The Gene Is Having an Identity Crisis

gollum123 writes "New large-scale studies of DNA are causing a rethinking of the very nature of genes. A typical gene is no longer conceived of as a single chunk of DNA encoding a single protein. It turns out, for example, that several different proteins may be produced from a single stretch of DNA. Most of the molecules produced from DNA may not even be proteins, but rather RNA. The familiar double helix of DNA no longer has a monopoly on heredity: other molecules clinging to DNA can produce striking differences between two organisms with the same genes — and those molecules can be inherited along with DNA. Scientists have been working on exploring the 98% of the genome not identified as the protein-coding region. One of the biggest of these projects is an effort called the Encyclopedia of DNA Elements, or 'Encode.' And its analysis of only 1% of the genome reveals the genome to be full of genes that are deeply weird, at least by the traditional standard of what a gene is supposed to be and do. The Encode team estimates that the average protein-coding region produces 5.7 different transcripts. Different kinds of cells appear to produce different transcripts from the same gene. And it gets even weirder. Our DNA is studded with millions of proteins and other molecules, which determine which genes can produce transcripts and which cannot. New cells inherit those molecules along with DNA. In other words, heredity can flow through a second channel."

Comments

Memory RNA

[CRCulver]

A thread on DNA and its relationship to RNA gives me a chance to ask: what ever happened to the idea that memory was encoded in RNA? In 1970s science fiction novels like Niven's A World out ot Time , you had people learning new skills through the injection of RNA. When did it become clear that RNA had nothing to do with memory?

Re:Memory RNA

[Ethanol-fueled]

The answer lies in the RTFW (Read The F'in Wikipedia) article about Memory RNA:

One experiment that was purported to show a chemical basis for memory involved training planaria to solve an extremely simple "maze", then grinding them up and feeding them to untrained planaria to see if they would be able to learn more quickly. The experiment seemed to show such an effect, but it was later determined that the original planaria had left chemical tracks inside the maze itself that were not properly cleaned away before the next set of planaria were run.

It's not a complete explanation, but it implies that pathfinding behavior(e.g. getting out of a maze) had much more to do with following a chemical "bread crumb" trail than using memory alone.

Re:Memory RNA

[thepotoo]

Well, I've not learned about RNA holding memory in any of my classes, and even Wikipedia has little to say on the subject.

I'd venture a guess that it's not correct (simply not enough evidence supporting it, but that has not yet been ruled out either.

The bottom line is that we do not yet fully understand memory, in much the same way that we do not fully understand synapse formation in the brain. We should just wait and see before jumping to any conclusions (and maybe write a grant proposal or two along the way).

Re:Memory RNA

[SlashThat]

Well, it might sound like a cool idea, but this just wouldn't work. This kind of "memory" would be to slow to be useful, since it would involve long biological processes to decode the RNA (or DNA). It would be like storing a program's memory page on an external floppy disk.

Re:Memory RNA

[Atmchicago]

A very simple answer is that RNA degrades *extremely* rapidly. Injecting RNA could feasibly give a short change in phenotype, but it is hard to imagine that RNA would be able to encode something as long-lasting as memory.

Re:Memory RNA

[joe_bruin]

RNA is a copy of DNA created by an enzyme called RNA Polymerase. All RNA Polymerase does is a simple copy. There is no mechanism for creating "new" RNA that contains data that is not already present in your genes. That is, your body does not contain any device that can write memory information to RNA strands.

Re:Memory RNA

[postbigbang]

More interesting still was his machine that took cell detritus and 'instant elsewhere'd' it to an adjoining chamber. The idea being to flush the junk from cells and cause a fountain of rejuvenation. FTA, it might be one day feasible to ride a cell of bad or junk RNA.

Re:Memory RNA

[ElBeano]

But... it only has to be decoded once, then stored in RAM.

Re:Memory RNA

[CODiNE]

Any new findings on instinct?

Re:Memory RNA

[rnaiguy]

Sorry, not true. There ARE mechanisms for creating new RNA not encoded in the DNA. Enzymes can shuffle around RNA sequence (as in RNA splicing), or change single nucleotides. Interestingly, the base changes occur most often in the nervous system of mammals. However, as mentioned, RNA doesn't stick around long enough to be responsible for memory. http://en.wikipedia.org/wiki/Rna_editing

Re:Memory RNA

[2nd Post!]

Can you define instinct so we can talk intelligently about it?

Re:Memory RNA

[Ollabelle]

Perhaps, but maybe that's where innate fear of certain predators originates.

Re:Memory RNA

[Anonymous Coward]

There is no mechanism for creating "new" RNA that contains data that is not already present in your genes. That is, your body does not contain any device that can write memory information to RNA strands.

That is not entirely true. Consider alternative splicing (can re-arrange or selectively express protein domains), trans-splicing (combining pieces of separate genes), and RNA editing (selective mutation of RNA independent of DNA).

Not to mention the case of C elegans, where small interfering RNAs can be stably expressed and even inherited (supposedly a defense against dsRNA viruses).

Re:Memory RNA

[lgw]

Stimulus-response patterns that are inherited, not learned. Some might exclude mere reflexes (patterns where the stimulus creates the response before/without brain activity) but I'm not sure that modifies the definition in a helpful way.

It's really an interesting question. Seeming complex behavior patterns are clearly not learned, but present in each generation - where do they come from? This would seem to be software, not hardware, but where and how it it stored/passed on?

Re:Memory RNA

[shawb]

I think what you are referring to is more closely related to instinct than memory. Instinct is related to sets of behaviors that are performed naturally, learned. These are to some extent controlled by genes, but can be overridden by learning. I.E. genes will encode for certain basic neural pathways to be formed, but the brain's development will then be left to augment or diminish that pathway's strength.

Memory is an entirely different system, in which patterns simulating previous stimuli are stored and available to be replayed or compared against. Calling the effect of instinct "ancestral memory" or "genetic memory" is at best a poetic interpretation, at worst a logical flaw similar to Lamarkian Evolution wherein giraffes have long necks because their ancestors stretched out trying to graze from tall shrubs, then trees, rather than the Darwinian idea that giraffes have long necks because short necked giraffes did not live to reproduce as well as long necked ones.

Re:Memory RNA

[popmaker]

In other words: "No conclusion"? It HASN'T been ruled out? The way I understand it is that a large part of evolutionary theory ASSUMES that memory can't be inherited.

Re:Memory RNA

[timeOday]

That's biology for you - everything that can happen does happen and every seemingly elegant mechanism turns out to be an incomplete story. Life on earth is a total mess and badly overdue for extensive refactoring :)

Re:Memory RNA

[2nd Post!]

Raising both a two year old and a seven month old, there appears to be precious little instinct. Maybe dancing to music.

Re:Memory RNA

[Anonymous Coward]

Well, never say never :)

Here's a twisted train of thought:

1) There are enzymes called "de novo DNA methyltransferases" whose job it is to (usually) stud DNA with CH3 groups at locations known as CpG islands. Methylating a CpG island typically stops or severely hinders the transcription of a coding region associated with it.

2) There are also cousins to these enzymes called "maintenance DNA methyltransferases" whose job it is to make sure that methylated DNA bases stay methylated. This becomes an issue during any sort of nuclear division, where DNA is copied in preparation and newly synthesized DNA lacks the methylation pattern of its parent strand.

3) Thanks to effects like alternative splicing, a "coding region" need not necessarily be an entire "gene". In fact, it's very possible to affect only certain coding regions (exons) of a gene, so that the final RNA product is wildly different than what one would expect from the whole gene's transcription.

4) ???

5) Profit!

So imagine a scenario where some external stimulus (say, the storage of a memory?) entices de novo DNA methyltransferase to start adding CH3 groups at particular locations and disabling certain coding regions. This changes the ultimate mRNA structure, which in turn changes the protein product. But what's more interesting is that during cell division, these methylation patterns get passed on to daughter cells. Or, to gamete cells...that end up making your daughter. Suddenly she's subject to the effects of a methylation pattern caused by YOUR experience.

Now, likelihood of this happening? Highly improbable that storage of a memory would somehow signal the cells involved in the production of your gametes to go on a methylating spree. Still, the point is that the mechanism DOES exist, even if it's not used in that way. The data stored in RNA is not at all solely governed by the sequence of bases in your DNA.

Re:Memory RNA

[Anonymous Coward]

That is, your body does not contain any device that can write memory information to RNA strands.

Hmm ... a good argument, but I don't think it's quite complete. For example - there are enzymes in cells that break RNA down into its component nucleotides. Some scraps of RNA (eg, with a G' cap) take longer to be broken down than others. Perhaps some enzymes, themselves regulated by other processes, can preferentially break down particular RNA sequences? Then information can be stored, not in the RNA sequences themselves, but in the relative concentrations of particular preexisting sequences.

Of course, this is pure speculation - I don't know of any research that actually implicates RNA as a mental memory mechanism.

Re:Memory RNA

[Anonymous Coward]

In 1970s science fiction novels

There's your answer.

Re:Memory RNA

[ShakaUVM]

>>The way I understand it is that a large part of evolutionary theory ASSUMES that memory can't be inherited.

Maybe not memory per se, but certain phenomena have demonstrated Lamarckian style inheritance.

Mm, DNA can be methylated, which modifies its behavior. A fat pregnant mother will methylate the genes in the fetus, resulting in a kid much more genetically prone to being fat. Experiments with dutch prisoners of war during WWII showed that even when raised under similar conditions, kids from mothers who ate more when they were pregnant were much more prone to obesity.

There's also effects like http://en.wikipedia.org/wiki/Genomic_imprinting which modify an offspring's genome on the fly between generation and generation.

Re:Memory RNA

[TheLink]

Yeah, I found it strange so many people were so confident that Lamarckian style inheritance does not happen.

Yes the naive Lamarckian stuff doesn't happen. But to me it seems rather advantageous for a species that some sort of Lamarckian style inheritance could occur at least in some circumstances - randomized a bit so that there's just a "higher chance". You don't want to "guarantee" changes are passed down since the environment might change in the future, so randomizing it a bit across the offspring will be better.

Re:Memory RNA

[Fumus]

One experiment that was purported to show a chemical basis for memory involved training planaria to solve an extremely simple "maze", then grinding them up and feeding them to untrained planaria to see if they would be able to learn more quickly.

This reminds me of VG Cats.
So wrong..

Re:Memory RNA

[FriendlyLurker]

Also Lamarckian style, or at least very flexible in the short term inheritance
http://www.nature.com/ejhg/journal/v14/n2/full/5201567a.html

http://en.wikipedia.org/wiki/Epigenetics

Re:Memory RNA

[aadvancedGIR]

Some time ago, I read about a good experiment (perhaps the only good one) about rat pathfinding learning.

