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New Code Discovered in DNA?
anthemaniac writes "The NY Times is reporting that scientists have found a second code in DNA that goes beyond the genes. The code is superimposed genetic information and 'sets the placement of the nucleosomes, miniature protein spools around which the DNA is looped. The spools both protect and control access to the DNA itself. The discovery, if confirmed, could open new insights into the higher order control of the genes, like the critical but still mysterious process by which each type of human cell is allowed to activate the genes it needs but cannot access the genes used by other types of cell.'"
like the critical but still mysterious process by which each type of human cell is allowed to activate the genes it needs but cannot access the genes used by other types of cell.
So my body has built in DRM?!
Monstar L
Does this mean that DNA has DRM?
So did we finally discover the Midichlorians that Qui-Gon was rambling about?
He who knows best knows how little he knows. - Thomas Jefferson
Personally, I think it's God's version of Sudoku.
Intron: the portion of DNA which expresses nothing useful.
I'll bet it is controlled by an Active Directory installation.
"I'm just here to regulate funkiness."
I think this kind of thing is an important reminder to all humans how much we really have to learn about this crazy but wonderful world we live in.
Only Go^H^Han intelligent designer could have implemented DNA with private and protected data. This sort of thing just can't randomly 'evolve'.
http://en.wikipedia.org/wiki/The_Chase_(TNG_episod e)
Karma: Excellent. 15 moderator points expire sometime.
Any software problem can be solved by adding another layer of indirection.
So apparenlty we are a software problem.
It's not like nucleosomes are anything new though, the real discovery here is that the scientists found a pattern to their binding.
Sadly the times article is filled with a lot of fluff. This isn't really a "second code" nor do I see why it's "hidden".
...a Whitespace program inside a C++ program. The Whitespace program coexists with the C++ program because of the "wiggle room" (to borrow a phrase from the article) that the C++ grammar givess you.
Doesn't it make you feel good to know that our freedoms are protected by politicans, lawyers and journalists.
Abstract and full text PDF. (currently freely available).
Any sufficiently advanced libertarian utopia is indistinguishable from government.
It is also why humans pass around so many damn virii. And how much junk mail do YOU get each week? We could go on and on, but I think it is fairly obvious that All Our DNA are Belong to Billy G.
"I'm just here to regulate funkiness."
That's the part that lets us read email.
have been discovered to be eighty units long and oriented face down, nine edge first.
"How to Do Nothing," kids activities, back in print!
Pardon? Your statement is nothing but a bald assertion. Error control mechanisms run in no way against the evolutionary grain. It's easy to imagine that an organism with a little error correction will be more fit in its niches than an organism without. Changing too rapidly, or too randomly, is as dangerous to an organism as not adapting fast enough.
Error control mechanisms, at the very least, would very much run against the flow of blind Darwinian processes.
Why? Why couldn't DNA evolve error control mechanisms over billions of years? Because you don't want it to?
Seems to me a mechanism to make the genes encoded into DNA more stable and reproduceable would produce enormous benefits to an organisms ability to rapidly and accurately reproduce and thus would have enormous evolutionary pressure behind it.
We're C++ code
I find it interesting that god/evolution/the great green arkleseizure/FSM/whatever invented metadata LONG before we did. Not surprising, just interesting.
"If you make people think they're thinking, they'll love you; But if you really make them think, they'll hate you." - DM
I have a lot of good code, ready for re-use!
This issue is a bit more complicated than you think.
Hidden message deciphered in nucleosomes: WE ARE SORRY FOR THE INCONVENIENCE.
"God uses DRM, SO CAN YOU!"
-EL
When am I going to see my first wetware virus that uses an "escalation of privileges" type attack?
Your sig(k) has been stolen. There is a puff of smoke!
"...like the critical but still mysterious process by which each type of human cell is allowed to activate the genes it needs but cannot access the genes used by other types of cell."
Personally I think some of these genes are not declared as 'public', but rather 'protected' or 'internal'.
Privacy is terrorism.
