User talk:Joannamasel - Misplaced Pages

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Evolvability

I noticed your edit at Evolvability. I haven't had a chance to examine your changes (although they look good), but I have a couple of comments that may be useful regarding Misplaced Pages styles. There are a lot of policies and guidelines, and you should not worry about them, but you might have a quick look. There is a Manual of Style with far too much information, but the thing relevant to this article is at WP:LEAD where it mentions that the first sentence of an article should begin with a definition, with the title of the article mentioned early, in bold. So, the article should start with something like "Evolvability is...", or "In , evolvability is...".

The other point to bear in mind is that all material must be verifiable: it's best to include at least a rough citation (perhaps just by putting author, title, publisher, page into the text, in brackets), although the policy merely requires that it is possible to verify assertions. The point is that anyone can edit the article and remove unreferenced material because such material is original research (that is, the text relies on the author's knowledge or opinion, rather than a reliable source). Misplaced Pages follows a fairly strict adherence to these policies to avoid having creationists and the like inserting text based on their opinion (such text can be reverted with edit summary "unsourced" if there are no references, or "unreliable source" if the source is plainly unscientific). Johnuniq (talk) 07:14, 18 August 2010 (UTC)

Genetic drift

I am delighted to see your changes and additions to Genetic drift. Know this is late, but found them today. --Ettrig (talk) 08:45, 25 November 2010 (UTC)

Need help with finding reference for mutation as a mechanism

Joanna, do you have a good introductory reference to recommend with respect to mutation as a mechanism of evolution? I teach an intro bio class and would like to incorporate some bits of it into my evolution lectures. By the way, we really appreciate your efforts on the evolution page. Thanks again! :D mezzaninelounge (talk) 18:20, 30 May 2011 (UTC)

I'm afraid I'm not sure about a good text at that level. The issue is clear enough in higher level texts: I teach Evolution also at the 600-level using Barton's textbook, but that's hardly accessible for Intro Bio. It's been some years since I taught at the 100-level.

I'm actually thinking of writing an education perspective piece advocating a shakeup in the "traditional" order in which students are introduced to evolutionary concepts. My reordering would consider how a more thorough understanding of probability and statistics content, taught in a stepwise building up fashion, can be effectively integrated into biology education. One of the suggestions I want to make is that mutation bias should be taught before drift because i) it relies on less difficult mathematical concepts of probability, ii) it is a simpler concept all-round that still teaches students that natural selection is not everything, and iii) unlike genetic drift, there are no grounds to dispute its importance in evolution.

Meantime, loss of pigments and eyes in cavefish is a pretty good and accessible example of a bias towards loss of function mutations, but you may find that many sources that discuss it confound drift and mutation bias. I think this eg will work best if you avoid teaching drift altogether at the 100-level, leaving that for later courses to cover, and avoiding confusion between the two. Another example you could pick is the evolution of genomewide GC content, which while affected by both selection and mutation bias, is driven more by bias in small populations, eg endosymbiotic bacteria.Joannamasel (talk) 18:38, 30 May 2011 (UTC)

Are you referring to this Evolution text by Barton et al.? If so, that is a good place for me to start as I'm not as familiar with mutation bias as I would like to be. I will see what I can do to dumb it down to the appropriate 100 level. I like those examples that you gave but as you correctly pointed out, students may confuse it with genetic drift. I just have to explain it delicately as I would like to keep genetic drift in my lectures.

With respect to reordering the "traditional education," I wholeheartedly agree! People definitely need to learn basic math and statistics first before proceeding to taking classes such as evolution or physiology, that do require some understanding of basic math and statistics. mezzaninelounge (talk) 18:54, 30 May 2011 (UTC)

Yes, that's the text I mean. I don't have it handy right now to doublecheck what it says on this topic, but generally it is a great book. My approximate memory is that he did have an experimental evolution eg in there on the effect of mutation over time, which in my lectures I ultimately replaced with a different experimental evolution by Maughan et al. 2007, which I thought captured the point better.

