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The Religious Origins of Science

Notedstrangeperson

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Mark Kennedy said:
You have a nerve to call someone ignorant while making such a fundamental mistake. Deleterious is by definition 'harmful'.
...
Now if you want to contrast deleterious effects with beneficial or neutral effects but pretending that deleterious does not mean harmful is silly.

I made a mistake, my bad. I intended to mean 'loss-of-function'.
When you speak of mutations you automatically seems to assume that mutations are damaging because they inhibit the genes normal functioning. They make it so that the gene works 'below normal capacity' or the genetic coding is lost altogether. To put it literally, the gene's code is deleted.

Now when I gave the example of telomerase and cancer I was using the word 'deleted' in it's literal sense. During cell division the very end of the chromosomes fail to replicate. They're missing. Normally this is a natural part of life, but if telomerase is present when it should not be it causes cells to keep replicating when they should have died - one of the many causes of cancer.

Mark Kennedy said:
I never argued that there was such a thing as a beneficial effect from a mutation.

Either you have changed your mind or worded your argument incorrectly, since on other occasions you have argued there are beneficial mutations, albeit rare ones:

(From my thread on Horizontal Gene Transfer):
Beneficial affects from mutations are among the rarest of mutations ...
Mutations with an effect strong enough for selection to act are almost always deleterious, the rarest of these errors have beneficial effects ...
I never said that beneficial effects don't happen, just not on the scale you are trying to make us believe.

I don't want to turn this into a petty "He said / She said" argument but your definition of mutations (from Wikipedia? There are far better sources than that) clearly has an effect on your understanding of evolution.

Mark Kennedy said:
Evolution is properly defined as the change of alleles in populations over time. The Darwinian a priori assumption of universal common descent by exclusively naturalistic causes is another definition you never own up to.

Evolution does indeed involve changes in alleles but it's much more than that - it involves the creation of new species. Macroevolution versus microevolution I think is the issue here. And marcoevolution involves the belief in universal common descent, which I believe. 'Exclusively naturalistic causes' I am dubious about.

(For the record this is an ad hominem argument) I guess you're just waiting for the right moment to say "Ha! I knew it, I knew it, she's a heathen!" :p
 
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Notedstrangeperson

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Shernren said:
The particular crux of the Intelligent Design movement is that, as Darrel Falk summarizes, naturalistic forces cannot produce "information"

Ah I see what you mean ... now that goes to the very root of the idea of a 'mechanical universe'.
I think something theistic evolutionists (including myself) are not very clear on is how God is involved with the creation of the universe. What, if anything, does he do exactly?
I think evolution damaged the idea that God created us in a specific way. It seems to rule out the idea of a designer - though not a creator, since perhaps insted of creating living beings in a certain way, he created a system which creates it's own lifeforms. This is nothing more than my own opinion, but to me it shows that God had a great deal more imagination and ingenuity than we first assumed.

But what about Darrel Falk's argument? How can natural forces produce information - or rather, how can order and meaning comes from a process which is unconcious and blind?
 
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shernren

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Ah I see what you mean ... now that goes to the very root of the idea of a 'mechanical universe'.
I think something theistic evolutionists (including myself) are not very clear on is how God is involved with the creation of the universe. What, if anything, does he do exactly?

The way I see it, God is the purpose of the universe. So who says God has to do anything? Creation will all be placed under the authority of the Son, who will in turn surrender it to the Father, and until that point in time God is free to act however He pleases in the world, whether to uphold the naturalistic processes that keep it running or temporarily suspend them. He is free to do whatever He pleases, however He pleases, to render the world a fitting gift from Father to Son.

And because we only dimly know what this gift is meant to look like, we can only dimly identify divine action in the world. We are told certain things in the Bible, but not others; indeed, if we could make a world pleasing to God, in our own intellectual and aesthetic capabilities, we would in a sense be God ourselves!

So I'm not particularly concerned with what God does. I am assured that if God showed it to me now, I wouldn't get it - nothing makes sense until it is seen in the light of eternity. I just need to obey what I do know for now, and - as a scientist - practice what I see as basically a codified kind of curiosity about the world, which God happens to have equipped me a little better for.

