Eisen Lab Blog

The flawed and offensive logic of "Academic Science Isn’t Sexist" in the @nytimes

OK.  It is Halloween night and I am tired and need to get my kids to sleep.  But someone on Twitter just pointed me to an opinion piece just out in the New York Times: Academic Science Isn’t Sexist – NYTimes.com and after reading it I felt I had to write a quick post.

The opinion piece is by Wendy M. Williams and Stephen J. Ceci and discusses work by them (and coauthors).  In particular they discuss findings in a massive report “Women in Academic Science: A Changing Landscape” by Stephen J. Ceci, Donna K. Ginther, Shulamit Kahn, and Wendy M. Williams in Psychological Science in the Public Interest.  I note – kudos to the authors for making this available freely and under what may be an open license and also apparently for making much of their data available behind their analyses.

The opinion piece and the associated article have a ton of things to discuss and ponder and analyze for anyone interested in the general issue of women in academic science.  I am not in any position at this time to comment on any of the specific claims made by the authors on this topic.  But certainly I have a ton of reading to do and am looking forward to it.

However, I do want to write about one thing – really just one single thing –  that really bothers me about their New York Times article.  I do not know if this was intentional on their part, but regardless I think there is a major flaw in their piece.

First, to set the stage — their article starts off with the following sentences:

Academic science has a gender problem: specifically, the almost daily reports about hostile workplaces, low pay, delayed promotion and even physical aggression against women.  Particularly in math-intensive fields like the physical sciences, computer science and engineering, women make up only 25 to 30 percent of junior faculty, and 7 to 15 percent of senior faculty, leading many to claim that the inhospitable work environment is to blame.

This then sets the stage for the authors to discuss their analyses which leads them to conclude that in recent times, there are not biases against women in hiring, publishing, tenure, and other areas.  Again, I am not in any position to examine or dispute their claims about these analyses – to either support them or refute them.

But the piece makes what to me appears to be a dangerous and unsupported connection.  They lump together what one could call “career progression” topics (such as pay, promotion, publishing, citation, etc) with workplace topics (hostility and physical aggression against women).  And yet, they only present or discuss data on the career progression issues.  Yet once they claim to find that career progression for women in math heavy fields seems to be going well recently, they imply that the other workplace issues must not be a problem.  This is seen in statements like “While no career is without setbacks and challenges” and “As we found, when the evidence of mistreatment goes beyond the anecdotal” and “leading many to claim that the inhospitable work environment is to blame.”

Whether one agrees with any or all of their analyses (which again, I am not addressing here) I see no justification for their inclusion of any mention of hostile workplaces and physical agression against women.  So – does this mean that a woman who does well in her career cannot experience physical aggression of any kind?  Also – I note – I am unclear I guess in some of their terminology usage – is their use of the term “physical aggression” here meant to discount reports of sexual violence?   This reminds me of the “Why I stayed” stories of domestic violence.  Just because a women’s career is doing OK does not mean that she did not experience workplace hostility or physical or sexual violence.  I hope – I truly hope – that the authors did not intend to imply this.  But whether they did or not, their logic appears to be both flawed and offensive.

UPDATE 1. November 1, 8:30 AM

Building a Storify about this.

UPDATE 2: Nov 3, 2014. Some other posts also criticizing the NY Times piece

UPDATE 3: Nov. 4, 2014.  More posts about the NY Times piece
——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Rediscovering some critical terms of use in microbial discussions: #microbiomania and #microbophobia

Earlier this week I was trying to come up with a short term to use when referring to the “Overselling of the Microbiome” and related hype. And I came up with one I really really like: microbiomania. The term just captures the essence of hype about microbiomes to me I guess.

So – of course – the first thing to do was to see if anyone else used this term.  And the number one thing I looked at was domain names.  Nope.  Microbiomania.Com and Microbiomania.Org are now mine.  And then I started to search the interwebs. And surprsingly there was not much (in English at least).  But some links showed up to books in Google Books with passages from > 100 years ago.  And this is when the digging got to be fun.  Here are some of the things I found.

1. A section from “The Medical Era“

When copying this section of the search results I discovered Google Books has an embed tool for Google Books though not sure how well it works: here is a try

Anyway – the text of this section of the book reads:

The Paris correspondent of the Chicago Tribune in a recent letter says We hear very little now of microbist or anti microbist theories Dr Koch’s so called discovery is regarded with skepticism though not refuted The truth is his assertions are generally held to be not proven Dr Peters the favorite pupil of the great surgeon Dr Trousseau denounces what he calls microbiomania as a social danger and declares that the micro bians doctrine is vain sterile and objectionable in every way as both needlessly alarming and wrongly reassuring 

So I guess there were some folks who did not like the Koch and his silly theories about germs.

2. The Eclectic Medical Journal Volume 48

OCR text:

Microbiomania For five or six years past says Semolla you could not open a journal without encountierng an alleged discovery of one or more pathogenic bacilla and it is not necessary for me to tell you that the surest means of attaining celebrity is to discover in such and such a malady a new bacillus or a minute micrococcus I can not tell you what ridiculous puerilities have been brought forth by the imagination of physicians who are incapable of serious work and according to the rules of experimental medicine mount every new idea as though it were a triumphal car and think that in celebrating and exaggeraring its praises they manifest their love of progress 

Pretty awesome stuff I think.

