Beneficial Mutations In Evolution

[BeeBeeramBeeBee]

Hello everyone.

 

So, I recently heard that, mutations that were considered beneficial, those observed in our time, in reality were detrimental.

 

Now, I brought up this mutation, the nylonase mutation in the discussion. The reply I had heard, was that, the mutation actually made a particular protein, less specific in what binds with, thus allowing the organism to consume nylonase.

 

The key point being that, the mutation basically decreased the specificity of a protein, which, in a sense, isnt really an advancement, rather just the breaking down of the specifics of a protein.

 

I hope that makes sense.

 

Has anyone heard this before? Also, is there such a mutation that makes a protein more specific in what it can do, which benefits an organism, which has been observed? Is this even a proper argument?

 

Thank you.

[sman]

Hello everyone.

 

So, I recently heard that, mutations that were considered beneficial, those observed in our time, in reality were detrimental.

 

.....

 

Has anyone heard this before?

 

 

Yes, I’ve heard this lots of times. The confusion comes from misunderstanding the way biologists use the word “benefit”, which - in biology - means something very specific.

 

A benefit is anything - anything at all - that statistically augments the number of grandchildren - in any way at all - of individuals with the trait.

 

That’s it..

 

It doesn’t mean any kind of graduation in complexity (although it can, if such a thing statistically augments the number of grandchildren in the individuals with the trait); It doesn’t mean increased specificity or efficiency (although it can… ). It doesn’t imply “advancement” in any sense. Nor does it imply that the trait “benefits” the individual carrying it in any way.

 

The term - used in this very technical way - is purely statistical. Therefore, whether a trait is a benefit or a detriment may be simply quantified (by counting the number of descendants) rather than judged subjectively.

 

Once we understand that biologists are using the word in this very odd way, the confusion usually melts. :D

Edited July 29, 2013 by sman

[BeeBeeramBeeBee]

Yes, I’ve heard this lots of times. The confusion comes from misunderstanding the way biologists use the word “benefit”, which - in biology - means something very specific.

 

A benefit is anything - anything at all - that statistically augments the number of grandchildren - in any way at all - of individuals with the trait.

 

That’s it..

 

It doesn’t mean any kind of graduation in complexity (although it can, if such a thing statistically augments the number of grandchildren in the individuals with the trait); It doesn’t mean increased specificity or efficiency (although it can… ). It doesn’t imply “advancement” in any sense. Nor does it imply that the trait “benefits” the individual carrying it in any way.

 

The term - used in this very technical way - is purely statistical. Therefore, whether a trait is a benefit or a detriment may be simply quantified (by counting the number of descendants) rather than judged subjectively.

 

Once we understand that biologists are using the word in this very odd way, the confusion usually melts. :D

 

Yes, thank you. That is essentially how I responded. A benefit is in the prosperity of the species, rather than the details of the proteins themselves.

 

However though, if a protein never became more specific or more precise in what it acts on, then we would never evolve to become anything at all.

 

Not to say this doesnt happen, but can anyone provide an example of a mutation in which a protein has become more precise, or refined in what it does?

 

This is interesting though, because in a sense, a protein losing specificity, while still gaining a capability, in a sense is growing more specific toward something that benefits it more than before. Which arguably isnt even losing specificity, and surely isnt losing its ability to augment the number of offspring in a species.

 

However, it would still be nice to have an example of a mutation that leads a protein to gain specificity while also benefiting the organism, otherwise people could very well argue for intelligently designed or guided evolution. (not that I am necessarily opposed to that, just curious to see what others have to say)

Edited July 30, 2013 by BeeBeeramBeeBee

[CraigD]

Welcome to hypography, BeeBeeramBeeBee! :) Please feel free to start a topic in the introductions forum to tell us something about yourself.

 

Has anyone heard this before?

Before your post, I’d never heard of the “nylon-eating” K172 strain of Flavobacterium.

 

Despite its popular name “nylon-eating bacteria”, I don’t believe this strain can actually digest nylon 6 or other types of nylon used in fabric, but 6-aminohexanoate, a byproduct of nylon 6 manufacturing found, along with this Flavobacterium strain, in factory waste water, which is chemically similar to the nylon 6 polymer, and also the amino acid lysine. Because there was practically no 6-aminohexanoate in water prior to the beginning of nylon manufacturing in the 1930s, it seems clear populations of Flavobacterium evolved the ability to digest it quickly, in less than 40 years!

 

The original research is pretty old – ca. 1975 – so this amazing adaptation was, I guess, rolled up in my general life science education under the aphorism “nature finds a way” (made famous in the 1993 movie Jurassic Park). :)

 

The subject seems to have become prominent again ca. 1995, from research in which Pseudomonas aeruginosa was forced to evolve the same ability in a lab, using different genes and enzymes.

 

Also, is there such a mutation that makes a protein more specific in what it can do, which benefits an organism, which has been observed? Is this even a proper argument?

