Monday, December 10, 2018

Twisted Tree of Life Award: University of Nebraska Lincoln Press Release on Archaeal Epigenetics

Well this one is really painful.  So painful I am re-starting my "Twisted Tree of Life" Award posts here.

See Tweets about it below:








Thursday, November 29, 2018

YAMMMM: Yet Another Mostly Male Microbiome Meeting - Gut Microbiota for Health World Summit 2019

Uggh. In the middle of a faculty retreat and saw a Tweet about this meeting and could not help looking at their speaker list. And am not impressed.  Too many male speakers.

Gut Microbiota for Health World Summit 2019
A Meeting to Hear Men (81%) Not Women (19%) Discussing Microbiota*, **
YAMMMM: Yet Another Mostly Male Microbiome Meeting

Gail A. Hecht, MD, MS, Loyola University Medical Center (U.S.)
Jack A. Gilbert, PhD, University of Chicago (U.S.)
Session Moderator: Giovanni Barbara, MD, University of Bologna (Italy)
Suzanne Devkota, PhD, Cedars-Sinai Medical Center (U.S.)
Magnus Simren, MD, PhD, AGAF, University of Gothenburg (Sweden)
Christoph Thaiss, PhD, University of Pennsylvania (U.S.)
Session Moderator: Purna Kashyap, MBBS, Mayo Clinic
Eric Martens, PhD, University of Michigan (U.S.)
Liping Zhao, PhD, Rutgers, The State University of New Jersey (U.S.)
Paul Cotter, PhD, University College Cork (Ireland)
Robert Britton, PhD, Baylor College of Medicine (U.S.)
Joseph Zackular, PhD, University of Pennsylvania (U.S.)
Premysl Bercik, MD, McMaster University (Canada)
Dirk Haller, PhD, Technical University of Munich (Germany)
Eran Elinav, MD, PhD, Weizmann Institute of Science (Israel)
Karine Clément, MD, PhD, Pitié-Salpêtrière Hospital (France)
Alexander Khoruts, MD, University of Minnesota (U.S.)
Diane Hoffmann, JD, MS, University of Maryland (U.S.)
Francisco Guarner, MD, PhD, University Hospital Vall d’Hebron (Spain)
Dylan Dodd, PhD, Stanford University (U.S.)
Stanley L. Hazen, MD, PhD, Cleveland Clinic (U.S.)
Rohit Loomba, MD, University of California, San Diego (U.S.)
Gary D. Wu, MD, University of Pennsylvania (U.S.)
Session Moderator: Hania Szajewska, MD, Medical University of Warsaw (Poland)
Purna Kashyap, MBBS, Mayo Clinic (U.S.)
Geoffrey Preidis, MD, PhD, Baylor College of Medicine (U.S.)
Pinaki Panigrahi, University of Nebraska (U.S.)

* Gender inferred by Google Searches, looking at personal websites, and some guessing
** Assuming just M:F genders which is clearly a bad assumption

Saturday, November 03, 2018

Pumpkin Carving as a model for Genome Assembly

So - we have this pumpkin carving contest every year in the UC Davis Genome Center.  And people from my lab have done some excellent pumpkins in the past.

See for example some details on their 2014 pumpkin:






And I have on and off carved pumpkins on sciency themes every once in a while.




So this year, when the Genome Center admins sent around an email saying they had bought pumpkins for people to use, I decided it would be fun to do something this year.  But then 10/30 came and we had still not done anything.

So I came up with a crazy idea.  Cut up pumpkins in different ways as an example of genome sequencing strategies.  And, with the help of a few people in my lab and some of the people in neighboring labs, this is what we did.

So - first - we took three pumpkins.

And we decided to make one of them a representation of long read sequencing and another a representative of short read sequencing.  So - using a saw provided by people in Justin Siegel's lab, I cut one pumpkin into horizontal slices and remove the innards and made that the "long read sequencing" example.  And then I took pumpkin #2 and again cut into horizontal slices but this time I  then cut those slices up into chunks.  And we then stored the pumpkin pieces overnight and Katie Dahlhausen in my lab made some nice signs to add to the display. In addition, the decorated pumpkin #3 with some "Shotgun sequencing" motifs.  And voila, we had our pumpkins ready for the contest for 10/31.

