Why didn't LUCA go extinct?

[Dan_Eastwood]

@colewd

@nwrickert

It isn’t trying to find any specific sequence. It is just trying to find one that works pretty well.

This sequence Dawkins used was 1 tenth the length of an average vertebrate protein. Even if half the amino acids of vertebrates are substitutable for a given protein the sequence problem still exists.

Hi Bill,
Does this moving of the goalposts indicate that you agree RMNS is able to find functional sequence?

@colewd

The only model I know of that can find a sequence through trial and error uses the specified sequence as the target. I think you are underestimating the difficulty RMNS faces. I have yet to see any realistic model that supports your assertion.

That probability of IID randomly generating such a sequence is irrelevant in the presence of selection. The conservation of critical sequences is also expected under selection.

[CrisprCAS9]

How many mutations do you think we should expect to see and why?

[Rumraket (Mikkel R.)]

@colewd

the sequence problem still exists

There is no such problem.

[AndyWalsh]

@Dan_Eastwood

The models you have never seen are discussed at great length in this forum and others. No specified sequence is needed, only a criteria to evaluate function.

Since it won’t come up in that search, I will shamelessly link to my own contribution:

X-Men Constructive Neutral Evolution

Don’t know if this is what you had in mind, but this is what I’ve got for you. http://www.faithacrossthemultiverse.com/DangerRoom.html What are you looking at? I’ve simulated the X-Men Danger Room, where the X-Men train to learn how to work together as a team. They have to defeat all the Sentinels (robots firing blue lasers) using a sequence of actions encoded in an X-Gene. They practice over and over, making random changes to their X-Gene each time. In the upper left room, Cyclops (shoots red optic blasts) is training by himself. His starting X-Gene already encodes a full solution to this scenario, but Cyclops is a dedicated team leader and so he practices over and over to make sure he can repeat the process. A new X-Gene only replaces the old X-Gene if it is still a full solution. Over time, you may observe some drift in his X-Gene - there is some redundancy in the genetic code, and some phenotype changes are also neutral. In the upper right room, Cyclops is joined by three team…

You can try it for yourself here and inspect the source code if you want. There is no prespecified sequence, just scores for different outcomes. Multiple sequences can achieve the same outcome, with enough variation to form phylogenies.

If this example isn’t satisfactory @colewd I’d be happy to discuss modifications or improvements to address whatever questions or concerns you might have.

[misterme987 (Andrew P.)]

@colewd

the sequence problem still exists.

Déjà vu.

[Dan_Eastwood]

This is both cute and brilliant!