Category Archives: Misc.

Today at #UCDavis: Giulio De Leo “Planetary Health: novel ecological solutions for the control of environmentally transmitted diseases”


Dr. Giulio De Leo is the seminar speaker for the Ecology and Evolution Seminar Series Today Thursday, Feb. 22nd at 4:10pm in 2205 Haring Hall.

His talk is entitled: “Planetary Health: novel ecological solutions for the control of environmentally transmitted diseases”

Abstract: In the past few decades, the unprecedented rate of technological innovation has contributed to the decline of diseases that have afflicted humanity for centuries. Yet, for diseases with obligate environmental transmission, such as malaria and schistosomiasis, targeting pathogens in the human host through vaccines and drugs might not be enough. In my talk, I present empirical evidence and theoretical considerations from a field project based in Senegal to promote a more holistic approach that acknowledges the ecological complexities driving disease dynamics and investigates the interactions of people and the environment. The ultimate goal is to identify "ecological levers" we can use to develop cost-effective solutions that can improve human health and protect the environment.

For more information on Giulio and his current work, please see the De Leo lab website, https://deleolab.stanford.edu/ .

mofofospoomics Solves #TomBrady “Injury” Mystery

So – there is great controversy surrounding the “Injury” to New England Patriots quarterback Tom Brady.  See for example:

And much much more.

So – in the interest of showing the power of science and the power of microbiome science, I have decided to tackle (so to speak) the topic.  If you are not familiar with the power of microbiome science in addressing Tom Brady related controversies then you must check out the use of microbial forensics to solve the #deflategate controversy.

See “Secret microbiome forensic study reveals #deflategate culprit” and the amazing video below

So given this prior record of the value of mofofospoomics (microbiome forensics for sports)  I decided to see what we could learn about Tom Brady’s injury.

I started, as any goo microbiome study does, with collecting all the relevant hypotheses to test and not in any way doing an exploratory analysis.  So I surveyed the internet by Googling, and searched around Twitter for 3-4 minutes and I found the following plausible hypothesis:

A: Brady was really injured in practice and got a cut that was then treated with stitches and topical antibiotics.

B. Brady had surgery to add an additional finger to hold a future Super Bowl championship ring. In addition, one would assume that oral or IV antibiotics were given as part of the post surgery treatment.

See for example:

https://platform.twitter.com/widgets.js

https://platform.twitter.com/widgets.js

C. Brady and Bill Belichick are faking it to force Jacksonville to alter practice plans.

All three seem completely plausible.  I would give them each equal wait in a Bayesian prior sense. So the key question was – could one develop some ways to use a mofofospoomics approach to test for which of these three hypothesis was most likely to be correct.


The first thing to do was to make some mofofospoomics related predictions based on each hypothesis.  This actually was relatively easy.

Under hypothesis A, I would expect one key mofofospoomics related signature.  Assuming the topical antibiotics were only applied to his right hand then one would expect his right hand to have a different microbiome than his left and to look abnormal like all antibiotic treated skin samples do.   So to test for this hypothesis A all we would need would be some hand microbiome samples from him.

Under hypothesis B, I would expect two mofofospoomics related signatures.  First, one would expect Brady’s hand to show the typical signature of post surgical changes in the microbiome (see for example Grice 2014). In addition, one would expect there to be affects of the antibiotics used.   The oral or IV antibiotics would be expected to affect all of his microbiome – skin and gut for example. Thus both his hands should look like apocalypse happened relative to the microbiome.   Also we might expect the new finger to look different from the other fingers since translated parts look more like the donor than the recipient. So to test for this hypothesis B all we would need would be some hand microbiome samples from him and also possibly a fecal sample.

Under hypothesis C,  I would expect no mofofospoomics related signatures. That his, his hands should look normal.  Or maybe they should look normal for a superstar athlete.  So one would need to compare to other well known athlete microbiome signatures.

So – from examination of the possible tests for the three hypothesis it seemed that getting hand microbiome samples for Brady would allow us to use a mofofospoomic approach to determine which of the three was best.

