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Scientists discover second code hiding in DNA

washington.edu

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Re: Scientists discover second code hiding in DNA

#41

Post by fivethree »

luketych wrote: post #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…

This is sort of a misunderstanding of evolution. It's not building to the most efficient or the greatest form of anything. It's spontaneous change that may or may not survive with no real reference to "the best."

Re: Scientists discover second code hiding in DNA

#42

Post by sounds »

skosuri wrote: post #35

I looked over the paper pretty quickly, but on a quick read it looks really nice. The data are really impressive, and they seemed to have pulled out really interesting trends for how transcription factors are affecting coding sequence. Furthermore, they map how variants found across the various cell lines they used (81!) to show that these variants actually are causal for transcription factor binding changes. For tho…

So I admit I haven't skimmed the paper yet.

Is it as comprehensive a map of DNA-encoded transcription factors as can be had? I ask because I can understand the way DNA codes for proteins–as a software-head–but the article definitely gets me with this "second language" and I want to think more about how the overlapping meanings might have developed (and how that might be apply to digital code).

Other than "start," "stop," "intron," "exon," and "suppress" (aka disable), what do the transcription factors do in terms of actual cell proteins?

I admit that a really detailed description of cell protein processes will be beyond my depth. :)

Re: Scientists discover second code hiding in DNA

#43

Post by mikecane »

taproot wrote: post #25
forgottenpaswrd wrote: post #16

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.

It's interesting to think of it like that but that's basing your understanding on something else that's just not as complex.

Re: Scientists discover second code hiding in DNA

#44

Post by kissickas »

forgottenpaswrd wrote: post #16

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" .

Any source on that bit about junk DNA?

I just completed a reasonably advanced course on computational biology and I was still taught that although we have found noncoding DNA performing functions, the majority of our DNA is both noncoding and not used for anything (i.e. evolutionarily obsolete, transposons, etc).

Re: Scientists discover second code hiding in DNA

#46

Post by maaku »

asveikau wrote: post #39
maaku wrote: post #28

Earlier quoted context omitted.

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

Your advice sounds a bit pretentious to me. Here I was under the mistaken impression that people should be themselves. (Downvoters in three, two, one...) RokStdy, don't be discouraged. You've done nothing wrong.

> Your advice sounds a bit pretentious to me. Here I was under the mistaken impression that people should be themselves.

No, no they shouldn't. Not if that means "take whatever action they feel like." One should take purposeful actions which serve to help their fellow HN'er and maintain the tremendously useful tool that this website has become. They should refrain from actions which decrease the signal to noise, or otherwise decrease the utility of HN.

That's not pretentious. That's the just an explicit statement of the implicit communal understanding which made this site what it is.

Re: Scientists discover second code hiding in DNA

#47

Post by kissickas »

damon_c wrote: post #32
forgottenpaswrd wrote: post #16

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 Properly referred to as "noncoding DNA"... until it is proved to be coding something.

There is, in fact, a difference between "junk DNA" and "noncoding DNA," now that we see some noncoding DNA performing functions as switches, promoters, TF-binding sites (like the article describes), etc.

Re: Scientists discover second code hiding in DNA

#48

Post by ddebernardy »

Honest question... How is this different from what was discovered around 2007?

I ask, because insofar as I'm aware, the moment geneticians parsed the human genome was the moment it occurred to them that most (90%?) of the information was missing. (As in, information to make the remaining proteins that we build in our body.)

I vaguely recollect 2007 being the year where they discoverned and/or described how ARN can influence how ADN is read and turn bits and pieces of information on and off to use the same code to build new proteins. And another team the same year described how injecting ARN could allow to use existing ADN to potentially build proteins that aren't synthesized in the body.

So... How is this different exactly? :-|

Re: Scientists discover second code hiding in DNA

#49

Post by kissickas »

mikecane wrote: post #45

So, can someone tie this into 23andMe? Wouldn't it change what they looked for?

It might indeed change our understanding of specific point mutations, for example, but it won't negate any of their research, as far as I can tell. On the contrary, it will help them moving forward as we now have some basis on which to understand what is going on a little better in the steps between genotype and phenotype.

Re: Scientists discover second code hiding in DNA

#50

Post by kissickas »

pvnick wrote: post #29
jnbiche wrote: post #26

Earlier quoted context omitted.

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 b…

You're correct in that this is not what the paper is talking about. However, there is a third layer (at least) beyond the gene-coding, most-studied area, and the article submitted; epigenetics studies how gene expression is modified by histone modification and DNA methylation, basically different ways of switching gene expression on/off or changing the amount of protein made from a certain gene.
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