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Author Topic:   Hello, cousin! (re: Recent common ancestors to all living humans)
randman 
Suspended Member (Idle past 4898 days)
Posts: 6367
Joined: 05-26-2005


Message 46 of 76 (330168)
07-09-2006 10:13 PM
Reply to: Message 45 by Wounded King
07-09-2006 6:42 PM


Re: Noah?
So you say, but you have no real evidence it isn't Noah, and the facts appear to fit the time-frame of Noah quite well.

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nwr
Member
Posts: 6408
From: Geneva, Illinois
Joined: 08-08-2005
Member Rating: 5.1


Message 47 of 76 (330184)
07-09-2006 11:19 PM
Reply to: Message 46 by randman
07-09-2006 10:13 PM


Re: Noah?
..., but you have no real evidence it isn't Noah, ...
If you would read the paper, or even read the rest of this thread, you might recognize that the paper being discussed has nothing to do with the idea that all descended from Noah, and it provides no evidence whatsoever to support such a view.

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RAZD
Member (Idle past 1404 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 48 of 76 (330193)
07-10-2006 12:03 AM
Reply to: Message 42 by nwr
07-09-2006 2:39 PM


Re: How many generations?
The set of MRCAs might not constitute a population, but instead are scattered among many populations. The term "population" is imprecise enough that I am not convinced MRCP is meaningful. The ancestor relation, on the other hand, is precisely defined so that MRCA is well defined (even if unimportant).
An MCRA does not function without being in a population.
Only for people who misunderstand what this paper is describing. Admittedly, that might be most readers.
It's a letter to Nature, not a peer reviewed paper in the journal.
I'm talking about what the term is used for, whether it is in this document or other. If this document is making a special usage of a previously defined term that is not in compliance with that definition then there may be an additional problem with the document version.
If the term promotes misunderstanding then it is a bad term and should be replaced.
You are still discussing this as if the paper were about genetics. It isn't.
Well I thought that section was about the genealogy of the human family tree - what exactyly about this statement:
Talking about a {most recent common ancestor population} on the other hand is a much more realistic an image - and no, that population does not all have to be descendent from a single person or pair of individuals, they are descendent from their MCRP. The Homo sapiens in Ethiopia did not propogate from a singe individual Homo heidelbergensis but from a population of them. The Homo heidelbergensis did not propogate from a singe individual Homo ergaster but from a population of them. Etc. How big that population was we don't know.
Says genetics to you instead of genealogy?
If we are talking about genetic ancestors, we should be concerned about how much of our DNA was derived from a particular ancestor. But that genetic inheritance was never a concern of the paper. It was concerned only about the ancestral relation. Once again, it isn't about genetics, it is only about the combinatorial relationship of ancestry.
ge·ne·al·o·gy n. pl. ge·ne·al·o·gies
1. A record or table of the descent of a person, family, or group from an ancestor or ancestors; a family tree.
2. Direct descent from an ancestor; lineage or pedigree.
It seems to me that genetics is an inseperable part of the package of descent from biological parents.
Are we or are we not talking about the sexual reproduction of children from parents, and who inherit genes from them in the process? Why do we need to know how much of which from who to know that they are genetic ancestors as well as genealogical? Perhaps your usage of genetic is more restrictive than mine -- I don't need to quantify beyond "some" -- am I missing something?
I notice the Wikipedia article on "Mitochondrial Eve" uses genealogy to explain the genetics ...
Imagine a family tree of all humans living today. Now imagine a line from each individual to their mother, and continue those lines from each of those mothers to their mothers, and so on.
If I'm confused by some subtle difference I don't appear to be the only one.
In my estimation, you are one of those promulgating false information by virtue of your repeated treatment of the paper as if it were about genetics.
My argument is based on the genealogy given the diagrams and discussion to date, so if you have a problem with my using "genetics" loosly in this context then change it -- I don't see a big distinction unless you replace biological parents with adoptive parents.
Regardless of what you call it the model still does not model reality. That's the issue.
The appropriate response of a biologist to this paper should be
Ho hum!
In any case, this paper is mostly a curiosity of little or no importance to biology.
Is it any different than creationist nonsense?
In this case, the model involves the ancestral relationship, and this is pretty much straight out of biology. If you think there is a problem there, it isn't in the math. The model also involves assumption about the mixing of different populations, and I expect that is over-simplified and not completely realistic.
I have a problem with the assumption of random mating when mating, especially in human society is both currently and historically anything but random. Not only are there social traditions and taboos in effect but there is only so much population available at any one time, most especially when you have isolated populations.
I have a real problem with sketchy theoretical considerations being presented as proven truth and with it being promulgated in other discussions as if it were fact. They adjusted the model to go from 800 years to 5000 years -- how do we know that this is any more valid than the 800 number? What would another 'adjustment' end up at -- 30,000 years? How would we know if THAT was valid?