I think evolution damaged the idea that God created us in a specific way. It seems to rule out the idea of a designer - though not a creator, since perhaps insted of creating living beings in a certain way, he created a system which creates it's own lifeforms. This is nothing more than my own opinion, but to me it shows that God had a great deal more imagination and ingenuity than we first assumed.

Sure evolution may have damaged a particular view of the world. But we are forgetting that in every generation science has "threatened" God, only to be assimilated and accepted.

It is interesting how little attention creationists pay to celestial mechanics, for example. Just four hundred years ago, Newton was convinced that the heavens were truly and literally the handiwork of God. He had developed the calculus, and the laws of gravity, with which he could predict the motions of the planets - but try as he may, he could not mathematically show that the Solar System is stable against perturbations. As such, he saw the imperfections of the Solar System as a testament to God's majesty and miraculous power - surely, in order to keep the Earth a habitable place, God is occasionally introducing comets and asteroids to perturb the Solar System and keep it stable.

No creationist today would dream of demanding equal time for such a theory next to Kepler's Laws. And yet this was the flashpoint of debate about theism. When Laplace solved Newton's problem, he thought he had eliminated God from the equation, as seen in the famous vignette where Napoleon asked him where in his treatise he mentioned God, and he replied: "I have no need of that hypothesis."

The irony is that we accept that "the heavens declare the glory of God", and yet, from an ID point of view, they are nothing more than meaningless, information-less husks of collapsing gases that happen to spew out a few photons our way. I think that tells us that the preoccupation with evolution disproving God says a lot more about the culture of our times than creationists like to admit.

But what about Darrel Falk's argument? How can natural forces produce information - or rather, how can order and meaning comes from a process which is unconcious and blind?

Looking inside a system to find the part or process which creates information is a bit like trying to learn Monopoly by writing down the physics of rolling dice. And dice are a perfect example of natural forces producing information: all that happens is that an oddly-shaped block of plastic hits the floor in a certain random configuration - and yet information has been produced! As far as I can see, information is produced not within systems, but as systems interact with their outside environments.

Of course, I'm sure that's not the whole story - but I think that must be the start.
 
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mark kennedy

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I made a mistake, my bad. I intended to mean 'loss-of-function'.

That doesn't explain the condescending tone, you were more interested in correcting me and making me foolish then what you were talking about. At any rate, a mutation wether it's a single-base substitution (missense mutation, nonsense, silent mutation, splice-site mutation) an insertion/deletion (indel), duplication or translocation. A mutation is a failure of DNA repair. Let's move on.

When you speak of mutations you automatically seems to assume that mutations are damaging because they inhibit the genes normal functioning. They make it so that the gene works 'below normal capacity' or the genetic coding is lost altogether. To put it literally, the gene's code is deleted.

I assume nothing of the sort, I realize that vast majority do nothing at all. What usually happens when there is an effect is a 'loss of function' or it is somehow disruptive. Indels for example:

Frameshift.gif

Indels involving one or two base pairs (or multiples thereof) can have devastating consequences to the gene because translation of the gene is "frameshifted"...Frameshifts often create new STOP codons and thus generate nonsense mutations. Perhaps that is just as well as the protein would probably be too garbled anyway to be useful to the cell. (mutations)​

Now when I gave the example of telomerase and cancer I was using the word 'deleted' in it's literal sense. During cell division the very end of the chromosomes fail to replicate. They're missing. Normally this is a natural part of life, but if telomerase is present when it should not be it causes cells to keep replicating when they should have died - one of the many causes of cancer.

Cancer cells contain mutated genes, they almost always contain genes that:

  • Control the cell cycle,
  • Mutations in these enable the cell to ignore signals telling it that it is irreparably damaged and should commit suicide.
  • Genes that maintain telomeres (the chromosome tips).
  • Genes that stimulate angiogenesis.
  • Metastasis genes: genes that enable cells of the tumor to separate from the primary tumor and migrate to other parts of the body.

