Comments on: A Switch is Born

By: sharon

sharon — Fri, 08 Sep 2006 03:50:35 +0000

IDers keep telling us that no one’s ever seen evolution happening,

What do they say about a fertilized egg which begins as a single cell (all of them look the same too!) rapidly, blink of an eye in geological time, all evolve into unique species…

Or a frog, starts out like a fish, sprouts legs, and moves on land.

or that only “microevolution” going back and forth between various pre-existing states can occur,

What about humans growing tails count, our ape ancestry, does that qualify as a pre-existing state…

By: Navneet

Navneet — Wed, 06 Sep 2006 16:49:24 +0000

I think the time point of 2 days should be replaced with the number of divisions that the cells might have undergone before getting a promoter sequence. The “2 days” sort of trivialises the fact that it contains roughly a hundred generations in it not to mention the number of organisms that might have been born and died.
Also what I wish to ask is that whether the study says that the promoter sites will spring up right before the first nucleotide that is “read” and copied into a messenger RNA…because there are chances that the promoter might spring up in unlikely locations making it less meaningful for the bacterium.

By: sharon

sharon — Wed, 30 Aug 2006 20:07:43 +0000

for all those IDers that this experiment occurred under “artificial,” “model” conditions, or they’d be left with very little to continue misleading their incurious followers about.
# soapbox
Incurious followers, more like, lack of understanding. Feel sorry for ‘em, maybe. Feel sorry for me. I know some in the ID/Evolution circles who purposely trivalize the controversies big mile-long words among and impressing their colleagues, and it alienates curiosity.. #insert mile long stretch of scientific babble-words here /
I’ve read the article a couple times, and still having a problem understanding, and its not that I don’t want to understand, and I certainly don’t believe Carl Zimmer is telling lies, however, truthfully, without understanding exactly what the point really is, I would be a liar to state with conviction, “He’s telling the truth.”

Point blank, it really is so much easier to believe Dembski, when he says “Goddidit”… not that anyone out in the real world really understands (or cares to) any of the science Dembski’s babbling about either, but “God”, people understand “God”.
/soapbox

- “Make everything as simple as possible, but not simpler.”
- “Any intelligent fool can make things bigger, more complex, and more violent. It takes a touch of genius — and a lot of courage — to move in the opposite direction.”
- “I want to know God’s thoughts; the rest are details.”
- Einstein
- rescomp.stanford.edu/~cheshire/EinsteinQuotes.html

By: Jim Hu

Jim Hu — Wed, 30 Aug 2006 09:31:30 +0000

Minor corrections:

The microbes were allowed to grow rapidly for 12 hours, producing a lot of sigma 70.

The Eσ70 is constant in the host cells in these experiments. The 12 hour growth allows the mutagenized plasmids to proliferate and make whatever chloramphenicol acetyl transferase they can make. There will be some additional mutations from this outgrowth as well.

The mutation rate refers to the fraction of promoter sequences that mutate in this stage of the cycle.

The frequency is expressed per bp sequenced, so it’s pretty high. The authors describe their low frequency (not rate) as:

The mutation frequency is 0.4% (13 mutations among 3198 bp examined)

The mutagenized segment is only 41 bp long. I get 13 mutations among 78 promoters sequenced. Although the paper is not totally clear, the correct way to do this is to sequence from the unselected population at each round. It looks like that’s what they did, since the sequences shown in Fig 5 have many more than 13 sequence changes.

In their low frequency experiment (Expt. 2), the dominant sequence seems to be derived from something that was not from the PCR mutagenesis (descendents of 2.1.15). The source of this DNA mystifies me…it would help if the papers was written more clearly wrt things like whether they sequenced both strands.

By: Paul Orwin

Paul Orwin — Tue, 29 Aug 2006 01:19:56 +0000

Carl, if you haven’t already, look into the work of Steve Finkel’s group at USC. They have been observing the GASP phenotype (basically, succession in old cultures) and the relationship to mutations in sigma factors. Some other big shots in the field are Roberto Kolter (Yale), Richard Lenski (Michigan State?), and Al Bennett (UCI). The switching stuff (stochastic controls on gene expression, single cells) is cool too; Mary Lidstrom is working on that with a neat methanogen system. If you ever look at “monocultures” of environmental bacteria, you know that the uniform colonies on a petri dish are a pure laboratory artifact – bacterial gene expression is heterogenous, and complex environmental cues are responsible, as well as stochastic processes – it’s fascinating stuff, and we have the tools to study it now.

By: Brian S.

Brian S. — Mon, 28 Aug 2006 21:37:11 +0000

I wouldn’t be surprised if the highly-resistant strains lost some fitness in other respects, and would be outcompeted by normal E coli in a “normal” petri dish environment. That would be pretty close to an Ernst Mayr definition of new species.

Do E. coli exchange DNA sequences amongst themselves? I know some bacteria do that, but I don’t know which ones or to what extent. If they did, they would even more closely resemble eukaryotic species.

By: Carl Zimmer

Carl Zimmer — Mon, 28 Aug 2006 02:49:22 +0000

djlactin: In each round of the experiment, the scientists sample bacteria, make copies of their promoter sequences and introduce mutations into those sequences through PCR mutategenesis. The mutation rate refers to the fraction of promoter sequences that mutate in this stage of the cycle.

By: djlactin

djlactin — Mon, 28 Aug 2006 01:09:38 +0000

just wondering how that mutation rate was determined/expressed? 18% of what? 18% substitution per codon per generation? 18%probability of 1 change per genome?…. need info here.

By: Natasha

Natasha — Sun, 27 Aug 2006 18:56:58 +0000

Just wondering if anyone else is reminded of the Luria-Delbruck fluctuation experiments. Hold a gun (Chloramphenicol) to a microbes head and its going to find a way to slip out from under it as soon as it can. If you have a very high selection pressure, things move quickly (and variably).

By: pdecell

pdecell — Sun, 27 Aug 2006 02:03:15 +0000

Stevie,

But of course the ID’ers really can’t rely on the excuse that the experiment happened under artificial conditions etc…after all, we don’t claim that there is really a difference say between natural and artificial electricity, do we? And since Dembsky’s ideas are supposedly mathematically based, they ought to apply equally to both natural and artificial situations!

By: Steviepinhead

Steviepinhead — Sat, 26 Aug 2006 22:50:49 +0000

But…but…but all those IDers keep telling us that no one’s ever seen evolution happening, or that only “microevolution” going back and forth between various pre-existing states can occur, that random mutation can’t produce new information, only dilute it…

Good thing for all those IDers that this experiment occurred under “artificial,” “model” conditions, or they’d be left with very little to continue misleading their incurious followers about.

By: Ian B Gibson

Ian B Gibson — Sat, 26 Aug 2006 16:01:56 +0000

It also lets us watch life defy the odds, day by day.

But life doesn’t really defy the odds, does it? I thought that we just have an intuitively poor understanding of the odds, which is why we are often surprised by certain things happening when we really shouldn’t be.

By: Michael Gray

Michael Gray — Sat, 26 Aug 2006 14:56:36 +0000

Very cool experiment. I wonder how long it would take and what sort of selection you’d need to evolve a regulator binding site. Maybe cyclic passages with and without chloramphenicol?

Pedantic aside from a molecular microbiologist: sigma factors aren’t enzymes…

By: Paul Decelles

Paul Decelles — Sat, 26 Aug 2006 03:15:07 +0000

Great find!

You mean random processes combined with deterministic processes can lead to new(at least for those artficial populations) information? Gee, I thought Dembsky said that wasn’t possible?