So - last week I participated in the City Nature Challenge 2019 Sacramento Area effort. See https://www.inaturalist.org/projects/city-nature-challenge-2019-sacramento-region for more details on the challenge.
My colleague Laci Gerhart-Barley was one of the co-organizers for our region and I saw some posts from her in the run up to the event and, as I have gotten more and more into iNaturalist I decided to participate. Fortunately in a way, I got a nasty bug with fever and chills and such and this meant (1) I did not want to go to work and (2) I wanted to avoid people. This gave me some extra time to go around. The vent ran from Friday to Monday April 26-29. And I tooled around UC Davis campus a few times and Sac State Campus once (on Saturday where my daughter had a concert) and around Yolo County and also my yard a bit. And I took a lot of pictures and posted as many as seemed interesting to iNaturalist. And the most amazing thing was the community of people that Laci and others had gathered together did an incredible job of helping ID many many many of my posts.
So I gave a lunchtime talk a few days ago for the New Lineages of Life 2019 meeting (aka #Nelli19) in San Francisco. My talk was on
The Twisted Tree of Life Awards and Why We Should Care About Misrepresentations of the Tree of Life
I will be posting a lot of notes about the talk soon but wanted to get at least some of the main material down here for people to look at if they are interested.
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:
So @PatSchloss had a Tweet a few minutes ago about a comment he got suggesting Twitter threads are more effective than blog posts and I thought I would comment about this in a thread 1/n https://t.co/WxHXyFTZOS
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.
I think this is only partially true. In the short term and for most purposes, Twitter threads are probably more effective. 2/n
Blog posts on the other hand have longer legs and also have the advantage in most cases of being updatable and more able to accommodate different formats and such 4/n
So what I have started doing in some cases is posting Twitter threads and then capturing them via @wakelet or embeds into a blog post with some other details and this then has a bit longer lifespan than the thread itself. 5/n
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.
Yes. I have a blog post I’ve given to 100+ people over they past few years. Tweets are pretty ephemeral. https://t.co/nc6fVcCmqw
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.
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 ...
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:
2012 Franklin Award Accepting Nominations - please consider nominating women - all past winners incl. me are male http://t.co/8DLeiPp6
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.
Nominations may be submitted by members of Bioinformatics.org using this form (you must be a member and logged in).
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).
The list of nominees will then be presented for a vote, on a ballot, to the members of Bioinformatics.org.
The time given for all votes to be collected will be specified on the ballot.
The nominee with the most votes will be the initial consideration for the Award. There will not be a run-off vote.
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.
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.
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:
And since the Ben Franklin award is basically only for men, it seemed inappropriate to have my plaque for the award hanging up, especially just below my "Everyone Needs Feminism" sign, so I took it down #GenderBias#STEMDiversitypic.twitter.com/DgxdgAIC3o
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:
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:
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.
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".
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.
