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Author Topic:   Wright et al. on the Process of Mutation
Percy
Member
Posts: 20112
From: New Hampshire
Joined: 12-23-2000
Member Rating: 4.2


Message 31 of 296 (628031)
08-06-2011 9:16 AM
Reply to: Message 30 by John Jones
08-06-2011 9:07 AM


How to Quote
Hi John Jones,

Where you said this:

quote If you don't understand the concept of fitness, that is no reason why biologists should abandon it; that's a sign that you should try harder to understand it.

What is it about this concept that is giving you trouble? unquote

Instead enter this:

[qs=Dr Adequate]If you don't understand the concept of fitness, that is no reason why biologists should abandon it; that's a sign that you should try harder to understand it.

What is it about this concept that is giving you trouble?[/qs]

This will result in this appearance:

Dr Adequate writes:

If you don't understand the concept of fitness, that is no reason why biologists should abandon it; that's a sign that you should try harder to understand it.

What is it about this concept that is giving you trouble?

Also, you can click on the "Peek" button for any message to see the markup text they used to produce quotes, images, smilies, colors, fonts, etc.

--Percy


This message is a reply to:
 Message 30 by John Jones, posted 08-06-2011 9:07 AM John Jones has not yet responded

  
John Jones
Junior Member (Idle past 3490 days)
Posts: 21
Joined: 08-05-2011


Message 32 of 296 (628032)
08-06-2011 9:17 AM
Reply to: Message 29 by Percy
08-06-2011 9:00 AM


quote As Dr Adequate implies, fitness has a well-defined meaning in biology. I can see that you're defining a "fit" offspring as one that has survived birth, but in biology fitness is measured by an organisms ability to generate offspring, or in genetic terms, to propagate its genes. Wikipedia has a good article on biological fitness. It actually calls it, and correctly in my view, "a central idea in evolutionary theory," so the odds are small that you're going to persuade evolutionary biologists to abandon the concept. unquote

As you can see from the rest of my initial post, I addressed the reproductive aspect of the "definition". But an excursion into reproductivity doesn't change the often tautologous, and always meaningless use of this term, which, I have argued in the post above this one, is a necessary condition of the "word" being employed as a syntactically disconnected (independent), promotional metaphor - a flag or mandala.

Many disciplines have these flags. For example, psychology uses "disorder", among others.

I wasn't able to follow your instructions for quotes. Do I have to type in a code? How do I easilyiest get or assemble the material that I want to quote?

Edited by John Jones, : No reason given.


This message is a reply to:
 Message 29 by Percy, posted 08-06-2011 9:00 AM Percy has responded

Replies to this message:
 Message 33 by Percy, posted 08-06-2011 9:22 AM John Jones has responded
 Message 34 by Percy, posted 08-06-2011 9:29 AM John Jones has not yet responded

  
Percy
Member
Posts: 20112
From: New Hampshire
Joined: 12-23-2000
Member Rating: 4.2


Message 33 of 296 (628033)
08-06-2011 9:22 AM
Reply to: Message 32 by John Jones
08-06-2011 9:17 AM


Sounds like a different topic. If you want to discuss biological terminology and the errors therein you might consider proposing a new thread over at Proposed New Topics.

This message is a reply to:
 Message 32 by John Jones, posted 08-06-2011 9:17 AM John Jones has responded

Replies to this message:
 Message 39 by John Jones, posted 08-06-2011 9:50 PM Percy has responded
 Message 40 by John Jones, posted 08-06-2011 10:00 PM Percy has acknowledged this reply

  
Percy
Member
Posts: 20112
From: New Hampshire
Joined: 12-23-2000
Member Rating: 4.2


Message 34 of 296 (628034)
08-06-2011 9:29 AM
Reply to: Message 32 by John Jones
08-06-2011 9:17 AM


John Jones writes:

I wasn't able to follow your instructions for quotes. Do I have to type in a code? How do I easilyiest get or assemble the material that I want to quote?

Yes, you have to type in a code. You can experiment just by clicking on the reply button for this message. Have you done that yet? Good.

Now type this verbatim into your message text box:

[qs]This is quoted text.[/qs]

Now click on the preview button and you'll see this:

This is quoted text.

You don't want to submit this as a message, of course, so don't click on "Submit Reply." You can use your back button to get back to the thread.

