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E-boy



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PostPosted: Wed Jan 06, 2010 5:25 pm    Post subject: Reply with quote

Prions evolve? Sure I suppose. They do replicate. There are a relatively limited number of ways a protein can mis-fold though and I'd imagine not all of them lead to prion like replicating abilities so that cuts it down even more still it's change in a replicating system over time. Which meets the criteria of at least one sense of the term evolve. If those changes increase the success rate of prion infections then it's adaptive change which would be even more interesting.

Now I have to go read the link. Smile Got over enthusiastic for a sec there.
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E-boy



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PostPosted: Wed Jan 06, 2010 5:36 pm    Post subject: Reply with quote

Good stuff High. Also very clear from the article that the changes are adaptive.

Really not a huge surprise to me considering they they replicate and hijack the cellular machinery of a host to do so. They're just going about it in a more economical way than viruses. The cells are already making the necessary raw material for them so they don't need DNA. They just need a means of disrupting protein folding which apparently their very presence does.

I read an article a while back about a guy working with recombinant DNA bacteria. They had a problem with what amounted to bacteria specific prions as a side effect of inserting human DNA into the bugs to make insulin. He came up with a solution to the problem that extended the life of individual bacteria and made them more productive in the insulin department. Research is now being done to determine if this same approach could offer a means of treating prion based illnesses in humans and animals. I will see if I can dig up the article but I read it at least two years ago so I'm not sure I can find it.
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mouse



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PostPosted: Wed Jan 06, 2010 11:24 pm    Post subject: Reply with quote

The Highlord wrote:
To which I'll cite Darwin's finches. New mutations aren't required for the beak sizes to shift: the variation in beak size is already present, and selection pressure shifts the modality of the population towards larger or smaller beaks.

Evolution is much more than just changes leading to speciation, of which mutations are a very important impetus. Just stirring the pot can lead to incredible diversity without new mutations being required due to redundancy and level of expressiveness of genes: except in the case of prions, it's due to protein-protein interactions.


i don't see how you can say evolution is more than 'just' speciation, and then say it's enough to just stir the pot and get new forms. this is the problem i had with a show i saw a few years ago, that purported to prove evolution. they were looking at a population of finches in the galapagos, with variable beak sizes. when environmental conditions shifted one way, there was selective pressure for one extreme of beak size, and that became predominant in the population. but when the environment shifted back, so did the distribution of beak sizes. so there was no net change, just some sloshing about.

"darwin's finches" are a group of distinct species; this presumes that some features are set, and if you put (for example) the cactus-eating finches on a diet of seeds, they wouldn't suddenly start showing seed-eating beaks.

actually, since i'm in wikipedia, let's look at the definition of evolution:

Quote:
In biology, evolution is change in the genetic material of a population of organisms through successive generations.


note: a change in genetic material. not just a shuffling of frequencies.

you can get a different-looking population if you change the frequencies, but they are still the same type of critters. you haven't moved things along in any way.
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WheelsOfConfusion



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PostPosted: Thu Jan 07, 2010 2:01 am    Post subject: Reply with quote

Actually from a genetic standpoint, it's the change in allele frequency in a population over time. If the anti-prion conditions persist for sufficient time to favor certain prion shapes over others, that could count. But then, a strict reading of that would mean prions don't count because they don't have genes.

I suppose you can say it's Darwin-like?
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The Highlord



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PostPosted: Thu Jan 07, 2010 4:10 am    Post subject: Reply with quote

Mouse: This discovery is novel, and beckons for a definition of evolution as affecting only things with genomes to be updated according to this new information. It's not a very large paradigm shift, mind you, but you cannot look at something newly discovered and criticize it for not fitting into the current model adequately. The problem's not the discovery, the problem's the model.
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E-boy



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PostPosted: Thu Jan 07, 2010 11:58 am    Post subject: Reply with quote

Darwin's idea applies beyond genetics. It's worth noting he was not familiar with Mendel's work and came up with his ideas in the absence of an understood means of information transmission.

