Home Archives for مارس 2015

Painful, kind of hilarious, typesetting error in a #PLOSOne paper from my lab - should I try to get it fixed?

Tags
Saw this tweet:

So I went and found the paper.

Wu D, Jospin G, Eisen JA (2013) Systematic Identification of Gene Families for Use as “Markers” for Phylogenetic and Phylogeny-Driven Ecological Studies of Bacteria and Archaea and Their Major Subgroups. PLoS ONE 8(10): e77033. doi:10.1371/journal.pone.0077033

And discovered what he was pointing to

Then I looked at the Pubmed Central version of the paper and it was the same.  So I wnet and found the arXiv version of the paper and it looked correct.



So apparently, PLOS One somehow replaced "nonmember" with



Brutal.  And even worse, this may have been there all along and I missed it.  So I responded:

And then Michael Hall pointed out another mistake.



Aaargh.  And funny too.  So now the question I guess is - should I fix it? And if so, how do I do that?

Calling attention to meetings with skewed speaker gender ratios, even when it hurts, part 2

Tags

A few weeks ago I gave a talk at the Future of Genomic Medicine 2015 (aka #FOGM15) meeting.  The talk seemed to go over well.  I talked right after Martin Blaser in a session on "The Microbiome".  I posted my slides and then a video of my talk as well as notes from the meeting: see My microbiome talk at #FOGM15 - the perils (and fun I guess) of redoing one's talk at the last minute.  And I met some really interesting people at the meeting and enjoyed most of the talks I went to.

But alas, one thing stuck in my head from this meeting.  One single Tweet from someone out there threw me for a loop:

And this let to a bit of soul searching on my part.  Some of the conversations on Twitter are captured in this Storify:


Which I guess culminated in a post to the organizers of the meeting


Then, when I left the meeting I went to say goodbye to the organizers.  And, well, one of them did not take too kindly to the critique of the meeting, saying that they were doing a better job than other healthcare meetings.  I disagreed and said I thought they could do much better, but I had no numbers to cite at the time and the conversation ended there.

So on the way to the airport I started digging around for some numbers and I found some great resources - especially this from Rock Health.

And for the last few weeks I have continued to fester wondering - well - should I post more about this?  Should I dig into the gender ratio of the FOGM meetings in more detail?  Well, why do it?  Because I think it is important to know how meetings perform in terms of diversity.  Why not do it?  Well, I like Eric Topol and the other organizers.  And the meeting has many strong points.  But, as I wrote a few days ago - sometimes one needs to call attention to meeting gender ratio issues, even when it hurts.  

So then I decided to dig a little deeper and look at past versions of the "Future of Genomic Medicine".  And, well, when I did this, things just do not look so good (detailed analysis is at the end of the post). (Note - for the numbers i counted all presenting slots - session chairs, keynotes, welcomes, etc.  The numbers are not much different if one counts just "talks").



If one compares these meetings to the ones catalogued by Rock Health, the FOGM meetings are at the low end.  Not the worst certainly.  But definitely not something to be proud of.  And certainly something that could be improved upon enormously.  So I repeat the Tweet I posted during the meeting, and I stand by it, even if it means I am unlikely to be invited back and even if it means pissing off some big shots in the world of genomics ...


If you are running a meeting, please consider the ways in which bias may creep into the speaker and session chair slots.  If speakers come from invitations, perhaps the invitation list is biased.  Perhaps certain types of people are more likely to say no to invitations.  Perhaps the timing of the meeting (e.g., on weekend) may lead certain types of people to not be able to participate.  Perhaps the meeting does not provide enough travel funds or child care or the right kind of schedule.  There are so many things that can lead to bias - from explicit bias against certain groups to very subtle implicit biases.  Consider inviting people from diverse career stages, which can open up speaking slots to more women and underrepresented minorities.  Consider providing child care.  Consider asking people why they say no to invitations to try and understand what is going on if many people say no.  Consider asking for help in finding speakers covering the diversity in the field.

If you do all these things, and the meeting still does not have diverse speakers, well, try some other things.  Keep trying to figure it out.  There are resources out there that can help.  Read things like Some suggestions for having diverse speakers at meetings (by me) and Ten Simple Rules to Achieve Conference Speaker Gender Balance (by Jenny Martin) and Increasing Diversity at Your Conference by Ashe Dryden (which is just completely awesome) and How To Create A More Diverse Tech Conference ... and Would I attend my own conference? - O'Reilly Radar by Sarah Milstein.

