Does the Darwinian theory require modification or replacement?

In message 643 I present evidence of dedicated, nonrandom, beneficial change.

In that some organisms may have developed an evolutionary mechanism by random mutation that allows them to identify and combat parasites by incorporating a portion of the invaders genome into their own thereby allowing them and their offspring to quickly identify like invaders and have responses ready that were already learned by random mutation and selection.

The mechanism appears to be specific to specific classes of pathogens and thus can be called dedicated. The evolved processes have been developed and put in place by random trial and error over many millions of years and are thus now non-randomly invoked by the presence of the specific pathogens.

None of this in any way indicates any directed intelligence performing predetermined modifications to the host genome for specific pre-need purposes.

What if any effect does this proof have on the modification of the MS?

None whatsoever.

Finally, am I misrepresenting Shapiro in message 643?

That does seem to be your purpose here.

What changes do you think your references would require of the Modern Synthesis?

The mechanism appears to be specific to specific classes of pathogens and thus can be called dedicated. The evolved processes have been developed and put in place by random trial and error over many millions of years and are thus now non-randomly invoked by the presence of the specific pathogens

Where are the data of this trial and error procedure?

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Information: It is time its undeservedly neglectet powerful role to evolution to be restored.

AZPaul3 writes: What changes do you think your references would require of the Modern Synthesis?

zi ko writes: Where are the data of this trial and error procedure?

You answer my question first and I'll answer yours in kind.

AZPaul3 writes: What changes do you think your references would require of the Modern Synthesis? zi ko writes: Where are the data of this trial and error procedure? You answer my question first and I'll answer yours in kind.

This question is not adressed to me. So what answer can i give?
I am still asking. What are the data for this random trial and error procedure?

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Information: It is time its undeservedly neglectet powerful role to evolution to be restored.

zi ko writes: What are the data for this random trial and error procedure?

This is a reference to evolution. Evolution by means of descent with modification and natural selection is a trial and error process. Trials are performed on random modifications, selection weeds out the "errors".

--Percy

zi ko writes: What are the data for this random trial and error procedure? This is a reference to evolution. Evolution by means of descent with modification and natural selection is a trial and error process. Trials are performed on random modifications, selection weeds out the "errors". --Percy

Are there ny data that exclude any information participation in procedure of evolution?

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Information: It is time its undeservedly neglectet powerful role to evolution to be restored.

zi ko writes: Are there ny data that exclude any information participation in procedure of evolution?

When scientists purposefully omit data from consideration in order to promote their own personal agenda they're always very careful to make sure it can't be detected.

Seriously, an information theoretic perspective is just one among many, and it isn't often the best one. For most problems in evolutionary theory, approaching them at the information theoretic level would be like calculating the path of a rolling ball through an analysis at the atomic level.

I share your fascination with information theory, but it isn't the best solution for every problem.

--Percy

Are there ny data that exclude any information participation in procedure of evolution?

In a broad sense the "information" content of the genome changes with random mutation (to include insertion, frame-shift etc.) and the resulting phenotype is matched against the "information" of the environment. The "information" in the environment determines if the "information" in the genome continues as part of the larger population or if it is lessened or eliminated from the larger population.

Taq writes: If which mutations are nonrandom? If 99.999% of mutations are random with a few examples of specialized systems that insert viral DNA into palindromic sequences would the entire theory need to be rewritten, or would a footnote do?

I take it you agree that the papers Shapiro referred to in his book and I cited on this board re CRISPR System is a process of nonrandom mutations for fitness.

If so does this process fit into the theory of evolution as it is known today?

Percy writes: Descent, modification and selection are natural processes. Planned and implemented by some entity is not a natural process. You seem to be trying to have it both ways.

What I am saying is that the whole process of evolution may in fact be planned.
Obviously I cannot prove that, nor can you disprove it.

But if in fact the process of evolution is planned then it still can be a natural process, planned by a Supernatural being.

Shad writes: What I am saying is that the whole process of evolution may in fact be planned. Obviously I cannot prove that, nor can you disprove it. But if in fact the process of evolution is planned then it still can be a natural process, planned by a Supernatural being.

The invisible hand of Zeus could be manipulating every ecoli experiment in order to dupe us into thinking that ecoli bacteria evolve. Likewise undetectable gravity gremlins could be manipulating reality to fool us into thinking that space-time curvature is responsible for gravitational effects.

Obviously I cannot prove that, nor can you disprove it.

So I guess these conclusions are as valid as the ones you are advocating?

AZPaul3 writes: The mechanism appears to be specific to specific classes of pathogens and thus can be called dedicated. The evolved processes have been developed and put in place by random trial and error over many millions of years and are thus now non-randomly invoked by the presence of the specific pathogens.

Not trying to be a jerk, but can you show by data that the processes have been developed and put in place by RANDOM TRIAL AND ERROR over many millions of years and are thus now nonrandomly invoked by the presence of the specific pathogens?

Or is this merely the assumption that that is how evolution works?
It seems to me to be a contradiction that the presence of specific pathogens would suddenly lead to a nonrandom process.

If it is a natural process then no supernatural being need apply.

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Anyone so limited that they can only spell a word one way is severely handicapped!

I don't think the question of fitness for any particular CRISPR incorporation event can be evaluated on the basis of the papers discussed so far. Certainly it is easy to appreciate how a defence system against bacteriophages in general should be beneficial to a bacterial population.

It isn't clear however to what extent any particular protospacer sequence will be an effective substrate for the CRISPR system to combat bacteriophage infection. The sequences the review discusses are ones already established in various bacterial populations, in other words they are ones that have already passed through several rounds of natural selection.

It may be that when a bacterial population is subject to a challenge from bacteriophage infection its constituent bacteria will incorporate dozens or hundreds of different spacer sequences depending on the prevalence of the particular PAM motifs that the CRISPR loci in the population targets. If a particular spacer sequence confers immunity to the bacteriophage challenge we would expect it to proliferate in the population. But we can't simply assume that all spacer sequences confer the same degree of immunity or even any immunity at all.

I'll have a look in some of the other CRISPR papers and see if there is anything about this. As it stands though I don't think we can say that every CRISPR locus spacer incorporation is a beneficial mutation even though we have specific instances where they have been.

TTFN,

WK

Not trying to be a jerk, but can you show by data that the processes have been developed and put in place by RANDOM TRIAL AND ERROR over many millions of years and are thus now nonrandomly invoked by the presence of the specific pathogens?

I have a thick skin. No 'jerk' assumed.

If you comprehended the papers you have been citing you would have answered your own question. All of them cite the usual and customary mechanisms to evolve what can now be seen as embedded non-random responses to external stimuli.

Similar, indeed, to the evolved non-random responses some people have to certain plant pollen: blind chemical cascades evolved to fight the effects of some specifically irritating external stimuli.

It seems to me to be a contradiction that the presence of specific pathogens would suddenly lead to a nonrandom process.

If you comprehended the papers you have been citing you would see the error in your statement.