3. The Louisville Medical Journal also comes up with a hit to microbiomania

Here is the attempt at an embed:

and the OCR interpreted text reads

and microbophobists The feeling against the theory of the microbial origin of cholera is very strong and was expressed by Prof Peter both at the Academy and the School of Medicine in these terms It is a pure satisfaction of natural history to say with the German School that there exists a microbe producer I say that there is a microbe product The parasitic doctrines have engendered a microbiomania which determined a terror which will be the opprobrium of the 19th century
Faris December 12 1884 

Now – nevermind that the OCR is not perfect (where is Faris?).  But not only is this fascinating.  But the beginning of the page has another word that seems worthy of resurrecting: microbophobists,  And this pulls up all sorts of fascinating discussions:


And the related search is perhaps more fascinating: microbophobia

So – in the end I did not come up with a totally new word.  But I do now have two words I really want to use more often and which I will use in the following ways:

  • Microbiomania which I define here as the overselling of the impact (beneficial or detrimental or otherwise) of microbiomes without the evidence to support such impact 
  • Microbophobia which I define here as the overwhelming and unreasonable fear of microbes (of any kinds).  This is similar in concept to “germophobia” but gets around the issue some people have with whether “germ” is a term that should be reserved for pathogens and thus that germophobia could be viewed as the fear of pathogens.  
——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

11/3 at #UCDavis: Dr. Sarah Mathew “The Evolution of Large Scale Cooperation in Humans: Insights from Turkana Warfare”

Evolutionary Anthropology Colloquium Series
Mondays at 4:10 pm in 273 SS&H

November 3rd:
The Evolution of Large Scale Cooperation in Humans: Insights from Turkana Warfare

Dr. Sarah Mathew
School for Human Evolution & Social Change
Arizona State University

CEO of Soylent goes even further off the deep end – going after his microbiome

Well, this is pretty deranged: Soylent CEO Is Lifehacking Water By Pissing In the Sink.  Forget all the wackiness of Soylent and the idea of limiting water intake.  And just look at the part of this on the micro biome

Feces are almost entirely deceased gut bacteria and water. I massacred my gut bacteria the day before by consuming a DIY Soylent version with no fiber and taking 500mg of Rifaximin, an antibiotic with poor bioavailability, meaning it stays in your gut and kills bacteria. Soylent’s microbiome consultant advised that this is a terrible idea so I do not recommend it. However, it worked. Throughout the challenge I did not defecate.

So – he took Rifaximin to kill his gut microbiome because he thought that would help him not defecate.  And then because he did not defecate he concluded that the Rifaximin played some role in such anti-defecation?  OMFG.  This is both bad science and some, well, crazy a*s-sh*t.  I – I – I – I just do not know what else to say.

Hat tip to Andrea Kuszewski.

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Worth a look: Article by John Bohannon about arXiv paper from Google Scholar

Definitely worth checking this out (by John Bohannon): Uprising: Less prestigious journals publishing greater share of high-impact papers.   The article discusses a paper recently posted to arXiv by Anurag Acharya (from Google Scholar) and others: Rise of the Rest: The Growing Impact of Non-Elite Journals.

Crosspost: Using Google Scholar in Scholarly Workflows

I wrote this for the Google Scholar blog where it was posted yesterday.  I am reposting it here, in part because comments are not allowed on the GS Blog (not sure why) and some people have asked me about that.  So here it is

When Anurag Acharya asked me recently if I would be interested in writing a guest post for the Google Scholar blog in relation to the 10th anniversary of Google Scholar I immediately responded “Yes.” Literally, that was the full content of my email response email response to his request. Why did I answer so enthusiastically? Well, I can put this down to three main reasons:

So – in thinking about what to write for this post, I came up with three main topics I thought would be good to cover – how I got interested in topics of searching for and sharing scholarly papers, how I use Google Scholar, and some ideas about future possible uses of Google Scholar.

Part 1: Some Background 

One day, in ancient history, my wife came home from work (at a biotech startup up focusing on bioinformatics) raving about this new search engine “Google” that people at her company were talking about. As someone who thought of himself as on the cutting edge of web technology, I was a bit dismayed that I had not somehow discovered this myself. But I got over that and tried it out. And, after searching for my name (and being impressed with how well this new search engine worked on such an important topic) I immediately started playing around with searching for scientific papers and data. I did this, I guess, because ever since I was in college, I had been becoming more and more interested in (or some would say obsessed with) issues relating to finding and sharing scientific knowledge.

Without going into two much detail some of the factors that contributed to my obsession included:

  • Working as a shelver and then assistant in the Museum of Comparative Zoology library in college and seeing how people struggled to find papers of relevance to their work;
  • Spending many years in graduate school (in the 1990s) working on projects that had been largely unstudied since the 1960s, including one (so called adaptive mutation) where researchers claimed to have discovered something new in the 1990s but had in fact missed a rich literature on the topic from the 1950s and 1960s (e.g., see this from 1955).
  • Building and sharing databases where I was trying to include a description of every paper that had been published about specific genes. I note – thanks to the Wayback machine my Stanford website from when I was a PhD student is still available – although alas the specific linked databases are not. I have reposted some of them for people to see what they were like (though many of the links in them are busted). See for example my sites on RecA, SNF2, MutS and more
  • Working on projects to catalog everything known about specific organisms in association with work I was doing to characterize the genomes of these organisms

In these and other projects I had seen and experienced just how much time could be spent on searching for papers and data about a particular topics. I am not sure I had a well-defined strategy in every case but I came to rely upon some preferred methods including:

  • “Citation walking” where one takes a paper of interest and then asks “how has this paper been cited?” and traverses across the literature via citations
  • Searching for keywords in abstracts and titles
  • Browsing through specific journals
  • Looking for papers by specific authors
  • For data, I mostly would look in specific centralized data repositories such as Genbank for DNA sequence information and PDB for three-dimensional structural data on proteins.

And of course many other approaches. Nothing really novel or brilliant here though I do think I got pretty good at how to carry out such searches. But one of the challenges was each approach had to be done in a different system and some of the systems were only available for a fee and some were not even online. And even with lots of time and pain, many things could be missed.

Thus when my wife introduced me to this new fangled Google thing my thoughts rapidly turned to – how can I use this new tool to help in finding and then sharing scientific papers or data about these genes and organisms I was studying? Did Google searches solve all my “issues” in this regard? Alas, no. But jump forward ~15 years to today and I am quite amazed in retrospect how much of my scholarly workflow flows through Google Scholar. But rather than try to recall and write about how my workflow changed with the advent of Google Scholar I thought I would just jump to the present time and discuss some ways that I use Google Scholar now.