Cancers are caused by anything that damages DNA; that is anything that is mutagenic. Or anything that stimulates the rate of mitosis. This is because a cell is most susceptible to mutations when it is replicating its DNA during the S phase of the cell cycle. (cancer)

Either you have changed your mind or worded your argument incorrectly, since on other occasions you have argued there are beneficial mutations, albeit rare ones:

Ok I really get tired of you putting words in my mouth. Stop it!!!

If you need some time to learn what you are talking about don't do it at my expense. What I have argued for years is that a failure of DNA repair is not the cause of most adaptive evolution.

(From my thread on Horizontal Gene Transfer):
Beneficial affects from mutations are among the rarest of mutations ...
Mutations with an effect strong enough for selection to act are almost always deleterious, the rarest of these errors have beneficial effects ...
I never said that beneficial effects don't happen, just not on the scale you are trying to make us believe.

I'm not chasing down the quotes, if you want to rehash a previous discussion then you are going to have to come up with direct quotes. I think it is pointless, in fact, I think it's a diversion. If you are trying to make a point then get on with it.

I don't want to turn this into a petty "He said / She said" argument but your definition of mutations (from Wikipedia? There are far better sources than that) clearly has an effect on your understanding of evolution.

If you don't like my definition of a mutation the try your own or find a suitable alternative. I don't intend to waste time fielding these pointless corrections since you have already demonstrated that you are struggling with the basics.

Evolution does indeed involve changes in alleles but it's much more than that - it involves the creation of new species. Macroevolution versus microevolution I think is the issue here. And marcoevolution involves the belief in universal common descent, which I believe. 'Exclusively naturalistic causes' I am dubious about.

Evolution is properly defined as the change of alleles in populations over time. That's the working definition I am using and what scale it is one does not effect the usefulness of the definition.

(For the record this is an ad hominem argument) I guess you're just waiting for the right moment to say "Ha! I knew it, I knew it, she's a heathen!" :p

Look, I enjoy talking about this sort of thing I would just like to focus on the molecular mechanisms, causes of change in the DNA sequences and how living systems adapt. I'm not your intellectual inferior simply because I don't subscribe to your a priori assumptions.

Take your time, lets focus on the facts and try to keep it civil.

Grace and peace,
Mark
 
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Notedstrangeperson

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Mark Kennedy said:
Ok I really get tired of you putting words in my mouth. Stop it!!! I'm not chasing down the quotes, if you want to rehash a previous discussion then you are going to have to come up with direct quotes.

I'm not trying to put words in your mouth, those are direct quotes cut and pasted from a separate thread. I provided the link for you. I added them because earlier you wrote "I never argued that there was such a thing as a beneficial effect from a mutation." As I said, either you have changed your mind or you worded your argument incorrectly.

Now correct me if I'm wrong but when you write "failure of DNA repair is not the cause of most adaptive evolution" you seem to be arguing that beneficial mutations, if they do exist, are too few and far between to have any noticable effect on a species. Since mutations are "a failure of DNA repair", how could a broken, flawed version somehow be better than the original version? But even calling it a 'failure' suggests that mutated version is somehow inferior to the non-mutaed version. Therefore by definition most effective mutations are damaging. But this isn't the case.

Whether a mutation is beneficial or not partly depends on circumstance. For example, there are several mutation which can cause and animals fur to turn white. If this animal lives in a European forest this would be a disaster as it makes them all-too obvious, even at night. If they live in the Arctic circle however this is a huge boost, as it allows them to blend in with their environment. The same mutation can be deleterious or beneficial depending on circumstance.

(BTW if "failure of DNA repair is not the cause of most adaptive evolution" than what is?)

Mark Kennedy said:
Evolution is properly defined as the change of alleles in populations over time.

Yes, you keep repeating this. It conveniently fits into microevolution but not macroevolution.

Mark Kennedy said:
notedstrangeperson said:
(For the record this is an ad hominem argument) I guess you're just waiting for the right moment to say "Ha! I knew it, I knew it, she's a heathen!"
Look, I enjoy talking about this sort of thing I would just like to focus on the molecular mechanisms, causes of change in the DNA sequences and how living systems adapt.