Basically, rat showed pathfinding abilities, so the reserchers tried to determine what information they used, so they gradually modified their maze to remove any external clue they could think of (odors, lighting, even vibrations) and do the experiment over and over, until the rats had no clue left to differentiate the various parts of the maze and couldn't learn the path anymore, demonstrating that they couldn't learn the path without memorizing hints.

Re:Memory RNA

[ByOhTek]

not necessarily true - there are forms of RNA that are more stable than DNA (I believe tRNA and maybe rRNA fall in to that category). And there are forms that are non-stable (mRNA if I remember my acronyms correctly).

Re:Memory RNA

[ErroneousBee]

A baby will pull back from a painful stimulus and show agitation. They also grab at hair, and cry when hungry.

I think if you drop one, their arms automatically go out, as if to catch on branches and break a fall.

Also, sneezing and closing of eyes.

Re:Memory RNA

[2nd Post!]

You call those instincts?

Pulling back from painful stimulus is probably hardwired (if you want to call it an instinct) because any creature who lack this "instinct" get killed/burned/maimed. So there is probably a portion of the brain stem responsible for this. You never lose this instinct.

Grabbing at hair is hardly an instinct. At least with my children, it was grabbing EVERYTHING. It was more likely a need to explore their surroundings and hair happens to be close by when someone is holding them.

Crying when hungry is also hardwired, I suspect. You see it in all animals, because if you never tell your parental unit you are hungry, you starve and fail to develop. In any case, this again is probably part of the brainstem. You lose this instinct pretty early.

Arms going out is something my son does, but my daughter lost this instinct very early. More likely it was a learned unlearning as she can now catch herself and prevent herself from falling. This is probably also hardwired, it is essentially a reflex, like blinking and ducking.

Sneezing while closing of eyes does not sound like instinct, it sounds like reflex.

Re:Memory RNA

[Raffaello]

Reflexes happen outside the brain proper. Instincts involve the brain (not merely a reflex arc between the peripheral nervous system and the spinal cord).

This being the distinction, any unlearned, inherited fixed response to stimulus that is mediated by the brain (not merely a reflex arc) is an instinct.

The wikipedia article on instinct gives the following (among others) as human instincts:

face recognition and perception,
disgust at noxious stimuli,
language acquisition,
so called "fight or flight" response,
sex drive,
aggression,
and others.

There is some purely definitional disagreement as to whether an unlearned inherited behavior can be called an instinct if it can be overridden by higher (i.e., cortical) brain processes, but this is just quibbling over terms, since even supposedly "lower" animals can be trained to override some instincts.

Human beings have much more powerful abilities to use cortical processes to override lower brain impulses and we are therefore less bound by instinct than other species. This does not mean that we don't have instincts, but rather that we are much more accomplished at suppressing them with cortical processing.

Re:Memory RNA

[zzsmirkzz]

at worst a logical flaw similar to Lamarkian Evolution [wikipedia.org] wherein giraffes have long necks because their ancestors stretched out trying to graze from tall shrubs, then trees, rather than the Darwinian idea that giraffes have long necks because short necked giraffes did not live to reproduce as well as long necked ones.

Those options do not seem mutually-exclusive to me. In fact, one would have to postulate that they both happened.

For those to tired to think, Darwin's theory only suggests why which of the two types of giraffes survived and still exist while the Lamarkian theory suggests why some giraffes were born with long necks.

Re:Memory RNA

[orclevegam]

They're stored in DNA, but they aren't "memory". Think of it as a bit like a base install. When we first form we have a simple pre-wired brain, that portion is encoded in our DNA, and it's these pre-wired synapses which are responsible for these basic instincts. During a persons lifetime some of these pre-wired synapses may be modified, enhanced, or even removed, but those changes will not be passed on as they aren't encoded in the DNA. How these pre-wired synapses came about is the same as how all genetic features came about, they were a mutation that conferred a advantage. The mammal that was born with the basic wiring to run from predators is more prone to survival than the one who has to learn that the hard way. These relatively simple low level instincts are simple to pre-wire as everything they interact with is already encoded. More advanced responses can not be encoded in DNA (at least not easily) because they rely on synapses structures that must be formed through learning, and are individualistic. Instincts can only work with what's already formed at birth, so things like recognizing a name, or the solution to a particular problem are impossible to code, without first encoding knowledge of that name or problem, which is highly unlikely to occur as doing so confers no evolutionary advantage.

Re:Memory RNA

[cpricejones]

This is partly incorrect. There are mechanisms for changing the RNA after RNA polymerase does its job, which is to simply copy. There are RNA-editing enzymes that edit your RNA after it has been transcribed, yielding mRNAs, tRNA, and other products that are not entirely from the data present in your DNA. In many cases, the editing can greatly affect the function of the RNA. In the case of one mitochondrial tRNA, editing the tRNA is essential for the RNA to correctly fold.

Re:Memory RNA

[dollargonzo]

Dawkins talks about this kind of supposed "Lamarckism" in "The Extended Phenotype." In many of these studies, the genome/replicating unit is in fact modified, which affects reproduction and heredity. Acquired characteristics of the replicating entity are passed on, *not* acquired characteristics of the organism, and that is fundamentally Darwinian. Some will argue that this isn't a valid difference, but consider things like myotic drive, cross-over etc. These are all modifications of the replicating entity, and in some sense are "acquired," because they depend on the embryological context. To be truly Lamarckian, characteristics *not* affecting the genome would have to have some heredity, which they don't.

Re:Memory RNA

[2nd Post!]

No disagreement from me, but I suspect this doesn't satisfy the original poster wanting to argue that instincts are poorly understood. Everything in the wiki article seems to have a strong evolutionary survival benefit, which means they would have been selected for without any "learning" necessary.

Re:Memory RNA

[Zerth]

It isn't so much Lamarackian as "Swiss-Army-Knife"ian or "Switch/Case"ian. The genetics are already present, but are only expressed in the appropriate environment, allowing you to carry genes that aren't always advantageous.

If I were a troll, I'd bring up something about certain groups and their thoughts on the why "fitness" would prevent the development of incomplete features.

Re:Memory RNA

[lgw]

But still, how do you inherit software? Reflexes may be "hardwired", but stimulus-response in the brain doesn't seem to be. Humans are *really* good at facial recognition - it's hard to imagine that this is the result of some physical pattern of neuron connections encoded in DNA. There certainly seems to be *software* at work here and in some other instincts - human and animal. How does tha software get installed, when these aren't learned behaviors.

A cat is born knowing how to stalk and pounce, but must be taught that a mouse is food. It's very strange, and it's hard to see how DNA would encode "how to stalk and pounce".

Re:Memory RNA

[ShakaUVM]

>>To be truly Lamarckian, characteristics *not* affecting the genome would have to have some heredity, which they don't.

Well, that's why I didn't call it truly Lamarckian, but Lamarckian-style. Call it Lamarckian-esque, if it makes you feel better. =)

Naive Darwinism says that you have these sorts of competitions for genes, and the conditions the parents go through don't really matter except 1) Mutations (that make it to the gametes) and 2) If they can successfully produce offspring.

On the contrary, there's a lot of interesting phenomena which show the parents' environmental conditions affecting the offspring.

Re:Memory RNA

[orclevegam]

It's because it's not really "software", it's more like a von neuman machine, it self modifies over its lifetime. Simply put, our DNA encodes a rudimentary brain with various stimulus-response pairs. Some of these may seem complex, such as a cat stalking and pouncing, but they're really just several complimentary and interlocking stimulus response pairs that combine in a favorable fashion. This can be demonstrated by the way in which cats will follow any fast moving object that crosses their vision, regardless of whether it's "food" or not. Once they engage the higher order learned responses and evaluate whether what they're following is food or not they may lose interest, but the behavior to track the item is pre-wired.

Imagine if you will, a plan for a machine that assembles a copy of itself based on a plan. Now further imagine that while the machine is running it can swap out and modify pieces of itself, but those modifications don't change the plan it has. This is essentially the relationship between the brain and DNA. The DNA encodes the starting condition of the brain, but once it reaches that starting condition it then proceeds to self modify itself. Those modifications do not get passed on through the DNA, but the initial starting condition does. Mutations to that starting condition, lets say a fear response to darkness, might confer a survival advantage and are likely to be passed on to further generations.

Re:Memory RNA

[shawb]

Way off target. Lamarckian Theory postulates that it is the physical stretching of the parent giraffe's neck that leads to offspring with longer necks. Darwinian evolution by natural selection plays with the random variance that exists in any population due to statistical chance. The key that allows Darwinian Natural Selection to push a given trait towards a trait more adapted for the environment is that the selective pressure itself is non-random, even if the natural variation within the population is itself random.

Re:Memory RNA

[dollargonzo]

Here's why I have an issue with talking about the environment of the parent as opposed to environment of the gene, which is what I think really matters. Consider a gene that causes an organism to be exposed to more radiation than its alleles (e.g. a small organism crawling around radio-active dumps seeking pockets of heat/moisture/whatever). This will likely cause faster mutation rates, which in turn is beneficial for smaller genes (since larger ones are less likely to have high copying fidelity in such an environment), causing them to become more frequent. I don't think that talking about these types of situations in terms of the organism's environment is remotely meaningful. So no, I don't think there is anything Lamarckian about it.

Re:Memory RNA

[Anonymous Coward]

In land vertebrates at least...

Methylating sperm DNA is plausible, sure, but having that sperm contribute to viable offspring is not really plausible.

Methylating egg DNA is implausible because of the timing of oogonium formation.

Also, even assuming that a zygote is produced with methylated DNA. How do you propose to have the methylation expressed in the downstream somatic cells?

Spermatozoa are not exactly capacious with respect to heritable material outside the haploid DNA.

So, what we REALLY need is . . .

[StefanJ]

. . . A Human Genome Interpreter Project.

Re:So, what we REALLY need is . . .

[Anonymous Coward]

The Parrot folks hope that Perl, Python and human DNA will compile to the same bytecode.

Re:So, what we REALLY need is . . .

[jd]

Yes, but Deep Thought says Earth will take some time to figure it out.

Re:So, what we REALLY need is . . .

[Yvan256]

How long does it take to compute 42?

Oh wait, we already have 42. What was the question again?

Re:So, what we REALLY need is . . .

[jd]

How many genes must a geneticist wear out before we call it a gene?

Re:So, what we REALLY need is . . .

[evilbessie]

I like that they were allowed to call 98% of their results junk without having much understanding of the other 2%.

Re:So, what we REALLY need is . . .

[rubycodez]

I thought we had those, and called them "mom"

Re:So, what we REALLY need is . . .

[ScrewMaster]

What was the question again?

"What do you get when you multiply 9 times 5."

Re:So, what we REALLY need is . . .