I'm not entirely sure this is a problem. We have a heirachy of media that cascades, simplifying down at each stage. In this case we normally have something like Nature article (for the practicing biologist) -> Nature News and Views (for the lazy people who read Nature but can't be arsed to read the article) -> New Scientist article/comment (for the interested layman) -> traditional news media (the proletariat). At each stage something is lost. I don't expect the public to care about a prediction method for the sequences involved in higher ordering of chromatin structure, but the fact they might find out that DNA does more than just 'make genes' I think is a relevant point.
The headline however, is unnecessarily sensationalist..
I don't read your sig, why do you read mine?
Error control mechanisms, at the very least, would very much run against the flow of blind Darwinian processes.
You mean like white blood cells?
What he can't kill, he has sex on. Trent.
New Code Discovered in DNA
b-e-s-u-r-e-t-o-d-r-i-n-k-y-o-u-r-o-v-a-l-t-i-n-e
Man! How long did it take evolution to figure that one out?
What time is it?
(Did you meant figure out how to do it, or figure out how it does it?)
I'm anticipating the time when we realize that life and evolution is an example of Reflections on Trusting Trust and thus that the origin of some aspects of DNA and life may be unknowable, and yet explicable, and thus not be of divine origin.
Oh, say does that Star-Spangled Banner entwine / The myrtle of Venus with Bacchus's vine?
wow we have discoved that genes use encapsulatio now.. OOPS is the way to go... no wonder it cant access private members of other classes erm.... genes..
If you put the new code together correctly will it form the plans for a dimensional portal?
Ummm, error control mechanisms are EVERYWHERE in biology and are nothing new. Take a look at:
kinetic proofreading
programmed cell death
nucleotide excision repair
base-excision repair
http://en.wikipedia.org/wiki/DNA_repair
I'm sure a real biologist could point out even more points to note. From an evolutionary point of view, an organism that couldn't control its cell growth or repair damaged DNA strands probably wouldn't last that long!
The placement of histones on DNA is something I learned about 10 years ago in my genetics textbooks. This is merely a slight addition to our current knowledge of which sequences histones are likely to bind.
Over ten years ago, the hot new field in biology was "gene expression". We already knew about DNA, but there was a lot of "junk DNA" that seemed weird, as well as lots of questions around when and how DNA was actually turned into working proteins.
It turns out there's some vastly complex actions around how genes are actually expressed. Methylization semi-permanently deactivates DNA. Other things control the unfolding of DNA so that they're accessible to be exposed. Much of the "junk dna" is probably not junk, but rather controls gene expression to some degree.
The bottom line is that DNA is only the bottom rung of how information is stored and manipulated in the nifty little computers that are our cells. This is also a great context to talk about evolution - no sane intelligent designer would make a cell this way. If you think about small changes over billions of years, though, you can see how the warping and twisting of DNA could produce interesting results that are passed down from generation to generation.
Science is rarely boring.
"The discovery, if confirmed, could open new insights into the higher order control of the genes."
Perhaps this may provide additional information as to the usefullness of the supposed "junk DNA" that fills the human g-nome.
We're all hypocrites. We all have hidden parts, it's the contrast between them that make us more a hypocrite than others
From TFA: A histone of peas and cows differs in just 2 of its 102 amino acid units.
Mmmm, a histone of peas... Seriously, let me be the first to say: I smell a Nobel prize for this one.
But, then we must of course examine our creator/creators.
The creator(s) are one of:
1) more complicated than us. So they even more likely created by another being than us. by the "intricate things have a creator" theory.
2) more complicated than us as a whole. The creator society as a whole created us.(**)
2) less complicated than us. Our creators used there intelligence, and directed evolution to create us. (***)
3) we are not allowed to think about this according to our religion, sorry.
(**) Similar to how a single person cannot build a jumbo jet, but thousands of people can.
(***) Note that we can create machines that can make calculations faster than any human. Note also that we can use software evolution to create efficient algorithms.
Everybody knows there's a hidden code in our DNA... Leonardo DaVinci put it there!
GetOuttaMySpace - The Anti-Social Network
I find it fascinating how cells are amazingly complex, and yet are able to reproduce of themselves. It is like there is a whole world found in a cell, and it is able to transfer all this needed information accurately to the next generation. I think we are just beginning to understand cells and there is a lot more complexity to be discovered.
