tag:blogger.com,1999:blog-10781944.comments2024-03-17T21:38:11.530-07:00 The Tree of LifeJonathan Eisenhttp://www.blogger.com/profile/07953790938128734305noreply@blogger.comBlogger5541125tag:blogger.com,1999:blog-10781944.post-27772213278575461422022-08-22T17:02:34.327-07:002022-08-22T17:02:34.327-07:00I am not in favor of the current campus COVID-19 p...I am not in favor of the current campus COVID-19 plan, particularly the removal of the mask mandate.<br /><br />When we resumed in-person instruction at UC Davis in Fall 2021, I was prepared for lots of arguments and non-compliance with the mandatory mask policy. I developed a plan for how to deal with non-compliance and trained my TAs on the plan. Over the course of the 2021-2022 school year, with a combined enrollment of over 2300 students, I heard zero complaints about the masks and didn’t have a single case of non-compliance that even came to my attention, let alone rising to the level of needing to initiate a disciplinary referral. Zero. That shows that, at least in my very large sample size of biology students, students will wear masks without complaint if they are required to do so. Given that there didn’t seem to be much of a push from students to drop the mandate, I’m confused about the rationale to do so, particularly when other universities and colleges have either kept their mandates or have reinstated them for Fall semester. <br /><br />I understand that running the testing program is very expensive and likely isn’t sustainable long-term. However, if we need to cut the testing program for financial reasons, it would make sense to at least keep the mask mandate as a precaution. During the last school year, I averaged 1-2 students per week that were testing positive (mostly through the campus surveillance program). I always asked how they were doing after they let me know that they had tested positive – most said that they were either asymptomatic or had very mild symptoms. This means that in the absence of required surveillance testing, those students would have come to class.<br /><br />If we’re not testing anymore, there will be more students with COVID in the classrooms, so requiring masks would be a sensible precaution. Now that masks are optional, I’m seeing only about 40% of my students wearing masks. Given the still high levels of community spread, some of those unmasked students are likely to be positive.<br /><br />I think it’s also important to consider the impact of students and staff testing positive. For students, immediate make-up work may not be an option (particularly near the end of the quarter), resulting in them needing to complete the course in a future quarter, potentially delaying graduation. I currently have one TA and my co-instructor that are out sick, which has resulted in us needing to temporarily shift to remote lectures and in me needing to cover 12 hours of lab instruction. That’s not sustainable and doesn’t provide a consistent learning experience for students.<br /><br />I’m really concerned about what’s going to happen in Fall quarter if we proceed with the current plan. The course I support will have 32 lab sections and 16 TAs, so staffing shortages could quickly overwhelm my ability to provide coverage for absences, leading to some lab sections needing to go remote, resulting in those students missing the hands-on aspects of the lab. In my opinion, dropping mandatory testing, but keeping the mask mandate would be a reasonable and relatively low-cost intermediate step on our road to the post-COVID era. Requiring masks would reduce transmission, reduce student absences, and cut down on staffing shortages – a lot of benefit for a relatively low impact intervention.gkbennhttps://www.blogger.com/profile/08743882908582790383noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-40600447474067356272019-10-09T00:40:03.595-07:002019-10-09T00:40:03.595-07:00Do you feel his books are basically the same? Any ...Do you feel his books are basically the same? Any value out of them? I just read microbiome diet and it seems full of quackery.Coultashttps://www.blogger.com/profile/04105978408078264152noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-7484728022235035462019-09-30T06:36:45.786-07:002019-09-30T06:36:45.786-07:00What do you think about Raphae kellman publishing ...What do you think about Raphae kellman publishing three different microbiome books? But not explaining why he needs three?Coultashttps://www.blogger.com/profile/04105978408078264152noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-8564733647012710362019-07-29T08:29:03.917-07:002019-07-29T08:29:03.917-07:00Sadly, as I sit here in July 2019 it appears SRA h...Sadly, as I sit here in July 2019 it appears SRA has improved little. I am trying my best to meet the requirements for a Nature Communication manuscript that has been accepted for publication. After 5 days now I am ready to submit a couple of files just to get the SRA id and call it good.pkMyt1https://www.blogger.com/profile/08886404667475830627noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-65194866087754589142019-03-11T19:41:18.459-07:002019-03-11T19:41:18.459-07:00Hi Jonathan,