So I headed in to work early, and set up our display.





And I posted about it to Twitter.


But something seemed lacking.  So I went and got another pumpkin


And now it felt complete.

And then, after the symposium I decided - hey - we should try to reassemble these.  I took some pics of this and made them into videos / gifs.
Long piece assembly. 

Assembling the long piece pumpkin shotgun was easy.



Linking assembly.

Assembling from the linking pieces was harder.  And in the end we did not quite get it back together.




We did not even try to assemble the small pieces. But the next day I did ponder recovering them and the other pieces and doing a meta pumpkin assembly.


Anyway - this ended up being pretty fun.  Lots of ideas about how to do it better (e.g., we should have barcoded / labelled the pieces so that we could guide the assembly if we failed to do it without guidance).   And thanks to all the discussions with people out there and to the people in my lab who helped put this all together.

Also I made a Wakelet of some of the Twitter discussion

Wednesday, October 31, 2018

And today in #microbiomania (aka overselling the microbiome) - ridiculous claim from Raphael Kellman's book marketing group



Just got this email below.  It is from a marketing person promoting Raphael Kellman's new book.  And it has an absolutely dangerous, ridiculous claim in it.  They claim that if you have memory loss, or mood problems, these are not in your head at all - this is caused my problems in your microbiome. What absolutely bullshit.  Sure, the microbiome can impact the brain and mood.  But to go from that to claiming that all memory loss and mood issues are due to problems with the microbiome.  Dangerous.  Deceptive.  Scary.  Snake oil.

But yes, I would be happy to write about your book.  Right here.  Right now.

Here is the email

Hello!

We are excited to announce the publication of The Microbiome Breakthrough: Harness the Power of Your Gut Bacteria to Boost Your Mood and Heal Your Body by Raphael Kellman, M.D. This revolutionary guide by the author of The Microbiome Diet offers a medication-free, scientifically-based approach to healing depression, anxiety, and brain fog by focusing on your “whole brain” – the brain, the gut, the microbiome, and the thyroid. 

If you are one of the millions of people who feel that you have memory loss or an inability to maintain a balanced, happy mood, the problem is not “in your head,” it is in your microbiome (the trillions of health-promoting bacteria in your body) and your gut. In The Microbiome Breakthrough, you’ll learn about the latest cutting-edge science and discover the Whole Brain Protocol, a powerful four-week plan that advises you on what to eat and which supplements and probiotics to take, so that your brain functions at its best level. Along with delicious, health-supporting recipes, meal plans, and other tips and strategies, The Microbiome Breakthrough will help make your brain work better, enabling you to feel calm, energized, and clear headed without prescription medications.

We would love to partner with you to spread the word about this groundbreaking book from a pioneer in holistic and functional medicine. If you would like to review it on your blog or website, promote it on your social media or email newsletter, or host a giveaway, we would be more than happy to send you a copy.

I look forward to hearing from you!

Thank you,
NAME 
--

NAME 
Marketing Department
Da Capo Press | Lifelong Books | Seal Press
An Imprint of Perseus Books | A Hachette Book Group Company
53 State St., 9th Fl. | Boston, MA 02109

Saturday, October 27, 2018

A 22 step guide to how to write a story to stir up germophobia.