This isn't a second code. The second code is the binding sites for proteins that activate and inhibit gene expression. Then there are a number of other codes already known that affect replication or expression in various ways.
This is way down on the list of discoveries of patterns in DNA, and it's really more a storage medium property than a code. This is more like sector markings on a hard drive platter than anything to do with data or filesystems. It's important, but because it will tell us where DNA is likely to get damaged, but these sequences are not functional components of the actual use of DNA.
42
Error control mechanisms, at the very least, would very much run against the flow of blind Darwinian processes.
No, error correction would counter the mutation process. Given that, generally, more mutations are harmful than beneficial, error-correcting genetics would be a short-term benefit in reducing genetic disorders. The downside would come if another species with a higher mutation rate evolves into a more successful form and crowds out the now-obsolete organism with rigid genetics. The overall winners would likely be organisms within some range of error-correction--neither a total free-for-all, nor a very rigid genome. This seems pretty well reflected in real life, unsurprisingly.
Yes, this discovery does not hurt the ID movement at all.
This is also true; no scientific discovery will hurt the ID movement, since it has precisely nothing to do with science...
What we need to find are the comments!
// FIXME: should check for overflow here!
if (replication_count < MAX_REP_COUNT){
childcell = new Cell;
replication_count++;
}
The short answer is this: "selfish" DNA like transposons invade a genome, they replicate and produce many copies, some preferentially insert near genes. These transposons over time degenerate but their ability to create mutations, including using their own proteins to control expression of some genes leads to diversity = better ability to cope to environmental pressures. This leads to a better capacity for evolution than waiting for single base mutations from cosmic radiation and the like. When a transposon has gone from genomic invader to a productive member of the gene pool it is said to be domesticated. Over long periods of time (hundreds of millions of years) a lot of the copies of the transposons, which are not necessary, and therefore not selected for, are allowed to mutate, degenerate and appear to be "junk".
Pah.
I can't be bothered to read Nature and Science these days. The damn articles are so long and hard to read. I mean, have you any idea at all how busy I am? How am I supposed to do any science if I spend all my days reading papers.
Phil
In response to a small percentage of posts, I can't help but make this comment: As usual, when there's a new scientific discovery that proves nature is more "complex" (a totally subjective word in and of itself) than we once thought, there's a surge of morons shoving the word "god" in where the words "I personally have no explanation" should be used instead.
Currently theta testing the prototype "Event Horizon" server-scaled desktop box with a 50 Gigameg of Ram.
FTA: "Biologists have suspected for years that some positions on the DNA, notably those where it bends most easily, might be more favorable for nucleosomes than others, but no overall pattern was apparent. Drs. Segal and Widom analyzed the sequence at some 200 sites in the yeast genome where nucleosomes are known to bind, and discovered that there is indeed a hidden pattern."
Honestly, many of us biologists are kind of giggling at how the NYT (and I guess Slashdot) have been hoodwinked by hot headlines. We have known for decades that histones bind DNA and organize it (into nucleosomes), periodically, all along its length. Now, this group has identified some concensus sequences where the nucleosomes are most likely to form. Turns out, yeah, it's what we thought, with the little twist that precise positioning of nucleosomes could help regulate gene expression (also heavily predicted and fully expected). There are new articles about DNA organization weekly. I think the NYT just picked one and labeled it as a "code beyond genetics", which is absurd, since the organization of DNA is controlled ultimately by DNA sequences. Also, if you want to talk about codes beyond genetics, there is a whole field of study called "epigenetics", which is "the study of reversible heritable changes in gene function that occur without a change in the sequence of nuclear DNA".
Personally, I find epigenetics http://en.wikipedia.org/wiki/Epigenetics more interesting than this article. It also explains the "mysterious process" of cell types.
The world is made by those who show up for the job.
The existence of nucleosomes is well known. It is not a secondary dna, simply a packing/folding mechanism for DNA, and it may have a role in regulating gene expression.
http://en.wikipedia.org/wiki/Nucleosome
The paper itself is as bad as the press reporting it. Slashdot is hardly the avenue to discuss the fine points of a research, but here is something to chew on: note how the authors claim that they predict 54% of nuclesomes ... yet a little later note how by random chance this so called "prediction" would yield a 39% accuracy anyhow. I guess that 54% accuracy is a whole lot less impressive.