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RAZD
Member (Idle past 1404 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 49 of 76 (330194)
07-10-2006 12:04 AM
Reply to: Message 46 by randman
07-09-2006 10:13 PM


Re: Noah?
... and the facts appear to fit ...
What facts?

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randman 
Suspended Member (Idle past 4898 days)
Posts: 6367
Joined: 05-26-2005


Message 50 of 76 (330196)
07-10-2006 12:07 AM
Reply to: Message 49 by RAZD
07-10-2006 12:04 AM


Re: Noah?
the timing

This message is a reply to:
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RAZD
Member (Idle past 1404 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 51 of 76 (330198)
07-10-2006 12:10 AM
Reply to: Message 44 by sfs
07-09-2006 5:07 PM


Re: Got the paper, but ...
No, there is nothing wrong with your calculation. If humans had had a panmictic population of size 1 million for their entire history, the most recent common ancestor in the maternal line would have occurred something like 1 million generations ago(*).
In other words the letter throws out figures without adjusting them for population nor mentioning that such should be done, meanwhile claiming to have solid proof of a theoretical result?
(*) There is one mistake, in fact, but it's not yours: the expected time to the MRCA for purely maternal inheritance is N/2 generations, not N generation. (Also, 20-25 years is a more realistic generation time for most of this period than 30 years.)
I had wondered about that with the result I had for my theoretical populations of 10 couples. Thanks.
On your other points, read nwr's responses. He or she understands the paper, and so far you don't.
Thanks for the kind comment. So far I don't see anything WORTH understanding, it's a flawed model.

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RAZD
Member (Idle past 1404 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 52 of 76 (330200)
07-10-2006 12:14 AM
Reply to: Message 50 by randman
07-10-2006 12:07 AM


Re: Noah?
the timing
That's not a fact.
That is a theoretical result from a model based on a bunch of erroneous assumptions.
Of course, if you accept it as factual, then it also means that Noah was living in Asia after his world cruise.
Enjoy.

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pink sasquatch
Member (Idle past 6022 days)
Posts: 1567
Joined: 06-10-2004


Message 53 of 76 (330453)
07-10-2006 2:45 PM
Reply to: Message 41 by RAZD
07-09-2006 1:36 PM


incorrect ideas about peer-review and ancestry
None of the math is in the {document\letter} -- we should also note that this is NOT a {presented peer reviewed paper} but a LETTER to the journal, and that there are different standards for peer review for letters compared to papers.
You are absolutely off the mark here. The "Letter" is the standard "paper" format for Nature, and the vast majority of Nature papers are "Letters". "Letter" simply describes the length and format, and "Letters" undergo rigorous peer-review identical to "Article" submissions. The current issue of Nature has thirteen Letters and only one Article.
If we are talking geneological ancestors we are talking genetic ancestors by definition of ancestor.
You seem to be stuck on a simple point here - you have genealogical ancestors whose genomes have contributed absolutely zero to your genome. It isn't a simple halving of a genome at each step.
You inherit 50% of your genome (in a simple sense) from your mother and 50% from your father. When you go back to grandparents however, you don't inherit 25% of your genome from each grandparent, due to variability in recombination and chromosome segregation. Potentially (though very improbably), one of your grandparents may have contributed zero to your genome.
In other words, it's possible 50% of your genome came from your mom's mom, and thus 0% from your mom's dad. However, your grandfather is still your genealogical ancestor.
Get it? Genealogical ancestry is not equivalent to genetic ancestry.

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sfs
Member (Idle past 2533 days)
Posts: 464
From: Cambridge, MA USA
Joined: 08-27-2003


Message 54 of 76 (330642)
07-10-2006 9:53 PM
Reply to: Message 53 by pink sasquatch
07-10-2006 2:45 PM


Re: incorrect ideas about peer-review and ancestry
quote:
Get it? Genealogical ancestry is not equivalent to genetic ancestry.
One way of thinking about it is that your genealogical ancestors are the set of people from whom it is possible for you to have inherited genetic material.

