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Random Acts of Evolution - Comments

Friend Giskard's Avatar Comment 1 by Friend Giskard

If you like puffer fish you'll like this vid.
http://youtube.com/watch?v=kJEacTZmd7I

Sun, 01 Jun 2008 10:37:00 UTC | #177697

Auraboy's Avatar Comment 2 by Auraboy

I wonder if random repeat transcription was the reason we got half of the article repeating itself? Was that a clever example ploy? Repeating itself? Was that a clever example ploy?


Damn. That God sure was a Microsoft code writer...Useless junk everywhere...

Sun, 01 Jun 2008 10:40:00 UTC | #177699

epeeist's Avatar Comment 3 by epeeist

Comment #187155 by Auraboy

Damn. That God sure was a Microsoft code writer...Useless junk everywhere..
Yeah, the worrying thing though is that no MS software works properly before version 3.

I wonder what version we are?

EDIT: And you note that he has written any documentation for the last 2000 years either.

Sun, 01 Jun 2008 10:45:00 UTC | #177703

Chrysippus_Maximus's Avatar Comment 4 by Chrysippus_Maximus

Referring to 'junk DNA' as "Useless junk" is a bit of a mistake.

Teleology anywhere in a biological description must be very carefully considered...

SINE and LINE copies are useless in terms of the strict biological function of the particular organism they are in, but that does NOT entail that there's nothing evolutionary 'useful' about them...

Especially since they do seem particularly useful to themselves. (i.e. from the gene's eye view).

Sun, 01 Jun 2008 10:49:00 UTC | #177708

Auraboy's Avatar Comment 6 by Auraboy

Excellent. And how much will we be charged for the upgrade? I know Vista pretty much drives me to random acts of violence so perhaps we have certain human traits explained...

Sun, 01 Jun 2008 10:50:00 UTC | #177710

Szymanowski's Avatar Comment 5 by Szymanowski

Heehee, was that deliberate? The article is totally messed up; some of it has replicated, à la junk DNA.

Otherwise, that was a very interesting read :)

Sun, 01 Jun 2008 10:50:00 UTC | #177709

JanChan's Avatar Comment 7 by JanChan

Argh... I see LINE everywhere!

(Well, at least I learnt something new)

Sun, 01 Jun 2008 10:52:00 UTC | #177713

Agrajag's Avatar Comment 8 by Agrajag

5. Comment #187165 by Szymanowski on June 1, 2008 at 11:50 am
Heehee, was that deliberate? The article is totally messed up; some of it has replicated, Ã la junk DNA.

"Tonight, on 'It's the Mind', we examine the phenomenon of deja vu..."
Ste5e

Sun, 01 Jun 2008 10:55:00 UTC | #177714

mejdrich's Avatar Comment 9 by mejdrich

What a delightful mistake: junk text added in the process of reproduction in an article about the same.

It's just to perfect.

Sun, 01 Jun 2008 12:22:00 UTC | #177744

justinesaracen's Avatar Comment 10 by justinesaracen

It's a fascinating article (and amusing due to the repetition). I had NO IDEA that our genome was mostly junk. And here I thought that nature just plowed along, saving things that were efficient and discarding things that didn't work. And that nothing totally functionless stayed around very long.
Apparently not. We have a tiny (5% !!!) engine that drives us and makes us what we are, and boxcars and boxcars of trash dragging along behind us.

Would some of the biologists in the group also please explain to me how a creature can have a bigger genome than homo sapiens? Or a 'more efficient' one?

And I want to hear more about those onions.

Sun, 01 Jun 2008 12:48:00 UTC | #177758

SteveN's Avatar Comment 11 by SteveN

Spinoza wrote in #4...

Referring to 'junk DNA' as "Useless junk" is a bit of a mistake.

Teleology anywhere in a biological description must be very carefully considered...

SINE and LINE copies are useless in terms of the strict biological function of the particular organism they are in, but that does NOT entail that there's nothing evolutionary 'useful' about them...

Especially since they do seem particularly useful to themselves. (i.e. from the gene's eye view).


I think that this is the whole point of PZ's post. Integrated (endogenous) retroviral sequences exist for the sake of themselves, not for the sake of the host organism. They are basically parasitic genes. Interestingly enough, there is considerable evidence that the human (and other mammal) host has co-opted some of these human endogenous retrovirus (HERV) genes to suppress immunological rejection of the 'foreign' (i.e. foetal) tissue at the placental/embryo interface. We might carry a lot of junk, but sometimes we make good use of it!