Behind the mumbo-jumbo, p-values, Komolgorov-Smirnoff tests, Boltman partition functions, etc all they do it match a set of 146 bp (start,end) intervals to another one. They are very-very skilled at hiding the simplicity of what they do behind a whole lot of fancy plots and words.
Nature should be ashamed of themselves ... the literature on this subject goes back many decades, besides doing more experimental work none of this is new, novel or even interesting. I also expect a significant backslash from people that are far more knowledgeble than I am in the matter.
Yes, that assertion most definitely lacks hair...?
-K
The only way this code was hidden was that we didn't know about it before. It took a whole bunch of yeast work and number crunching to see it.
God put a rainbow in the sky to remind man that he would never flood the Earth with water again.
Yes, we can explain exactly why it appears there using elementary physics and predict exactly where it will appear at any given time of day based on the position of the sun in the sky.
But that doesn't diminish its divine origin.
The problem with this silly statement is that it would mean that there were no rainbows before the flood, and that the laws of physics were changed to enable rainbows to appear.
"There are about 30 million nucleosomes in each human cell. So many are needed because the DNA strand wraps around each one only 1.65 times, in a twist containing 147 of its units,..."
.....1.618 The Divine Proportion....damnit i was soooo close to finding the meaning of life this time!
1.65 hmmmmm thats awfully close to
SMD
over and out
I'm not disagreeing with you.
Except for ending slavery, the Nazis, communism, & securing American independence, war has never solved anything.
Case in point: the HIV virus. It's an RNA virus. Most enzymes cells use for replicating DNA (called DNA polymerases) have a proofreading skill: if they detect that what they're reading is incorrect they'll rip it out and try again. Most RNA polymerases lack proofreading skill (because it's expensive: it takes a lot of energy, and RNA is, in the grand scheme of things, considered throwaway material, a transition from the data storage system to the actual machinery.) So, the viruses that rely on RNA as their data storage have a much higher rate of mutation. The result is that they have a vastly higher rate of nonviable viral particles, and a small number of extremely viable particles, which have found, by chance, better ways of evading host immune response. It's a main reason that HIV is so difficult to treat or cure.
Here is some information about reverse transcriptase error rates. In contrast, here is some for one of the DNApolymerases. As I recall, in eukaryotes there are three DNA polymerases, and only DNApolyIII has bidirectional proofreading ability (I may be wrong) so only it can scan finished DNA, but all three can scan DNA while it's being built. In contrast, I don't believe there are any enzymes that can scan finished RNA (since it's not, to my knowledge, found double-stranded in anything we've found, and you'd have no way of determining that there was an error) so the best you can hope for is really good DNA->RNA fidelity, and as I said earlier, there's not much evolutionary pressure FOR that in the rest of nature, while there's some evolutionary pressure AGAINST it (because it's expensive) so if it were to exist, it would only exist in things that would benefit from it, those being small RNA viruses that are much less likely to have either the history, the machinery, or the overhead to afford proofreading replication enzymes. Besides which, if their gain (number of viruses produced for each cell infected) is high enough, they A: don't care about individual viral particle loss from bad fidelity, and B: actually benefit from high mutation rate because of its help in evading host response.
whew. that was wordy. sorry.
Nostalgia's not what it used to be.
The argument those of us are making is more complex than "we don't understand it, therefore God."
The arguments are closer to "the more you understand, the better our case is."
Except for ending slavery, the Nazis, communism, & securing American independence, war has never solved anything.
This is why I always wondered why people fund/do research on if prayer? What good does it do? Now in science, that is never a good attidtude, but... You aren't going to convince anyone of anything and you can't prove anything. When you're dealing with God, all bets are off. I never insert God as a crutch in science. So what is the point?
OK, on topic:
This is why I want to go into molecular/computatioal bio. Weird, exciting, important things are always there tobe discovered (ok, so you can make that assertion about any science, but I prefer bio).