Part 2: Using Google Scholar today

When working on this post I started to look around at how I use Google Scholar and I confess I was amazed at how many different ways I use it in my work. Here are some examples:

Tracking and using citations. One major general use of Google Scholar lies in tracking of citations to specific scholarly works. Here are some ways that I use such information:

  • Citations to individual works. A key aspect of scholarly work in many fields is examining how specific works are cited. Such information has many uses include discovering new works on a topic by seeing how specific papers from the past are cited, assessing impact of works, ego satisfying, and more. For many years, information on how a specific work was cited was nearly impossible to come by without paying for access to citation tracking databases. Now, with Google Scholar I (and others) can very rapidly gather such information.
  • Citation from diverse sources. One aspect of using Google Scholar to track citations to individual works is the way GS finds citations in diverse sources – not just in the peer reviewed scholarly literature. Now, in some ways this can be viewed as a limitation (some may not want to count or even know about citations from self published white papers, for example). But in others ways this is a wonderful thing as one can find citations to one’s work from very diverse sources outside of the “normal” mold.
  • Citation metrics. It is not a large conceptual leap to go from the ability to track citations to individual works to the ability to create summary statistics about citations across many works. There are many indices for such purposes – some useful and some not. But whatever you think of such indices – Google Scholar has opened up the ability for people to calculate such metrics for oneself or to offer services to calculate metrics for others. Such indices can be used in many ways but perhaps the most common is to summarize the citations for one individual researcher. Which leads into my next topic …

Google Scholar Pages. Perhaps my favorite development from Google Scholar in the last 10 years has been the introduction of Google Scholar Pages for individuals. I make use of my Google Scholar page and pages of others for dozens of things including these:

  • Citation metrics for myself. See above for a discussion of citation metrics in general. I use Google Scholar pages to examine citation metrics for myself and my papers all the time (right now GS shows two summary statistics H-index and I-10 index). And I use this information in many ways including putting it on my CV, including it in grant reports, and examining which of my scholarly works have had more “impact”.
  • As landing page for my publication list. Once one has a GS page, GS automatically adds new publications to one’s list and also updates citation counts and other information regularly. Thus I now include a link to my GS page on my blogs, my work web sites, and in my email signature.
  • To keep track of my coauthors. I have been blessed (and perhaps a bit cursed) to work in a field (genomics) where many projects involve large-scale collaborations across many institutions, involving many researchers. And I have found that a nice way to track these coauthors is via GS (although – note to GS folks – there used to be a way to show, publically, all coauthors in a list but I cannot seem to figure out how to do this anymore).
  • Author disambiguation. For people like myself with a relatively unique name, when others search for my scholarly works, they are pretty easy to find (although I note the fact that there is another Jonathan Eisen out there who publishes some works with a bit of a conspiracy theory angle has been both good and bad for me at times). But for many others, their name is not a perfect way to find their work. This may be because they have a name that is relatively common, or it may be because they have changed their name (e.g., after marriage). For such people creating a GS page can be very useful because once one trains GS with a set of works, it can find new works by that same person quite well (I first found out about this author disambiguation by GS when Anurag gave a talk at a meeting I organized last year). GS is certainly not the only tool in author disambiguation and others – like author UIDs (e.g., ORCID) are almost certainly better long term options. I note – author disambiguation may seem like a esoteric topic to many but it has major implications on important issues such as gender equity in academia, since women are much more likely to change their names during their career than men are.
  • Automated updates of new papers by specific authors. One option associated with GS author pages I use extensively is the ability to “follow” specific authors and get notified of new publications of theirs.
  • To keep track of a collection of people. Most researchers do not regularly update their individual publication pages on their websites. However, if those researchers have GS pages one can keep track of their new papers quite easily (either by the follow option mentioned above or just by browsing occasionally). For example, for my microBEnet project I curate a list of GS pages for researchers in the whole field with connections to studies of “microbiology of the built environment” and thus (hopefully) help others keep up with what is going on in the field.
  • Who is in a specific field? One feature of GS author pages that is not used a lot as far as I can tell, but which has some value is the “areas of interest” tag one can add to one’s profile. Though not everyone uses such tags, I have found they are a useful tool in finding researchers working on specific topics. For example, I list “symbiosis” as one of my areas of interest and if I click on the link for that on my page I get a list (sorted by citation counts – which is both useful and annoying) of others who have listed that same area of interest. And many of the people in this list I am not familiar with yet they do work on topics in which I am very interested.

Automated discovery of new papers by topic. Pretty much all scholars these days are drowning in information and in keeping up with scholarly works. There are many reasons for this of course, and there are also some solutions. I find, for example, that social media is a great way to keep up to date on what new papers are coming out or have come out recently. But social media does not find everything and as someone who is responsible for keeping others up to date on various fields (e.g., this is one of my jobs at microBEnet) I also rely on both manual and automated searchers of the scholarly literature to find new papers or old papers I have missed. GS has two key ways to help in this regard. The first is relatively simple in concept but takes advantage of the power of Google indexing – which is just directly searching GS for papers on particular topics. And the advanced search options allow some customization of such searches. But as someone who is quite busy, I do not actually end up searching GS for new papers all that often. Instead I rely upon automated searches through various services including Pubmed, Pubchase, and GS. I use GS in two ways for such automated searches:

  • Create an alert. When one does a search on GS, in addition to results one is presented with an option to “Create an alert” (which I think may only come up if one is logged in with a Google account). I now have dozens of such alerts in operation. To avoid getting drowned by the results I set them up to send only once a week and I filter them into a separate mail folder that I only look at when I have time. But I frequently find interesting new papers this way.
  • GS Updates. Another option now available, if one has a GS profile, is to use the GS Updates system (which I have written about before here and here for example). This system uses one’s publication list to scan for new papers that are related in some way to one’s prior work.

Many other uses of GS. I have gone on perhaps way too long here so I am only going to briefly mention a few other uses of GS.

