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rms2
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« Reply #25 on: October 28, 2012, 03:46:39 PM »

It would be interesting to put the question "What happened to the YCC?" on Rootsweb. I venture that there are folks on there who know the story.

That's probably a good idea.

The implication in Bennett's email to me was that the YCC is still in existence. I asked him if it was. While he didn't answer that question specifically, he did say Dr. Hammer manages (present tense) the YCC and that it was the YCC that approved FTDNA's shorthand, etc.
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« Reply #26 on: October 28, 2012, 04:56:33 PM »

It would be interesting to put the question "What happened to the YCC?" on Rootsweb. I venture that there are folks on there who know the story.

That's probably a good idea.

The implication in Bennett's email to me was that the YCC is still in existence. I asked him if it was. While he didn't answer that question specifically, he did say Dr. Hammer manages (present tense) the YCC and that it was the YCC that approved FTDNA's shorthand, etc.

BG's reply is somewhat enigmatic.

Nowadays, when you try the original YCC website URL, you are asked to login:

http://ycc.biosci.arizona.edu/

I don't have an account on Rootsweb. Maybe somebody here does.

Meanwhile, I continue to ask around in as many quarters as I can. So far the silence I'm getting feels like a "pregnant pause" ...
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« Reply #27 on: October 28, 2012, 05:24:13 PM »

It would be interesting to put the question "What happened to the YCC?" on Rootsweb. I venture that there are folks on there who know the story.

That's probably a good idea.

The implication in Bennett's email to me was that the YCC is still in existence. I asked him if it was. While he didn't answer that question specifically, he did say Dr. Hammer manages (present tense) the YCC and that it was the YCC that approved FTDNA's shorthand, etc.

BG's reply is somewhat enigmatic.

Nowadays, when you try the original YCC website URL, you are asked to login:

http://ycc.biosci.arizona.edu/

I don't have an account on Rootsweb. Maybe somebody here does.

Meanwhile, I continue to ask around in as many quarters as I can. So far the silence I'm getting feels like a "pregnant pause" ...

Interesting. A "members only" thing, I guess.

I just posted the following on Rootsweb under the rubric "The YCC: Still active?":

Quote
Does anyone know if the YCC is still alive and kicking? What can you tell me about it?

Thanks in advance.

Rich


I don't generally post on Rootsweb these days. We'll see if anyone replies.
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Mike Walsh
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« Reply #28 on: October 28, 2012, 05:57:32 PM »

I heard from Mr. Greenspan, but his answer was brief. He said Dr. Hammer is the head of the YCC and approved the current shorthand FTDNA is using. I hate to pester Bennett, but I think I will write him again and ask for some clarification.

He did say they want to drop the longhand entirely because it will be "changing SO much with the introduction of the Nat Geo Geno 2.0 product" (his words, including the caps).

As I've said before, I'm all for dropping the long hand for conversations and articles. I'm just worried the real reason for dropping the long hand is just that they've thrown in the towel on keeping track of the full haplotree.  I guess, they could've reasoned we (the company) are a genealogical (as opposed to deep ancestral supporting) DNA company, therefore the only thing that counts is the terminal SNP... and besides, this is cheaper/less to support. I hope I'm wrong.
« Last Edit: October 28, 2012, 06:02:20 PM by Mikewww » Logged

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« Reply #29 on: October 28, 2012, 06:13:32 PM »

I'm just worried the real reason for dropping the long hand is just that they've thrown in the towel on keeping track of the full haplotree.

I've been thinking it's to do with that NextGen stuff and a pre-programmed chip that will quickly and inexpensively tell you Yes or No -- for the stuff it's designed to detect.

And for other stuff -- somebody else can discover it, maybe feed them the primers, and then for some fixed fee (probably greater than $27) they will still be willing to do an "Advanced" test, for any SNP too new to be on their current "Geno2" type chip.  I *think* that requires the additional PCR step, that is unnecessary with the NextGen techniques and chip technology.  More manual, less automated, therefore slower and more expensive.