Maughan H, Masel J, Birky WC, Nicholson WL (2007). "The roles of mutation accumulation and selection in loss of sporulation in experimental populations of Bacillus subtilis". Genetics. 177: 937–948. doi:10.1534/genetics.107.075663.{{cite journal}}: CS1 maint: multiple names: authors list (link)Joannamasel (talk) 19:34, 30 May 2011 (UTC)

Thanks for the references. By the way, in the interest of resolving the issue of mutation as a mechanism on the Evolution Talk page, could you list some references, peer-reviewed or graduate college texts, on the talk page to buttress the statement that mutation is a mechanism of evolution? I'm only asking because you're most familiar with this topic and probably know the key or seminal papers on this topic. We definitely need to resolve this issue. mezzaninelounge (talk) 19:41, 30 May 2011 (UTC)

For textbooks, I will have to wait until I am in the office, and then other things are always pressing... The citations already in the mutation bias section are all very sound, though. And by no means all of them are self-cites. The Yampolsky & Stoltzfus papers are particularly decisive and I believe they should be enough.Joannamasel (talk) 19:47, 30 May 2011 (UTC)

Also, thanks so much for the backup on this mutation-mechanism issue! Without your help and that of others, I would have given up by now. You make me believe that this wikipedia method really works!Joannamasel (talk) 19:52, 30 May 2011 (UTC)

Hmm, we'll just have to lay them (references) out then. No rush, but a textbook would be a nice as they usually summarize the trends of a field. :D mezzaninelounge (talk) 19:54, 30 May 2011 (UTC)

May 2011

You currently appear to be engaged in an edit war according to the reverts you have made on Evolution. Users are expected to collaborate with others and avoid editing disruptively.

In particular, the three-revert rule states that:

Making more than three reversions on a single page within a 24-hour period is almost always grounds for an immediate block.
Do not edit war even if you believe you are right.

If you find yourself in an editing dispute, use the article's talk page to discuss controversial changes; work towards a version that represents consensus among editors. You can post a request for help at an appropriate noticeboard or seek dispute resolution. In some cases it may be appropriate to request temporary page protection. If you continue to edit war, you may be blocked from editing without further notice. OrangeMarlin 20:36, 30 May 2011 (UTC)

Just Saying Hi

Noticed that you are down in UT of A. I thought about applying to Mark Kirkpatrick's lab. I have read some of your papers and, in retrospect, I think your research is more along the lines of what I am interested in than Kirkpatrick's. Anyway, it is nice to see serious people doing serious work on here, rather than people like. . . me.

PS: even though I am in the Lynch lab, my opposition to the concept of evolvability isn't all that deep. Matthew Ackerman (talk) 20:11, 31 May 2011 (UTC)

I'm not sure Lynch's opposition is that deep either, if he would admit it. I was recently carefully reading Lynch & Gabriel 1983. Whatever words he uses, in fact the paper is all about cryptic genetic variation, evolvability, and um, evolutionary capacitance!

I'm still reasonably new to wikipedia. In a dream world of mine, in which most serious scientists become editors, I imagine scientific consensus reached or controversies clarified... Meantime I thought I had better lead by example. Joannamasel (talk) 20:21, 31 May 2011 (UTC)

Evolution lead discussion

I realize that I have pretty much done the same thing as you, bowing out of the discussion because of the way it is conducted. Years ago, when I brought the natural selection article to Good Article Status, I had the unpleasant experience with an editor who was convinced that he was right and that Darwin was the only way to go. Needless to say, once the article was finished, it slowly but surely deteriorated because the same discussion was renewed over and over again. The same pattern as here is arising, a editor with a lot of time who will throw reference after reference to you in order to make his point. For small article for which there are a limited number of articles, that could work, but when you have an expansive topic like evolution, it only muddles the waters. Anyway, just wanted to let you know that your experience is not unique. I might drop back in the discussion if I feel it can be productive, but I have learned that endless discussions like the current one only cost a lot of time and frustration and I rather work on an article like the History of horse domestication theories were the atmosphere is far more relaxed and productive. -- Kim van der Linde 19:37, 11 October 2011 (UTC)

I am sorry to see that you have left the discussion. I hope it is just temporary as you are a valuable resource to that page. Do not feel too bad by the heated discussions. Believe me, it was much worse at one time. See Archive 55 for example. So do not be disheartened. As time passes, these things tend to get a little easier. danielkueh (talk) 21:08, 11 October 2011 (UTC)

Sure, things can always be worse.-- Kim van der Linde 21:15, 11 October 2011 (UTC)

I believe it that things can be worse, but still, this has reached the point where it is just not worth my time. Right now I should be writing a review for BioEssays on how to teach evolution... the question arises as to which activity is more time-effective. Thank you both for writing here, and for your hard work, past and present, on evolution. For all that it could be better, it is still pretty good. Joannamasel (talk) 21:37, 11 October 2011 (UTC)