Thus the next issue was – how to get hand microbiome samples from Mr. Brady.  First, we tried to get the gloves he has been wearing since the “injury” assuming we could turn them inside out and do all sorts of cool things.  Alas, apparently, he has not taken them off at all.rom Boston Globe

So we were left with one alternative possibility.  It is well known that before every major game, Mr. Brady destroys his cell phones to make sure that nobody can find directions to his house.  Or for some other reason. Well this is key because it is well known that phones contain a signature of the users finger microbiome whereby one can identify individuals using the phones for criminal or other investigations (see also this).

So all we would need would be to get his latest phone. To do this, we placed fake garbage cans on the path from the parking area to their training facility yesterday and .. voila .. Brady walked by and tossed something into the can.  Using our patented SmartGarbage sample collector, what he threw in was sealed inside sterile, DNA free plastic.  And later in the evening we collected it and … voila voila .. we had a smashed phone itself in a plastic bag (I guess Brady does not want people to get exposed to the cell phone dust).  Thanks Tom.

So we took the phone back to our private lab and we asked one key question that was critical to whether we could proceed.  Will it blend?  And it did.

So then we took the cell phone dust and did standard mofofospoomic analysis on it (DNA isolation, both rRNA gene PCR and sequencing and shotgun metagenomic sequencing, de multiplexing, QC).  Kit and other controls were included in every step. And we also downloaded and added sequences from studies of human skin, hands, antibiotic treated or not, cell phones, and also some controls like sports objects.

And then we we fed all the data into the new integrated MAQDADDY pipeline (a combination of Mothur, Anvi’o, QIIME, and DADA).  And we used it to test the three hypotheses.  Amazingly none of them showed a good match to the data.

For example, the Brady phone sample did not really even resemble a phone well

So this was really disappointing.  But as one last ditch effort, we decided to download all of the available microbiome data from any sample on the planet.  Like all of it.  We then reran the MAQDADDY pipeline and found an amazing result.

What I think this means is that Tom Brady had a Luke Skywalker operation.  That is, his hand is robotic.  So cool.

I just love mofofospoomics.

 

Today at @ucdavis: Katie Hinde ” More than food: how hormones in mother’s milk organize infant behavior”

​Updated with location …

This week’s Animal Behavior Graduate Group seminar:

More than food: how hormones in mother’s milk organize infant behavior

Dr. Katie Hinde

Associate Professor, Arizona State University

Friday, January 19th, 12:10 pm in Young Hall 194
Coffee and cookies will be available

"Dr. Hinde’s research focuses on how mother’s milk contributes to infant development and behavior in socially complex taxa, particularly humans and monkeys. This includes not only provision of energy and materials for growth, but also milk constituents that shape immunological, neurobiological, and behavior development. She investigates how variation in mother’s milk and behavioral care influences infant outcomes from post-natal life and into adulthood, and subsequent generations.” – The Evolution Institute

For more information on Dr. Hinde’s research: http://mammalssuck.blogspot.com/?view=classic

At #UCDavis 1/19: Katie Hinde “More than food: how hormones in mother’s milk organize infant behavior”

This week’s Animal Behavior Graduate Group seminar:
**please note that the location will be announced prior to Friday’s seminar**

More than food: how hormones in mother’s milk organize infant behavior

Dr. Katie Hinde

Associate Professor, Arizona State University

Friday, January 19th, 12:10 pm – LOCATION TO BE DETERMINED
Coffee and cookies will be available

"Dr. Hinde’s research focuses on how mother’s milk contributes to infant development and behavior in socially complex taxa, particularly humans and monkeys. This includes not only provision of energy and materials for growth, but also milk constituents that shape immunological, neurobiological, and behavior development. She investigates how variation in mother’s milk and behavioral care influences infant outcomes from post-natal life and into adulthood, and subsequent generations.” – The Evolution Institute

For more information on Dr. Hinde’s research: http://mammalssuck.blogspot.com/?view=classic

1/24 and 1/25 at #UCDavis: Peter Mumby, Storer Lecturer, on Coral Reefs

Posting as requested:

PLEASE POST AND DISTRIBUTE:

We are pleased to announce that Peter Mumby, Professor of Marine Spatial Ecology Laboratory from the University of Queensland in Australia, will be presenting two lectures in the Storer Lectureship in Life Sciences Series, “The Future of Coral Reefs,” at 4:10 p.m. on Wednesday, January 24, 2018 in the Alumni and Visitors Center and “The Connectivity, Ecosystem Overfishing and Rebuilding of Coral Reef Fisheries” at 4:10pm on Thursday January 25, 2018 in Haring Hall. Please see the attached flyer for additional information.

