Wikipedia:Reference desk/Archives/Science/2015 December 4

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December 4

Humans without junk DNA

Yes, I know that the question of whether apparently useless DNA has in fact some purpose is a controversial one, but it still seems strange that some organisms are virtually free of non-coding DNA while others, including our own, have genomes which are more than 97% junk. If junk DNA does have some purpose, why this disparity? And, following on from this, we would now have the capacity to delete all such DNA from a genome. Would a human be in any way different if they had no such DNA in their genome? Myles325a (talk) 04:35, 4 December 2015 (UTC)

These categorizations are controversial, because they often work from different definitions. When one decides that DNA is "junk" DNA (formally noncoding DNA, there are many ways one can define the terms. Strictly speaking, noncoding DNA is merely DNA which does not directly translate to a protein's amino acid sequence. Claims of "97% junk DNA" generally work from this most restrictive application, while lower estimates (including the low value of 20% junk DNA) are based on notions that DNA have other important biological function aside from merely being a code to create proteins. When you have reliable, scientific bodies varying in estimates as wide ranging as 20%-97%, it's quite clear there's major definitional problems that need to be solved before one can even start to approach to answer the question of "why", the why question is irrelevent until we get an agreed upon answer to the "what" question, and "what" is all over the map. --Jayron32 04:43, 4 December 2015 (UTC)

OP myles325a back live. See, this is what really gets me down on the floor and dragging up carpet tacks wid my teeth while making noises like a Tasmanian Devil on crack. I ask a perfectly sensible question which would be comprehensible to 99.0% of WP readers and I get a brusque note from a trophy polisher basically telling me nothing except that I am an ignoramus and a dickhead. Your answer is nought but garrulous and pompous evasiveness. I note that you make no attempt to say what the “useful” component of non-coding DNA actually does. In any case, even if you knew, my question would still stand. Is that component of DNA which does not “merely” code for proteins necessary for life, and what would happen if you deleted it? I’m a plain-speaking Australian, who has asked an honest and sensible question. It is your answer which is “irrelevent” (sic). Myles325a (talk) 02:44, 7 December 2015 (UTC)

To answer the second question, a human embryo with all noncoding DNA removed would just die. We know that at least some of noncoding DNA is essential to life; one example is telomeres in eukaryotic cells. This is largely why scientists don't like the term "junk DNA", because it has misleading connotations. --71.119.131.184 (talk) 05:18, 4 December 2015 (UTC)

OP myles325a back live. Waaahh, pooor bubba. However, I am supposing that telomere length in a new cell IS determined by DNA coding, else male sperm cells produced by a 60 year old man would inherit the truncated version, and this would be passed down to his progeny. So bubbs lives after all. Not too sure about this, but in any case, one instance can hardly champion the 97% of DNA which does not code. Myles325a (talk) 02:54, 7 December 2015 (UTC)

@Myles325a: See Telomerase. There are special issues involved at the ends of chromosomes - DNA there may shorten, or in the presence of the right gene activity, lengthen. Technically I suppose such DNA is not genetic material at all! It is simply a structural sugar in that region, much as scientists imagined before the bases were discovered. However, adjoining sequence doubtless has some sort of effect on how much telomeres are extended. Wnt (talk) 16:32, 7 December 2015 (UTC)

Coding DNA determines which proteins the body can make, but it says nothing about where and when they should be made, or in what quantity. That information is contained in the noncoding DNA, encoded by a variety of mechanisms. Also, as the answer above points out, noncoding DNA serves several mechanical functions. Looie496 (talk) 13:37, 4 December 2015 (UTC)

So you're saying that non-coding DNA is involved in gene expression, right? That article mentions non-protein coding DNA, and also non-coding DNA, and non-coding RNA, and a few other categories that seem hard to keep straight. Non-coding DNA can also affect mechanical properties of DNA, such as DNA supercoiling, and that can also affect gene expression in some organisms. SemanticMantis (talk) 14:11, 4 December 2015 (UTC)

OP myles325a back live. See, SOMEONE thinks that I am asking a reasonable question. We know that the genome has vast real estate of evolutionary dead ends and meaningless repetitions. (I believe that about 3% of DNA comprise these repetitive strings, so we have as much DNA devoted to accidental repetition as we have to the coding DNA. It is interesting to think that the long stretches of DNA deriving from now non-functional phenomes is necessary for proper genome and phenome expression today. But what then about the organisms, like puffer fish, who have next to no non-coding DNA. And why would organisms like wheat need so much of it. Myles325a (talk) 03:14, 7 December 2015 (UTC)

That's why "junk" DNA is misleading, and also why placing such an emphasis on "noncoding DNA" vs. "coding DNA" is also misleading. The fact that some string of DNA doesn't directly code for a protein sequence doesn't mean it isn't necessary, or that you could remove it with no harm. --Jayron32 14:19, 4 December 2015 (UTC)