Another day.  Another excessively germophobic news story. Today it is:

What's the dirtiest surface on an airplane? The result may surprise you | CBC News

In reading this article I realized, as others have before me, that these tend to follow a simple script.  Swab. Report on how dirty things are.  But I decided to dig in a little more.  And I have come up with  a foolproof way to write such stories. Just follow these 13 steps. These do not have to be done in the order below.
  1. Swab something
  2. Send swabs off for testing with a microbiologist or testing company to make it seem like there is some serious science going on. 
  3. Bonus points for showing microscopes or bacterial plates or other science things.
  4. Don't report the full methods or data. Just make it seem like you know what you are doing.  Be vague some of the time.  And use really big #s other times.
  5. Report on the results that make things seem way dirtier than people might have expected.  Say things like "Dirtier than a toilet seat". 
  6. Mention feces.  Or fecal matter.  Pretend or just flat out lie about how the testing you did shows that feces was in the samples.
  7. Mention something else that is gross. Condoms.  Bodily fluids.  Vomit.  Disease.  Vermin.
  8. Repeatedly use synonyms of "dirty" or "gross". 
  9. Mention human illness.  Often. 
  10. Bonus points for telling people they "could" or better yet - "likely will" - get specific diseases from touching these sites even when there is likely absolutely no evidence regarding likelihood of transmission.  
  11. Bonus points for mentioning nasty symptoms of human illness like diarrhea or vomiting or things involving bleeding.
  12. Mention specific microbes but only ones that make people sick and don't mention all the other microbes in samples.
  13. Definitely do not mention that some microbes you are calling dangerous also frequently come in non dangerous forms.
  14. Get a known fear mongering germophobe to comment about the results. 
  15. Bonus points if the person you get to comment has a nickname involving microbiology.
  16. Bonus points if the person you get to comment runs a company involved in infection prevention.
  17. Tell people to use hand sanitizer.
  18. Discuss how nobody cleans the surfaces swabbed in the story as often as you would have thought.  
  19. Bonus points for misleadingly saying that you can say something about how often or how well people clean the sites being studies from a limited amount of indirect swab data.
  20. Link to other germaphobic stories or videos.
  21. Ask the people responsible for the sites that were swabbed to comment without really providing them with enough details to be able to know what exactly was done or whether it means anything.
  22. Ask employees or other personnel to comment about other gross things they have seen associated with the sites being sampled.
And today's article has most / all of these.  I will leave it to you, dear readers, to figure out how to map these 22 things onto this and other stories.

Friday, September 07, 2018

Friday, May 18, 2018

Koalas, Chlamydia, Microbiomania, Katie Dahlhausen, John Oliver, Russell Crowe, and me.

I love Chlamydia.  Really I do.  It was in a paper analyzing two Chlamydial genomes that I first noticed a very strange pattern of genome evolution.

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This in turn led to our discovery that large genome inversions in bacteria and archaea are most common when they are symmetric around the origin of replication.

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This may be my favorite paper from my entire career and I owe it all to Chlamydia.

Plus, there are all sorts of jokes one can make with the Giant Microbe Chlamydias like

and


Monday, April 30, 2018

No Microbiome Santa Claus we cannot magically convert correlative studies into causal ones. And scientists dishing out medical advice about vaping based on such bad science is ridiculous.

Aaarrrrrrrg.  That is how I feel right now.

Many microbiome studies involve examining the microbiome in various samples and asking and answering "Are there differences in the microbiome between my sample types?".  This is a standard correlative analysis used in all sorts of areas of science. and it can be quite useful in many cases.

However, in most cases it is not OK to take information from a correlative study and infer that the microbiome was "changed" due to some factor that differed between the samples.  Generally this would only be possible to do in some sort of controlled experimental manipulation experiment.  But so so so many people make such inferences and I am going to highlight an example that relates to a new study of vaping and the microbiome.

There is a new paper on this topic and an associated press release:
Basically the researchers compared microbiomes in three groups of people who had different behaviors (some non smokers, some smokers, some papers vapers).  Note - they did not study people before and after vaping or smoking.  They compared different people who differed in these behaviors but also differ in 100s to 1000s of other things like diet, gender, age, activity, housing, childhood, and more.

And when they did comparisons in relation to the main variables of non smoker, smoker, vaper, they found some differences in microbiomes and some similarities.  Small study.  But potentially interesting.