As you wish, but I dislike having macroevolution / universal common descent referred to as 'blasphemous'. :p
 
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mark kennedy

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I'm not trying to put words in your mouth, those are direct quotes cut and pasted from a separate thread. I provided the link for you. I added them because earlier you wrote "I never argued that there was such a thing as a beneficial effect from a mutation." As I said, either you have changed your mind or you worded your argument incorrectly.

These quotes never say that there is no such thing as a beneficial effect from a mutation:

  • Beneficial affects from mutations are among the rarest of mutations ...
  • Mutations with an effect strong enough for selection to act are almost always deleterious, the rarest of these errors have beneficial effects
  • I never said that beneficial effects don't happen, just not on the scale you are trying to make us believe
.

I have neither changed my mind nor changed my wording. Your quoting me out of context and misrepresenting my meaning, it's as simple as that.

Now correct me if I'm wrong but when you write "failure of DNA repair is not the cause of most adaptive evolution" you seem to be arguing that beneficial mutations, if they do exist, are too few and far between to have any noticable effect on a species. Since mutations are "a failure of DNA repair", how could a broken, flawed version somehow be better than the original version? But even calling it a 'failure' suggests that mutated version is somehow inferior to the non-mutaed version. Therefore by definition most effective mutations are damaging. But this isn't the case.

Actually most mutations that have an effect are deleterious (harmful), I'm not making this up:

In the living cell, DNA undergoes frequent chemical change, especially when it is being replicated (in S phase of the eukaryotic cell cycle). Most of these changes are quickly repaired. Those that are not result in a mutation. Thus, mutation is a failure of DNA repair. mutations

Although mutations are an essential component of adaptive evolution, most mutations that affect fitness are deleterious...Under extreme circumstances, the process of fixing deleterious mutations and subsequent fitness decline can perpetuate itself and eventually drive extinction PLoS Morran LT, Ohdera AH, Phillips PC (2010)

The PLoS article cites 2 papers that I have quoted and cited for years and base my statements about mutations on. I'm not making this up and I have not changed my view of mutations one iota based on my discussions with you or anyone else on here. It doesn't mean that mutations are not a part of adaptive evolution but there has to be a better explanation then errors in DNA repair.

Whether a mutation is beneficial or not partly depends on circumstance. For example, there are several mutation which can cause and animals fur to turn white. If this animal lives in a European forest this would be a disaster as it makes them all-too obvious, even at night. If they live in the Arctic circle however this is a huge boost, as it allows them to blend in with their environment. The same mutation can be deleterious or beneficial depending on circumstance.

Yes I know and deleterious or slightly deleterious mutations can become beneficial under certain circumstances.

(BTW if "failure of DNA repair is not the cause of most adaptive evolution" than what is?)

There are a number of things that I will touch on briefly. Changes in gene expression, genes can be turned on and off, chromosomal rearrangements. The thing is for them to be adaptive on an evolutionary scale they have to occur in the germline cells and this is precisely where they are least likely to occur. Now if I didn't have to spend so much time fielding arguments about deleterious mutations we could talk some more about how living systems adapt without DNA even having to change at all. But under the circumstances we will have to do that another time.

Yes, you keep repeating this. It conveniently fits into microevolution but not macroevolution.

I have never had the slightest interest in distinguishing between the two.

As you wish, but I dislike having macroevolution / universal common descent referred to as 'blasphemous'. :p

That's not what is blasphemous, this is:

Either concede that if God created the world he also created all the fossils, including the transitional ones, or at the very least think of new ways to argue your point - insted of repeated the same ones over and over again like a broken record

I've looked at the fossils and found them to be misrepresented by Darwinians desperate to demonstrate transitionals. That does not make God a liar because you think they prove macroevolution or universal common descent.

Once again you have quoted me out of context and twisted my words to mean something I never intended. When you call God a liar and deceiver based on fragmentary fossil evidence you don't even describe, it's blasphemous. That's the kind of inflammatory rhetoric TEs come into this forum with and you pretend you have done nothing wrong.

Now knock it off, try reading a couple of scientific publications or other resources and we can talk some more. Its only fair to warn you though, I'm wise to your rhetoric and I'm not impressed.

