Is information added to genome by evolution?

[apeiron]

As Jon said, some testing really has confirmed the "junk" nature of some, but others do seem to be useful in odd ways (mRNA as referenced earlier). That said, you assign too much purpose to our genome, which as always, is concerned with the survival of the genes, not us.

As for mechanisms to remove junk, that would take evolution, and we're not that old as a species, and everything else evolves as well. Remember, that "Drag" has to be significant enough to be a selective trait, or not, and it may be that once it DID have a function. Now, it's junk...

Maybe some of those stretches are useful for the next ice age, or like, or not. Either way, we're efficient in terms of what is transcribed and codes proteins, but not necessarily in terms of what sticks in the DNA as a whole.

This sounds like a reply, but it really isn't.

 

[Frame Dragger]

This sounds like a reply, but it really isn't.

Ok, if you want a technical reply, there's that as well.

By thinking of the human organism as a whole, with its genome being entirely streamlined for current conditions is a fantasy. Each cell in our body has the same copy of our DNA, and it is the propagation of those genes that is subject to this discussion. We are in direct competition with much of the life in this planet (or all of it from the genetic point of view), and the assumption that we have the capacity to simply remove junk code in a time-frame such as the one you specify is unlikely.

To be "visible" to selection is the issue, but you're being anthrocentric, when the issue really is much more global. You posit that some is not "visible" to selection, and my reply is that is simply silly from the view of molecular biology, although bioinformatics sometimes gets into that. Our DNA is simply not subject to a mechanism for hiding, except by symbiosis, or just parasitism.

Of course, as I mentioned earlier in the thread referencing SCD and Malaria, some adaptations become less useful, then junk. Assuming no medicine, SCD would be highly visible, and selection would do the rest. That's obviously not the case now, but what of regions for more hair, or a bit of tail, etc...?

This is all complicated by the fact that again, reading a genome is extremely UNilluminating on its own. So, if you want to say that this junk is there for mutation, who can say otherwise at this point? I doubt that, as mutation can occur without the junk, and selection for potential future mutations is not really natural. Perhaps those regions provide material for 5`, 3`, or other portions used during transcription, editing, etc... That doesn't work to express proteins, but again, who knows. Some genes regulate other genes expression, and that can be hard to see, but it's not junk. That said, I can see such genes becoming junk over time, and being harder than most to 'remove'.

What IS known now, is that mRNA and miRNA play much larger roles than previously thought, and no, I don't know (nor does anyone) what the full extent of that role is. Remember when people thought that simply mapping our genome would be the end of all mysterious illness and such? Yeah, now we worry about how they code proteins, why some are activated by environment, and the realization that genes act in concert beyond (any) expectations.

That's damned complex, and therefore what is junk and what is not may be up for grabs. There is JUNK however... but maybe the issue is how you define junk. Finally, while we're up for selection always, we're following the model of an apex predator and then some. It's hard to say why, but our DNA is full of junk compared to saaaay, the favourite of biologists everywhere: Drosophila (melanogaster).

What can I say, mammals in general, and humans in particular just have not been subject to natural selection for the duration that saaaaaaay... crocodilians have. That has a profound effect, especially when I question the impact of this "drag". It's not as though much of that material won't be recovered upon apoptosis (traumatic damage... who knows).

You asked a brief and general question. You got a brief and general answer... I don't believe that it requires the response you gave it. If you'd like to offer your view beyond vagaries, I'd be more than happy to engage more deeply.

 

[apeiron]

You asked a brief and general question. You got a brief and general answer... I don't believe that it requires the response you gave it. If you'd like to offer your view beyond vagaries, I'd be more than happy to engage more deeply.

You are responding to something you imagined.

I said if there is junk DNA, then it is indeed an issue over how it is invisible to the winnowing force of selection.

1) It could be just that the timescales don't allow a clear-out (selection would act very weakly on the junk).

2) It could be that the junk is functional in some fashion (either as a reserve of mutation potential or because it is actually epigenetic machinery - and the existence of epigenetic machinery of course does not rule out also the existence of an element of junk).

3) The actually different possibility I then raised was that junk DNA is properly parasitic and has evolved defences against being noticed, therefore being removed by selection.

Parasites do evolve to fly below the radar of a host's immune system, a genome's selective processes. And the mRNA example is relevant if you take the very attractive symbiotic hypothesis of Lynn Margulis concerning organelles generally.

So 3) was the question, as much as I was raising a question here. You can focus on that if you like.

 

[Frame Dragger]

You are responding to something you imagined.

