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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 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
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.
Epigenetics
RNA Splincing
siRNA
Who would have thought God coded DNA using Perl...
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.
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
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.
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.
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