However, the PR significantly misrepresents what they did and found. Here are some examples of wording I have a problem with:

Press Release:
  • "Vapers and non-smokers have the same flourishing gut flora."
    • OK this has nothing to do with the point of my post but they do not in any way show "flourishing" flora.
  • "whilst smokers have significant changes to their microbiome".  
    • No.  They show differences.  Not changes
  • Significant changes were found in the gut bacteria of the smokers, with an increase in the Prevotella bacteria which is linked to an increased risk of colon cancer and colitis.
    • Again.  No.  They show differences.  They do not know if they are changes since they do not know what these people had before smoking. And thus they cannot show "increases" either.
  • There was also a decrease in the presence of Bacteroides in smokers, a beneficial bacteria or probiotic.
    • No - no decrease shown.  And for that matter - not all Bacteroides are beneficial or probiotic. 
  • More investigation is needed but to find that vaping is less-damaging than smoking on our gut bacteria adds to the incentive to change to e-cigarettes and for people to use them as a tool to quit smoking completely.
    • Jesus #(@(@.  No.  They did not show this. 
  • This revealed significant changes in the gut bacteria of the faecal samples.
    • Again, no. 

Monday, March 26, 2018

Monday, March 19, 2018

Science Magazine publishes "opinion" piece targeting a specific student w/ sexist "critique" and then won't publicly discuss what happened or what they will do about it



Well, I can't even begin to explain how disappointed I am in AAAS and Science Magazine over their actions recently. An "opinion" article was published last week in the "Working Life" section of Science which was stunningly inappropriate for Science Magazine. I first found out about this when I saw a Tweet from a colleague and friend Rebecca Calisi Rodriguez.
And when I started to dig into the story I was nauseated.

 To sum up - the article was by a student who was apparently trying to express some thoughts about #SciComm activities by others that she did not like. And in the piece she named and mocked the activities of another PhD student at her own institution who does SciComm in ways she does not feel comfortable with. Fortunately, when I started looking at social media responses to this, they were overwhelmingly in support of this targeted student - Samantha Yammine who does really quite phenomenal SciComm work. (See for example her Twitter feed and her Instagram feed.

 I am really thrilled and proud of the community that came out in support of her.

There have also been a few news stories related to or directly about the topic which are worth reading.
Also some of the Tweet streams about this are really worth reading. For example, this one from @christineliuart is a must read:



YAMMMM: Yet another mostly male microbiome meeting - Microbiome Therapeutics Europe Meeting


YAMMMM: Yet Another Mostly Male Microbiome Meeting:
Microbiome Therapeutics Europe Meeting

From their speakers page I estimated gender balance of speakers 

19:6 M:F 
or 75% male

Thursday, March 15, 2018

YAMMMM - Yet another mostly male microbiome meeting - 2018 Translational Microbiome Conference

Uggh.

Here is a sad sad example of a YAMMMM - yet another mostly male microbiome meeting (a phrase first coined by Carly Rosewarne).

The 2018 Translational Microbiome Meeting.
https://www.microbiomeconference.com

From my estimates there are 47 speakers of which 41 are male (note - these are inferences of gender and may be inaccurate).  That comes out to an estimate of 87% male speakers.  That is just not good.  The microbiome field has a good sample pool of people of diverse backgrounds that could be speakers at meetings and thus meetings that are this skewed in diversity should not be supported.

  

-------------------
UPDATE 3/20/2018

The organizer of the meeting Mollie Roth has written to me to object to my post. She says she tried to have a more diverse collection of speakers. She says she invited many other women to speak, some who did not answer, and some who could not come, and some women who could not come sent men to replace them.

She wrote (I have removed names here)

  • XXX from YYY was committed to speak and had to drop out due to work commitments, 
  • that XXX of YYY was invited to speak and declined, 
  • that XXX of YYY was invited to speak and choose to send a man instead, 
  • that XXX committed to speak and had to drop out due to other commitments and is sending a man instead
  • that XXX of YYY was invited and never responded
  • that XXX andXXX of YYY were invited and never responded
That’s 7 women off the top of my head without going into my files and pulling up all the ones that were invited and never responded or declined because they could not make it or accepted and ultimately sent a man from their companies instead. I wonder what that number alone would do to your stats?