Sun, 01 Jun 2008 12:50:00 UTC | #177760

Carl Sai Baba's Avatar Comment 12 by Carl Sai Baba

esuther:

Matt Ridley talks about "junk" DNA at the 30th anniversary gathering for The Selfish Gene.

http://richarddawkins.net/audio/SelfishGene30.mp3
(Ridley starts at about 32:00, but don't skip over Dennett!)

You can probably find more detailed information elsewhere, but I immediately thought that if you didn't already know about our upside-down genome, you must have missed out on this wonderful little event for Dawkins.

Edit:
Ridley does address frogs having more DNA than humans, to answer that question.

Sun, 01 Jun 2008 13:25:00 UTC | #177767

shanek's Avatar Comment 13 by shanek

"Our human CD contains, in effect, the equivalent of one really good, but short, pop song, with the rest of the tracks being staticky hisses, noise, and repetitions of the same short phrase, over and over again. "

Our genome is the White Album???

Sun, 01 Jun 2008 17:10:00 UTC | #177816

Wosret's Avatar Comment 14 by Wosret

10. Comment #187214 by esuther

As I understand it homo sapiens have a relatively small genome compared to many other animals. Also, if I'm not mistaken I believe that I read somewhere that an Ameba has the largest genome of all.

I believe (though again, I'm not sure, and I've read very little about it) this is because a lot of mutations actually delete genes from the genome. Then I believe I remember someone (maybe Dawkins in "The Ancestor's Tale"?) using a hard drive as an analogy for a genome, and saying how different animals actually have different size "hard drives" as it were. So not only difference in amount of genes, but in capacity of the genome.

Sun, 01 Jun 2008 18:28:00 UTC | #177830

therussmeister's Avatar Comment 15 by therussmeister

Anyone else wonder whether P K Dick's middle name is Kipple?

Sun, 01 Jun 2008 19:08:00 UTC | #177835

Shuggy's Avatar Comment 16 by Shuggy

esuther asked:

Would some of the biologists in the group also please explain to me how a creature can have a bigger genome than homo sapiens? Or a 'more efficient' one?

Why not? We are among the least specialised of the animals. To make a big brain, our main specialisation, you need a gene that says "make brains" (and all animals with any brain have that) and a gene that says "make this much" which is the same as the gene in the other animals but with a higher value of "this". I am of course speaking in crude terms of something that is very complicated, but it's just as complicated for all animals.

Two factors that make our development look more complicated than it is:

1. The most complicated element in it is the working cell, and one of those is carried forward from each generation to the next, like the bug that makes yoghurt or ginger beer.

2. Much of the development is shaped by earlier and adjacent development. So a muscle attachment will cause the development of a bone of a particular shape, and vice versa. This was borne home to me strikingly in a pathology lab when I examined the skulls of two-headed - or rather two-faced, single-craniumed lambs. Clearly there has been no evolution of two-headed lambs, but the separate parts had more or less normal bone-structure (more where they were far from the join, less where they were closer), while the joins themselves had bones that were variants of the normal, modified by the presence of the other half. They did their best to work as well as they could with what they had, which in two faced animals is not often very well.

Sun, 01 Jun 2008 20:32:00 UTC | #177849

jo5ef's Avatar Comment 17 by jo5ef

"Our genome is the White Album???"
That gave me my first good laugh for the day!

Sun, 01 Jun 2008 22:19:00 UTC | #177861

j.mills's Avatar Comment 18 by j.mills

Does anyone of a biological bent know what it COSTS us to carry around all that junk? I realise that DNA makes up only a tiny fraction of each cell, but then again we have trillions of cells. Does a lot of our food go into maintaining freeloading genes, or is the resource requirement trivial?

Mon, 02 Jun 2008 06:50:00 UTC | #178013

Geodesic17's Avatar Comment 19 by Geodesic17

Is there a relationship between the size of an organism's genome and how quickly it reproduces?

