Saturday, March 23, 2019

Blog post w/ Twitter thread about Twitter threads & blog posts & how to turn a Twitter thread into a blog post

So I am writing a blog post here where I have captured a Twitter thread about blog posts and Twitter threads. I saw a Tweet from Pat Schloss and responded to it:
But that was not the only Tweet I made about this. I made a whole frigging thread. You can see the thread in most Twitter clients by clicking on the Tweet. But I figured I would also capture the thread here in this blog post. Tweet #2 in the thread.
Tweet #3 in the Thread.
Tweet #4 in the Thread.
Tweet #5 in the Thread.
Note - I got the embed codes for these Tweets from Twitter by selected the drop down menu in the upper right of the Tweet which I see in Safari at the Twitter site. I am not sure if this shows up in all Twitter clients but it works on the Twitter web site.



This gets me this menu


I then selected "Embed Tweet" and it gives me this



I then selected customization options because when posting all the Tweets I wanted just the Tweets and not the full conversation of the Tweet. First you get this menu:



I then selected "Hide Conversation"


And clicked update and then it showed me the new Embed code.  I then copied it and inserted it into this blog post.  I did this for each of the five tweets shown above.

And Voila - I have a blog post with a Twitter thread embedded in it where the thread discusses blog posts vs. Twitter threads.

Also - one can also include other Tweets about the same topic here.  So for example I can include responses too ...

Like this one.

If a thread is long, this is a real pain.  A much easier though less controllable approach is to use Wakelet or Twitter moments.  However, since Twitter seems to be abandoning moments as far as I can tell, Wakelet seems a better option


Here is the Wakelet I made --- Anyhow - there you go. A quick guide to turning a Tweet thread about blog posts and Tweet threads into a blog post.

Playing with iNaturalist Places ..

So - have been experimenting a bit with iNaturalist. Just testing some embedding here. This embed is for a "place" where I do a lot of birding - the rural areas between Davis and Woodland. I love that with iNaturalist I can outline my own places on maps so am going to see how this goes. It should show observations from this area ...

The place is: https://www.inaturalist.org/places/rural-areas-between-davis-and-woodland
 

Friday, March 15, 2019

The "Ben Franklin Award for Open Access in the Life Sciences" should be renamed as a "#Manward"

Uggh.

So in 2011 I won this award called the "Benjamin Franklin Award for Open Access in the Life Sciences. "  I was happy about it at the time.  I got a book and a plaque and was toasted at a meeting in Boston.  A few years ago I and others noted that the award had been given only to men.  Then Helen Berman won the award in 2014 and it looked like maybe the process was starting to not be so biased.

But I got alerted to the ongoing issues again by an email a few days ago.  And not only have the other winners all been men, all four nominees this year are men too.

Past Winners
  • 2002 – Michael B. Eisen
  • 2003 – James Kent
  • 2004 – Lincoln D. Stein
  • 2005 – Ewan Birney 
  • 2006 – Michael Ashburner 
  • 2007 – Sean Eddy 
  • 2008 – Robert Gentleman 
  • 2009 – Philip E. Bourne 
  • 2010 – Alex Bateman 
  • 2011 – Jonathan A. Eisen 
  • 2012 – Heng Li 
  • 2013 – Steven Salzberg 
  • 2014 – Helen M. Berman 
  • 2015 – Owen White 
  • 2016 – Benjamin Langmead 
  • 2017 – Rafael Irizarry 
  • 2018 – Desmond Higgins
That comes to 16:1 M:F.  

Yuck.  This just is not reflective of the contributions of people to open access in the life sciences. There are many many many women who have made important contributions in this general area.  

When I won the award I was happy but I did notice the gender bias of the winners although that was when I was kind of just waking up to the issue of gender bias in STEM.  I tried to get people to nominate more women for the award the next year via FriendFeed, Twitter, email and other means.  For example: 


But that effort went nowhere I guess.  Helen Berman did win in 2014, but for the last four years it has been all men again.  Uggh.  At this point I think the only conclusion is that there is some bias in the system.  It is actually quite hard to figure out on the web just who is behind the whole award thing anyway.  It is given out by the "Bioinformatics.Org" group.   But the web site does not really have any details about what the group actually is.  There is a page for the award: https://www.bioinformatics.org/franklin/. And then there is a link to information about the selection process.

