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Author Topic: Truth be Told about Human Chimp DNA  (Read 1023 times)
daedalus 2.0
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« Reply #45 on: November 12, 2007, 02:59:48 PM »

how fast are they evolving? Or, anytime intelligence is involved (e.g., drugs), you get to declare it not applicable?  Do other organisms include in this subset, since you presume they were designed by God, you must conclude that even things evolving far from man's reach are ID'd... and on it goes...
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« Reply #46 on: November 15, 2007, 05:41:50 PM »

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Sickle Hb is a special case of protein-protein interaction.
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Considering that protein-protein interaction are difficult to study (=expensive and time consuming) most of studied interactions are special cases. Except antigen-antibody.
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True enough, but I'm not sure we are using the term in the same sense.

Antibody - protein, antigen - for example foreign proteins.

Again I do not disagree.  These interactions though do not occur by evolutionary processes and this is why I say they are not the same sense.  They are managed by a series of finely tuned nanobots that effectively search shape space and chemical affinities to result in identification and generation of specific proteins with appropriate binding sites.  Remarkably designed mechanism that totally defies a materialistic explanation.

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Instead we find evolution damaging coherent funtion, generating incoherent byproducts and only preserving these changes when selection pressure is such that the damage also disrupts an even more damaging system

"Damaging coherent function" is a relative term. How about bacteria gaining resistance against antibiotic? Is that a good example of gaining function by mutation?

I don't think so.  When we look at specifically what is going on, we don't find new functionality.  Instead we find that preexisting function is damaged and in the process the bridge or key that used to allow the antibiotic to exploit a vulnerability has been blocked or the keyhole has been filled with gum so to speak. 
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Reasoned Faith
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« Reply #47 on: November 17, 2007, 02:38:08 PM »

how fast are they evolving?

Yes, that is the question I ask.

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Or, anytime intelligence is involved (e.g., drugs), you get to declare it not applicable?

No, selection pressure is selection pressure regardless of the source.  At what rate are parasites, bacteria and insects evolving in response to the selection pressure of drugs and chemicals?  Experimental analaysis shows it is not very fast and not very far.  But don't take my word.  Research it and then tell me, how fast is it?

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Do other organisms include in this subset, since you presume they were designed by God, you must conclude that even things evolving far from man's reach are ID'd... and on it goes...

Show me any organism you wish and tell us what rate is it evolving?
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tejtej
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« Reply #48 on: November 17, 2007, 11:53:45 PM »

how fast are they evolving?

In this the question about drug resistance?

We have done this in microbiological practicum. A culture of E.coli is divided in half. One half goes on a first petri dish with antibiotic (kanamycin or ampicillin, I forgot), the other half goes under a UV light for a minute or so and then on a second petri dish with antibiotic. Overnight incubation -> first petri dish is clean, no bacteria survives. The second has a few colonies.

Without such mutagens like UV, mutation rate is somewhere between 1 nucleotide in 10 000 and 1 in 1 000 000 per generation. E. coli has about 3 500 000 nucleotides, generation time about 30 minutes, number of cells per milliliter of liquid media about 100 000 000. This is about how fast they mutate not about how fast these changes are selected (=how fast they evolve).

Show me any organism you wish and tell us what rate is it evolving?

The speed of evolution is not a constant value. The speed of evolution of genes in the same organism is not a constant value.
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« Reply #49 on: November 18, 2007, 07:07:04 PM »

how fast are they evolving?

In this the question about drug resistance?

We have done this in microbiological practicum. A culture of E.coli is divided in half. One half goes on a first petri dish with antibiotic (kanamycin or ampicillin, I forgot), the other half goes under a UV light for a minute or so and then on a second petri dish with antibiotic. Overnight incubation -> first petri dish is clean, no bacteria survives. The second has a few colonies.

Without such mutagens like UV, mutation rate is somewhere between 1 nucleotide in 10 000 and 1 in 1 000 000 per generation. E. coli has about 3 500 000 nucleotides, generation time about 30 minutes, number of cells per milliliter of liquid media about 100 000 000. This is about how fast they mutate not about how fast these changes are selected (=how fast they evolve).

Thank you tej, that was interesting.  Your job sounds fascinating to me.  And thanks for pointing out that the restatement barney offered was vague, I should not have accepted it. That was my fault.  I was asking about selection.  Specifically I was challenging those who view drug resistance as good examples of how evolution accounts for observed diversity to estimate the rate that these evolutionary processes are generating new biological information, the kind required for new form and function.

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Show me any organism you wish and tell us what rate is it evolving?

The speed of evolution is not a constant value. The speed of evolution of genes in the same organism is not a constant value.

Fair enough.  I should have asked for an average over an observed period.  I also once again intended to ask about accumulating new function and the corresponding new biological information.
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« Reply #50 on: November 18, 2007, 09:59:36 PM »

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Show me any organism you wish and tell us what rate is it evolving?

