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Mutation And Natural Selection


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Poll: Given the assumptions in this thread, would evolution be possible? (21 member(s) have cast votes)

Given the assumptions in this thread, would evolution be possible?

  1. Yes and I believe evolution is possible (10 votes [47.62%])

    Percentage of vote: 47.62%

  2. No and I believe evolution is possible (0 votes [0.00%])

    Percentage of vote: 0.00%

  3. Yes and I believe evolution is impossible (3 votes [14.29%])

    Percentage of vote: 14.29%

  4. No and I believe evolution is impossible (8 votes [38.10%])

    Percentage of vote: 38.10%

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#101 Bruce V.

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Posted 09 June 2009 - 03:27 PM

I think my 'model' is exactly RM + NS, but with inclusion of the understanding of genetics, genomics etc which has come since Darwin.  This includes things like endosymbiosis as the origin of eukaryotic cells, large numbers of neutral mutations, some horizontal gene transfer, imprinting, etc. 
If some additional effects are discovered I am confident that they can also be fitted into this framework.
I think it is wrong to see each complication revealed by genetics as a refutation of RM + NS, instead they are refinements.  If anything, these refinements increase the power of mutation to explain our evolutionary history.

I also do not believe there is any need for any other 'force' to explain evolution.  This includes theistic involvement in any way.
I realize abiogenesis is an unexplained area, but think we will find that too does not require any magic.

As to my alternative to the computer analogy, think of a teletype terminal or computer printer.  That takes any 'message' in ascii code and prints it out.  Any message, mutated or not, is printed.  There is no need for error-correction because errors will not jam the printer etc.
Think of the 'messages' which are printed out as individual organisms.  Natural selection can then screen messages and make additional copies of those which are particularly effective (but not necessarily understandable as English).

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Hi Kieth,

I am totally sure I understand your view of evolution, but I am getting closer. TY for the effort you put into explaining it.

I will attempt to summarize your view in my own words. I know I will get some of it wrong but I am trying to understand.


1. RM + NS are still in play but we have learned evolution uses more than single point mutations to create diversity. For example, horizontal gene transfer, epigenetics and other mechanisms all play significant roles.

2. That there are many mutations of genes, proteins, DNA fragments ... which enters into some kind of queue or holding bin (like Junk DNA) as copies of the original. Now random selection mechanisms work on the queue of available options and selects the best one. There is no real need for error correction in this model because the less fit options are selected out as part of the process.

Keith, I am not trying to create a straw man. I really am just trying to understand, so feel free to correct me. TIA

Bruce

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Posted 10 June 2009 - 02:41 PM

I think you are trying too hard to condense what I was saying, and that simplification produces problems - if only in that I am not sure what you mean.

1. Natural selection + S@xual selection + random drift & founder effect are the effects which change allele frequencies in populations. NS and SS operate on the expressed phenotypes of individuals. Random drift and founder effect are important in small populations and in colonization.

2. Mutations occur randomly (without relation to need or desirability) and are of several types, single nucleotide changes, insertions and deletions, plus insertions and deletions of longer sections, inversions, duplications and chromosome breaks and fusions. Some locations (hot-spots) are frequent sites of mutation, sometimes because of repeated sequences.

3. Mitochondria, chloroplasts and probably other organelles are the result of endosymbiosis, with many of the symbiont's genes incorporated in the host nucleus. Viral infection and reverse transcription of messenger RNA inserts foreign DNA into genomes and some insertions are able to jump to other locations (jumping genes).

4. Many genes consist of several parts, exons, divided by intervening sequences, introns, which are cut out of the RNA copy before translation into protein. Alternative splicing together of exons increases the number of different proteins which can be produced from a single gene. A single gene may produce several different effects on the organism.

5. Control of gene expression is determined in at least 2 ways. In cells with some specialized function, those genes not required are tightly bound with chromatin and are not transcribed. For other genes, control regions upstream of the start location act as switches, and can be turned on and off by molecules which bind to particular DNA sequences. Various other RNA molecules can also influence gene activity.

6. In multicellular organisms, growth of the embryo is controlled by the switching on and off of a series of master genes, which in turn switch particular genes in particular tissues and appropriate times. This modular organization means some mutations are limited to particular organs. Proportions of different body parts are easily influenced by timing of switches.