Mon, 02 Jun 2008 08:23:00 UTC | #178059

kleb's Avatar Comment 20 by kleb

I think it's fair to say that no scientific undertaking has done so much to corroborate and demonstrate the idea of the Selfish Gene as the various genome mapping projects have. We're so accustomed to speaking, however carefully and with a mental asterisk firmly in place, of the various features of bodies in a purpose-oriented language - you know: the heart serves the purpose of pumping blood, a receptor protein on the cell membrane serves the purpose of transmitting hormonal signals to the inside of the cell, and so on - that we've come to view the genome in the same way; as a tool that serves the higher purpose of bringing about and operating an organism. One could say that the genome functions as a blueprint of the body which at the same time controls its own execution. That's perfectly correct, but that's not the genome's "purpose". On the contrary, the whole body is only constructed to serve the genome, so that it can survive and replicate. And as it turns out, only a minority of the genes are actually doing the whole body-construction work; large parts of the genome are only along for the ride and don't contribute anything themselves. Only now that we humans are acquiring the ability to manipulate our own genome may the power of who serves whose purpose be transferred to ourselves.

As for the selective pressure to eliminate junk DNA: I've read that DNA constitutes about 1% of the mass of the human body. That's not a lot, but it has to be synthesized and renewed continuously, and the raw materials don't grow on trees (well, they do, but we have to acquire them nonetheless). If the amount of completely unnecessary DNA were to spiral out of control, then the cost of duplicating those sequences for every single cell of the body would soon become, if not prohibitive, then at least disadvantageous.

Another thought: It might well be that in some way or other bodies might have a selective incentive to keep all forms of reverse transcriptase at bay. Artificial reverse transcriptase inhibitors are nowadays used to treat HIV infections.

By the way: The fact that lots of apparently useless and random stuff is going on in nature deserves to be pointed out more. It isn't very glamorous, but it's simply sick to hear creationists go on again and again about how they cannot fathom it all arose "by random chance" and all looks so "designed" when in fact a lot of it looks like the designer was on crack.

Mon, 02 Jun 2008 08:53:00 UTC | #178089

nilou's Avatar Comment 21 by nilou

But what about structure? The architectural packing of the genome may be essential to its function, which is to relay functional information. This may result in seemingly useless complexity in terms of sequence, but functionally essential complexity in terms of structure.

See Albert et al.(2007) Nature, 446:572-576

Also see: Ahnert et al. (2008) Journal of Theoretical Biology, 252: 587-592

They conclude "This minimum (of "junk") increases quadratically with the amount of DNA located in exons".

Quadratically hmmm... interesting that nucleosomes have cylindrical surfaces...


"We'd be better off reconciling ourselves to the notion that much of evolution is random, and that nothing prevents nonfunctional complexity from simply accumulating"

lets not jump the gun

Mon, 02 Jun 2008 11:04:00 UTC | #178176

Carl Sai Baba's Avatar Comment 22 by Carl Sai Baba

Ridley says more DNA makes the entire cell larger overall. It also tends to make the animal's brain smaller, due to slowed cellular reproduction when growing the brain.

Mon, 02 Jun 2008 17:39:00 UTC | #178352

amalthea's Avatar Comment 23 by amalthea

I have to agree with kleb on the last comment, bad design does show the IDiots up a little.

As for the whole concept of junk DNA, I think it's probably to show that he human genome is essentially bureaucratic, lots of form and no actual content :)

But seriously, I was hoping that at least some of that 'junk' DNA coded for something interesting that we hadn't elucidated yet. Maybe a propensity towards intelligence or something.......... then I saw the ID description of the banana. Nah.

Tue, 03 Jun 2008 13:09:00 UTC | #178790

SteveN's Avatar Comment 24 by SteveN

In answer to j.mills question (#18) and to add to kleb's answer (#20), I expect that, with the exception of the few occasions in which a piece of integrated junk DNA provides an actual benefit to the host, the use of resources needed to replicate all that DNA is indeed a significant disadvantage that would normally be weeded out by natural selection over time. The problem as I see it is that the host's molecular machinery has no way of distinguishing between 'good' and 'bad' DNA. The potential gain in efficiency by randomly deleting chunks of DNA is far outweighed by the high risk of doing harm.

By the way, the recently published sequence of the platypus genome has revealed that about 50% is comprised of interspersed repeats derived from transposable elements. This, the authors claim, is higher than for any other previously characterised metazoan genome.

Wed, 04 Jun 2008 02:11:00 UTC | #178909

Koreman's Avatar Comment 25 by Koreman

@Comment #187159 by epeeist on June 1, 2008 at 11:45 am

Thankfully it's open source so we can engineer patches and service packs ourselves. Well documented as well. Too bad that some of this documentation conflicts with some of the manuals that were written by people in the bronze age, so now I am in doubt.

Wed, 04 Jun 2008 22:18:00 UTC | #179406