OP myles325a back live. Groan, the trophy polishing hair splitter is back. The reason we would place such an emphasis on DNA which "merely" codes, is that just about all we know about the makeup of an organism comes from there. You seem sure that non-coding DNA is important, but you provide no clue as to why it is. And yes, as you say, the fact that "some string of DNA doesn't directly code for a protein sequence doesn't mean it isn't necessary". Agree, but it also does not, ipso facto, guarantee that it IS necessary. The SCIENTIFIC way to ascertain the truth in such circumstances, is to do as I have suggested and delete the non-coding DNA of an neonate. If doing this to a human embryo is considered unethical, we could use a hamster or a rat or a pig or such. Myles325a (talk) 03:14, 7 December 2015 (UTC)

@Myles325a: Doing this experiment on a genome-wide scale in a mammal is beyond present capability. See minimal genome/synthetic life - to test the deletion of unnecessary DNA from one of the smallest known genomes is a massive undertaking. Wnt (talk) 16:32, 7 December 2015 (UTC)

If there's selective pressure to reduce DNA length, this can be done, but normally I think it takes a long time. Some of the deletions could turn out to be deleterious after all, and then the organism needs a way to compensate for them. Doing it as an engineering project requires absolute confidence in one's knowledge of what every base-pair is for, and we don't have that.

OP myles325a back live. Hmmm Wnt, I appreciate your thoughts, but in the above you seem to have segued between deletion via natural selection and deletion by geneticists. Luckily, the quality improves after this initial blooper. Myles325a (talk) 03:21, 7 December 2015 (UTC)

No matter how the deletion happens, it has the same effects. When it occurs naturally, many generations separate each random experiment, and so it is possible that if it reduces or increases the expression of a nearby gene, a corresponding promoter variant will turn out to be selected to reverse that effect: the deletion might be retained and some other change made. But in an artificial experiment, if you wanted to delete hundreds of noncoding sequences at once, all the minor decreases in fitness would take effect in the same moment, and you might simply fail to produce viable offspring. Wnt (talk) 16:47, 7 December 2015 (UTC)

A specific role of the junk DNA is in posttranscriptional regulation. Something like an Alu element can occur in a sense or antisense configuration in an mRNA. If so, that mRNA becomes subject to a network of sense-antisense interactions that may affect where it goes in the nucleus and how active its translation will be.

OP myles325a back live. Ok, Wnt, but while I understand but little of the page you refer to, it DOES seem to be devoted to the special role of RNA on posttranscription processes. That means there are certain changes which are not the result of DNA coding, but there is nothing there, as I read it, relating to the usefulness of stretches of non-coding "junk" DNA. Myles325a (talk) 03:33, 7 December 2015 (UTC)

The simplest case is the interaction between sense and antisense. It doesn't matter what the sequence of an element is - if it finds a corresponding antisense RNA, the two will interact in a way that has effects on the entire transcribed gene. See shRNA, siRNA. Also, I suppose the insertion of a transposon changes the structure of an mRNA, which might affect how it is spliced among other things.

Even when a transposon is not part of the transcribed gene, it is possible that specific regulatory elements in the transposon have a beneficial effect on nearby transcription, or that by producing heterochromatin it creates a context where the activity of a nearby gene is repressed unless something binds to a specific factor on it. Biology doesn't have a sense that these genes are spam and can't be used for anything (except in the general but unreliable sense that they might lead to heterochromatin formation, gene silencing, etc.); it can and will have gone ahead and worked with any activity they happen to have. Over time, some of these will have evolved to be important. Wnt (talk) 16:47, 7 December 2015 (UTC)

In the longer term, purging genomes of junk DNA could be a bad thing. The junk elements have a tendency to sit down in introns, because otherwise they disrupt genes - they sort of "press" on the genome with a constant stream of deleterious mutations, which might seem good to get rid of.... but later on, homologous recombination can create what you might call "Hopeful Monster" genes, some exons of this spliced onto some exons of that, in a way that random breakage or less specific homologous recombination would rarely manage (i.e. with many fewer translatable genes produced per mutation, and therefore, with a much higher cost for the same amount of evolutionary experimentation). So it's possible you might purge these genes and a hundred million years out the species hasn't had the opportunity to change as much as another. But here I'm just guessing, because how do you test that? It's really, really hard to predict what messing with biology in a new way will do, that's all. Wnt (talk) 15:54, 4 December 2015 (UTC)

