Great Video on the Extend Evolutionary Synthesis by Zack Hancock

[heymike3]

By the same token, what counts as fitness? Earlier T said fitness is the same as a function that is beneficial to the organism.

[heymike3]

@T_aquaticus

Why not just use fitness?

Probably because Noble is a physiologist. If beneficial function = fitness, why accuse him of strawmanning when he uses a different term that carries the same meaning?

[heymike3]

@T_aquaticus

“I think what we find emotionally or aesthetically more appealing is not the basis for science"–Douglas Futuyma

Sure, the question for me is whether the organism can change its DNA? That changes in DNA are not strictly random with respect to fitness (or physiological function).

[T_aquaticus]

@heymike3

If beneficial function = fitness, why accuse him of strawmanning when he uses a different term that carries the same meaning?

Because a loss of function can be beneficial. Fitness is modeled as an allele, not as a function. An allele can be a non-functional version of a gene. That would be one issue with what you are describing. You may want to check out the Price equation:

Price equation

Noble is also claiming his ideas “extend” the evolutionary synthesis. If all he is doing is renaming stuff we already have, is that an extension? If I renamed North America “New Taqland” could I claim I have discovered a new continent?

[T_aquaticus]

@heymike3

Sure, the question for me is whether the organism can change its DNA? That changes in DNA are not strictly random with respect to fitness (or physiological function).

I know of no evidence demonstrating non-random mutation with respect to fitness, and I haven’t seen Noble nor any EES supporter present any such evidence. In fact, that is one of the main points of the video in the opening post.

[heymike3]

@T_aquaticus

Because a loss of function can be beneficial.

I think function is with respect to the organism as a whole. How well does it function as an aggregate of its particular functions. Noble being a physiologist, it’s not a stretch to see function in that sense.

[T_aquaticus]

@heymike3

I think function is with respect to the organism as a whole. How well does it function as an aggregate of its particular functions. Noble being a physiologist, it’s not a stretch to see function in that sense.

How Noble “sees things” is immaterial to science. What matters is the data. If Noble wants to change or extend a scientific theory he needs evidence, not opinions. Enough with the rhetoric and semantics. Let’s see the science.

[heymike3]

Now that is some serious strawmanning. We are merely talking about terms. He gets to the evidence. Are you aware of the evidence he cites?

[T_aquaticus]

@heymike3

He gets to the evidence. Are you aware of the evidence he cites?

Yes.

Among the members of the audience was a biologist named David Shuker. After listening quietly for a day and a half, the University of St Andrews researcher had had enough. At the end of a talk, he shot up his hand.

The talk had been given by Denis Noble, a physiologist with a mop of white hair and a blue blazer. Noble, who has spent most of his career at Oxford, said he started out as a traditional biologist, seeing genes as the ultimate cause of everything in the body. But in recent years he had switched his thinking. He spoke of the genome not as a blueprint for life but as a sensitive organ, detecting stress and rearranging itself to cope with challenges. “I’ve been on a long journey to this view,” Noble said.

To illustrate this new view, Noble discussed an assortment of recent experiments. One of them was published last year by a team at the University of Reading. They did an experiment on bacteria that swim by spinning their long tails.

First, the scientists cut a gene out of the bacteria’s DNA that’s essential for building tails. The researchers then dropped these tailless bacteria into a petri dish with a meager supply of food. Before long, the bacteria ate all the food in their immediate surroundings. If they couldn’t move, they died. In less than four days in these dire conditions, the bacteria were swimming again. On close inspection, the team found they were growing new tails.

“This strategy is to produce rapid evolutionary genome change in response to the unfavorable environment,” Noble declared to the audience. “It’s a self-maintaining system that enables a particular characteristic to occur independent of the DNA.”

That didn’t sound right to Shuker, and he was determined to challenge Noble after the applause died down.

“Could you comment at all on the mechanism underlying that discovery?” Shuker asked.

Noble stammered in reply. “The mechanism in general terms, I can, yes…” he said, and then started talking about networks and regulation and a desperate search for a solution to a crisis. “You’d have to go back to the original paper,” he then said.

While Noble was struggling to respond, Shuker went back to the paper on an iPad. And now he read the abstract in a booming voice.

