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[LordBaal]

I think there's some Russian billionaire funding research into mind-computer transfer, with the goal of livingdrinking vodka forever.

Immortality would be only a side effect.

[Dutrius]

Junk DNA is a bit of a misnomer. If it were really junk, it would get removed from the genome pretty quickly naturally. It's not so much "Junk" DNA, it's more "We don't know what it does yet" DNA.

DNA is far more convoluted and complex than anything we've ever done. Codes for proteins, control codes for gene expression, one gene might do one thing when another gene is active, and do another thing entirely when it's not. &c. &c.

[jaked122]

That's fair, but I'm just not sure that it is feasible to upload brains if it takes a whole simulation with all of the components.

I was tempted to mention junk-dna, but knowing that it has a lot of actual purposes that they've found, using it to control transcription for example.

What I'm trying to get to is that building abstractions to avoid dealing with complicated debugging(I.E. the fluid doesn't work right in this one circumstance that only happens once every 10^4 simulations over the course of 10^5 seconds. These abstractions that tell us how things generally work in situation X and situation Y may be more efficient through approximating all of the factors in subsystem W and Z.

Alternately, if someone can actually make cryogenics work, I wouldn't balk at that for space travel either. Though reading Alistair Reynolds and all of those protagonists that don't remember things due to minor malfunctions that didn't kill them outright makes me very hesitant. He's not really a scientific authority on that matter anyway, so those problems might not even exist.

I just don't want something silly like philosophy and the ideas about qualia preventing us from trying these potentially useful methods.

[i2amroy]

Junk DNA is a bit of a misnomer. If it were really junk, it would get removed from the genome pretty quickly naturally. It's not so much "Junk" DNA, it's more "We don't know what it does yet" DNA.

DNA is far more convoluted and complex than anything we've ever done. Codes for proteins, control codes for gene expression, one gene might do one thing when another gene is active, and do another thing entirely when it's not. &c. &c.

There's also a fair bit of DNA that is "junk" in the sense that while it doesn't actively do anything, but it's mere presence serves to alter the things around it. Look at this example algorithm:
index starts at 1, perform each instruction and then advance 1
1) Go forward 2 instructions
2) Jump twice
3) Pat your head
4) Stomp your feet
Following this algorithm would lead to you just stomping your feet because you skip steps 2 and 3. However if there wasn't actually something present in steps 2 and 3, then we would skip stomping our feet because it would be included in the "skipped" instructions. In the same way there are some bits of DNA that's only purpose is to "pad" instructions so that certain things aren't skipped that function as "junk" DNA.

[Sheb]

But then, you also have stuff like transposon, which acts mostly like viruses that decided that leaving the cell was a bother. Although of course some of them are being used in some case...

The thing is, nature mostly just take whatever is around and use it to McGyver a living being. Junk might be used, or it might stay around. I mean, if you take that big rusted washing machine and use it to hold your door open, does it stop being junk?

[i2amroy]

I mean, if you take that big rusted washing machine and use it to hold your door open, does it stop being junk?

If it's the only thing I have available to hold the door open, and I really need that door held open or the building becomes unusable, then yes, it magically changes from being a junky rusted washing machine into just a very oversized doorstop. That doesn't necessarily mean it's a very good doorstop, of course, but it does mean that it becomes essential to functionality and thus no longer "junk" IMO.

[Sheb]

But what if you just grabbed it because it was the closest thing around, and your neighbour actually made a real one, is it still junk?

I guess my point is that since organism are incredibly jury-rigged (seriously, if a human designer had come up with the human eye, he would have been fired on the spot), distinguishing between what is junk or not is hard. Especially since many things are only tangentially useful. Think of the appendix. It's very obviously a remain from a previously more develloped cecum. But it also seems to play a role as a haven for gut bacteria in some conditions.

So, is it leftover junk or not? Would it disappear under the pressure of natural selection over time or not?

[Starver]

Junk DNA is a bit of a misnomer. If it were really junk, it would get removed from the genome pretty quickly naturally. It's not so much "Junk" DNA, it's more "We don't know what it does yet" DNA.

Just in case you missed it, that was my gist.  Possibly you didn't and you were expanding on what I said, though, in which case thank you.

[Sheb]

Why would it be removed though? The cost of DNA replication for a large organism is pretty low. I mean, you shouldn't assume that just because something is there, it is useful.

[Starver]

Sheb raised the point I wanted to. Organisms are filled with redundant stuff. I've said before, nature trends towards two things: Hack jobs and efficiency, and somehow the latter comes from the former.

It's all a hack job.  But it's also all (at least anything that's been around for a handful of generations and not causing you problems) a hack-job that generally works.  Which is obviously more efficient than a hack job that doesn't, or an efficiency that falls over due to a critical loss of redundancy.

