Leisola: Cited to Attack Darwin Devolves, Study Devolves on Close Inspection

Design

(Wayne Rossiter) #22

I’m still pouring over the details (some of the methods in the supplementary materials are foreign to me). However, Ann did ask (apparently she’s not on here anymore?) that I pass along her rebuttal. So, this is literally cut-pasted from her message to me:

[@moderators: the email from @agauger was moved to this thread: Gauger: Answering Art Hunt on Real Time Evolution. This thread will be reserved for dialogue with @Wayne_Rossiter]


(S. Joshua Swamidass) split this topic #24

A post was merged into an existing topic: Gauger: Answering Art Hunt on Real Time Evolution


(Arthur Hunt) #25

Thanks for this @Wayne_Rossiter. However, I would recommend that we discuss your own ideas, and not ask you to be a messenger for Ann. Any sort of back and forth with Ann will get very cumbersome and (I expect) use too much of your time. Ann left this group - if she wants to discuss the matter more with us, she should re-enlist (or whatever one might call it).

With that in mind, I will wait on @Wayne_Rossiter’s own remarks before adding anything to this discussion.


(S. Joshua Swamidass) #27

@Wayne_Rossiter, I agree with @art on this. This thread will be reserved for your thoughts, as it was originally set up to engage with you. I do not want there to be distractions here from others.

I emailed @Agauger asking what she wanted to do. I’m pleased to report she wants to be reinstated. I have just reinstated her account. She can respond to @art here: Gauger: Answering Art Hunt on Real Time Evolution.


@Wayne_Rossiter, as you see fit, you may quote from her as needed. I do caution you that @Agauger has explained the past that she is not allowed to concede any points on behalf of Behe or Axe. If you do quote from her, I hope you can explain for yourself the reasoning. Honestly, I’m very puzzled by the ID response to this paper. I am hopeful you can help me understand.

I look forward to the conversation developing from here!


(S. Joshua Swamidass) #28

@art, I had one question about the system. I could sort this out by reading the paper again, but it will better to just ask you so we are all on the same page. During the “amplification” phase of the experiment, @Rumraket says that the gene was placed on a plasmid. Is this correct? I thought it was placed into the salmonella genome. Was it a plasmid or integrated into the genome when the bacteria duplicated it?


(Mikkel R.) #29

It was on a plasmid, Real-Time Evolution of New Genes by Innovation, Amplification, and Divergence

We placed this bifunctional parental gene (dup13-15, D10G) under the control of a constitutive promoter that cotranscribed a yellow fluorescent protein ( yfp ) gene. We also placed the T- his operon in a transposition-inactive transposable element Tn 10d Tet close to the lac operon on the low–copy number (about two copies per chromosome) (11) F′128 plasmid (Fig. 1C). Duplications and amplifications of this region are frequent and have low fitness cost (3), allowing experimental study of the process within a reasonable time frame. An F′ plasmid with the bifunctional gene inside T- his was introduced into a S. enterica strain with deleted hisA and trpF genes, dependent on the bifunctional gene for synthesis of both histidine and tryptophan. In the absence of both amino acids, the bifunctional gene supported a generation time of ~5.1 hours in minimal medium with doubling times of ~2.8 hours in the presence of tryptophan alone, ~2.6 hours in the presence of histidine alone, and ~1.5 hours in presence of both amino acids.


(S. Joshua Swamidass) #30

Interesting. What is the mechanism that maintains these plasmids at low copy number?


(Mikkel R.) #31

Good question, I don’t know.


(S. Joshua Swamidass) #32

It seems that this might have been a difference between @Agauger’s study and the RTE study. Did @Agauger use a high copy number plasmid? If so, this difference might explain why she saw a loss of duplications.


(Arthur Hunt) #33

I think this is an inherent feature of F plasmids.


(Mikkel R.) #34

If you’re referring to their Axe and Gauger’s bio-complexity paper, they did not do anything involving duplications at all.