I said if there is junk DNA, then it is indeed an issue over how it is invisible to the winnowing force of selection.

1) It could be just that the timescales don't allow a clear-out (selection would act very weakly on the junk).

2) It could be that the junk is functional in some fashion (either as a reserve of mutation potential or because it is actually epigenetic machinery - and the existence of epigenetic machinery of course does not rule out also the existence of an element of junk).

3) The actually different possibility I then raised was that junk DNA is properly parasitic and has evolved defences against being noticed, therefore being removed by selection.

Parasites do evolve to fly below the radar of a host's immune system, a genome's selective processes. And the mRNA example is relevant if you take the very attractive symbiotic hypothesis of Lynn Margulis concerning organelles generally.

So 3) was the question, as much as I was raising a question here. You can focus on that if you like.

Again, the notion of parasitic genes is one that I don't feel requires any more answer than #1. Given time, it COULD be winnowed out... remember, no plan means that chance plays a factor as well. The other side of #1, is that while our machinery removes the junk, more junk is inserted. In 100K years, what will be junk? I'm saying your entire premise is essentially flawed; our genome has had viral success, and when our species inevitably perishes, it will be the genetic material that is in the game for selection, or not.

Again, I believe you need to define the magnitude of "drag" that parasitic genetic material exerts. The symbiosis hypothesis works well in my mind, but not for ALL of this material, nor does the epigenetic approach. I also question how a virus for instance, evolves outside of the context of a host? It comes down to genomic war, and I don't know that it matters if the DNA is HIGHLY visible. In the end it will be raw material again, with fairly minimal loss. Unless the material results in saaay... genital warts (or any Herpes)... where I think everyone appreciates that in a different time it would be a HIGHLY selective feature.

If you simply have a few hundred base-pairs however, that is normally used during transcription... well, maybe junk material in small quantities is useful, but not inherently so.

As for a question... fair enough, but this is at least a discussion. Replace "asked a brief and general question" with "Made brief and general statement I disagree with.". I didn't imagine what you said, and I am deeply unimpressed that you are leading with rhetoric first.

Clearly you favour Lynn Margulis... who's hypothesis (or wild swing...) is far from mainstream, or accepted. She's under constant fire for pushing her views, and using her position to do so. I am unimpressed by her theory compared with timescales. Anthrocentrism... again.

If you don't want to talk about this, probably, this isn't the right thread for you? If you do, at least have the courtesy to do more than be terse. I certainly won't retain anything like this semblance of polite discourse in that case, nor do I feel I should. If this were in Physics end, I'd just reply "ATM", and blow you off, and rightly so. Proof, if such were needed that biology is a truly weak and derivative science. At this point molecular genetics, physics and chemistry are far better lenses into these matters... biology is merely the result of that. My view of course, but I figure... one ATM view for another.

 

[apeiron]

Again, the notion of parasitic genes is one that I don't feel requires any more answer than #1.

I wish you could follow the simplest of arguments. If the answer is 1, then there is just junk and no need to invoke the higher level of complexity that a parallel with parasitism implies.

I'm saying your entire premise is essentially flawed

What entire premise? The standard idea that selection reduces variety?

I didn't imagine what you said, and I am deeply unimpressed that you are leading with rhetoric first.

That made me laugh out loud. Someday you will surprise me by referring to recognisable bodies of theory and offer clear references. Windy, unfocused rhetoric is all we get instead from you.

Clearly you favour Lynn Margulis... who's hypothesis (or wild swing...) is far from mainstream, or accepted. She's under constant fire for pushing her views, and using her position to do so. I am unimpressed by her theory compared with timescales. Anthrocentrism... again.

Why the ad hominen attack on Margulis? Can you cite who these people are who feel it is a wild swing, that she is using her position to push her views?

And then what else do you do in academia? If you don't have view that you are pushing, and you haven't earnt a position, then you are in the wrong game.

If you don't want to talk about this, probably, this isn't the right thread for you? If you do, at least have the courtesy to do more than be terse. I certainly won't retain anything like this semblance of polite discourse in that case, nor do I feel I should. If this were in Physics end, I'd just reply "ATM", and blow you off, and rightly so. Proof, if such were needed that biology is a truly weak and derivative science. At this point molecular genetics, physics and chemistry are far better lenses into these matters... biology is merely the result of that. My view of course, but I figure... one ATM view for another.

Oh yeah. We've heard all this before. How you are being very patient with a lightweight like me and at any moment you are going to pull out your super-duper intellectual weaponry (which has been cleverly concealed thus far) and terminate me, dude. Physics uber alles! you will holler as you pull your (sadly imaginary) trigger.