I mean, why even have two sets of genes?  Surely once the whole hot, steamy gamete-on-gamete mix'n'matching action is concluded, everyone could get away with one of each.  Except for the XX/XY pairing, where us men, at least, need the pair... but women can use just the single X though, right?

(We should all know the answer to those questions.  Consider them rhetorical.  Polyploidy (>2N) also seems to help greatly with adaptability of organisms (up to 12N, last I heard!), but it looks like we manage well enough at the level of diploid (2N), whether or not we could somehow reduce our functional genome to the haploid level if we really tried, by deliberate hacking and patching back up with the molecular equivalent of duct-tape.)

[i2amroy]

Junk DNA is a bit of a misnomer. If it were really junk, it would get removed from the genome pretty quickly naturally. It's not so much "Junk" DNA, it's more "We don't know what it does yet" DNA.

Just in case you missed it, that was my gist.  Possibly you didn't and you were expanding on what I said, though, in which case thank you.

More a case of me typing up my post, forgetting to hit send, and then coming back 50 minutes later with some ninja posts having happened and going "Screw it! Posting anyways!"

[origamiscienceguy]

I've heard that most of the "junk" DNA is  different genomes that are triggered by environmental conditions. So somebody born in environment A would be different than someone born in environment B. Even if their DNA was exactly identical.

[wierd]

What is this? I leave for a month or two, and the space thread devolves into some kind of horror show hybrid of a David Icke and Jack Chick marathon. WTF.

Anyway....

Concerning "Green cows"- Chlorophyll is not the most efficient quantum energy shuffling molecule out there. Recently, there was research into synthetic viral capsids that are more efficent at collecting photons and concentrating the resulting electron/hole pairs. The figures put clorophyll to shame. It should be noted that the capsid does not direct the energy into an actual process-- however, modifying the structures involved so that the energy actually is used for something seems to be a technically plausible scenario. 

http://news.mit.edu/2015/quantum-physics-engineered%20viruses-1014

The deal here is that chloropyll is only receptive to photons of certain narrow bands in the visible spectrum, where the synthetic chromophore compounds used in Loyd and Blecher's work can potentially use much wider bands, meaning much better overall energy absorbtion, coupled with an efficient transport system. If applied to actual organisms, the potential for vastly improved cellular processes in plants is quite apparent.

I somehow doubt that, given the potential for much wider bandwidth of useful spectra, that the resulting humans with such modifications would be green.  The ideal color would be black. (as in, REALLY black. Not brown.)


Concerning "Junk DNA", I direct you to the plant with the single largest genome-- It contains 'Junk DNA" from many different plant, bacterial, (and even animal) species, as the result of some SERIOUS horizontal gene transfers.
http://www.the-scientist.com/?articles.view/articleNo/38729/title/Genomes-Gone-Wild/

[Reelya]

I've heard that most of the "junk" DNA is  different genomes that are triggered by environmental conditions. So somebody born in environment A would be different than someone born in environment B. Even if their DNA was exactly identical.

Even if their DNA was exactly identical.

Just 100% no on this. "Junk" DNA is part (most) of the total DNA, and all DNA resides in your 23 chromosome pairs. So someone with differing junk DNA cannot have "exactly identical" DNA at all.

What you're talking about - the genome triggering differently in different environmental conditions is called "epigenetics", i.e. changes independent and at a higher level than whatever DNA you happen to have, "junk" or otherwise. Yes, this happens, but the concept has 0% relationship with the "junk DNA" concept.

There's no objective basis for DNA being "junk". A "gene" means a section of DNA which codifies a protein or RNA sequence, and scientists took this to be the main building-block of the DNA. The set of all DNA was then called the "genome". So, semantically it made no sense to say that DNA which isn't part of a gene is part of the "genome" as well, so it got the "junk" label. But nature doesn't even know what "genes" are, it only knows DNA base pairs. Where one "gene" starts and ends is a human distinction, not something encoded into DNA in any objective sense.

[wierd]

Pretty much-- but there is also genuine "junk" in there. Things like deactivated retroviral DNA that became part of the germ line, repeating sequence transposons, run of the mill copy-errors, etc.

Another useful role for carrying such "junk" around, is that it reduces the likelihood that a random mutation (say, caused by a cosmic ray particle, or by UV exposure, or (insert ionization source here) happening in a vital section of DNA. If you carry around lots of non-coding junk, a mutation there wont kill you.  If your genome is "Super efficiently lean"-- a mutation is pretty much always a bad thing.

Evolution deals with the "Good enough"-- not with the "Theoretically ideal maximimum"

Another really interesting theory for carrying around lots of "junk", is that it helps with efficient chromosome packing (physical folding geometry of the chromosome) within the nucleus.

To wit:
http://jcb.rupress.org/content/157/4/579.abstract