Human Evolution-Bacteria Conjugation

  • #26
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All valid points....I am still intrigued, in reference to the E.coli evolution experiment, about the odds of the Citrate + ( mutation resulting in E.coli that are able to utilize Citrate in aerobic conditions) occurring. There are 4288 genes found to be coding for proteins in E.coli (see https://en.wikipedia.org/wiki/Escherichia_coli#Genomics). If we conservatively estimate that it requires 2 potentiating mutations to allow for a final actuating mutation to develop, which then results in a new trait (such as the Citrate utilizing protein), then the number of potential mutations would be described by the permutation formula. C representing the maximum number of possible combinations and n the total subjects in a field, r the number of subsets, thus based on the formula C = n!/ (r! ( n-r )! ), we arrive at 13,131,343,936 possible combinations/ mutations! The Citrate + mutation seems to have developed very early in the total pathway of the C number of possible mutations. How did that happen?!! by anyones understanding of this?
I don't know where your number comes from, but the approach does not work.
All the bacteria accumulated many mutations. Mutations that don't change fitness can easily stay in the pool, so you always have a huge amount of different DNA sets in the sample. It's not like the bacteria need exactly two changes and no changes anywhere else.
 
  • #27
Ygggdrasil
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It's not necessarily the case that the Cit+ phenotype requires a unique genotype. In other words, there may be more than one combination of potentiating mutations that enable the identified actualizing mutations to work, and there could be entirely different actualizing mutations that work via a different biochemical mechanism. It is difficult to estimate the probabilities involved.
 
  • #28
Yes, the study references 2 potentiating mutations and 1 actualizing mutation leading to the Cit+ phenotype, and the estimate number of total potential mutations, utilizing the permutation formula, may actually be a very conservative one with the r or subset number, being 3 only.
 
  • #29
Drakkith
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If the mutation indeed occurred early on, then the implications are as prior noted.

Or, if it did indeed occur 'early', it could simply have been due to plain old probability. An event with a one-in-a-million chance of happening can certainly occur the first time. People win the lottery every day.

If conversely, the mutation occurred in the latter part of the mutation spectrum, then this too has implications. Namely, that the E.coli are still very phenotypically recognizable as the progenitor E.coli. i.e., they have not evolved into something in any way unrecognizable from the original.

I don't see how the mutations occurring 'later' as apposed to 'earlier' has anything to do with whether or not the bacteria have evolved into something beyond the original species.
 
  • #30
Or, if it did indeed occur 'early', it could simply have been due to plain old probability. An event with a one-in-a-million chance of happening can certainly occur the first time. People win the lottery every day.
Well, yes but realistically....one can say still understand that probability wise, an early onset Cit + mutation has remarkable implications.
 
  • #31
I don't see how the mutations occurring 'later' as apposed to 'earlier' has anything to do with whether or not the bacteria have evolved into something beyond the original species.

If indeed the mutation occurred in the latter phase of the full spectrum of possible mutations, then there really are not many mutations 'left' so to speak....Very logical...
If it did occur in the latter phase, then we also can interpret that there is a a finite limit of possible phenotypic variation, that being the case since there is an X amount of maximum possible mutation combinations per aforementioned computation.
 
  • #32
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Yes, the study references 2 potentiating mutations and 1 actualizing mutation leading to the Cit+ phenotype, and the estimate number of total potential mutations, utilizing the permutation formula, may actually be a very conservative one with the r or subset number, being 3 only.
Assuming only three mutations underestimates the probability massively.

Take 10 million possible places for a mutation, assume that every cell randomly has 25,000 of them (corresponding to ~.5% genetic difference between cells, the level humans have - probably an underestimate), calculate the probability that a cell has three specific mutations (plus about 25,000 mutations elsewhere). It is about 1 in 60 millions. The experiment had way more cells, so even a much smaller number of mutations is sufficient to get a reasonable chance of three mutations at specific places. In addition, see above: it does not have to be the only combination that leads to the same result.
 