Here is the summary:

The selection process

  1. Nominations may be submitted by members of Bioinformatics.org using this form (you must be a member and logged in).
  2. Any person may be nominated, but the final list of nominees will be determined by Bioinformatics.org, based on the following criteria:
    • All nominations must be submitted by current members of Bioinformatics.org.
    • Self-nominations will not be counted.
    • Nominations of past laureates will not be counted.
    • There must be evidence that the nominee has done something to promote open access in the life sciences.
    • After the above exceptions have been considered, there must remain at least two (2) nominations per nominee (a member must ``second'' each nomination).
  3. The list of nominees will then be presented for a vote, on a ballot, to the members of Bioinformatics.org.
  4. The time given for all votes to be collected will be specified on the ballot.
  5. The nominee with the most votes will be the initial consideration for the Award. There will not be a run-off vote.
  6. The initial consideration for the Award will then be contacted. He or she must be willing and able to accept the Award in person at the time of the ceremony.
  7. If the initial consideration will not accept the Award in person at the time of the ceremony, then the nominee with the next most votes will be considered. And the process will be repeated until a laureate is found or until the list of nominees is exhausted.
  8. An announcement about the identity of the laureate will be made sometime prior to the ceremony.
Well, that sounds, umm, not ideal.  No committee.  No names of members who do any of the reviewing.  So - my guess is that the gender bias in the award is connected to this highly anecdotal review process.  Pretty disconcerting.  I thus think this award should be renamed "The Ben Franklin Award for Men"


UPDATE:

Sunday, March 10, 2019

Stalking the wild garganey in West Sacramento #birding #eBird #iNaturalist #birdphotography #nikonD500

So - I did a thing today.  A new thing for me.  I officially became a bird nut.  For the first time in my life, I went on an outing to see a rare bird that I read about online.

I went to West Sacramento, to a pond there, to see, and hopefully take pictures of, a garganey.  What, you ask, is a garganey?  It is a kind of duck.  According to Wikipedia:
The garganey (Spatula querquedula) is a small dabbling duck. It breeds in much of Europe and western Asia, but is strictly migratory, with the entire population moving to southern Africa, India (in particular Santragachi), Bangladesh (in the natural reservoirs of Sylhet district) and Australasia in winter,[2] where large flocks can occur. This species was first described by Linnaeus in 1758. Like other small ducks such as the common teal, this species rises easily from the water with a fast twisting wader-like flight.

So - kind of boring in some sense.  Just another duck right?  But the key for my outing today is that it is not a normal resident of Wast Sacramento, or Central California, or California, or North American even.  It is, as my National Geographic bird field guide says in a colonialist phrasing "An old world species" 

So when one was spotted a few weeks ago in the West Sacramento area, the birders got very excited.  And they started to share information about it on Facebook, and eBird (which is where I heard about it) and Twitter and such.  And it even made the news: Bird Watchers Flock To West Sacramento To Catch A Glimpse Of Rare Bird

So why, you may ask, did this interest me?  Well, I have been a birder, on and off, since I was a kid.  Birds, and birdwatching, are what got me into nature, which then got me into natural history, which then got me into biology, which then got me to where I am now.  For example, my first science job, doing field in the summer of 1988, involved studying hummingbirds in Colorado at the Rocky Mountain Biological Laboratory with Bill Calder from Arizona.  

More recently, I have rediscovered birding and bird science.  From a birding point of view, I got back into birding when we went on a trip to Costa Rica a few years ago.  For that trip, I got my first good pair of binoculars (Leica Trinovid 8 x 42) I have ever owned.  And I got my first digital SLR camera (a Nikon D80) and a nice lens (a Nikkor 70-200 f/2.8).  This was a great set up to have. although I confess I never fully learned all the ins and outs of using it for photography.  I mean, I used it a lot, but I never learned how to do much other than leave it on auto settings and use some of the "scene" settings to vary things up.  I wrote some blog posts about birding in the area on and off too and also started to spend a lot of time in Yolo Bypass nearby Davis.  See for example:
I even made some collections of my better pics. For example see

From a science point of view, I have been slowly trying to do more bird work in my lab.  And since I study microbes, the easiest thing to do seemed to be to study bird associated microbes.  I tried to get a project going on microbes of Darwin's Finches and to jump start this I even helped sequence one of the finch genomes.  See Nice timing: Our paper on the Darwin's Finch genome is out today on Darwin's birthday.  But we never got funding to work on the finch microbiomes (though am still interested in that).  But I have gotten involved in a few bird microbiome projects recently and am doing a few more now and looking for others.  See for example  The cloacal microbiome of five wild duck species varies by species and influenza A virus infection status and Community-level differences in the microbiome of healthy wild mallards and those infected by influenza A viruses and Genome Sequence of a Multidrug-Resistant Strain of Bacillus pumilus, CB01, Isolated from the Feces of an American Crow, Corvus brachyrhynchos

And I should note that I also have been going on and on and on about how microbiologists could learn a lot from birders and how I think we need a "Field Guide to the Microbes."

So, yeah, birds and birding were and are bigs parts of my life.