As best I can tell, the mutant gene expressed “nylonase” enzymes (there are, I believe, 3, not just 1, or these proteins) in Flavobacterium K172 are no less “specific” than the versions of them in its ancestors – that is, the bacterium gained the ability to digest 6-aminohexanoate, but lost the ability to digest other molecules.

 

While it seems proper to call a collection of enzymes that can metabolize a smaller collection of molecules more “specific” than one that can metabolize a larger collection, I don’t know that this concept is very useful to biologists. Knowing specifically what and how enzymes catalyze biochemical reactions is more useful, I think, than assigning them general traits like more or less “specific”.

[BeeBeeramBeeBee]

Welcome to hypography, BeeBeeramBeeBee! :) Please feel free to start a topic in the introductions forum to tell us something about yourself.

 

 

Before your post, I’d never heard of the “nylon-eating” K172 strain of Flavobacterium.

 

Despite its popular name “nylon-eating bacteria”, I don’t believe this strain can actually digest nylon 6 or other types of nylon used in fabric, but 6-aminohexanoate, a byproduct of nylon 6 manufacturing found, along with this Flavobacterium strain, in factory waste water, which is chemically similar to the nylon 6 polymer, and also the amino acid lysine. Because there was practically no 6-aminohexanoate in water prior to the beginning of nylon manufacturing in the 1930s, it seems clear populations of Flavobacterium evolved the ability to digest it quickly, in less than 40 years!

 

The original research is pretty old – ca. 1975 – so this amazing adaptation was, I guess, rolled up in my general life science education under the aphorism “nature finds a way” (made famous in the 1993 movie Jurassic Park). :)

 

The subject seems to have become prominent again ca. 1995, from research in which Pseudomonas aeruginosa was forced to evolve the same ability in a lab, using different genes and enzymes.

 

 

As best I can tell, the mutant gene expressed “nylonase” enzymes (there are, I believe, 3, not just 1, or these proteins) in Flavobacterium K172 are no less “specific” than the versions of them in its ancestors – that is, the bacterium gained the ability to digest 6-aminohexanoate, but lost the ability to digest other molecules.

 

While it seems proper to call a collection of enzymes that can metabolize a smaller collection of molecules more “specific” than one that can metabolize a larger collection, I don’t know that this concept is very useful to biologists. Knowing specifically what and how enzymes catalyze biochemical reactions is more useful, I think, than assigning them general traits like more or less “specific”.

 

Thank you.

 

Ive seen, here is the topic here, that I was reading.

 

http://www.shiachat.com/forum/index.php?/topic/234989658-the-theory-of-evolution/?p=2369365

 

The person, "Ibn-Ahmed Aliyy Herz ", uses these words "break down, or damaged", when describing the proteins after mutation. After mutation, could the alteration in the number of compounds that they break down, can it be compared or described as damaged? For example, if a protein can break down 1 protein, but then alters and loses that capability, but then can break down 2 different ones, could it be damaged?

 

It sounds kind of stupid.

 

Wouldnt the breaking down of more proteins equate to a greater skill for survival of a species. In this case, the bacteria being able to break down this by product, that is prominant in its environment, it seems like a blatant advancement in capability. While, simultaneously, could it be said that the proteins have a greater specificity for breaking down nylonase by products?

 

Can any merit be extracted from this persons argument at all?

Edited August 1, 2013 by BeeBeeramBeeBee

[BeeBeeramBeeBee]

Bump

[Rade]

Beneficial mutations are difficult to detect because their detection requires analysis of changes in gene frequency over many generations. So, as expected, bacteria are excellent organisms to use to study beneficial mutations, and as you read here, in a 10,000-generation experiment beneficial mutations were observed:

 

 

 

Papadopoulos, D., Schneider, D., Meier-Eiss, J., Arber, W., Lenski, R. E., Blot, M. (1999). Genomic evolution during a 10,000-generation experiment with bacteria. Proc. Natl. Acad. Sci. U. S. A. 96: 3807-3812

 

 

Molecular methods are used widely to measure genetic diversity within populations and determine relationships among species. However, it is difficult to observe genomic evolution in action because these dynamics are too slow in most organisms. To overcome this limitation, we sampled genomes from populations of Escherichia coli evolving in the laboratory for 10,000 generations. We analyzed the genomes for restriction fragment length polymorphisms (RFLP) using seven insertion sequences (IS) as probes; most polymorphisms detected by this approach reflect rearrangements (including transpositions) rather than point mutations. The evolving genomes became increasingly different from their ancestor over time. Moreover, tremendous diversity accumulated within each population, such that almost every individual had a different genetic fingerprint after 10,000 generations. As has been often suggested, but not previously shown by experiment, the rates of phenotypic and genomic change were discordant, both across replicate populations and over time within a population. Certain pivotal mutations were shared by all descendants in a population, and these are candidates for beneficial mutations, which are rare and difficult to find. More generally, these data show that the genome is highly dynamic even over a time scale that is, from an evolutionary perspective, very brief.

 

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Edited August 30, 2013 by Rade