“‘Our results demonstrate that natural selection can rapidly rewire regulatory networks,’” Shuker said. He put down the iPad. “So it’s a perfect, beautiful example of rapid neo-Darwinian evolution,” he declared.
Scientists Seek to Update Evolution | Carl Zimmer

[heymike3]

What’s that mean?

I believe Noble cites a similar phenomenon with the cardiac rythm of the heart. But that’s not in the section of the book where he cites the evidence in support of his view. I’m currently rereading it now, but some major things may be sidetracking me over the next couple of days.

[T_aquaticus]

@heymike3

What’s that mean?

It means Noble takes someone else’s research describing standard evolutionary pathways and tries to change its meaning into something else.

@heymike3

I believe Noble cites a similar phenomenon with the cardiac rythm of the heart.

What does that have to do with mutations or natural selection?

@heymike3

But that’s not in the section of the book where he cites the evidence in support of his view. I’m currently rereading it now, but some major things may be sidetracking me over the next couple of days.

An analogy I would recommend you keep in mind. If someone wins the lottery, does it mean the lottery isn’t random? The answer is obviously no. If Noble’s argument boils down to “mutations aren’t random because beneficial mutations happen” then he doesn’t understand what he is talking about.

[heymike3]

@T_aquaticus

It means Noble takes someone else’s research describing standard evolutionary pathways and tries to change its meaning into something else.

Standard evolutionary pathways is a merely a term. How did the bacteria regrow the tale once the DNA responsible for the tale was removed?

[glipsnort (Steve Schaffner)]

@heymike3

By the same token, what counts as fitness?

Fitness is determined by the expected number of offspring (with a bunch of nuance that needs to be added). The point is, it’s an objective, numerical value that you can estimate through experiment or observation. It’s also the thing that directly affects evolution, that is, the change in the genetic makeup of the population over time.

[heymike3]

@glipsnort

Fitness is determined by the expected number of offspring

I looked it up now and see it is based on survival and reproduction

[glipsnort (Steve Schaffner)]

@heymike3

I looked it up now and see it is based on survival and reproduction

Exactly.
[filler]

[heymike3]

I don’t see anything Noble would disagree with once we set aside his use of physiological function in place of fitness

[heymike3]

@T_aquaticus

What does that have to do with mutations or natural selection?

I believe it has to do with how the physiological system can reproduce the behavior apart from the chemistry responsible for the behavior, which seems to be the point he is making with bacteria regrowing a tail without the DNA responsible for the tail.

[heymike3]

@T_aquaticus

If Noble’s argument boils down to “mutations aren’t random because beneficial mutations happen” then he doesn’t understand what he is talking about.

You should read Noble for yourself…

Either way, I am very interested in an explanation of how the bacteria regrew a tail once the DNA responsible for the tail was removed.

[paleomalacologist (David Campbell)]

“…whether the organism can change its DNA? That changes in DNA are not strictly random with respect to fitness (or physiological function).”

Organisms can have mechanisms that promote changes in DNA. Unsurprisingly, such ability is highly nonrandom with regard to fitness and physiological function - promoting change in the DNA is advantageous if having something new would often be helpful and not when what it has works well. Different parts of the genome have higher or lower mutation rates, as do different organisms.

But, as far as we can tell, the changes themselves are random with regard to fitness and function. Bacteria cannot say “Those sneaky scientists mutated my gene; I need to get a G at location 32586 to modify another protein to cover the job of the one they deleted.” If all the bacteria are having problems, there’s less competition, and an individual with a higher mutation rate may have an advantage of being more likely to change to something functional. Or it may just be that, with huge population size and fast generation, a few individuals happened to have a mutation that was useful. But for every bacterium that had the right mutation to be successful under the particular conditions, we would expect to also have some with other, non-useful mutations.

Curiously, the Discovery Institute tried to downplay the study rather than promoting it as an example of “non-Darwinian” evolution - “Evolution News” has a piece by Behe dismissing the change as minor.

Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system - White Rose Research Online should give free access to the paper on re-enabled flagellar function.

[glipsnort (Steve Schaffner)]

@heymike3

Either way, I am very interested in an explanation of how the bacteria regrew a tail once the DNA responsible for the tail was removed.

Have you looked at the paper in question? The DNA for the flagellar proteins was still intact. It was just one regulatory gene that was knocked out, and that could be replaced by a mutated version of a different gene. Nothing here looks like anything other than Darwinian evolution at work.