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Scientists Measure How Quickly Plant Genes Mutate

Soulskill posted more than 4 years ago | from the starting-countdown-to-triffid-massacre dept.

Biotech 67

eldavojohn writes "A recent study puts observed numbers on genome mutations in plants. This kind of research is becoming more popular in understanding evolution. The research 'followed all genetic changes in five lines of the mustard relative Arabidopsis thaliana that occurred during 30 generations. In the genome of the final generation they then searched for differences to the genome of the original ancestor.' A single generation has about a one in 140 million chance of mutating any letter of the genome (which has about 120 million base pairs). Sound like bad odds? From the article, 'if one starts to consider that they occur in the genomes of every member of a species, it becomes clear how fluid the genome is: In a collection of only 60 million Arabidopsis plants, each letter in the genome is changed, on average, once. For an organism that produces thousands of seeds in each generation, 60 million is not such a big number at all.' The academic paper is available in Science, though seeing more than the abstract requires a subscription."

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evolution ? (5, Insightful)

polar red (215081) | more than 4 years ago | (#30632082)

Plants don't evolve, they get changed by the touch of his noodly appendages

Hah. (0, Redundant)

bmecoli (963615) | more than 4 years ago | (#30632222)

Modded as informative. I'm amused. Only on Slashdot.

Re:Hah. (1)

hrimhari (1241292) | more than 4 years ago | (#30646888)

I bet that you didn't see the "Insightful" coming up.

Re:evolution ? (2, Interesting)

tomhath (637240) | more than 4 years ago | (#30632256)

there are climate scientists trying to disprove global warming, but they fail,... what does THAT tell you?

It tells me that you can't prove a negative.

Re:evolution ? (-1, Flamebait)

Anonymous Coward | more than 4 years ago | (#30632382)

You can prove a negative, it's easy. I can prove your mother isn't a cankerous whore. That's because I have been fucking her monogamously.

Re:evolution ? (1)

somersault (912633) | more than 4 years ago | (#30632406)

I thought global warming was just observed fact, and the thing that is trying to be proven is the actual cause of it. Actually though, because of the strange climate we have here, global warming is only going to make my country colder at first. Hah.

Re:evolution ? (4, Insightful)

Maxo-Texas (864189) | more than 4 years ago | (#30633010)

Bonus points for introducing a second unrelated hot topic.

What I want to know is the impact of gay marriage, and dating co-workers on all this.

Re:evolution ? (0)

Anonymous Coward | more than 4 years ago | (#30638246)

Well, it's really not that complicated. These are simply the kind of things that happen when you live in a country where the government allows mothers to murder their unborn babies.

Re:evolution ? (2, Insightful)

hey (83763) | more than 4 years ago | (#30632420)

If you are having troubling proving negative hypothesis A ... try proving "not A".

Re:evolution ? (0)

Anonymous Coward | more than 4 years ago | (#30632460)

there are climate scientists trying to disprove global warming, but they fail,... what does THAT tell you?

It tells me that you can't prove a negative.

I know that the creationists and the anti-climate change groups are different, however.... what do you expect when you are dealing with people who espouse the idea of "irreducible complexity"?

On the same note, let me share with you a conversation that I was part of:

My Father: You know what? God put the Earth here, and it's been around for forever. It's crazy for anyone on this Earth to think that they can have a greater impact than his will!
My Aunt: (laughing out loud) Yeah!
Me : Chernobyl. North America Dust Bowl. Acid Rain. Smog in Mexico.
My Father: How can anyone believe in God and, at the same time, think that humans are more powerful than he is?!
Me : I'm an atheist. Lets presume I believe in God. I'd consider this planet a gift. Whether or not global warming is true or not, It's your duty as a "child of god" to take care of this planet.
Me: Yeah...
My Father: So, son, what do you think about global warming?!
Me: Uh, I don't discuss three things: Religion, law, and politics. Most people are too uninformed to have a proper discussion on the subject.
My Father: Is that so?
My Father: Global warming is all about government control. They just want another way to control your life
Me : I don't disagree too much.
Me: Yep.

The big issue with the whole god damned thing is... There are people who stand to make a profit on either side of the issue. If we say "Fuck you, environment", there are tons of companies who will laugh all the way to the bank because they don't need to follow environmental guidelines. If we go all "Tree-hugging-hippie" on the issue, then our tax dollars will be taken (with aid of the police-power of the state) to pay for projects which simultaneously do nothing for the environment and line some corrupt businessmen pockets.