I don't have much of a problem with that, in that if I were in business I'd be looking at profit or loss columns, too.   
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« Reply #30 on: October 28, 2012, 06:22:28 PM »

I'm just worried the real reason for dropping the long hand is just that they've thrown in the towel on keeping track of the full haplotree.  

How's this for another bit of crystal ball gazing ...

YCC, in a second coming, agrees to provide academic oversight of ISOGG (sort of a Board of Advisers thing). In turn, ISOGG becomes the official keeper of the Y tree, and FTDNA simply links to that. In other words, it outsources tree upkeep to a trusted party.

It's known that ISOGG has been working to replace the current HTML version of the tree with a proper database from which the tree can be depicted. If that's done properly, then a public API into the database would support my conjecture.
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« Reply #31 on: October 29, 2012, 12:24:45 AM »

I'm just worried the real reason for dropping the long hand is just that they've thrown in the towel on keeping track of the full haplotree.  

How's this for another bit of crystal ball gazing ...

YCC, in a second coming, agrees to provide academic oversight of ISOGG (sort of a Board of Advisers thing). In turn, ISOGG becomes the official keeper of the Y tree, and FTDNA simply links to that. In other words, it outsources tree upkeep to a trusted party.

It's known that ISOGG has been working to replace the current HTML version of the tree with a proper database from which the tree can be depicted. If that's done properly, then a public API into the database would support my conjecture.

I think FTDNA's hope has always been that YCC would provide the academic backing for a Y DNA tree that FTDNA would essentially discover via the FTDNA labs which do National Geno testing also.

I don't know if a testing company or academic institute can effective let a band of hobbyists set standards, but I think in this case its a good idea.  In any case, I don't think that hobbyists* have to follow blindly whatever terms a testing company, or an academic institution or two set. I think we have to give credit to FTDNA, though. Even though they couldn't keep up the haplotree formally, they (via Thomas Krahn) kept an accurate draft tree going. Krahn showed exceptional skills in cooperation by working with citizen-scientists and the like. I think he showed great initiative and innovation.

* I don't know if we are there yet, but at some point the hobbyists/consumers form enough power in numbers and dollars that they become the big dog, and the testing companies will just follow whatever sells most. I'm sure they'd be happy with that. I'm not sure if the academic institutions would be bothered by NOT providing the leadership, but I think commercial entities care more about market share/revenue leadership than standards leadership.
« Last Edit: October 29, 2012, 09:44:52 AM by Mikewww » Logged

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« Reply #32 on: October 29, 2012, 04:54:44 AM »

Another stakeholder to take into account is
http://www.yhrd.org/
They look after standardisation for the Forensic DNA community.
They generally deal in low number of STRs, typically 14.
Forensic reporting crucially depends on the scientific acceptance, standardization and reproducibility of the applied methodology. They tend to be more conservervative in acceptance of new technological breakthroughs than for example the Genetic Genealogy community.They are probably overwhelmed by the explosion in new SNPs.
My preference is still for the ISOGG approach. I would like to see groups like ISOGG, the Welcome Trust Sanger Institute, Genographic, the Testing Companies and others come together to nail down one standard which everyone can live with.
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« Reply #33 on: October 29, 2012, 10:00:08 AM »

I don't know what's up with the YCC, but my impression is that it's not totally defunct. We definitely have a situation right now in the world of genetic science and genetic genealogy that resembles the early USA under the Articles of Confederation: a very loose jumble of sometimes-cooperative independent entities, none of them beholden to any central, unifying authority.

Maybe that's good. George Mason and Patrick Henry probably would have liked it.

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gtc
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« Reply #34 on: October 29, 2012, 11:00:03 PM »

I think FTDNA's hope has always been that YCC would provide the academic backing for a Y DNA tree that FTDNA would essentially discover via the FTDNA labs which do National Geno testing also.

I don't know if a testing company or academic institute can effective let a band of hobbyists set standards, but I think in this case its a good idea.  In any case, I don't think that hobbyists* have to follow blindly whatever terms a testing company, or an academic institution or two set. I think we have to give credit to FTDNA, though. Even though they couldn't keep up the haplotree formally, they (via Thomas Krahn) kept an accurate draft tree going. Krahn showed exceptional skills in cooperation by working with citizen-scientists and the like. I think he showed great initiative and innovation.

