Sunday, July 07, 2019

Early AM at #YoloBypass and a brief encounter with a bald eagle #Birds #BirdPhotography

So yesterday I went out early in the morning to Yolo Bypass Wildife Area. I had not been in a few weeks and wanted to get out for a hike and some birding.

Thankfully, even though it was really early (like 6:30 AM) my wife had already prepared coffee for the two of us since she had been woken by the strange yowling beast that lives in our house.



So I packed up some gear, put on long pants and boots and a long sleeve shirt (mostly to deal with the brambles in my favorite hiking spot) and headed out in my car (I note - I would love to bike there and then bike through Yolo Bypass but bikes are not allowed - so the car is the only way).



And then withinYolo Bypass I headed to the Southern edge to my favorite hiking spot along Putah Creek.
 

And I wandered into this area:



I took some panoramic pics and video and texted them to my wife ...






And then hiked around for a few hours. Here are some of the things I saw there:

Belted kingfisher:


Black crowned night herons


Spotted towhees


Egrets



Lots of nice plants, such as these: 





Wood ducks


Pied billed grebes


Black phoebes


Other misc. birds



Butterflies


And lots of otter poop



Oh - and some more panoramas and a selfie




And then I headed back to my car and drove to the end of the road just for completeness and headed back out towards the exit.  I took a few pics from my car long the way:



Oh, and then it happened.  Was heading back out and along the dirt/ gravel road a black town car was pulled over.  So I slowed down, not wanting to disturb them if they saw some cool creature.  And I slowly pulled up on their left.  And there was a woman in the car looking through binoculars.  I pulled up to be almost beside her car and she pointed up and ahead and whispered "Bald Eagle."

OMG.

There was one on the telephone pole.  I had been coming to Yolo Bypass for almost 15 years with 100s of visits and had never seen one here.  And so I got out my camera and at this bad angle started taking pics.  After 10 minutes or so I told the woman I was going to pull ahead and to the side to get a better view.  And I thanked her over and over, told her I would post pics to iNaturalist (and told her what that was) and then pulled up and took some more pics.  And this is where I got some of the better ones that I am sharing here:



And I followed it East down the road towards the Deep Water channel and watched as it flew far far away.  I chatted with some of the people fishing and then went for another walk to see some more birds.  There were a lot of interesting shorebirds in particular but also saw some others.
Here are some of those pics:

Shorebirds galore:


Blackbirds and such


Sparrows and phoebes and other small birds


Sheep (I know, they are not birds but nobody's perfect)


Hummingbirds


And even some insects such as this one:


Any many other things along the way. I then headed out taking pics along the way.  Some of the better pics include these:


And then I was out of Yolo Bypass.  I took the scenic route home and took some more pics.  Here are some:



And then I went home and posted everything to iNaturalist.  See the collection here



Monday, June 24, 2019

Microbe Themed Comics and Cartoons #ASMicrobe #Microbiology

Posted a request to Twitter about microbe themed comics and cartoons and am posting some of the Tweets here.


Saturday, May 25, 2019

My observations for the City Nature Challenge 2019 - Sacramento #iNaturalist

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 here are some more details

Day 1. Link to observations.  Screen capture below.






Day 2. Link to observations


Day 3. Link to observations



Day 4. Link to observations.



Some of my favorite observations from these days are below;


And many many more.

Thanks to all the people who helped ID many of my pics and thanks to Laci and the other coorganizers for running the show.  It was a great experience.



Thursday, April 04, 2019

My talk on "The Twisted Tree of Life Awards" for #Nelli19

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.

Slides:



Screencapture video with Audio

 


Some Tweets about the Talk

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:

Most recent post

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