I really don't know what to say, other than this: between the deniers, the undecided, and the devout, so many important science issues are being decided by emotion. Unfortunately, that's not going to change any time soon.

In short, the issue is fucked up. I'm done thinking about it right now. I'll go pour myself another alcoholic beverage and try to pretend like the big purple elephant isn't in the room for another day.

-ss

Re:evolution ? (1)

radtea (464814) | more than 4 years ago | (#30632736)

I know that the creationists and the anti-climate change groups are different, however.... what do you expect when you are dealing with people who espouse the idea of "irreducible complexity"?

Creationism and climate change scepticism are distinguished precisely by the practical role of "irreducible complexity" in each field. Evolution is demonstrably highly reducible to nothing more than the laws of probability. We have endless amounts of experimental and observation evidence to that effect, to the point that creationists have to deny what amounts to simple arithmetic to claim that evolution has not occurred.

Young Earth Creationists are actually more consistent than Old Earth Creationists because the former merely have to invoke a great big miracle: the Earth was created with the appearance of being old 6000 years ago, implying just that God is a liar, a charlatan and a cheat. If Young Earth Creationists admit that then they have an unassailable albeit insane argument. Old Earth Creationists on the other hand have to accept what physics, chemistry and geology tell us about the age of the Earth, while denying the laws of probability, which isn't even remotely self-consistent.

Climate change sceptics (at least the honest ones) are legitimately concerned regarding the known problems of modelling complex fluids on coarse grids precisely because we know that it the nature of the Navier-Stokes equations to be sensitive to phenomena on all scales. This is not quite formally "irreducible complexity" but it comes close enough in practical terms. It is doubtful (although given advances in turbulence research in the past twenty years no longer quite inconceivable) that anyone will ever produce a physically legitimate model of the Earth's atmosphere that is remotely predictive or even usefully non-predictive (that is, which reproduces the statistical behaviour of the climate but can't be used for prediction due to sensitivity to initial conditions.)

Climate change sceptics are also concerned about the anti-scientific attitude of AGW proponents who claim to be so terrified that their data and methods will be cherry-picked by "the other side" that they won't release them to full public scrutiny, despite the huge public policy implications of their claims and conclusions.

Such people are obviously either hiding something, or hate the scientific process, which ultimately depends on revealing the full body of your work to scrutiny by anyone who cares to scrutinize it, not just the anointed priesthood. Science, even in recent times, has had too many contributions made by gifted amateurs to justify any claims that the debate ought not to be open to all.

Re:evolution ? (1)

khallow (566160) | more than 4 years ago | (#30632994)

Young Earth Creationists are actually more consistent than Old Earth Creationists because the former merely have to invoke a great big miracle: the Earth was created with the appearance of being old 6000 years ago, implying just that God is a liar, a charlatan and a cheat. If Young Earth Creationists admit that then they have an unassailable albeit insane argument. Old Earth Creationists on the other hand have to accept what physics, chemistry and geology tell us about the age of the Earth, while denying the laws of probability, which isn't even remotely self-consistent.

I don't get this at all. The Young Earth Creationists have a huge inconsistency to explain. Why God chose to make a young Earth appear old. Also from the point of view of effort, that's quite a bit of effort to go through. In comparison, the Old Earth Creationists need explain nothing, not even the laws of probability. It's a perfectly unfalsifiable theory.

Re:evolution ? (0)

Anonymous Coward | more than 4 years ago | (#30633850)

I'm going to reiterate what khallow just wrote. In order for YEC to make sense, Yahweh would have to interfere every time any radiometric dating of anything takes place, or set up the laws of physics such that things only appear old. And since sciences are necessarily only concerned with the observable world anyway, for all intents and purposes that's the same thing as saying the earth is old. Occam's razor and all that.

YEC is *almost* as crazy as the flat-earthers (yeah, they're still around) but stupefyingly is believed by many, many more people. We really need to get our science education in order.

It is doubtful (although given advances in turbulence research in the past twenty years no longer quite inconceivable) that anyone will ever produce a physically legitimate model of the Earth's atmosphere that is remotely predictive or even usefully non-predictive (that is, which reproduces the statistical behaviour of the climate but can't be used for prediction due to sensitivity to initial conditions.)