Copying Storify of Phil Campbell talk at UC Davis

Philip Campbell of @nature talk at @ucdavis met w/ some skepticism …

Philip Campbell of @nature talk at @ucdavis met w/ some skepticism …

Sir Philip Campbell gave a talk at UC Davis on “Challenges for Research Group Leaders”. A few people Tweeted during his talk. Here is a recap. I threaded all my Tweets with my first one below so it might be better / easier to follow the discussion if you just go directly to that Tweet.

  1. At @ucdavis: Philip Campbell of @nature talking about “Challenges for research group leaders and the support they need”
  2. @ucdavis @nature Sir Philip Campbell at @ucdavis: been on a tour of universities to push for more discussion about the “health” of research groups
  3. @ucdavis @nature Sir Philip Campbell at @ucdavis: demands on PIs have never been greater and set to grow – and system is doing less than justice to grad students, PIs, post docs, etc
  4. @ucdavis @nature Sir Philip Campbell at @ucdavis: thinks that we need to shift how we evaluate academics away from impact factor towards personal narratives and selection of key products
  5. @phylogenomics @ucdavis @nature LMFTFY Campbell will speak on “Challenges for WHITE MALE research group leaders and the support they need” Maybe a toss away slide for POC/Women pic.twitter.com/rnLITkvsIo
  6. @ucdavis @nature Sir Philip Campbell at @ucdavis: discussing benefits of preprints but also pressures that come to PIs after publications
  7. @ucdavis @nature Sir Philip Campbell at @ucdavis: supports post publication review but says some aspects of places like PubPeer can be very harsh
  8. Hey @PsyArXiv - you're in Philip Campbell's talk (EiC of Nature). He's encouraging authors to use preprint servers. @improvingpsych https://t.co/Uzbji33LZR

    Hey @PsyArXiv – you’re in Philip Campbell’s talk (EiC of Nature). He’s encouraging authors to use preprint servers.
    @improvingpsych pic.twitter.com/Uzbji33LZR
  9. When @nature editor Campbell was in MN giving a similar talk, multiple women said he spent downtime joking about “women in the kitchen” and such. HILL-arious.  https://twitter.com/phylogenomics/status/935207488084893696 
  10. @ucdavis @nature Sir Philip Campbell at @ucdavis: going through list of many of the new @nature journals (though I am not sure what the point of this list is)
  11. @ucdavis @nature Sir Philip Campbell at @ucdavis: says he thinks @nature adds value to publications (peer review, editing, distributions, visibility, amplification, permanence, etc)
  12. @ucdavis @nature Ugh – Sir Philip Campbell at @ucdavis just gave props to Kent Anderson of Scholarly Kitchen – says he is worth reading – I disagree
  13. Apparently I’m just going to sit here from afar and heckle @phylogenomics twitter stream on @nature editors blah-blah about promoting science. pic.twitter.com/GDm1tE8U3w
  14. @McLNeuro @nature please continue – I am trying for now to post what he is saying and don’t have time to heckle much
  15. @ucdavis @nature Campbell at @ucdavis: making claims about the editorial process at @nature and says they have a strict focus on the significance of the research not other values (though I don’t believe this ..)
  16. @phylogenomics @ucdavis @nature Pressures on PIs like needing to have 4 post docs work for 4 years to get a @nature publication? Like that kind of pressure? pic.twitter.com/36n3pVwwrU
  17. @ucdavis @nature Campbell at @ucdavis: claims that they don’t think about citations when reviewing papers (again, I don’t believe this) ..
  18. Wait….sprinkle some holy water on Sir Phillip and see if he burns for this lie! Also, WTF is up with their dumbass editorials and mansplaining?  https://twitter.com/phylogenomics/status/935210672954081280 
  19. @phylogenomics Sure, not when reviewing; when deciding to send out to review 🙂
  20. Editor in Chief of Nature: editors don't consider who author is, "authorship is not the point" (See pic) But double-blind review is optional https://t.co/jWuIm9VN77