[jd]

If I could have gotten away with calling 98% of my exams "junk", not understood the remaining 2% of the questions, and passed with grades so good that people would give me the kind of cash genetics labs are getting, I'd have retired at age 30 to my own island.

Re:So, what we REALLY need is . . .

[Tolkien]

How many genes must a geneticist wear out before we call it a gene?

The answer my friend,
is bubbling in a lab.

The answer is bubbling in a lab.

Re:So, what we REALLY need is . . .

[Anonymous Coward]

Wait, that doesn't sound right... does it?

Re:So, what we REALLY need is . . .

[againjj]

Actually, it's "What do you get if you multiply six by nine?"

Six by nine. Forty two.

That's it. That's all there is.

I always thought something was fundamentally wrong with the universe.

Re:So, what we REALLY need is . . .

[Marillion]

Yes we do.

In computers have a static runtime (the CPU) and you change the instructions to get different results.

In biology, the instructions (DNA) are mostly static, but the runtime (cell cycle regulation and other pathways) changes to get different results.

Re:So, what we REALLY need is . . .

[ScrewMaster]

Yes, well, it's been a long time since I read the book. Or saw the movie.

I Knew It

[Nyall]

Not only does God code in machine language, but it is all spaghetti. Thats probably why eventually malfunction and die.

Re:I Knew It

[Anonymous Coward]

Well, yeah. Some of the best evidence that christian or muslim creationists are full of shit is that, well, god's "designs" *suck*. An omniscient, omnipotent, benevolent god should be less of a freaking moron. About the only religion in that general abrahamic family that made a slight bit of sense there was gnostic christianity - the mad, retarded but nigh-on all-powerful demiurge Samael spewed out the sucky material world.

Re:I Knew It

[Pichu0102]

Thats probably why eventually malfunction and die.

Some faster than others, apparently.

Re:I Knew It

[Bryansix]

Fallen Man Much?

Re:I Knew It

[Yvan256]

You have it backwards. God doesn't code in spaghetti machine language. The FSM itself coded God.

Re:I Knew It

[Anonymous Coward]

Reality much?

Re:I Knew It

[Anonymous Coward]

I have tomato in my harddrive

Re:I Knew It

[Anonymous Coward]

Can't be spaghetti - Collins' book say "God's language is DNA and mathematics". The question is the intrinsic mathematics of Genome Informatics. By now, gene has long become "FractoGene"; one part here, another a chromosome away... Type "Pellionisz" into your YouTube field for a Google Tech Talk on fractal mathematics of the web AND the genome.

Pellionisz_at_junkdna.com

Re:I Knew It

[Anonymous Coward]

I know! You'd have to be some kind of a Perl hacker to suggest we're intelligently designed.

Re:I Knew It

[Repton]

Well, what do you expect when you knock off a major project in under a week?

Re:I Knew It

[Nyall]

ha, just got that.

Re:I Knew It

[speedingant]

Oh no!!! You angered the flying spaghetti monster!! RUN FOR YOUR LIVES!!!!!!!

Re:I Knew It

[Anonymous Coward]

Look, I made God and I killed God end of story.

-FSM

Re:I Knew It

[Anonymous Coward]

I've read the Bible cover to cover. That's actually pretty much WHY I'm an atheist. Have you read that it? It's retarded. Seriously. It was obviously written by a bunch of primitive hicks millenia ago. It's just superstition.

Re:I Knew It

[servognome]

Death is a feature... please consult your owners manual or contact customer service for more information - God

Re:I Knew It

[jamesh]

I bet that obscure comments in God's code would put Larry Wall to shame too :) /* FIXME: Is free will a good idea? Review after beta testing... */

Re:I Knew It

[ScrewMaster]

Well, yeah. Some of the best evidence that christian or muslim creationists are full of shit is that, well, god's "designs" *suck*.

True, you'd think He would be a better engineer. Of course, if you make that point, they'll just tell you that God's will is not obvious. Furthermore, they'll tell you that we must be better designed than we appear, because otherwise we could not have been made in God's image. Ha ... tell that to all the people who died before their time because of the quality engineering that went into their bodies. If God is a Lamborghini then people are Yugos.

I have friends who tell me they can see signs of the Creator in all manner of living things. Oddly, I find myself unable to perceive these subtleties (they just look like camouflage markings and so forth to me.) They look at me sadly when I say, "Sorry, I'm just not getting it."

Oh well.

Re:I Knew It

[ScrewMaster]

Thats probably why eventually malfunction and die.

Some faster than others, apparently.

I guess we live in the Age of the Killer Typo.

Re:I Knew It

[Anonymous Coward]

You have it backwards. God doesn't code in spaghetti machine language. The FSM itself coded God.

Great. Now that you let the secret out about how the Flying Spaghetti Monster was a Finite State Machine, the cellular automata people will come crawling out of the woodwork.

Re:I Knew It

[ScrewMaster]

But hey, don't let the tenets of MY PERSONAL FAITH get in the way of your petty jokes....

That's not the issue. The question is why should your personal faith (or lack of it) have anything whatsoever to do with what anyone else says or does? As you say, that's your personal business. It is not ours, and we are under no obligation to avoid offending you, especially when you can so easily avoid being offended.

And from a practical standpoint (as someone who has been a regular reader/poster on this site for years) you'd best learn to grow a thicker skin. Or find a tamer forum. Nobody here cares what either of us think, and there will always be someone ready to poke holes in someone else's belief system. That's what I enjoy about Slashdot: sometimes (not often, but sometimes) I'm made to think outside my usual round. That's not necessarily easy, but it's always entertaining, and I walk away a better person for it.

Re:I Knew It

[ScrewMaster]

I've read the Bible cover to cover. That's actually pretty much WHY I'm an atheist. Have you read that it? It's retarded. Seriously. It was obviously written by a bunch of primitive hicks millenia ago. It's just superstition.

I read it a long time ago, and didn't manage to read it cover to cover. I figured I should try to understand what all the fuss was about, since I wasn't raised in any religion.

Some of my more pious friends occasionally attempt to explain to me where my thinking has gone wrong. So far, the've not met with much success. Neither have I, for that matter: they can't figure me out, and I can't figure them out either.

Re:I Knew It

[ScrewMaster]

I bet that obscure comments in God's code would put Larry Wall to shame too :) /* FIXME: Is free will a good idea? Review after beta testing... */

There was a comic strip I read years ago that had God in a kitchen, in the process of removing Planet Earth from the oven. He was saying, "Hm. Something tells me this thing is half-baked."

Re:I Knew It

[darkvizier]

Hahahahaha.

-Nietzsche

Re:I Knew It

[BorgCopyeditor]

I thought it was the MCP.

Re:I Knew It

[Nyall]

From the farside gallery

Re:I Knew It

[Mr. Slippery]

But hey, don't let the tenets of MY PERSONAL FAITH get in the way of your petty jokes....

Well, my personal faith says, "Fuck 'em if they can't take a joke." So, yeah, I won't let the tenets your faith get in the way of my jokes. Priorities, man, priorities. I mean, have you ever even actually READ the Book of The SubGenius?

Re:I Knew It

[acheron12]

Sounds like a Far Side :)

Re:I Knew It

[Anonymous Coward]

My brains exploded as well thinking about the complexity...

Re:I Knew It

[Anonymous Coward]

I read it as "Fallen Man Munch". The new cereal. At stores, now...

Re:I Knew It

[Anonymous Coward]

Mind sharing it with us? I don't get it.

Re:I Knew It

[Anonymous Coward]

Sears appliances, a cute but annoying boozehound, and lots of cloying dramatics - at least that's what I remember from watching "Extreme Makeover: Home Edition" years ago.

Re:I Knew It

[Schadrach]

One of the four preachers at my place of employ has tried to "reach" me several times, but whenever I point out the gaping logical holes in whatever the point of the moment is, his answer is that the Bible has to be "spiritually received" rather than understood. Which then leads to the situation you mentioned where "they can't figure me out, and I can't figure them out either". It's like we're talking past each other.

Re:I Knew It

[Raffaello]

If you meet the FSM on the road...

kill him!

sincerely,

the Buddha

Re:I Knew It

[Nyall]

I accidentally left out a word. 'why eventually' should have been "why we eventually". By leaving out this word I 'malfunctioned'

Re:I Knew It

[orclevegam]

I have friends who tell me they can see signs of the Creator in all manner of living things. Oddly, I find myself unable to perceive these subtleties (they just look like camouflage markings and so forth to me.) They look at me sadly when I say, "Sorry, I'm just not getting it."

You know what they say, "Ignorance is Bliss". They're just sad that you're not as blissful as them.

Re:I Knew It

[orclevegam]

It's like we're talking past each other.

That's because you are. You're attempting to apply logic and reason to the inherently illogical and unreasonable. Likewise he's attempting to convince you using logically flawed arguments that he adheres to not out of any careful study or reasoning, but because he was indoctrinated not to question those arguments. He willfully denies any arguments that are counter to his world outlook because to do otherwise would violate a large portion of his world view, something that everyone avoids, and many people are incapable of admitting.

Re:I Knew It

[CyBlue]

This is pretty clearly delineated in the Holy Bible (I can send you one if you like).

Yaaa! Free rolling papers! Anyone have suggestions for suitable passages? Maybe Psalm 23:4 or the one with the burning bush. yeah yeah.. offtopic

Re:I Knew It

[ScrewMaster]

One of the four preachers at my place of employ has tried to "reach" me several times, but whenever I point out the gaping logical holes in whatever the point of the moment is, his answer is that the Bible has to be "spiritually received" rather than understood. Which then leads to the situation you mentioned where "they can't figure me out, and I can't figure them out either". It's like we're talking past each other.

The source of the conflict is that "spiritually received" is considered semantically equivalent to "accepted as fact" to such people. Now, spiritualism is one thing (it can't be tested, can't be disproved, and can be accepted on those terms.) My disagreements come in when people simply point-blank deny what is. Not only that, but they do it in large groups, as if it's some kind of mass psychosis.

Remarkable really.

Surprise, surprise!

[Anonymous Coward]

This from the people who claimed that most of the DNA in our cells was just junk. I wonder why they were so bloody arrogant? Couldn't they just have acknowledged that they had no clue?

Re:Surprise, surprise!

[Yvan256]

Real scientists will know and acknowledge they don't know everything. The hacks think and try to convince you otherwise.

Re:Surprise, surprise!

[GigaHurtsMyRobot]

I wish humility, modesty, and reality crept into science more often. We don't have half a clue to be able to emphatically declare much at all. Just about every conclusion that is drawn should be followed by, ".. but we could totally be wrong, so don't bet your life on it or start a new diet fad or anything like that."

Re:Surprise, surprise!