* I don't know if we are there yet, but at some point the hobbyists/consumers form enough power in numbers and dollars that they become the big dog, and the testing companies will just follow whatever sells most. I'm sure they'd be happy with that. I'm not sure if the academic institutions would be bothered by NOT providing the leadership, but I think commercial entities care more about market share/revenue leadership than standards leadership.

In one sense, academia is between a rock and a hard place with this issue. Authors of academic papers only reference other peer-reviewed academic material and the YCC tree provided that "cred". FTDNA followed that convention, too (not surprising since their Chief Scientist is Michael Hammer).

However, as structured, the YCC can/could not hope to keep up to date with the discoveries occurring outside of academia.

On the other hand, because of its structure, ISOGG is very fleet of foot.

So, it strikes me that a happy solution might be for academia to recognize ISOGG by taking an advisory role ensuring that its processes and protocols are sufficiently rigorous to satisfy academic peer review standards, but without burying ISOGG in procedural molasses in the process. (At the practical level, these aims may be mutually inconsistent.)

Under that proposal, the ISOGG tree would always be described as a working draft.
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« Reply #35 on: October 30, 2012, 09:11:40 AM »

I think FTDNA's hope has always been that YCC would provide the academic backing for a Y DNA tree that FTDNA would essentially discover via the FTDNA labs which do National Geno testing also.

I don't know if a testing company or academic institute can effective let a band of hobbyists set standards, but I think in this case its a good idea.  In any case, I don't think that hobbyists* have to follow blindly whatever terms a testing company, or an academic institution or two set. I think we have to give credit to FTDNA, though. Even though they couldn't keep up the haplotree formally, they (via Thomas Krahn) kept an accurate draft tree going. Krahn showed exceptional skills in cooperation by working with citizen-scientists and the like. I think he showed great initiative and innovation.

* I don't know if we are there yet, but at some point the hobbyists/consumers form enough power in numbers and dollars that they become the big dog, and the testing companies will just follow whatever sells most. I'm sure they'd be happy with that. I'm not sure if the academic institutions would be bothered by NOT providing the leadership, but I think commercial entities care more about market share/revenue leadership than standards leadership.

In one sense, academia is between a rock and a hard place with this issue. Authors of academic papers only reference other peer-reviewed academic material and the YCC tree provided that "cred". FTDNA followed that convention, too (not surprising since their Chief Scientist is Michael Hammer).

However, as structured, the YCC can/could not hope to keep up to date with the discoveries occurring outside of academia.

On the other hand, because of its structure, ISOGG is very fleet of foot.

So, it strikes me that a happy solution might be for academia to recognize ISOGG by taking an advisory role ensuring that its processes and protocols are sufficiently rigorous to satisfy academic peer review standards, but without burying ISOGG in procedural molasses in the process. (At the practical level, these aims may be mutually inconsistent.)

Under that proposal, the ISOGG tree would always be described as a working draft.

GTC, I don't know what's practical in the world of academia, but your suggestion makes perfect sense to me. Perhaps the ISOGG tree should be recognized as THE working draft.

From what I've seen, ISOGG members track references to testing that defines where an SNP gets placed. I don't think they publish those references, though. If they did, I think that would make their tree sufficient to be recognized. However, as you said, probably, you'd need some peer review process on all of this so maybe the working draft concept is the way to go. The formal academic trees will never catch up. I guess that's okay. We just need to live with that.  We've seen that the formal trees are going to be forced into changing their rooting anyway so maybe formal recognition doesn't mean correctness, anyway.

Please consider posting your thoughts on http://groups.yahoo.com/group/ISOGG/
« Last Edit: October 30, 2012, 09:27:56 AM by Mikewww » Logged

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« Reply #36 on: October 30, 2012, 10:15:26 AM »

I think FTDNA's hope has always been that YCC would provide the academic backing for a Y DNA tree that FTDNA would essentially discover via the FTDNA labs which do National Geno testing also.