I responded that I did not feel this was in any way sufficient but she disagrees.  I pointed her to some suggestions for how to run a more diverse meeting that do not simply involve inviting more women to speak.

She also noted that she offended by my post and that I did not continue a private conversation we had on Linked In regarding this meeting.  I note I did not continue the private conversation, and chose to post this post, because her response to my private critique made it seem that she was not interested in having a private conversation about the meeting.

-----------------------------
UPDATE 2.  3/20/2018 3 PM PST.

The organizer of the meeting Mollie Roth apparently thinks that I have deleted her "comment" on this blog.  I have not done that.  The 1st comment made to this blog is the one where she is accusing me of deleting a comment.  I note - blog comments are open for anyone to post here for 2 weeks and then comments get moderated.  I checked the Blogger SPAM comment filter but there is nothing there.  So I can only conclude she did not make a comment.  I emailed her to try to find out what she meant but she did not answer directly.  I think what she may have meant is that she wanted me to post the full email of her communication with me to the blog but I am honestly not sure. I am pondering posting all my communications with her but am not sure if that is a good idea at this point.

So for now I am posting the entirety of her first message to me which I had edited a bit above.  I am still editing out identifying features of others however. See below.

Professor Eisen

XXX was kind enough to forward your email to me encouraging him not to participate in the Arrowhead conference. 

Really? Rather than engaging in a conversation with me on LinkedIn and learning more about this year’s gender imbalance, you are posting about it on your blog and reaching out to speakers encouraging them to drop out. 

Would you care to take a moment to learn that -


  • XXX from YYY was committed to speak and had to drop out due to work commitments, 
  • that XXX of YYY was invited to speak and declined, 
  • that XXX of YYY was invited to speak and choose to send a man instead, 
  • that XXX committed to speak and had to drop out due to other commitments and is sending a man instead
  • that XXX of YYY was invited and never responded
  • that XXX andXXX of YYY were invited and never responded

That’s 7 women off the top of my head without going into my files and pulling up all the ones that were invited and never responded or declined because they could not make it or accepted and ultimately sent a man from their companies instead. I wonder what that number alone would do to your stats?

I will ask, although I am sure you will neither respond nor do the right thing, that you primarily stop contacting speakers to ask them not to participate. But secondarily you should really if not retract your offensive post add some of this information to inform it and perhaps encourage the women to own some of this issue themselves this year.

I am sure you will do neither, unfortunately. I will be sure we do address this issue in our conference blog and in our social media channels.
----------------------------

UPDATE 3 3/20 11 PM PST

I guess my inclusion of this additional information was not enough for the organizer Mollie Roth.  She seemed to imply that I was hiding her explanations from the public.  So ... I am going to post them all here.

This all started with a Linked in message from her to me on March 5 telling me about this meeting.
I wrote back a few days later - obviously not enthusiastic about this meeting



She then wrote back, clearly not impressed with me.  I am not sure if she would be OK with me posting all of the comments she made in that thread so I am just posting the most relevant one here which is how she ended the discussion.

 

Sounded to me like she did not want anything to do with me ever again.  I pondered what to do for a while.  Was writing back a good or a bad thing?  I did not know.  But I decided to try. I wrote a response and tried to send it but the message would not go through.  I assumed she blocked me or disconnected / delinked me (I don't know what that is called on Linkedin).  I thought about emailing her back but the last message from her implied to me that she wanted nothing more to do with me.

So a few days later I wrote a blog post about YAMMMMs in relation to this meeting.  And then I wrote this blog post here.  And then I engages in some discussion about the post on Twitter and asked some of the speakers to not speak at the meeting.  I emailed one that I knew well and he forwarded the email to Mollie. She then sent me an email. I have deleted names and other identifying features of other people from this and other messages.