 

[Frame Dragger]

Wow... you are one angry, uninformed person. You ascribe to Margulis, but you have no notion of any controversy regarding her, or that her theory is increasingly... fringe.

That said, always good to know when a nerve is struck, although I have to say the ad hominem attacks seem to be coming from you... circa #31.

Oh, and if you've been paying such close attention to my posts in the past, that you believe I'm full of wind, you'd long since know that I've made it clear quite a few times just how INexpert I am, and that I'm NOT in academia. Really, if you can't engage on substance, don't, because as far as "gun" metaphors go, you've been shooting blanks for a while on this thread... which really isn't your style usually (from what I've seen).

EDIT: As for #1, the lack of need, vs. timescale is your answer. It WAS parasitic, now it's junk, with a metabolic "Drag" as you so eloquently put it. It isn't JUNK, if it is surviving the process of selection, and it is still parasitic to some degree by demanding metabolic resources. That is junk, and it's origins are parasitic or accidental. I'm still waiting for you to quantify and clarify the metabolic drag, or answer any question put to you that isn't fitting your internal narrative.

 

[Jon Richfield]

I'm more with the camp that expects junk DNA to actually have epigenetic function, so it would be visible to selection anyway.

There is a lot to be said for this. It is hard to imagine DNA that has exactly zero effect, either positive or negative. However:
1: Bear in mind that some DNA has a slightly negative effect, and some not so slightly, also some has a slightly positive effect and some not so slightly (I leave the exact accountancy to you, because in practice there are all sorts of multidimensional, multifactorial effects that I ignore here, out of sheer prudence!) The implication is that there should be some in the continuum that has zero effect. More to the point <ahem!> there is a fair amount of scope for harm or function too slight for us to detect the effect in any reasonable time.
2: Something else that escapes my memory.

But it there is actual junk, then as you say, it would seem to be at least weakly visible. So it may pay for itself by occasionally being a useful pool of mutation - enough to balance its metabolic drag.

Yes, junk DNA is a useful concept in terms of mental stimulus. Another possible function that springs to mind is as a target for viruses, such that a virus that lands in junk does no harm because there is no activation code to activate it.

However another thought. If junk DNA is actually parasitic, then it may have evolved mechanisms so as not to be visible. It may have evolved mechanisms to ensure it stays switched off and out of the gene pool. It may have evolved to be non-living, or non-evolving, in effect.

Yes, I think it was Francis Crick who proposed parasitic DNA back in the late seventies or so - early eighties perhaps? It was a good bit of thinking, but last I heard it had turned out about as hard to show that a piece of DNA was parasitic as to show that it is junk - possibly harder. It is a very tricky concept in practice.

After all, parasitism itself is very tricky! How much of our so-called "normal flora" is parasitic and how much is symbiotic? And for whom?

And think of hedgehog fleas; remove them as a favour to the hedgehog and it is likely to languish or even die. The suspicion is that it needs their stimulation, though I am not aware of definitive research on the subject.

Let's just sign off before I get too itchy!

Jon

 

[apeiron]

Wow... you are one angry, uninformed person. You ascribe to Margulis, but you have no notion of any controversy regarding her, or that her theory is increasingly... fringe.
.

Richard Dawkins: I greatly admire Lynn Margulis's sheer courage and stamina in sticking by the endosymbiosis theory, and carrying it through from being an unorthodoxy to an orthodoxy. I'm referring to the theory that the eukaryotic cell is a symbiotic union of primitive prokaryotic cells. This is one of the great achievements of twentieth-century evolutionary biology, and I greatly admire her for it.
http://www.edge.org/documents/ThirdCulture/n-Ch.7.html

Wow... you are one angry, uninformed person. You seem to have no ability to sort out what is generally accepted as a likely mechanism in evolutionary biology and the other stuff Margulis might have said.

I've made it clear quite a few times just how INexpert I am, and that I'm NOT in academia.
.

Yes, your every post confirms this. So why do you always jump in so confidently with no facts to back you up?

EDIT: As for #1, the lack of need, vs. timescale is your answer. It WAS parasitic, now it's junk, with a metabolic "Drag" as you so eloquently put it. It isn't JUNK, if it is surviving the process of selection, and it is still parasitic to some degree by demanding metabolic resources. That is junk, and it's origins are parasitic or accidental. I'm still waiting for you to quantify and clarify the metabolic drag, or answer any question put to you that isn't fitting your internal narrative.

You would have to untangle your garbled logic here before any response would be possible.

