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Scientists discover second code hiding in DNA
- RokStdy 13y agoThe second code is: Up Up Down Down Left Right Left Right B A
- AnthonBerg 13y agoComments like this encourage me to write more quality posts so I can get downvote rights. Sorry.
- gregschlom 13y agoWhy 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 :)
- lukifer 13y agoHN 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++".
- RokStdy 13y agoI 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. </derail>
- outworlder 13y agoYou should delete you comment while you still have some karma left.
- maaku 13y agoDon't try to be funny here. Be insightful.
- asveikau 13y agoYour 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.
- maaku 13y ago> 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.
- asveikau 13y agoI hope that one day you can grow enough as a person to realize that authenticity is an important trait. I don't think I've very often heard "no, no you shouldn't" as a direct response to a claim that one should avoid being something you are not.
- maaku 13y agoAuthenticity doesn't mean broadcasting every little thought that enters your head.
- icholy 13y agothis isn't reddit ...
- skosuri 13y agoActually the reddit discussion on the paper is much more informative [1]. [1] http://www.reddit.com/r/science/comments/1sqj63/scientists_discover_second_code_hiding_in_dna/ http://www.reddit.com/r/science/comments/1sqj63/scientists_d...
- mtdewcmu 13y agoThat's kind of funny.
- LionRoar 13y agoThis is funny AND insightful. Reminds me of folding proteins. So, I guess it is a good moment to point to http://folding.stanford.edu/ http://folding.stanford.edu/
- bananacurve 13y agoCan someone with an AAAS membership please post the full article? https://www.sciencemag.org/content/342/6164/1367.full.pdf 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.
- bede 13y agohttp://bede.im/Science-2013-Stergachis-1367-72.pdf http://bede.im/Science-2013-Stergachis-1367-72.pdf
- bananacurve 13y agoThank you.
- bede 13y agoThank my university :) ...And perhaps my server, which definitely isn't accustomed to HN traffic.
- atmosx 13y agoThanks!
- bede 13y agoTL;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.
- dl8 13y agoAfter 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.
- contingencies 13y agoDoes this affect assumptions made within genetic engineering of agricultural crops?
- csours 13y agoMy 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.
- bede 13y agoAgreed. The finding is hardly surprising, but this paper appears to formalise things very nicely.
- jnbiche 13y agoI 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?
- pvnick 13y ago
- tokenadult 13y agoIt's a university press release.[1] I'm sending the link to the published paper from Science kindly shared in an earlier comment here to some geneticists I know locally, who have just been in a seminar together this afternoon, I'm pretty sure. The editors of Science evidently agreed that there is something interesting here, but they have been wrong before.[2] [1] http://www.phdcomics.com/comics.php?f=1174 http://www.phdcomics.com/comics.php?f=1174 [2] http://www.slate.com/articles/health_and_science/science/2010/12/this_paper_should_not_have_been_published.html http://www.slate.com/articles/health_and_science/science/201... https://www.sciencenews.org/node/5635 https://www.sciencenews.org/node/5635 http://www.nature.com/news/arsenic-life-bacterium-prefers-phosphorus-after-all-1.11520 http://www.nature.com/news/arsenic-life-bacterium-prefers-ph... AFTER EDIT: I heard back from one of my local geneticist friends, a mathematician turned psychologist by higher education who largely does statistical analysis as part of a team of researchers on behavior genetics. He writes, from the perspective of behavior genetics research, "That is fascinating, but if duons are also tagged by SNPs, and especially if they are in the exomic DNA, we've already been studying them and finding very little. In other words, this is huge for molecular genetics and physiology, but I'm not so sure it changes what we do in genotype-phenotype association research." So I take that to say that this could be quite a big deal for molecular genetics and physiology, if this finding is confirmed in follow-up research.
- forgottenpaswrd 13y agoIt 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" .
- taproot 13y agoJunk dna is just header files and whitespace.
- deleted 13y ago[deleted]
- mikecane 13y agoIt's interesting to think of it like that but that's basing your understanding on something else that's just not as complex.
- damon_c 13y ago> junk DNA Properly referred to as "noncoding DNA"... until it is proved to be coding something.
- kissickas 13y agoThere 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.
- kissickas 13y agoAny 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).
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- tsenkov 13y agoI 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.
- deleted 13y ago[deleted]
- schiffern 13y ago>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? ;)
- dragonwriter 13y ago> > ground-braking > That's like aerobraking, right? ;) More like lithobraking [1]. [1] http://en.wikipedia.org/wiki/Lithobraking http://en.wikipedia.org/wiki/Lithobraking
- tsenkov 13y agoOooops. :> It should've been groundbreaking*. Well, the "therapeutic applications" were kind of what I meant. I hope "some time" is not more than 5 years.
- qrybam 13y agoThis is very interesting. Makes me imagine that there might be even higher levels of control/abstraction over the top of this.
- luketych 13y agoFunny 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.
- fivethree 13y agoThis 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."
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- skosuri 13y agoI 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 those saying this is not a big deal, or is obvious; it is, and is not (respectively). It's been pretty clear for some time that codon choice is not random (hence codon optimization is useful when taking a gene from one organism to another), and 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). For example, we published a paper a few weeks back [1] showing that in bacteria (and probably higher organisms), the N-terminus of genes has a lot of rare codons and this is due to other constraints such as relieving mRNA structure to allow better translation of proteins. I think in the coming years, we will find that other regulatory elements also shape this code, including sequences that control splicing, small RNAs, mRNA degradation and transport, et cetera Anyways, it's a pretty fun time in biology. The tools we have now make studies that were ridiculously impossible just a few years ago, a reality for an individual lab. I can't wait to see what the next few years bring. [1] http://arep.med.harvard.edu/pdf/Goodman_Sci_13.pdf\ http://arep.med.harvard.edu/pdf/Goodman_Sci_13.pdf\ EDIT: Since my comment has hijacked the most useful comment linking to the original study, I'll link to the comment here: https://news.ycombinator.com/item?id=6897122 https://news.ycombinator.com/item?id=6897122
- daemonk 13y agoAgreed. 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.
