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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

#51

Post by waterlesscloud »

sounds wrote: post #42
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," "st…

I know next to nothing about this field, but I just sort of brute-forced my way through the OP paper with the help of wikipedia. It's a painful process. :-)

But it has piqued my curiosity about the field. Are there any good introductory books/websites for the curious layman to get a grounding?

Re: Scientists discover second code hiding in DNA

#52

Post by dnautics »

This is very similar to earlier discoveries that the choice of codon can be intimately tied in with protein domains folding; allowing proteins to partially fold while the remainder is "stalled" on the ribosome waiting for the rare codon. It's interesting, but I would hardly call it a "second code".

Re: Scientists discover second code hiding in DNA

#53

Post by skosuri »

waterlesscloud wrote: post #51
sounds wrote: post #42

Earlier quoted context omitted.

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," "st…

I know next to nothing about this field, but I just sort of brute-forced my way through the OP paper with the help of wikipedia. It's a painful process. :-) But it has piqued my curiosity about the field. Are there any good introductory books/websites for the curious layman to get a grounding?

Depends on what level. Wikipedia is actually quite good for this sort of thing. The classic book as a basic overview of molecular biology in general is the Molecular Biology of the Cell [1]. A really cool website to look at on cutting edge studies such as these is the ENCODE consortium's publications in Nature [2]. They simultaneously published 30 papers last year, and this is a really cool meta page that explains the ENCODE project and what they found.

[1]. http://www.ncbi.nlm.nih.gov/books/NBK21054/

[2]. http://www.nature.com/encode/

Re: Scientists discover second code hiding in DNA

#54

Post by skosuri »

waterlesscloud wrote: post #51
sounds wrote: post #42

Earlier quoted context omitted.

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," "st…

I know next to nothing about this field, but I just sort of brute-forced my way through the OP paper with the help of wikipedia. It's a painful process. :-) But it has piqued my curiosity about the field. Are there any good introductory books/websites for the curious layman to get a grounding?

Oh and for Codon usage in general, a really good review can be found here [1].

[1]. http://people.cs.vt.edu/~heath/VTMENA/CodonBias/PlotkinKudla...

Re: Scientists discover second code hiding in DNA

#56

Post by kissickas »

sounds wrote: post #42
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," "st…

In case you were unaware, another really amazing example of overlapping meainings is in "normal" DNA code, where genes can overlap themselves.

Because a stop codon would kill transcription, these are either on alternate reading frames (i.e. the codons begin on a different one of the three possibilities) or on the antisense side of the gene (the opposite base pairs from those corresponding to the original gene).

It blows my mind that such an incredible amount of stuff could go wrong if there is just a single mutation, and that such an incredibly delicate system arose through evolution and survived billions of years of natural selection.

Re: Scientists discover second code hiding in DNA

#57

Post by gizmo686 »

fivethree wrote: post #41
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."

This also seems to misunderstand evolution. You can think of evolution as a hill climbing optimization algorithm, with a complicated and constantly changing fitness metric. While it is true that any given change is random, and even 'good' changes still only succeed with some probability, over a long time period we see a series of incremental improvements. If there is an opportunity to increase efficiency it is likely that evolution would have found it, given how long the process has been running. Of course, this become less likely when we are discussing new features (the thumb is less optimized than DNA because it is so recent), and as the benefit of these optimizations becomes less. They also become less likely if their are fewer evolutionary paths that might lead to them.

Re: Scientists discover second code hiding in DNA

#58

Post by possibilistic »

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" .

DNA is a machine. It encodes information, but it also lives and breathes through interaction with various TFs, methylation events, packing, etc. There many types of epigenetic "state information".

We've known this for a looong time, it's just that it's so damned complex that we have trouble grappling with it.

And let's not forget the rest of the cell and all of the information encoded at the protein/messenger level.

Re: Scientists discover second code hiding in DNA

#59

Post by mvleming »

waterlesscloud wrote: post #51
sounds wrote: post #42

Earlier quoted context omitted.

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," "st…

I know next to nothing about this field, but I just sort of brute-forced my way through the OP paper with the help of wikipedia. It's a painful process. :-) But it has piqued my curiosity about the field. Are there any good introductory books/websites for the curious layman to get a grounding?

The Machinery of Life [1] is a fantastic book, I was one of those curious laymen and boy did it saturate my thirst for learning about microbiology. I think it's close to the time I read it again.

[1] http://www.amazon.com/The-Machinery-Life-David-Goodsell/dp/0...

Edit: Whoops, no Markdown support. Revised link to use footnote.

Re: Scientists discover second code hiding in DNA

#60

Post by Estragon »

daemonk wrote: post #38
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…

Agreed. It's an interesting trend. I also just skimmed over it; however, I wonder how significant is their initial TF binding occupancy data. There are a bunch of papers recently that looked at binding sites and found that they don't really correlate well with transcription. The cell is just a stochastic bag of molecules. TFs bind whereever they can. I wonder if they are just seeing noise.

Yes, so much bullshit has been published over the last decade as a result of artifacts in the measurement of TFBS that you have to be skeptical.
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