I don't know if a testing company or academic institute can effective let a band of hobbyists set standards, but I think in this case its a good idea.  In any case, I don't think that hobbyists* have to follow blindly whatever terms a testing company, or an academic institution or two set. I think we have to give credit to FTDNA, though. Even though they couldn't keep up the haplotree formally, they (via Thomas Krahn) kept an accurate draft tree going. Krahn showed exceptional skills in cooperation by working with citizen-scientists and the like. I think he showed great initiative and innovation.

* I don't know if we are there yet, but at some point the hobbyists/consumers form enough power in numbers and dollars that they become the big dog, and the testing companies will just follow whatever sells most. I'm sure they'd be happy with that. I'm not sure if the academic institutions would be bothered by NOT providing the leadership, but I think commercial entities care more about market share/revenue leadership than standards leadership.

In one sense, academia is between a rock and a hard place with this issue. Authors of academic papers only reference other peer-reviewed academic material and the YCC tree provided that "cred". FTDNA followed that convention, too (not surprising since their Chief Scientist is Michael Hammer).

However, as structured, the YCC can/could not hope to keep up to date with the discoveries occurring outside of academia.

On the other hand, because of its structure, ISOGG is very fleet of foot.

So, it strikes me that a happy solution might be for academia to recognize ISOGG by taking an advisory role ensuring that its processes and protocols are sufficiently rigorous to satisfy academic peer review standards, but without burying ISOGG in procedural molasses in the process. (At the practical level, these aims may be mutually inconsistent.)

Under that proposal, the ISOGG tree would always be described as a working draft.

GTC, I don't know what's practical in the world of academia, but your suggestion makes perfect sense to me. Perhaps the ISOGG tree should be recognized as THE working draft.

From what I've seen, ISOGG members track references to testing that defines where an SNP gets placed. I don't think they publish those references, though. If they did, I think that would make their tree sufficient to be recognized. However, as you said, probably, you'd need some peer review process on all of this so maybe the working draft concept is the way to go. The formal academic trees will never catch up. I guess that's okay. We just need to live with that.  We've seen that the formal trees are going to be forced into changing their rooting anyway so maybe formal recognition doesn't mean correctness, anyway.

Please consider posting your thoughts on http://groups.yahoo.com/group/ISOGG/

Given that a number of papers germane to this issue are expected to be given at various conferences in a little over a week from now, I'd like to hold off on that suggestion until we see what emerges then.
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« Reply #37 on: October 30, 2012, 10:35:04 AM »

I think FTDNA's hope has always been that YCC would provide the academic backing for a Y DNA tree that FTDNA would essentially discover via the FTDNA labs which do National Geno testing also.

I don't know if a testing company or academic institute can effective let a band of hobbyists set standards, but I think in this case its a good idea.  In any case, I don't think that hobbyists* have to follow blindly whatever terms a testing company, or an academic institution or two set. I think we have to give credit to FTDNA, though. Even though they couldn't keep up the haplotree formally, they (via Thomas Krahn) kept an accurate draft tree going. Krahn showed exceptional skills in cooperation by working with citizen-scientists and the like. I think he showed great initiative and innovation.

* I don't know if we are there yet, but at some point the hobbyists/consumers form enough power in numbers and dollars that they become the big dog, and the testing companies will just follow whatever sells most. I'm sure they'd be happy with that. I'm not sure if the academic institutions would be bothered by NOT providing the leadership, but I think commercial entities care more about market share/revenue leadership than standards leadership.

In one sense, academia is between a rock and a hard place with this issue. Authors of academic papers only reference other peer-reviewed academic material and the YCC tree provided that "cred". FTDNA followed that convention, too (not surprising since their Chief Scientist is Michael Hammer).

However, as structured, the YCC can/could not hope to keep up to date with the discoveries occurring outside of academia.

On the other hand, because of its structure, ISOGG is very fleet of foot.

So, it strikes me that a happy solution might be for academia to recognize ISOGG by taking an advisory role ensuring that its processes and protocols are sufficiently rigorous to satisfy academic peer review standards, but without burying ISOGG in procedural molasses in the process. (At the practical level, these aims may be mutually inconsistent.)

Under that proposal, the ISOGG tree would always be described as a working draft.

