SFT, TMR4A, and Created Heterozygosity

[SFT]

@John_Harshman

It’s the recombination rate that’s the obvious problem

Read my responses carefully.

[evograd (Blogging Graduate Student)]

@SFT

You seem to be forgetting my answers to this: gene conversion helps break up the alleles fairly quickly.

What TMR4A shows is that you would need to invoke rates of recombination, mutation, gene conversion, far in excess of what we observe today in order to generate the required diversity in just a few thousand years. At current rates, ~500,000 years is required. That’s the point. if you have all these densely packed heterozygous sites then you need a lot of fine-scale (intragenic) recombination you break them and and produce new alleles from the created heterozygosity. This isn’t what we observe in modern populations.

@SFT

Also, Evograd, I did an entire video addressing your arguments on the Y chromosome specifically pertaining to the papers you say Dr. Jeanson ignored (Balanovsky and Scally?). I also reiterated the questions and challenges in the comment sections for sake of you not having to watch the entire videos.

Start a new topic if you want to discuss that.

[T.j_Runyon]

@SFT

I challenged you to refute my “Refuting Critics” book that addresses all of these typical arguments

You did?

@SFT

I challenged you to refute my “Refuting Critics” book that addresses all of these typical arguments. Heck, if you email me, I will even send you a free PDF! And that goes for anybody here who thinks they can refute it. It definitely beats me having to spend hours a day in blog wars. Comment on my channel and I will give you me email IF you are willing to take up the challenge.

I don’t do YouTube, but I’d definitely love a copy of the book. I don’t care enough about this debate to dedicate some thorough review of it (I’m also a paleontologist so this is somewhat out of my comfort zone) . Everyone accepts evolution and everyone accepts common ancestry. On all sides. The disagreements are how much can known evolutionary processes can accomplish, is the common ancestry separate or universal and over what timescales. That’s not enough of a disagreement for me to care that much. But I’d be more than willing to read your book If you’d provide it.

[SFT]

@swamidass

I think the poor guy is confused.

I have explained everything very thoroughly in my “walls of text”. You seem to be incapable of reading through them in order to engaged in honest discussion. I do see why experts such as Jeanson Sanford and Carter would never bother with these blogs. I am quickly seeing why they are a waste of time. Like I said, I am going to enjoy analyzing this on my channel. I am still awaiting excitedly for some kind of response to my refutations in regards to the critics (evograd, Dan, etc…) misrepresentations of Jeanson’s Y chromosome papers.

[evograd (Blogging Graduate Student)]

@SFT

I want to add that if we are defining alleles the correct way, then MANY, MANY alleles can arise from a created heterozygosity model.

Define “allele” for us the “correct” way then. Be as specific and detailed as possible.

[SFT]

@evograd

Define “allele” for us the “correct” way then. Be as specific and detailed as possible.

Unbelievable. I have at least 3 times alone in this thread. I am done here.

Good talk guys.

Much like the previous thread I engaged in, I am yet again very enlightened.

[Mr_Wilford]

@SFT

I am yet again very enlightened.

I think everyone is.

[SFT]

@evograd

What TMR4A shows is that you would need to invoke rates of recombination, mutation, gene conversion, far in excess of what we observe today in order to generate the required diversity in just a few thousand years. At current rates, ~500,000 years is required. That’s the point. if you have all these densely packed heterozygous sites then you need a lot of fine-scale (intragenic) recombination you break them and and produce new alleles from the created heterozygosity. This isn’t what we observe in modern populations.

Exactly what my latest video addresses as well as my comments here in this thread. And yet Swamidass accuses me of not understanding. This is a dishonest tactic and turns me off from participating in these discussions. In all fairness, it seemed like you did indeed understand what I was saying. Scroll up and look for my definition of alleles and you will see that I have answered this thoroughly. Dan even responded to my definition of alleles quite thoroughly in his most recent video.

[swamidass (S. Joshua Swamidass)]

@SFT

And yet Swamidass accuses me of not understanding. This is a dishonest tactic

Is it dishonest when you accuse us of misunderstanding?

[T.j_Runyon]

@evograd

Define “allele” for us the “correct” way then. Be as specific and detailed as possible.

One of two or more versions of a particular DNA position”

It was buried DEEP in a wall of text

[evograd (Blogging Graduate Student)]

@SFT

Unbelievable. I have at least 3 times alone in this thread.

You gave this definition (Frello’s definition that Jeanson approved of):

@SFT

“One of two or more versions of a particular DNA position”

But then later said:

@SFT

Only when alleles are defined as single nucleotides does the maximum “4 limit exist”

A particular DNA position = a single nucleotide, so you seem to be contradicting yourself. That’s why I’m asking for clarification.

[evograd (Blogging Graduate Student)]

@SFT

I am still awaiting excitedly for some kind of response to my refutations in regards to the critics (evograd, Dan, etc…) misrepresentations of Jeanson’s Y chromosome papers.

Make a thread about it here then, and I promise that I (and maybe even others) will respond. This forum is a far better place to have these kinds of discussions than the comments section of a YouTube video that no one else will ever read.

It’s simply not worth my time to write detailed responses if only you will read them, I’d prefer to do it much more publicly. You should want the same thing, so I suggest again - make a thread here about it.

[Rumraket (Mikkel R.)]

@evograd

A particular DNA position = a single nucleotide, so you seem to be contradicting yourself. That’s why I’m asking for clarification.

I have to second this. Can’t make sense of his given definition.

[Mr_Wilford]

@evograd

You should want the same thing, so I suggest again - make a thread here about it.

As I said earlier, I’d be happy to start a discussion if he isn’t. This time I could probably be more helpful by sitting down and summarizing his video, so there’s something to bite. Anyone interested?

[dsterncardinale]

I’m going to be the one to point out that having this conversation with someone who lacks a basic understanding of the relevant concepts is going to be challenging and confusing for the other participants.

[swamidass (S. Joshua Swamidass)]

I agree. I think explaining the concepts that are correct, clearly to people, is better than a detailed back and forth. Right now there is a gap. We haven’t really explained a lot of this in away that makes sense to most people.

[Timothy_Horton]

@dsterncardinale

I’m going to be the one to point out that having this conversation with someone who lacks a basic understanding of the relevant concepts is going to be challenging and confusing for the other participants.

Especially when the one who lacks the basic understanding has already made a strong commitment to not understanding and to remaining scientifically unaware.

[evograd (Blogging Graduate Student)]

I think explaining the concept of how TMR4A interacts with created heterozygosity graphically would be helpful. A diagram showing Adam and Eve with some created heterozygosity, how genomes change over generations in their offspring, and how the algorithms used in TMR4A reconstruct this history would be very valuable.

I also wonder if it might be helpful to show TMR4A working on simulated data. You could simulate 2 genomes with created heterozygosity, have the population grow and genomes recombine for a given period of time, then show that your method is accurate. This is standard practice in developing new popgen tools, after all.

[swamidass (S. Joshua Swamidass)]

Yes we have some unpublished data on this. I wonder if @GutsickGibbon might want to do a video on it too .

[evograd (Blogging Graduate Student)]

Any idea when/where you’ll publish on this?