Not to be rude, but I thought this too, when was learning about chaos theory and fluid dynamics and began to "treat everything as if it were a nail." To be sure, climate models fall prey to the same types of problems of other models, but that does not destroy their usefulness. The thing to remember is that nobody has come forward with a model that's as accurate as the current ones that doesn't take human CO2 output into account. Yes, it's a challenge to model climate. But the world's top meteorologists are working on it, and the vast majority of them are in agreement on the matter. What do you know that they don't?

Re:evolution ? (2, Insightful)

radtea (464814) | more than 4 years ago | (#30632512)

It tells me that you can't prove a negative.

You most certainly can prove a negative, and scientists do so all the time. The argument is generally of the form, "If X is true, the phenomenon Y must be observed under conditions Z. We have created conditions Z, proved by positive calibration that if Y occurred we would see it. Therefore X is false."

Only people who are completely ignorant of exactly the kind of experimental science that has driven our understanding of the universe in the past century would claim that you can't prove a negative. I blame first year introductions to logic, which teach some medieval nonsense in the guise of "logic" that doesn't even touch on the empirical falsehood of Leibniz's Law, much less introduce the logic of science, which is Bayesian.

Re:evolution ? (0, Offtopic)

tomhath (637240) | more than 4 years ago | (#30632880)

Yea, I took symbolic logic too. In your example you've proven that the conditions you believe represent Z did not produce Y. So either you didn't really produce condition Z (even though you thought you did), or your assumptions are wrong. But none of that matters, nor does it matter that some people cling to a supernatural explanation of what they observe in the real world.

What's more important is whether transferring hundreds of billions of dollars from developed countries to less developed countries [newsdaily.com] is a better idea than using that money to minimize further change or adjust to the change as it happens. The AWG alarmists need to distance themselves from the one world government crowd.

Re:evolution ? (5, Insightful)

polar red (215081) | more than 4 years ago | (#30633216)

It's funny the people warning us about one world (elected)government don't issue warnings about our (unelected)corporate overlords.

Re:evolution ? (1)

RockDoctor (15477) | more than 4 years ago | (#30638872)

It's funny the people warning us about one world (elected)government don't issue warnings about our (unelected)corporate overlords.

That's probably because they (the one-world-government-warning people) probably consider themselves to be likely members of the corporate overlord group, not of the boot-trampled masses. That's capitalism for you.

Re:evolution ? (1)

Hurricane78 (562437) | more than 4 years ago | (#30698914)

Because they are the same thing! Duh!

Re:evolution ? (1)

Abcd1234 (188840) | more than 4 years ago | (#30633402)

You most certainly can prove a negative, and scientists do so all the time.

Um, no, they don't.

Scientists never "prove" negative statements. They falsify (ie, provide counter-evidence for) positive statements.

Re:evolution ? (1)

jjohnson (62583) | more than 4 years ago | (#30633758)

Negating a positive statement yields another positive statement: "There are elephants in my office" becomes "There are no elephants in my office", which is an assertion susceptible to falsification (i.e., looking for and finding no elephants in my office). Thus, I've proved a negative.

The slogan "you can't prove a negative" is meaningless outside a fairly narrow use in logic.

Re:evolution ? (1)

Maxo-Texas (864189) | more than 4 years ago | (#30637284)

Proving a negative is more like, "There have never been elephants in my office" without a 100% accurate historical record.

And "There will never be elephants in my office" could be proved only by destroying the office.

Re:evolution ? (1)

jjohnson (62583) | more than 4 years ago | (#30641762)

Your example is correct, but it doesn't have to do with negatives. It's as hard to prove the statement "there have always been elephants in my office" without the same 100% accurate historical record (more plausibly, and as difficult to prove, "All life on Earth is carbon-based").

Re:evolution ? (5, Informative)

polar red (215081) | more than 4 years ago | (#30633254)

Scientists are always trying to disprove. 'proving' a new theory is much harder than disproving the most widely adopted theories. see 'falsifiability' http://en.wikipedia.org/wiki/Falsifiability [wikipedia.org]

Enough Already ! (4, Insightful)

daveime (1253762) | more than 4 years ago | (#30632154)

The academic paper is available in Science, though seeing more than the abstract requires a subscription

I thought this was "news for nerds, stuff that matters", not "Science magazine touting for subscriptions".

