Clade

[juvenissun]

We rarely look at changes in a family across generations. Occasionally we'll look at changes within a population over a few generation, usually in organisms with short reproductive times like viruses or malaria.

What we do is look at genetic differences between individuals. For what I do, it's usually individuals within a single species; for others, it's individuals in different species. In either case, we use common descent for all sorts of things, as I already noted.

Now, could you please tell me why the practical uses I have for the idea of common descent don't exist?

You used the term with the same problem as using the term evolution. Evolution to you could happen in one hour or in one minute. In that sense, it has no problem. However, I do NOT take this process as an "evolution" change. It is simply a change.

The cladistics is NOT made for genetic study, but is made for biology/paleontology study. The change of species does not take place in days or anytime shorter than a few decades. Your use of the term evolution is not the same as it is used in non-genetic study. You borrowed the cladistics for genetics does not mean the genetic study verifies the common ancestor idea embedded in cladistics.

So, you said the common ancestry idea is practical and is used in your study. In fact, you only borrow the term and apply it to the change of an entirely different time scale. And this is NOT an example for the practical use of the idea.

 

[juvenissun]

It is really efficient to use DNA evidence to trace a genetic trait. Especially ones that aren't obviously expressed.

That has nothing to do with biological evolution, and has nothing to do with the idea of common descendant.

 

[sfs]

So, you said the common ancestry idea is practical and is used in your study. In fact, you only borrow the term and apply it to the change of an entirely different time scale. And this is NOT an example for the practical use of the idea.

Your response has no connection to reality. There's only one concept of common descent: different species share a common ancestor. That's the concept we use, and which is of great practical importance. Humans share a common ancestor with chimpanzees, and before that with gorillas, and before that with monkeys and on back through the tree of life.

I have used chimpanzee sequence to tell me which human genetic variant is ancestral. I have used the differences between humans and chimpanzees to tell me what the local mutation rate is in a section of the genome. How could I be doing that without using the ordinary meaning of common descent?

So please try again: why don't the uses I've listed for the concept of common descent exist?

 

[PsychoSarah]

That has nothing to do with biological evolution, and has nothing to do with the idea of common descendant.

It has everything to do with biological evolution and common descent! DNA mutation is the mechanism by which evolution occurs (well, one of them, anyways) and by which we can confirm common ancestry!

 

[juvenissun]

Your response has no connection to reality. There's only one concept of common descent: different species share a common ancestor. That's the concept we use, and which is of great practical importance. Humans share a common ancestor with chimpanzees, and before that with gorillas, and before that with monkeys and on back through the tree of life.

I have used chimpanzee sequence to tell me which human genetic variant is ancestral. I have used the differences between humans and chimpanzees to tell me what the local mutation rate is in a section of the genome. How could I be doing that without using the ordinary meaning of common descent?

So please try again: why don't the uses I've listed for the concept of common descent exist?

Hmm... Very good. You get to the meat of it. And I have to think about it.

 

[juvenissun]

Your response has no connection to reality. There's only one concept of common descent: different species share a common ancestor. That's the concept we use, and which is of great practical importance. Humans share a common ancestor with chimpanzees, and before that with gorillas, and before that with monkeys and on back through the tree of life.

I have used chimpanzee sequence to tell me which human genetic variant is ancestral. I have used the differences between humans and chimpanzees to tell me what the local mutation rate is in a section of the genome. How could I be doing that without using the ordinary meaning of common descent?

So please try again: why don't the uses I've listed for the concept of common descent exist?

By that quote, are you saying:

1. You check the chimp sequence.
2. You try to match human sequence with chimp sequence.
3. If they matched, then you said: that particular chimp sequence is the ancestral sequence of the human sequence.

If that is the case, I do not see any use on the conclusion of item 3. You could perfectly save that, and simply use the FACTS found in items 1 and 2. for a particular purpose.

What is the use of implication in item 3 except it supports the idea of evolution?

 

[juvenissun]

Your response has no connection to reality. There's only one concept of common descent: different species share a common ancestor. That's the concept we use, and which is of great practical importance. Humans share a common ancestor with chimpanzees, and before that with gorillas, and before that with monkeys and on back through the tree of life.

I have used chimpanzee sequence to tell me which human genetic variant is ancestral. I have used the differences between humans and chimpanzees to tell me what the local mutation rate is in a section of the genome. How could I be doing that without using the ordinary meaning of common descent?

So please try again: why don't the uses I've listed for the concept of common descent exist?

For the above quote:

1. You select a particular section of chimp genome
2. You select a "correspondant" section of human genome
3. You compare the difference between item 1 and item 2
4. You assume a period of time, during which item 1 changed to item 2.
5. you calculate the rate of the change.

Am I right on that?

I am not quite sure about this one. I will raise my question once you confirmed that the steps and the works are correct.

 

[Subduction Zone]

By that quote, are you saying:

1. You check the chimp sequence.

Correct.

2. You try to match human sequence with chimp sequence.

Correct again.

3. If they matched, then you said: that particular chimp sequence is the ancestral sequence of the human sequence.

Correct again.

If that is the case, I do not see any use on the conclusion of item 3. You could perfectly save that, and simply use the FACTS found in items 1 and 2. for a particular purpose.

What is the use of implication in item 3 except it supports the idea of evolution?