Have a nice day :wave:
Mark

P.S. There's one in every thread...
 
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Notedstrangeperson

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Mark Kennedy said:
These quotes never say that there is no such thing as a beneficial effect from a mutation:
Sigh.
Yes, I know. I added them because on the thread on Horizontal Gene Transfer you wrote you did believe in beneficial mutations whereas earlier on this thread - the Religious Origins of Science - you wrote "I never argued that there was such a thing as a beneficial effect from a mutation."
So to avoid confusion, do you think beneficial mutations exist or not?

Mark Kennedy said:
Yes I know and deleterious or slightly deleterious mutations can become beneficial under certain circumstances.

Ah, so you do. In which case what is the point of repeatedly inisisting that that most mutations are harmful and therefore are evidence against evolution?

Mark Kennedy said:
Changes in gene expression, genes can be turned on and off, chromosomal rearrangements. The thing is for them to be adaptive on an evolutionary scale they have to occur in the germline cells and this is precisely where they are least likely to occur. Now if I didn't have to spend so much time fielding arguments about deleterious mutations we could talk some more about how living systems adapt without DNA even having to change at all.

You mean epigenetics? Why do you chose this option over the traditional evolutionary one? I'm not being facetious - how does it effect your view on Creationism / evolution?
Epigenetics focuses on individuals rather than entire speices since they are not inherited, so they are not especially useful mutations. However there is some (very scant) evidence that epigenetic changes can be passed on, which would support Lamarckian evolution rather than Darwinism. But I can't see how this would support Creationism ...

Mark Kennedy said:
When you call God a liar and deceiver based on fragmentary fossil evidence you don't even describe, it's blasphemous.

I did not call God a 'liar' :| You inferred that yourself - "You have the unmitigated gall to come in here and pretend that these contrived fossils turn the Word of God into a lie?" I wrote that if God created the world and everything in it presumably he also created the fossils.
 
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shernren

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There are a number of things that I will touch on briefly. Changes in gene expression, genes can be turned on and off, chromosomal rearrangements.

You might want to know that chromosomal rearrangements are mutations.

I'm more than happy to talk about this. We could start with the question:

Are changes in gene expression, or "genes being turned on and off", heritable?

(I hope you can see the relevance of this question. I'm sure you'll agree with me that any change to a genome that isn't heritable can't, by definition, go into defining the differences between species.)

EDIT: I don't think I want to hijack this thread - not that it's still on topic, heh. I'll open this up in the main OT forum. How about that?
 
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Notedstrangeperson

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Shernren said:
I'm more than happy to talk about this. We could start with the question:

Are changes in gene expression, or "genes being turned on and off", heritable?

(I hope you can see the relevance of this question. I'm sure you'll agree with me that any change to a genome that isn't heritable can't, by definition, go into defining the differences between species.)

EDIT: I don't think I want to hijack this thread - not that it's still on topic, heh. I'll open this up in the main OT forum. How about that?

Yes that would be interesting. This thread has gone the way of all flesh. :p
 
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Papias

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Mark wrote:

Actually most mutations that have an effect are deleterious (harmful), I'm not making this up:

Mark, we know that most mutations are harmful. Since natural selection removes the harmful ones and geometrically multiplies the beneficial mutations, why does it matter if there are more harmful mutations to start with? I hope you recognize that we aren't arguing that there are more beneficial mutations originally.

Papias
 
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Papias

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So Mark is again denying that beneficial mutations are plentiful and build up by natural selection?

Earlier, I posted a list of examples where Mark posted a falsehood, was shown to be wrong, and then later on posted the same falsehood again as if no one would notice that he's been corrected before.

Apparently now we have another example of this behavior. One of the many times Mark has been shown some of these beneficial mutations and how they accumulate was at these posts:

http://www.christianforums.com/t7513938-6/ See around post #56 on.