[Cassius Corodes]

It has been known for a long time that junk DNA wasn't junk. However its one of those catchy memes that has persisted it the general public far longer then it was believed to be true.

Re:Surprise, surprise!

[Lemmy Caution]

There are plenty of very good scientists who actually are blindly arrogant, but still able to produce important work. And there are some modest people with a realistic understanding of the limitations of human kowledge who nonetheless have very little to contribute in terms of significant research.

Crick, for example, really believed that he had pretty much covered it all. He was arrogant beyond belief. Yet he is still a real scientist.

Re:Surprise, surprise!

[DragonWriter]

This from the people who claimed that most of the DNA in our cells was just junk.

Really, the same people? I think not. DNA that doesn't seem to get used in protein synthesis in the well-understood mechanisms as "junk" is, as I understand it, mostly an misperception of popularization, not something that has ever been the dominant understanding in the field.

Re:Surprise, surprise!

[thasmudyan]

Computer memory is actually a pretty good analogy for this: the "unused" DNA is not reachable by any "pointers" and thus wasn't important when eucaryote evolution began. Some of these areas are obviously non-coding ever-repeating nonsense sequences, others appear to be random information - exactly like unused RAM in a computer system. Of course, nothing in there is really random, it's just a product of whatever process happened to use the areas before.

Here's the catch, however. Just like a programmer who develops against an ancient API with a lot of well-known bugs and workarounds, some transcription mechanisms actually began to rely on the presence of the "useless" areas in order to work.

It's all a huge mess, the deeper you look, the less elegant it all becomes. For example, epigenetic mechanisms modify the meaning of DNA code depending on different contexts, as the article mentioned. But that's still not the whole picture. In order to create a protein, DNA is first transcribed into RNA, which then in turn gets executed in order to assemble the protein. However, the intermediate RNA information is modified beyond recognition before it is used. Then, after the protein is finally assembled, it too can be modified extensively. All of these steps are hopelessly interwoven, and they use zillions of chemical messenger signals in order to tweak an manipulate each other.

Genetics really is the worst spaghetti code project ever and I assume that more advanced (=complex) organisms really paint themselves into an evolutionary corner eventually, because the whole system - while beautifully specialized - is essentially becoming more and more difficult to alter meaningfully when radical change needs to happen.

Re:Surprise, surprise!

[evolvearth]

None of what was mentioned in the article is even new to biologists, or at least geneticists. This stuff is taught in a general genetics course, suggesting that this has been accepted for years prior.

"Junk DNA" probably hasn't been stated in any serious, meaningful way by genetics in decades, and probably was never meant to be taken seriously--especially since research in gene expression took off. Not to say that there aren't any junk DNA, there certainly are, but the media took something interesting and blew it out of proportion like they always do. The real clue was how some supposedly junk DNA was very conserved, and the fact that you'd think that a genome full of junk would eventually get smaller and smaller with time considering the amount of energy it takes to replicate and package such a load. To think that geneticists simply thought it was all useless junk flies in the face of logic.

Re:Surprise, surprise!

[Anonymous Coward]

Actually thats exactly one of the problems with catchy memes, they propogate misinformation when they're incorrect.

IE: Humans only use 10% of their brains!

I hate hearing that.

Re:Surprise, surprise!

[PitaBred]

Anyone who claims they do know everything about something is either lying or trying to sell you something.

I know this because I know everything about how people work.

Re:Surprise, surprise!

[PitaBred]

Global warming? Bueller? Bueller?

Re:Surprise, surprise!

[Cyberax]

Surprise!

We now know that most of junk DNA is STILL junk - it serves no direct purpose. That's about 60% of DNA. Of that 60% more than 45% consist of transposons.

Re:Surprise, surprise!

[Cassius Corodes]

It really depends on your definition of purpose: some of the junk is virus DNA that got incorporated that seems to have some purpose (retrotransposons), others are believed to have some regulatory function, while the rest could conceivably serve as constantly randomising raw material for new genes. There is also the possibility of self-replicating parts of the DNA (ie. the real selfish genes) that have no use for the body which would be the true junk DNA.

Re:Surprise, surprise!

[Cyberax]

Retrotransposons do not have a direct purpose. In fact, you'll quickly develop multiple cancers if retrotransposons are allowed to propagate. They ARE selfish DNA.

For example, 13% of human genome consists of repeating http://en.wikipedia.org/wiki/Alu_sequence which can cause multiple diseases.

It's speculated that junk DNA might be beneficial because it works as a buffer against mutation (unlikely) or as intra-genome source of additional mutations.

Re:Surprise, surprise!

[Retric]

The hacked nature of DNA is what let's things evolve quickly. Think of how well conjoined twins work. You can build a person with 4 limbs that are "useless" but still under control of a single brain. You can have 2 harts in the same body and blood still flows etc etc. All of this from minor mutations or defects in the gestation process.

EX: The arrangement of your blood vessel's are not designed at the lowest level. They self balance and repair so each cubic mm of your body gets all the nutrients it needs. Your bones work the same way with minor breaks being repaired so the overall structure just as strong as it needs to be while still being light.

What limits higher organisms is how well thing already work. We don't need 4 arms so a second set that does not really work is not helpful. etc.

Re:Surprise, surprise!

[Cassius Corodes]

Retrotransposons are very interesting from an evolutionary perspective as they have co-evolved with their host. No doubt some are harmful, but some have beneficial properties as well (co-operation is more stable then competition). I can't remember now where I have read the article on them but one example is mentioned here tho no details are provided http://www.pnas.org/content/98/25/14497.abstract

Re:Surprise, surprise!

[daeg]

Sometimes you have to ignore the bigger picture to make progress in the short term. Very few problems are solved trying to solve the macro picture without focus on the micro, IMO, and most macro problems are solved only after a shit-ton of micro problem solving. [Note: macro/micro doesn't refer to physical scale]

Re:Surprise, surprise!

[gregbot9000]

because the whole system - while beautifully specialized - is essentially becoming more and more difficult to alter meaningfully when radical change needs to happen.

I am so tired of people raging on the US government on slahdot!

Re:Surprise, surprise!

[eli pabst]

They do have a benefit in that they are believed to occasionally aid in the creation on the elements that control gene expression (promoter and enhancer elements) upstream of genes. So keeping them present does serve an evolutionarily beneficial purpose. However making the claim they *all* of the transposons and repetitive elements in the genome have a purpose is extending that to a point where it is a false statement.

Re:Surprise, surprise!

[lelio180]

Actually, most evolutionary biologists would argue that animals aren't written into an evolutionary corner. The gene regulatory networks that make up how we develop are highly conserved between us and other species. Our genome, in terms of development, is written in an object oriented manner. The pathways and genes involved in 'make back leg" or "make eye" are essentially exactly the same in us as it is in lizards or birds. There is a common developmental toolkit for all animals to use. You can change where you call each subroutine or make subtle alterations to it to change where you place a limb or exactly how it will look. By separating the 'house construction blueprints' or developmental genes from the 'interior decorating genes' or species specific genes, you dont get written into a corner evolutionarily

Re:Surprise, surprise!

[burris]

What limits higher organisms is how well thing already work. We don't need 4 arms so a second set that does not really work is not helpful. etc.

Everyone knows an extra arm does wonders for your ski-boxing.

Re:Surprise, surprise!

[c6gunner]

Think of how well conjoined twins work.

They don't. That's a horrible example. In nature, most such mutations die either during childbirth or shortly after. The fact that they can now survive for long periods of time isn't so much an example of the redundant nature of DNA as a testament to modern medical science.

Re:Surprise, surprise!

[operon]

One time I see a very good scientist saying that since they have low salaries (for the long years of study needed to take a PhD), low recognition (you are a nerd!) and low success with girls (you are a nerd!) the only thing left is to take pleasure with arrogance. (and irony, for sure).

Re:Surprise, surprise!

[Retric]

I would like to point out that for a wide rang of these cases the body works. Servival for an hour or two requires an amazing amount of the body's systems to work an complex balancing act. In nature there is little long term gain, but plenty of people have found fully grown frogs with extra legs ect. And there where plenty of "freak" shows in the early 1900's where people had an extra limb or where joined at the hip etc.

My point is while modern medicine let's us remove "extra" parts from people the human body is not a rigid design like a CPU where a tiny defect prevents it from working at all.

Re:Surprise, surprise!

[ByOhTek]

I found it interesting this artical was called 'news'. 'olds' might be more like it. This stuff was covered in my undergraduate Genetics classes in 03 and 04. Well, a good part of it was in a class for grads and undergrads, but still, it's no longer novel. As far as 'junk DNA', what's the definition of that? It's still probable (I've never heard it said as 'definitive', just 'likely', 'most likely' or 'probable'), that most (by a large factor) of the human genome IS "junk" DNA - that being DNA that doesn't code for anything, or belong to a promotor region. Considering propensities for provide structural purpose (cause DNA sections to be more likely to form tight packages, such as by forming around nuclear proteins), or epigenetic factors (methylation, etc), most of the genome would still be 'junk'. Also, the definition of gene should be properly defined here, and the difference between an [i]allele[/i], [i]gene[/i] and a [i]gene locus[/i]. [b]allele[/b]: One variant of a gene - different alleles can cause different phenotypes. [b]gene[/b]: Often used as a lazy shorthand for an allele (the gene for red hair - yes, I know this is actually a combination of alleles in different locations, simplified example) or gene locus (the hair color gene - yes, again I know there are multiple gene locations, simplified example). It can also be a set of alleles, which are in most cases mutually exclusive on a given chromosome/monoploid set. [b]gene locus[/b]: The location of a gene on the chromosome. Usually one location for any given gene, but it is possible for a gene to be found in more than one location, usually not both at the same time. If it is both locations at the same time, things get fuzzy...

Re:Surprise, surprise!

[flinnb]

Fantastic. So we're all going to become Windows over time? So:

• A stroke == blue screen
• Cancer == corrupt registry
• Lots of other bad analogies, I'm sure...

Too bad we can't always be rebooted effectively...

Re:Surprise, surprise!

[Muad'Dave]

I've always thought the same thing. To a lesser extent the 'dark matter' and 'dark energy' folks are guilty of the same sort of excess. They don't know what it is (if anything) but you'll hear statements like 'Dark matter is matter than doesn't generate or reflect light but interacts gravitationally". We have no idea if that's really the case. I'm one to always use more circumspect language - "There is an effect present that mimics a distribution of currently-unseen matter" or some such.

I agree wholeheartedly with this quip from the Wikipedia page on Dark Matter:

It has been noted that the names "dark matter" and "dark energy" serve mainly as expressions of human ignorance, much as the marking of early maps with "terra incognita."

Re:Surprise, surprise!

[Anonymous Coward]

"difficult to alter meaningfully when radical change needs to happen." -- Dinosaurs, anyone?