Evolution has already been proven by many many other methods. The amount of DNA that matches alone is all but proof positive for evolution. We are long past the days of needing to prove evolution. What we are doing now is seeing exactly how we are related to other creatures. That is the purpose of this exercise.

 

[sfs]

By that quote, are you saying:

1. You check the chimp sequence.
2. You try to match human sequence with chimp sequence.
3. If they matched, then you said: that particular chimp sequence is the ancestral sequence of the human sequence.

If that is the case, I do not see any use on the conclusion of item 3. You could perfectly save that, and simply use the FACTS found in items 1 and 2. for a particular purpose.

Great. How do I use those facts? Why should I think the human sequence was ever the same as the chimp sequence? And why would I even be looking at the chimp sequence in the first place, if I hadn't started with the knowledge that they share a common ancestor?

 

[sfs]

For the above quote:

1. You select a particular section of chimp genome
2. You select a "correspondant" section of human genome
3. You compare the difference between item 1 and item 2
4. You assume a period of time, during which item 1 changed to item 2.
5. you calculate the rate of the change.

Am I right on that?

Yes, that's right. That tells me what the mutation rate is in this region of the genome.

 

[juvenissun]

Yes, that's right. That tells me what the mutation rate is in this region of the genome.

OK, before I ask details of the process, let me ask this:

How do you USE this calculated rate in a practical sense?

 

[sfs]

OK, before I ask details of the process, let me ask this:

How do you USE this calculated rate in a practical sense?

I'd use it to see if human genetic diversity was unusually low in a region of the genome. If diversity is low because the mutation rate is low, that's not interesting. If the mutation rate is high, low diversity suggests that natural selection has had an impact on that region.

 

[juvenissun]

I'd use it to see if human genetic diversity was unusually low in a region of the genome. If diversity is low because the mutation rate is low, that's not interesting. If the mutation rate is high, low diversity suggests that natural selection has had an impact on that region.

I believe you are (or your group is) not the only one who is doing this kind of study. Is there a good example on this nature of study which strongly suggested such an impact of natural selection? Has there been a case that such a process of natural selection was identified by the genome comparison and rate calculation?

 

[sfs]

I believe you are (or your group is) not the only one who is doing this kind of study. Is there a good example on this nature of study which strongly suggested such an impact of natural selection? Has there been a case that such a process of natural selection was identified by the genome comparison and rate calculation?

I've seen this correction for mutation rate used in a number of publications, e.g. Mike Zody used it in the chimpanzee genome paper to identify probable regions of positive selection in humans.

We also used the human-chimpanzee divergence estimate of local mutation rates for a different purpose in this paper, which provided the first evidence for wide-spread large variation in recombination rate in humans.

So far you haven't answered my question: why aren't this practical uses of the concept of common descent?

 

[juvenissun]

I've seen this correction for mutation rate used in a number of publications, e.g. Mike Zody used it in the chimpanzee genome paper to identify probable regions of positive selection in humans.

We also used the human-chimpanzee divergence estimate of local mutation rates for a different purpose in this paper, which provided the first evidence for wide-spread large variation in recombination rate in humans.

So far you haven't answered my question: why aren't this practical uses of the concept of common descent?

I do not understand the specifics. So I can not evaluate if it practical or not. I am trying to find out:

May I learn the the following:
1. How to identify the positive selection in humans (by the mutation rate)?
2. What is the positive selection in that particular study?

In order to see if the study has any practical value, I need to know the practical implication. I am not going to read the papers. If you could not (or would not) make an simple explanation which I can understand, then you can simply stop. But the question in my OP is not answered either.

 

[juvenissun]

I've seen this correction for mutation rate used in a number of publications, e.g. Mike Zody used it in the chimpanzee genome paper to identify probable regions of positive selection in humans.

We also used the human-chimpanzee divergence estimate of local mutation rates for a different purpose in this paper, which provided the first evidence for wide-spread large variation in recombination rate in humans.

So far you haven't answered my question: why aren't this practical uses of the concept of common descent?

How is the recombination rate related to the local mutation rate?

(Sorry, I am actually testing your ability of teaching. If you can not teach me, then there is probably few you can teach)

 

[Mr Strawberry]

(Sorry, I am actually testing your ability of teaching. If you can not teach me, then there is probably few you can teach)

Lol. Breathtaking.

 

[PsychoSarah]

How is the recombination rate related to the local mutation rate?

(Sorry, I am actually testing your ability of teaching. If you can not teach me, then there is probably few you can teach)

Teaching requires an able instructor and a willing student.

 

[sfs]

How is the recombination rate related to the local mutation rate?

It's a somewhat subtle analysis. The best description of it is in the paper itself, which you can read here. We worked quite hard on making the paper clear, going through more than 100 drafts. I'll be happy to answer questions about it.

(Sorry, I am actually testing your ability of teaching. If you can not teach me, then there is probably few you can teach)

Many people have read and understood the paper.

 

[Loudmouth]

I do not understand the specifics. So I can not evaluate if it practical or not.

And yet you have no problem telling experts in the field that there is no practical use of common ancestry and evolution, even though you don't even understand the research they are doing.

The word "hubris" comes to mind.

In order to see if the study has any practical value, I need to know the practical implication. I am not going to read the papers. If you could not (or would not) make an simple explanation which I can understand, then you can simply stop. But the question in my OP is not answered either.

You want to know how it works, but you refuse to be told how it works, and you also refuse to learn on your own.

You can lead a horse to water . . .