User talk:Felsenst

Hello there Felsenst, welcome to the 'pedia! I hope you like the place and decide to stay. If you ever need editing help visit Wikipedia:How does one edit a page and experiment at Wikipedia:Sandbox. If you need pointers on how we title pages visit Wikipedia:Naming conventions or how to format them visit our manual of style. If you have any other questions about the project then check out Wikipedia:Help or add a question to the Village pump. Cheers! --maveric149

Getting at older edits of Sewall Wright

Kind of wish the stuff in the old Sewall Wright page was accessible now (it has vanished) as I thought it read better. (Of course I wrote some of it). Joe Felsenstein

Joe-- You can get the old Sewall Wright page edits if you know the IP address from which you made the edits. Go to the User Contributions for that IP, and there will be a list of your edits. Click on the Sewall G. Wright edits, and you'll have access to the text as it existed at that time. You can then cut and paste from there into the current article. Cheers, Greg Mayer. MayerG 08:32, 2 February 2006 (UTC)

The administrator who deleted the old Sewall Wright page on 4 January, 2006 helped out by restoring the old one at my request. You can see a copy of it here: [1]. It's not very long, though. EdJohnston 02:31, 3 January 2007 (UTC)

Your sig

Hi Joe, you need to sign your posts with four tildes please ~~~~ — Dunc|☺ 13:58, 7 June 2006 (UTC)

JBS Haldane

Dear Professor Felsenstein, if that image is not of him but of his father, you should perhaps suggest its removal on the talk page. Shyamal 04:46, 24 July 2006 (UTC)

Yes, changing the title was wicked of me, but effective -- the image is gone now. It was definitely his father, not him. The pipe-smoking image on the infobox that was recently there and is now on the talk page is an excellent one, and I hope that it becomes the image on the main page. I am glad that he is once again listed as British rather than Scottish, as that is more accurate. [[Felsenst 21:27, 1 August 2006 (UTC)|Joe Felsenstein]]

Picture of you needed

Hello Professor Felsenstein,

Do you know the copyright status of the picture of you that is posted at http://www.gs.washington.edu/faculty/felsenstein.htm? It seems to me that it could be used in Wikipedia's article Joe_Felsenstein. Do you have the power to release it? Wikipedia is fussy about copyrights. If not, do you have a picture that you took yourself?

The page that is used to describe 'requests for permission' is at WP:ERP. Essentially the picture would have to be released under the Gnu Free Documentation License.

If you reply that it's OK, I'll try to upload the picture and include it in the article. Thanks, EdJohnston 20:57, 8 September 2006 (UTC)

Ed Johnston --

Yes, that is a photo taken in 2005 by my wife in our backyard. I own it. I can if needed supply a higher-resolution version. However although I am happy to release it under the GFDL, I have no idea how to do so and cannot devote the hours needed to persuade the avid photo-deleters at the Wikipedia to stay their hand. Felsenst 21:12, 8 September 2006 (UTC)

I think you've just uttered the magic words! Your verbatim response (as above) will be captured and saved by the Wikipedians in their archives as evidence of your consent. Let me know if that's the wording you'd like to use. It might be better not to say anything about the photo-deleters. I'll take care of filing the paperwork. EdJohnston 21:45, 8 September 2006 (UTC)

Photo has been posted in the Joe Felsenstein article. The GFDL image is at Image:Felsenstein.jpg in commons.wikimedia.org. EdJohnston 02:17, 9 September 2006 (UTC)

Cladistics - adding to the word soup

Dear Professor, I hope you get working on the cladistics and related articles soon. The article suggests that phenetics is polythetic (overall) whereas cladistics is not. My belief was that phenetics differed in that it was strictly based on morphology. The word phyletic is nowhere used. Is it synonymous with phylogenetic. cheers Shyamal 01:33, 22 September 2006 (UTC)