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sfs
Member (Idle past 2533 days)
Posts: 464
From: Cambridge, MA USA
Joined: 08-27-2003


Message 55 of 76 (330644)
07-10-2006 10:05 PM
Reply to: Message 51 by RAZD
07-10-2006 12:10 AM


Re: Got the paper, but ...
quote:
In other words the letter throws out figures without adjusting them for population nor mentioning that such should be done, meanwhile claiming to have solid proof of a theoretical result?
The paper is here using the example of a simple model to explain the conceptual difference between Mitochondrial Eve and the MRCA they're talking about. The simple model has nothing to do with their theoretical results.
quote:
Thanks for the kind comment. So far I don't see anything WORTH understanding, it's a flawed model.
My comment was not intended to be unkind. In science there is no point in pretending to understand something when one doesn't, and it is important to know what one understands and what one doesn't. (If you want a list of things I don't understand, I could supply one, but it will be lengthy, and only a small sample.) Since you don't understand it (or didn't when you were writing), you aren't able to judge the flaws in the paper.
I don't think the paper has obvious major flaws, since its main result is likely to be quite robust under a wide range of models. I just don't think it's very interesting. Genealogical relationships without consideration of genetics have little biological relevance, although I suppose they might be useful for encouraging everyone to join hands and sing Kum Bah Ya or something.

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RAZD
Member (Idle past 1404 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 56 of 76 (330666)
07-10-2006 11:15 PM
Reply to: Message 53 by pink sasquatch
07-10-2006 2:45 PM


I stand corrected - now lets deal with the math problem ...
The "Letter" is the standard "paper" format for Nature, and the vast majority of Nature papers are "Letters". "Letter" simply describes the length and format, and "Letters" undergo rigorous peer-review identical to "Article" submissions.
I didn't know that. I stand corrected.
You seem to be stuck on a simple point here - you have genealogical ancestors whose genomes have contributed absolutely zero to your genome. It isn't a simple halving of a genome at each step.
You inherit 50% of your genome (in a simple sense) from your mother and 50% from your father. When you go back to grandparents however, you don't inherit 25% of your genome from each grandparent, due to variability in recombination and chromosome segregation. Potentially (though very improbably), one of your grandparents may have contributed zero to your genome.
I figured that out from nwr's posts since last go round. The irony (to me) is that now we are talking about someone who was (potentially) totally insignificant to most people alive today then eh?
This becomes no more significant than having "six degrees of separation" between all living individuals. Whoopie: my dad shook hands with Nixon (reluctantly) so that leaves me connected to how many people?

Now perhaps we can get back to the maths issue ...
I still have a LOT of trouble with treating (any) mathematical model like this as anything more than a faint possiblity at best. It may help define limits within which reality acts, at best, and is totally dependent on getting all the input factors correct to end up with the correct results. My hackles are also raised when they use terminology like "would have lived" when they can really only mean "could at a minimum have lived" at best, and thus give a false sense of {truth\validity} to what is at best a very hypothetical and untested result.
This model assumes a random mating of individuals - mating is not random with males and females mating at every chance meeting (and even if they did there would be regional selection due to distance between populations). There is structure in reproductive behavior. They go from 600 years ago for a purely random result based on 1 million people (why one million?) to 5000 years by applying "more realistic" factors ... how do we know it shouldn't be 30,000 years ago? The upper limit would logically be the younger of the {matrilineal\patrilinial} ancestor (here the 60,000 to 90,000 years ago of yDNA Adam)
They apply "structure" by dividing the world up:
... consider a population of size n divided into randomly mating subpopulations that are linked by occasional migrants.
Whoops, they still use random mating within each sub-population?
They then get involved in modeling hypothetical migration numbers and percentages ... and conclude:
Arguably, this simulation is far too conservative, especially given its prediction that, even in densely populated Eurasia, only 55.3 people will leave each country per generation in AD 1500. If the migration rate among towns is increased to 20%, the local port users are reduced to 80%, and the migration rates between countries and continents are scaled up by factors of 5 and 10, respectively, the mean MRCA date is as recent as AD 55 and the mean IA date is 2,158 BC.
The biggest hole in this is using random mating in the subpopulations. Judging by what we know from history, traditions and anthropological evidence it seems to me that the smaller the population gets the more it would be modeled by a completely structured pattern of mating behavior than a random one - that random would best apply to the chance interaction between structured sub-populations.
Now consider that social conventions and taboos act as a control on random mating to a certain level. If nothing else, a basic human pattern is for sexually active individuals to have several children with the same mate. Every additional child by the same parents cuts severely into the random equation. If we assume a minimum structured mating pattern holds over a 2 generation period then the MCRA 'advances' n/2=2/2=1 generation during those 2 generation periods.
How does this affect the overal calculation? It would make the time period develop like n/2 half the time and like log2n half the time.
It seems to me that log2n is a more logical lower limit and that n/2 (for a purely structured population that matches matrilineal\patrilinial ancestry) is an upper limit: 5,000 to 90,000 years ... that's a pretty big range.
If I take half of one and half of the other (to simulate the effect of structure over two generations per above) I get 47,500 years.
It almost appears that they stopped evaluating the results when they got the 5000 year figure. That's not a good feeling.

