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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

#101

Post by Double_Cast »

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…

That's not how it works. There's no single "global optimum" that lifeforms are evolving towards; there's no final hilltop; there's no intent. This notion of "Evolutionary Teleology" is how we get things like X-Men (which I enjoy for the record, it's not like X-Men is taught in biology class). If there were some global optimum, we'd all have eyesight like Legolas and the color-pallete of a Mantis-Shrimp, instead of a blind spot in the center of our retina.

Evolution just happens, and it is what it is. E.g. Natural Selection didn't "optimize" giraffes so they could reach leaves. Natural Selection is simply a way of explaining that some giraffes had long necks, some had short, and the shorter just happened to die out. Similarly, NBA players didn't "evolve" to play basketball. Some people are tall, and some are short, and the short people just didn't make the cut. "Select" != "Optimize". Evolution is better thought of as a historical accident. We're talking monkeys on a flying rock.

Re: Scientists discover second code hiding in DNA

#102

Post by bananacurve »

Here 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.

Re: Scientists discover second code hiding in DNA

#103

Post by asveikau »

coldtea wrote: post #94
asveikau wrote: post #83

Earlier quoted context omitted.

Right, because what constitutes a "dumb joke" can be universally agreed upon.

No, because any joke is a "dumb joke" in the context of a HN discussion. There's no debate about the smartness of them. The "dumb" part is about it being a joke, as opposed to a serious contribution, argument or commentary. Not about the joke's quality as a joke. That is, even if you're Woody Allen, HN does not want you to write jokes in here -- and especially one liners without any other content.

Is it wrong that I find your anti-joke stance somewhat humorous?

I sometimes find it strange how much this community values orthodoxy. People work really hard to appear to be totally conventional HN readers. To share the same mannerisms, attitudes and opinions of the idealized HN user. I guess that this includes denying humor does not totally surprise me. It seems to be a caricature of itself.

One reason I value humor in my own life is that it reminds everyone of the absurdity which we are all living. I can't escape that this makes an HN user wrapped up in a culture of orthodoxy a bit uncomfortable.

Re: Scientists discover second code hiding in DNA

#104

Post by Myrmornis »

kissickas wrote: post #56
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…

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 bl…

That's only known in viral genomes, right?

Re: Scientists discover second code hiding in DNA

#105

Post by Myrmornis »

xerophtye wrote: post #86

I 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…

Yes, 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.

Re: Scientists discover second code hiding in DNA

#106

Post by coldtea »

mtdewcmu wrote: post #100
coldtea wrote: post #94

Earlier quoted context omitted.

No, because any joke is a "dumb joke" in the context of a HN discussion. There's no debate about the smartness of them. The "dumb" part is about it being a joke, as opposed to a serious contribution, argument or commentary. Not about the joke's quality as a joke. That is, even if you're Woody Allen, HN does not want you to write jokes in here -- and especially one liners without any other content.

>> HN does not want you to write jokes in here -- and especially one liners without any other content. But humor is insight, and brevity is the soul of wit. I saw it as commentary on the headline itself, which was ambiguous and vague. I thought it meant scientists had found an easter egg or the Enigma code hidden in DNA.

>But humor is insight

Not really. Most of the time is just the mental analogue of fart jokes.

>and brevity is the soul of wit

No, that's just a cliche.

Re: Scientists discover second code hiding in DNA

#107

Post by mtdewcmu »

coldtea wrote: post #106
mtdewcmu wrote: post #100

Earlier quoted context omitted.

>> HN does not want you to write jokes in here -- and especially one liners without any other content. But humor is insight, and brevity is the soul of wit. I saw it as commentary on the headline itself, which was ambiguous and vague. I thought it meant scientists had found an easter egg or the Enigma code hidden in DNA.

> But humor is insight Not really. Most of the time is just the mental analogue of fart jokes. > and brevity is the soul of wit No, that's just a cliche.

>Not really. Most of the time is just the mental analogue of fart jokes.

I didn't say all insights were equal. If this was just a fart joke, I wouldn't have thought it was funny. But you can't draw a line between insight and humor, can you?

>No, that's just a cliche.

It's a cliche because it's Shakespeare. That doesn't make it less true.

Re: Scientists discover second code hiding in DNA

#108

Post by ConceptJunkie »

jonathansizz wrote: post #78
kissickas wrote: post #44

Earlier quoted context omitted.

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.

You know, if we really wanted to be sure about that, we could just check the commit comments.
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