"You will do foolish things, but do them with enthusiasm." - S. G. Colette
I wasn't referring to the 2nd law of thermodynamics. I was referring to information.
Except for ending slavery, the Nazis, communism, & securing American independence, war has never solved anything.
Some jokes just write themselves.
What if the Hokey Pokey really is what it's all about?
That's what I love about evolution :) It is pretty easy to imagine up an evolutionary advantage about absolutely any biological feature that ever existed. Just read something like New Scientist to see what I mean. Evolution has an answer to everything.
Great Windows SFTP Server!
With much fear, surprise, and surprise for some of the scientists, they began to read the new code... it began:
......
#!/usr/bin/perl -ane
One scientist looked at the other, and said "This explains everything!"
For every problem, there is at least one solution that is simple, neat, and wrong.
Darwin's Radio? (Greg Bear)
Yeah, right - were a quarter million people killed by their own imaginations? There are floods even with the fricking rainbows. Read a newer book.
.. paranoid crackpot leftover from the days of Amiga.
Mod parent down. He has just screwed a wonderful joke and explained something we already know =)
Changing too rapidly, or too randomly, is as dangerous to an organism as not adapting fast enough
As in cases of cancer, mutation, and other such things. We want our bodies to adapt, but not necessarily mutate (and I don't mean in the X-men way)
Exactly. Evolution is the basic tenet of modern biology. All biological realities are explained by it. It's one of the most successful theories in existence.
There exists no way of exchanging information without making judgments. --Bene Gesserit Axiom
Sounds like a legitimate point, not a troll.
I mean, honestly. The creationist tactic of taking plausible-sounding premises and coming up with utter bullshit conclusions is frustrating, amusing, and finally just boring. You've said nothing of actual useful interest here, and it's a good solid bet that 90% of the premises you've put forward are complete garbage anyway. You numbskulls do not now and never will understand what science is actually about. Real knowledge is real power. Fake knowledge will give you the illusion of power, and the moment the sand shifts under your feet you will have nothing except a bunch of people laughing at what jackasses you are.
My book, podcast
Exactly. I have often mentioned that sexual reproduction is essentially an anti-mutational adaptation. Homologous recombination prefers LIKENESS to UNLIKENESS, so the chances that truly "unique" genes wind up in the recombination product (the child genome) is lessened. Sex keeps known working genes around, and largely prevents completely novel genetic information from being passed on.
There exists no way of exchanging information without making judgments. --Bene Gesserit Axiom
If you play my genes backwards, you hear a car accident and then someone says "Paul is dead. Paul is dead."
-- I have monkeys in my pants.
as well as lots of questions around when and how DNA was actually turned into working proteins.
DNA is transcribed into mRNA which is then translated by ribosomes in the cytoplasm. DNA is not "turned into" proteins.
Methylization semi-permanently deactivates DNA
Methylation is just one aspect of chromatin structure. It's not semi-permanent, it's dynamic.
The bottom line is that DNA is only the bottom rung of how information is stored and manipulated in the nifty little computers that are our cells.
DNA is the fundamental unit of information, which is the source of all gene regulation. If the DNA wasn't what it was, nothing would work in the cell. Afterall, "junk DNA" as you call it is not junk and is responsible for gene silencing (microRNA) other forms of gene regulation.
This is also a great context to talk about evolution - no sane intelligent designer would make a cell this way. If you think about small changes over billions of years, though, you can see how the warping and twisting of DNA could produce interesting results that are passed down from generation to generation.
To claim that you are smarter than the creator of the universe is pure hubris. Who are you, o little man? You are but a speck in the ocean of the universe.
I am defenseless. Use your button. Mod me down with all of your hatred.
This is called the argument from personal incredulity, and is a favourite of the IDers. See http://www.millerandlevine.com/km/evol/design2/art icle.html for an excellent example of how this argument fails spectacularly with the nature-evolved wheel, the eubacterial flagellum.
Call me old fashioned, but I like a dump to be as memorable as it is devastating - Bender
Without being able to view your premises I can only guess at what they are, but I assume they include ideas like "irreducible complexity" which has been violently debunked a number of times now.