If we can't even RTFA without paying first, then it has no place on this site IMHO, as we have all come to realize that TFS is at best "a summary", and at worst, complete BS.

Re:Enough Already ! (4, Funny)

RDW (41497) | more than 4 years ago | (#30632306)

Sounds like you might be interested in this exciting new media access concept!:

http://en.wikipedia.org/wiki/Library [wikipedia.org]

Re:Enough Already ! (5, Funny)

daveime (1253762) | more than 4 years ago | (#30632386)

Morpheus

This is the construct. It's our loading program. We can load anything from clothing, to equipment, weapons, training simulations, anything we need. But if you want to read a Science article linked from Slashdot, you'll have to get on the bus and nip down to the local library.

Re:Enough Already ! (1)

noidentity (188756) | more than 4 years ago | (#30633668)

Morpheus: This is the construct. It's our loading program. We can load anything from clothing, to equipment, weapons, training simulations, anything we need. But if you want to read a Science article linked from Slashdot, you'll have to get on the bus and nip down to the local library

Oh, come on, you can't expect us to be able to computerize everything! Accessing magazine articles online has been a very tough problem to solve, due to the inherent difficulties in the process. Enjoy the advances we have made.

Re:Enough Already ! (1)

mkarcher (136108) | more than 4 years ago | (#30769062)

Morpheus

This is the construct. It's our loading program. We can load anything from clothing, to equipment, weapons, training simulations, anything we need. But if you want to read a Science article linked from Slashdot, you'll have to get on the bus and nip down to the local library.

Wasn't that the entire plot of the movie? They couldn't jack in from their comfy cave complex.

Re:Enough Already ! (4, Insightful)

Daniel Dvorkin (106857) | more than 4 years ago | (#30632364)

Slashdot regularly reports on new products costing hundreds or thousands of dollars, sometimes tens of thousands. You don't get to use the product (particularly if it's hardware) without paying for it, yet many more people will talk about it than will pony up the cash.

If you want to read the article without a subscription, you can do so for fifteen bucks. If you're in school, or know anyone who is, there's a good chance you can do so for free.

For those of us in bioinformatics, this kind of thing is our bread and butter. Don't dismiss this as "not news for nerds" just because it doesn't happen to relate to one of the particular kinds of nerdiness about which you care enough to pay a small amount of money.

Re:Enough Already ! (1, Insightful)

daveime (1253762) | more than 4 years ago | (#30632444)

I don't care to pay *any* amount of money for nerd news, that's why I'm here in the first place.

Having essentially a "free" news for nerds site, then linking it to paid-only subscription articles kind of defeats the purpose, wouldn't you agree ?

Which was my original point and seems to have got lost. It's not about whether or not I'm prepared to pay X amount to get Y information, it's about the fact that this is supposedly a "free" site.

It's the same kind of scam which means when I search for "free software" on Google, I end up on websites that offer "free downloads of software that needs to be paid for".

Re:Enough Already ! (1)

Daniel Dvorkin (106857) | more than 4 years ago | (#30632552)

Slashdot calls itself "news for nerds," not "free stuff for nerds." There is no requirement that linked information be free. It's nice when it is, of course, but that's a bonus.

Again, do you have a problem with articles that discuss proprietary hardware or software? You can't, I hope you'll agree, get complete information on the latest offering from, say, Apple or Oracle, without buying and using it.

Re:Enough Already ! (1)

Tranzistors (1180307) | more than 4 years ago | (#30632632)

I don't care to pay *any* amount of money for nerd news, that's why I'm here in the first place.

You got the news - "Scientists Measure How Quickly Plant Genes Mutate". Even more so, you got some numbers - 1:1,4*10^8 per gen. This is news.

What you are asking is "Science papers for nerds", or maybe you want a free book with book review.

Re:Enough Already ! (0, Troll)

Anonymous Coward | more than 4 years ago | (#30632876)

Are scientists so greedy, they need each person to pay 15$ for a fucking glance to what they are doing? Do they have shyness to speak in public so severe, that they can't publish on the Internet? Or are they so stupid they can't learn how to build a web server?

And scientists wonder why there is so much creationism and anti-intellectualism out there...

Re:Enough Already ! (2, Insightful)

dkf (304284) | more than 4 years ago | (#30633404)

Are scientists so greedy, they need each person to pay 15$ for a fucking glance to what they are doing?