- skosuri 13y ago
- mikecane 13y agoSo, can someone tie this into 23andMe? Wouldn't it change what they looked for?
- kissickas 13y agoIt 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.
- ddebernardy 13y agoHonest 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? :-|
- dnautics 13y agoThis 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".
- atmosx 13y agoThat's a Nobel prize imho. Good going :-)
- xerophtye 13y agoI am confused. I have absolutely zero biology background so please, bear with me. So genes only code how to make proteins? That's IT? What about all the other stuff like what you look like, what diseases you may or may not get, some special functions of your body, your biological strengths and weaknesses, etc etc. Or defining protein generation actually defines all of that? (that would be so fascinating). And 90% of the DNA is labeled as "non-coding?" ?!?!? Seriously? well it can't be "junk" can it? Or maybe its like a long bitcoin chain with only the latest commit relevant....
- Myrmornis 13y agoYes, specifying which proteins are made, and how much of each and how that varies with cell type is most of what determines an organism's phenotype. This is largely because enzymes are proteins, and enzymes control all the biochemical reactions in a cell. But proteins can also be transcription factors, which control which other proteins are produced, and they can be important for their mechanical properties, etc. So, not some boring category of biomolecule that gets listed on nutritional information section on food packaging.
- mseepgood 13y ago64 letter alphabet? Base64 encoded?
- chmike 13y agoA protein is a chain of amino acids. There are 21 different amino acids. The alphabet of proteins is made of 21 different letters. DNA strings are sequence of Deoxyribose Nucleic Acid (DNA). There are only 4 of them named A, T, C, G. The alphabet of DNA is thus made of 4 letters. One needs at least 3 DNA letters to encode one of the 21 amino acids. These 3 DNA letters are called codon. But with 3 DNA letters there exist 4^3 = 64 different codons. This is similar to a Base64 encoding just by the number of letters in the codon alphabet. Since 64 is much more than 21, many different codons encode the same amino acid. This provides a liberty degree which is apparently used to encode something else. As suggested by this research result, the secondary encoding would sort of encode the predicate specifying when and maybe how the DNA sequence encoding a protein should be decoded.
- coldtea 13y agoSo, there was a second code hiding in DNA, with different types of instructions, and those scientists discovered it. That's nice, that's how science progresses. Now, let's go to how business works. What about all those "scientists" (nay, engineers doing whatever for a payroll) and all those corporations, cocky and convinced that they had all the knowledge they needed, working as amateur magicians with DNA to create synthetic food, organs, new drugs, etc? They essentially said "fuck" to a better and timely scientific understanding, in order to greedily rush to market some half baked results -- and consequences (medical or otherwise) be damned.
- tgb 13y agoLike this one? http://dresdencodak.com/2009/07/12/fabulous-prizes/ http://dresdencodak.com/2009/07/12/fabulous-prizes/
- vincie 13y agoThe Trekkies were right all along: http://en.wikipedia.org/wiki/The_Chase_(Star_Trek:_The_Next_Generation) http://en.wikipedia.org/wiki/The_Chase_(Star_Trek:_The_Next_...
- wbhart 13y agoThe wording of the news is quite similar to a discovery reported in 2006: http://www.nytimes.com/2006/07/25/science/25dna.html?_r=0 http://www.nytimes.com/2006/07/25/science/25dna.html?_r=0 So is this a third code? A rediscovery of the same thing? Or a refinement of that earlier work?
- brutopia 13y agoSeems like scientists haven't discovered yet how not to include unencrypted resources on https sites.
- bananacurve 13y agoHere is a decent analogy I read: >Suppose we have a computer program which makes books. All of the commands which tell your computer program how to write a book are stored as sequences of 0's and 1's. Also, all of the letters, punctuation marks, and formatting symbols (line break, indent etc) are stored as specific sequences of 0's and 1's. The commands which control the computer program and the actual text of the book are both stored in the same file. Up until now, we thought that these were placed side by side in the file, so you would have a segment saying "at 6am every day, print the following text in 12 pt font, and bind it in a hard red cover", followed by a text containing segment, and then another command segment saying "when you finish, print a copy of the book 134 positions further along in the file. We thought this was the case because we have known the sequences of 0's and 1's that stand for each letter for a long time now. When we looked at a file and attempted to interpret it as If it all stood for letters which made up words' we would see something like "fffffgfgy6- fsjjjjjj the quick brown fox jumped over the lazy dog.bttt68-%jjjjjjfffffffff". After a while, we learned that the 'gibberish' segments were actually full of meaningful statements, but they were in a different language and contained the commands for the program. Now getting to today's article, this group has found that inside those sections which code for the actual text of the book, there are some commands that run the program. This is accomplished because there is more than one way to write most of the letters. As an example, you could have one segment of text which says "It was the best of times, it was the worst of times", and another segment which says "It was the best of times, it was the worst of times" and also tells the book program to bind the book in gold leaf. And the only difference between the two is that the first one wrote the 's' in 'best' as 00010110, and the second one wrote it as 00010111.