Also there's the simple matter of a testable hypothesis, which by the very definition that is given is impossible. In the meantime, real scientific knowledge advances despite all Creationist efforts to prevent it. I find it variously hilarious and very irritating (as I've posted before) that Creationists try to glom onto every new scientific fact before it can get out into the world and cast it as some sort of religious revalation. The problem is, and has been, that if you come up with bogus conclusions and are later trumped by reality, you end up looking just plain stupid.
But that's a choice you make for yourself. Filling in the gaps with God has been the tactic for centuries and we can always look back into the past and see that in those gaps were always more revealing and far more compelling real-world explanations than the unimaginative God-obsessed dullards could ever come up with. Fake knowledge is fake power. Real understanding leads to real illumination. I always prefer the real thing.
My book, podcast
--Rob
Towards the Singularity.
I suppose by "semi-permanent", I meant that methylization was a fairly sturdy structure compared to other methods of blocking transcription. This is in comparison to RNAi, which is fairly temporary.
:)
DNA is the fundamental unit of information
I suppose we could go over semantics forever. Lots of stuff carries information. I'd argue that everything carries information in some form or another. Prions, viruses, and raw RNA seem to do just fine without any DNA. What I was trying to get across is that there were lots of biological mechanisms that carried and processed information, not just DNA.
To claim that you are smarter than the creator of the universe is pure hubris.
Guilty as charged.
I am tempted to summon Occam's Razor in this case. It's sort of like the "Little Man in the Coke Machine" argument. Sure, the Coke cans might be dropped down by a little man inside the vending machine when I put in my money. The simpler mechanical answer is more likely, though.
In this case, I'd argue that a super-intelligent being might take pity on me and make DNA that didn't fall apart and get cancer, make my knees non-screwed up, and my sinuses drain outside my body instead of down my throat.
Who knows? Maybe the universe was created by a Book of Job God who likes to punish us to teach us to be good. I never did understand the part about Job being okay with getting a new wife after God killed off his old one, but maybe Job was a swinger or something.
Sorry for wandering off topic. I blame the coffee.
I don't think that PHP is the best solution here. If you want sequence processing, you will need... wait for it... wait for it...
:D
Lisp!
"All you have to do is be fragile and grateful. So stay the underdog." Chuck Palahniuk, Choke
I find this akin to a computer trying to reverse engineer itself. For instance: I am a software program (mind) that is running on organic hardware (body). Whatever designed me probably coded me in Jah++, I can compile Jah++ natively, but I don't really know what any of it means - because I only understand binary. Is it even possible to understand how we are coded? I mean we can see that there is input and it is n characters long, and it affects the eyeballs. But can we really fully understand why? Why were we coded this way in the first place, and how are we able to understand what little bit we can? Finding comments and metadata etc. in our DNA should come as no surprise to anyone here. We have crudely reproduced the most basic inner workings of animal deduction in modern PCs. We didn't invent the PC, we observed and deduced things that occur naturally. PCs are built the same way we are, foreground processes (listening, watching, reading, consciousness) running on top of background processes (breathing, blood circulation, subconsciousness) inside of a case that cools and provides structure. There are input and output devices, microphone, camera, scanner, printer, speaker, etc. We are the creator's computers. We are a part of a grand design for a self contained network of evolving machinery. As far as our computers go, we are building the dinosaurs and hard shelled organisms, slowly we will evolve into making organic computers that are made out of the same stuff we are and can reason - way beyond AI, I am talking about proper intelligence being built into an organism. Arms being recreated, lungs being grown for implants, brains being repaired after car accidents. It is not a far fetched sci-fi scenario. We are able to interface brain to computer right now. Give us time and we will have a Data, we will not know the difference between man and machine. Just my observations. I could be wrong.
-Scottux
Message finally revealed to be: "All your bases are belong to us..."
any biologists have any recommended reading / courses for this kind of stuff ... ie what's the best starting point etc
I've been reading a lot of Richard Dawkins - find it interesting - gave up biology at GCSE level (exam in UK we take at 16yo) - but could do some OU (www.open.ac.uk) courses etc.
The 2nd Law of Thermodynamics is that closed systems move towards greater states of entropy, i.e. disorder. The appearance of more order in an isolated area of a closed system (i.e. more information) is not problematic so long as the sum entropy of the whole system is not reduced.