I am busy with other (non-Wikipedia) work right now -- in any case the whole miasma surrounding "cladistics" makes it difficult to even start. Is cladistics a method of classification? Or a method of inferring phylogenies? I think the former, but a lot of systematists disagree with me on that. You will find lots of people who say cladistics is simply inferring phylogenies by using neatly nested synapomorphies. If pressed they might later admit that it isn't quite that simple (homoplasy happens, and we don't usually know which state is ancestral). The classification is described as a phylogeny and vice versa. I think this is disastrous. It is not unique to Wikipedia, but this mess is common everywhere. BTW phenetics is not restricted to morphology. It is either (according to me) classification on the basis of overall similarity (not phylogeny) or (according to the majority of everyone else) a method of inferring phylogenies by using distance matrix methods -- and about half the time they include maximum likelihood as phenetic, and half the time not. (AARGH!) It's a total muddle reflecting muddled thinking. Phenetics is polythetic, but then phylogenetics is too if there is a reasonable amount of homoplasy. In saying cladistics isn't they are implicitly assuming that there is little homoplasy. They are using the Walt Disney version of cladistics, as people usually do in their teaching. You can make up data sets where not one derived state avoids homoplasy. Felsenst 04:16, 22 September 2006 (UTC)

I imagine that the Cladistics journal would have a definition and scope defined somewhere. Shyamal 08:10, 22 September 2006 (UTC)

Cladistics is up for featured article review

You might be interested in this - the article cladistics was, a long time ago, identified as a featured article, and is now up for featured article review, meaning it will no longer be considered one of Wikipedia's best articles if it does not get some substantial improvement. The article as it stands is frankly quite poor, and is neither comprehensive nor well-written, suffering in particular from muddled terminology. A few of us who contribute regularly to biology-related articles were asked to do some work on it a couple of weeks ago, but the subject is really outside my field, and it needs the attention of an expert. If you get a chance, anything you can contribute - either editing the article itself or offering suggestions for improvement - would be appreciated. Opabinia regalis 03:02, 3 January 2007 (UTC)

I don't think I can be of much help. My own view on all this is considered borderline-crackpot, and editing it to reflect my views would make it conflict with most researchers' views. The article assumes that "cladistics" is the use of nested synapomorphies, and that this is practical in essentially all real cases. (In reality this is the Mickey Mouse view, and real life does not afford us knowledge about ancestral states or give us sets of uncontradicted characters). The article goes on to equate this analysis with "phylogenetic systematics" but then later equates it with "cladistic taxonomy". I always thought that phylogenetic systematics was the construction of a monophyletic taxonomy, but the article separates the two. The article has many problems:

• Getting confused over what is classification and what is inference of phylogenies.
• Making it sound as if nesting synapomorphies is the usual method
  • Leaving the impression that we know ancestral states, and that there is no homoplasy in practice.
  • Then adding in parsimony as if it was the same thing, which it isn't
  • Then mentioning other methods such as maximum likelihood for inferring phylogenies (but never having made clear what is the connection between phylogenies and cladograms, if any).

The reason I just don't sail in and edit it to correct these problems is that the formulation in the article does fairly reflect the dominant-consensus view. In short, that view is badly muddled. This can be seen in many textbooks, whose elementary introductions to modern systematics are a total mess. It would be highly controversial of me to resolve the muddle in the article. Felsenst 13:12, 3 January 2007 (UTC)

Thanks for your comments. This is why I haven't edited the article - I can't reliably distinguish between "rather controversial" and "considered borderline crackpot" :) If the reason the article seems muddled to me is due to the field itself and not to my inadequate understanding of it, then I'll keep my proboscis out of it. ('No homoplasy in practice' is really a 'consensus' view?) Opabinia regalis 06:05, 4 January 2007 (UTC)

No homoplasy in practice is an extreme view, of course. But the simple description of "cladistics" as involving nesting homoplasies is a practice that can only really work if there is no homoplasy in practice (and if we do know which states are ancestral). So the standard description of cladistics blatantly violates reality. Which is my point -- the standard textbook descriptions are a mess, and the article faithfully reflects that mess in its mess. Felsenst 08:00, 7 January 2007 (UTC)