  • Finding online versions of papers. Unquestionably one of the most valuable uses of GS is to find online versions of scholarly works. But since others have written extensively about this I will just say the following: if you publish any scholarly work I recommend you make it freely and openly available AND that you make sure that it gets indexed by GS.
  • Full text searches of the literature. Another critically important aspect of GS is that it facilitates full text searching of the scholarly literature which is important for many reasons.
  • Finding works outside of the “normal” places to publish. Another key feature of GS is that it indexes much more than just publisher’s sites. If one posts a preprint on one’s own web server, that paper may show up in GS (which I think is a good thing). GS also indexes many diverse sources of scholarly works and thus helps in finding works that may otherwise not see the light of day.

Part 3: Where do we go from here?

As an active user of Google Scholar I of course have many comments, complaints, ideas and thoughts about what it could do better and where it might go in the future. And there are SO many things that could be added or improved upon – things like better figure and table searching, better exporting of information, better abilities to curate and create collections and to then use such collections as training sets for automated searchers, and more and more and more.  I have written about some such issues and suggestions from time to time in my blog (see for example, this and this and this).  There is certainly lots of work to be done.

But in thinking about this I realized that making a list of issues and suggestions is only of limited value. What I think GS really needs is a better public forum where GS can discuss what their plans are for the future and also where users and developers can discuss what they would find useful. And though I see some places for such discussions on the Google Scholar blog and in related sites, I don’t see a lot. So – I would like to end with a call for GS to create a better site for such discussions of the future of GS …

Update – Adding some comments and responses from Twitter

La Biology and Mathematics in the Bay Area (BaMBA) at #UCDavis 11/22

Got this in the old email tubes (note – I spoke at BaBMA a few years back – great meeting).

Dear Colleagues,

The Biology and Mathematics in the Bay Area (BaMBA) Day is an annual meeting aimed at creating a fairly informal atmosphere to explore the role of mathematics in biology. Going beyond traditional applied mathematics, the topics include sophisticated computational methods, biophysical methods, discrete mathematics and topological methods. Our goal is to encourage dialogue between researchers and students from different disciplines in an atmosphere that promotes the open exchange of ideas and viewpoints to discuss the role of mathematics in modern molecular biology. Please join us for a day full of enticing discussions!

BaMBA 9 will be held 9am-6pm on Saturday, November 22nd, in 1002 Geidt Hall on the UC Davis campus. The talks by keynote speakers will be followed by a poster session. Continue reading “La Biology and Mathematics in the Bay Area (BaMBA) at #UCDavis 11/22”

#UCDavis teaching position for Experimental Ecology and Evolution in the Field Winter & Spring

DEPARTMENT OF EVOLUTION AND ECOLOGY

TEACHING POSITION AVAILABLE

WINTER & SPRING 2015

(Jan. 2, 2015 through Jun. 12, 2015)

LECTURER

Experimental Ecology and Evolution in the Field

EVE/ENT 180A (Winter) and EVE/ENT 180B (Spring)

Responsibilities: A 100% position teaching EVE/ENT 180A and EVE/ENT 180B Experimental Ecology and Evolution – (4 units each). Lecture/laboratory – 3 hours, fieldwork – 3 hours. Experimental design in field ecology. Examination of primary literature, experimental design, independent and collaborative research, analysis of data, development of original research paper based on field experiments.

Continue reading “#UCDavis teaching position for Experimental Ecology and Evolution in the Field Winter & Spring”

Some suggestions for having diverse speakers at meetings

Been having a lot of discussions online in response to my post (Apparently, the National Academy of Sciences thinks only one sex is qualified to talk about alternatives to sex #YAMMM) tracking the awful gender ratio for speakers and session chairs at meetings run by the National Academy of Sciences in their Sackler series.  Some people were asking what one can do to improve gender diversity at meetings so I thought I would post this which I was meaning to do anyway …

——————————————————-

I wrote this in an email to a meeting organizer after I had turned down their invitation due to the imbalance in gender of the speakers (more about this another time — this is not the same case as the one I wrote about here: Turning down an endowed lectureship because their gender ratio is too skewed towards males #WomenInSTEM). 

Anyway, my colleague wrote a long and very helpful email to me after I withdrew from the meeting when I saw the speaker list.  In the email she detailed things that her organization was trying to do to increase diversity of speakers at meetings.  She ended it with this:

Thus, I take your comment to heart and wanted you to know that I care about this issues as well.  I would love to hear how you balance these inequities at your meetings and learn as much as I can.  Thank you for taking the time to bring this up I know how busy you are and appreciate your candor. Truly looking forward to more scientific exchanges and perhaps some education around gender issues.

And I wrote back, quickly, without digging into the literature or all the posts in the world about this some quick suggestions which I think others might find useful. So here is my response – again – was not meant to cover all the things one can do – just examples:

Thanks so much for the response and I am really glad to see all you are trying to do in this area. 

In terms of how we try to balance inequities at meetings I organize I would note a few simple things

  1. Do not try to invite only the famous people or the people doing the “top” work.  This usually biases one towards more established researchers (as in, older) and this alas also usually is accompanied by distortion of diversity.
  2. DO try to invite people across the breadth of career stages.  Meetings to me should not be only about getting the PIs whose labs are doing the best work to talk.  It should also be about giving opportunities to junior researchers – PhD students, post docs and junior faculty who are doing exciting work – perhaps more focused or smaller scale – but nevertheless exciting.  If one opens up a invited speaker list to people at diverse career stages one generally greatly increases the gender and ethnic diversity. 
  3. DO try to invite people from diverse institutions – research universities, research institutes, companies, non profits, NGOs, the press, non research universities, and more.
  4. DO try to be flexible about times and dates for talks – I have found that women more than men have other commitments (e.g. kids) for which they cannot change dates of activities. 
  5. DO try to provide child care assistance (as you are doing).
  6. DO try to make sure women are on the organizing committee See http://www.theatlantic.com/technology/archive/2014/01/the-easiest-possible-way-to-increase-female-speakers-at-conferences/282858/
  7. DO make sure to provide travel funds.
  8. DO try to include some talks on related areas that may not be the main theme of the conference.  For example history of science and ELSI related topics increase the pool of women and speakers with diverse backgrounds which can be invited.
  9. DO ask the women who turn down invitations if they care to say why.
  10. DO commit to spending a decent amount of time searching for qualified female speakers.  Sometimes there are people who fit ALL the goals of a meeting and they are just missed because women on average have lower public profiles than men doing the same type of work.