The point is that the 2nd law is about information.
"Stumble before you crawl"
With loose hanging comments like: "I think it's really interesting," said Bradley Bernstein, a biologist at Massachusetts General Hospital. and a link to the hospital web site, I think this article was for publicity purposes and nothing else. It really says nothing new, nothing that matters and nothing for nerds. Who let this one through the editorial process?
So it's like Object Oriented Genetics?
While I'm on the subject, there is no such thing as a red blood cell or white blood cells. These objects are corpuscles, or bodies, not cells because they have no genetic material.
Now, what kind of a Nazi am I?
You're not allowed to bring up Goodwin's Law. :)
We have always been at war with Eurasia!
When I read articles about biology, especially molecular biology/genetics, I see lots of interesting "facts" about the field given by various members of the slashdot crowd. I'm not a leader in the field, but I feel knowledgeable enough working in the field to know just how wrong these "facts" are, yet get modded insightful.
What scares me are all the articles about topics that I'm not an expert in, where I can't judge the veracity of comments. I've realized that if you guys are so terribly wrong here, that you're probably not believeable anywhere else, either.
Not that this news to anyone. It just depresses me everytime I see this type of story come up.
*sigh*
I'm guessing it's the flood with the Noah's ark etc.
Isn't that similar to the ID argument? How the hell can we use science to deduce if a external being has changed the laws of our universe and is able to manipulate time at will? I was just pointing out that it doesn't matter if we could scientifically deduce how rainbows could have been created by god, because we first have to make a faith-based assumption that god did create rainbows.
Wheels within wheels, code within code. How much more intricate can it get?
Jedis are stupid. If they were so powerful, why couldn't they handle counseling for a kid who missed his mom?
Well, clearly I should go reread my college textbooks...
But I thought that tRNA and mtRNA, while certainly coiled into an enzyme-like shape, were not double-stranded so much as held together by short runs of complimentary sequences. I know, that's splitting hairs, but my understanding was that 80% or so of the structure was held together by 20% or so of complimentary runs, and that's not going to be very useful for proofreading.
Now, viral dsRNA is entirely new to me. Do you know if there's any evidence of proofreading enzymes that can work with it? It'd be an interesting tactic to use the host cell polymerases to fix your RNA.
I also seem to remember that the proofreading enzymes rely on methylation of the ribose/phospates to decide which strand to trust for mismatches (aside from obvious errors like thymine dimers and uracils.) Would this hold with RNA? Are there RNA phosphorylases to even provide this functionality? I'm in areas I don't remember well enough.
Nostalgia's not what it used to be.
I actually did a short research rotation in Jon Widom's lab at the beginning of grad school, 3 years ago. If anyone has any more specific questions regarding the implications of this work, let me know and I'll post something useful.
I'm not a biologist, and as much as I'm interested in this kind of thing I don't have the time, inclination or background to keep up with such old, old stories.
./ may have been hoodwinked by it, but I don't really mind - one of the great things about /. is that when you get an article like this, folks who actually *do* know what they're talking about will chime in with links to better info, better commentary, explanations of their own... which means that I get to vaguely edumacate myself over lunch.
Sure, it's a hot headline &
It's not like it's another "Google releases x beta" story - it's a starting point for discussion. Just my £0.018
I am a Molecular Biology major. Biologists have known about histones (that's what they are called) for years now. I don't see how the NYtimes can play this up as something new.
Error control mechanisms, at the very least, would very much run against the flow of blind Darwinian processes.
Error control mechanisms, which have been known for many years to exist, in no way run counter to expectations from Darwinian theory. In the short term, error correction improves fitness, because any given mutation is more likely to be deleterious than beneficial. In the long-run, however, too much error correction would be bad for the species, because the ability to evolve is required to adapt to changing conditions, and evolution depends upon a pool of variation, derived from those mutations that have not turned out to be particularly deleterious. Evolution has no foresight, so in most situations it is unable to produce change "for the good of the species," so one might worry that species might error correct themselves out of the evolution business. However, there is a short-term disadvantage to error correction--it costs metabolic energy that might offer a greater yield in fitness if used for other purposes. So selection supports the evolution of "just enough" error correction, where the fitness benefit in terms of reduced deleterious mutations just balances the fitness cost in terms of poorer energy "mileage."