migration rates and patterns ...
The model uses a simplified migration system in which each person has a single opportunity to migrate from his or her town of birth. The probabilities of leaving a town or a country are set at various levels to reflect different migration patterns.
It seems from the letter that the only real attempts to input historical data is by setting date limits at certain bottlnecks and in introducing population loss due to disease introduction post columbus. They do say that:
Actual migration rates among populations are very poorly known and undoubtedly have varied considerably in different times and places.
They briefly discuss the effect of changing the migration rate at one locus, but do not say what happens when you change all of them.
There is no mention of testing their modelled migration rates against any known migration pattern to ground truth their assumptions.
A mathematical model that hasn't been ground-truthed is worthless.

I also have a LOT of trouble with the "MRCA" terminology. You suggested MRCP, but nwr takes exception to that.
Most people seem to assume a single ancestor from the term (see Randman's post for example) in spite of explanations to the contrary. This means the term contributes to the confusion.
Not sure what to do about that. Last Universal Connection?
Enough for tonight.

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This message is a reply to:
 Message 53 by pink sasquatch, posted 07-10-2006 2:45 PM pink sasquatch has replied

Replies to this message:
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pink sasquatch
Member (Idle past 6022 days)
Posts: 1567
Joined: 06-10-2004


Message 57 of 76 (330670)
07-10-2006 11:55 PM
Reply to: Message 56 by RAZD
07-10-2006 11:15 PM


still haven't read thoroughly, it seems...
If nothing else, a basic human pattern is for sexually active individuals to have several children with the same mate. Every additional child by the same parents cuts severely into the random equation. If we assume a minimum structured mating pattern holds over a 2 generation period then the MCRA 'advances' n/2=2/2=1 generation during those 2 generation periods.
Unless I'm reading something horribly wrong, it's already in the model:
After the first child, there is an 80% chance that the father of the previous child will also father the next one, thus simulating marriage.
It seems your criticism is not valid. They also include sex-based differences in marriage potential and fertility, as well as individual differences in mating success and fecundity.
It almost appears that they stopped evaluating the results when they got the 5000 year figure.
What specifically leads you to this accusation? Considering you didn't even read the methods to see that mating within subpopulations was non-random, I find it beyond the pale that you are suggesting fraud.
I also have a LOT of trouble with the "MRCA" terminology. You suggested MRCP, but nwr takes exception to that.
I merely suggested the acronym. I haven't made up my mind about the MRCA concept yet. You, on the other hand, had made up your mind and discounted the model before having even examined it.

This message is a reply to:
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nwr
Member
Posts: 6408
From: Geneva, Illinois
Joined: 08-08-2005
Member Rating: 5.1


Message 58 of 76 (330672)
07-11-2006 12:00 AM
Reply to: Message 56 by RAZD
07-10-2006 11:15 PM