Many lovely shots there, I've be...Hi Jonathan,<br /><br />Many lovely shots there, I've been following you on Instagram for a while now. I have a Nikon D7200 and a manual focus 300mm lens from the 80s that also has a learning curve. There's a rule of thumb that you want your shutter speed to be at least the inverse of the focal length, so at 500mm a shutter of 1/500th or less, which I think works well at normal ranges but does not scale to long zooms. For my 300mm (which on my smaller sensor works out to more like 420mm) I find I have to be at 1/2000 or faster to get a nice result. The other thing I've found with this zoom is the depth of field at wide apertures is quite shallow, so if you're set at f5.6 for example only a few inches of the depth will be in focus. I get substantially nicer results at f11 or f16, however that wants to slow down the shutter speed. So I end up using manual mode (M on the dial) and underexposing a couple of stops if necessary, and then bringing back that detail in post. Plus I set the ISO max to about 6400 I think to avoid too much noise in the monochromatic sections. Here are some shots from a political thing I went to last summer, this is where I learned that people at a podium moved back and forth too quickly to use an aperture larger than f8:<br /><br />https://www.facebook.com/brettrpike/media_set?set=a.663208384060558&type=3<br /><br />And here is a parade at the capitol, lots of light made it easy to shoot fast enough to capture motion crisply. I do photograph things other than leftists but, well, it's a small sample. <br /><br />https://www.facebook.com/brettrpike/media_set?set=a.572607203120677&type=3<br /><br />I'd be happy to discuss more; I don't think I can stop using Nikon at this point as I finally know where most of the menu options are. See you around. Brett Pikehttps://www.blogger.com/profile/03467997066673161501noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-21592011367453060322019-03-07T17:17:48.917-08:002019-03-07T17:17:48.917-08:00This is a dog bites man posting, Jonathan. Not a c...This is a dog bites man posting, Jonathan. Not a cheap shot at Marie Claire perhaps, just an obvious one if you're feigning shock that a fashion magazine tailors its editorial to advertisers (potential or real). That said, Mother Dirt is a pretty good product. Like "unsteadily" I've been using since 2016 with similar results. Diminished need to shower, less dermal dryness and itchiness (although that could be a function of only needing 90 seconds shower time). I ditched the shampoo (too astringent and the packaging design was not durable )and found the mist product to be pointless. (Isn't the point of a probiotic additive supposed to be microbial diversity? How does an unchanging mist provide diversity?) But the cleanser is an excellent product and not much of a price premium over some OTC soaps. I did all this when I went vegan and wanted my exterior biome to be as healthy as my gut biome.Mark Reiterhttps://www.blogger.com/profile/12394336937441767154noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-58725785592768472532019-02-27T17:38:52.903-08:002019-02-27T17:38:52.903-08:00Jon.. Thanks, as always, for your blog.
Below is a...Jon.. Thanks, as always, for your blog.<br />Below is a copy of an opinion I made yesterday in response to the Mark Perry post:<br /><br />"Those of us old enough to have routinely attended many all-male symposia in the past will tell you the difference between them and the current UCSD symposium is that, until recently, few of those past speakers felt anything was amiss and needed to change. In contrast, I don't think anyone honestly believes that any of the speakers in the UCSD symposium want to continue to be part of single-gender presentations. This meeting is obviously a one-off, meant to make a splash, which it successfully has. <br /><br />The fact is that men still hold a vast majority of STEM faculty positions in essentially every university, in spite of women receiving 13 million more degrees than men since 1982. So, we men continue to get more than our share, and should stop looking whiny or hysterical until, if ever, there's an actual problem.<br /><br />I am delighted to be one of the (hopefully numerous) senior men in the microbiome field who will attend the UCSD symposium, and I am also confident that women, unlike men, will never let such single-gender events become the norm."Anonymoushttps://www.blogger.com/profile/10491383809672434739noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-42432086774673045532018-09-09T18:03:45.264-07:002018-09-09T18:03:45.264-07:00Hooray for sea cucumber poop! Hahahahaha!