Bounded mutation

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Sherlock Holmes

Bounded mutation

Post #1

Post by Sherlock Holmes »

I was reading this article earlier, in there we read:
To better understand the impact of this situation, think of it this way: With a genome size of 2.8 × 10^6 and a mutation rate of 1 mutation per 10^10 base pairs, it would take a single bacterium 30 hours to grow into a population in which every single base pair in the genome will have mutated not once, but 30 times! Thus, any individual mutation that could theoretically occur in the bacteria will have occurred somewhere in that population—in just over a day.
This seems to be an admission that even if every possible mutation (from the finite set of possibilities) occurs at some point in the colony, then we still have - bacteria, surely with these rates of reproduction and probabilities of mutation and so on, doesn't this show that the bacteria evolving never leads to anything other than a variant of the bacteria? That the set of all possible mutants is either dead or still more or less the same bacteria.

Given the rate at which bacteria reproduce and their number on earth and in societies, shouldn't we see evidence that the genome has developed more and more novelty? yet it seems all we see is just bacteria...

So is there evidence that bacteria can become something quite different given enough time and if not, why not? are the possible states that the genome can get into simply insufficient to ever lead to escalating novelty?

Sherlock Holmes

Re: Bounded mutation

Post #21

Post by Sherlock Holmes »

DrNoGods wrote: Thu Feb 24, 2022 5:36 pm [Replying to Sherlock Holmes in post #19]
What does it mean in your opinion? and other than the obvious religious connotations what is it about the About page that makes you think it doesn't have a peer review process?
Do they send submitted manuscripts out to qualified experts NOT on their editorial staff for unbiased, independent peer review? Or do they only let the editorial staff do the reviews (or another biased creationist organization)? Their bias is stated right there on their About page ... they support a young earth and a literal interpretation of Noah's flood and its biblical time frame. Try submitting a manuscript showing that a global flood could not possibly have covered the entire earth to above the highest mountains a measly 4400 or so years ago and see if they'll publish it.
Do you consider The Journal of Neuroscience and Journal of Leukocyte Biology to be peer reviewed scientific publications?

I'll address your other points later, I think we need to clear this up first.

Also why is this an example of bias:
The International Conference on Creationism has been recognized as the world's premier gathering of young earth creation researchers and has, since the first conference in 1986, served to greatly further the creation model of origins. The mission of the ICC is to promote the development and dissemination of positive contributions to a young earth creationist model of origins and models of earth history that recognize the reality of the global Flood described in Genesis.
yet this is not:
The Journal of Evolutionary Biology is a peer-reviewed, international journal owned by the European Society of Evolutionary Biology. We consider submissions describing research from across the field of evolutionary biology, such as molecular evolution, evolutionary genetics and genomics, life histories, evolutionary ecology, development or morphology.

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Re: Bounded mutation

Post #22

Post by DrNoGods »

[Replying to Sherlock Holmes in post #21]
Do you consider The Journal of Neuroscience and Journal of Leukocyte Biology to be peer reviewed scientific publications?
If they send manuscripts out for peer review outside of their editorial board, to multiple reviewers who are qualified in the subject matter, then yes I'd consider them proper scientific journals. I'm not familiar with these journals personally though. I served as Associate Editor for 7 years for a journal relevant to my field (Journal of Quantitative Spectroscopy and Radiative Transfer) and distributed submitted manuscripts to multiple reviewers when I received them for that purpose, after reading them myself. The process is well established.
Also why is this an example of bias:

The International Conference on Creationism has been recognized as the world's premier gathering of young earth creation researchers and has, since the first conference in 1986, served to greatly further the creation model of origins. The mission of the ICC is to promote the development and dissemination of positive contributions to a young earth creationist model of origins and models of earth history that recognize the reality of the global Flood described in Genesis.

yet this is not:

The Journal of Evolutionary Biology is a peer-reviewed, international journal owned by the European Society of Evolutionary Biology. We consider submissions describing research from across the field of evolutionary biology, such as molecular evolution, evolutionary genetics and genomics, life histories, evolutionary ecology, development or morphology.
Seriously? You're joking, right? The first one specifically states that their mission is to promote a young earth creationist model of origins and models of earth history that recognize the reality of Noah's flood. What do they do with manuscripts (or articles more appropriately) that do NOT recognize the reality of Noah's flood? Would they likely have a bias against such a submission? What do you think?

