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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

#71

Post by lukifer »

gregschlom wrote: post #8
AnthonBerg wrote: post #4

Earlier quoted context omitted.

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

Why hate? Why wish downvoting? His comment will get buried down while more informative comments bubble to the top. Personally, I found his comment funny and I also learned about Konami codes, which I knew nothing about. So it satisfied my intellectual curiosity :)

HN discourages humor without content, to keep the culture focused around serious discussion. You can have a sense of humor, but it should be in the context of the topic and add something meaningful to the discussion.

There's nothing wrong with the Reddit culture of competing for top joke, but HN strives to be something different. The internet already has plenty of homes for "$nerdReference + $nostalgia == $karma++".

Re: Scientists discover second code hiding in DNA

#72

Post by timr »

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…

"over the last few years it's also been clear that codon bias can be evolutionarily constrained. For a while, it mostly thought to be based on tRNA levels (basically anticodons). However, it's been increasingly clear that there are other constraints to protein coding sequences than just the decoded protein sequence (aka the genetic code)."

This is a much older question than the last few years -- it's one of those "evergreen" questions that's been around for almost as long as we've been able to do statistics on codon prevalence. You'll see hand-wavy explanations for differences in codon usage in really old textbooks. The tRNA one is a particularly old chestnut -- I think I read about that one in my first undergrad course on molecular biology.

Re: Scientists discover second code hiding in DNA

#73

Post by smartial_arts »

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?

"Tales from Genome" course on Udacity is pretty awesome, although at times painfully anal/detailed with regards to assignments.

I think you can skip those, though.

https://www.udacity.com/course/bio110

Re: Scientists discover second code hiding in DNA

#74

Post by refurb »

kissickas wrote: post #44
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).

Huh. I haven't heard that take on "junk DNA" in a long time.

http://www.princeton.edu/~achaney/tmve/wiki100k/docs/Noncodi...

Re: Scientists discover second code hiding in DNA

#75

Post by [deleted] »

mvleming wrote: post #64
fivethree wrote: post #41

Earlier quoted context omitted.

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."

Your comment reminds me of this discussion I had before here on HN and someone made a reply that has stuck with me to this day in its eloquence. I'll quote it here because I want to share what comment I'm talking about but out of context I think it makes little sense and I think you should read the thread [1]–it's very relevant to what we're talking about here. > Essentially it is trying to say that we are at a globa…

[deleted]

Re: Scientists discover second code hiding in DNA

#76

Post by jonathansizz »

gizmo686 wrote: post #57
fivethree wrote: post #41

Earlier quoted context omitted.

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…

No. You're equating evolution with adaptation, and also making assumptions about beneficial mutations occurring as and when needed.

Re: Scientists discover second code hiding in DNA

#77

Post by [deleted] »

gizmo686 wrote: post #57
fivethree wrote: post #41

Earlier quoted context omitted.

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…

[deleted]

Re: Scientists discover second code hiding in DNA

#78

Post by jonathansizz »

kissickas wrote: post #44
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).

You are correct. Most non-coding DNA is junk, which amounts to around 90% of the genome. Dead transposons alone make up just under half of the human genome.

Re: Scientists discover second code hiding in DNA

#79

Post by [deleted] »

kissickas wrote: post #44
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).

[deleted]

Re: Scientists discover second code hiding in DNA

#80

Post by [deleted] »

kissickas wrote: post #44
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).

[deleted]
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