------------------------------
Professor Eisen 
XXX was kind enough to forward your email to me encouraging him not to participate in the Arrowhead conference. 
Really? Rather than engaging in a conversation with me on LinkedIn and learning more about this year’s gender imbalance, you are posting about it on your blog and reaching out to speakers encouraging them to drop out.  
Would you care to take a moment to learn that -
XXX from YYY was committed to speak and had to drop out due to work commitments,   
that XXX of YYY  was invited to speak and declined, 
that XXX of YYY was invited to speak and choose to send a man instead, 
that XXX committed to speak and had to drop out due to other commitments and is sending a man instea
that XXX of YYY was invited and never responded that XXX and XXX of YYY were invited and never responded 
That’s 7 women off the top of my head without going into my files and pulling up all the ones that were invited and never responded or declined because they could not make it or accepted and ultimately sent a man from their companies instead. I wonder what that number alone would do to your stats? 
I will ask, although I am sure you will neither respond nor do the right thing, that you primarily stop contacting speakers to ask them not to participate. But secondarily you should really if not retract your offensive post add some of this information to inform it and perhaps encourage the women to own some of this issue themselves this year 
I am sure you will do neither, unfortunately. I will be sure we do address this issue in our conference blog and in our social media channels. 

Mollie
Mollie Roth, J.D.Managing PartnerPGx Consulting

-----------------------

I wrote back

Mollie 
In our conversation on Linked In you basically told me you were not interested in discussing the issue. Your last message was "I am sorry I reached out to you and will not make the mistake of doing so again. Good day." 
Regardless, I tried to write back but was unable to respond to you via the messaging system.  I assumed that was because you blocked me in some way.  
Given that you did not seem to want to discuss it further in private, I decided to take it public.  I would be more than happy to add whatever response you want to my blog post or you can post there. I stand by my critique of your meeting.  It is not enough to just invite a few women to speak in my opinion and there is much literature on this out there if you are interested.  In order to achieve a diverse meeting one must work a bit more on it.  If you are interested in suggestions for how to do this, please see this part of my blog.
https://phylogenomics.blogspot.com/p/posts-on-women-in-science.html 

Jonathan
-----------------------

She then wrote back
Jonathan  
I neither blocked you nor impeded your communication in any way on LinkedIn or anywhere else. I have my doubts that you are so easily put off, I think you prefer the hype and hyperbole of being the individual who “outs” the bad actors, regardless of whether they are or they are not. 
I take offense at your characterization that I did no more than invite a few women, I do substantial research and go well beyond a bald faced email with no followup. I know many of these women personally from interactions over the years from prior conferences - where we have agreed women were well represented - but saying my conference fails on this front from a single year is a slant helpful only to you. 
I will be more than happy to have you demonstrate your acuity with gathering these women and getting them to the table next year. Writing about these issues from an academic perspective is one thing, actually driving engagement is quite another.  
In fact I will be more than happy to make a space for you on the podium this year if you would like to come speak about these issues and commit to lending your knowledgeable hand as a consultant next year to demonstrate how these “suggestions” work in practice. What say you Professor Eisen, willing to put your academic suggestions to the test in the real world? 
So I responded
Mollie 
In your 1st communication with me in September of 2015, you wrote 
"Let me start by applauding you for the commentary in your blog post on overselling the microbiome about the gender imbalance in Dr. Roizen’s conference. " 
So back then you supported a public critique of a meeting in relation to its gender balance of speakers.  This is why I wrote back to you privately on Linked In in such a shocked state regarding your current meeting. 
So -what has changed since then?  Your meeting has an unbalanced gender for speakers.  And I bogged about it.  Just like I did previously and which you applauded me for. 
Again, I stand by my critique of your meeting.  And no, I am definitely not interested in attending it in any way or for any purpose.  And I will continue to recommend other people not attend it or speak at it as it now stands.  If you run a meeting with a better gender balance I would be more than happy to participate in some way in a discussion of gender issues in STEM.
She wrote back
It is not until one is unfairly targeted that one understands how skewed people pointing these types of things out are. Knowing what I know now about your skewed attacks, I was perhaps unfair in assuming others were acting in bad faith. I d not believe you are acting in good faith, nor do I believe you will do so. I think you like the fight, I think you like the hyperbole and I think you like pointing fingers with no intention of trying to understand the other side. 
I wrote back

