod.
Or a more tolerant outlook. TFA may not always be all that interessant to read, and anyway, the point is, should we mod people down for being too lazy to RTFA, when we are too lazy to type in a proper comment?
Missing Variable (Score:1)
Reminds me of taking out that missing variable in the source code that you figure isn't being used for anything, except there's no search function to find out what it impacts.
Re: $1000 for a genome? (Score:2)
Yes - Illuminas HiSeq X machine (family) is one of the machines marketed as this. Please note that this is the projected internal per-genome cost of a dedicated sequencing facility - before any customer markup is applied, and only if you have the high quantity of data required to get your money's worth.
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Last time I checked (about 6 months ago), MacroGen up in Korea will do a whole genome (30X coverage) for $1,500 - but the minimum order is 50 genomes. If you only want one genome sequenced then the cost is $4,500.
It's worth noting also that you don't need blood, per se. DNAGenotek sells saliva collection kits ($20/kit but 25 kit minimum order). Basically you just spit in a tube, FedEx it to Korea and a few months later they're send you a USB external hard drive with a few hundred GB of your genome sequence
Curb your enthusiasm (Score:2)
It's the comments (Score:4, Funny)
Don't delete anything, comment it out! You never know, you might need to put it back.
https://www.gnu.org/fun/jokes/... [gnu.org]
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Nature is one step ahead of you [wikipedia.org]. :)
Up next (Score:2)
Up next, the four limbs you can live without.
Not so sure (Score:2)
let's see...... (Score:1)
Gene Simmons..........no
Gene Wilder...............no
Gene Siskel................yes
Gene Hackman..........no
this could take a while......
Weight Loss (Score:2)
What if genes didn't evolve and were created? (Score:1)
No, I am not saying "believe in God over evolution." I am just saying that looking at DNA without considering the possibility of intelligent design is myopic.
At least some DNA studies should assume intelligent design.
Start looking at DNA and everything that interacts with it as a programming language created by something intelligent.
In a programming language, there is code and data. Code contains all the method and functions to do small amounts of work. Data is used or acted upon by the code. Data can be re
Just like new programmers (Score:1)
That sounds just like a new programmer faced with working on legacy code. The first thing they want to do is delete everything that they don't understand!
If we didn't need it, it would not be there. There is no room in nature for wasted effort.
They said the same thing about the appendix, for decades, but now we know it's not true. The appendix is necessary for propper digestion, look it up...
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