    Editor in Chief of Nature: editors don’t consider who author is, “authorship is not the point” (See pic) But double-blind review is optional pic.twitter.com/jWuIm9VN77
  21. @ucdavis @nature Campbell at @ucdavis still spending a lot of time praising the @nature review system and nothing about research groups and the support they need …
  22. Tell me more about the values of @nature editors who doxx pseud female bloggers. 🍿🍿🍿  https://twitter.com/phylogenomics/status/935210672954081280 
  23. This doesn’t work. Editors and reviewers are human. You can’t just tell them to ignore who the authors are.  https://twitter.com/siminevazire/status/935211323423571968 
  24. Only someone who hasn’t read Anderson, or tried to argue in good faith with him, could say that. Than again, Nature is a for-profit anti-science scam so perhaps ol’ Phil believes his own bullshit.  https://twitter.com/phylogenomics/status/935210038594912257 
  25. @ucdavis @nature Campbell at @ucdavis: discussing most cited and least cited papers from 2010 (again, not sure of the point here)
  26. Don’t forget the @nature thought piece where they let a @UofR male faculty member speak out about…using the word ‘obviously’. While neuroscience women were being harassed and silenced by their administration.  https://twitter.com/phylogenomics/status/935212221054861312 
  27. @ucdavis @nature Campbell at @ucdavis: now discussing other demands on PIs including refereeing papers (note – I recommend nobody review for @nature doe to their #closedaccess policies)
  28. Also, the submission and publication fees to glam journals – those will set a new PI back a bit!  https://twitter.com/phylogenomics/status/935213122926690304 
  29. At @ucdavis talk by Nature editor in chief. Can’t wait for Q & A – pretty sure @phylogenomics will make it interesting.
  30. @ucdavis @nature Campbell at @ucdavis: editorial preoccupations at @nature – multidisciplinary, reproducibility, pressures on younger researchers, mentoring
  31. Editor in chief of Nature: survey results, what would improve reproducibility? "Journals enforcing standards" towards the bottom 🤔 https://t.co/tcE4yCUNU3

    Editor in chief of Nature: survey results, what would improve reproducibility? “Journals enforcing standards” towards the bottom 🤔 pic.twitter.com/tcE4yCUNU3
  32. @phylogenomics @ucdavis @nature Are you KIDDING ME??? Nature publishes all the punching down editorials on trainees about how there are no jobs, they need to work more – UGH. @nature is the problem. pic.twitter.com/wGDAcd2PbC
  33. I bet Campbell isn’t even at UCDavis and @phylogenomics is just tweeting to make me have a stroke. pic.twitter.com/QP9LEV3L5u
  34. @siminevazire @ucdavis @phylogenomics You should make it interesting. They are notoriously anti-female, beat down on trainees and driven by money not science.
  35. @phylogenomics @ucdavis @nature So…he’s just making a list of problems that @nature contributes to? Is that a fair summary of his talk thus far? Let’s get to some solutions there, Sir Phillip pic.twitter.com/BsTHoQJ8m3
  36. @phylogenomics @ucdavis @nature I did think they had dropped it from their advertising tho.
  37. @ucdavis @nature At @ucdavis Campbell says should ask who is setting the pathological incentives for publishing in @nature – implies @nautre has 0 to do with this
  38. @sennoma @siminevazire @ucdavis @phylogenomics I’m an assistant professor. You never have enough power, money or friends. I don’t get paid enough to not have an opinion when people are being punched down on.
  39. @sennoma @McLNeuro @siminevazire @ucdavis @phylogenomics Is @phylogenomics willing to communicate questions from the Twitter audience? 😈 The speaker should know that the world is watching & listening….
  40. Editor in chief of Nature: "Everyone complains about incentives. Who is in charge of incentives?" https://t.co/aMb0qrV7OM