Just some ideas off the top of my head.

Jonathan

see also 

http://www.stemwomen.net/jonathan-eisen/ 

and 

http://phylogenomics.blogspot.com/p/posts-on-women-in-science.html

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Apparently, the National Academy of Sciences thinks only one sex is qualified to talk about alternatives to sex #YAMMM

Just got this email from Francisco Ayala:

January 9-10, 2015 

In the Light of Evolution IX. Clonal Reproduction: Alternatives to Sex 

Organizers: Michel Tibayrenc, John C. Avise and Francisco J. Ayala 

Beckman Center of the National Academies, Irvine, CA 

Evolutionary studies of clonal organisms have advanced considerably in recent years, but are still fledgling. Although recent textbooks on evolution and genetics might give the impression that nonsexual reproduction is an anomaly in the living world, clonality is the rule rather than the exception in many viruses, bacteria, and parasites that undergo preponderant asexual evolution in nature. Clonality is thus of crucial importance in basic biology as well as in studies dealing with transmissible diseases. 

This Colloquium will bring together specialists in various disciplines, including genetics, evolution, statistics, bioinformatics, and medicine. A balance will be sought between the various disciplines, including clonal animals and plants, animal and human cloning, pathogens, and cancer studies.   

Registration is now open http://www.nasonline.org/programs/sackler-colloquia/upcoming-colloquia/ILE_IX_Clonal_Reproduction.html

Registration fee is $150. 

Graduate students and postdoctoral researchers are eligible for discount fee of $100. 

All meals, break and reception refreshments listed on the agenda are included in the registration fee.
For more information, contact sackler@nas.edu.

Could be interesting right?  Alas, then, I clicked on the link.  And I discovered the meeting could also be referred to as “Only one sex talks about alternatives to sex”.  Men are highlighted in yellow. Women highlighted in green. (Note – I am making some guesses as to gender but I think these are reasoably accurate).

Organizers: Michel Tibayrenc, John C. Avise and Francisco J. Ayala 

I. General Considerations  

  • 8:30 AM Overview: The ILE Series. John C. Avise  
  • 8:40 AM Introduction and Chair, John C. Avise  
  • 8:40 AM  Can eukaryotes be considered clonally propagating cell lines with intermittent sex?, Dave Speijer, University of Amsterdam 
  • 9:30 AM Cancer in Parasitic Protozoan Trypanosoma brucei and Toxoplasma gondii, Zhao-Rong Lun, Sun Yat-Sen University 
  • 10:40 AM Mathematical Models of Clonality, Dominik Wodarz, University of California, Irvine 
  • 11:30 AM The Cost of Sex: Why Aren’t We All Clonal?, Claus-Peter Stelzer, University of Innsbruck 

II. Clonality in Multicellular Organisms  1:30 PM Chair, Zhao-Rong Lun

  • 1:30 PM  Genets, Ramets and Unisexual Reproduction in Plants, Spencer C.H. Barrett, University of Toronto
  • 2:20 PM Clonality in Asexual Invertebrate Animals, John M. Logsdon, Jr., University of Iowa
  • 3:30 PM Natural Clonality in Vertebrate Animals, John C. Avise, University of California, Irvine
  • 4:20 PM Artificial Cloning of Domestic Animals, Carol L. Keefer, University of Maryland

Keynote Address 

  • 6:45 PM Introduction, Michel Tibayrenc
  • 6:50 PM Cloning Humans: Biological and Ethical Considerations, Francisco J. Ayala, University of California, Irvine

III. Clonality in the Microbial World  

  • 8:00 AM Chair, Carol L. Keefer  
  • 8:00 AM Clonality and Intracellular Polyploidy in Virus Evolution and Pathogenesis, Esteban Domingo, Universidad Autónoma de Madrid
  • 8:50 AM The Impermanence of Bacterial Clones, Howard Ochman, University of Texas, Austin
  • 10:00 AM Clonal Reproduction in Fungi, John Taylor, University of California, Berkeley
  • 10:50 AM Clonal Reproduction in Parasitic Protozoa, Michel Tibayrenc, IRD, Montpellier, France

IV. Clonality, Cancer, and Evolution

  • 12:50 PM Organismal Fitness, Somatic Evolution, and Cancer, James DeGregori, University of Colorado School of Medicine
  • 1:40 PM Cancer and Pathogens as Clonal Processes, Edwin L. Cooper, University of California, Los Angeles
  • 2:50 PM Stem Cell Competitions: Evolution, and Cancer Progression, Irving Weissman, Stanford University
  • 3:40 PM Clonal Reproduction: An Evolutionary Curse or Blessing?, Marcel E. Dorken, Trent University
  • 4:30 PM Concluding Remarks, Francisco J. Ayala, University of California, Irvine

So – whether you count just speakers, or speakers plus session chairs, the gender ratio is not good.  Really there is only one woman as far as I can tell involved with this meeting.  Sadly this is not the only meeting at the NAS Beckman Center with gender issues.  See this post for example Today’s YAMMM (Yet Another Mostly Male Meeting) Brought to You by CIFAR & NAS.  Does NAS even make any effort in regard to diversity of speakers?

UPDATE 10/25/14 – Some responses from Twitter

//platform.twitter.com/widgets.js

//platform.twitter.com/widgets.js

//platform.twitter.com/widgets.js

For more on this topic see my other posts on “Diversity in STEM“

UPDATE 2: 10/26 – New NAS Sackler meeting after this one – better but barely in gender ratio

The next Sackler meeting after this one is on “Drawing Causal Inference from Big Data”.  Here are the speakers they list with the same colors as used above.