I understand your frustration. Why do you think I have been taking a backseat role and give my two cents now and then? :D

For what it was worth, I really appreciate your contributions to that page. I have a learned a great deal from you. Your students must be lucky. Cheers, danielkueh (talk) 21:46, 11 October 2011 (UTC)

Thanks for the feedback on my proposal. I did it in a whim and did not take it too seriously. I have incorporated the suggestions (including yours) from several different editors. Let me know how I can improve the last paragraph (I admit it is not my favorite). Thanks for that reference by Provine. I'm going to check it out. danielkueh (talk) 22:49, 14 October 2011 (UTC)

And thanks for taking feedback seriously! I'm trying to post infrequently, maybe once a day, but am always happy to chip in more when someone actually wants to listen! When the question is what is most important rather than what is scientifically true, then regular science articles by scientists are very subject to POV issues as sources. At that point, turning to professional historians and philosophers of the discipline in question as the best NPOV sources seems appropriate to me. Joannamasel (talk) 23:01, 14 October 2011 (UTC)

I understand the need for infrequent posts. I have papers that need to be done and submitted. Like you, I'm just chipping in from time to time. danielkueh (talk) 23:03, 14 October 2011 (UTC)

With respect to references, I think you might make more headway if you just cite graduate level texts. Since they constitute secondary/tertiary sources and represent mainstream views, they are much closer to the recommendations of WP:source and WP:NPOV. I think they would help resolve many of these back and forth debates. Just a suggestion. danielkueh (talk) 14:08, 15 October 2011 (UTC)

Almost every time!!!

Almost every damn time we come up with a proposal for Evolution you have something to say... ...forcing us to dig deeper, do better and thoroughly cover every important aspect that somehow has slipped by us!!

And for that, I thank you. :-) Best, Rob ROBERTMFROMLI | /_CN 23:33, 27 October 2011 (UTC)

Thanks Rob! Joannamasel (talk) 23:39, 27 October 2011 (UTC)

I second this!! A big token of appreciation for the work of Joannamasel.Thompsma (talk) 17:59, 8 November 2011 (UTC)

A barnstar for you!

	The Barnstar of Diligence
	Much thanks for pushing us (and thus the article) to be the best and bringing up so many good points, rewordings and suggestions! ROBERTMFROMLI \| /_CN 23:35, 27 October 2011 (UTC)

Feedback in Evolution as theory and fact

Hi Joannamasel!! It was a pleasure working with you in evolution - even though we had a bit of a rough beginning, toward the end I felt we had made an excellent team. I recently launched a proposal for a new lead in evolution as theory and fact and I am hoping that you could drop in for some critical feedback. I'm sure that you will have some critical feedback that I'm not going to like (at first), but in the end I see the advantage in your intelligent critical review as it leads toward superior content.Thompsma (talk) 17:56, 8 November 2011 (UTC)

I noticed your recent change - I question if population genetics is mathematical language. See discussion in talk pages.Thompsma (talk) 01:15, 10 November 2011 (UTC)

A barnstar for you!

	The Brilliant Idea Barnstar
	Joanna - You are a dedicated scientist and you have contributed brilliant work to Misplaced Pages. Thank you very much for your hard work and all the improvements you have made advancing knowledge in evolution and science. This is a small token of appreciation. Thompsma (talk) 17:44, 9 December 2011 (UTC)

Straw poll on fate of Evolutionary Biology article

Hi, this is to notify you that I have started a more indept discussion about whether the Evolutionary Biology article should be restored and in what form exactly. Please see Talk:Evolutionary_biology#Restoration_of_Evolutionary_biology for the discussion. -- Kim van der Linde 03:46, 10 December 2011 (UTC)

The IP who doesn't understand amyloid

Hi. Just in case you hadn't had all the relevant pages watchlisted, you should know that the increasingly unpleasant IP editor is playing games with signed posts. He's added {{fact}} tags a couple of times now to talk page comments from other editors (yours and mine) when he doesn't understand the stuff we've been laying out in front of him; he's also taken to deleting posts and moving them to where he thinks discussions should talk place, since we're "not following directions". You may want to know that you're now being (mis)represented as having commented directly at Talk:Amyloid precursor protein#Difference between APP and prion.