7. Gene expression can also be modified by chemical changes, such as methylation of specific nucleotides which do not change the inherited DNA. Gene activity can thus be dependent on which parent it is inherited from and other factors.

The importance of all these factors is that they show how small DNA changes produce have large phenotype effects.
"Junk DNA" does provide a reservoir of DNA which can be inserted into genes or transcribed independently. NS then retains those few examples which prove beneficial. Since any such re-activated sequence is trying out for a new role, what was deleterious previously may be quite functional.
This is definitely not a queue in which sequences are tried in some systematic order.

You also wrote:-

There is no real need for error correction in this model because the less fit options are selected out as part of the process.

My comments about error correction were related to the difference between the DNA-as-computer-program analogy and the real situation of DNA in a cell. A random change to a computer program is almost invaringly fatal. However, for DNA, transcription and translation into protein will continue regardless of any mutation. This means that all phenotypes resulting from mutations are expressed and evaluated by NS. There is no intrinsic need to avoid errors and this feature may not have been needed for the first living organisms..
Error correction (proof-reading) becomes required to avoid error catastrophy in producing more complex organisms if DNA copying does not have sufficient fidelity for longer genomes. The various correction mechanisms could then have evolved by natural selection as complexity increased, rather than being part of an irreducibly complex system.
If a genetic system were designed with the intention of avoiding mutations, then a true error-correcting code could have been used.

#103 Adam Nagy

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Posted 10 June 2009 - 05:13 PM

I think you are trying too hard to condense what I was saying, and that simplification produces problems...

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...or maybe that simplification produces unwanted clarity? ;)

#104 Bruce V.

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Posted 10 June 2009 - 05:30 PM

"Junk DNA" does provide a reservoir of DNA which can be inserted into genes or transcribed independently.  NS then retains those few examples which prove beneficial.  Since any such re-activated sequence is trying out for a new role, what was deleterious previously may be quite functional.


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Note: RM + NS = Random mutation + natural selection

Hi Kieth,

A nice overview and as originally posted your evolutionary view has evolved well past random mutation and natural selection (RM + NS) or Darwinism. Modern Evolution theory is more or less saying that Darwinism (RM + NS) doesn't explain much - we need more, much more to explain life.

Junk DNA

The reason chromosome duplication (polyploidy) is of so much interest is that the duplicate DNA segment can accumulate mutations and build something useful while leaving the original DNA to do its normal job. The key words are "multiple mutations" . Polyploidy is moving beyond RM + NS and trying to create modular units rather than building something incrementally.

NS then retains those few examples which prove beneficial.  Since any such re-activated sequence is trying out for a new role, what was deleterious previously may be quite functional.



Problems I have with the above statement:

1. Gene duplication is testing a group of mutations, the whole DNA segment, not one mutation at time. The whole unit is tested in a "go - no go" situation- all or nothing.

2. If the DNA fragment is not expressed then natural selection has no selective power. DNA fragments are only tested by natural selection when they are expressed. Therefore, the junk DNA segment is ambivalent toward accumulating good, neutral or deleterious mutations. The DNA fragment is simply a holding bin and there is no force like natural selection that can cause an increase in complexity or weed out deleterious mutations.

3. The ratio of negative mutation to positive mutations is over 100,000/1. (Well over). This causes a sever problem with testing a group of mutation because you will have many more negative than positive mutations in a junk DNA fragment.

4. As time goes by the accumulation of negative mutations gets worse and worse. Therefore, the DNA fragment does not hang around and test for various roles, because the DNA fragment is undergoing genetic entropy. (time and mutations ultimately become the enemy)

5. The DNA fragment is inserted into DNA. It matters where it is inserted into the DNA. For one thing DNA is very large and right spot is very small. The probability of the DNA fragment finding the tight niche is next to zero. Moreover, if this beneficial DNA fragment is inserted into the wrong spot, it would normally create problems.

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Posted 12 June 2009 - 11:05 AM

A nice overview and as originally posted your evolutionary view has evolved well past random mutation and natural selection (RM + NS) or Darwinism. Modern Evolution theory is more or less saying that Darwinism (RM + NS) doesn't explain much - we need more, much more to explain life.

Modern discoveries about genetics, genomics etc just smake natural selection more powerful

You go on to list 'problems':-

1. Gene duplication is testing a group of mutations, the whole DNA segment, not one mutation at time.  The whole unit is tested in a "go - no go" situation- all or nothing.