Re: I stand corrected - now lets deal with the math problem ...
The irony (to me) is that now we are talking about someone who was (potentially) totally insignificant to most people alive today then eh?
That's the point I have been trying to make. I'm glad you finally get it.
My hackles are also raised when they use terminology like "would have lived" when they can really only mean "could at a minimum have lived" at best, and thus give a false sense of {truth\validity} to what is at best a very hypothetical and untested result.
Why allow your hackles to be raised about something that is totally insignificant?
To me, looking at it as a mathematician, it doesn't much matter if the MRCA is 1000 years earlier than they suggest. The interesting thing is that it is far earlier than the time of mitochondrial eve. Note that this is interesting in the sense that it is counter-intuitive. I still agree that the result is totally insignificant.
This model assumes a random mating of individuals
This doesn't really seem to be a big problem. Unless the mating is constrained to be within a bunch of separate inbreeding groups, it will be random enough for the kind of mixing needed.
Looking at the case of the Australian aboriginals, it is my understanding that they lived in relatively isolated tribes. In my opinion, they should have considered each tribe as if an island in their analysis. Within each tribal group the mating was probably random enough. But even if each tribe were considered an island, this would probably push the MRCA date back only 1000 years, and I don't see that as a big deal.
If nothing else, a basic human pattern is for sexually active individuals to have several children with the same mate.
The reports I hear, are that there is a lot of sleeping around that actually goes on.

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RAZD
Member (Idle past 1404 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 59 of 76 (330739)
07-11-2006 8:09 AM
Reply to: Message 57 by pink sasquatch
07-10-2006 11:55 PM


After the first child, there is an 80% chance that the father of...
It seems your criticism is not valid.
I did a search for 80% in the letter and only got one hit:
If the migration rate among towns is increased to 20%, the local port users are reduced to 80%, and the migration rates between countries and continents are scaled up by factors of 5 and 10,
I also don't find it in {Modeling the recent common ancestry of all living humans Supplementary Methods A: Further Explanation and Derivations of Mathematical Results} - suppliment 1, that's in suppliment 2 - {Modeling the recent common ancestry of all living humans Supplementary Methods B: Further Details of the Computational Model}. I scanned that one for migration.
What happens if they change that to 90%? How sensitive is the result to the {randomness\lack of}?
But I'm not just saying that {monogamism} was the only structure. The prince(ss) does not mate with the beggers at the beggers choice. Look at all the class structures in all the cultures in known history.
Suppliment 2 again:
The father of a woman's first child is selected at random from the men who are at least as old as the woman.
Why at random? Because it is computationally easy? Again what is the sensitivity of the result to changing the randomness of this choice?
and they also say:
It sometimes happens, especially early in the simulation when populations are low or when a new area is first colonized, that there are no suitable fathers living in the same town as a woman who is to have a child. In this case, fathers are sought in the other towns within the same country.
Again they could assume incest or adultry instead of forced migration of a mail-order male. What is the sensitivity of the result to the degree of importing a M-O M?
Seems to me the cling to a random metric in their model. It also seems to me that a little loss of randomness has a significant effect on the result - that the model is very sensitive to the degree of randomness.
What specifically leads you to this accusation?
Because they present that as a final result without giving a range of possibilities and say it could be as low as 2000 years and it could be as high as 45,000 years. They appear to stop and the 2nd\3rd level of evaluating effects rather than continue to see how far it leads and when it becomes unreasonable at the far end.
It's not because the number is 5000, but because they don't develop a larger range of possibilities even though they state several (significant) uncertainties - they don't model the uncertainties (5,000 +40,000/-3,000) in the results.
Enough for now.

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sfs
Member (Idle past 2533 days)
Posts: 464
From: Cambridge, MA USA
Joined: 08-27-2003


Message 60 of 76 (330748)
07-11-2006 8:22 AM
Reply to: Message 58 by nwr
07-11-2006 12:00 AM


Re: I stand corrected - now lets deal with the math problem ...
quote:
To me, looking at it as a mathematician, it doesn't much matter if the MRCA is 1000 years earlier than they suggest. The interesting thing is that it is far earlier than the time of mitochondrial eve. Note that this is interesting in the sense that it is counter-intuitive. I still agree that the result is totally insignificant.
When you think about it, it's actually a pretty trivial result (that the common ancestor was very recent, I mean). The number of ancestors increases exponentially as you go back in time, so the time to the MRCA has to be logarithmic in the population size, for a single population. Since your ancestors quickly take over your own population, any migration rate at all means that one of them had to have come from a different population. In the source population, the migrated ancestor will also take logarithmic time to have an MRCA there. So for a widely dispersed island model with local migration only, I'd expect a logarithmic dependence on population size with a multiplicative factor for the number of populations. The details of their demographic and mating models will modulate this a little, but not much.
I don't think this is a really deep result, since the logarithmic dependence was already known. Mind you, I'd never thought about how recent the MRCA must be until I heard about this paper -- but I still can't think of a reason why I should have thought about it. So I find the idea moderately interesting, but not worth publication in a top journal.

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