Responding to Justa's Comments On Evolution

Loudmouth · Aug 20, 2015

whois said:
really?
We performed a classic MA experiment in which frequent sampling of MA lines was combined with whole genome resequencing to develop a high-resolution picture of the effect of spontaneous mutations in a hypermutator (ΔmutS) strain of the bacterium Pseudomonas aeruginosa.

notice the word SPONTANEOUS.

Notice the word "hypermutator".

whois · Aug 20, 2015

Loudmouth said:
Notice the word "hypermutator".

and?
please demonstrate how this disqualifies the results.
also, please present something other than your opinion in doing so.

Oncedeceived · Aug 21, 2015

whois said:
and?
please demonstrate how this disqualifies the results.
also, please present something other than your opinion in doing so.

Silence.....

Loudmouth · Aug 21, 2015

whois said:
and?

What happens for strains with normal rates of mutation?

"The average fitness of bottlenecked nonhypermutator control lines did not change significantly over the course of the experiment (ANOVA: P = 0.712, F1,118 = 0.137), indicating that the loss of fitness in hypermutator lines was due to mutation accumulation."
http://www.genetics.org/content/197/3/981.full

Oh, wouldn't you know it . . . the fitness of nonhypermutator control lines did not decrease over time. Why did you fail to mention this?

It is also worth mentioning that they observed beneficial mutations in this experiment:

"Although the average fitness effect of a step was deleterious, there were numerous steps in which fitness increased (Figure 4). To confirm the presence of steps containing beneficial mutations, we repeated the competitive fitness assays for the 11 steps with the largest increases in fitness. Even after false discovery rate correction (Benjamini and Hochberg 1995), fitness increased significantly (P < 0.05) in 6/89 (6.7%) of the measurable steps."

You failed to mention that as well. Why?

lasthero · Aug 21, 2015

Oncedeceived said:
Silence.....

Yes, Once. If someone does not answer a question within a few hours, they must be completely stumped.

whois · Aug 21, 2015

oh, wouldn't you know it . . . bottlenecked mutations aren't normal mutation rates.
why didn't you mention that?

BTW, this MA experiment is not the only one that shows evolution in ways that often decrease fitness of an organism.

Loudmouth · Aug 21, 2015

whois said:
oh, wouldn't you know it . . . bottlenecked mutations aren't normal mutation rates.
why didn't you mention that?

I didn't say that because that sentence makes no sense. Bottlenecking and mutation rate are two different things.

whois · Aug 21, 2015

loudmouth,
you apparently missed the entire point of the paper.
this paper PROVES that increasing fitness is effected by rare mutations of large effect.
in other words evolution DOES NOT proceed by infinitesimal small increases in fitness.
next.

Loudmouth · Aug 21, 2015

Just to be clear what the experiment is, here is how they created the hypermutating clone of P. aeruginosa:

"The eight replicate clones used in this study were founded from the P. aeruginosa hypermutator strain PAO1ΔmutS, which was created by replacing mutS—part of the methyl-directed mismatch repair pathway—with the antibiotic resistance marker aac1 using the Cre-lox system for gene deletion and antibiotic resistance marker recycling following the methods of Mandsberg et al. (2011). Deleting mutS increases the mutation rate by ∼70-fold in P. aeruginosa (Torres-Barcelo et al. 2013), primarily by increasing the rate of transitions (Miller 1996)."
http://www.genetics.org/content/197/3/981.full

So the hypermutating strain had a 70 fold higher rate of mutation than the control strain. They then used 30 bottlenecks (i.e. used a single bacterium to found a new population) to fix mutations immediately in a new population:

"Eight replicate mutation accumulation lines were generated by streaking randomly selected colonies of PAO1ΔmutS onto individual M9KB agar plates (glycerol, 10 g/liter; peptone, 20 g/liter; M9 salts, 10.5 g/liter; agar, 12 g/liter; and MgSO4, 2 mL/liter). Plates were incubated at 37° for 18 hr before repeating the process of picking a random colony and streaking it on a fresh plate. This process was repeated daily for 30 days."
http://www.genetics.org/content/197/3/981.full

They then compared the fitness of these populations against a standard strain. They did the same experiment for both the hypermutating strain of P. aeruginosa and a control strain where the mutS gene was not deleted.

What did they find? The control strain did not have a reduction in fitness while the hypermutator did. Whois only likes to mention the results from the hypermutator strain.

Loudmouth · Aug 21, 2015

whois said:
loudmouth,
you apparently missed the entire point of the paper.
this paper PROVES that increasing fitness is effected by rare mutations of large effect.
in other words evolution DOES NOT proceed by infinitesimal small increases in fitness.
next.

Affected by what again? Mutations? Do these mutations accumulate?

Since these populations were a single species with identical starting genomes, these mutations could not have come about by HGT, correct? They certainly weren't epigenetic. These were mutations that were vertically inherited, correct?

Oncedeceived · Aug 21, 2015

lasthero said:
Yes, Once. If someone does not answer a question within a few hours, they must be completely stumped.

I thought this was posted several days ago.

whois · Aug 21, 2015

Loudmouth said:
Affected by what again? Mutations? Do these mutations accumulate?

apparently not, they were apparently the same species they started with.

Since these populations were a single species with identical starting genomes, these mutations could not have come about by HGT, correct?

i don't know if this was stated in the paper, but seeing as they are bacteria, the prospect seems highly likely.

They certainly weren't epigenetic.

this also wasn't mentioned, so i wouldn't say "certainly".

These were mutations that were vertically inherited, correct?

like i said, these are bacteria, the prospect of HGT seems likely but wasn't mentioned.

Loudmouth · Aug 21, 2015

whois said:
apparently not, they were apparently the same species they started with.