(yes, I&#...Hooray for sea cucumber poop! Hahahahaha!(yes, I'm a grown woman)Anonymoushttps://www.blogger.com/profile/14085388098942870218noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-8129197531676749212018-07-07T19:42:50.529-07:002018-07-07T19:42:50.529-07:00Perhaps time would be best spent studying, and com...Perhaps time would be best spent studying, and commenting, how indigenous tribes have been found, and studied, to have twice the diversity in their microbiome that other people do. Shame when so many people, especially children, who suffer from what may most likely be due to long term scientific ignorance/ ego's... others chose to sit and argue against issues that they know little about. As it can be now seen... science and modern medicine are simply BEGINNING to learn about the different types, and roles, of what is now being called "Friendly bacteria" not long ago most bacteria were simply called GERMSAnonymoushttps://www.blogger.com/profile/07671849838921402253noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-29119614206789919142018-06-25T01:05:18.599-07:002018-06-25T01:05:18.599-07:00And then there is the fact that they used the word...And then there is the fact that they used the word "flora". AaarrrgggghhhhhDr Anitorihttps://www.blogger.com/profile/01562449380059332412noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-64334276283944491632018-03-20T14:23:02.802-07:002018-03-20T14:23:02.802-07:00I have not removed a single comment here Mollie. I...I have not removed a single comment here Mollie. I have no clue what you are talking aboutJonathan Eisenhttps://www.blogger.com/profile/07953790938128734305noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-19157578305362715172018-03-20T14:21:52.791-07:002018-03-20T14:21:52.791-07:00Why have a comment section Professor Eisen if you ...Why have a comment section Professor Eisen if you are simply going to remove people's comments and recharacterize them as you see fit? And by taking down my comment, a WOMAN who is very active in the microbiome space, aren't you doing exactly the same thing you accuse almost everyone else of? Silencing women's voices in the space? As unfair a characterization I am sure as the one you have leveled against me.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-10781944.post-43924154325056635582018-03-19T22:31:07.958-07:002018-03-19T22:31:07.958-07:00This comment has been removed by the author.Skin Care Junkiehttps://www.blogger.com/profile/10461640929599600621noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-29973905640476429372018-03-19T11:55:09.593-07:002018-03-19T11:55:09.593-07:00Thanks Jonathan. As you know from our emails, I h...Thanks Jonathan. As you know from our emails, I have had a similar email conversation with Jeremey Berg with a similar outcome. This is a great summary of a very unfortunate decision by Science's editors, and as a AAAS Fellow I am disappointed.Mark Phttps://www.blogger.com/profile/14462250693712068754noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-17816234541438501252018-03-09T19:08:15.576-08:002018-03-09T19:08:15.576-08:00This is awesome. I think you probably did coin it....This is awesome. I think you probably did coin it. Jonathan Eisenhttps://www.blogger.com/profile/07953790938128734305noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-89887621343268191312018-03-09T19:03:25.726-08:002018-03-09T19:03:25.726-08:00Leaving this article here too - I used the term YA...Leaving this article here too - I used the term YAMMMM in my piece from last year. Not sure if I coined it or not �� Carly Rosewarne (@microbialme) https://npjbiofilmscommunity.nature.com/users/36624-carly-rosewarne/posts/15921-we-re-in-a-state-of-dysbiosis-gender-inequity-on-microbiome-conference-speaker-panelsAnonymoushttps://www.blogger.com/profile/14444909433603274747noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-8044774356176069912018-03-04T17:40:06.416-08:002018-03-04T17:40:06.416-08:00Thanks for posting this. Not sure if you say the ...Thanks for posting this. Not sure if you say the Twitter Moment I made about the criticisms of this idea, many of which I think are valid. I am a bit torn - I really want Acknowledgements to be more useful but some of the criticisms about where this could lead are kind of spot on so am rethinking the idea. Jonathan Eisenhttps://www.blogger.com/profile/07953790938128734305noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-66780193927666169272018-03-04T16:37:04.672-08:002018-03-04T16:37:04.672-08:00My experience today, doing this for a manuscript w...My experience today, doing this for a manuscript where I am turning in the final post-revisions version today, so I figured I would add this:<br /><br />Of eight academics we had decided to thank in Acknowledgements, all of them active and publishing, only 4 had ORCID IDs that we could be reasonably sure were correct. Two of these, however, had no public information linked to them, so technically we were just assuming we had the right person. One name was common and there were dozens of ORCID IDs to try and search through to find the guy, and after clicking on them all, most of those were set to private, none were clearly him, so I put nothing for that one. The others brought up nothing on the ORCID search page.