Tuesday, February 26, 2019

A conference where all the speakers are women - happening this week #YAMMM #manels #STEMDiversity #GenderBias

It was now six years ago that I wrote here wondering if it would be a good idea to have a conference where all the speakers were women.

See The Tree of Life: A conference where the speakers are all women?

I wrote about this because of the general issue with excessive numbers of conferences where most or all of the speakers were men.  I had come up with a term for such meetings - YAMMM.  Yet Another Mostly Male Meeting.  I even made some little pics / images to represent such YAMMMs.

And I blogged and Tweeted about such meetings a lot (and still do).  See STEM Diversity posts and related links here for example.

When I wrote the post I was wondering if this would be a good counter to the problem of these YAMMMs (also called manels by others).  The feedback (much of it on Twitter) was really useful, mostly.  And over the years I pondered doing such a thing but to be honest, never felt really comfortable with the idea.  I worried about some of the possible negative sides of doing this, such as how the speakers might get unwanted attention and critiqued for being selected solely because of their gender.  And I also worried about whether this would be viewed in some way as a form of "reverse discrimination".

But I did try to do other analogous things where one reversed the normal gender skew (which is almost always towards males).  For example, when I found out, kind of at the last minute, I was speaking at a meeting with a very very skewed gender ratio of speakers, I gave my talk, but changed only referenced the work of women in the field.  See What to do when you realize the meeting you are speaking at is a YAMMM (yet another mostly male meeting)?  And in a class I teach I decided to basically replace most of the white male scientists I had been referencing with women and people of color.  Small things I know.  But I was pleased when people noticed these efforts and commented on how it made them think a bit about the examples we use when we give talks and teach.

Mind you, I have organized or helped organize a lot of meetings and seminar series since that post six years ago.  And I have tried to have the speakers at these be representative of diverse backgrounds in terms of gender, ethnicity, career stage, type of institution, and more.  But I myself have never gone to the next level and flipped the standard gender bias on its head.

Thus I was intrigued in September last year when I found out that my friend and colleague Dr. Rob Knight was co-organizing (with Dr. Sandrine Miller-Montgomery) a meeting in San Diego on "microbiomes" (my main area of research) where all of the invited speakers were women.  I blogged briefly about this here: 1st annual CMI International Microbiome Meeting (CIMM) w/ a great #STEMDiversity statement & plan.  I include below the material from the conference site that I included in that post:

On behalf of Dr. Rob Knight, the Center for Microbiome Innovation is pleased to host the 1st annual CMI International Microbiome Meeting (CIMM) on February 27–28, 2019 in San Diego. Additionally, we are pleased to announce that the 1st Urobiome Meeting on February 26, 2019, led by Linda Brubaker MD, will occur in conjunction with CIMM to make the most of your visit to San Diego. 
During the first day of this event, leading researchers will present on the emerging science of the Urobiome and its recently discovered implications for human health, including common conditions such as urinary tract infection, urinary incontinence and bladder overactivity. 
The following two days will feature high-impact presentations on the latest discoveries in microbiome sciences, with sessions on topics ranging from the microbiome in human disease and wellness and the metabolome, to primate microbiomes, to environmental and ocean microbiomes. For this first edition, we have decided to demonstrate that it is possible to have a large representation of women presenters in a scientific meeting by inviting only women speakers. Be prepared to hear from fantastic presenters such as Dr. Katie Amato (Northwestern University), Dr. Rita Colwell (University of Maryland), Dr. Merete Eggesbo (Norwegian Institute of Public Health), Dr Susan Prescott (University of Western Australia), Dr. Lita Proctor (NIH), and many more!
In addition, I agreed to serve on a panel at the end of the meeting discussing "Breaking the Glass Ceiling: How do we solve the gender imbalance in STEM?" (I had found out about their plans for the meetings when they invited me to serve on the panel). As someone who has critiqued meetings for egregiously skewed gender ratios of speakers and as someone who has called attention to in particular the many microbiome focused meetings with gender balance issues, the whole idea behind this conference was in essence represented by this statement:
For this first edition, we have decided to demonstrate that it is possible to have a large representation of women presenters in a scientific meeting by inviting only women speakers
This was certainly a bold move by the organizers. So - now zoom to today.

Today I am heading down to San Diego for the meeting.  And yesterday I found out that there was an editorial in the Wall Street Journal apparently critiquing the plan for having only female speakers.  It is entitled "No Men Allowed" by James Freeman. Alas, I do not have access to the editorial as it is behind a paywall.  There is also an editorial by Mark Perry at the American Enterprise Institute web site: Can the University of California bar males from presenting research at a biology conference?

So -- clearly, some people do not like the idea of a conference where all the speakers are women.  I confess I am still torn about the whole concept for the reasons I mentioned above.  However, even though I am torn, I do think it is important to push back against the clear implicit and explicit biases that have occurred against women in relation to speaking at conferences.  There is an extensive literature on this topic and on the topic of implicit and explicit biases that may be involved.  And I think this conference is an important form of push back.  The organizers may in fact get a bunch of grief over not having any male speakers.  But they will also provide an important venue for people to get challenged.  Conferences with only male speakers occurred for many many years without too many people raising any complaints.  And now some still occur but they are generally frowned upon in most places and are becoming rarer at least in my fields.  So in a way this conference can serve a similar function as Ruth Bader Ginsburg's dream of an all female US Supreme Court (this analogy was pointed out to me by Karen James). In reference to this concept Ruth Bader Ginsburg said:
"So now the perception is, yes, women are here to stay. And when I'm sometimes asked when will there be enough [women on the supreme court]? And I say when there are nine, people are shocked. But there'd been nine men, and nobody's ever raised a question about that."
Of course, gender bias is just one of the forms of bias that happens in STEM fields and with STEM conferences.  It is not the only issue we need to worry about or work on.  But it is a big one.  And the organizers of this meeting have done something bold and risky to confront this issue.