Anyway, back to the garganey.  Why was I checking out eBird reports and following reports of bird sightings?  Well, because I REALLY rediscovered birding in the last two months.  This happened because after about two years of pondering, and about 1 year of serious research, I got a new camera and lens specifically to do more bird photography.  In order to choose what camera to get, basically, I looked and looked and looked and finally found someone online who made recommendations for bird photography that I really trusted.  This person is Mark Smith.  And I found his recommendations via the oracle of Google and then watched a series of his videos on Youtube about comparing and contrasting different set ups for bird photography.  Especially bird in flight photography.  This had been my bane in a way.  I just felt like with my current birding set up I was not able to get close enough to birds or get good pictures of them in flight. And Mark Smith's videos showed me how I could get to the next level.  Based on his videos I finalized my choice to a Nikon D850 w/ a crazy fancy lens (for more than $10,000) or a Nikon D500 with a Nikkor 200-500 mm lens for about $3000.  I decided on the $3000 option both to save money and because I was not sure I would really use the rig enough to justify $10K.  So here is what I got, based on Mark Smith's guidance:
All purchased from B&H photos.

Everything showed up in early January.  And I started to try to learn how to use everything.  And things were slow at first.  I went out for a few weeks taking pictures using auto settings. And, well, it was nice, occasionally.  But the pics just were not as good as I thought they would be. It all came to a head when I went on a local little outing with Jim Koenigsaecker.  And he kept asking me about all the settings I was using.  And I kept saying "blarg" or something like that (actually, I said mostly I was using just the automated settings).  And when I went home from that day, I had some good pics.  And a lot of crummy ones.

So then I decided to consult the oracle again.  Google that is.  And I found Mark Smith had a bunch of videos on how to set up the Nikon D500 for shooting birds in flight



And I watched these. A few times. And then set up my camera with those settings.  And I went out again that afternoon.  And BOOM.  The pics were way way way better.

See for example these.

Anyway - more about my pictures from the past another time.  Back to the garganey.  As part of taking better pictures I started wanting to share them more.  And I started being able to ID birds better and in some cases also wanted help confirming IDs.  So I started using iNaturalist and eBird more.

See my iNaturalist posts here.
See my eBird posts here.

And I signed up for notifications about bird sightings via eBird.

And this is FINALLY where the garganey comes in.  A few weeks ago I saw that some people had reported a rare bird on eBird - a garganey.  I also saw these were reported in the West Sacramento area, near the deep water channel and near where UC Davis students do crew and sailing.  So this stuck in my head somewhere for a few weeks.  And I talked about possibly going to check it out with some birding friends like Mei Yamaguchi. And then, a few days ago my friend from TIGR Karla Heidelberg contacted me and told me she was going to be in the Davis area this weekend since her daughter would be racing in two crew regattas.  So yesterday we met up to see Captain Marvel with my wife, daughter, mom and step dad.  And Karla came with her son, who it turns out, is getting interested in bird photography.  And while chatting before or after the movie I asked where her daughter was going to be racing Sunday and she said "somewhere near West Sacramento".

Thursday, March 07, 2019

Kisaco Research - sponsoring YAMMMM - yet another mostly male microbiome meeting - again - not their first biased rodeo

Well, sadly, I am not shocked by this. Disappointed, yes.  But not shocked.  Just got an announcement sent to me for this meeting: Animal Microbiome USA 2019 | Kisaco Research

Happening next week in Kansas City.  Run by Kisaco Research.  I have written about their propensity to have meetings where most of the speakers were white men previously.  See
People from the company claimed they were going to do better in the future.  And maybe they have for some meetings.  But alas not for this one.  By my estimate the speakers are ~ 85% male.  15% female.  Grrr.  Not good.  Not representative of the field.  Most  likely some sort of implicit or explicit bias going on.   

Tuesday, March 05, 2019

If a body wash falls in the forest, is it gentle on the microbiome?

Well, I guess I am happy Dove is interested in the microbiome. My exposure to Dove's thinking on the microbiome started with an ad that was shared with me by Christine Parks.




The ad claims that Dove is gentle on the microbiome.  OK.  I am not sure I get what that means completely.  But I think they are saying "Our product does not mess up your microbiome".  I guess this could be good for some people if it were true.  But for others, maybe you want to mess up the microbiome.  Regardless, I would love to see data, if it exists, behind such a claim because my guess is that any body wash affects up the microbiome in many ways.

