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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."
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?
. . . A Human Genome Interpreter Project.
Not only does God code in machine language, but it is all spaghetti. Thats probably why eventually malfunction and die.
http://en.wikipedia.org/wiki/Jury_nullification
Epigenetics
RNA Splincing
siRNA
Who would have thought God coded DNA using Perl...
Don't take my word for it, take the word of a cellular biologist.
Those who fail to understand communication protocols, are doomed to repeat them over port 80.
...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.
It's a small world and it smells funny; I'd buy another if it wasn't for the money; Take back what I paid (SoM)
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
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.
Control is an illusion, order our comforting lie. From chaos, through chaos, into chaos we fly
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.
If you post it, they will read.
I'm sorry to say,
your genes are a complete mess
and not poetic.
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/ )
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.
The enemies of Democracy are
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.
The enemies of Democracy are
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.
"FDA staff reviewers expressed concern about the number of patients who were left out of the study because they died."
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.
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.
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.
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: 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.
D6 63 0D 70 89 81 BB 8E 7B 7C 5F 5D 54 EA AB 73
I guess science is coming up with a better explanation every day why your neighbour's youngest boy has the milkman's hair color!
There was Frontline and a Nova on this like 2 years ago.
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.