All the dBCodes are documented here: dBCode Help. This same link appears to the left of the message box where you enter text. You can also use HTML in messages. And smilies, too, click on the Smilies Table link that also appears to the left of the message box.

--Percy


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Doctor Witch
Junior Member (Idle past 3517 days)
Posts: 27
From: Both Sides
Joined: 08-05-2011


Message 35 of 296 (628049)
08-06-2011 12:41 PM
Reply to: Message 27 by Dr Adequate
08-06-2011 8:45 AM


A Wider Reaction
Whilst DNA is not changed in aligning animo acids into proteins, it is eventually broken down into individual molecules. I am considering this overall 'reaction' in the cytoplasm.

I am considering the reverse of the reaction that we usually consider. The bonding of an animo acid to an RNA triplet is independent of whether the amino acid and the triplet are 'free' or a part of a chain.

The reaction that we normally consider is where RNA is in a chain and the amino acids free. I am asking you to visualise the reverse situation where the amino acid enters in a chain in an environment of free RNA triplets. The triplets will be aligned then acted upon by the polymerase to form a chain. The end product is the same as in the 'forward' reaction. There is an RNA chain that 'matches' the protein chain.

However, the protein has now transcribed the RNA.

Similarly, with free triplets of DNA can be 'coded' by a formed RNA strand.

So whilst we are considering the overall results of a complex chain of reactions, I believe that the concept of Natural Equilibrium is appropriate and also conceptually useful. It is the situation where we have a big forwards arrow to show a reaction that a reaction predominantly progresses in one direction, but then there is the smaller arrow that cannot be overlooked beneath going in the reverse direction.

It would appear that we have overlooked that little reverse arrow which would explain how prokaryotes produce biologically active new genes and leads to an explanation of the mechanical weighting of the randomness of creating completely new genes in evolution.

Or has anybody done the experiment? I have not heard of it.


This message is a reply to:
 Message 27 by Dr Adequate, posted 08-06-2011 8:45 AM Dr Adequate has responded

Replies to this message:
 Message 36 by Taq, posted 08-06-2011 1:23 PM Doctor Witch has not yet responded
 Message 38 by Dr Adequate, posted 08-06-2011 2:25 PM Doctor Witch has not yet responded

  
Taq
Member (Idle past 0 days)
Posts: 8482
Joined: 03-06-2009


Message 36 of 296 (628053)
08-06-2011 1:23 PM
Reply to: Message 35 by Doctor Witch
08-06-2011 12:41 PM


Re: A Wider Reaction
Whilst DNA is not changed in aligning animo acids into proteins, it is eventually broken down into individual molecules. I am considering this overall 'reaction' in the cytoplasm.

I am considering the reverse of the reaction that we usually consider. The bonding of an animo acid to an RNA triplet is independent of whether the amino acid and the triplet are 'free' or a part of a chain.

The reaction that we normally consider is where RNA is in a chain and the amino acids free. I am asking you to visualise the reverse situation where the amino acid enters in a chain in an environment of free RNA triplets. The triplets will be aligned then acted upon by the polymerase to form a chain. The end product is the same as in the 'forward' reaction. There is an RNA chain that 'matches' the protein chain.

However, the protein has now transcribed the RNA.

Similarly, with free triplets of DNA can be 'coded' by a formed RNA strand.

So whilst we are considering the overall results of a complex chain of reactions, I believe that the concept of Natural Equilibrium is appropriate and also conceptually useful. It is the situation where we have a big forwards arrow to show a reaction that a reaction predominantly progresses in one direction, but then there is the smaller arrow that cannot be overlooked beneath going in the reverse direction.

It would appear that we have overlooked that little reverse arrow which would explain how prokaryotes produce biologically active new genes and leads to an explanation of the mechanical weighting of the randomness of creating completely new genes in evolution.

Or has anybody done the experiment? I have not heard of it.

How does this specifically relate to the paper we are discussing? Is the process of transcribing and translating the leuB gene any different than how the rest of the genes in the genome are treated?

Also, did you have any questions about the information presented thus far? Do you understand how leuB is derepressed and how reversion rates are related to mRNA abundance?