The second only states that they "consider submssions describing research" from acrosss the fields their journal is specific to. It does not state any bias towards promoting a specific viewpoint, only that manuscripts will be considered describing research in the relevant fields.

If you can't see the drastic difference between these two I don't know what to tell you. The first explicitly states a bias, while the second does not.
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Re: Bounded mutation

Post #23

Post by benchwarmer »

DrNoGods wrote: Thu Feb 24, 2022 7:17 pm If you can't see the drastic difference between these two I don't know what to tell you. The first explicitly states a bias, while the second does not.
I'm thinking your interlocutor considers "reviewed by people who already agree with the conclusions" the same as "reviewed by relevant experts in the field".

Perhaps the word 'peer' is confusing to some. It doesn't mean 'friend', 'ally', 'within same belief circle', etc. It means (please correct me if I've got it wrong as well), others within the same or similar domains of research who have the knowledge and resources to attempt to actually falsify the conclusions.

I believe a real scientist wants their peers to try and find any and all flaws in their methodology and conclusions (while hoping that all bases are covered and no holes or faulty conclusions are found).

When groups like AIG, etc do 'peer review', what they mean is that within their belief circle, they will rubber stamp approval as long as it fits within their already decided conclusions. Anything that does not line up with their predetermined beliefs will 'fail' their 'peer review'. It's really quite ridiculous and laughably transparent as to what they are doing, but it seems to fool some people into thinking some real science is going on.

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Re: Bounded mutation

Post #24

Post by DrNoGods »

[Replying to benchwarmer in post #23]
When groups like AIG, etc do 'peer review', what they mean is that within their belief circle, they will rubber stamp approval as long as it fits within their already decided conclusions. Anything that does not line up with their predetermined beliefs will 'fail' their 'peer review'. It's really quite ridiculous and laughably transparent as to what they are doing, but it seems to fool some people into thinking some real science is going on.
Exactly! When the "journal" explicitly states that they are promoting a young earth model and the reality(!) of Noah's flood, it is hard to imagine how anyone could not see the obvious bias towards any submitted manuscripts that do not conform to this view.

Queue up a post claiming that evolution is not a valid theory, so any journal accepting manuscripts on that subject are biased towards a belief that evolution is a valid theory, and so are no different.
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Re: Bounded mutation

Post #25

Post by Sherlock Holmes »

DrNoGods wrote: Thu Feb 24, 2022 7:17 pm [Replying to Sherlock Holmes in post #21]
Do you consider The Journal of Neuroscience and Journal of Leukocyte Biology to be peer reviewed scientific publications?
If they send manuscripts out for peer review outside of their editorial board, to multiple reviewers who are qualified in the subject matter, then yes I'd consider them proper scientific journals. I'm not familiar with these journals personally though. I served as Associate Editor for 7 years for a journal relevant to my field (Journal of Quantitative Spectroscopy and Radiative Transfer) and distributed submitted manuscripts to multiple reviewers when I received them for that purpose, after reading them myself. The process is well established.
So you don't know if the two journals I asked you about are or are not peer reviewed scientific publications (did you even make an effort to find out) yet you are adamant the Creationist one is not, that's quite an interesting unscientific way of responding to my question.

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Re: Bounded mutation

Post #26

Post by DrNoGods »

[Replying to Sherlock Holmes in post #25]
So you don't know if the two journals I asked you about are or are not peer reviewed scientific publications yet you are adamant the Creationist one is not, that's quite an interesting unscientific way of responding to my question.
More word twisting. Can you ever stop doing this? I did not say I didn't know if they were peer reviewed scientific publications. Here is what I actually said:

If they send manuscripts out for peer review outside of their editorial board, to multiple reviewers who are qualified in the subject matter, then yes I'd consider them proper scientific journals.

