61–70 of 108 posts
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…
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'm also not quite sure what is meant by suppress.
Really all transcription factors do is up-regulate or down-regulate genes, i.e. make more proteins from this gene or make less. However simple that seems this is actually an extremely important function. Other than enabling cells to respond to say, heat, stress, or tension by making proteins that help them cope, gene regulation levels are important in differentiation. This is the process by which cells 'pick' a destiny, i.e. brain cells, kidney cells, etc.
Generally, you can think of every cell in your body (with some limited exceptions) as containing all genes in your body, so how does the cell know what type of cell it should be? One way is by transcription factors, which will tell the cell make more of this kidney-related protein, or other proteins that help determine its fate.
They have also been implicated in memory formation and almost everything else you can think of. But for the actual process of what transcription factors do they just regulate how much protein should be made from this gene.
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."
> Essentially it is trying to say that we are at a global maximum in a space that is probably more nonlinear. In fact our genes may well be suboptimal in some respects even if you think they have "control".
[1] https://news.ycombinator.com/item?id=4906810, just read the first four comments from the top, mvleming -> mcherm -> mvleming -> justincormack
Can someone with an AAAS membership please post the full article? https://www.sciencemag.org/content/342/6164/1367.full.pdf $20 for one day access! Fucking obscene. I should join AAAS, it is only $50 for the year, but I can't swing it just now.
http://bede.im/Science-2013-Stergachis-1367-72.pdf
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 reevaluat…
>How long before this discovery can be used in mainstream medicine? Almost immediately. While it won't have therapeutic applications for some time, the first benefit will be helping scientists better understand the cause of certain diseases. >ground-braking That's like aerobraking, right? ;)
> That's like aerobraking, right? ;)
More like lithobraking [1].
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.
The "machine" you are referring two, can be a set of enzyme complexes which performs the DNA transcription, as you said at the messenger RNA level.
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.
http://www.paulgraham.com/hackernews.html
"The most dangerous form of stupid comment is not the
long but mistaken argument, but the dumb joke. [...]
Bad comments are like kudzu: they take over rapidly.
Comments have much more effect on new comments than
submissions have on new submissions. If someone submits
a lame article, the other submissions don't all become
lame. But if someone posts a stupid comment on a thread,
that sets the tone for the region around it. People
reply to dumb jokes with dumb jokes."
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…
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?