Interestingly, humans have ways to adapt themselves without relying on genomic evolution. It's called technology. If that doesn't work out, there's always the cockroaches to carry on..

Re:Surprise, surprise!

[Anonymous Coward]

The actual published papers generally DO cage things in those terms.

The journalists, text-book writers, and popular authors, however, usually edit all the hedging out in the name of clarity and conciseness.

(Sorry about the AC-- already used mod points up-thread)

Re:Surprise, surprise!

[benthurston27]

But with the brain this process came up with we'll be able to intelligently make changes to our dna and then we're out of the box.

Biology 101

[Anonymous Coward]

Apparently some of us haven't taken it. Its been known for a very long time exons, introns, methylation, etc. all play roles in expression of a protien. Congratulations for sitting through the second day of the class. Now lets continue the real news please.

I hate the New York Times

[Anonymous Coward]

I hate the New York Times with their obsession to make me register. I of course don't but it sucks to go to read a news article and then find their annoying sign-in page. And I don't really understand it because I'd assume they'd want me to go to their page but I guess they don't want it that much.

How is any of this new?

[repapetilto]

Epigenetics
RNA Splincing
siRNA

Re:How is any of this new?

[Anonymous Coward]

I was just thinking the same thing, I thought that epigenetics was quite well-established already. BTW, for anyone who's interested in a decent documentary about the subject should check out Nova's 'Ghost in your genes'.

Re:How is any of this new?

[repapetilto]

OK, well now that I actually read the article its a pretty good one. Anyway heres what is new (at least to me): "the Encode scientists estimate that a staggering 93 percent of the genome produces RNA transcripts"

Re:How is any of this new?

[visualight]

http://www.pbs.org/wgbh/nova/sciencenow/3411/02.html

I'm waiting longer before hitting submit.

Re:How is any of this new?

[repapetilto]

Nevermind they were just talking about transcription factor binding sites. None of this is new stuff.

Re:How is any of this new?

[Anonymous Coward]

Among many other things: pervasive trans-splicing and large scale transcription out of coding frame.
If that is not new and strange for you, you might want to sent a letter to nature.

Re:How is any of this new?

[TimFenn]

I find the article to be more of a review of past work than actual news. It covers several topics that anyone could read about by picking up a recent biology textbook (siRNA, the ribosome, alternative splicing, etc). I'm surprised this is on the front page of slashdot, while Nature dedicated almost an entire issue regarding the future of DNA technology, including the current state-of-the-art on personalized genomes. Now that is news for nerds.

Re:How is any of this new?

[keypox]

yeah and on top of that the genetics class i took a few years ago had all this "new" info lol. Also DNA never goes straight to protein. It goes DNA > RNA > protein... Also DNA is coiled to either turn it on or off. This is all old commonly known.

Re:How is any of this new?

[radtea]

Some of it is new, but none of it is surprising to anyone who has been paying attention for, I dunno, the past decade.

It's been clear since the mid-90's when we learned that there were only 44k "coding" genes but at least ten times that many proteins that more was going on than simple templating.

Things like methylation of double-stranded DNA have been known to be important in oncogenesis for at least ten years. miRNAs have been considered important for five years or more. Other conserved non-coding regions have been known for almost as long or longer.

This story is going to be like that "green" story that reports breathlessly every year or so that some company has instituted green policies because they save money! Just like Interface did fifteen years ago, and hundreds of others have done since.

The interesting thing is that these persistently "new" stories give us a measure of how slowly what can fairly be called "general knowledge" changes. Based on evidence from the "green" story we can expect to be hearing the AMAZING NEWS that there's more to genes than template coding until at least 2020.

Following the details as we learn them is fascinating. Being told that an uncontroversial fact we've known for a decade or more is "news" is very, very irritating.

Re:How is any of this new?

[freddy_dreddy]

Second that, nothing is news in this report. Common knowledge on genetics is portrayed as fresh from the press. Probably every medium-size gene-annotation research facility, small or medium, has their private version of a gene database.

Mod Parent Up

Re:How is any of this new?

[Anonymous Coward]

Your big words scare me.

methylation: the process of replacing a hydrogen atom with a methyl group.
oncogenisis: the generation of tumors.

(all definitions)
Dictionary.com Unabridged (v 1.1). Random House, Inc. 11 Nov. 2008. http://dictionary.reference.com/browse/methylation>.

Re:How is any of this new?

[eli pabst]

Nevermind they were just talking about transcription factor binding sites. None of this is new stuff.

No, you were right. The ENCODE group published a paper last year claiming that virtually all of the genome is transcribed (ENCODE Project Consortium in Nature, 2007). While it's an interesting observation that is probably true, the question is what does that really mean? Unlike translation which is a deterministic process (e.g. the codon AAA will always code for the amino acid lysine), transcription is a relatively sloppy probabilistic process where the DNA signals to start and stop don't always work properly, so you end up with things like aborted and run-off transcripts. However, the cell has control measures in place to degrade abnormal protein and RNA transcripts. So if you take a snapshot of the cell at a particular moment, you'll find all of these artifacts that are destined for the genetic dustbin and will never be translated into proteins. Add onto that, that these are relatively rare events, so if you find 1 of these long run-off transcripts in a sea of 50,000 normal ones, does that really matter?

Re:How is any of this new?

[benthurston27]

Well its the first time I had heard about any of it.

So, as a car analogy...

[RabidMoose]

...we had been assuming that the layout of cupholders determines what the make/model is?
Somebody help me out here, I'm on pain meds and not thinking at 100% capacity...

Re:So, as a car analogy...

[Zekasu]

Sort of like that. Take it more as, "The layout of the cupholders determines what shape the console/dash of the car is, which determines what kind of lights are used for the dash, which determines what kind of seats can be put in the car, [...], which determines what make/model you eventually get."

At least that's how I understand it. Too many assumptions, if you ask me, but I'm not a biologist.

Re:So, as a car analogy...

[Simply Curious]

We had been assuming that the blueprints to the car are always kept in the glove compartment.

Instead, we found out that most of the blueprints are in the glove compartment, but that they need the secret decoder rings that are kept in the trunk, under the seats, and in the gas tank. Furthermore, parts of the blueprint simply say "Look at how it was made in this car and do the same thing."

Re:So, as a car analogy...

[Anonymous Coward]

We had been telling people (newspaper reporters) that the easiest way to tell the difference between two types of cars is to look at the hood ornament, and the people (newspaper reporters) disseminated this information, leaving out the 'easiest way' part.

anyone educated in the field knows that ornaments are capable of lying, and are shared between different models, but as a first approximation its pretty decent.

What you read in the news about science is 30% factual but irrelevant, 50% inaccurate but in a not-that-harmful way, and 20% wildly wrong.

(And my statistics are 100% off the top of my head)

Re:So, as a car analogy...

[reverseengineer]

Think of it this way- if your protein-coding genes are the blueprints for a car, then epigenetics are the blueprints, operating procedures, and logistics for a mass production automobile factory. By reading your genes, you can find out the kinds of proteins that make you up. Similarly, car blueprints tell you how to make a car. A car, just one car. However, your cells are not putting out handbuilt cars. It's a modern Toyota factory going on in there, with continuous production and assembly. It's a marvel of mass production, with transcription, splicing, translation, post-translational modification, and relocation to the site of use all going on in multiple sites constantly. Production has to be carefully coordinated to make sure you have the right amounts of the right proteins delivered at the right times.

Epigenetics is the guy at the factory who knows how many cars to build this month, and the guy who makes sure that 10,000 cars have 10,000 steering wheels available to put in. Epigenetics is the guy who tells the line to hold up on building doors, because there's a surplus of doors in the warehouse already and we should use those first. Epigenetics is not the stuff you are made of, but rather a system of production control of that stuff.

Re:So, as a car analogy...

[shawb]

What you read in the news about science is 30% factual but irrelevant, 50% inaccurate but in a not-that-harmful way, and 20% wildly wrong.

That's a pretty reasonable guess, but you can leave out that "about science" part. Every time I see something in the news that I have been personally involved in, there seem to be mistakes and flat out made up information while the important details and overreaching problems are completely omitted. It gets worse if you start cross-checking against various "new sources." I fairly consistently find every outlet making up their own little details to fill word space while giving the image of gritty journalism.

Which is actually the only way to do business in an advertising funded media. Once advertisers start paying the bills the audience is no longer the customer, but the product. Every company strives to deliver the best product they can to the customer... and in this case the best possible product to deliver is gullible people. Therefore it becomes the medias responsibility to attract gullible people, and beyond that to ensure that people become more and more so.

Shades of Star Wars

[Marxist Hacker 42]

And do the midichlorians also carry the force?

Seriously, though, I thought we already had mitochondria living in our cells that were also inherited...

Re:Shades of Star Wars

[Bryansix]

In Episode V Yoda said the force is everywhere. In the trees, in the rocks, between the earth and the X-Wing. How do midichlorians even come remotely close to explaining any of that?

Re:Shades of Star Wars

[Marxist Hacker 42]

Perhaps they infect everything.

Re:Shades of Star Wars

[Anonymous Coward]

Option 1 - Yoda was wrong/lying

Option 2 - Yoda was using a metaphor to help luke train up quicker (the boy ain't too bright, better not confuse him with all the technical mumbo jumbo)

Re:Shades of Star Wars

[Chris Burke]

The Force is everywhere, just as Yoda said. The ability for a sentient being to manipulate the Force comes only via midichlorians.

There's your explanation.

And yes, it's still retarded. Best to pretend that never happened.

Re:Shades of Star Wars

[Anonymous Coward]

Well, when you're 900 years old, you'll probably sometimes get "The Buddha Nature" and "The Force" confused sometimes too!

Re:Shades of Star Wars

[elthicko]

Seriously, though, I thought we already had mitochondria living in our cells that were also inherited...

You are correct, mitochondria are inherited (maternally). http://en.wikipedia.org/wiki/Mitochondrial_DNA

Re:Shades of Star Wars

[Opyros]

Yep. And there are other kinds of non-chromosomal bodies which transmit genetic information, too — see the Wikipedia article on Extranuclear inheritance, to start with. And this has been known for a very long time; the book I just used to check my recollection of this was copyrighted in 1970!

Re:Shades of Star Wars

[jdoss]

Option 3 - George Lucas is an asshole.

Re:Shades of Star Wars

[Anonymous Coward]

I thought that the midichlorians were simply attracted to the force. So a large amount of midichlorians would imply a large amount of the force.

Correlation, causation, etc., etc.

Re:Shades of Star Wars

[Bryansix]

As opposed to when I'm 880 years old and I can bounce off walls like flubber and wield a light saber better then any Sith Lord out there...

Re:Shades of Star Wars

[LanMan04]

And yes, it's still retarded. Best to pretend that never happened.