Then what caused the changes in fitness if it wasn't mutations?

i don't know if this was stated in the paper, but seeing as they are bacteria, the prospect seems highly likely.

The prospect of what? You are being ambiguous.

like i said, these are bacteria, the prospect of HGT seems likely but wasn't mentioned.

What would the source of HGT be?

Loudmouth · Aug 21, 2015

Reading the paper further, none of the mutations were described as HGT events.

"Of the 944 mutations, 778 (82.4%) were base substitutions, 164 (17.4%) were short indels (<10 bp), and 2 (0.2%) were large structural variations, consisting of a partial gene duplication event (pvdD) and a 1880-bp intergenic deletion."

The only mutation that could have been from HGT is the one partial gene duplication. Base susbstitutions and short indels are not from HGT.

Loudmouth · Aug 21, 2015

More from whois' paper. I am starting to suspect that whois is suddenly regretting ever using this paper. Time will tell.

As discussed earlier, the bacterial populations go through sudden and severe bottlenecks. The population goes from a single bacterium, to a few hundred thousand, and back to a single bacterium in one fell swoop about every 30 generations. Each new population is a randomly selected individual. This, in effect, removes natural selection from the process.

What you see with a hypermutator and these extreme bottlenecks is what happens when you have a lot of mutations and no natural selection. Wouldn't you know it, fitness goes down.

"Using detailed fitness measurements and whole genome resequencing, we studied the evolutionary dynamics of eight replicate mutation accumulation lines of a hypermutator strain of the pathogenic bacterium Pseudomonas aeruginosa. MA lines were passaged through 28 single-cell bottlenecks followed by rapid population growth over a period of ∼644 generations. Under this regime, we estimate that the effective population size of MA lines had a lower limit of ∼16, which should be sufficient to prevent natural selection on the vast majority of spontaneous mutations."
http://www.genetics.org/content/197/3/981.full

Just hoping that whois is still willing to discuss the paper.

crjmurray · Aug 21, 2015

Loudmouth said:
More from whois' paper. I am starting to suspect that whois is suddenly regretting ever using this paper. Time will tell.

About as much as he regrets using that Ayala quote.

bhsmte · Aug 21, 2015

Loudmouth said:
More from whois' paper. I am starting to suspect that whois is suddenly regretting ever using this paper. Time will tell.

As discussed earlier, the bacterial populations go through sudden and severe bottlenecks. The population goes from a single bacterium, to a few hundred thousand, and back to a single bacterium in one fell swoop about every 30 generations. Each new population is a randomly selected individual. This, in effect, removes natural selection from the process.

What you see with a hypermutator and these extreme bottlenecks is what happens when you have a lot of mutations and no natural selection. Wouldn't you know it, fitness goes down.

"Using detailed fitness measurements and whole genome resequencing, we studied the evolutionary dynamics of eight replicate mutation accumulation lines of a hypermutator strain of the pathogenic bacterium Pseudomonas aeruginosa. MA lines were passaged through 28 single-cell bottlenecks followed by rapid population growth over a period of ∼644 generations. Under this regime, we estimate that the effective population size of MA lines had a lower limit of ∼16, which should be sufficient to prevent natural selection on the vast majority of spontaneous mutations."
http://www.genetics.org/content/197/3/981.full

Just hoping that whois is still willing to discuss the paper.

This is what happens, when someone selectively reads papers.

Loudmouth · Aug 21, 2015

bhsmte said:
This is what happens, when someone selectively reads papers.

At least it is a peer reviewed paper instead of a NY Times article.

What I think happens many times is that people read the section quoted by a creationist website. It isn't selective reading within the paper itself, but never actually reading the paper.

On top of that, people don't even understand the experiments and project their own beliefs onto it. I think that is what happened in this case. Whois reads that single mutations can have large effects. Whois automatically assumes that these mutations have to come from horizontal genetic transfer because they have a large effect. They never stop to see exactly what the real mutation is. As it turns out, a substitution mutation as part of vertical genetic transfer can produce a large effect.

whois · Aug 21, 2015

Loudmouth said:
At least it is a peer reviewed paper instead of a NY Times article.

the boyce article?
this was an article where an evolutionist was interviewing an evolutionist.
i guess they just decided to lie their butts off, right?

What I think happens many times is that people read the section quoted by a creationist website. It isn't selective reading within the paper itself, but never actually reading the paper.

i have no idea why you make assumptions like that.
seldom do i skim creationist sites for material.

On top of that, people don't even understand the experiments and project their own beliefs onto it. I think that is what happened in this case.

again, you believe wrong, the entire point of the paper was to prove fitness is strongly influenced by rare mutations of strong effect.

Whois reads that single mutations can have large effects. Whois automatically assumes that these mutations have to come from horizontal genetic transfer because they have a large effect.

wait a minute, i never mentioned HGT, YOU DID.

They never stop to see exactly what the real mutation is. As it turns out, a substitution mutation as part of vertical genetic transfer can produce a large effect.

see upload for the source of this material:

whois · Aug 21, 2015

Our experimental approach allowed us to experimentally demonstrate that it is highly likely that at least 0.64% of the mutations that fixed during our MA experiment were beneficial. For these mutations to have been fixed by drift, the beneficial mutation rate in a nonhypermutator population with a genomic mutation rate of 3 × 10−3 mutations/genome/generation would have to have been ∼5 × 10−6 mutations/genome/generation, which is two to three orders of magnitude higher than existing estimates.
-ibid

Additionally, we found no evidence of positive selection on the same genes in different MA lines. Surprisingly, we found that nonsynonymous mutations in highly conserved core genes can have strong deleterious effects on fitness (Figure 2), and yet we found no evidence that these mutations were removed by natural selection.
-ibid

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