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  • #33
Ygggdrasil
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The question is an important one. Perhaps someone very familiar with the intricacies of the E.coli evolution study can add to this? If the mutation indeed occurred early on, then the implications are as prior noted. If conversely, the mutation occurred in the latter part of the mutation spectrum, then this too has implications. Namely, that the E.coli are still very phenotypically recognizable as the progenitor E.coli. i.e., they have not evolved into something in any way unrecognizable from the original.

Why would you expect the E. coli to evolve into something unrecognizable from the original? The culture conditions for the LTEE are fairly close to optimal growth conditions for an organism like E. coli. If you were to seed the cultures with E. coli and a number of other species, it's likely, that the E. coli would win out and dominate the culture over time. In these cases, most traits are under purifying selection which in general, will help to disfavor change over time (because most changes are deleterious).
 
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  • #34
All the bacteria accumulated many mutations. Mutations that don't change fitness can easily stay in the pool, so you always have a huge amount of different DNA sets in the sample.
Ok but the question remains, where in the spectrum of all of the possible mutations (let us call this the X amount) did the Citrate +[set] of mutations occur? [If] it was earlier on (in this pathway of total possible mutations), then it stretches probability theory for such a beneficial trait to emerge in the time that it did. It was mentioned by Drakkith earlier that it would be analogous to winning the lottery.

The experiment had way more cells, so even a much smaller number of mutations is sufficient to get a reasonable chance of three mutations at specific places.
I understand with more clarity your point.

The culture conditions for the LTEE are fairly close to optimal growth conditions for an organism like E. coli.

Yes, near optimal environment and growth medium for the E.coli experiment. It would be quite interesting to implement and then observe the effects of varied and more challenging environments for the E.coli to evolve in a way that is phenotypically different than their progenitors.
Respects to all...
 
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  • #35
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Ok but the question remains, where in the spectrum of all of the possible mutations (let us call this the X amount) did the Citrate +[set] of mutations occur? [If] it was earlier on (in this pathway of total possible mutations), then it stretches probability theory for such a beneficial trait to emerge in the time that it did. It was mentioned by Drakkith earlier that it would be analogous to winning the lottery.
I don't see any indication that it would have occured very early or very late. Estimating the probability precisely looks like a huge challenge.

You can edit your posts if you want to add something. I merged your posts.
 
  • #36
I don't see any indication that it would have occured very early or very late. Estimating the probability precisely looks like a huge challenge.
So, with regards to the E.coli evolution experiment, would modifying the culture medium of the E.coli change it from, as noted earlier, a purifying selection process to a diversifying one? If the E.coli were placed in a more natural environment with amplified survival pressure, could we expect diversification of E.coli phenotypes?
 
  • #37
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That is possible.
 
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  • #38
It would be remarkable to see if this diversification (over many generations) led to something similar already seen in nature, or if entirely new phenotypes came about.
It would conversely, be quite consequential if the diversification process (in this setting) fell flat and not much came from it, beyond prior observations.
 
  • #39
So the different kinds of environments could be: varied temperatures, light/dark exposure, pH variances, tepid versus turbulent environments (that which would simulate wave action, for example) and variations in nutrients and base chemistries. This would mimic conditions found in nature.
 
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  • #40
Drakkith
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So the different kinds of environments could be: varied temperatures, light/dark exposure, pH variances, tepid versus turbulent environments (that which would simulate wave action, for example) and variations in nutrients and base chemistries. This would mimic conditions found in nature.

There have been a great many such experiments. One of the first was William Dallinger's experiment from 1880-1886 in which he gradually increased the temperature of samples of bacteria from 60 F to 158 F. The initial population of bacteria couldn't survive at a temperature anywhere near 158 F. Conversely, the population that could survive at 158 F could no longer survive at the original 60 F temperature.

A huge number of similar experiments have been performed since then that do exactly what you're asking about. Here's a PHD thesis from Alex Hall on the subject: https://www.era.lib.ed.ac.uk/handle/1842/3977
 
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