  • Edoardo Airoldi, Harvard University
  • Susan Athey, Stanford University 
  • Leon Bottou, Microsoft Corporation 
  • Danah Boyd, Microsoft Corporation
  • Peter Buhlmann, ETH Zurich 
  • Susan Dumais, Microsoft Corporation
  • Dean Eckles, Facebook 
  • James Fowler, University of California, San Diego  
  • Michael Hawrylycz, Allen Institute 
  • David Heckerman, Microsoft Corporation 
  • Jennifer Hill, New York University 
  • Guido Imbens, Stanford University
  • Michael Jordan, University of California, Berkeley 
  • Steven Levitt, The University of Chicago 
  • David Madigan, Columbia University
  • Thomas Richardson, University of Washington 
  • Bernhard Schölkopf, Max Planck Institute 
  • Jasjeet Sekhon, University of California, Berkeley 
  • Cosma Shalizi, Carnegie Mellon University  
  • Richard Shiffrin, Indiana University 
  • John Stamatoyannopoulos, University of Washington 
  • Hal Varian, Google, Inc. 
  • Bin Yu, University of California, Berkeley 

That is a ratio of 18:5 or 21% women.  Not sure what the gender balance is for people working on “big data” but still, given the Sackler’s recent issues with gender ratio in fields with an almost 50:50 ratio of men:women I am not willing to give them the benefit of the doubt here.  And I note – the link they provide for Susan Athey goes to the web site of Richard Shiffrin.  So I am just going to assume that the name on the list is correct not the link to Shiffrin.

UPDATE 3: 10/26 – Made a Storify to track discussion of this.

UPDATE 4: 10/26 — and another recent Sackler meeting

Epigenetic changes in the developing brain: Effects on behavior

This meeting was held March 28-29, 2014 at the National Academy of Sciences in Washington, D.C. and organized by Donald W. Pfaff (The Rockefeller University) and Eric Barrington Keverne (King’s College, Cambridge).

  • Introduction and welcome, Donald Pfaff and Barry Keverne
  • Session I. DNA methylation (Chair, Tom Insel)
    • Mechanisms that establish and maintain genomic methylation patterns in mammalian tissues, Tim Bestor, Columbia University
    • Signaling networks that regulate synapse development and dysfunction, Michael Greenberg, Harvard University
    • Impact of early life experiences on DNA methylation: Implications for brain development and behaviour, Frances Champagne, Columbia University
  • Session II. Histone modifications (Chair, Barry Keverne)
    • A histone methylation network regulates epigenetic inheritance, Yang Shi, Harvard University
    • Global Epigenomic Reconfiguration during Mammalian Brain Development, Joseph Ecker, Salk Institute for Biological Studies
    • H3.3 nucleosomal dynamics regulate synaptic development and plasticity in postreplicative neurons, Ian Maze & David Allis, The Rockefeller University
    • Steroid hormone actions on histone tail modifications in the brain, Donald Pfaff, The Rockefeller University
  • 14th Annual Sackler Public Lecture
    • Introduction – Diane Griffin, Vice President, National Academy of Sciences
    • Deconstructing circuits for motor behavior, Thomas Jessell, Columbia University
  • Session III. Genomic imprinting (Chair, Rusty Gage)
    • Genomic imprinting,action and interaction of two genomes in mother, Barry Keverne, Cambridge University
    • Epigenetic regulation of imprinted gene loci, Marisa Bartolomei, University of Pennsylvania Medical School
    • Monoallelic gene expression, Andrew Chess, Mount Sinai Hospital
  • Session IV. Non-coding RNA’s (Chair, Don Pfaff)
    • Linking RNA to Nuclear Architecture, John L. Rinn, Broad Institute of Harvard and MIT
    • Human retrotransposons (“jumping genes”) in health and disease, Haig Kazazian, Johns Hopkins University
  • Session V. CNS applications (Chair, Tim Bestor)
    • Mobile Element Activity in Evolution and Disease, Fred Gage, Salk Institute
    • The Epigenetic Language of the Circadian Clock, Poalo Sassone-Corsi, University of California, Irvine
    • Epigenomics of Major Psychiatric Disease, Art Petronis, University of Toronto
    • Imprinting mechanisms underlying Prader Willi and Angelman syndromes, James Resnick, University of Florida
  • Closing remarks: Brain Exceptionalism, Tom Insel, Director, National Institute of Mental Health, NIH

So – if you just count all the speaking / session chair slots that comes to 24 slots to men and 3 to women for a wonderful 11% female percentage.  Even if you count just speakers (and not session chairs) the #s don’t look good.  Looking pretty bad NAS Sackler meetings.

UPDATE 5: Copying in my analysis of gender ratio at the most recent Sackler meeting on Symbioses becoming permanent: The origins and evolutionary trajectories of organelles which I refer to above but only via a link out to my post.  Here is the speaker analysis:

  • Organizers: W. Ford Doolittle, Patrick Keeling, and John McCutcheon
  • Distinctive Voices Public Lecture presented by Michael Gray, CIFAR Advisor, Dalhousie University
  • Session 1: Genomes (evolutionary rates, oddities, and reduction)
    • Introduction and welcome remarks – W. Ford Doolittle, CIFAR Advisor & Patrick Keeling, CIFAR Program Director and Senior Fellow
    • John McCutcheon, CIFAR Associate Fellow, University of Montana
    • John Archibald, CIFAR Senior Fellow, Dalhousie University, Nuclear organelles 
    • Andrew Roger, CIFAR Senior Fellow, Dalhousie University, Organelle reduction 
    • Siv Andersson, Uppsala University, Alphaproteobacterial genome evolution 
    • David Smith, University of Western Ontario, Roots of genomic architecture variation 
    • Daniel Sloan, Colorado State University, Cytonuclear co-evolution under extreme mitochondrial mutation rates
    • John Allen, University College London, Why keep genomes?
  • Session 2: Integration/Control (trafficking, signaling, transporters)
    • Debash Bhattacharya, Rutgers University, Transporters in organellogenesis 
    • Nancy Moran, University of Texas, Austin, Insect endosymbionts 
    • Geoff McFadden, University of Melbourne, Diversity of protein trafficking
    • Chris Howe, Cambridge University, Why integrate?
    • Steve Perlman, CIFAR Fellow, University of Victoria, Maternal transmission, sex ratio distortion, and mitochondria 
    • William Martin, Düsseldorf University, Endosymbiont and organelle, what’s the difference? 
    • Moriya Okhuma, Riken University, Metabolic integration across endosymbiotic communities
  • Session 3: Theories and Models
    • Eors Szathmary, Loránd University, A fresh look at cooperation in some major transitions, especially the origin of eukaryotes
    • Marc Ereshefsky, University of Calgary, Evolutionary individuality
    • Peter Godfrey-Smith, City University of New York, Individuality and the egalitarian transitions 
    • Maureen O’Malley, University of Sydney, Philosophical Reflections on Endosymbiosis: Implications for Evolutionary Theory
    • Toby Kiers, University Amsterdam, Bacterial cooperativity
  • Closing remarks J. McCutcheon