2.  If the DNA fragment is not expressed then natural selection has no selective power.  DNA fragments are only tested by natural selection when they are expressed.  Therefore, the junk DNA segment is ambivalent toward accumulating good, neutral or deleterious mutations.  The DNA fragment is simply a holding bin and there is no force like natural selection that can cause an increase in complexity or weed out deleterious mutations.

3.  The ratio of negative mutation to positive mutations is over 100,000/1.  (Well over).  This causes a sever problem with testing a group of mutation because you will have many more negative than positive mutations in a junk DNA fragment. 

4.  As time goes by the accumulation of negative mutations gets worse and worse.  Therefore, the DNA fragment does not hang around and test for various roles, because the DNA fragment is undergoing genetic entropy. (time and mutations ultimately become the enemy)

5.  The DNA fragment is inserted into DNA.  It matters where it is inserted into the DNA.  For one thing DNA is very large and right spot is very small. The probability of the DNA fragment finding the tight niche is next to zero.  Moreover, if this beneficial DNA fragment is inserted into the wrong spot, it would normally create problems.

This reference:-
http://www.pnas.org/.../98/3/1113.fullestimated beneficial mutation frequency of 4 x 10^(-9) /cell/generation.
Deleterious mutation rate about 10^(-4) / cell /generation.
Deleterious to beneficial - 250,000 to 1, which is in the range you like.

Note that for each deleterious mutation, there will be 9,999 cells without a deleterious mutation.
Think now of a section of DNA which is re-activated in some way. How many generations before this gene suffers the first deleterious mutation changing its sequence from what it was at the time of reactivation?
That is the time for natural selection to act on the initial sequence.

Look hard at the reference. Data shows 66 advantageous mutations, each of which was able to out-compete previous advantageous mutants even with the handical of adverse mutants to give real net improvement in growth rate.

Experiment proves your reasoning is faulty.

#106 Adam Nagy

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Posted 12 June 2009 - 11:34 AM

Modern discoveries about genetics, genomics etc just smake natural selection more powerful

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I'm not sure Natural Selection has 'power' considering what it's describing. From an evolutionist's perspective Natural Selection has the same kind of power that randomness does... it doesn't, because it is merely our description of other forces in play.

Now accepting the reality of natural selection as a realistic and reasonable result based on the tautology 'survival of the fittest', it is true that healthy and well adapted creatures should survive and be more attractive for furthering the kind through reproduction.

Now the dilemma is this... Did natural selection produce itself accidentally, or is natural selection a functional result of already fully created creatures designed for diversity and adaptation?

Sure natural selection happens but is its origin logically accidental? Does natural selection, assuming it has power, :lol: have the capacity to take an imaginary spontaneously duplicating polymer, to cascade outwards and upwards, hobbling along, designing itself, over billions of years, to produce features that trick the most conscious, and accidental result of this unguided process, humans that is, to come to the faulty conclusion that living organisms are designed? When it's really all just an illusion... :blink:

#107 CTD

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Posted 12 June 2009 - 02:05 PM

Note that for each deleterious mutation, there will be 9,999 cells without a deleterious mutation.

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That is a misrepresentation. There will be no cells without a deleterious mutation. The trick here is that "mutations/cell/generation" has been carelessly replaced with "cells".

"Deleterious mutation rate about 10^(-4) / cell /generation"

Unless they're being spontaneously generated, the cells will have accumulated plenty, even under these silly numbers.

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Posted 12 June 2009 - 06:43 PM

I'm not sure Natural Selection has 'power' considering what it's describing. From an evolutionist's perspective Natural Selection has the same kind of power that randomness does... it doesn't, because it is merely our description of other forces in play.

What other forces?

Now the dilemma is this... Did natural selection produce itself accidentally, or is natural selection a functional result of already fully created creatures designed for diversity and adaptation?

I have no idea what you mean by natural selection producing natural selection?

It is even harder to interpret NS being a result of diversity and adaptation.

Sure natural selection happens but is its origin logically accidental?

Do you perhaps mean, 'Was the universe set up in ways which ensured NS would operate or is NS just an unintentional side effect?"
Only way I could see that being consistent with what I assume is your theology is that NS is one of the consequences of original sin.