Ah yes, the Highlander method. Now also works with Star Wars!

Those bastards.

[Brian.Kirby]

Damnit! I get a C in biology, and now they go and change the curriculum. I knew I was right when I decided to focus on physics and math.

Re:Those bastards.

[Anonymous Coward]

Well, math anyway, because physics is next...

Well..

[Zekasu]

For the sake of efficiency, it would make sense that some of our DNA is RNA, considering you'd be holding somewhere between the massive amount of information DNA would normally carry, and copies of that massive amount of data.

The thing that truly bothers about this article, disregarding the whole "double helix is no longer a viable model" part, is the fact that it's taken so long for someone to admit that the old presumption of, "Okay, so... See this pair of A-G molecules right here in your genome? That means you have blue eyes.", is an incorrect way of thinking. I mean, for the sake of efficiency, changing one pair of DNA molecules around would probably have multiple changes, rather than just one. I mean, how could a piece of information that describes virtually every feature of the human body store information about how a cell is reflective of blue light, 2 picometers wide, and takes a certain combination of chemicals to make.

Personally, I think this "advancement", if it's true and not another kdawrson new story, could help immensely in decoding DNA sequences and modifying DNA. Heck, it might even one day eliminate cancer.

Re:Well..

[maxume]

You are making a presumption about the old presumption.

Inteligent Design

[EEPROMS]

Who would have thought God coded DNA using Perl...

Re:Inteligent Design

[Zekasu]

Shoo, at least he didn't use Visual Basic.

Re:Inteligent Design

[RuBLed]

You forgot the link

Re:Inteligent Design

[rrohbeck]

Come on, intelligently designed Perl is quite readable.

Re:Inteligent Design

[mysticgoat]

Well, we thought She was doing it with regexes, some of them a thousand characters or more long, but still basically pattern matching. But now it turns out that She's doing some of it with evals and self-modifying code, which opens up an entirely different beastiary. And who can guess what other clever little tricks She is using?

The gene is dead. NYT confirms it...

Re:Inteligent Design

[rrohbeck]

Well, we thought She was doing it with regexes, some of them a thousand characters or more long, but still basically pattern matching.

That was Jeffrey Friedl. You got something wrong there.

so what to call the full package?

[khallow]

Since the genome doesn't contain all the information that a person inherits biologically, what should we call the full package of inherited RNA, proteins, bacteria cultures, and who knows what else?

Re:so what to call the full package?

[Anonymous Coward]

Mom and dad?

Re:so what to call the full package?

[postbigbang]

Imagine: a little molecular salt on that embryo, and we could make Johnny a genius and 7 feet tall!!

Re:so what to call the full package?

[khallow]

Mom and dad?

Nope. Even if you just consider the genome, you only get half from each. The other half of their genome you don't get.

Re:so what to call the full package?

[Anonymous Coward]

Anon for mod points. From my understanding of the article, the additional "information" is more like a modified config file, which will naturally slowly revert to defaults, not any further programming.

Re:so what to call the full package?

[khallow]

I disagree. At the moment of fertilization, anything in there that modifies the genome or how it expresses (even temporarily) changes the program. It's very possible that these proteins are inheritable. Given where they operate, that means they can have a significant though blunt effect on early development and should be considered along with the genome. Inherited bacteria cultures also should be considered. They probably have a profound affect on how well the child digests various types of food.

New cells inherit those molecules along with DNA..

[Anonymous Coward]

> "In other words, heredity can flow through a second channel"

This is not heredity unless these molecules self-replicate. But they don't - they are transcribed or translated from DNA or created by the products of DNA.

...or not

[Relic of the Future]

Don't take my word for it, take the word of a cellular biologist.

Re:...or not

[Anonymous Coward]

Don't take my word for it, take the word of a cellular biologist.

Some good points, but in the old model all promoters etc. interact with proteins.
Hence I would call the fact that not all gene effects are mediated by protein (maybe not even the majority) a paradigm shift. Especially considering that a lot of these ncRNAs might be much weirder then microRNAs.

Re:...or not

[tobiah]

He doesn't really refute anything in TFA, he just complains that this is old news, and gives his own summary.

Re:...or not

[Serious Callers Only]

Thanks for that link. The NYTimes article was hyperbolic, but the Slashdot summary is hyperbolic and hopelessly confused -

most of the molecules produced from DNA may not even be proteins, but rather RNA.

??

As a layperson, I was under the impression that the standard model was DNA -> RNA -> mRNA -> Proteins, but the summary implies that this is somehow a new idea and we previously thought proteins came straight from DNA....

Wow!

[PineHall]

I did not really understand how complex and complicated the whole genome is. It is not a surprise then that I am a mess.

Re:Wow!

[tobiah]

Ya, consider my mind blown. Particularly the epigenetic factors.

It is all about EPIGENETICS

[Anonymous Coward]

DNA is a dead sequence that is stripped bare.

In vivo, DNA is configured in chromosomes with surrounding structure and with methylation patterns to cause gene expression for a particular runtime configuration of each cell type. From sex cell, to embryo, to full grown adult. Different configurations with different outcomes based on the actual life experiences encountered in each individual.

The idea of the first sequences of genomes as an endpoint is replaced by a genome that is just the beginning of a beginning. All the meat exists in the runtime of all these cells and cell lines and each instance of cell and cell lines.

Should keep the scientists happily busy forever.

Obligatory

[cashman73]

In Soviet Russia, YOU encode your own DNA!

Re:Obligatory

[Anonymous Coward]

Uuuuughhh, if you're going to continue to whip that dead horse, you could at least bother to get it right.

"In Soviet Russia, (noun) (verb)s you!"

Re:Obligatory

[gregbot9000]

So, In Soviet Russia, (DNA) (encodes)s you?

But thats not funny.

And apparently only partially true.

Not funny at all.

Re:Obligatory

[Raffaello]

In Soviet Russia, organism encodes DNA!

Not so very funny, but it does match the meme's regex.

Re:Obligatory

[Anonymous Coward]

no, it doesn't! how hard is it for people who are presumably smart enough to understand regex, to get a simple sentence correct?

~$ echo In\ Soviet\ Russia,\ organism\ encodes\ DNA\! | grep In\ Soviet\ Russia,\ [a-z]*\ [a-z]*s\ YOU\!
~$

This is why...

[jd]

...I'm not (yet) convinced of the value of the gene-mapping you can currently buy. $1000+ and you get back a description that is essentially meaningless because they don't really understand how the genes work yet. You get tested for a handful of conditions which have genetic links, but not all. (Genetic studies have shown there to be 7 forms of ME, according to the specific genetic cause, but very few labs will test for any of them yet.) Without knowing more about how genes work, it is impossible to know if what these studies reveal is even an accurate reflection of the genetics behind such conditions.

Alongside that is an argument in the reverse direction. If genes are not necessarily contiguous and/or can have ill-defined boundaries and/or can have components off the main DNA itself, then there is a definite possibility that there may be additional regions that could be useful for deep ancestry and genealogical DNA testing. This could help enormously as current research is pushing the limits of what is knowable using the regions and markers that are currently available. Entire haplogroup trees have been redefined because new information has revealed flaws in the previous models. More data, preferably more data that changes slowly, could be useful in getting these models right rather than continuously patching them.

Re:This is why...

[swid27]

Entire haplogroup trees have been redefined because new information has revealed flaws in the previous models.

Not just that, but the redefinitions have come about in large part due to the efforts of hobbyists (the YDNA SNPs spreadsheet).

How many genes does it take to invent a light bulb

[cutecub]

I recall people freaking out when the human genome project revealed that Humans only have about 30,000 genes rather than the previous estimate of 150K.

It always seemed to me that measuring Human complexity based on the number of our genes is a little like judging a book by the number of words it contains. It completely ignores the fact that words have Meaning.

Poetry is both the most compact and the most subtle form of written expression.

This latest finding suggests to me that something similar applies to our genetic heritage.

-S

 

What is a gene? - history and updated definition

[Anonymous Coward]

latest updated definition What is a gene? http://www.ncbi.nlm.nih.gov/pubmed/17567988

Re:New cells inherit those molecules along with DN

[Bill, Shooter of Bul]

I think what they are saying is that they are present in the sperm and/or egg along with the dna. That they don't come from dna. You could have two exact sets of dna, but different other molecules, which would result in different proteins being created. Those molecules must be create from dna at some point, but not with out the help of other pre-existing molecules of non dna. So DNA doesn't have all of the information needed to create everything in the cell.

Evolution is bound to be messy.

[Melibeus]

I'm not surprised that this is very complex. There's no reason that we should expect the outcome of a stochastic process to be elegant and simple. It's more evidence (as if we really need more!) that there is no designer.

Pfft.

[MostAwesomeDude]

Can't be harder than programming a graphics card.

An analog?

[jlowery]

Does anyone else see the resemblence between DNA and crufted up old legacy software? Concepts about how heredity works get turned on their head once the mechanisms are examined in detail. I expect next it will be discovered that there are bugs in the DNA transcoding that are fixed by patches which in turn have patches.

Re:An analog?

[JesseMcDonald]

Does anyone else see the resemblence between DNA and crufted up old legacy software?

Well, imagine that this software started out as a simple "hello-world" program, and that every time the requirements changed -- a frequent occurence -- it was updated by repeatedly making the smallest change required to bring it a bit more in line with the requirements, with no regard at all to readability or maintenance. Further assume that random changes are being made all the time, and are only removed when a customer registers a complaint.

The result would probably look something like DNA.

Re:An analog?

[tfoss]

I expect next it will be discovered that there are bugs in the DNA transcoding that are fixed by patches which in turn have patches.

Already discovered.

-Ted

Re:An analog?

[modulo]

Or it's a very sophisticated decompression hardware and software, all rolled up in one.

Re:An analog?

[Anonymous Coward]

Declare a, b, c
a = b = c = 1
One:
If a = 0 Goto Three
c = 5
If b < 3 Goto Four
b = 3
Two:
a = 0
If c > 4 Goto One
b = 4
Three:
c = 2
a = 1
Four:
If b > 3 Goto Two
Else If c > 1 Goto One
Else Goto Three

Re:An analog?

[jlowery]

Actually, I was thinking of something even more confounding: superficial "fixes" that cover up an underlying problem, such that the the core problem can never be corrected because to do so will break the patch (and the patch of the patch). I see that sort of thing occurring where I work. (I'd run screaming, but they keep throwing benefits and bonuses at me. I sometimes wonder if I still have a soul.)

Re:An analog?