That is a ratio of 19:4 for speakers slots for men vs. women.  Sensing a pattern anyone?

UPDATE 6: I feel much better now looking at the meeting before the developing brain meeting.  It is so much better (not). 

In the Light of Evolution VIII: Darwinian Thinking in the Social Sciences. January 10-11, 2014 at the Arnold and Mabel Beckman Center in Irvine, CA. 

  • Organized by Brian Skyrms, John C. Avise and Francisco J. Ayala
  • I.  Evolution of Social Norms
    • Bargaining and Fairness, Kenneth Binmore, University College London
    • Cooperation, Natalia Komarova, University of California, Irvine
    • Friendship and Natural Selection, James H. Fowler, University of California, San Diego
    • Reputation and Punishment, Michihiro Kandori, University of Tokyo
  • II. Social Dynamics
    • The Replicator Equation and Other Game Dynamics, Ross Cressman, Wilfrid Laurier University
    • Payoff-Based Learning Dynamics, Alvin Roth, Harvard University
    • Strategic Learning Dynamics, David K. Levine, Washington University
    • Cultural Evolution, Marcus W. Feldman, Stanford University
  • Keynote Address:  Public Goods: Competition, Cooperation, and Spite, Simon A. Levin, Princeton University
  • III. Special Sciences
    • Evolutionary Demography, Kenneth W. Wachter, University of California, Berkeley
    • Folklore of the Elite and Biological Evolution, Barry O’Neill, University of California, Los Angeles
    • Economics, Ted Bergstrom, University of California, Santa Barbara
    • Psychology, Dale Purves, Duke-National University of Singapore Graduate Medical School
  • IV. Applications
    • Evolutionary Implementation in Mechanism Design, Éva Tardos, Cornell University
    • Some Dynamics of Signaling, Brian Skyrms, University of California, Irvine
    • The Rate of Innovation Diffusion in Social Networks, H. Peyton Young, Oxford University
    • Homophily, Culture, and Coordinating Behaviors, Matthew O. Jackson, Stanford University

That is 15:2 males to females in speaking slots and also three main organizers. 

Update 7: A trend in meetings coorganized by John Avise and Francisco Ayala

I note the meeting above in Update 6 is the second recent meeting coorganized by John Avise and Francisco Ayala with a highly skewed gender ratio.  So I decided to go back and look at other meetings they coorganized.  For example here is the next most recent one.

In the Light of Evolution VII: The Human Mental Machinery

Organized by Camilo J. Cela-Conde, Raúl Gutiérrez Lombardo, John C. Avise and Francisco J. Ayala

This meeting was held January 10-12, 2013 at the Arnold and Mabel Beckman Center in Irvine, CA.

  •  I. Theory of Mind 
    • Theory of Mind: Darwin’s legacy, John Searle, University of California, Berkeley
    • Human mind and brain – pathological evidence, Robert E. Clark, University of California, San Diego 
    • Theory of Mind in Other Primates, Robert M. Seyfarth, University of Pennsylvania
  • II. Cognition
    • Evolution of Working Memory, Peter Carruthers, University of Maryland
    • The evolution of episodic memory, Norbert Fortin, University of California, Irvine
    • Natural Basis of Cognition, Terrence J. Sejnowski, Salk Institute for Biological Studies
    • Human and Animal Consciousness, Michael T. Alkire, University of California, Irvine
    • Co-Evolution: Culture, mind and brain, Chet C. Sherwood, George Washington University 
  • Keynote Address 
    • Unusual and Exceptional Capacities of the Human Mind, James L. McGaugh, University of California, Irvine     
  • III. Evolving Piece by Piece: Levels of Modularity in Neurobiology
    • Neuronal Networks of the Moral Judgment, Patricia Churchland, University of California, San Diego
    • Pathological Altruism, Barbara A. Oakley, Oakland University
    • Theory of Justice in Non-Human Primates, Sarah F. Brosnan, Georgia State University
    • Evolutionary Dynamics of Altruism, Martin Nowak, Harvard University
    • Human and Animal Neuroeconomics, Michael Platt, Duke University 
  • IV. Aesthetics 
    • Music and the Brain, Robert Zatorre, Montreal Neurological Institute 
    • Aesthetic and Ethnic Emotions, Oshin Vartanian, University of Toronto, Scarborough
    • Aesthetic Perception: Mind and Brain , Camilo J. Cela-Conde, University of the Baleares Islands, Spain

That is a ratio of 14:3 for speakers of men: women. //platform.twitter.com/widgets.js

UPDATE 8: The next most recent meeting coorganized by Avise and Ayala

In the Light of Evolution VI: Brain and Behavior
January 19-21, 2012
Arnold and Mabel Beckman Center
Organized by Georg F. Striedter, John C. Avise and Francisco J. Ayala

