The Gene Is Having an Identity Crisis 257
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."
So, what we REALLY need is . . . (Score:5, Insightful)
. . . A Human Genome Interpreter Project.
Re:I Knew It (Score:0, Insightful)
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:Memory RNA (Score:3, Insightful)
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:Surprise, surprise! (Score:2, Insightful)
Real scientists will know and acknowledge they don't know everything. The hacks think and try to convince you otherwise.
This is why... (Score:3, Insightful)
...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.
And you know this because (Score:1, Insightful)
Right?
Re:Shades of Star Wars (Score:3, Insightful)
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:So, as a car analogy... (Score:5, Insightful)
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, what we REALLY need is . . . (Score:3, Insightful)
Re:Memory RNA (Score:2, Insightful)
Re:Memory RNA (Score:3, Insightful)
Can you define instinct so we can talk intelligently about it?
Re:Surprise, surprise! (Score:5, Insightful)
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:So, what we REALLY need is . . . (Score:3, Insightful)
Re:Memory RNA (Score:3, Insightful)
Re:Memory RNA (Score:1, Insightful)
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:Surprise, surprise! (Score:1, Insightful)
Old News... (Score:1, Insightful)
Re:Which came first, RNA or DNA? (Score:1, Insightful)
A cosmic version of you got my peanut butter in your chocolate.
2 girls, 1 cup?
Re:An analog? (Score:1, Insightful)
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.