This message is a reply to:
 Message 35 by Doctor Witch, posted 08-06-2011 12:41 PM Doctor Witch has not yet responded

  
Taq
Member (Idle past 0 days)
Posts: 8482
Joined: 03-06-2009


Message 37 of 296 (628057)
08-06-2011 1:35 PM
Reply to: Message 21 by Doctor Witch
08-06-2011 12:25 AM


Re: Hasn't the fundamental study been done yet?
This paper appears to be yet another fragment of evidence for the non-random evolution of protein codes that carry biological advantage at the cellular level which pretty much started in the study of bacterial resistance to antibiotics.

Just so that we are on the same page, I will fully agree that the process of evolution is non-random. If evolution were random then deleterious mutations would have just as much a chance of being passed on as beneficial mutations. This is not the case.

However, one of the mechanisms within the process of evolution is random, and that process is mutation. I will show that the processes that produced the leuB reversions in the Wright et al. paper are incapable of determining if the mutations are helpful or harmful to the overall fitness of the organism.

At this point, I have discussed a table that listed the number of leuB reversions due to a single nucleotide substitution. The rate at which this occurs is 2 per billion cell divisions. Just 2 bacteria out of every 1,000,000,000 are able to gain an advantageous mutation in their leuB gene. If this process is a guided process, then why is the reversion rate so low?

I think I will hold off on discussing new material in this paper until Monday to give people time to discuss why the reversion rate is 2 per billion cells.

Edited by Taq, : No reason given.


This message is a reply to:
 Message 21 by Doctor Witch, posted 08-06-2011 12:25 AM Doctor Witch has not yet responded

  
Dr Adequate
Member
Posts: 16112
Joined: 07-20-2006


Message 38 of 296 (628065)
08-06-2011 2:25 PM
Reply to: Message 35 by Doctor Witch
08-06-2011 12:41 PM


Re: A Wider Reaction
Whilst DNA is not changed in aligning animo acids into proteins, it is eventually broken down into individual molecules.

And the reverse of this would not be a protein producing DNA coding for that protein from its constituent bases. Just a bunch of bases chaining together to make DNA.

I am considering the reverse of the reaction that we usually consider.

No.

The bonding of an animo acid to an RNA triplet is independent of whether the amino acid and the triplet are 'free' or a part of a chain.

The bonding of an amino acid to an RNA triplet does not in fact happen. You seem to think that translation is like transcription. It is not.

Moreover, since translation does not destroy RNA, reversing the process would not create any.


This message is a reply to:
 Message 35 by Doctor Witch, posted 08-06-2011 12:41 PM Doctor Witch has not yet responded

  
John Jones
Junior Member (Idle past 3490 days)
Posts: 21
Joined: 08-05-2011


Message 39 of 296 (628119)
08-06-2011 9:50 PM
Reply to: Message 33 by Percy
08-06-2011 9:22 AM


It isn't a different topic to enquire about the significance of a term that is employed in that topic. It would, rather, seem to be key to it.

This message is a reply to:
 Message 33 by Percy, posted 08-06-2011 9:22 AM Percy has responded

Replies to this message:
 Message 44 by Percy, posted 08-07-2011 6:35 AM John Jones has not yet responded

  
John Jones
Junior Member (Idle past 3490 days)
Posts: 21
Joined: 08-05-2011


Message 40 of 296 (628121)
08-06-2011 10:00 PM
Reply to: Message 33 by Percy
08-06-2011 9:22 AM


quote
Sounds like a different topic. If you want to discuss biological terminology and the errors therein you might consider proposing a new thread over at Proposed New Topics
unquote

It isn't a different topic to enquire about the significance of a key term in that topic.
It's significance is, rather, key to the whole topic. Surely so.

However, if by "the topic" you mean just the original post, then I agree with you. But the original post had some problems that cast a shadow on its own case, and these needed examining. My examination used an example taken from many other, similar problems in that original post.

We cannot take what we read for granted. A post isn't just factual, it is conceptual, and in the latter the origin, I argued, was found lacking.

Will study your instructions for quoting.