  • Session I. Brains in History: Descent with Modification
    • Chair, John C. Avise, University of California, Irvine
    • Evolution of Brain Development, Georg Striedter, University of California, Irvine
    • Evolution of Neuronal Cell Types, Nipam H. Patel, University of California, Berkeley
    • Homology and Homoplasy of Behavior and Neural Circuits, Paul S. Katz, Georgia State University
    • Evolution of Cognitive Traits, Lucia F. Jacobs, University of California, Berkeley
  • Session II. Brains in Ecology: Adapatation by Natural Selection
    • Chair, Georg Striedter, University of California, Irvine
    • Adaptation of Neuron-typical Molecules and Processes, Harold H. Zakon, University of Texas, Austin
    • Evolution of Specialized Sensory Systems, Kenneth C. Catania, Vanderbilt University
    • Evolution of Specialized Motor Systems, Andrew H. Bass, Cornell University
    • Evolving Neural Mechanisms of Social Diversity and Cognition, James L. Goodson, Indiana University
  • Keynote Address
    • Introduction, Francisco J. Ayala, University of California, Irvine
    • Evolution of Centralized Nervous Systems, R. Glenn Northcutt, Scripps Institution of Oceanography
  • Session III. Evolving Piece by Piece: Levels of Modularity in Neurobiology
    • Chair, Lucia F. Jacobs, University of California, Irvine
    • Molecular Models in Neurobiology, Kenneth S. Kosik, University of California, Santa Barbara
    • Devolpmental Modules in Nervous Systems, Leah A. Krubitzer, University of California, Davis
    • Neuroanatomical and Physiological Modules, Jon H. Kaas, Vanderbilt University
    • Modularity of Cognitive Processes, Jessica F. Cantlon, University of Rochester
  • Session IV. Human Evolution: Brains and Behavior
    • Chair, Francisco J. Ayala, University of California, Irvine
    • Molecular Aspects of Human Brain Evolution, Todd M. Preuss, Emory University School of Medicine
    • Evolution of Primate Brain Morphology, Suzana Herculano-Houzel, Universidade Federal do Rio de Janeiro
    • Evolution of Primate Brain Functions, Lizabeth M. Romanski, University of Rochester
    • The Evolution of Human Cognition, Clark Barrett, University of California, Los Angeles
  • Concluding Remarks
    • Francisco J. Ayala, University of California, Irvine
That isa ratio of 17:6 if one includes all slots (chairs, speakers, etc) or 14:5 if you just include speaking slots. 

UPDATE 9: This is NOT just about speaking at meetings.

I note – many of the Sackler meetings turn into special collections in PNAS and thus the limited representation of women speakers (which is a problem) is made worse by then directly affecting publishing in PNAS.

UPDATE 10: 10/27/14. Going back to another Avise/Ayala meeting from 2001

In the Light of Evolution V: Cooperation

Organized by Joan E. Strassmann, David C. Queller, John C. Avise, and Francisco J. Ayala
January 7-8, 2011

(Note Joan Strassmann is one of my favorite scientists and people on the planet – great to see her in a role as coorganizer here)

  • Session I. Foundations of Cooperation
    • John C. Avise, University of California, Irvine, Chair
    • Insect Societies: pinnacles of cooperation – Peter Nonacs, University of California, Los Angeles
    • Families in vertebrates – Dustin R. Rubenstein, Columbia University
    • The major evolutionary transitions In bacterial symbiosis – Joel L. Sachs, University of California, Riverside
    • Kin, kith, and kind: the varieties of social experience – David C. Queller, Rice University
  • Session II. Genetic Basis of Cooperation and Conflict
    • David Queller, Chair
    • Altruism and cheating in a social microbe, Dicytostelium discoideum – Joan E. Strassmann, Rice University
    • A prokaryotic model system –Greg Velicer, Indiana University
    • The evolution of restraint in simple communities – Ben Kerr, University of Washington
    • Selfish genetic elements – Jack H. Werren, University of Rochester
  • Banquet Lecture
    • Francisco J. Ayala, University of California, Irvine, Introduction
    • Evolution of insect society: eat, drink and be scary – Gene E. Robinson, University of Illinois at Urbana-Champaign
  • Session III. Hamiltonian Medicine
    • Joan E. Strassmann, Chair
    • Genomic imprinting, helpers at the nest, and age at menarche David Haig, Harvard University 
    • Pathology from evolutionary conflict – Steven A. Frank, University of California, Irvine 
    • The sociobiology of drug resistance and pathogen virulence – Andrew Read, Pennsylvania State University
    • Microbial sociality: implications for disease – Kevin Foster, Harvard University
  • Session IV. Are Humans Different?
    • Francisco J. Ayala, Chair
    • Cooperation and conflict in traditional cultures – Beverly I. Strassmann, University of Michigan 
    • The cultural niche – Robert Boyd, University of California, Los Angeles
    • Social Bonds to Social Preferences; the foundations for human moral sentiments  – Joan Silk, University of California, Los Angeles
    • What does primate cooperation tell us? – Dorothy Cheney, University of Pennsylvania
  • Concluding Remarks
    • John C. Avise, University of California, Irvine

So – for speaking and chairing slots – that comes to a ratio of 17:5 male to female.  Even with Joan Strassmann being involved as a coorganizer (and she is truly wonderful in a million ways) this meeting still has the NAS and Avise/Ayala pattern of very few female speakers or session chairs, even in fields where ther are many candidates.  Yuck.

I think I would make one recommendation out of this to begin with – John Avise and Francisco Ayala should not be allowed to run any NAS meetings again.  And NAS needs to have and use policies on educating meeting organizers about gender bias and requiring some type of efforts to have reasonable representations of diversity among speakers and chairs.

UPDATE 11: Meetings from 1990s I went to while in graduate school

Just scanned in notes from some of these NAS Beckman Center meetings that I attended while in graduate school at Stanford.  I added them to my collection of “Retroblogging Meetings and Seminars: Posting Scans of Notes“.  The meetings then had even worse gender ratios of speakers.

1994: Tempo and Mode in Evolution.  See scans here. All speakers except one were male.
1997: Genetics and the Origin of Species. See scans here.

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–