[Anonymous Coward]

Oh, you have no idea. Some genomes look like the equivalent of someone making a printout of spaghetti code, then getting half of it copied (badly) on the photocopier, pages getting mixed up, accidentally mixing up some pages with code for viruses, etc., and then someone typing it back in and simultaneously trying to fix it all up to keep it working. Not only does look like "crufted up old legacy software", but it was really badly maintained software, with a weird combination of elegantly optimized bits, functional but Rube Goldberg-like systems, and completely irrelevant garbage. One issue that's probably relevant is the fact that this code was ALWAYS running in "production systems" that could not be temporarily shut down, and the copying process was always imperfect. Even weirder, code was merged from slightly different versions all the time. You can imagine the mess that would cause if you were trying to maintain it "live" while the interpreter is always running, and if it crashes, well, that copy is dead, but there are zillions of others.

This stuff is code with a deep, deep history. The result is impressive and horrifying at the same time.

Re:An analog?

[Anonymous Coward]

running in "production systems" that could not be temporarily shut down, and the copying process was always imperfect. Even weirder, code was merged from slightly different versions all the time

A self-correcting parallel system. Large scale parallelism not only for the effiency, but for fault tolerance. Perhaps here is a useful way to spend hundreds of cores of the future in an always-on system.

Re:How many genes does it take to invent a light b

[Anonymous Coward]

I'm sorry to say,
your genes are a complete mess
and not poetic.

I welcome our new found transcription gene powers

[SirusTV]

Hello new field of medicine.

Not at all surprising, given the history

[Mode_Locrian]

The term 'gene' has undergone quite a bit of change in its history, so this isn't really all that surprising in light of this. The term was originally coined (probably by Mendel himself, but I don't remember) to mean roughly "whatever is responsible for the observable results of hybridization experiments" and later, with the advent of molecular biology, came to be shorthand for referring to a molecular structure of a certain kind. It's an interesting question of course, whether those definitions are coextensive (my bet is they aren't) and these latest findings are just evidence of a new conceptual (or at least terminological) shift. See Stotz and Griffiths "Gene" (2005) (to appear in Cambridge companion to philosophy of biology, and also can be viewed online at http://philsci-archive.pitt.edu/archive/00002494/ )

Re:Not at all surprising, given the history

[Mode_Locrian]

Hah, well I just RTFA and it turns out that it was Johanssen that coined the term.

And you know this because

[Anonymous Coward]

...you have exhaustively searched through every gene in the human genome, conclusively proven that there is no such structure, and can link to several of the thousands of papers that you published on the topic for which you won your second Nobel for.

Right?

Re:And you know this because

[malkir]

ding ding ding, anyone can link to wikipedia.

Re:New cells inherit those molecules along with DN

[repapetilto]

Your DNA is actually wrapped around complexes of protiens called Histones and these protiens can be modified to stick together or not. Ones that don't stick together make the genes easy to be expressed, and those that do aren't expressed. This along with modification of the actual DNA making it harder to be expressed (methylation) is what is passed down via the sperm/egg.

Iron.

[Fantastic Lad]

As much as I was unpleasantly gobsmacked by the Midichlorians thing, I do recognize it as an earnest attempt on Lucas' part to match up his universe with the real one.

In Star Wars, the Force IS out there, like water in a river and we are all little row boats bobbing in the current. --To manipulate the water, (the Force), you need something to stick in the water. Like midichlorians, the more 'Oars' you have to work with, the more you can alter how the Force affects you. (Sorry. That's a horrible metaphor, but it's the best I was able to come up in the moment).

In our reality, one opinion is that the vital particles in question are Iron atoms. --Our version of the 'Force' is simply referred to as 'Energy', and it has both similar and very different properties as compared to the Star Wars simplicities. --Keeping in mind that Lucas scooped the Star Wars magic system whole cloth from our own world.

But of course, there is not 'magic'. Nothing happens without a reason, and the same is true of our world. There is always an underlying mechanic which can be measured and understood given enough time and insight.

-FL

Re:How many genes does it take to invent a light b

[Chris Burke]

I recall people freaking out when the human genome project revealed that Humans only have about 30,000 genes rather than the previous estimate of 150K.

It always seemed to me that measuring Human complexity based on the number of our genes is a little like judging a book by the number of words it contains. It completely ignores the fact that words have Meaning.

Uh, I remember when they discovered that too, and I don't recall any scientists "freaking out" because the low number of genes implied we had low "complexity". Instead, I remember them being very excited, because they already knew there are far more than 30,000 proteins generated from our DNA, meaning that the 1:1 gene:protein mapping theory had to be wrong, and the mechanism was far more complicated than previously thought.

This sounds to me like a continuation of the line of inquiry opened by that discovery years ago, where now they're gaining a better idea of how the genes really code for proteins. With the extremely interesting aspect that some of this is controlled by things not part of the DNA itself, yet which can still be inherited.

To (ab)use your analogy, if the human body is a work of literature then proteins are the words, and genes are characters. The number of words hasn't changed, it's just that before we thought the language was like Chinese, where a single character mapped to a single word. Now we realize it's more like English, where the interactions between characters create different words. Oh and now we've discovered that there's also punctuation like apostrophes and hyphens which can significantly alter the meaning of the resulting words.

Isn't the gene...

[elthicko]

Isn't the Gene the front man for KISS?

So...

[andr00oo]

So I'm not descended from the milkman after all?

Re:How many genes does it take to invent a light b

[tonytnnt]

Nah, it's just all coded recursively.

Re:argh!

[tonytnnt]

There's a lot of people still trying to find genetic proof of homosexuality, in many cases for purely scientific reasons, in others, to justify the naturalness of homosexuality. Anyways, some links: http://www.livescience.com/health/080617-hereditary-homosexuality.html http://en.wikipedia.org/wiki/Biology_and_sexual_orientation

Re:How many genes does it take to invent a light b

[evolvearth]

The debate was philosophical at the heart of it, because at the root of the debate was the problem of nature vs nurture. Many happy about the discovery were using it ease their fear that human behavior could be traced to genes.

DMCA Takedown

[servognome]

RE: NOTICE OF COPYRIGHT INFRINGEMENT

Ladies and Gentlemen:

We act on behalf of God (the "Owner").

As required under Sections 512(c)(3) and 512(d)(3) of the Digital Millennium Copyright Act (17 U.S.C. ??512(c)(3) and 512(d)(3)), we are instructed to place you on notice that:

1. The Owner is the exclusive owner of the copyrights in and to the human DNA, RNA, and all other information contained therein

2. Decryption of aforementioned encrypted information constitutes an unlawful cicumvention of encryption technology

Please cease and desist from further decryption of stated copyright information and publication of previously acquired DNA information.

Re:DMCA Takedown

[astralpancakes]

Does that mean you'll change your sig to the human genome?

Re:How many genes does it take to invent a light b

[Artifakt]

I don't recall the professionals as a whole 'freaking out' either, but when that 30,000 number began being bandied about, there were scientists who pointed out that some other species seemed to have a lot more than 30,000 genes (some amphibians in particular, had anomalously high numbers). I also recall comparisons to the numbers found in fruit flies, which led to comments that either fruit flies were a lot more complex than we had thought, or there was something else very strange going on.
      There were estimates for humans based on the measured number of proteins (which was still a pretty incomplete count too at that time), but there were also alternate estimates for humans based on other things, such as assuming that with 23 chromosomes, the average number of genes per chromosome in humans ought to go up very close to linearly with the weight of a given chromosome, and the same ratios should apply across species (so as soon as you know how many genes are on any one chromosome of any species, you can extrapolate). When the 30,000 count was first announced, there was still a lot of debate between several different theorems such as these, so I can see both how the press had trouble explaining this well, and how at least some professionals gave some pretty awful interviews.

He is?

[MrKaos]

I thought there was only one Gene Simmons, who does he think he is, Sting, Flea?

Re:How many genes does it take to invent a light b

[Anonymous Coward]

And like poetry, looking at DNA without context means you could read any meaning into it you wanted to, whether that meaning was meant or not. Poetry for meaning always seemed like the old joke of DEL *.*, 100% compression! It's only worthwhile (outside of entertainment) if you can get out the same meaning that was put in.

God uses operator overloading

[Anonymous Coward]

heh

Re:God uses operator overloading

[Tablizer]

Me to boss: "If God can use Go-to's and spaghetti code, so can *I*!"

g=c800:5

[Mal-2]

Where you start in a code has an awful lot to do with the output, or if it runs at all. First of all, there are base triplet "synonyms" aplenty since there are many more base triplets than there are amino acids. This means there are a variety of ways to code the same protein, so it is possible to tweak a sequence without changing its function. What if you were to start some number of base pairs into a sequence -- might it also code for a valid protein? Would changing a base pair change the output of this new sequence while leaving the original function unchanged? What happens when the bases are read back in reverse, starting at some arbitrary point?

Just like you can find just about any reasonably short sequence of digits in the first million digits of pi, maybe one gene can "run" multiple programs depending on where you start and which way you go.

Mal-2

Re:How many genes does it take to invent a light b

[ScrewMaster]

This latest finding suggests to me that something similar applies to our genetic heritage.

The problem is that we're looking at a vast encoded and compressed dataset with only the barest clue as to how the decryption/decompression engine works.

good lord

[Anonymous Coward]

>>New large-scale studies of DNA Are you joking??? These features have been known about for years upon years. Maybe your textbook was lacking?

Re:How many genes does it take to invent a light b

[grouchomarxist]

we thought the language was like Chinese, where a single character mapped to a single word.

For the most part Chinese doesn't work that way either. Quoting wikipedia:
"A majority of words in all modern varieties of Chinese are poly-syllabic and thus require two or more characters to write."

...from the makers of South Park

[darkvizier]

So the FSM is a Finite State Machine, and God is a Perl hacker. Man, South Park's successor is going to be so awesome! Instead of Jesus packing heat we'll have God trying to hack into Ala's mainframe while an angel's going down on him. Just when you thought you couldn't be any more offended by television. Let the good times roll!

Cytosine methylation

[MillionthMonkey]

> "In other words, heredity can flow through a second channel"
This is not heredity unless these molecules self-replicate.

The article uses the cytosine methylation as an example all throughout, but it talks about it in this popularized way that doesn't make a lot of sense. Your DNA is full of crap like dormant viruses and transposons and other little vicious stretches of nucleic acid, and if it's left sitting around for the transcription machinery to find, you'll generally end up with undesirable RNA and undesirable proteins.

Methyl groups on cytosine bases will jam all this stuff up, so even if the DNA is somehow hostile, it can still be "commented out" by cytosine methylation. But cytosine methylation doesn't give you /* */ comments for your DNA- it's more like a // comment mechanism in that to comment out a region you can't just stick methyl groups at the ends; you have to carpet the whole stretch of DNA with methyl groups on all the cytosines.

