What is evolutionary theory?


(Bill Cole) #42

Thanks Neil
How do you work through almost infinite sequence space without a mechanism that very specifically moves from function to function. I have been studying eukaryotic cells fairly intensively for the last 3 years and there are no mechanisms that do anything but try to preserve sequences with the exception of the adaptive immune system that has substrates with 10 amino acids or less.

Shapiro and his group talk about natural genetic engineering where there is some trace of evidence but this is mostly in bacteria and plants and is simply and adaptive force. There is nothing here powerful enough for a dramatic speciation event.

Neil, what mechanism am I not seeing that carries the power of a real scientific claim?


(Timothy Horton) #43

Evolution didn’t have to search through almost infinite sequence space. Once the first imperfect self replicators got going evolution only had to search the sequence space immediately next to already functioning entities for small better functioning changes.

What’s that make, about the 10th or 11th time you’ve made the same argument now and ignored the explanation?


(Neil Rickert) #44

A biologist publishes a paper announcing a newly discovered species.

That is a dramatic speciation event.

If you are looking for a case where an organism reproduces, and the offspring are a different species from the parent – I doubt that this ever happens. Speciation doesn’t require that it happen that way.

Reality is full of fuzzy boundaries. It is part of human cognition – part of human categorization – to treat some of those fuzzy boundaries if they were sharp boundaries.


(Bill Cole) #45

Unless the speciation event was observed wouldn’t you call it an observation of a newly discovered specie?

The real challenge here is how a process that has mechanisms to minimize variation generates enough directed variation for an evolutionary event.

At the end of the day no one has identified a mechanism of directed variation during reproduction beyond what occurs during meiosis and mitosis.

I don’t think the current molecular evidence supports the theory. Maybe someday.


(Timothy Horton) #46

Sigh. Another episode of the long running series Willful Ignorance On Display.

Mechanisms of Speciation

You should have stopped after the first three words.


(John Harshman) #47

It isn’t clear what you mean by that.

More evidence that you don’t know what “speciation” means.

Is that evidence that you don’t know what “speciation” means? Please explain.

We’ve been over this. The mechanisms that minimize variation are proofreading and repair mechanisms. We see only the mutations that get past those. They’re included in the mutation rate. And directed variation isn’t necessary; you just made that part up.


(Neil Rickert) #48

Fair enough. But you wanted it to be a dramatic event, so I described it so as to emphasize the drama.

That already seems to be a misunderstanding.

I don’t see a mechanism to minimize variation. Rather, I see a mechanism to limit variation to what the population can bear, yet to maintain enough variation to allow the population to cope with change in the environemt.

And I do not see any need for such a mechanism.


(Neil Rickert) #49

@colewd wanted a dramatic event, so I described something that roughly fitted the “dramatic event” part. I don’t know where he got the idea that there should be “a dramatic speciation event”.


#50

Unless you show us what those facts are it is a bare assertion.

How would you describe the connection between you and your cousins?


#51

It would appear that you haven’t looked very hard. In this paper there is a gain in function in the mc1r gene of pocket mice which involves a change in DNA sequence.

Would you classify the genetic differences between humans and chmips as enough for a dramatic speciation event? If so, those are the mutations you are looking for.


#52

Let’s do the math. Each human is born with around 75 mutations. It’s been around 5 million years since the chimp and human lineages split. Let’s use a 25 year generation time and a constant population of just 100,000 in the human lineage.

100,000 people and 75 mutations each comes to 7.5 million mutations in each generation. With a generation time of 25 years there would have been 200,000 generations. Therefore, there would have been 1.5 trillion mutations that occurred in the human lineage.

Now let’s look at the chimp and human genomes. We are separated by 40 million mutations. Let’s say that half of those mutations happened in each lineage, so all we need is 20 million mutations to accumulate in the human lineage to produce the differences we see. There were 1.5 trillion mutations that did happen, so all that needed to happen is for about 0.00001% of those mutations to stick around.

Can you please tell us why this would be a challenge?


(John Mercer) #53

Random sequence space has plenty of function, as we can easily see from 32 years of catalytic antibodies (utterly ignored by the ID crowd), and evolutionary mechanisms do NOT specifically move from function to function.


(John Mercer) #54

I don’t think you’ve looked at the current molecular evidence, Bill, or even the old molecular evidence. Unless you have, it’s not ethical for you to be making claims that refer to evidence.


(Bill Cole) #55

There are less then 10^10 humans on earth. There are 10^1000000000 ways to arrange the human genome. If we take all the animals that have ever lived we have less than 10^50.

The fact is that the KNOWN limit of functional sequences is 10^50. Any number larger is speculation.

This is the problem evolution faces. How do you find function in this almost infinite sequence space through trial and error. Your calculations are not able to search a tiny piece of this space. Change will be minimized by biological mechanisms and purifying selection as evidenced of the lack of genome variation between humans.


#56

Meiosis does not randomly mix up the entire genome, so your model doesn’t apply.

Through random mutation of a limited number of bases, as already described.

Then you need to reread it, because it does. There were over 1 trillion mutations that would have happened in the human lineage, and we are only separated from chimps by 40 million mutations.

With a mutation rate of 75 mutations per person, a 6 billion base diploid genome, and 3 possible substitution mutations at each position it would only take 240 million births to produce every possible substitution mutation in the human genome.


(Neil Rickert) #57

No, this is not a problem that evolution faces.

Evolution is not playing the slots at Vegas.


(Bill Cole) #58

Do you realize this is a tiny fraction of the search space? Sampling individual mutations is very different then
-sampling the entire search space
-any of those mutations becoming fixed in the population


#59

You don’t need to cover the entire search space to evolve new species. Again, chimps and humans are separated by just 40 million mutations.


(Bill Cole) #60

Evolution is facing combinatorial mathematics as biological information is an organized sequence.


(Bill Cole) #61

Only if the mechanism is directed otherwise mutation will get you lost in the search space.