The speed of evolution is not a constant value. The speed of evolution of genes in the same organism is not a constant value.

Fair enough.  I should have asked for an average over an observed period.  I also once again intended to ask about accumulating new function and the corresponding new biological information.

Some genes seem to have almost zero changes among all organisms compared, like histones in eucariotes, molecules that hold the DNA. And some seem to evolve very fast. At the 1. FEMS congress there was a presentation about comparing genomes of different strains of E.coli. Whole sections (up to the third of the genome) were different (or present/absent), mostly genes involved in host:pathogen interaction. How to tell at all if this functions were gained from a simpler ancestral E.coli or lost from a more complex ancestral E.coli?
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Slovenc, tvoja zemlja je zdrava in pridnim nje lega najprava.
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« Reply #51 on: November 19, 2007, 05:24:25 AM »

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Show me any organism you wish and tell us what rate is it evolving?

The speed of evolution is not a constant value. The speed of evolution of genes in the same organism is not a constant value.

Fair enough.  I should have asked for an average over an observed period.  I also once again intended to ask about accumulating new function and the corresponding new biological information.

Some genes seem to have almost zero changes among all organisms compared, like histones in eucariotes, molecules that hold the DNA. And some seem to evolve very fast. At the 1. FEMS congress there was a presentation about comparing genomes of different strains of E.coli. Whole sections (up to the third of the genome) were different (or present/absent), mostly genes involved in host:pathogen interaction. How to tell at all if this functions were gained from a simpler ancestral E.coli or lost from a more complex ancestral E.coli?

Right, It appears that some conserved proteins are critical for biological function in many organisms.  Any modification of these genes cause failure so they don't carry forward.  Other sections of the genome are not critical and are subject to modification without significant effect.  It is consistent with my original premise that you would see evolutionary modification in genes involved in pathogen interaction since these pathogen pathway blocking techniques that damage or degrade function but block out the even larger threat seem to be one thing evolution is quite proficient at accomplishing.

Returning to your previous example of bacteria exposed to (high energy) UV radiation which is also known to damage genes should have a similar effect.  UV is completely random in its damage and some of the billions of organisms will have just the right genes damaged to block the antibiotic pathway but still allow the weakend bacteria to survive and duplicate in an environment now free of competition.

These are all good examples of the evidence that evolution damages function to block pathogen and damaging chemical pathways but does not seem to build new function.  If evolution also built new function we would predict the conserved genes to also show evolutionary characteristics and also they should be identified as sources for evolved genes but they don't. 

Once again analysis from probability provides the basis to explain why we don't see behavior.  Evolution can and does successfully mutate to alternate functional forms when the probability involved in the alteration is greater than the inverse of the number of probabilistic resources available (organism count is the primary resource) but does not when the probability involved in a new or alternate functional protein is less than the inverse of the resources.  Bacteria counts on this earth are estimated at 10^35 or so but the probability of obtaining a functional protein from random change is less than 10^-55 for even the shortest ones.
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« Reply #52 on: November 19, 2007, 07:52:15 AM »

Going in circles.

Once again analysis from probability provides the basis to explain why we don't see behavior.

Explained when I compared flagellin to a human protein with a different function.

...a new or alternate functional protein is less than the inverse of the resources. Bacteria counts on this earth are estimated at 10^35 or so but the probability of obtaining a functional protein from random change is less than 10^-55 for even the shortest ones.

Again the subjective "what is a new protein". Under UV a functional protein able to digest (or avoid) antibiotic can be produced in minutes from a protein that lacked this ability.
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« Reply #53 on: November 20, 2007, 08:16:07 AM »

Going in circles.

Indeed.  We have a different view about what counts for evidence for a pathway.  You seem to count the outcome as evidence of a specific path, but the outcome is explained by many possible paths.

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Once again analysis from probability provides the basis to explain why we don't see behavior.

Explained when I compared flagellin to a human protein with a different function.

By this I take it to mean that the reason we don't observe the expected behavior is because it is obscured by the large number of posible pathways and potential starting points in attempting to recreate history from a narrative.  Instead let's stick with what we can and do observe and test.  We observe mutations occuring and we even know how to accellerate mutation rates, but we don't observe a progression of changes building on each other to produce new functional components.

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...a new or alternate functional protein is less than the inverse of the resources. Bacteria counts on this earth are estimated at 10^35 or so but the probability of obtaining a functional protein from random change is less than 10^-55 for even the shortest ones.

Again the subjective "what is a new protein". Under UV a functional protein able to digest (or avoid) antibiotic can be produced in minutes from a protein that lacked this ability.

Have we confirmed that these protiens have new function with no loss of old function?  My understanding is that function is lost (or reduced) and in the process the antibiotic pathway is also lost.
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