I've removed the abusive {fact} tags and restored the comment of yours he deleted from Talk:Prion, but I've left the duplicate of your comment on the APP talk page, as it very succinctly points out where the IP is utterly mistaken. TenOfAllTrades(talk) 15:12, 9 March 2012 (UTC)

Thank you so much for the headsup! I hadn't noticed these things, I'll try to pay closer attention now, thanks for the reversions! Yes, leaving the comment up as duplicate in both places is an excellent idea. Joannamasel (talk) 19:29, 9 March 2012 (UTC)

Proof by Sabotage of the opposing viewpoint

Do you see the problem with making a point weak, and then calling it fringe material, indirectly attacking Pub Med's credibility on talk:prion? 142.59.231.219 (talk) 06:57, 12 March 2012 (UTC)

Let's get the history straight here. You cited a paper on PubMed, and I rejected its relevance to the article "prion" on the grounds that the article in question did not mention prions. While a single PubMed article may not in fact mean much, notice that in this I did not in fact challenge the quality of the article in question, simply its relevance to the point you were using it to make. I then called the material you inserted in the prion article "fringe" on the basis of its lack of peer-reviewed support. A good standard for being mainstream rather than fringe would be for the material not to contradict a typical, mainstream peer-reviewed review articel on the topic of prions, and in fact, to be mentioned in at least some such reviews. Your "argument" then degenerated to throwing around words like "sabotage", and now taking this to my talk page rather than staying at talk:prion, a move that further makes things personal rather than concentrates on the material. Joannamasel (talk) 15:08, 12 March 2012 (UTC)

Dude—not cool. You've been misunderstanding or misrepresenting the literature, and Joanna's been a lot more patient with you about it than I would have been in her place. Keep discussions about the article on the article talk page; don't just show up on the talk pages of editors who have disagreed with you in order to attack them. Trying to bully someone who actually has worked professionally in the field is not a good way to improve Misplaced Pages. TenOfAllTrades(talk) 15:24, 12 March 2012 (UTC)

Discussion on lede sentence of evolution article

There is another round of discussions on the lede sentence of the evolution article, which I think could benefit greatly from your input. Cheers. danielkueh (talk) 15:40, 16 August 2012 (UTC)

There is another one, again. :| danielkueh (talk) 05:03, 17 September 2012 (UTC)

Epigenetics in evolution

Do you have any thoughts on this? Talk:Evolution#Heredity_and_Epigenetics_2 danielkueh (talk) 23:04, 12 December 2012 (UTC)

Adaptive function of meiosis

Hi Joanna, when you get a chance, could you take a look at this proposed edit (Talk:Evolution#Response_to_removed_paragraph) on the Evolution Talk Page? Although I am not fully convinced of its merits, I would prefer someone with expertise in genetics and evolution to take a gander and see if it is worth incorporating into the article. Thanks! danielkueh (talk) 02:18, 6 November 2013 (UTC)

Sequence space

I've recently started a sequence space (evolution) page and I thought you might have some good input on it given your research field. In particular, if you've any relevant diagram that might help. T. Shafee (Evo&Evo) (talk) 10:58, 16 January 2014 (UTC)

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Genetic entropy

Hello,

Would you like to take a look at genetic entropy? I get a feeling that it's just a creationist take on genetic load, and the "article" should be turned into a redirect to load, while what little content there is should be merged into John C. Sanford, since it's basically an ad for that guy's book. This is not my field however, so I'd like to check that I'm not missing something here. Since I frequently see you on genetic load, you seem like the person to ask.

Cheers — Gamall Wednesday Ida (t · c) 18:57, 1 November 2016 (UTC)

I agree with you. I think the best redirect is Genetic_load#Deleterious_Mutation, linking just to one section because the rest of the genetic load page isn't so relevant. An alternative option is Muller's ratchet, but that's only about asexual populations, so I think not as good.Joannamasel (talk) 20:09, 1 November 2016 (UTC)

Waddington and Lamarck

Hi Joanna, you certainly know far more than I do about this. However, a range of books do discuss the question of whether people thought Waddington's work was in a (neo-)Lamarckian tradition, such as Scott F. Gilbert's Conceptual History of Modern Embryology (it's easy to find others). Note 53 on page 205 says "That was not, however, how Waddington's 'genetic assimilation' was usually interpreted. While Lerner, 1958 and Merrell, 1962 saw as a way of explaining so-called Lamarckian inheritance in terms of orthodox Darwinism, two of the major interpreters of evolutionary theory, Theodosius Dobzhansky and Ernst Mayr, interpreted Waddington's theory as being a failed attempt to support Lamarckian inheritance. Both Mayr, 1963 and Dobzhansky, 1970 claimed that there was no genetic assimilation, and what Waddington saw in his experiments was merely the selection of preexisting variants in the population." It goes on to mention Lysenko (sigh).