From there, here are some beneficial mutations:

There is plenty of evidence for many observed beneficial mutations. For example, here is an observed beneficial mutation for better immune cells in humans: Enhanced fMLP-stimulated chemotaxis in human neutr... [FEBS Lett. 1998] - PubMed result, an observed beneficial mutation for bigger muscles in humans: A Very Muscular Baby Offers Hope Against Diseases - NYTimes.com, in bacteria, an observed beneficial mutation for the ability to eat citrate Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli — PNAS , and an observed beneficial mutation for the ability to digest nylon Emergence of nylon oligomer degradation enzymes in Pseudomonas aeruginosa PAO through experimental evolution -- Prijambada et al. 61 (5): 2020 -- Applied and Environmental Microbiology,

and if all those weren't enough (and there are plenty more), then here are literally hundreds of beneficial mutations intentionally induced by radiation exposure, where crop seeds are irradiated to cause mutations, then the plants are grown, the deletrious mutants thrown out, and the beneficial mutants kept : http://www.google.com/url?q=http://webapp.ciat.cgiar.org/biotechnology/cbn/sixth_international_meeting/pdf_presentations/dia%252012/Chikelu_Mba2.pdf&sa=U&ei=Ion2TLEqgaafB9yqmaMJ&ved=0CB0QFjAD&usg=AFQjCNG4z8GeHJC7MRMGAH_QcyyFkg6wsg

(go to original post for links)

Plus, simple common sense shows that there are plenty of beneficial mutations. A mutation will cause a change in the offspring. So look at your arm - a mutation would make it longer, or shorter. Which is "beneficial", and which is "harmful"? Well, that depends on the environment. If you are living in the trees, the longer arm is beneficial for reaching branches. If you are a runner on the plains,the longer arm is harmful, because it's more weight to carry.


Mark was also directed to post #75, here:

http://www.christianforums.com/t7512492-8/

Which shows mathematically that natural selection will cause beneficial mutations to be dominant, even if the mutation rate makes many more harmful mutations than beneficial mutations.

Mark, do you remember those instances?

Do you agree there are beneficial mutations, and that natural selection will naturally multiply them, while removing the harmful mutations?

Papias
 
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mark kennedy

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So Mark is again denying that beneficial mutations are plentiful and build up by natural selection?

I deny the naturalistic assumptions of Darwinians who conflate real world science with pithy rhetoric while neglecting the genuine artlcle of science. Natural selection is nothing more then the death of the less fit and if you don't know that then you don't know the first thing about it.

By the way, addressing me in the third person is something I have very little patience for. If you want to perform I suggest you get a soap box and go down to the local park.

Earlier, I posted a list of examples where Mark posted a falsehood, was shown to be wrong, and then later on posted the same falsehood again as if no one would notice that he's been corrected before.

You mean you went on an error fabrication campaign and succeeded in alienating someone who was trying to share with you what he learned. That's fine, if you want to define the discussion in those terms I'm always ready to defend my position against the fallacious rhetoric of Darwinian minions.

Apparently now we have another example of this behavior. One of the many times Mark has been shown some of these beneficial mutations and how they accumulate was at these posts:

So you cut and past another link that gets us to a discussion of this source material:

To untangle the different possibilities, we performed MA experiments on lines differing by approximately 300-fold in fitness to characterize the distribution of deleterious mutation effects on fitness (Figure 4). This distribution of mutational effects is leptokurtic, with most mutations being of small effect, and a few having large effects (Figure 4A). Across a very wide range of fitness values, this distribution of effects appears to remain approximately constant (Figure S1). Additionally, the shape of the distribution is strongly supported by the genomic data, which show that even when populations are maintained at large population sizes and fitness does not change, substitutions continue to accrue; these must be of very small effect. However, if all mutations were of small effect, they should be immune to selection in small populations. This was not observed; both deleterious and beneficial mutations were subject to selective forces, even in the smallest of the populations (citation unavailable)​

  • Across a very wide range of fitness values distribution appears to remain approximately constant.
  • Even when populations are maintained at large population sizes and fitness this does not change.
  • Both deleterious and beneficial mutations were subject to selective forces even in the smallest populations.

Notice my comments below the quote in a three point list is just a summary and paraphrase of the quote. The quote is really just saying that the beneficial and deleterious effects are the same in small and large populations. The comments shrenern makes are aimed exclusively at me, he never makes a substantive point and the topic is hopelessly mired in personal remarks.