By "Sure natural selection happens" do you really mean you accept its operation in cases such as evolution of anti-freeze glycoproteins, or is that just a hypothetical?

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Posted 12 June 2009 - 06:54 PM

That is a misrepresentation. There will be no cells without a deleterious mutation. The trick here is that "mutations/cell/generation" has been carelessly replaced with "cells".

"Deleterious mutation rate about 10^(-4) / cell /generation"

Unless they're being spontaneously generated, the cells will have accumulated plenty, even under these silly numbers.

Since you do not like my numbers, this is your opportunity to present your own estimates of mutation rates, perhaps giving neutral, deleterious and beneficial separately, and with the source or data you have used.

Note that mutation rate will have units like mutations/cell per generation or perhaps mutations/nucleotide per generation if the genome length is known.

#110 CTD

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Posted 12 June 2009 - 09:36 PM

Since you do not like my numbers, this is your opportunity to present your own estimates of mutation rates, perhaps giving neutral, deleterious and beneficial separately, and with the source or data you have used.

Note that mutation rate will have units like mutations/cell per generation or perhaps mutations/nucleotide per generation if the genome length is known.

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Regardless of the rate, it must be applied as a rate. It isn't x mutations per individual. It's x mutations per individual per generation. As generations pass, they accumulate.

Therefore,

Note that for each deleterious mutation, there will be 9,999 cells without a deleterious mutation.

is just wrong.

You should've said "for every cell generated with a new deleterious mutation there'll be 9,999 cells generated without a new deleterious mutation."

Which is the case? Is it too troublesome to double-check your work, or is it too troublesome to be honest?

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Posted 13 June 2009 - 07:17 PM

Regardless of the rate, it must be applied as a rate. It isn't x mutations per individual. It's x mutations per individual per generation. As generations pass, they accumulate.

Therefore,


Note that for each deleterious mutation, there will be 9,999 cells without a deleterious mutation.

is just wrong.

You should've said "for every cell generated with a new deleterious mutation there'll be 9,999 cells generated without a new deleterious mutation."


I am happy with your correction.
You are also right that 9,999 to 1 ratio only applies to the first generation.
However, deleterious mutations do not accumulate without limit. Because they are deleterious, they are gradually lost. It is the beneficial mutations which can accumulate [although random chance also affects individual cells.]

#112 Adam Nagy

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Posted 13 June 2009 - 07:28 PM

You are also right that 9,999 to 1 ratio only applies to the first generation.
However, deleterious mutations do not accumulate without limit.  Because they are deleterious, they are gradually lost.  It is the beneficial mutations which can accumulate [although random chance also affects individual cells.]

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This sounds good until you try to put numbers on actual beneficial mutation rates (or beneficial expression) which is zero, or to be generous, really close to zero, and then to infer that this almost immeasurable, if not immeasurable, beneficial movement is the thing that accounts for all the diversity of life from bacteria to worms to fish to monkeys to people.

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Posted 14 June 2009 - 11:43 AM

This sounds good until you try to put numbers on actual beneficial mutation rates (or beneficial expression) which is zero, or to be generous, really close to zero, and then to infer that this almost immeasurable, if not immeasurable, beneficial movement is the thing that accounts for all the diversity of life from bacteria to worms to fish to monkeys to people.


The actual experiment found 66 beneficial mutations in 1000 generations (about 2 month's growth) in 50 ml (about 1/4 cup) of cell suspension.
http://www.pnas.org/.../98/3/1113.full

That seems very clearly measurable to me.

Since you are clearly wrong in your assessment of the frequency of favorable mutations, (really close to zero), your final conclusion is unjustified.

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Posted 14 June 2009 - 02:24 PM

The actual experiment found 66 beneficial mutations in 1000 generations (about 2 month's growth) in 50 ml (about 1/4 cup) of cell suspension.
http://www.pnas.org/.../98/3/1113.full

That seems very clearly measurable to me.

Since you are clearly wrong in your assessment of the frequency of favorable mutations, (really close to zero), your final conclusion is unjustified.

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This type of "study" is just silly.

Determination of Fitness Parameter m.

The Malthusian fitness parameter m can be determined from the frequency increase of the carrier of the advantageous mutation (12): Formula where m ij is given per generation. P i is the frequency of the selected lineage at the time point when a statistically significant increase in allele frequency was detected. P j = 1 − P i. Time measured in generations is specified by t.