Ok. 
Believe what you want. 
I still welcome any comments you would like to make on my blog and whether you believe it or not I truly believed you did not want to hear a anything more from me in private.  I certainly could have made more of an effort to figure that out.  But your response led me to believe that that path was closed.
Molly wrote
If you were sincere Professor Eisen you would amend or include further information you have been provided on your blog post yourself. Of course I am going to contradict what you said or have a different perspective but it really only has substantial meaning if you are willing to say “ok hang on, here are some things I did not know” and further inform the conversation yourself. 
I will get in touch with our speakers and let them know the nature of your communications and how you have refused to take the information you have been provided and adjust your outrage. 
So I decided to do what she asked.  It seemed only fair.  And I updated my post with a summary of her comments.  I did not say I agreed with her but I did try to provide her perspective.


I thought I was doing what she asked.  To give her side of the story.  I did not think I was obliged to agree with her but she then wrote back something which I just do not understand.
I just went to remove my response to your post realizing the fact that you are not really interested din the reality of these situations to find you had removed it and, no surprise, recharacterized it all in your own words. That’s not open discourse Professor Eisen now is it, more evidence that you simply like being the finger pointer and are not actually interested in honest and open engagement. 
This was so strange because she never posted a comment to my blog.  I went and checked SPAM and comments awaiting moderation and -- nothing.  I was very very confused.  So I wrote back

Mollie 
I have no idea what you are talking about here. 
When did you write a response and post it to my blog?  Did you submit a comment? I have no record of that. How could you then remove it?  How could I then remove it?  You have not as far as I know posted any comment anywhere. I have certainly not removed a single thing you posted to my blog nor would I. 
She then wrote
Oh my goodness. You literally wrote on your blog that the organizer responded on your blog and then recharacterized what I said and you are now playing DUMB?
So so weird.  I did not delete any comment.  She never made any comment.  And now her explanation what that she was claiming I had written that she made a comment.  But I did not write that.  My guess is she either (1) thought that her email to me was automatically posted to my blog (seems unlikely that she thought that) or (2) that I had posted her comments to my blog directly and then deleted them.  Seemed like 2 was the only plausible option But since she had already told me she did not want me to post her comments directly to my blog this seemed weird. So I wrote back again.  

No Mollie 
I wrote "The organizer of the meeting Mollie Roth has written to me to object to my post"
I did not say you wrote on my blog. 
And when I asked you in email if I should post your comments to my blog directly you wrote 
"If you were sincere Professor Eisen you would amend or include further information you have been provided on your blog post yourself. Of course I am going to contradict what you said or have a different perspective but it really only has substantial meaning if you are willing to say “ok hang on, here are some things I did not know” and further inform the conversation yourself. " 
Clearly saying you did not want me to just post what you wrote.
I did not hear back immediately so I wrote a follow up:
Here is a proposal.  I will post the entire contents of these emails to my blog in the interest of transparency.  Are you OK with that?
And she wrote back:
It is your blog Professor, you are free to do with it anything you wish, clearly
So here we are.  I still do not know what she meant by me deleting her comments from my blog, which I did not do.  But in the interest of transparency I am posting all of our emails here.