 

[Jon Richfield]

Congrats on finding such a clearly compatible wife as well (golf aside)!

Sorry I gave the impression that SHE likes golf! That was another relative by marriage! My wife is far too involved with things that matter and are of more practical or intellectual interest. (This makes for a wearing life, but satisfying!  )
Oh, and btw, she had the camera that day, and took the picture. The blasted birds were so well camouflaged that the pics were practically worthless!

Oh, and I had no CLUE what a "frogmouth in a banksia" was, but thanks to the wonders of the internet, I do now! They rest horizontally?! Australia... love the people, but the fauna seems to range from beautiful and odd, to deadly and odd. I'm not even touching the flora... no pun intended.

You are prudent. As a biologist I did a lot of touching. Among other things I touched a soft-looking cushiony grass that grew in expanding circles. I later discovered without the slightest surprise that its local name is porcupine grass!

Wow, something about the way you said "I spotted a pair of frogmouths in a Banksia..." that made me think of, "A damsel with a dulcimer in a vision once I saw..." ... and I'm not sure why...

Well, I am not into opium, though I have been known to commit public alliteration, but I confess to considerable pleasure on the occasion. I had had a soft spot for frogmouths ever since having seen them in pictures as a child, but had never expected to see them in the wild because I had realized that their camouflage was something impressive (It IS!) So really, it would have had to be quite a special damsel whose dulcimer could have given me anything like the same thrill!

On another subject, I have had a great respect for Margulis ever since I first encountered her work (nth-hand) in promoting the concept of endosymbiosis. I realize that it goes back a long way before her time, but she certainly put it on the map. Now, admiration need not entail undue lack of critical appraisal, and I have serious, though not as yet coherent, reservations about the generality of her views on (largely endo-)symbiotic communities as organisms. That strikes me as Gaia-like hand-waving. You see, the concept of how an association amounts to an entity, and when an entity comprises an “organism” in a non-trivially useful sense, is far from obvious in any cogent sense. I have not yet had the time and impetus to think it all out satisfactorily, but I am at least sure that whereas extremely intimate endosymbiosis can be regarded as comprising an organism even when it is reasonable simultaneously to regard that very association as an association of conceptually distinguishable individuals, there are looser associations that one need not regard as organisms in any non-trivial sense. For example, one of my sons attended a lecture she gave at a time when he was a chemical engineer, but not yet formally a biologist. He asked her whether in the light of several themes in her lecture she regarded a ruminant plus its rumen flora as an organism. The response was essentially “Yes.”
Now, he said that she seemed ill at the time and the questions were cut short about then, but taking the event at face value, while I take the point, I think the point is stretched in such an example, much as I take the point of regarding Gaia as an organism as decidedly over-stretched. Considering Gaia as an organism with homeostatic functions and what amounts to teleologically self-preservational capacities, I regard as irrational mysticism.

I still regard her with respect, and I still regard the concepts of endosymbiosis and even eusociality as ranging from association to integration in various concepts. Some forms of hydrogenosomes for example, I see as exceptionally interesting and intellectually exciting.

But not appropriate for getting into a spat over, if it is possible for me to say so without annoying anyone.

Cheers,

Jon

 

[Frame Dragger]

Well, if Dawkins admires her, that's all the proof I need. Certainly that not a fallacious appeal to authority.

As for the rest, it's just childish. I can't claim that I've seen you behave this way elsewhere, so I assume you simply dislike me for the reasons states. I'm sure you can imagine how deeply that wounds me. I'll leave it to those whom you respect to correct your errors, or not. If you feel the need for a "last word", by all means, feel free to have it. I'll simply continue as though you were making 0 meaningful contributions... which is surprisingly easy.

Oh, and if you want to research Lynn Margulis, beyond simply quoting Richard Dawkins, you could start with this, from Wikipedia. Not the greatest source, but then, I'm sure you can take it from here.

Controversy
In addition to rejecting Neo-Darwinian evolution as an explanation for diversity, Margulis holds a number of opinions outside of mainstream science. In 2009 she co-authored a paper [7] arguing that the change in spirochete form, from more motile helical to more inactive cyst and back, may be a causal contributor to AIDS. In 2009 she also pushed the journal Proceedings of the National Academy of Sciences (PNAS) to publish a paper by Donald I. Williamson arguing that butterflies are the result of hybridization of a now extinct insect and velvet worms[8][9]. As a member of the National Academy of Sciences, Margulis has the privilege of "communicating" scientific papers, allowing them to be published with minimal review. Williamson's paper provoked immediate response from the scientific community, including a paper in PNAS [10]. Developmental Biologist and Professor at Duke university Fred Nijhout was quoted as saying that the paper was better suited for "National Enquirer than the National Academy.". In September it was announced that PNAS will eliminate Communicated submissions in July 2010 but PNAS stated that the decision had nothing to do with the Williamson controversy.[9]

http://en.wikipedia.org/wiki/Lynn_Margulis

From there, I suppose you just have to check the footnotes. Have fun!