Any research institution worth the name will have a site license for the journal. The rest of you should try googling for a preprint...

Re:Enough Already ! (0)

Anonymous Coward | more than 4 years ago | (#30638810)

The rest of you

99% of the population, including researchers in the first and second worlds.

Proprietary science publishing these days is largely a scam and should not be supported in any shape or form. They add little to no value, they're just middlemen leeching off others.

Re:Enough Already ! (2, Insightful)

Beezlebub33 (1220368) | more than 4 years ago | (#30633990)

It's definitely not the scientists themselves. The scientists that I know would be happy to have you read their research (for free). You can get preprints, reprints, research papers, and all sorts of documents that discuss research.

The thing here though is that it's printed in a refereed journal, specifically Science, that is a really big deal to most scientists. The scientists are plenty willing to let their paper be published in a journal that costs money to have the ability to put 'Science' on their CVs (actually, they are more than 'plenty willing', they are probably willing to give their left nut for it). The prestige associated with getting published in Nature or Science is well worth losing some readership on the internet. In addition, the paper will be available to the people that really need the paper itself (other scientists) because they all have access to Science through their institutions, or they are willing to pay $15 for it. The general public is almost certainly not that interested in the details of the paper, and they can get the info through other means (popular press, reviews), or they can pony up the $15 for it.

When someone write a book, and it is discussed on Slashdot, do you complain that the book is not available on Slashdot? Why is this different?

Not their fault: scientific publishing model sucks (2, Insightful)

SlashBugs (1339813) | more than 4 years ago | (#30634030)

Given the choice, all scientists would probably publish their research freely; it's actually pretty common practice in physics and maths. However, in other fields -- including biology -- this isn't realistically possible.

A scientist's career and a department's funding are entirely dependent on their reputation, which is almost completely dependant on getting your work published in high profile (a.k.a "high impact factor") journals. In order for these journals to accept amd publish your work, you have to sign over copyright to the publishing company, and agree that you won't distribute the article for free.Scientists get completely shafted in this system: We raise money, do the work, write the article, sign over copyright to the publisher then pay for the privilige of them selling our work for their own profit. Then we're contractually forbidden from passing on copies of our work to interested colleagues (or potential employers, etc), much less the wider world.

There are some exceptions to this. In the UK, certain funding bodies and research charities insist that all work funded by their money must be made freely available, either at time of publication or, more commonly, after a delay of half a year or more. In the USA, work funded by the NIH must be made freely available. This is still generally restricted to the researcher's own version of the paper (i.e. without the journal's professional typesetting), but at least the information gets out.

Scientists hate this system, but an individual scientist simply doesn't have the bargaining power. You want to negotiate with a journal? They'll simply refuse your paper and run one of the tens or hundreds of others competing for your spot. Want to make a principled stand and only submit to open-access journals? You can, but you can basically kiss your career and funding prospects goodbye. So it's simple pragmitism: not many people are willing to risk throwing their careers away in the fight to let non-professionals (and a huge number of cranks, if you've ever read the Nature comments boards) read their article for free.

So what? (1)

Junior J. Junior III (192702) | more than 4 years ago | (#30632490)

Slashdot posts news stories about hardware that you can't get your hands on without paying for it. It posts reviews of books that you can't read without paying for them (short of going to a library). Why should it be any different for a scientific journal that happens to have an online edition? The news is the discovery. The article happens to contain more information about the methods, data, and the findings. So what if it costs money to read it? Isn't supporting the scientific community worth something?

Re:So what? (0)

daveime (1253762) | more than 4 years ago | (#30632550)

You wouldn't buy a house without seeing inside first and having a full structural survey done.

You wouldn't buy a car without test driving it first, and having the engine checked over thoroughly by a mechanic.

But you say to me, "Here's an article on Science, it's really interesting, honest. But if you want to know the nitty-gritty, you'll have to pony up 15 bucks first" ?

The Honest Indian Business Model is a bit outdated, don't you think ?

Re:So what? (1)

Junior J. Junior III (192702) | more than 4 years ago | (#30632812)

You wouldn't buy the article AFTER reading the whole thing and knowing what it already says, either, would you? Ah!

I guess scientists should spend years studying and researching and publish their findings for free, and for dinner they can eat the rainbows that shoot out of your butt.