--------------------------

UPDATE 4. 3/21/18

Mollie Roth, the organizer of the meeting sent an email to all the speakers of the meeting and cc'd me.  In the interest of transparency, especially since she accused me of deleting comments that she never posted here, I feel comfortable posting her email here.
Dear Speakers  
It has come to our attention that you may have received a message from a Professor Jonathan Eisen at UC Davis encouraging you to boycott the Arrowhead conference next month because of the lack of gender diversity on the speaking faculty. 
Unfortunately Professor Eisen is absolutely correct, the speaking faculty is predominantly male this year. Highlighting the role of women in this industry has been a top priority since I started this conference four years ago and prior years were much more gender balanced. Professor Eisen is well aware of this from our prior discussions on the issue. His dissatisfaction this year is equal to mine - in spite off having identified and invited numerous women to speak, they did not respond to my invitation or accepted and subsequently had to withdraw or in two cases decided to send men in their places.
Several of you have been in touch asking what WE are going to do to address this issue. I will turn that question around as gender diversity in the sciences is all of our responsibility - what are YOU going to do to address this?  
I encourage all of you to identify a women in your organization and send her to speak in your place if this issue is of concern to you. There is only so much I can do as an outsider to drive this issue, it requires everyone working together. 
If this is possible, please let us know as soon as possible and we will switch out her name and bio for yours on the online agenda and before it goes to press for printing. It would be my great pleasure to highlight this happening next month. 
And I will extend the same invitation to Professor Eisen who is copied here that I did privately, please consider lending your substantial knowledge and expertise on this issue to making this gender diversity happen not simply in your academic writing but in the real world. I welcome your time and assistance in pulling together the faculty for the conference next year. The experience will no doubt further inform your understanding of just how difficult this task is to accomplish in the real world. 
If you have any questions or continuing concerns, please do not hesitate to be in touch. 
Best regards
Mollie
Mollie Roth, J.D.
Managing Partner
PGx Consulting
Founder and Chair
Arrowhead Translational Microbiome Conference
www.microbiomeconference.com
I wrote back
Mollie (cc'ing speakers) 
Thank you very much for working to improve the diversity of speakers at this meeting. I think asking for help in identifying and selecting speakers that represent a broader sample of diversity is a great idea. In addition, I would be more than happy to help you organize a conference next year.   
Contrary to your comments, I have extensive experience planning and running conferences in various STEM area including the microbiome space.  And though it can be difficult to achieve, for these we have had excellent diversity of speakers.  You can see a partial list here.  
For each of the meetings I have organized in the last 5 or so years (I became interested to speaker diversity about 10 years ago but have been more committed to it in the last 5) we have been able to achieve a strong representation of diversity among the speakers.  This is however not easy in every case and takes a strong commitment to diversity and sometimes significant amounts of work. 
I would suggest that for your future meetings you do some of the things recommended in the articles I list at the bottom of my web page on Diversity at Conferences. One example article worth looking as is this https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4238945/.
Some examples of things that can improve the diversity of speakers include 
  1. Develop a diversity policy and publicly post it stating your commitment to diversity for speakers. I would be happy to help you develop one.  Many people basically copy a template that has come up from the technology world. I note this should not just be about gender diversity but about diversity broadly (i.e., racial, ethnic, gender, career stage, background, country, type of institution, etc). An example is https://us.pycon.org/2017/about/diversity/
  2. When people turn down invitations, ask them why and whether you could do anything to make it more likely the next time for them to accept.  It may be that some simple changes might make it more likely for people to accept.
  3. Broaden the invitation pool by expanding topics or types of people you invite.  This could, for example, include having a student or post doc presentation in each session, or including sessions focused on related topics such as press coverage of the field, or such.
  4. Ask people in the field for help in identifying speakers.  Ideally this would happen at the planning stage but could happen any time.
  5. Record and share data about speaker diversity.
  6. Make use of and contribute to diversity related lists for speakers.  For example Elisabeth Bik, now at uBiome maintains a great website and list of women in microbiome and related fields who could be invited speakers. See https://microbiomedigest.com/sample-page/women-in-microbiology-for-keynote-lectures/ . There are many other such lists around and they can be very useful. 
I would be happy to work with you on crafting a speaker diversity statement for your future meeting(s) and work with you on planning a meeting. 
Again, thank you for working to improve the diversity of this meeting.
Jonathan Eisen