    Editor in chief of Nature: “Everyone complains about incentives. Who is in charge of incentives?” pic.twitter.com/aMb0qrV7OM
  41. @JoshFessel @sennoma @siminevazire @ucdavis @phylogenomics Actually, it’s just the five of us who are riled up. Everyone else is on about the royal wedding.
  42. @McLNeuro @siminevazire @ucdavis @phylogenomics I may have misread and/or miscommunicated. I meant that I didn’t feel right telling someone they should stir shit, when it’s them not me who’s going to live with the fallout. But I’m 100% pro-shit stirring!
  43. @ucdavis @nature At @ucdavis: Philip Campbell lists some solutions to PI challenges – none of which seem to involve any changes by @nature
  44. @phylogenomics My favorite quote so far: every year we give a mentor award in a different country, last year was in the west coast. CA, OR, WA. Ha! The #bluewall has begun.
  45. @ucdavis @nature At @ucdavis: Philip Campbell says people can apply pressure to make change (e.g., refs using Athena SWAN system for awarding grants but then says Nature would not use such information to decide on papers
  46. @phylogenomics @ucdavis @nature If decisions abt promotion, tenure, & funding continue to be at least in part “outsourced” to high impact journals, that means @nature is in a powerful position as a change agent.

    How is @nature going to use that power to the benefit of scientists & science? Help us.

  47. @ucdavis @nature At @ucdavis: Campbell – I asked what @nature is doing in regard to better support advancement of minorities and women
  48. @ucdavis @nature At @ucdavis: Campbell in response to my ?? mentions the whitewashing Editorial and says it was bad … and then is now discussing the editorial I referred to  http://www.nature.com/news/nature-s-sexism-1.11850 
  49. @ucdavis @nature Now @siminevazire following up my question saying that there almost certainly is status bias and other biases in review and suggests they should address that
  50. @ucdavis @nature Also @siminevazire points out that @nature is partly responsible for the problems for PIs even though Campbell implied otherwise
  51. @ucdavis @nature Question for Campbell – asking about gaming the system and bad papers in high profile journals – those people benefit from this
  52. Mindless data-crunching made bearable with 2nd monitor showing live tweet commentary by @phylogenomics during Nature’s editor-in-chief talk at @ucdavis. I feel like I should pay for this entertainment.
  53. @phylogenomics @ucdavis Not to take anything away from the serious issued being raised though. Just loving the approach…
  54. @phylogenomics @ucdavis @nature Q re: overhyped writing style you sometimes see in Nature. How do you keep editors from rejecting papers that are conservatively written?
  55. @phylogenomics @ucdavis @nature A: point me to papers you think are overstated and we’ll take a look.
    [His email is p.campbell@nature.com]
  56. @phylogenomics @ucdavis @nature Doesn’t answer question about how to give cautiously written papers a chance, which is great question.
  57. In response to my Q, editor in chief of Nature says they’re now trying to make desk reject decisions w/o editor knowing author’s identities.
  58. All journals/editors should do this, in my opinion. Perhaps the easiest change we can make with potentially big impact.  https://twitter.com/siminevazire/status/935232856242077697 
  59. @McLNeuro @phylogenomics Oh gawd that gif brings back memories.
    “Ya hear that Elisabeth? I’m coming to join ya honey!” Lol #GoogOldDays
  60. I like the phrase “credibility revolution” – it captures both openness/transparency & reproducibility/rigor goals
     https://www.econstor.eu/bitstream/10419/36365/1/621208477.pdf 
  61. Like this thread @phylogenomics but Pro-Tip: You don’t have to call him “Sir” every time just ‘cos some hereditary rich old cow across the pond 🇬🇧 says so!  https://twitter.com/phylogenomics/status/935207488084893696 
  62. @PSBROOKES I stopped it a few Tweets in – I think I copied that from somewhere and just pasted it in for a few tweets and then felt embarrassed …
  63. @phylogenomics @ucdavis @nature As a former Nature imprint interviewee I LOL hard at this. It was obvious from the interview what they were looking for (not that it isn’t blatantly obvious…)