If you're casually interested in the topic, probably you don't want to bother paying money for it. Bitch about it if you want to; the unfair world doesn't publish scientific findings for free and hand deliver them to your doorstep on demand. Boo hoo.

If you're professionally or academically interested, you're probably more willing to pay for it. If the publication or the authors are reputable, you're probably not going to be disappointed with the investment. The work necessary to acquire a reputation has costs associated with it, which are in part recouped by the sale of access rights to published works. It might not be a perfect utopia, but it works.

I'm not going to pay for the privilege of reading the article, but thanks to the free coverage that I did read, I now know a little bit more about something interesting going on in the scientific community. And just maybe, a few more dollars are flowing to scientific work because of the publicity. Hardly a bad thing.

Re:So what? (1)

jbengt (874751) | more than 4 years ago | (#30636940)

I guess scientists should spend years studying and researching and publish their findings for free, and for dinner they can eat the rainbows that shoot out of your butt.

Well, that might be better than the current situation, where in order to get published by a reputable journal they must give up their copyrights for free and agree to not publish their own works elsewhere, and for dinner they eat the funding that they begged for in order to do the research, which funding they will probably not get without the prestige of having articles published in a reputable journal that charges you money for reading but pays no money to the scientist for writing, depending on how good those rainbows taste.

Re:Enough Already ! (2, Insightful)

one cup of coffee (1623645) | more than 4 years ago | (#30632596)

"If we can't even RTFA without paying first, then it has no place on this site IMHO"

WTF!? IANAL but AFAIK on Slashdot, RTFA-ing is BS! LMAO!

I'm sorry,,, I'll leave now....

Re:Enough Already ! (1)

noidentity (188756) | more than 4 years ago | (#30633644)

Wait a minute, you're complaining that you can't RTFA? You must be new here.

Re:Enough Already ! (1)

daveime (1253762) | more than 4 years ago | (#30636932)

Not reading TFA and not being *able* to read the TFA without paying first, are two different things ;-)

I'm really just trying to shame them into not linking to paid articles, so then I can safely ignore TFA, and in principle, save myself 15 bucks in the process ;-)

(For those with sleepy neuron deficiency, the above *IS* sarcasm).

eldavojohn is gone! (0)

Anonymous Coward | more than 4 years ago | (#30632326)

The stories posted by eldavojohn lately make me want to stop reading /. until eldavojohn returns to school and/or goes back to packing groceries.

Oh great. (0, Troll)

Strep (956749) | more than 4 years ago | (#30632374)

Oh great. Now the greenies are going to start claiming that each variant is a new species and that we have to drop everything to save them. On the other hand, the eco-diversity crowd should be pleased by this.

Re:Oh great. (2, Insightful)

Daniel Dvorkin (106857) | more than 4 years ago | (#30632458)

As far as wilful misinterpretation goes, you have to worry a lot more about the creationists on this one than the "greenies." It doesn't really affect the environmentalist viewpoint in any meaningful way, but it requires the more sophisticated creationists to move the goalposts again to maintain the artificial "microevolution/macroevolution" dichotomy they're so enamored of.

Re:Oh great. (0, Troll)

Strep (956749) | more than 4 years ago | (#30632484)

Yeah, whatever. Creationists aren't taxing my a$$ off to save some freaking flies...

Re:Oh great. (1)

Daniel Dvorkin (106857) | more than 4 years ago | (#30632636)

Nobody is "taxing your ass off to save flies." If you think they are, you've been sadly misinformed.

Re:Oh great. (5, Insightful)

bcmm (768152) | more than 4 years ago | (#30632612)

Genetic diversity is useful, as it make it much harder for a single pathogen to wipe out a population in a short space of time.

As for the rest, nobody is going to claim that each individual is a species. You've constructed a rather unconvincing straw man to hijack an interesting article, because you have a problem with some imaginary "greenies".

shut it (0)

Anonymous Coward | more than 4 years ago | (#30632376)

it was a good article, so shut your face. don't get a subscription, no one gives a damn, the dude doesn't work for the mag he is just informing you that you can't view the whole thing. lay off.

Re:shut it (1)

daveime (1253762) | more than 4 years ago | (#30632662)

Very eloquently said, Sir. Consider my face shut, at least for the next 8 hours.