And you warp this to claim I said I didn't know if they were scientific journals, presumably so you could dodge the issue (again).

The creationist "journal" is biased towards articles that favor a young earth model and the reality of Noah's flood, exactly as they state on their About page. Why don't you comment on why you think that isn't biased, rather than twisting what I actually said into something completely different, then dodging the issue entirely?
In human affairs the sources of success are ever to be found in the fountains of quick resolve and swift stroke; and it seems to be a law, inflexible and inexorable, that he who will not risk cannot win.
John Paul Jones, 1779

The man who does not read has no advantage over the man who cannot read.
Mark Twain

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Re: Bounded mutation

Post #27

Post by Sherlock Holmes »

DrNoGods wrote: Fri Feb 25, 2022 9:59 am [Replying to Sherlock Holmes in post #25]
So you don't know if the two journals I asked you about are or are not peer reviewed scientific publications yet you are adamant the Creationist one is not, that's quite an interesting unscientific way of responding to my question.
More word twisting. Can you ever stop doing this? I did not say I didn't know if they were peer reviewed scientific publications.
Well I inferred that you don't know because you introduced a conditional, and did not indicate the values of it. If you do know then tell us else I'm taking it as either you do not know or do not want to reveal your opinion.
DrNoGods wrote: Fri Feb 25, 2022 9:59 am Here is what I actually said:

If they send manuscripts out for peer review outside of their editorial board, to multiple reviewers who are qualified in the subject matter, then yes I'd consider them proper scientific journals.
Well you obviously answered this "if" in the case of the creationism journal so can't you do the same thing and answer it for these other two? I mean is this a hard question or just unwelcome?
DrNoGods wrote: Fri Feb 25, 2022 9:59 am And you warp this to claim I said I didn't know if they were scientific journals, presumably so you could dodge the issue (again).
Hardly a warp, I ask if you know if X is true, you answer with X is true if Y is true and refuse to state if you regard Y as true, it's reasonable in a debate to suspect that you do not know if Y is true or simply do not want to share your answer, could it possibly mean anything else?
DrNoGods wrote: Fri Feb 25, 2022 9:59 am The creationist "journal" is biased towards articles that favor a young earth model and the reality of Noah's flood, exactly as they state on their About page. Why don't you comment on why you think that isn't biased, rather than twisting what I actually said into something completely different, then dodging the issue entirely?
I'm happy to answer that question but I'm a bit old fashioned you see, I think that questions in a debate between two parties should (where possible) be answered in the same order they were asked.

Are The Journal of Neuroscience and Journal of Leukocyte Biology peer reviewed scientific publications? Why is this such a big deal for you? is even a simple question like this too controversial for you now?

It seems that if two candidates were being considered and one had a paper published in The Journal of Neuroscience and the other had a paper published in The Proceedings of the International Conference on Creationism you'd be able to say right away that the latter was not a peer reviewed publication but how is that fair? You must apply unbiased fair criteria to each candidate, seems you have a rule for the second candidate that you don't have for the first, tell me more about how you'd make this decision?

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Re: Bounded mutation

Post #28

Post by DrNoGods »

