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#48322 - 03/14/13 01:09 PM Re: 'The Scars of Human Evolution' [Re: Bill]
ImagingGeek Offline
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Registered: 05/19/10
Posts: 410
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Originally Posted By: Bill
Now here Motl seems to be to be saying that for larger systems, such as life, there is no visible difference between classic and QM entropy.

LOL. Bill manages in one short paragraph to explicitly show what I've spent pages trying to say.

Bryan
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#48323 - 03/14/13 01:31 PM Re: 'The Scars of Human Evolution' [Re: Orac]
ImagingGeek Offline
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Originally Posted By: Orac
Firstly to store quantum information it must pack into a quantum spin. How that spin is encoded by the organisms DNA we don't have to get involved in it will be very complex. DNA will only have the ability to encode a certain number of spins per base pair and it may not even be per base pair it may need sequences that is all biological stuff I don't study perhaps ImagingGeek knows. I think it has something to do with protein foldings or something like that.

Biological information is not stored as quantum states - and again, I'm questioning your knowledge of QM. By its very nature, spin is both unstable (indeed, we manipulate electron spin all the time, in several forms of microscopy & biomedical imaging), and generally you cannot extract the information stored in quantum states (i.e. spin) without altering other aspects of the quantum state.

Biological 'information' (whether that is a meaningful term in biology, and whether information theory can be applied to it, is hotly debated) is stored in a much more stable form than a quantum state - it is stored in chemical form, specifically in the form of triplets of DNA (or in some cases, RNA) nucleotides. The closest you get to 'quantum' interactions in the system is in read-out. Genetic information is 'read' from the DNA strand via non-covalent chemical bonding (hydrogen + ionic) of the mRNA intermediary by pair-bonding with tRNAs. Again, the readout isn't dependent on the quantum state of the electrons forming the bonds (indeed, spin, excitation state, etc, are all irrelevant to the process).

Originally Posted By: Orac
Now your argument that the organism can stay the same is the same as saying I can hold a computer byte to a set value. I can do any problems I like so long as I don't require more than 256 different values.

The problem becomes the moment I need to add in a 257th entry I need to expand the information base and on a computer you could jump to a 9th bit but for simplicity they don't they jump to 16 bits.

You're making a fatal flaw here - assuming that different or better adapted always requires more information. This is not the case - indeed, outside of eukaryota, there is a strong selective force against the accumulation of additional DNA.

Originally Posted By: Orac
For animals to evolve ergo they must encode more information or else they violate this central tennant of QM or don't evolve take your pick.

And again, you've made assumptions about evolution & biology that are false, and on those falsehoods your claims fail.

You do not need more biological 'information' to evolve; indeed, loosing unneeded information is observed as often as is the formation of new information. Information is not free - it carries a very real biological expense (notably, the energy and resources needed to replicate, maintain and process your genetic material). Nor do you need new information to increase complexity - few would argue that an amoeba or onion are more complex than humans, and yet they have more information. I'd argue a human is more complex than a mouse, and yet we have roughly the same amount of DNA with mice having slightly more functional genes.

What you've left out of your equation is the very principal of emergence. Emergence allows for the formation of hugely complex structures based on minimal information. Biology relies heavily on this. You DNA doesn't say "to make a person put protein X in position Y). Rather, it says "make proteins X, Y, Z; the interactions between them will the create a person". Very minute changes to "X, Y and Z" - rather than new proteins/information, are what creates the vast majority of the differences between you and a less 'complex' organisms such as a fly.

The standard metaphor for biological information (and a surprisingly accurate one at that) is that of a cake recipe - our DNA does not say "put a chocolate chip at 1.2,3.4,7.8cm [x,y,z coordinate]"; rather, it says "mix flour, eggs, milk, sugar, chocolate chips & yeast". Most evolution - including changes in apparent complexity - arise simply through minor tweaks to the recipe, rather than the addition of new ingredients.

Bryan
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#48324 - 03/14/13 01:43 PM Re: 'The Scars of Human Evolution' [Re: Orac]
ImagingGeek Offline
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Registered: 05/19/10
Posts: 410
Loc: Canada
Originally Posted By: Orac
I would leave a little open excercise for ImagingGeek if he wants to take up the challenge.

The nasty problem I am left with he is how do we measure and define complexity or if you prefer "information left to learn" it is not going to be a simple as count genomes or anything like that because the fitness criteria imposed was complex.