Perhaps tomorrow you'll learn the difference between the Reply button at the top of the page, and the Reply button under my actual post(s) ?

huh? (1)

jbengt (874751) | more than 4 years ago | (#30632650)

With four different DNA letters, there are six possible changes . . .

Can anyone explain this? Are they saying that a change from, say, for example, T to A is the same as a change from A to T? Are they just wrong? Or is there some good explanation that eludes me?

Re:huh? (0)

Anonymous Coward | more than 4 years ago | (#30632780)

If you were A, you could change to T, G, or C.
That's three.

The other three come from... uh... umm....
I don't even see how six is possible as a number of total possible changes (too low).

Maybe plants code for stuff differently than animals or something (that is transcribing dna (well, RNA) to proteins or whatever it is plants have). But even then, the mutations happen on the DNA themselves, even if they aren't expressed (sort of a low level genotype vs phenotype), so that line of thinking is stupid as well.

Re:huh? (1)

mikael (484) | more than 4 years ago | (#30632980)

Wikipedia has a better explanation of the genetic code [wikipedia.org] . It's probably better to understand that
in just about every species, groups of three letters form a codon [bioephemera.com] , which defines a particular amino acid, of which there are 30 or so, but most species only seem to use around 24, along with a STOP command.

Some funky stuff goes on, with some DNA being used in reverse, or offset by one or two letters, so that you get six possible sequences from the same set of letters.

Re:huh? (1)

jbengt (874751) | more than 4 years ago | (#30637102)

Still looks like there would be a lot more than 6 possible mutations, even if they're only counting the mutations that make actual functional changes to the codons. I have a feeling that TFA got something confused or left something out.

Re:huh? (1)

kmcarr (1185785) | more than 4 years ago | (#30643436)

First the "six possible changes" is only referring to single nucleotide polymorphisms (SNPs), which is the substitution of on one base for another. There are more complex alteration, insertions, deletions, inversions, etc. are not counted among these six. For a SNP to become "fixed", that is stably maintained through subsequent replication cycles you have the initial mutation event (altering a base) but then you must also have the complementary substitution on the other strand of the double helix. If an A is changed to a T on one strand then the complementary T must subsequently be changed to an A to maintain complementarity of the double helix. Once the mutation is fixed it is impossible to tell if the original mutation was the A->T, with complemnting T->A, or vice-versa. More properly these mutations are written as change in the paired bases AT->TA. An AT->TA is indistinguishable from TA->AT. The six possible changes are:

AT->GC
GC->AT
AT->CG
AT->TA
GC->TA
GC->CG

Great piece of work! (5, Informative)

elyons (934748) | more than 4 years ago | (#30633714)

For those that don't know much about either the significance of the science or the technology involved with generating the data, this might be useful. One big gray area in our understanding of evolution is how quickly genomes are changing, where they change, and the types of changes that are occurring. Yes, a genome is usually made up from DNA (RNA viruses being the major exception), and encoded in the DNA are genes, many of which get translated into proteins that do much of the "work" in an organism. However, depending on the organism, much of the DNA does not code for genes. The human genome for example is ~3,100,000,000 nucleotides (DNA's building blocks) long. Of that, ~1.5 percent codes for protein. Of the rest, the vast majority are ancient, dead, "selfish" chunks of DNA such as retroviruses (RNA viruses that convert to DNA and integrate into a genome. HIV is an example of one of these guys) and transposons (a major class of which are just like retroviruses but lack the genes for cell-to-cell transfer). Periodically in the evolution of many multicellular organisms (e.g. plants and animals), there are explosions or blooms of these types of elements that suddenly take off and integrate around a genome. This is one type of mutation (or genome evolution), and there are many others. Single nucleotides can change (e.g. C->T, as discussed in the paper), individual genes can get duplicated through a process known as unequal crossing-over or nonhomologous recombination, and the entire genome can be duplicated (known as polyploidy and is a dominant feature in flowering plant genome evolution.)

Our current understanding of how dynamic a genome is, the types of changes that occur, and the factors that limit these changes is very limited. Much of this is because getting a genome of an organism can be expensive and laborious, depending on the size of the genome (RNA virus 15,000 nt, DNA virus: 150,000 nt, bacteria: 5,000,000 nt, yeast: 20,000,000 nt, multicellular organisms: 100,000,000-10,000,000,000). Since our understanding of how genomes evolve depend on getting genomes sequenced that are appropriately related to one another (e.g. populations of organisms versus diversity of organisms), we can only get answers for those genomes we currently have (current ~8000 for all viruses, bacteria, archaea, and eukaryotes). Fortunately, there is currently a major technological revolution happening in biology: generating DNA sequences fast and cheap. For example, the first human genome was approx a 10 year project and cost ~$1,000,000,000. Now, the record for a human genome takes less than a week and costs ~$15,000.

