Jonathan Bartlett: Measuring Active Information in Biological Systems

[swamidass (S. Joshua Swamidass)]

@johnnyb

@Dan_Eastwood -

I think you are still thinking of the paper in the same way that Swamidass started out thinking.

To be clear, I have not stopped thinking this is what you are doing.

@johnnyb

This is a complete misunderstanding of what I am doing. I am not testing whether or not mutations follow a uniform probability. I am testing whether or not mutations, as they occur in nature, are more successful or less successful (or even) than they would be if they did follow a uniform probability.

Yes, that is what I thought from the beginning. Our point is that this doesn’t make much sense.

@johnnyb

When someone says that “mutation is random with respect to function”, they are saying (or at least most people are understanding) that the outcome of the mutation is no more or less functional than any other arbitrary transformation on the genome.

I’ve already granted you that mutations are not independent of function. They are skewed to functional mutations that are beneficial in important ways. That is true, but we don’t know that from your work and analysis.

They are still random, in that we cannot fully predict the mutations we will see. That’s why the whole “random with respect to” is a very poor way to put this.

@johnnyb

Anyway, this has been fun, and I appreciate everyone’s thoughtful contributions. Unless anyone has specific questions for me, I’m happy to leave y’all with the last word.

Thanks for joining the conversation. I do have some specific questions.

Do you understand why the focused issues I just raised here are a deal breaker for us? Do you still think your argument is valid?