Edited by John Jones, : left bits out


This message is a reply to:
 Message 33 by Percy, posted 08-06-2011 9:22 AM Percy has acknowledged this reply

Replies to this message:
 Message 41 by Taq, posted 08-06-2011 10:20 PM John Jones has responded

  
Taq
Member (Idle past 0 days)
Posts: 8482
Joined: 03-06-2009


Message 41 of 296 (628123)
08-06-2011 10:20 PM
Reply to: Message 40 by John Jones
08-06-2011 10:00 PM


We cannot take what we read for granted. A post isn't just factual, it is conceptual, and in the latter the origin, I argued, was found lacking.

Perhaps you could explain how it is lacking? Are you saying that fitness is not a factor in the propagation of a genome?


This message is a reply to:
 Message 40 by John Jones, posted 08-06-2011 10:00 PM John Jones has responded

Replies to this message:
 Message 42 by John Jones, posted 08-06-2011 11:49 PM Taq has responded
 Message 46 by John Jones, posted 08-09-2011 6:53 PM Taq has responded

  
John Jones
Junior Member (Idle past 3490 days)
Posts: 21
Joined: 08-05-2011


Message 42 of 296 (628136)
08-06-2011 11:49 PM
Reply to: Message 41 by Taq
08-06-2011 10:20 PM


"Perhaps you could explain how it is lacking? Are you saying that fitness is not a factor in the propagation of a genome?"

I couldn't begin to say what fitness is, nor its scope. Is the scope of fitness the continuance of the species, or individuals with greater number of offspring? The two aren't the same.


This message is a reply to:
 Message 41 by Taq, posted 08-06-2011 10:20 PM Taq has responded

Replies to this message:
 Message 43 by Panda, posted 08-07-2011 6:23 AM John Jones has not yet responded
 Message 45 by Taq, posted 08-08-2011 3:15 PM John Jones has not yet responded

  
Panda
Member (Idle past 2613 days)
Posts: 2688
From: UK
Joined: 10-04-2010


Message 43 of 296 (628161)
08-07-2011 6:23 AM
Reply to: Message 42 by John Jones
08-06-2011 11:49 PM


You seemed to have missed Percy's explanation of how to use quotes.
Copy and paste this into your previous post:

[qs=taq]Perhaps you could explain how it is lacking? Are you saying that fitness is not a factor in the propagation of a genome?[/qs]
I couldn't begin to say what fitness is, nor its scope. Is the scope of fitness the continuance of the species, or individuals with greater number of offspring? The two aren't the same.

Edited by Panda, : clarity


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Percy
Member
Posts: 20112
From: New Hampshire
Joined: 12-23-2000
Member Rating: 4.2


Message 44 of 296 (628163)
08-07-2011 6:35 AM
Reply to: Message 39 by John Jones
08-06-2011 9:50 PM


John Jones writes:

It isn't a different topic to enquire about the significance of a term that is employed in that topic. It would, rather, seem to be key to it.

Inquiring about the definition of a term is fine, encouraged in fact, but disputing the definition of a term fundamental to evolution probably deserves its own topic. Back in Message 29 I said that in biology fitness is measured by an organisms ability to generate offspring, or in genetic terms, to propagate its genes. I also pointed you at Wikipedia's article on biological fitness. If you have more questions about the definition of fitness I'm sure everyone would be glad to answer them.

But if you don't like the definition and have problems with the concept itself, this probably isn't the right thread for discussing it.

--Percy


This message is a reply to:
 Message 39 by John Jones, posted 08-06-2011 9:50 PM John Jones has not yet responded

  
Taq
Member (Idle past 0 days)
Posts: 8482
Joined: 03-06-2009


Message 45 of 296 (628299)
08-08-2011 3:15 PM
Reply to: Message 42 by John Jones
08-06-2011 11:49 PM


I couldn't begin to say what fitness is, nor its scope. Is the scope of fitness the continuance of the species, or individuals with greater number of offspring? The two aren't the same.

The two aren't the same, but they are both measures of fitness. Obviously, an organism that has one offspring is more fit, on average, than an organism that has none.

It is worth mentioning that the authors are using different environments to test the fitness of the organisms. For example, the bacteria in these experiments are descendants of a leuB- strain that is not able to produce it's own leucine. Some of those descendants do spontaneously acquire the ability to make their own leucine, and therefore reproduce at a higher rate than the other descendants. Is this a valid definition of increased fitness in your eyes?


This message is a reply to:
 Message 42 by John Jones, posted 08-06-2011 11:49 PM John Jones has not yet responded

  
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