I will report more from the meeting. I would also love to hear what other people think about the plan for this conference.

PS. Thanks to multiple colleagues for some private feedback on this conference.  If I get permission I will post details of their comments.

Saturday, February 09, 2019

Symbiosis paper of interest: Host-Microbe Coevolution and Complex Marine Invertebrate Holobionts | mBio

This looks potentially interesting.

Host-Microbe Coevolution: Applying Evidence from Model Systems to Complex Marine Invertebrate Holobionts | mBio

O’Brien PA, Webster NS, Miller DJ, Bourne DG. 2019. Host-microbe coevolution: applying evidence from model systems to complex marine invertebrate holobionts. mBio 10:e02241-18. https://doi.org/10.1128/mBio.02241-18.

Marine invertebrates often host diverse microbial communities, making it difficult to identify important symbionts and to understand how these communities are structured. This complexity has also made it challenging to assign microbial functions and to unravel the myriad of interactions among the microbiota. Here we propose to address these issues by applying evidence from model systems of host-microbe coevolution to complex marine invertebrate microbiomes. Coevolution is the reciprocal adaptation of one lineage in response to another and can occur through the interaction of a host and its beneficial symbiont. A classic indicator of coevolution is codivergence of host and microbe, and evidence of this is found in both corals and sponges. Metabolic collaboration between host and microbe is often linked to codivergence and appears likely in complex holobionts, where microbial symbionts can interact with host cells through production and degradation of metabolic compounds. Neutral models are also useful to distinguish selected microbes against a background population consisting predominately of random associates. Enhanced understanding of the interactions between marine invertebrates and their microbial communities is urgently required as coral reefs face unprecedented local and global pressures and as active restoration approaches, including manipulation of the microbiome, are proposed to improve the health and tolerance of reef species. On the basis of a detailed review of the literature, we propose three research criteria for examining coevolution in marine invertebrates: (i) identifying stochastic and deterministic components of the microbiome, (ii) assessing codivergence of host and microbe, and (iii) confirming the intimate association based on shared metabolic function.

Found out about it on Slack, Twitter and via Google Scholar automated searches so .. caught my attention.

Today's microbial diversity reading: A census-based estimate of Earth's bacterial and archaeal diversity

Looking at this today: A census-based estimate of Earth's bacterial and archaeal diversity

Louca S, Mazel F, Doebeli M, Parfrey LW (2019) A census-based estimate of Earth's bacterial and archaeal diversity. PLoS Biol 17(2): e3000106. https://doi.org/10.1371/journal.pbio.3000106

Definitely worth a look:

The global diversity of Bacteria and Archaea, the most ancient and most widespread forms of life on Earth, is a subject of intense controversy. This controversy stems largely from the fact that existing estimates are entirely based on theoretical models or extrapolations from small and biased data sets. Here, in an attempt to census the bulk of Earth's bacterial and archaeal ("prokaryotic") clades and to estimate their overall global richness, we analyzed over 1.7 billion 16S ribosomal RNA amplicon sequences in the V4 hypervariable region obtained from 492 studies worldwide, covering a multitude of environments and using multiple alternative primers. From this data set, we recovered 739,880 prokaryotic operational taxonomic units (OTUs, 16S-V4 gene clusters at 97% similarity), a commonly used measure of microbial richness. Using several statistical approaches, we estimate that there exist globally about 0.8–1.6 million prokaryotic OTUs, of which we recovered somewhere between 47%–96%, representing >99.98% of prokaryotic cells. Consistent with this conclusion, our data set independently "recaptured" 91%–93% of 16S sequences from multiple previous global surveys, including PCR-independent metagenomic surveys. The distribution of relative OTU abundances is consistent with a log-normal model commonly observed in larger organisms; the total number of OTUs predicted by this model is also consistent with our global richness estimates. By combining our estimates with the ratio of full-length versus partial-length (V4) sequence diversity in the SILVA sequence database, we further estimate that there exist about 2.2–4.3 million full-length OTUs worldwide. When restricting our analysis to the Americas, while controlling for the number of studies, we obtain similar richness estimates as for the global data set, suggesting that most OTUs are globally distributed. Qualitatively similar results are also obtained for other 16S similarity thresholds (90%, 95%, and 99%). Our estimates constrain the extent of a poorly quantified rare microbial biosphere and refute recent predictions that there exist trillions of prokaryotic OTUs.

Author summary
The global diversity of Bacteria and Archaea ("prokaryotes"), the most ancient and most widespread forms of life on Earth, is subject to high uncertainty. Here, to estimate the global diversity of prokaryotes, we analyzed a large number of 16S ribosomal RNA gene sequences, found in all prokaryotes and commonly used to catalogue prokaryotic diversity. Sequences were obtained from a multitude of environments across thousands of geographic locations worldwide. From this data set, we recovered 739,880 prokaryotic operational taxonomic units (OTUs), i.e., 16S gene clusters sharing 97% similarity, roughly corresponding to prokaryotic species. Using several statistical approaches and through comparison with existing databases and previous independent surveys, we estimate that there exist globally between 0.8 and 1.6 million prokaryotic OTUs. When restricting our analysis to the Americas, while controlling for the number of studies, we obtain similar estimates as for the global data set, suggesting that most OTUs are not restricted to a single continent but are instead globally distributed. Our estimates constrain the extent of a commonly hypothesized but poorly quantified rare prokaryotic biosphere and refute recent predictions that there exists trillions of prokaryotic OTUs. Our findings also indicate that, contrary to common speculation, extinctions may strongly influence global prokaryotic diversity.

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