OP myles325a back live. This is a beautiful concept. Much of evolution proceeds via random mutations, and if there was a storehouse of abandoned genome sequences, and even sequences from other organisms, held in escrow in the genome, then there might be a rich treasure house of genomic sequences which could be recombined and brought back from the wings to centre stage again (to mix a metaphor in a context which invites such). Thus, the happy monster. I did have an idea earlier that such a treasure house could be opened by excessive radiation, which accelerates mutation rates. Thus, a dystopia occurring after a nuclear war, when new phenotypes are needed, might trigger the reactivation of ancient phenotypes like body hair. As the dying sun expands and solar radiation begins to strip away the atmosphere, high radiation rates might foster de-evolution, reintroducing hardy organisms which can withstand such ferocious conditions. Then again, evolutionary processes are not teleological (end-directed) so it is hard to see how they could be favored by natural selection on a generation by generation level. But I digress.....Myles325a (talk) 04:04, 7 December 2015 (UTC)

Well, as seen at Chernobyl, life can withstand increased mutation rate with relatively little obvious harm, but it can impose a heavy cost in terms of spontaneous abortion. I am eager to see whether it has long term effects on lifespan, but I'll avoid too much hypothesizing at the moment. Much of what you say above seems unlikely - when environments change, life struggles to adapt. Sometimes it succeeds, sometimes it fails. When the Earth enters its final greenhouse phase (definitely within one or two billion years, perhaps within one or two hundred) I don't expect much to survive, though some organisms can survive autoclave conditions and might linger on for a fairly long time deep below the surface. Wnt (talk) 16:54, 7 December 2015 (UTC)

(ec)If we assume (keeping in mind it's a controversial assumption) that "junk DNA" is unnecessary for humans to function, the question naturally arises of why it's kept around. (For the persnickety pedants, treat this as a Gedankenexperiment.) But one possible explanation that doesn't necessitate function is similar to that for neutral drift. The extra DNA may be kept around because there's no strong selective pressure to remove it. Humans have several years to replicate our germline cells. Even our somatic cells are able to be somewhat leisurely in replicating - normally taking several hours for each doubling. There's plenty of time to replicate all of that DNA. Material costs aren't really limiting either - if humans were resource starved, it's easier to remove whole cells (e.g. not grow as big) than try to trim fractions of a percent of the metabolic cost by reducing the amount of DNA. Contrast this to organisms which are lean, mean, "junk DNA"-free machines. These are normally bacteria and viruses who take the tactic of replicating fast and reproducing as much as possible as quickly as possible. For them, every second they don't have to spend synthesizing DNA is one second faster on the replication cycle, and by reducing the amount of DNA, you can possible squeak out an extra generation or two in a resource poor environment. Also, with a quick reproductive cycle and a boom-and-bust population dynamic, there's many more opportunities for small selective pressures to act on the population. (Remember, there's no junk DNA specific cleaner. Excess DNA has to be removed via random deletions, which are as apt to remove a stretch of DNA with a necessary function as to remove a stretch which is superfluous. This means that insertions can be less disruptive than deletions, leading in an asymmetry in the unselected DNA growing/shrinking balance.) Finally, even if portions of the "junk DNA" are doing things like serving regulatory or structural functions, those quickly-reproducing organisms have an incentive to find alternative mechanisms for those functions, ones which are less time and resource intensive. Humans don't necessarily have the same selective pressure to the same extent. - So in addition to "Why don't humans get rid of junk DNA?", it might be helpful to consider "Why would they?" -- 160.129.138.186 (talk) 16:19, 4 December 2015 (UTC)

Nature is doing try and error. Some of the junk DNA might still have an epigenetic background. Some of it makes its owner resistent to several unknown conditions. Influenca can kill people never came in touch with its successors. Corn has no brain but several times the amounth of DNA as human have. As the decoded the chapters of the DNA, we still can not read it. We can identify the letters, but we do not understand the information, expressed by the DNA code. --Hans Haase (有问题吗) 11:27, 5 December 2015 (UTC)

Endogenous retrovirus makes good reading. Still, the example of Takifugu rubripes tells us that organisms can purge most "junk" without obvious ill effect, at least in the short term. Wnt (talk) 16:07, 5 December 2015 (UTC)

Alcohol rubs when drawing blood

Why is it that some places use alcohol wipes on your skin before drawing blood and others don't. 2A02:C7D:B901:CC00:CCA2:261C:1C78:FFEE (talk) 14:10, 4 December 2015 (UTC)

It may have to do with whether or not the alcohol wipes are adjudged by the organization to be effective or not in disinfecting the injection site. There are some studies on the use of such wipes and their effectiveness; like many such practices there's some information out there to indicate that it isn't all that effective in preventing infection. So depending on which studies the organization is reading up on, may determine the policies of said organization. Some such studies include [1], [2], and there are many more out there. I did also find this forum discussion which cites some more studies. The literature is decidedly mixed. --Jayron32 14:18, 4 December 2015 (UTC)