ANY replicator of sufficient but not perfect fidelity in a varying environment and with differential survival can experience evolutionary change. This is a point many scientists make over and over and it's not terribly controversial. It almost sounds as though people are giving special status to DNA without providing any reason for doing so. It's basically an information medium. A four letter alphabet for information encoding. Any medium that can hold and copy information will do though. It's also worth noting that a lot of the information in living things is 'assumed' information. Living things develop differently in zero g for a reason. So the environment contains some information as well.

Studies on the origins of life are rife with differing theories on wether metabolism or replicators came first. What is known is that evolution as we know it in biology wouldn't be possible without replicators.

Heck Dennet even wrote a book about the broader implications of Darwin's ideas "Darwin's Dangerous Idea".
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E-boy



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PostPosted: Thu Jan 07, 2010 12:03 pm    Post subject: Reply with quote

Oh and Mouse (you know I love ya so don't get mad) but the key words in your quote are "IN BIOLOGY". Prions don't have their own biology. And evolution is as I mentioned not restricted to DNA and RNA. Biology is necessary for their existence, but only as a substrate.
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mouse



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PostPosted: Fri Jan 08, 2010 12:35 am    Post subject: Reply with quote

The Highlord wrote:
Mouse: This discovery is novel, and beckons for a definition of evolution as affecting only things with genomes to be updated according to this new information. It's not a very large paradigm shift, mind you, but you cannot look at something newly discovered and criticize it for not fitting into the current model adequately. The problem's not the discovery, the problem's the model.


no - the problem is, you haven't read what i said.

back in my first post on this, i said:

Quote:
it looks like there aren't new variants created,


and in my second post, i said:
Quote:
if there are mutations in prions, then that fits with my definition of evolution.


the issue is, are there any new variants coming into the population of prions? if there are a fixed number of prions, and there are never any additional variants of prions arising however is that prions might possibly come up with new variants, then i hold that prions don't evolve, there is simply selection from among an eternally fixed set of possibilities. if, as i said in my second post, there _are_ new variants created, then the issue (as it pertains to prions) becomes moot. from there on, the discussion is just 'what is necessary to have a process defined as an evolutionary one' which, as i have said repeatedly, to my mind requires both a) selection among variants and b) addition of new variants.

now, the article, to my mind, didn't address adding new forms of prions, just selecting among an existing population. that's selection, which is a part of evolution - but it's not _all_ of evolution.

and it doesn't matter a flying fuck if they have genes or not. it's whether you have new forms available for selection, however you want to define those new forms.

you are fixed on the notion of selection, and persist in limiting evolution to that. i say, and the definition appears to say, that YOU ARE WRONG.

and e-boy - babycakes, seriously? prions don't have biology? they can't be defined in terms of biology? they are made of a substance found only in biological matter (proteins), they reproduce - where else are you going to put them, than under 'biology'? sociology? linguistics? mineralogy? biology is only necessary to them as a substrate? well, hell - the rest of the biological kingdom is only necessary to _us_ as a substrate (i.e., that which we live on, and from which we derive substance). so is every other living thing not biology? or are we humans not?
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The Highlord



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PostPosted: Fri Jan 08, 2010 1:30 am    Post subject: Reply with quote

I respectfully* disagree.

*By which I mean calm the fuck down.
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mouse



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PostPosted: Fri Jan 08, 2010 2:10 am    Post subject: Reply with quote

so you are saying, if i have a population with a fixed gene pool (or a set of prions of fixed amino acid sequences), and i let selection happen until only one sequence is present in the population, and that population then continues that way forever - evolution has happened?

ok, now i know how i should interpret your further posts on biology.
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Dro



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PostPosted: Fri Jan 08, 2010 6:27 am    Post subject: Reply with quote

From looking at the article, I would say that new genetic material is entering the population of prions. It suggests as proteins are converted there is a low rate of altered conformations, some of which have higher fitness in certain environments. The odd thing here is that the number of possible conformations is somewhat low, so it's as if a very simple genome was being mutated. So all these variants get created at a low level, and the typical population does have sort of a fixed 'allele' frequency.