Any mutation - good, bad, or indifferent, is designated "beneficial" if the numbers increase to satisfy the formula. It's totally useless, except that it might provide a clue where to start looking for the mythological "beneficial mutation". ...And as a propaganda tool, as one must expect.

Now then,

Ten parallel cultures were propagated for about 1,000 generations by serial transfer, and 66 adaptive events were identified. From this data set, we estimate the rate of beneficial mutations to be 4 × 10−9 per cell and generation.

After accounting for measurement errors, we identified 66 significant increases of a single allele in the 10 replicate cultures (see supplementary Figs. 4–12, which are published as supplemental data on the PNAS web site, www.pnas.org). Hence, at least 66 advantageous mutations have occurred over approximately 10,000 generations.

This just makes it worse. There are several known mechanisms which cells use to adapt to their environment. No attempt at all was made to determine whether an "adaptive event" was actually the result of a mutation, or whether any of these mechanisms were responsible. None! They're trying to steal credit from all the pre-programmed devices and apply it to actual mutations.

Also,

Second, because the deleterious mutation rate in E. coli is estimated to be in the order of 10−4 (22), we can assume that favorable mutations do not appear in deleterious mutation-free genomes. Thus, those cells carrying a new beneficial mutation but suffering a negative net selection coefficient cannot be identified.

(my bold) They're assuming deleterious mutations will always be present. They're saying that the omnipresent bad may overshadow some of the good, so their count of good is probably low. Compare this to the earlier argument in the thread, which maintained the good could be expected to go unopposed.

This "Malthusian fitness" also shows how such low rates for "deleterious mutations" can easily be obtained. If a mutation is deleterious enough to die out before spreading, they'll never even detect it in this kind of study. They don't examine each and every bacteria cell individually. A mutation has to spread enough to get their attention, and then turn around and diminish in numbers. What percentage of mutations would one expect to be up to such a task? "Malthusian fitness" studies of bacteria cannot yield sensible results for either beneficial or deleterious mutation rates.

"Malthusian fitness" isn't the only formula, but every evolutionist formula for calculating "fitness" will employ similar circular reasoning.

#115 Guest_Keith C_*

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Posted 15 June 2009 - 07:37 PM

This type of "study" is just silly.

Could you give a little more detail of the criteria you use to reach this conclusion?
It seems from the rest of your reply that your technique was to use 'find' to get to passages you can misrepresent without bothering to read the actual paper.

Any mutation - good, bad, or indifferent, is designated "beneficial" if the numbers increase to satisfy the formula. It's totally useless, except that it might provide a clue where to start looking for the mythological "beneficial mutation". ...And as a propaganda tool, as one must expect.

The 66 mutations each multiplied more rapidly than the original cells and any earlier mutant.

This just makes it worse. There are several known mechanisms which cells use to adapt to their environment. No attempt at all was made to determine whether an "adaptive event" was actually the result of a mutation, or whether any of these mechanisms were responsible. None! They're trying to steal credit from all the pre-programmed devices and apply it to actual mutations.

The genetic marker system used in the experiment showed that each identified 'mutant' really was genetically distinct.

(my bold) They're assuming deleterious mutations will always be present. They're saying that the omnipresent bad may overshadow some of the good, so their count of good is probably low. Compare this to the earlier argument in the thread, which maintained the good could be expected to go unopposed.

Since deleterious mutations are far more frequent than beneficial mutations by factor >100,000 by your own estimate, they certainly will be present.
Just read more carefully and all will be clear!

This "Malthusian fitness" also shows how such low rates for "deleterious mutations" can easily be obtained. If a mutation is deleterious enough to die out before spreading, they'll never even detect it in this kind of study. They don't examine each and every bacteria cell individually. A mutation has to spread enough to get their attention, and then turn around and diminish in numbers. What percentage of mutations would one expect to be up to such a task? "Malthusian fitness" studies of bacteria cannot yield sensible results for either beneficial or deleterious mutation rates.

"Malthusian fitness" isn't the only formula, but every evolutionist formula for calculating "fitness" will employ similar circular reasoning.

Since the experiment does not measure 'deleterious mutations' at all, I have no idea what strange notion has distracted your attention.
Neither do I understand what 'circular reasoning' you imagine you have spotted.