Nils Barricelli

Hi I noticed you recently added a reference to Barricelli, Nils Aall (1963), Numerical testing of evolution theories. Part II. Preliminary tests of performance, symbiogenesis and terrestrial life, Acta Biotheoretica, 16: 99-126. On the Genetic algorithm article. I was just wondering if you could give me a source to this paper or any other early work by Barricelli, I can only find one pay for article on the net... I'd be interested in reading these papers, I just finished my undergrad dissertation adding in a symbiogenetic operator to a Genetic Algorithm, so it would be really nice to see what was done 44 years ago :) Thanks for editing! MattOates (Ulti) 10:01, 2 May 2007 (UTC)

I have found Matt's email address and replied to him privately about how he can get this article. Felsenst 13:17, 3 May 2007 (UTC)

Infobox

Hi Felsenst, I've had a go at correcting the errors in the infobox in my sandbox. I still think there's a problem with my understanding though. I wonder if you could take a look and see if you can spot my mistake. In Edwards' paper he has a graph showing how the chance of misclassification decreases when the number of loci is increased, but when I produced a similar graph it looked quite different to his, for example I don't get any better resolution with two loci than I do with a single locus, and four loci is no more discriminatory than three. There must be some flaw with my understanding here. I'd appreciate your input if you have the time, though of course I understand if you can't find the time. Thanks for any help in advance. My attempt to correct my initial errors is here. All the best. Alun (talk) 17:08, 28 September 2008 (UTC)

What is the rule you use for classification in the two-locus case? When a haplotype has a mixed signal (+-) what do you do? Do you (I hope) assign the individual half to each population, and count that as half a misclassification, instead of as a misclassification? I think this will cause the misclassications to be fewer when there are 2 loci than 1, and fewer when there are 4 loci than 3. Also I think Edwards's calculation is for diploids, so we do not expect the two calculations to be the same -- his should be close to what you would get with twice the number of loci. Felsenst (talk) 01:38, 29 September 2008 (UTC)

Oh wait, I see. Yes, you get no better misclassification with two loci, you are right. I think the simple rule being used for classifying is at fault. Let me look into this. Felsenst (talk) 01:42, 29 September 2008 (UTC)

Thanks, yes I classify half the probability for +- etc. If Edwards misclassification rates are for diploid organisms then it would explain the difference. But I thought he'd said in his paper that his graph referred to his first example, which I think he says is for a haploid population. I really appreciate your help. Thanks. Alun (talk) 06:08, 29 September 2008 (UTC)

You're right, Edwards's example is haploid. He says classification in his example is "simply on the basis of counting the number of + genes" but he does not say what the criterion is. If you use whether the majority of the loci do or do not have +, and divide the ties equally between the two populations, yes, I get misclassification rates of 0.3, 0.3, 0.216, and 0.216 for 1, 2, 3 and 4 loci. If that is what Edwards does his figure is simply wrong, and you are right. I think he may have used a normal approximation. You might email him and ask. Note, however that a more sophisticated method would have assign each individual a probability of being in each population. In fact the odds favoring it being in population 1 would be multiplied by 7/3 for each + in its genome, and by 3/7 for each -. I haven't yet tried to see what that does to misclassification rates but it is the Bayesian solution under a prior that has equal probabilities of being in each population. Felsenst (talk) 06:55, 30 September 2008 (UTC)

Never mind. I just calculated misclassification probabilities under the "Bayesian" scheme. They do decline smoothly as the number of loci increases -- but counting mislassified fractions of individuals, it actually gives a higher probability of misclassification! I was able to verify that in the counting-plus-alleles method you get the same misclassification probability for an even number of loci as for the next smallest number. Thus the misclassification probability for 10 loci is the same as for 9, etc. Felsenst (talk) 14:24, 30 September 2008 (UTC)