[Replying to Sherlock Holmes in post #27]
Well I inferred that you don't know because you introduced a conditional, and did not indicate the values of it. If you do know then tell us else I'm taking it as either you do not know or do not want to reveal your opinion.
What is so hard about this? The conditional related to whether the journals you mentioned send manuscripts out for normal external review as any legitimate science journal does. I'm not familiar with those specific journals myself, so why don't you tell me (since you chose them) if they do this, and that will be your answer. I would assume they do but am not going to contact them and ask. You chose them, you can find out the answer.
Well you obviously answered this "if" in the case of the creationism journal so can't you do the same thing and answer it for these other two? I mean is this a hard question or just unwelcome?
Again, this is very simple. The creationist journal specifically states that they are biased in favor of young earth and a literal Noah's flood. The other two make no such biased statements in the section you posted, along with the creationist About page section that I had posted. So all you have to do is read them both to see that one is biased (they explicitly state it) and the other has no such statements. If you want to dig deeper into their manuscript review processes, do that work yourself. Why did you choose the two journals that you did?
Hardly a warp, I ask if you know if X is true, you answer with X is true if Y is true and refuse to state if you regard Y as true, it's reasonable in a debate to suspect that you do not know if Y is true or simply do not want to share your answer.
See above ... just more word twisting. I'm not "refusing" to state if I regard Y as true ... it is up to you to investigate (Sherlock Holmes) the manuscript review policies of the two journals you chose.
It seems that if two candidates were being considered and one had a paper published in The Journal of Neuroscience and the other had a paper published in The Proceedings of the International Conference on Creationism you'd be able to say right away that the latter was not a peer reviewed publication but how is that fair? You must apply unbiased fair criteria to each candidate, seems you have a rule for the second candidate that you don't have for the first, tell me more about how you'd make this decision?
What are you talking about? The PICC is NOT a peer reviewed scientific journal for one thing. But if you go back and read what I actually wrote regarding this issue (post 10) I clearly said that I'd consider their knowledge of the subject, not what journal they may have published something in. You're just twisting things up as usual to build a strawman. Here is what I actually said:

No, but I'd probably read the article and see if it conflicted with the job requirements being hired for, ie. if it showed that the person did not understand the subject well enough to do the job. I'm a spectroscopist by trade, and if their article considered something related to spectroscopy (eg. red shifts, the H2 spectrum characteristics, selection rules, etc.) that conflicted with what we know to be correct (eg. because they argue that the universe is only 6000 years old), then yes ... I'd disqualify them on the basis that they do not understand the subject well enough. But if their article didn't relate to the job being considered, I wouldn't care.

Nothing to do with whether the journal is a proper peer-reviewed journal or not. Just more word twisting on your part to produce a false argument.
In human affairs the sources of success are ever to be found in the fountains of quick resolve and swift stroke; and it seems to be a law, inflexible and inexorable, that he who will not risk cannot win.
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Sherlock Holmes

Re: Bounded mutation

Post #29

Post by Sherlock Holmes »

DrNoGods wrote: Fri Feb 25, 2022 11:51 am [Replying to Sherlock Holmes in post #27]
Well I inferred that you don't know because you introduced a conditional, and did not indicate the values of it. If you do know then tell us else I'm taking it as either you do not know or do not want to reveal your opinion.
What is so hard about this? The conditional related to whether the journals you mentioned send manuscripts out for normal external review as any legitimate science journal does. I'm not familiar with those specific journals myself, so why don't you tell me (since you chose them) if they do this, and that will be your answer. I would assume they do but am not going to contact them and ask. You chose them, you can find out the answer.
Right so like I said already you don't know!
DrNoGods wrote: Fri Feb 25, 2022 11:51 am
Well you obviously answered this "if" in the case of the creationism journal so can't you do the same thing and answer it for these other two? I mean is this a hard question or just unwelcome?
Again, this is very simple. The creationist journal specifically states that they are biased in favor of young earth and a literal Noah's flood.
This is no different to arguing that The American Journal of physics is biased toward physics, a frankly cringeworthy, embarrassing position to take.
DrNoGods wrote: Fri Feb 25, 2022 11:51 am The other two make no such biased statements in the section you posted, along with the creationist About page section that I had posted. So all you have to do is read them both to see that one is biased (they explicitly state it) and the other has no such statements. If you want to dig deeper into their manuscript review processes, do that work yourself. Why did you choose the two journals that you did?
Lets be clear the term "bias" you like to use is not applicable nor is it helping you make your case.
DrNoGods wrote: Fri Feb 25, 2022 11:51 am
Hardly a warp, I ask if you know if X is true, you answer with X is true if Y is true and refuse to state if you regard Y as true, it's reasonable in a debate to suspect that you do not know if Y is true or simply do not want to share your answer.
See above ... just more word twisting. I'm not "refusing" to state if I regard Y as true ... it is up to you to investigate (Sherlock Holmes) the manuscript review policies of the two journals you chose.
Well you surely investigated the The Proceedings of the International Conference on Creationism in order to claim it is not really peer reviewed, yet can't do the same for these other magazines? You say also "am not going to contact them and ask" yet did not contact the The Proceedings of the International Conference on Creationism adding even more doubt to your claimed objectivity.
DrNoGods wrote: Fri Feb 25, 2022 11:51 am
It seems that if two candidates were being considered and one had a paper published in The Journal of Neuroscience and the other had a paper published in The Proceedings of the International Conference on Creationism you'd be able to say right away that the latter was not a peer reviewed publication but how is that fair? You must apply unbiased fair criteria to each candidate, seems you have a rule for the second candidate that you don't have for the first, tell me more about how you'd make this decision?
What are you talking about? The PICC is NOT a peer reviewed scientific journal for one thing.
Yes I know you truly believe that, prejudices do that, they often blind one.
DrNoGods wrote: Fri Feb 25, 2022 11:51 am But if you go back and read what I actually wrote regarding this issue (post 10) I clearly said that I'd consider their knowledge of the subject, not what journal they may have published something in.You're just twisting things up as usual to build a strawman. Here is what I actually said:

No, but I'd probably read the article and see if it conflicted with the job requirements being hired for, ie. if it showed that the person did not understand the subject well enough to do the job. I'm a spectroscopist by trade, and if their article considered something related to spectroscopy (eg. red shifts, the H2 spectrum characteristics, selection rules, etc.) that conflicted with what we know to be correct (eg. because they argue that the universe is only 6000 years old), then yes ... I'd disqualify them on the basis that they do not understand the subject well enough. But if their article didn't relate to the job being considered, I wouldn't care.

Nothing to do with whether the journal is a proper peer-reviewed journal or not. Just more word twisting on your part to produce a false argument.
Yes you did say that AFTER you'd already said this:
First, what you linked isn't a scientific paper published in a peer-reviewed journal.
Now you say that this doesn't matter? is that because you don't really want to talk about this any more?

You're all over the place!

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Re: Bounded mutation

Post #30

Post by DrNoGods »

[Replying to Sherlock Holmes in post #29]
Right so like I said already you don't know!
And neither do you apparently, even though you suggested those two journals as a comparison to a creationist "journal." Do your homework next time.
This is no different to arguing that The American Journal of physics is biased toward physics, a frankly cringeworthy, embarrassing position to take.
It is not at all the same. Physics has not been thoroughly debunked, whereas a young earth and the reality of Noah's flood have. Claiming physics has been debunked as you just did (see how two can play the strawman building game?) is indeed an embarrassing position to take.
Well you surely investigated the The Proceedings of the International Conference on Creationism in order to claim it is not really peer reviewed, yet can't do the same for these other magazines? You say also "am not going to contact them and ask" yet did not contact the The Proceedings of the International Conference on Creationism adding even more doubt to your claimed objectivity.
No ... you are the one who brought up PICC in the first place, and it is you who have claimed repeatedly that they are a bona-fide, peer-reviewed scientific journal. Go back and read your own posts.
Now you say that this doesn't matter? is that because you don't really want to talk about this any more?
What is "this"? You continue to make up stuff and attribute your random reinterpretations it to me.
You're all over the place!
Only because of your incessant word twisting, strawman building and goal post moving as you continuously dodge questions and reinterpret what people say, then present these warped revisions as a basis for some point you want to make. It has gotten old and boring, but at least you're consistent.
In human affairs the sources of success are ever to be found in the fountains of quick resolve and swift stroke; and it seems to be a law, inflexible and inexorable, that he who will not risk cannot win.
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The man who does not read has no advantage over the man who cannot read.
Mark Twain

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