Papias is celebrating the fallacious line of reasoning and pretending to prove something.

Shernren is making a mockery of the paper as well as engaging his standard ad hominem attack, it's his whole function on here. If you want to see his intellectual integrity in full swing you should come and see how he refuses to acknowledge that 3 + 1 = 4. Is that science?

I ask a simple question, based on the findings of the Chimpanzee Genome consortium are we 98% the same as Chimpanzees or 96%. Not a single evolutionist will admit this clear statement of fact:

Chimpanzee/Human Genome Difference. 98% or 96%?

  • Single-nucleotide substitutions occur at a mean rate of 1.23% between copies of the human and chimpanzee genome, with 1.06% or less corresponding to fixed divergence between the species.
  • Insertion and deletion (indel) events are fewer in number than single-nucleotide substitutions, but result in ~1.5% of the euchromatic sequence in each species being lineage-specific.

(Initial sequence of the chimpanzee genome and comparison with the human genome, Nature 2005)​

Not one evolutionist will admit that 3 + 1 = 4 and this is a prime example of that kind of fallacious rhetoric. They don't care about science, they come here to make personal attacks on creationists.


Yea check it out, the argument is so important it is represented here by papias as a cut and paste link and an inflammatory personal attack.

Repeatedly I have told this guy that I do not deny beneficial effects from mutations. Repeatedly he sets up a strawman attack on an argument I have never made. Mutations are a failure of DNA repair, when they have an effect the vast majority are deleterious. Researchers emphasis this point and this in no way distracts them from the fact that mutations are essential to improved fitness in populations over time.

That is not a contradiction of what I'm saying nor is it an indictment against evolution. It's simply a fact of life, especially for single celled populations like bacteria. If you are not well read in the scientific literature it's hard to grasp and papias would know this by now if he were focused on something other then personal attacks.

From there, here are some beneficial mutations:

Notice to this point he has not quoted me once. He calls me a liar but he never quotes the lie. This is called a strawman argument, he sets up an argument against someone who is denying that there is such a thing as a beneficial effect from a mutation. He calls that person Mark but I never said that. Now he is going to do his standard cut and paste link intermingled with his pedantic, sophomoric quips. He doesn't even put a title in the link

This mess is what he is passing off as an argument:

There is plenty of evidence for many observed beneficial mutations.

An argument I never made...

For example, here is an observed beneficial mutation for better immune cells in humans:

This is the first line of the abstract he linked to without any substantive remarks.

We have recently described a C825T polymorphism in the gene encoding for the Gbeta3 subunit of heterotrimeric G proteins. (Pub Med 1998)​

This is describing a polymorphism in highly technical language I guarantee you papias cannot read. He doesn't pick a paper in PLoS where the whole thing is available or make the slightest effort to describe how this spam salad has any relevance. He calls me a liar without quoting me, cut and pastes a link with a one line comment on nothing to nobody.

It's a polymorphism in a protein coding gene, so what?

an observed beneficial mutation for bigger muscles in humans...

This kid has a deactivated gene that has this effect on him:

''At first we thought it might be epilepsy,'' Dr. Schuelke said.

After two months, the jerking movements had subsided, but the puzzle of the baby's muscles remained. Then Dr. Schuelke had an idea. He knew that Dr. Se-Jin Lee at Johns Hopkins University, working with mice, had found that when both copies of a gene for a protein called myostatin were inactivated, the animals grew up lean and so muscular that Dr. Lee called them ''mighty mice.''

It turned out that cattle breeders, decades ago, had stumbled upon the same genetic trick, developing a strain known as Belgian Blue, or double muscle cattle. The cattle are hefty, very meaty and lean, and they, too, researchers later found, had inactive myostatin genes...

...The mother had one nonfunctioning copy of the gene. In the boy, both copies of the gene were inactive; he was making no myostatin at all. (A Very Muscular Baby Offers Hope Against Diseases - NYTimes.com)​

That's the new article he is going to submit, a kid that jerked so much that they thought he have epilepsy. There you have it, two inactive copies of a gene presented as an example of a beneficial effect from a mutation.

