Responding to Justa's Comments On Evolution

[DogmaHunter]

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?

Obviously, because that didn't agree with the point he wanted to make.

 

[DogmaHunter]

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.

I think it's safe to say that whois got served.

This thread is hilarious.

 

[whois]

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

yes, i am.
but you seemed to have disappeared.
are you going to respond to post 1040?

 

[Loudmouth]

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?

Was Koonin lying when he wrote this?

"The comparative infrequency of HGT in the eukaryote part of the biological world means, however, that in this case the conceptual implications for the TOL might not be as drastic: the evolutionary histories of many eukaryotes appear to produce tree-like patterns."
http://www.biologydirect.com/content/6/1/32

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

It was more of a general statement. As an example, there are a few famous quote mines from Origin of Species that creationists like to use. Anyone who read Darwin's work would never use them since it is so obviously taken out of context. For example,

To suppose that the eye, with all its inimitable contrivances for adjusting the focus to different distances, for admitting different amounts of light, and for the correction of spherical and chromatic aberration, could have been formed by natural selection, seems, I freely confess, absurd in the highest possible degree.​

They leave off the rest of section which says just the opposite:

Yet reason tells me, that if numerous gradations from a perfect and complex eye to one very imperfect and simple, each grade being useful to its possessor, can be shown to exist; if further, the eye does vary ever so slightly, and the variations be inherited, which is certainly the case; and if any variation or modification in the organ be ever useful to an animal under changing conditions of life, then the difficulty of believing that a perfect and complex eye could be formed by natural selection, though insuperable by our imagination, can hardly be considered real. How a nerve comes to be sensitive to light, hardly concerns us more than how life itself first originated; but I may remark that several facts make me suspect that any sensitive nerve may be rendered sensitive to light, and likewise to those coarser vibrations of the air which produce sound. . .

In the Articulata we can commence a series with an optic nerve merely coated with pigment, and without any other mechanism; and from this low stage, numerous gradations of structure, branching off in two fundamentally different lines, can be shown to exist, until we reach a moderately high stage of perfection. In certain crustaceans, for instance, there is a double cornea, the inner one divided into facets, within each of which there is a lens shaped swelling. In other crustaceans the transparent cones which are coated by pigment, and which properly act only by excluding lateral pencils of light, are convex at their upper ends and must act by convergence; and at their lower ends there seems to be an imperfect vitreous substance. With these facts, here far too briefly and imperfectly given, which show that there is much graduated diversity in the eyes of living crustaceans, and bearing in mind how small the number of living animals is in proportion to those which have become extinct, I can see no very great difficulty (not more than in the case of many other structures) in believing that natural selection has converted the simple apparatus of an optic nerve merely coated with pigment and invested by transparent membrane, into an optical instrument as perfect as is possessed by any member of the great Articulate class.
http://www.talkorigins.org/faqs/origin/chapter6.html​

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

None of which were produced by HGT.

 

[Loudmouth]

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

And?

The whole point of the methodology was to remove natural selection in order to get a better idea of what the deleterious mutation rate really is. They did this by selecting random bacteria as the founders of new populations. If natural selection were allowed to act on these populations, one way or the other, then the would overestimate the beneficial mutation rate and underestimate the deleterious mutation rate.

What did you think those quotes were trying to say?

 

[whois]

And?

The whole point of the methodology was to remove natural selection in order to get a better idea of what the deleterious mutation rate really is. They did this by selecting random bacteria as the founders of new populations. If natural selection were allowed to act on these populations, one way or the other, then the would overestimate the beneficial mutation rate and underestimate the deleterious mutation rate.

What did you think those quotes were trying to say?

you are indeed a riot loudmouth.
you know for a fact your post is garbage.

 

[bhsmte]

you are indeed a riot loudmouth.
you know for a fact your post is garbage.

Is that the best you can do?

 

[whois]

Was Koonin lying when he wrote this?

"The comparative infrequency of HGT in the eukaryote part of the biological world means, however, that in this case the conceptual implications for the TOL might not be as drastic: the evolutionary histories of many eukaryotes appear to produce tree-like patterns."
http://www.biologydirect.com/content/6/1/32

http://www.biologydirect.com/content/6/1/32
what does koonin have to do with the boyce article?
exactly zero, that's what.
more waffling on your part.

http://www.talkorigins.org/faqs/origin/chapter6.html

​

yes indeed, a respected, peer reviewed source if i ever seen it.

 

[Loudmouth]

the adaptive nature of darwinism is also incorrect as one of my recent posts shows.
the MA experiment conclusively shows a linearly decreasing fitness with the accumulation of mutations.

I wanted to highlight this post once again (post 152).

If I am understanding this post correctly, whois attempts to claim that the accumulation of mutations can not increase fitness through Darwinian mechanisms.

Am I reading this wrong?

 

[Loudmouth]

what does koonin have to do with the boyce article?
exactly zero, that's what.
more waffling on your part.

Will you acknowledge that you have read this quote and understand that Koonin sees very little role for HGT in the evolution of complex eukaryotes like humans?

"The comparative infrequency of HGT in the eukaryote part of the biological world means, however, that in this case the conceptual implications for the TOL might not be as drastic: the evolutionary histories of many eukaryotes appear to produce tree-like patterns."
http://www.biologydirect.com/content/6/1/32

​

yes indeed, a respected, peer reviewed source if i ever seen it.

"more waffling on your part"--whois

 

[whois]

Will you acknowledge that you have read this quote and understand that Koonin sees very little role for HGT in the evolution of complex eukaryotes like humans?

other scientists do.
and i uploaded the peer reviewed paper.

 

[Loudmouth]

you are indeed a riot loudmouth.
you know for a fact your post is garbage.

"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

It says right in the paper that they removed selection pressures.

 

[Loudmouth]

other scientists do.

Why are you suppressing Koonin's work?

 

[whois]

"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

It says right in the paper that they removed selection pressures.

you know full well that your post refers to the test samples and not the controls.
just stop it already loudmouth.

 

[Loudmouth]

you know full well that your post refers to the test samples and not the controls.
just stop it already loudmouth.

I know no such thing. They treated the control strain identically to the hypermutator strains.

"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."

The control strains went through the same bottlenecking that removes natural selection.

[added in edit: another quote from same paper]

"One of the most widely used methods for determining the rate and fitness effect of spontaneous mutations is the MA experiment. Following the pioneering work Bateman (1959) and Mukai (1964), MA experiments involve propagating many replicate lines at very small effective population sizes so that the effect of natural selection is swamped out by that of genetic drift, allowing weakly selected mutations to accumulate randomly."