EDIT:
@Jon Richfield: Well, it's good to hear that you can appreciate the poetry without the aids Coleridge "used". I've had some similar experiences when it comes to "touching the pretty flower"... or in my case, the pretty razorgrass... which is WELL NAMED.

Anyway, glad to hear that your wife isn't a golfer, I was reaching deeply into my bag of diplomacy in responding there! As for damsels... Angie Everheart, in her prime... Hmmmm.

As for Margulis, that is essentially my impression, although I don't believe she's TRYING to formulate something quite that... spiritual or off-kilter. Then again, it's what she seems to be pushing more and more. It's one thing to respect her, but as you say, another to accept her current theories which were based on notions of how DNA could be "read" and "understood" that simply have not been realized. I appreciate her ability to look beyond the obvious darwinian model, but an interesting personal hypothesis has taken her down an unfortunate road in my view.

Then again, how many people respect Stephen Hawking, but also think he's utterly wrong re: Information Paradox? "Spukhafte Fernwirking"... 'nuff said.

 

[apeiron]

Oh, and if you want to research Lynn Margulis, beyond simply quoting Richard Dawkins, you could start with this, from Wikipedia. Not the greatest source, but then, I'm sure you can take it from here.

You ask why I might dislike you. I don't know you. I can only judge your online behaviour.

This is precisely an example of the behaviour I dislike.

I show you that Dawkins endorses not only endosymbiosis but even Margulis herself (which is going quite far really). Then you respond with a wiki reference as if I've only just heard of Margulis, endosymbiosis, and any controversy. As if I need the educating here.

I've read her papers. I've got her books on my shelf.

What gives you the right to be so insulting? Next time you decide to mount an attack on me, just do a little homework first.

 

[Frame Dragger]

You ask why I might dislike you. I don't know you. I can only judge your online behaviour.

This is precisely an example of the behaviour I dislike.

I show you that Dawkins endorses not only endosymbiosis but even Margulis herself (which is going quite far really). Then you respond with a wiki reference as if I've only just heard of Margulis, endosymbiosis, and any controversy. As if I need the educating here.

I've read her papers. I've got her books on my shelf.

What gives you the right to be so insulting? Next time you decide to mount an attack on me, just do a little homework first.

You didn't really need to say that, it was obvious from the moment I showed disrespect for someone you like. Again... childish. As for Richard Dawkins, see my comment regarding Stephen Hawking. You're making the same appeal to authority, and this from someone who throws about "ad hominem". What a shock. If you ever decide to respond to substance, go for it, but it seems to me that you're simply advocating her theory. Again, I'm unimpressed.

As for my behaviour, it would seem that it has been a mutual escalation, one I'd say that you began with "that sounds like a response..." You set the tone, and defended what you perceived as an attack on Margulis, with purely ad hominem **** directed at me. The most I can say is that, like Fox News, you are at least relentless in your narrative.

 

[apeiron]

Well, if Dawkins admires her, that's all the proof I need. Certainly that not a fallacious appeal to authority.

As for Richard Dawkins, see my comment regarding Stephen Hawking. You're making the same appeal to authority, and this from someone who throws about "ad hominem".

So which is it? Do you feel Dawkins is an authority or not?

 

[Frame Dragger]

So which is it? Do you feel Dawkins is an authority or not?

Your appeal to his authority is fallacious... again, more rhetoric, and even less substance. Take this up in a PM (which, to be fair, I will ignore) if you like, but you're cluttering the thread.

EDIT: Have fun talking to yourself or others apeiron, I'm done with you.

 

[apeiron]

Your appeal to his authority is fallacious... again, more rhetoric, and even less substance. Take this up in a PM (which, to be fair, I will ignore) if you like, but you're cluttering the thread.

No, you appear to make two completely contradictory responses here. Are you saying that if Dawkins gives a clear endorsement of endosymbiosis/Margulis then:

a) You do not view Dawkins' endorsement as authoritative.

b) You do view Dawkins' endorsement as authoritative.

As to PMs, why should I spare your blushes if you continue to make a fool of yourself with disorganised and unreferenced responses?

 

[berkeman]

Closed pending moderation.