So, if they were not going to show evidence for this claim, I wondered, what are the ingredients of this Dover product? Fortunately the company provides them readily: https://www.dove.com/us/en/washing-and-bathing/body-wash/deep-moisture-body-wash.html. And here they are:
  • Water (Aqua), 
  • Cocamidopropyl Betaine, 
  • Sodium Hydroxypropyl Starch Phosphate, 
  • Lauric Acid, 
  • Sodium Lauroyl Glycinate, 
  • Sodium Lauroyl Isethionate, 
  • Hydrogenated Soybean Oil, 
  • Glycine Soja (Soybean) Oil, 
  • Sodium Chloride, 
  • Glycerin, 
  • Fragrance (Parfum), 
  • Phenoxyethanol, 
  • Guar Hydroxypropyltrimonium Chloride, 
  • Stearic Acid, 
  • Citric Acid, 
  • Sodium Isethionate, 
  • BHT, 
  • Tetrasodium, 
  • Iodopropynyl Butylcarbamate (IPBC)
This last one, Iodopropynyl Butylcarbamate (IPBC), is interesting since there is a paper discussing its effect on the microbiome. See "Effect of cosmetic chemical preservatives on resident flora isolated from healthy facial skin". They report "MTI and IPBC displayed the strongest effect on all tested strains (MICs ≤0.01%), followed by EHG and MP (MICs ≤0.3%), and finally PE with the weakest effect (MIC ≤1%)."  IPBC apparently is a known antibacterial and anti fungal agent.  Unclear how that being in the product is consistent with being gentle on the microbiome.

BHT is also interesting as it has been known as an antimicrobial for a long time (e.g., see this 1980 paper). It is used widely as a "preservative" but one of the ways it works as a preservative appears to be that it is anti microbial. 

Phenoxyethanol is also an antimicrobial.  See for example this where they report things like:
The study reveals that the six preservatives-Phenoxyethanol, Methyl paraben, Propyl paraben, Sorbic acid, Potassium sorbate and Sodium benzoate shown antimicrobial activity with the three test organisms at various concentrations and time periods.
My guess is many of the other ingredients can also affect the microbiome.  This would not really be surprising as lots of things affect the microbiome.  So, sorry Dove, but just saying your product is "gentle on the microbiome" just does not cut it for me.

I decided to see if I could find out anything else about Dove's claim of being gentle on the microbiome so I did the usual thing and Googled "Dove microbiome" and found some of their material on the microbiome.  And I guess I could say I was pretty disappointed. For example see this:Introducing your skin’s microbiome – Dove Nothing there providing data on just how gentle Dove really is or is not on the sin microbiome.  And in addition there was a statement I was not so fond of:
"Think of it as an invisible eco-system that lives on the skin that’s working to help keep it healthy and in good condition. "
Umm -- no -- no evidence for this.  The microbes on your skin appear to mostly be working for themselves.  Some of the time they are harmful. Some of the time they are helpful.  Some of the time they are neither.  But they are certainly not "working" to keep skin healthy.

So - it seems like Dove wants to get in on the microbiome hype.  I guess I am glad they are interested in the microbiome.  But they cannot just make claims about things like "being gentle" on the microbiome without evidence.  Especially when their ingredient list contains a collection of known antimicrobial chemicals.

Interesting and important story on fecal transplants in @nytimes



This is definitely worth a read:

Drug Companies and Doctors Battle Over the Future of Fecal Transplants - The New York Times. By Andrew Jacobs. March 3, 2019.

The lead in is good:
CAMBRIDGE, Mass. — There’s a new war raging in health care, with hundreds of millions of dollars at stake and thousands of lives in the balance. The battle, pitting drug companies against doctors and patient advocates, is being fought over the unlikeliest of substances: human excrement.
The story is both interesting and includes some very important stuff going on behind the scenes that may affect the future of fecal transplants as a treatment in t. It seems that a variety of folks including those from companies who are trying to develop treatments mimicking fecal transplants are trying to get the FDA to crack down on the use of actual feces for carrying out fecal transplants.
“The first principle of medicine is do no harm, and at the moment we don’t have a long-term track record of F.M.T.’s adverse effects,” said Dr. Sahil Khanna, an associate professor of gastroenterology at the Mayo Clinic who has conducted industry-funded clinical trials on fecal transplants. “We also need to move away from transferring poo from one person to another.”
and
Drug companies, which have been struggling to funnel patients into the clinical studies that are required for F.D.A. approval, would like federal officials to restrict the stool bank’s ability to distribute fecal matter in the hope that more patients will enroll in their trials.
On the other side are those from places like OpenBiome as well as many clinicians who think that the regulation may have already gone far enough or even too far.
“It is very frustrating to see hyperregulation again ruining a good thing in health care,” said Dr. Colleen Kelly, a gastroenterologist at the Brown University medical school.
and
“I never imagined the solution to my nightmare could be so simple,” he said. “I just hope Big Pharma doesn’t make it unaffordable for the people like me.”