, in bacteria, an observed beneficial mutation for the ability to eat citrate

My often made statement that the overwhelming majority of effects from mutations that have an effect are deleterious is confirmed in no uncertain terms here:

No population evolved the capacity to exploit citrate for >30,000 generations, although each population tested billions of mutations. A citrate-using (Cit+) variant finally evolved in one population by 31,500 generations, causing an increase in population size and diversity. The long-delayed and unique evolution of this function might indicate the involvement of some extremely rare mutation.(PNAS 2008)​

I don't know if he thinks this will scare me away from the scientific literature but he has still, not quoted me once. He has still not made a single substantive remark or elaborated with more then a single off the wall remark on the sources he uses.

This is nothing more then spam intended to flood the thread and discourage creationists from posting to their own forum. It is a shameless empty post that unfortunately is typical of his tactics.

Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli” PNAS[/I][/URL] ,

and an observed beneficial mutation for the ability to digest nylon http://aem.asm.org/cgi/pmidlookup?view=long&pmid=7646041


I'll make my last point with this one because it's the best one I've ever seen. All the evolutionists love using this one because it's an example of a frameshift mutation that improves a protein product that is not only beneficial but adaptive. A frameshift in the protein coding genes are highly disruptive, this is what happens most of the time:

Indels involving one or two base pairs (or multiples thereof) can have devastating consequences to the gene because translation of the gene is "frameshifted". This figure shows how by shifting the reading frame one nucleotide to the right, the same sequence of nucleotides encodes a different sequence of amino acids. The mRNA is translated in new groups of three nucleotides and the protein specified by these new codons will be worthless. Scroll up to see two other examples (Patients C and D). ([URL="http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/M/Mutations.html"]mutations​
)

Frameshift.gif

Frameshifts often create new STOP codons and thus generate nonsense mutations. Perhaps that is just as well as the protein would probably be too garbled anyway to be useful to the cell.​

Ok, that's what a frameshift mutation does the overwelmning majority of the time. In the case of the nylon bug a frameshift created the ability of this population to digest nylon right?

Wrong!!!!

The mechanism of gene duplication as the means to acquire new genes with previously nonexistent functions is inherently self limiting in that the function possessed by a new protein, in reality, is but a mere variation of the preexisted theme. As the source of a truly unique protein, I suggest an unused open reading frame of the existing coding sequence. Only those coding sequences that started from oligomeric repeats are likely to retain alternative long open reading frames.​

Birth of a unique enzyme from an alternative reading frame of the preexisted, internally repetitious coding sequence.

This swapped out reading frame of simple repeats is very similar to the Arctic fish that not only had a unique sequence but a new gene. I won't go into the details any further because I doubt seriously anyone is reading these insufferable cut and paste spam attacks. I'll tell you this, what you are looking at with the nylon bug is not a random mutation or natural selection. What you are seeing is an adaptation from a molecular mechanism.

and if all those weren't enough (and there are plenty more),


No body is reading these cut and paste spam ramblings. I sorted through them because I enjoy the literature and I've read a lot of it, something you should try at least once in a while.

Plus, simple common sense shows that there are plenty of beneficial mutations. A mutation will cause a change in the offspring. So look at your arm - a mutation would make it longer, or shorter. Which is "beneficial", and which is "harmful"? Well, that depends on the environment. If you are living in the trees, the longer arm is beneficial for reaching branches. If you are a runner on the plains,the longer arm is harmful, because it's more weight to carry.

Pure, undiluted Darwinian rhetoric without scientific merit and requiring no substantive or empirical support.


Mark was also directed to post #75, here:

http://www.christianforums.com/t7512492-8/

I'm through following you down these pointless rabbit hole posts.

Which shows mathematically that natural selection will cause beneficial mutations to be dominant, even if the mutation rate makes many more harmful mutations than beneficial mutations.

Mark, do you remember those instances?

Do you agree there are beneficial mutations, and that natural selection will naturally multiply them, while removing the harmful mutations?

Papias

I don't agree with anything you say. I think you are a shameless liar. You didn't have the decency to even quote me your fallacious debate tactics, frankly, disgust me.

Have a nice day :)
Mark
 
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