OK, thanks a lot. I'm considering trying to include something like Edwards' second example in the article, as this shows how individuals are sorted into groups without a priori information. I want to make this box so people can come here and see how it's done, so I want to make the explanation as transparent as possible. My thinking is that we have the infobox as it is for articles that discuss these issues, but that the Lewontin's Fallacy article might be better served with additional information about how sorting is achieved. I'll have a go at explaining Edward's second example, and I'll run it by you before I add it to the article if that's OK? Cheers. Alun (talk) 06:16, 1 October 2008 (UTC)

Bio stub creation alert

Suresh Jayakar and Helen Spurway - could do with some additions. Shyamal (talk) 14:20, 19 October 2008 (UTC)

Perhaps they could. I met Jayakar years ago, and he did some nice work. But in his case and Spurway's, I know too little about the rest of their achievements to do these updates, and I don't have time to work on this. Felsenst (talk) 18:38, 19 October 2008 (UTC)

Understand, no problem. I figured you might know, having browsed through your bibliography of theoret. pop. genetics many years ago. Shyamal (talk) 03:57, 20 October 2008 (UTC)

Noticed that only 500 copies were ever printed ! The one I got my hands on was at the Indian Agricultural Statistics Research Institute. Shyamal (talk) 07:10, 20 October 2008 (UTC)

But notice that (at the link you gave) that you can download the entire list of publications. It is only about one megabyte. Using an editor to search for keywords you can do about as well as if you owned a print copy. Felsenst (talk) 11:22, 20 October 2008 (UTC)

:) A bit late, unfortunately. Not in that field now... ! Shyamal (talk) 12:30, 20 October 2008 (UTC)

Reliable sources noticeboard

Hi, I'd really appreciate your opinion as a scientist, regarding the reliability of this sort of source if you have the time. Thanks. Alun (talk) 12:26, 15 January 2009 (UTC)

I don't have time, and am not familiar enough with Wikipedia's standards to comment. Felsenst (talk) 18:18, 16 January 2009 (UTC)

Hello Sir

Being a renown computer scientist, this fellow computer science/business undergraduate asks you your advice. Which major would you recommend? I love to travel and work with computers. Is there anything you can recommend me? And sorry for posting such a random question. Have a good day! --DarkKunai (talk) 04:06, 6 April 2009 (UTC)

My email address is easily available on the web. Felsenst (talk) 13:59, 6 April 2009 (UTC)

Linkage disequilibrium

Hi Joe. I added some stuff about the Finnish disease heritage to the lead of Linkage disequilibrium, as a notable application for those who read about LD and wonder "so what?" I think it would be better as a section in the article, with a precis in the lead. I also noticed Genetic isolate needs work to connect it to LD. --Una Smith (talk) 04:26, 26 May 2009 (UTC)

Hi, Una. Go right ahead, I am not in charge of that page, I just intervened when it became a mess with wrong formulas and irrelevant stuff cluttering up what could have been a simple explanation. I have not even looked at Genetic isolate. The example you use of Finnish diseases seems to be to be an example of among-population LD: are the two diseases in LD within the Finnish population? That is not clear to me. Felsenst (talk) 13:15, 26 May 2009 (UTC)

Opinion sought

With reference to this discussion, I would like to know if phenetics and numerical taxonomy are one and the same. Would be grateful if you gave your opinion here or at the discussion or even privately on my email if you so prefer. AshLin (talk) 15:31, 12 April 2010 (UTC)

Thank you for your input. AshLin (talk) 03:20, 13 April 2010 (UTC)

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Sewall Wright: Revision history

Hi! I have no idea why you think I did anything to Sewall Wright! Do you know how to check the Revision history? If not, ask at the teahouse. Also, if you want to discuss something with another editor, you really should do it on their talk page, not their userpage. DennisPietras (talk) 02:04, 8 March 2017 (UTC)

Apologies. I somehow misinterpreted an edit made by another editor as having been made by you. Felsenst (talk) 23:00, 8 March 2017 (UTC)

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