GTC, I don't know what's practical in the world of academia, but your suggestion makes perfect sense to me. Perhaps the ISOGG tree should be recognized as THE working draft.

From what I've seen, ISOGG members track references to testing that defines where an SNP gets placed. I don't think they publish those references, though. If they did, I think that would make their tree sufficient to be recognized. However, as you said, probably, you'd need some peer review process on all of this so maybe the working draft concept is the way to go. The formal academic trees will never catch up. I guess that's okay. We just need to live with that.  We've seen that the formal trees are going to be forced into changing their rooting anyway so maybe formal recognition doesn't mean correctness, anyway.

Please consider posting your thoughts on http://groups.yahoo.com/group/ISOGG/

Given that a number of papers germane to this issue are expected to be given at various conferences in a little over a week from now, I'd like to hold off on that suggestion until we see what emerges then.

I don't want push you into a strong advocacy position, but I like your idea. I guess, in a sense, the ISOGG tree already is THE defacto standard working draft for the on-line community.

I don't think it will be hard to figure out what will happen. There will be scientific papers that up date the tree. I think scientists greatest focus will be at the root and at early branches, though. That is population genetics at the broad and very ancient levels, getting into philosophical discussions on the origins of man (see Dr Hammer Youtube video.)  This is where headlines will be made and books with broad readership written. Why would we think that YCC wants to support genetic genealogy? as opposed to ancient population genetics?

Out here on the small branch and twig parts of the tree, I think academic community will always be behind. It's just a factual matter of their constraints and requirements. It's not bad. It just is.  When Spencer Wells produces his paper, if it is Geno 2.0 based, it will already be behind.  What about this time next year? Will Wells or YCC or someone else produce a paper every six months to keep up?

A different process is needed, and probably ISOGG is the best bet for executing that.
« Last Edit: October 30, 2012, 10:38:36 AM by Mikewww » Logged

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« Reply #38 on: October 30, 2012, 11:13:34 AM »

(... trimmed ...)

I don't want push you into a strong advocacy position, but I like your idea. I guess, in a sense, the ISOGG tree already is THE defacto standard working draft for the on-line community.

I don't think it will be hard to figure out what will happen. There will be scientific papers that up date the tree. I think scientists greatest focus will be at the root and at early branches, though. That is population genetics at the broad and very ancient levels, getting into philosophical discussions on the origins of man (see Dr Hammer Youtube video.)  This is where headlines will be made and books with broad readership written. Why would we think that YCC wants to support genetic genealogy? as opposed to ancient population genetics?

Out here on the small branch and twig parts of the tree, I think academic community will always be behind. It's just a factual matter of their constraints and requirements. It's not bad. It just is.  When Spencer Wells produces his paper, if it is Geno 2.0 based, it will already be behind.  What about this time next year? Will Wells or YCC or someone else produce a paper every six months to keep up?

A different process is needed, and probably ISOGG is the best bet for executing that.


S'okay, I don't feel pushed in that sense, and if no news of a re-engineered and streamlined YCC-type process emerges from these conferences, then I'm happy to b-a-n-g a drum for change, for what it's worth.

I have mentioned elsewhere that I think there may be an embargo situation pending imminent official announcements. IMO, too many people who should be in the know about YCC status are either not replying, or replying in enigmatic terms, to questions on that subject.

Meanwhile, another model that could be considered is the one used for mtDNA: namely the Phylotree which is maintained by Mannis van Oven, Department of Forensic Molecular Biology, Erasmus MC, University Medical Center Rotterdam, The Netherlands.

His update policy is "The tree will be updated at least every six months (unless no new data has appeared)". Now, granted that the mt-tree is smaller and arguably less chaotic than the Y-tree, but here we have one guy within the academic community with a commitment to regular revisions, as opposed to a committee with no such commitment.

http://www.phylotree.org

[Edit: why the heck is the word b-a-n-g (with no hyphens) erased by this site's software???]
« Last Edit: October 30, 2012, 11:16:26 AM by gtc » Logged

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« Reply #39 on: October 30, 2012, 06:30:31 PM »

Somewhat enigmatic is how I would characterize Mr. Greenspan's replies to me via email. Reading between the lines, I would say something is definitely up.
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