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Scientists discover second code hiding in DNA

washington.edu

21–30 of 108 posts

Re: Scientists discover second code hiding in DNA

#21
I am not a biologist, but this discovery seems ground-braking to me.

What strikes me as an interesting question (I hope someone of you can answer) is: How long will it be, before physicians/gene specialists/biologists/etc. will use the new way of DNA interpretation in cases for regular people? How long before this discovery can be used in mainstream medicine?

My (uneducated) guess is: there has to be a huge reevaluation of the accumulated data (and assumptions) about gene connections with deceases.

Re: Scientists discover second code hiding in DNA

#23
post #9

TL;DR for biologists: synonymous codon variation is heavily constrained by the need to maintain transcription factor binding motifs. While I found the article very interesting as a new postgraduate student, it seems like such a straightforward deduction that I find it difficult to believe no one has ever put it into words until now.

Codon usage bias is a pretty well-described phenomenon. You can read more about it here http://en.wikipedia.org/wiki/Codon_usage_bias

Re: Scientists discover second code hiding in DNA

#25

It looks like there is software in DNA, not just firmware. We are just starting to understand that gene expression is very important too, code that express(is executed) or not based on the environment, and that junk DNA is probably "not understood code" .

Junk dna is just header files and whitespace.

Re: Scientists discover second code hiding in DNA

#26
post #12
post #9

TL;DR for biologists: synonymous codon variation is heavily constrained by the need to maintain transcription factor binding motifs. While I found the article very interesting as a new postgraduate student, it seems like such a straightforward deduction that I find it difficult to believe no one has ever put it into words until now.

After talking to someone who knows quite a bit about this stuff, apparently most people in the genomics/bioinformatics community kinda already knew about this, just that the researchers who wrote the paper were the first one to officially categorize them.

I agree. I believe I recall my biologist friend saying at one point that there are up to three such "layers" of genetic code, depending on where you start reading the sequence. Am I understanding that correctly?

Re: Scientists discover second code hiding in DNA

#27
Funny how discoveries like this don't surprise me at all anymore. After embracing concepts such as fractal geometry, recursion and the demand for efficiency in nature, it makes sense that in nature everything has evolved in a way in which every layer is a part of the next layer above it (quarks -> electrons, protons -> elements -> compounds -> amino acids -> proteins -> information -> abstract information -> ..., or binary -> hexadecimal -> assembly -> low-level code -> high-level code -> abstractions -> ...), and everything has value in more than one way. DNA, proteins, muscles, neural clusters, even programming are all based around this principle. If you were building two programs that were identical in many ways why wouldn't you abstract out the commonalities, instead of building them twice?

The brain is no exception. I think musicians, for example, are better at math because at the heart of music and at the heart of math, many of the same brain circuits are involved. It is more efficient to have one copy of these circuits and just apply them to both music and math, rather than having two copies of nearly identical circuits. Proteins have more than one use in our bodies, because if each only had only one use we would need an inefficient number of them, possibly more than what exists. Same for neurotransmitters. When nature is limited by constraints it usually finds a way to fold into a higher dimension around that constraint (such as the neocortex wrinkling to increase surface area, or DNA containing information on more than a single level, or even how grass grows over a fallen log instead of "choosing" to just grow somewhere else, or if you are into String Theory, how the universe/multiverse has folded into 11 dimensions, possibly because that was the most efficient way for our universe to exist.)

It reminds me of a river when it is initially forming down the side of a mountain. The water takes the most efficient path at any given instance from the top of the mountain to the bottom. The process is like a greedy algorithm. The water cannot foresee where it will end up, it just flows. The water won't always find the most efficient solution, but give it enough time and will find an efficient-enough solution.

Re: Scientists discover second code hiding in DNA

#28
post #11

Earlier quoted context omitted.

Comments like this encourage me to write more quality posts so I can get downvote rights. Sorry.

I figured I might get downvoted, but when I read the headline the konami code stuck in my head and I couldn't resist. It made me laugh, and I thought it might make others laugh. Which to me has (a little) value. But now, you are pot and I am kettle (or vice versa). Your comment adds no value or, I'd argue less value, because at least I was trying to be funny.

Don't try to be funny here. Be insightful.

Re: Scientists discover second code hiding in DNA

#29
post #26
post #12

Earlier quoted context omitted.

After talking to someone who knows quite a bit about this stuff, apparently most people in the genomics/bioinformatics community kinda already knew about this, just that the researchers who wrote the paper were the first one to officially categorize them.

I agree. I believe I recall my biologist friend saying at one point that there are up to three such "layers" of genetic code, depending on where you start reading the sequence. Am I understanding that correctly?

Well, yeah, if what he's talking about are nucleotide bases, it takes three of them to make a codon. So if you have a sequence ABCABC, then ABC might be a codon (which codes for an amino acid, like a "bead" in a necklace that makes up a protein), BCA might be a codon, and CAB might be a codon. Then at the same time you could go backwards. So really there's six potential different codons that a single basepair might be involved in. But that's probably not what this paper is talking about.

Re: Scientists discover second code hiding in DNA

#30
post #12

Earlier quoted context omitted.

After talking to someone who knows quite a bit about this stuff, apparently most people in the genomics/bioinformatics community kinda already knew about this, just that the researchers who wrote the paper were the first one to officially categorize them.

Does this affect assumptions made within genetic engineering of agricultural crops?

My understanding is that GMO crops have snippets taken from other species' DNA. Those sequences would be internally consistent, and only the patch between the native and foreign sequence would be affected.
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