Prions are interesting because they are both the information carriers (the amino acid sequence) but also exhibit the phenotype upon which selection acts (the altered conformation that can inflict that conformation on normal proteins). Other examples are DNA transposons (bits of DNA that have evolved to hop around a genome and copy itself) and RNA enzymes (sequence of RNA that form structures with catalytic activity). All of them pretty much sit in gray areas of most definitions of how things act.
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The Highlord



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PostPosted: Fri Jan 08, 2010 9:19 am    Post subject: Reply with quote

Mouse: It's important to realize that selection pressure does not (excepting a purported increase in genetic shuffling in response to stress observed in some plants) cause the mutations to happen. The drug resistant bacteria in a culture (or the humans with tough enough faces to survive being shot by Dick Cheney) are already there, and the selection pressure simply brings the mutants out as the dominant trait.

Would you say that drug resistivity in bacteria isn't evolution because of your narrow definition? Or is it only evolution for the first part of the scenario, which also occurs in prions except with folding instead of DNA? If so, I must once again reiterate that the problem is your definition, bolstered though it is by wikipedia. Also, once more for the record, novel forms of prions do pop up, so there is an element of random mutation among the forms, even if this isn't necessary to say that evolution is taking place. I'd confine such a definition to a sub-category such as speciation or simply evolution by means of stochastic mutation, but evolution is a big, big tent.
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mouse



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PostPosted: Fri Jan 08, 2010 8:05 pm    Post subject: Reply with quote

i am quite aware that selection is not the same as mutation. even an increase in genetic shuffling is not mutation, if it does not change the sequence of nucleic acids in a dna strand (unless the shuffling is on a sub-genetic level, which would indeed alter the makeup if individual proteins).


and yes, drug resistivity in bacteria is evolution because such resistivity is CAUSED by mutations in the bacterial genome. which mutations are then acted upon by the process of selection, which can either fix them in a population, or cause them to be lost.

it's all about getting some level of variability in the population for selection to act upon. you have to have the variability first. and for the population to change in a quantifiable way from the initial population, you have to keep having a source of variability. otherwise, you are just talking about a change in allele frequencies, or prion morphologies, or whatever you want to talk about.

i'm glad i have dro around, for some intelligent discussion. yes, it will be interesting to see how much "evolving" prions can do, given the limited number of possible variations. one wonders if this will give us some further insight into drug resistance - can a relatively limited tool set give you resistance to a wide array of drugs? is there then some simple underlying key to drug resistance? (or at least perhaps resistance to major groups of drugs) this might explain why drug resistance in bacteria seems to be evolving at such frightening speed - maybe there's some basic thing, and once you get that, you're golden.
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The Highlord



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PostPosted: Sat Jan 09, 2010 11:08 am    Post subject: Reply with quote

I too am glad when people don't disagree with me when I'm wrong, hyuk hyuk.
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E-boy



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PostPosted: Sat Jan 09, 2010 3:04 pm    Post subject: Reply with quote

I love when you get all scientific and sassy mouse. Smile

I would have served my point better if I said Prions have neither metabolism or DNA/RNA. They don't live, don't even come as close as viruses do. Yes they are a product of biological processes and dependent on them and I acknowledged that. They themselves are not biological in the sense that they can't do any of the above. They are too complicated to exist without biology and too simple to achieve it themselves and yet they reproduce apparently with some minor variation allowing for flexibility in the face of a changing environment. I re-read your posts though and have a better understanding of where you are coming from.

To be more accurate I fully read your post for the first time when I went back to catch up. I very much doubt prions have the capacity to mutate and directly introduce enough variation to create whole new kinds. They'd be utterly dependent on host biology for that as they don't carry instructions for manufacturing different amino acid strings. Read understood and agreed with.
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