That is very much an open question in biology. People have tried to apply classical information theory (Shannon entropy, etc) to the problem, and generally have failed. The issue is that not all genetic material is information - some of it is structural, some of it has functions other than passing on information, some of it (most, in humans) is junk, in many cases even functional elements like genes are disposable (so the value of the information in them is hard to quantify), etc.

Restricting the analysis to regions which encode functional elements - proteins, RNAs, etc - also doesn't seem to provide any meaningful measure. Often, the amount of these present seems to have nothing to do with the complexity are degree of adaptation of the organisms, and instead reflect a combination of genetic chance and the strength of selection against increasing genome size.

IMO, the best measure of 'information' is one not currently in reach - a bioinformatic description of all the protein (and other functional elements) interactions required for the organisms survival. This avoid the complexities of genome architecture, junk DNA, etc, by quantifying only those interactions which impact the biology of the organisms. we are, however, likely decades away from that capacity.

Bryan
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#48326 - 03/14/13 01:55 PM Re: 'The Scars of Human Evolution' [Re: Orac]
ImagingGeek Offline
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Registered: 05/19/10
Posts: 410
Loc: Canada
Originally Posted By: Orac
So the most evolutionary advanced animal using that criteria is the marbled lungfish at a whopping 130Gb and the most evolved plant is the Japanese-native, pale-petal at 150Gb.

I would need ImagingGeek to explain what the hell that DNA much is needed for, I guess alot of it is junk.

Yes & no. In animals there is a tenancy to accumulate both extra genes and towards the accumulation of junk DNA (junk meaning the DNA is not required to maintain the fitness of the organism). This is a product of the cross-over process which occurs during the formation of eggs/sperm. The process is error-prone, with unequal cross-overs leading to duplication or deletion of DNA. Deletions are less likely to be passed on (simply because you may delete something important) so the net trend is towards genome growth.

When discussing agricultural plants things get complex. Plants have a tendency to duplicate their entire genomes (called polyploidy). Normally, polyploids don't survive well, but they do tend to have characteristics humans like - bigger fruits/seeds/flowers, etc. Paris japonica is octaploid - its whole-scale duplicated its genome 3 times, and is also allopolyploid, meaning its crossed with an unrelated species and retains some of that species genome. Whether polyploidy can be considered more information (as its simply a duplicate of what was already there) is unclear.

What sets the upper limit to genome growth is the energy required to maintain the genome relative to the organisms other needs. In the case of agricultural plants, human intervention provides a selective pressure that counters the natural selection that would normally suppress polyploidy.

Originally Posted By: Orac
If you think that is a fair criteria there is an obvious flaw in it and it comes up in the entry that things with this length DNA replicate very slowly because it takes a very very long time to replicate that ammount of DNA.

Actually, it doesn't take long to replicate the DNA. Again, you need to learn some biology before you start pontificating on it. DNA replication in eukaryotes does not start at a single site and progress from there. Rather, it starts at multiple sites within each chromosome. Since chromosomes typically grow via duplications, these sites are duplicated at the same rate as the chromosome in general, and thus you maintain a proportionate number of start sites relative to genome size.

Bryan
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#48329 - 03/14/13 03:47 PM Re: 'The Scars of Human Evolution' [Re: ImagingGeek]
Bill Offline
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Registered: 12/31/10
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Originally Posted By: ImagingGeek
Yes & no. In animals there is a tenancy to accumulate both extra genes and towards the accumulation of junk DNA (junk meaning the DNA is not required to maintain the fitness of the organism).

Bryan, this is something I have wondered about. I think I recall that all of the DNA that wasn't genes was considered junk, then they found out a lot of the junk was actually there to control the transcription of the genetic information. How confident are we that the rest is really junk? I know that one thing you mentioned is that it does take resources to support the extra, so it might seem that it would get deleted over time.

Bill Gill
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#48331 - 03/14/13 08:07 PM Re: 'The Scars of Human Evolution' [Re: Bill]
redewenur Offline
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Registered: 02/14/07
Posts: 1840
Good question, Bill, and awaiting Bryan's reply.

Evidently, the first doubts re 'junk' DNA arose some 50 years ago. In the last decade the doubts have increased:

"Transposable elements (TEs), also known as "jumping genes" or transposons, are sequences of DNA that move (or jump) from one location in the genome to another. Maize geneticist Barbara McClintock discovered TEs in the 1940s... McClintock, however, was among the first researchers to suggest that these mysterious mobile elements of the genome might play some kind of regulatory role, determining which genes are turned on and when this activation takes place (McClintock, 1965)."