I am DEFINITELY on the wrong planet...
Previously: "Linux... Toward the Sunrise..." Now: "Linux... Toward the-- No, now, part of Every Sunrise"
Did anyone else think this was a perfect summary of TFA?
Don't believe the nonsense, unless you hear it from me directly.
And you trust ancient peoples who didn't even realize that the world was not flat to determine that the entire planet was flooded?
Oh, say does that Star-Spangled Banner entwine / The myrtle of Venus with Bacchus's vine?
> Just because something might be explicable, doesn't preclude it being of divine origin.
And that's precisely the problem with supernatural "explanations".
I dropped my pen and gravity drew it down to the floor, accelerating it along the way. No, wait - pixies pulled it down, and the acceleration was the result of more pixies joining in as it fell.
When you start invoking supernatural "explanations", evidence becomes irrelevant, and one claim is just as good as any other. Any other.
Sheesh, evil *and* a jerk. -- Jade
I think the moderator failed to learn PHP during an introduction programming class. Such incidents usually leads to a life of bitterness for falling so short on something so easy to learn. Not everyone has the ability to re-program their DNA with PHP.
> Yes, this discovery does not hurt the ID movement at all.
No discovery will ever hurt the ID movement, because it's based on bullshit rather than evidence.
Sheesh, evil *and* a jerk. -- Jade
To add to what you said, I read an article in Scientific American a few years ago (The Hidden Genetic Program of Complex Organisms, John S. Mattick, Scientific American, October 2004, p62).
It seems that the "junk DNA" may actually code for RNA molecules that perform a bunch of regulatory functions. Removing some of this "junk DNA" seems to have ill effects on some organisms.
There's also more here.
Vivin Suresh Paliath
http://vivin.net
I like
My first thought was "oh my $DEITY, they *ACTUALLY* found it". But thun again, of course I've been reading too much sci-fi. It's just that this one story ....... well, here it is:
t ml
"We'll Return, After This Message" by John Walker, December 1st, 1989
http://www.fourmilab.ch/documents/sftriple/gpic.h
"Good news, everyone!"
Whilst (mature) red blood corpuscles don't have nuclei, I was under the impression that white blood cells are genuine cells, and do have nucleii.
Looks like all that time they took to map the human genome could be a waste of time. They may have to do it all over again.
Nature wouldn't evolve as system as wasterful as 2-3% useful DNA (0.1% in some amoebas). The other stuff is doing something, either rarely used or relatively transient.
Also Wik.
"I'm just here to regulate funkiness."
No. It is about entropy, not information. They are different categories.
Except for ending slavery, the Nazis, communism, & securing American independence, war has never solved anything.
Let me correct your correction then. Once the sperm enters the Oocyte it is then considered a cell. It's after this point that the mitochondria introduced by the sperm is destroyed. Clearly it wouldn't have happened before because the mitochondria wasn't in the Oocyte. The embryo is the egg cell I speak off, not the precursory elements of it.
You are checking your backups, aren't you?
it [the ID movement] has precisely nothing to do with science...
That is true IFF you take science==evolution.
Unfortunately no other theories on species origins can every be considered scientific by that definition.
For proper objective science that actually looks at evidence without prejudice, ID is significantly more scientific than evolution.
"Nine times out of ten, starting a fire is not the best way to solve the problem." - my wife
faith: the capacity to believe what you know isn't true.
Oh, say does that Star-Spangled Banner entwine / The myrtle of Venus with Bacchus's vine?
Except that the amino acid code existed in Bacteria long before the Eukarya and Archaea, and Bacteria don't have histones, the core feature of nucleosomes. There may be another code that explains the redudancy, but it's probably not a nucleosome code.
"I'm so moist I'm sticking to the leather." -Kermit the Frog on The Late Late Show
I find your ideas intriguing and wish to subscribe to your religion. Please present more evidence for intelligent design than there is for evolution and I'll begin throwing away my money to your church immediately.