When a cell divides, both strands of its DNA have methylated cytosines in the same regions. After the DNA replicates you have two methylated daughter strands, each coupled with a brand new complimentary strand. This complimentary strand has no methyl groups on it, which is a problem. So a clever enzyme comes along, DNA methyltransferase. It has a regulatory domain and a catalytic domain. The regulatory domain runs across the DNA feeling it for methyl groups. If it finds them on one strand, the catalytic domain deposits methyl groups on nearby cytosines on the other strand. That way, the stretch of DNA can be marked and disabled in a way that is heritable. The cytosine methylation signal is propagating on a separate channel of the DNA than the one that carries the actual DNA base sequence. Both are shaped by natural selection.

Which came first, RNA or DNA?

[huckamania]

There's only a few possibilities:

1.RNA then DNA, same place
2.DNA then RNA, same place
3.1 but different place
4.2 but different place
5.Same time, different place
6.Same time, same place

RNA has been found in nature and both have been artificially created. It appears that 3 is the most likely candidate. Lots of RNA pooled or gelled or what ever form it would collect into, sitting around waiting for some DNA, any DNA. A cosmic version of you got my peanut butter in your chocolate.

Re:Which came first, RNA or DNA?

[Anonymous Coward]

A cosmic version of you got my peanut butter in your chocolate.

2 girls, 1 cup?

After 'experts' cleared for release into the wild

[D4C5CE]

...all sorts of "safe" GM critters (with associated business models), we learn that there is no 1:1 correlation of what a snippet of DNA does - i.e. "nature finds a way"...

The Encode team estimates that the average protein-coding region produces 5.7 different transcripts. [...] New cells inherit those molecules along with DNA. In other words, heredity can flow through a second channel.

...at its worst, in a Jurassic Park kind of way, only that the threat won't be as "easy" to detect and defend from as a T-Rex.

What are genes

[eennaarbrak]

I am not a geneticist, but if I recall correctly according to Dawkins' Selfish Gene theory a gene is defined as a replicating entity that have selection pressure acting upon it. He specifically excluded it to mean a specific part in the DNA sequence - a single gene can be encoded with many different proteins all over the DNA sequence, as long as it replicates as a unit.

I'll give you "The Gene" having an identity crisis

[syousef]

http://www.imdb.com/title/tt0115685/

Sense-- and I don't mean the reading frame

[drunkenoafoffofb3ta]

"Most of the molecules produced from DNA may not even be proteins, but rather RNA." Perhaps "Almost all of the molecules produced from DNA are RNA, but not all of these RNA species are translated into protein; rather, RNA has lots of functions that we've previously not known about... etc." Bloody hell, the statement half-implies DNA->proteins in one step-- which is nothing short of magic.

Old News...

[Anonymous Coward]

Hmm, I'm not a fan of the article's beginning sensationalist vocabulary... it starts out by declaring a crisis and implying that a gene encoding for RNA is something 'new', but ends up explaining the basics of introns/exons, etc. But it's quite eukaryote-centric, as prokaryotes generally do not have introns in genes coding for mRNA. This is the source of all that alternative splicing referenced in the article and as much as I love us eukaryotes, prokaryotes are dominant on this planet. There's also this tone in the article about genes being thought of as less important. This is certainly not the case - genes are still extremely important, but regulatory elements have been discovered to have a significant heritable impact as well. This doesn't actually weaken the 'status' of genes, but rather strengthens the dynamic of heredity. Now don't get me wrong, so far as science articles go this was a good one. I just don't think the contrived 'science dramas' are necessary to keep people's attentions and they tend to mislead.

Not new

[DerCed]

This has been known for a long time now and is certainly not newsworthy. Wasting my time has never been more wasteful, thanks Slashdot!

Re:How many genes does it take to invent a light b

[Anonymous Coward]

oh how beatiful!

Re:How many genes does it take to invent a light b

[jez9999]

It always seemed to me that measuring Human complexity based on the number of our genes is a little like judging a book by the number of words it contains. It completely ignores the fact that words have Meaning.

Yep. The most advanced animal possible has a gene sequence that represents but one solitary number: 42.

Well, what do you expect?

[Arancaytar]

Billions of lines of undocumented spaghetti code with randomly commented-out sections, it will take you decades to understand all that.

"Intelligent"? The people who designed that were grade-A morons.

Phew! What a relief

[AlecC]

I was always worried by the "traditional" gene as one block of DNA coding for one protein. There simply wasn't enough code there to generate the complexity we see. When they say each such block cosed for an average of 5.7 proteins, plus lots of other info in methylation and teleomeres. Which means that there is much more information being transferred. Much more messily, but who said it had to be simple?

Makes sense

[Drakkenmensch]

I guess science is coming up with a better explanation every day why your neighbour's youngest boy has the milkman's hair color!

Epigenetics... google for it

[Anonymous Coward]

There was Frontline and a Nova on this like 2 years ago.

Re:How many genes does it take to invent a light b

[noidentity]

It always seemed to me that measuring Human complexity based on the number of our genes is a little like judging a book by the number of words it contains. It completely ignores the fact that words have Meaning.

Since we're on the subject, what is the meaning of the capitalization of the words "human" and "meaning" above? The latter seems to be for emphasis, but I don't see why emphasizing "human" would help make the point.

nothing to see here .. move along ..

[Anonymous Coward]

just like everything else in modern human MIS-understanding .. of just about everything else .. economics .. physics .. politics .. health .. human nature .. and the list goes on and on ..

let's do a little free thinking ..

something that according to studies done by the CIA .. also only exists in about 1 to 2% of the general population .. where public education and mass media is driving the agenda .. established by the Ruling Class .. which is also about 1 to 2% .. in ORDER to fulfill their self-interests .. of their understanding .. of what is RIGHT and how thing should and do work ..

http://www.johntaylorgatto.com/

DNA 64 .. RNA 64 total 128 ..

so it would be a reasonable assumption that it is probably 50% of the whole story .. and we are only now gaining a crude understanding of 1% of DNA .. which if you look at the Whole is actually only 1/2 of a percent ..

welcome to the Brave New(old) World Order .. the future for humankind indeed looks bleak ..

as Timothy Leary was reported to have said:

"ALLWAYS question authority .. and think for yourself" and may the force be with you ..

5.7 figure

[mapkinase]

"The Encode team estimates that the average protein-coding region produces 5.7 different transcripts."

I failed to trace this number to any peer-reviewed publication. Do you have any? Are they talking only about eukaryots (I guess, it's only humans, but...)?

Gotta Quote Firesign Theatre....

[zzsmirkzz]

There is a theory that states that whenever anybody discovers exactly what The Universe is and what it should be called, it will instantly disappear and be replaced with something even more bizarrely inexplicable. There is another theory that states that this has already happened.

Re:Gotta Quote Firesign Theatre....

[MadMidnightBomber]

Douglas frickin' Adams. Beginning of Restaurant at the End of the Universe.

No such thing as Memory

[DrYak]

The bottom line is that we do not yet fully understand memory, in much the same way that we do not fully understand synapse formation in the brain. We should just wait and see before jumping to any conclusions

This is even made more complex by the fact that there's no real such thing as "memory" (at least not in the way the /. geeks might think about it).
You don't keep a "recording" of events or such. We don't have a video recorder inside our skull.

The closest neurologist and neuropsychiatrist have come to understanding how the brain works, is that it function in a way which could briefly described as "making some association stronger".
(And there lies currently the problems there's still a lot to progress beyond the brief description).

At this point, searching how information is stored is hard, because we don't even know *what* information is stored.

(and maybe write a grant proposal or two along the way).

Yup. Good ideae. Do have any idea how we could cram "... and this will cure cancer" or "... and is also the perfect way to fight pedo-terrorist pirates" or "... can be turned into a powerful weapon of mass destruction to be sold to the US Army" or "... is a perfectly good reason to authorize un-warranted wiretaping"?
That would probably increase the chance of obtaining the grand :-)

OT: How do I learn more?

[JakartaDean]

Ok, sorry to interrupt the thread. I've got a degree in mechanical engineering, and a graduate degree in science. I'm happy with what I know and what I don't know, in a very general sense, with one exception: I don't get genetics. I know there's DNA, I know there are things called genes, which I think are strands of DNA coded in some specific ways. What makes something a gene, versus the wasted space bits. What do genes do (general sense)?

Rather than answers to those specific questions, which I'm sure are the tip of the iceberg, can someone point me to a useful resource / reference?

Dean

P.S. In general I am generally comfortable with my level of knowledge of things, at the age of 45. Genes are the exception: I know nothing, and it's frustrating.

Another botched science story

[virtualXTC]

This article is about 50 yrs late. FTA: "Most of the molecules produced from DNA may not even be proteins, but another chemical known as RNA"

It has been know for years that DNA doesn't directly encode proteins (see the 2006 Nobel prizes in chemistry and medicine), but rather is translated to and RNA message first. Further, overlapping genes were discovered years ago, same goes for rybozymes. Finally methylation has been a suspected epigenitic control mechanism since the 80's.

Nothing new to see here; move along.

Old Testament. Nowadays they'd be locked up

[ErkDemon]

Try approaching them with a troubled look and asking if they can explain to you the business about Noah, and what the moral of the tale is.

I don't mean the bit about the boat. I mean afterwards. When Noah gets blind drunk, and wakes up the next morning in his tent, stark naked, with one of his sons. Um.
And his son tells his other sons, and Noah is furious, and punishes his son for "telling" by disinheriting him and declaring that he and all his children , ad his children's children, will now be slaves forever. Or something.

Anyway, ask the priest whether the moral of the story is that if a grown-up gets inappropriately drunk and naked with you in their tent, that if you tell anyone, it means that you're Bad and deserve to be punished?

Or is the moral of the story that Noah, God's Chosen, was a evil vindictive child-abusing drunk?

I read through the Old Testament when I was little and I was horrified. It seemed to me that most of the "heroes" were lying/cheating/thieving/murdering/relative-shagging/slavekeeping/mass-murdering/two-faced cunts.

The bad guys always seemed to come out on top, and the worse they were, the more successful they got, and the more they were hero-worshipped.

And THAT's supposed to be the basis of a moral code? Jeez.

that's nice

[Anonymous Coward]

There is a single gene, Dscam, implicated in Down's Syndrome, which is believed to encode 38,000 proteins (via alternative splicing). Wiki it.

Spageti code

[Anonymous Coward]

"while beautifully specialized - is essentially becoming more and more difficult to alter meaningfully when radical change needs to happen."
This has already been seen, on the scale of species. I for one am glad that some of Homo sapiens specializations includes the possibility simulation and prediction (this conversation). I wonder about the upper limits of computational power. Will we at some time posses the power to do near real-time virtualization of whole organic systems? Is real-time genetic debugging, code optimization on the fly to much to ask? What would we call the result; Homo Optimus Prime?