#116 CTD

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Posted 17 June 2009 - 03:36 AM

This type of "study" is just silly.

Could you give a little more detail of the criteria you use to reach this conclusion?

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More detail was given. Didn't you read my post?

It seems from the rest of your reply that your technique was to use 'find' to get to passages you can misrepresent without bothering to read the actual paper.

I misrepresented nothing. You can keep that trash. If you continue, expect to be reported.

The 66 mutations each multiplied more rapidly than the original cells and any earlier mutant.

So what?

The genetic marker system used in the experiment showed that each identified 'mutant' really was genetically distinct.

Again, so what? None of this means they were beneficial. Neither does it mean they weren't the result of pre-programmed adaptation mechanisms.

Since deleterious mutations are far more frequent than beneficial mutations by factor >100,000 by your own estimate, they certainly will be present.
Just read more carefully and all will be clear!

What's clear is that you're clowning around. I have no "own estimate", and the nonsense you tried to pass off earlier is debunked by your own source.

Rather than continuing to assert that I misunderstand, why not put a little effort into understanding the issues and terms yourself? Either that, or try participating in threads where you're competent to do so.

Since the experiment does not measure 'deleterious mutations' at all, I have no idea what strange notion has distracted your attention.
Neither do I understand what 'circular reasoning' you imagine you have spotted.

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How would you know if it measured deleterious mutations? Anyone's who's educated and fluent in evospeak knows quite well they were measuring deleterious mutations and calling them "beneficial". It is certain in populations of that size that deleterious mutations will arise, and if they spread rapidly enough to satisfy the formula, they get designated "beneficial". I won't say it couldn't get any more bogus, but I do maintain it'd take some serious effort to pull it off.

As for what I'm talking about, it's right there for you to see. Read it again. "Malthusian fitness" is a bogus tool for generating bogus propaganda. "Malthusian fitness" doesn't amount to anything meaningful in the real world. Google it yourself and see. What am I talking about? "Malthusian fitness" is bogus. Got it this time? Just because a mutation spreads, that does not mean it actually confers a benefit.

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Posted 17 June 2009 - 06:31 PM

Again, so what? None of this means they were beneficial. Neither does it mean they weren't the result of pre-programmed adaptation mechanisms.

How would you know if it measured deleterious mutations? Anyone's who's educated and fluent in evospeak knows quite well they were measuring deleterious mutations and calling them "beneficial". It is certain in populations of that size that deleterious mutations will arise, and if they spread rapidly enough to satisfy the formula, they get designated "beneficial". I won't say it couldn't get any more bogus, but I do maintain it'd take some serious effort to pull it off.

As for what I'm talking about, it's right there for you to see. Read it again. "Malthusian fitness" is a bogus tool for generating bogus propaganda. "Malthusian fitness" doesn't amount to anything meaningful in the real world. Google it yourself and see. What am I talking about? "Malthusian fitness" is bogus. Got it this time? Just because a mutation spreads, that does not mean it actually confers a benefit.

What do you mean by 'pre-programmed adaptation mechanisms'?

The experiment started with a single cell which was allowed to multiply to give cells which were genetically identical (except for the marker which had been inserted for tracking purposes.) All cells had the same pre-programmed genes, except as changed by mutation during the experiment, either deleterious or more rarely beneficial. Beneficial in this experiment was defined to be anything which increased cell multiplication rate.
The marker enabled measurement of the relative numbers of the differently-marked cells. Results were the relative numbers of cells with the particular markers as a function of the numbers of cell generations. When a beneficial mutation occurred the number of cells with that marker would increase while the numbers with other markers would decrease. Total cell concentrations were constant during the experiment, so that slower-growing cells (either without the latest beneficial mutation or with adverse mutations) were diluted and eventually lost.
Mutants with growth rates from 1% to 6% greater than the previous fastest growing variant were detected.

The only 'defect' in the procedure I have detected is that cells were grown in 'rich media'. This means that some of the 'beneficial' mutations could be changes to shut off transcription of particular genes which were not needed. Importance of this problem depends on how effectively the bacteria were adapted to this growth media before the experiment began.
Better alternative would be growth on minimal media so that cells were required to use their entire metabolism.
If you had read more carefully you might have identified this problem instead of the various irrelevant objections you floated.




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