<br /><br />In terms of the likely rewards/credit, adding the ORCID IDs seems likely to be pointless to me at the moment. Perhaps if it were universally done, it would move up to a minor positive impact, but the work involved to make it "fair" - i.e., every academic has a public ORCID ID profile and sufficient identifying information - is substantial, and arguably yet another uncompensated burden. On the other hand, perhaps putting up your profile publicly indicates that you do consider labeled kudos worthwhile.<br /><br />Probably the main reason to give names in Acknowledgements is to let those people know themselves that their help is appreciated, it seems like that doesn't change with/without the ORCID ID. And, perhaps another potential criticism of ORCID IDs in the Acknowledgements is that it is yet another step towards pseudo-quantification and monetizing of academic labor.<br /><br />But, whatever, I figured I'll try it this time, mostly to see how the journal reacts.NickMhttps://www.blogger.com/profile/04765417807335152285noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-81081045717237458962018-01-21T08:21:33.943-08:002018-01-21T08:21:33.943-08:00Nice entry and cool blog :)
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Niskie ...Nice entry and cool blog :)<br /><br />_____________<br /><a href="http://www.ceneo.pl/" rel="nofollow">Niskie ceny</a>Georgehttps://www.blogger.com/profile/07693837900956930880noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-81531988196048533632018-01-11T21:17:34.155-08:002018-01-11T21:17:34.155-08:00That’s what I was looking for. I am talking about ...That’s what I was looking for. I am talking about all topics bundled in this blog. They all are really very useful for me as well as for my team. We are definitely going to use its highlighted information.<a href="https://www.fastvip2541.com/" rel="nofollow">แทง บอล ออนไลน์</a>Maichahttps://www.blogger.com/profile/12496451885881421230noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-79785383655371191942018-01-02T04:14:21.883-08:002018-01-02T04:14:21.883-08:00One of the most important considerations you'l...One of the most important considerations you'll need to give to your business meeting is where you're going to hold it. Whether you are going to use <a href="https://eventup.com/venues/san-francisco-ca/" rel="nofollow">meeting space San Francisco</a> or your own office or exploring potential alternatives, be sure that it fits the occasion.Rammy Joneshttps://www.blogger.com/profile/16867908057027874837noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-40558266139478023452017-12-29T12:37:18.458-08:002017-12-29T12:37:18.458-08:00Nice Its a Viral Video now Keep PostingNice Its a <a href="https://viralvidos.com/" rel="nofollow">Viral Video</a> now Keep PostingPaul Martinhttps://www.blogger.com/profile/13093904132973264479noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-89741242738154339982017-12-14T20:48:16.906-08:002017-12-14T20:48:16.906-08:00Look what else I found --- email announcing semina...Look what else I found --- email announcing seminar by you and David G (I think practice for your talk at Snowbird): (It looks better in Courier Font I think)<br /><br />******* SPECIAL SEMINAR ********<br /><br /> FRIDAY JUNE 4, 1993<br /> 12:00 NOON<br /> GILBERT 117<br /><br /> An Improved Molecular Distance Measure -<br />Noise Abatement in Phylogenetic Reconstruction<br /><br /> DAVIDS<br /><br /> G<br /> O<br /> POLLOCK<br /> D<br /> S<br /> T<br /> E<br /> I<br /> N<br /><br />*************************************************<br /><br />Anyone interested in molecular phylogenetics should<br />be interested in this. <br /><br />JonathanJonathan Eisenhttps://www.blogger.com/profile/07953790938128734305noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-46209870460616005402017-12-14T20:41:03.327-08:002017-12-14T20:41:03.327-08:00lmao, I was thinking that you were extremely kind ...lmao, I was thinking that you were extremely kind to Goldstein and I not to!David Pollockhttps://www.blogger.com/profile/05439014250240247459noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-12246073132023188242017-12-14T20:30:14.696-08:002017-12-14T20:30:14.696-08:00the real question is - should I comment about the ...the real question is - should I comment about the ride back?Jonathan Eisenhttps://www.blogger.com/profile/07953790938128734305noreply@blogger.com