This project is a major milestone as the authors sequenced 6 plant genomes (a mustard known as Arabidopsis thaliana) that are related to one another by 30 generations. Because of the close evolutionary relationships of these organisms, the authors can characterize the types of genomic change happening over very short time periods.

The emerging picture is that genomes, the fundamental genetic blueprint for a lineage of organisms, are much more dynamic than we had previously thought.

Re:Great piece of work! (2, Insightful)

grikdog (697841) | more than 4 years ago | (#30637592)

Mod this up to 10. This is important because plant genomes have been the source of some stupendously unexpected discoveries indicating that DNA is extremely plastic, and manages to squeeze into available ecosphere niches with ease -- resulting in closely related genomes that express forms as divergent as pineapples and plane trees. Linnaean classification schemes based on morphology therefore disconnect from reality and become first approximation maps. When the morphologies in question are fossils, the peril in drawing conclusions from shapes alone throws decades of curatorship into doubt. The greater implication is, that evolution is not only reasonable and easy but dirt cheap. The probability that life exists on other planets, in the galaxy if not the solar system, becomes a near certainty.

Re:Great piece of work! (1)

Xest (935314) | more than 4 years ago | (#30638744)

Can this data really be extrapolated beyond the genomes of the plants for which they have gathered data though?

The summary suggests 1 in 60 million for a plant that produces thousands of seeds isn't such a big number, but in contrast, take a plant like Carnegia gigantea which produces around 60 million seeds a year, but which is lucky to have even one of those survive beyond a few weeks if it even germinates at all, for species like this, it's still a big number. For these sorts of species then, we have a 1 in 60 million chance of carrying a mutation, coupled with a 1 in 60 million chance of that species being the one to germinate. Of course, even that is assuming that again, the chance of mutation is a roughly static value across all species.

So can we actually really say from this study that lifeforms are more dynamic than we thought in general? Or simply that some species are more dynamic than we thought as in the case of those species tested? Even with the given numbers if they hold the speed of change clearly isn't so fast in the likes of Carnegia gigantea. The species itself is quite numerous in population, but again, not so much as many other plants.

A question about Lenski's work. (1)

telomerewhythere (1493937) | more than 4 years ago | (#30637304)

Has the DNA Sequencing been done on his E. Coli?

If so, What was found?

If not, when do we expect it?

Re:A question about Lenski's work. (2, Informative)

elyons (934748) | more than 4 years ago | (#30637546)

Yes. His group had a recent paper in Nature where they sequenced genomes from their Long Term E. coli Evolution experiment at generations: 0, 2000, 5000, 10000, 15000, 20000, and 40000.

Absolutely stunning piece of work:
http://www.nature.com/nature/journal/v461/n7268/full/nature08480.html [nature.com]

Re:A question about Lenski's work. (1)

telomerewhythere (1493937) | more than 4 years ago | (#30639538)

I thought I remembered that, but I couldn't find it. Don't know why. I don't have access to Nature, and $32 is too much money to me just to find out if the article talks about how the Cit+ E. Coli came about genetically.

Did they discuss this mutation in this article? The abstract doesn't even mention the Cit+ E. Coli.

I wonder if they found the answer to Lenski's question near the end of his 2008 paper: "What physiological mechanism has evolved that allows aerobic growth on citrate?"

Is that discussed in the Nature paper?

Re:A question about Lenski's work. (1)

elyons (934748) | more than 4 years ago | (#30640964)

I'll need to re-read the article for the specifics, but this was just measuring the background rate of mutations without any form of selection. They found an initial burst of change as the bacteria adapted to the experimental conditions, then not much for the first 20,000 generations, then a continuous burst of new mutations between 20,000 and 40,000 generations. They could attribute those mutations to a mutation that knocked out one of the DNA repair enzymes.

Re:A question about Lenski's work. (1)

telomerewhythere (1493937) | more than 4 years ago | (#30649364)

Thanks for the info.
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