Better safe than sorry. If someone is intending to draw blood or otherwise insert a needle in you, and they don't wear fresh rubber gloves and/or they don't swab the spot they're sticking the needle in, you had best get up and leave ASAP, and find another clinic. ←Baseball Bugs ^{What's up, Doc?} carrots→ 18:15, 4 December 2015 (UTC)

Unless, let's say, that the swab only killed the harmless bacteria that were competing the harmful bacteria at bay, and keeping them from making you sick. If your swab kills the wrong bacteria, you're going to be quite unsafe, and equally as sorry. That's why some antibiotics mess up your gut flora. --Jayron32 19:04, 4 December 2015 (UTC)

And a respondent here telling someone to leave a medical clinic due to lack of alcohol swabbing seems rather close to medical advice, and specifically it seems like medical advice that is contrary to that clinic's professional practice. SemanticMantis (talk) 19:38, 4 December 2015 (UTC)

Also against the reliable references I provided. But Bugs just writing whatever he feels without regards to what reliable experts have already written about the subject is expected behavior based on past performance. --Jayron32 20:04, 4 December 2015 (UTC)

It should be pointed out that some people getting their blood drawn have filthy skin, and an alcohol wipe is an inoffensive way of cleaning that skin. - Nunh-huh 05:29, 5 December 2015 (UTC)

I thought most people naturally have a "filthy" skin as far as it being a nice place for bacteria to live. I'm not sure whether someone whose beliefs or lifestyle include avoiding alcohol would consider this inoffensive, if that's what you meant. Bazza (talk) 11:04, 5 December 2015 (UTC)

No, I meant filthy as in "covered in dirt". Using an alcohol wipe or two is an inoffensive way of cleaning that up without them feeling judged. - Nunh-huh 13:57, 5 December 2015 (UTC)

Some of this stuff is creeping toward medical advice, and I'm skeptical of some of it. Particularly, I doubt it matters whether you kill "good" bacteria on a small patch of skin before a needle pierce - the wound will clot soon afterward, and if there's a kind of bacteria that are demonstrably good to rub into an open wound in order to antidote the bad ones I don't know about it, though I couldn't actually rule it out. By definition, whatever a significant proportion of doctors routinely do is accepted medical practice. Wnt (talk) 15:42, 5 December 2015 (UTC)

Table 3

I believe the underlying question is the efficacy of the alcohol wipe. It is well accepted that alcohol kills a large amount of pathogens, but why are we now seeing the alcohol rub skipped altogether? The answer is that while it is a statistically significant amount of pathogens killed at the injection site, this isn't practically significant enough to show infection. This article referenced a World Health Organization bulletin , which I read and found Table 3 to be extremely useful.

Even with this bulletin released, which was for muscular shots and not blood draws, the WHO still recommends an alcohol wipe, but honestly I couldn't find a decent reason for this. Jasonmfisher (talk) 15:06, 6 December 2015 (UTC)

References

Holographic universe and Simulation hypothesis

This article:

http://news.sciencemag.org/2015/12/controversial-experiment-sees-no-evidence-universe-hologram

Basically says that the "holographic universe" hypothesis has just been effectively disproved. I know the results of the experiment are controversial - and might be wrong. But if it has indeed proved that there is no fine-scale jitter in the positions of objects, does that also disprove my favorite hypothesis - the Simulation hypothesis? Seems like if objects can be positioned without jitter then the amount of data to completely describe that position must be infinite - which means that the universe can't possibly be a giant computer simulation like The Matrix.

But I'm not entirely sure I understand the holographic universe hypothesis - so it's not clear that this approach to disproving it also disproves the simulation hypothesis too.

SteveBaker (talk) 20:06, 4 December 2015 (UTC)

Holometer is the article (and I guess it needs an update). The whole thing looks iffy to me. This blog post quotes Raphael Bousso and Leonard Susskind as saying that the experiment is useless (long before the results came in), which is pretty bad since they're two of the biggest proponents of gravitational holography. Sabine Hossenfelder and Luboš Motl also seemed to be suspicious of it. The experiment seems like a pet project of Hogan's, albeit one that he got $2.5 million in funding for. -- BenRG (talk) 23:00, 4 December 2015 (UTC)

Great answer - I should just point out that blog post leads on to [3], which is far, far more than I'm ready to digest currently. Wnt (talk) 05:36, 5 December 2015 (UTC)

I don't see how you can draw any conclusions about simulation, based on physics known inside the presumed simulation. Why should the simulators' physics look anything like ours? Maybe they're simulating some entirely counterfactual physics.

In other news, physicalism, materialism, and naturalism may all be false. --Trovatore (talk) 23:18, 5 December 2015 (UTC)

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