"...Moreover, in primates, scientists have identified a SINE known as Alu that seems to play an important role in gene regulation and evolution. These new discoveries are prompting scientists to think twice about dismissing such a large portion of the genome as nothing but 'junk.' "
Leslie Pray, Ph.D. 2008 Nature Education
http://www.nature.com/scitable/topicpage/transposons-or-jumping-genes-not-junk-dna-1211

Now it appears that the 'junk' notion is rejected:

"A staggering batch of over 30 papers published in Nature, Science, and other journals this month, firmly rejects the idea that, apart from the 1% of the human genome that codes for proteins, most of our DNA is "junk" that has accumulated over time like some evolutionary flotsam and jetsam."
Written by Catharine Paddock PhD, Article Date: 09 Sep 2012
http://www.medicalnewstoday.com/articles/250006.php

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#48334 - 03/15/13 06:13 AM Re: 'The Scars of Human Evolution' [Re: Bill]
Amaranth Rose II Offline

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Registered: 12/16/06
Posts: 962
Loc: Southeast Nebraska, USA
this goes to prove what I have been saying for years, that there is no such thing as junk DNA, just DNA whose function we do not know yet. Organisms don't carry loads of DNA just for the fun of it. It has some function, or it wouldn't be maintained. DNA is much too expensive for the cell to make just for the heck of it. I think we will find that more and more of the so-called "junk" DNA has functions that we have only begun to suspect.
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#48335 - 03/15/13 07:33 PM Re: 'The Scars of Human Evolution' [Re: redewenur]
Bill Offline
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Registered: 12/31/10
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Loc: Oklahoma, USA
Thanks Rede and Rose. That is pretty much what I was thinking. I suppose that there may be some left over unused DNA in there, but it does take precious resources to maintain it, so there would be a tendency to prune it over time. I had seen something like this before, and just wanted to verify it.

Bill Gill
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#48336 - 03/16/13 02:04 AM Re: 'The Scars of Human Evolution' [Re: Bill]
Bill Offline
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Registered: 12/31/10
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Loc: Oklahoma, USA
Update! On phys.org I found this posting: Not dead yet: Junk DNA is back.
And interesting read, defending junk DNA.

So now we have 2 different opinions.

Bill Gill
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#48337 - 03/16/13 04:43 AM Re: 'The Scars of Human Evolution' [Re: Bill]
redewenur Offline
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Registered: 02/14/07
Posts: 1840
Thanks for the news, Bill. An interesting topic to keep an eye on through the next few years, no doubt.
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#48339 - 03/16/13 02:31 PM Re: 'The Scars of Human Evolution' [Re: redewenur]
Bill Offline
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Registered: 12/31/10
Posts: 1858
Loc: Oklahoma, USA
Well, I did a quick read of the link and came up with what I said in my last post, but I didn't really follow it and think about it. Now I have read it more carefully and followed some of the links. Cryptogenomicon has a discussion of the matter with a huge number of comments following it. After reading through half or more of the comments I came up with the idea that we don't know enough to really say. In the comments there are a bunch of different ideas about what the 'junk' DNA is. Some suggest that it may not do anything directly, but it may have some kind of structural effect that influences what the active parts of the DNA do. And I think there are some other comments on what it might do.

The main thing I got out of the discussion was that we really don't know enough about how DNA works to really figure out what the junk does or doesn't do. It may be that a lot of it will turn out to be junk, or it may have some subtle effect that we just don't understand yet. In the meantime we people on the side lines will just have to wait and see what comes out of the ongoing research.

Bill Gill
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#48340 - 03/16/13 03:48 PM Re: 'The Scars of Human Evolution' [Re: Bill]
redewenur Offline
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Registered: 02/14/07
Posts: 1840
Yes, that's what I take it all to mean, too: we wait and see. Exciting times in biology, materials, nanotech, cosmology, and so much else...so much waiting to pop up over the horizon. I'm going to apply for a 100 year life extension smile
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#48678 - 05/15/13 02:01 AM Re: 'The Scars of Human Evolution' [Re: Bill]
Bill Offline
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Registered: 12/31/10
Posts: 1858
Loc: Oklahoma, USA
More news about junk DNA. Carnivorous plant trims its tiny genome

So we have huge amounts of so called junk DNA. And here is a plant that has almost none. 97% of its genome consists of genes and control sequences. So now we have to wonder just how much "junk" do we need in our genome.

One more complication in our understanding of genetics.

Bill Gill
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