Denis Noble's Conrad Waddington and the origin of epigenetics writes "He did not describe himself as a Lamarckian, but by revealing mechanisms of inheritance of acquired characteristics, I think he should be regarded as such. The reason he did not do so is that Lamarck could not have conceived of the processes that Waddington revealed. Incidentally, it is also true to say that Lamarck did not invent the idea of the inheritance of acquired characteristics. But, whether historically correct or not, we are stuck today with the term ‘Lamarckian’ for inheritance of a characteristic acquired through an environmental influence."

Whether this entitles us to use the adjective is debatable, but perhaps we should rather mention that others have discussed it? Would be very glad of your views on this. All the best, Chiswick Chap (talk) 09:10, 10 November 2016 (UTC)

I think this material is better discussed on the genetic assimilation page than the canalisation (genetics) page. Common usage of the term "Lamarckian" has so many problems (eg, not being central to what Lamarck said, being contrasted with Darwinism when Darwin in fact supported the inheritance of acquired characteristics), that when in doubt, I think it's better to avoid mention of it. I think it is peripheral to the case of canalisation, where the genetic assimilation section of that page serves to relate the two concepts, rather than give a comprehensive discussion of genetic assimilation.

I think it would be fine to add a "relationship to neo-Lamarckianism" section to the genetic assimilation page. In that context, the quotes you give only say that some people interpreted Waddington in neo-Lamarckian terms, not that Waddington himself saw things that way, nor that this is the consensus view of his work today, so the section would need some nuance.Joannamasel (talk) 18:30, 10 November 2016 (UTC)

Thank you for this. I'll see if I can add something sensible to genetic assimilation then. Do feel free to tweak it if I don't get the nuances exactly right! Chiswick Chap (talk) 18:58, 10 November 2016 (UTC)

I've given it a go; the article (and its referencing) remains somewhat scrappy, and the Darwinian explanation that was already there could certainly be improved. And Dobzhansky and Mayr proposed a different Darwinian explanation! If you're feeling strong ... All the best, Chiswick Chap (talk)

Hallo again (sorry), I saw your rationale for grading Genetic assimilation rather poorly, and have had another try to sort out the article, partly from one of your papers... I've cited and described Waddington's 1942 and 1953 experiments, and rationalised the repeated, fragmented and poorly cited accounts of conventional explanations of the results. It's a lot shorter, and I hope rather clearer. I'd be glad of any comments you have time to make. All the best, Chiswick Chap (talk) 15:19, 25 March 2017 (UTC)

Thanks! I had a go at improving it further. I think most of it is now in good shape, except the last section is still way off. In fact, there are a number of good empirical studies that seem to imply genetic assimilation in the wild, including Rick Shine's work on tiger snakes, and Rich Palmer's on phylogenetic patterns of symmetry breaking in lobsters and the like. One of my own papers https://doi.org/10.1093/molbev/msl172 points to a form of genetic assimilation too. I haven't followed developments super-carefully, but I would be surprised if there weren't a few more out there.

Many thanks for looking and for the leads, I'll see what I can do. Chiswick Chap (talk) 18:13, 26 March 2017 (UTC)

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Evolution discussion (new one)

Hi, Joannamasel. Long time no chat. There is a new discussion thread on the Evolution page regarding an edit made by Harvard2TheBigHouse with respect to "maximum genetic diversity." He has also edited several related pages such as "neutral theory of evolution." I don't have the time to thoroughly vet all these edits, but given your background and expertise in this area, I was wondering if you wouldn't taking a look and share your perspective? Much appreciated. Thanks. danielkueh (talk) 00:21, 14 November 2019 (UTC)

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Copyright problems

From here https://www.nature.com/articles/s41582-019-0295-9

Please be more careful. Best Doc James (talk · contribs · email) 07:29, 20 December 2019 (UTC)

Yikes! I just thought it was overly specialized material for the page, and was trying to move it somewhere more suitable. I don't know much about how to block the editor User_talk:128.12.252.4 who originally added it, and remove other damage they did, do you?Joannamasel (talk) 23:51, 20 December 2019 (UTC)

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