Why is this important?  Well, speaking at a meeting is important for people's careers.  It helps in merit and promotion and tenure cases.  It helps get their work recognized and known.  Speaking at a meeting is also good practice for speaking at other meetings.  Having diverse speakers also is important in terms of providing role models to attendees.  And having diverse speakers helps a meeting not just be about the same old, white, men talking about their ideas.  Or, in other words, it makes a meeting more, well, diverse.  And almost certainly more interesting.  And so on.  Diversity of speakers at meetings is important for 100s of reasons.  And don't just focus on one aspect of diversity.  I post a lot about women speakers because, well, it is easy to make a reasonable guess as to whether a person is male or female.  But there are MANY other aspects of diversity to consider (see Increasing Diversity at Your Conference by Ashe Dryden (which I referenced above and which really is awesome).

Anyway - if you are organizing a meeting, make sure to think about these issues.  And do something about them.  And if you are invited to a meeting, look at the speaker list (if it is available) and consider saying no to speaking if the meeting has diversity issues (see a post of mine about doing this here: Turning down an endowed lectureship because their gender ratio is too skewed towards males #WomenInSTEM).

And if you are considering attending a meeting, consider diversity of speakers when deciding whether or not to attend.  Meetings with high diversity of speakers should be supported.  Meetings with poor diversity relative to possible candidate speakers (e.g., who is in the field) should be avoided, shunned, and called out.  We need to force change upon some fields and the only way will be to call out the bad apples.  Mind you, it is not possible to know WHY a meeting has a skew in terms of diversity of speakers.  Thus one additional thing to consider is whether something is a consistent pattern.  For example see my post about meetings from the National Academy of Sciences Sackler Colloquia - Apparently, the National Academy of Sciences thinks only one sex is qualified to talk about alternatives to sex #YAMMM. Sadly it seems to me that the FOGM meetings have a consistent pattern of poor representation of women among the presenters.  Unless the organizers commit to changing this, I think people should not attend this meeting in the future.


Detailed analyses of these meetings are below.

People I have identified as males are labelled in yellow.  People I have identified as females are in green.  I realize that this is an imperfect thing to do.  I may make mistakes in my inferences.  And dividing people into two categories is not representative of the true diversity in the human population.  But I still think this is a useful, informative thing to try to do.

2015 FOGM (schedule is from the one sent around to participants on 3/4/15)
  • Welcome
    • Eric Topol
    • Pateint #1 - Eunice Lee and Nilesh Dharajiya
    • Francis Collins
  • Session 1
    • Moderator Ali Torkamani
    • Diana Bianchi
    • Evan Muse
    • Stephen Quake
    • David Hoon
  • Session 2
    • Moderator Ali Torkamani
    • Mark McCarthy
    • Christopher Austin
    • George Yancopoulos
  • Session 3
    • Moderators Nathan Wineinger and Andrew Su
    • Atul Butte
    • Eric Schadt
    • Andrew Su
    • Joe Pickrell
  • Welcome Day 2
    • Patient #2
    • Eric Topol
  • Session 4: 
    • Moderator Ali Torkamani
    • Cristian Tomasetti
    • Nazneen Rahman
    • Roni Ziegler
  • Session 5
    • Moderators Kristin Baldwin and Fyodor Urnov
    • J. Keith Joung
    • Fyodor Urnov
    • TBD
    • Kristin Baldwin
  • Session 5
    • Moderator Kristian Andersen
    • Martin Blaser
    • Jonathan Eisen
    • Stephen Steinhubl
  • Session 6
    • Moderator David Goldstein  (he did not show up)
    • Elizabeth Worthey
    • Ali Torkamani
    • Seth Mnookin
    • Virginia Hughes
All speaker and session chair slots
  • Male: 30 (81%)
  • Female: 7 (19%)
Just speakers
  • Male: 23
  • Female: 6
2014 - Future of Genomic Medicine VII -  schedule from here
  • Welcome
    • Chris Van Gorder, FACHE
    • Eric J. Topol, MD
    • Patient / Family #1
  • Session 1
    • Frank McCormick
    • Bert Vogelstein
    • Elaine Mardis
    • Robert Nussbaum
    • Sarah Jane Dawson
    • Michael Pellini
  • Session 2
    • J. Craig Venter
    • Eric Topol 
    • Al Gore
    • Heidi Rehm
    • Muin Khoury
  • Session 3
    • Moderator Katrina Kelner
    • Leonid Kruglyak
    • Carl Zimmer
    • Magdalena Skipper
    • Chris Gunter
  • Session 4
    • Patient / Family #2
    • Athur Beaudet
    • Jay Shendure
    • Howard Jacob
    • Hakon Hakonarson
    • David Epstein
    • Nir Birzalai
    • Ali Torkamani
    • Jeffrey Hammerbacher
  • Session 5
    • Michael Specter
    • Jessica Richman
    • Andrew Feinberg
    • Russ Altman
    • Anne Wojcicki
    • Harry Greenspun
    • Zubin Damania
Speakers
  • Male: 25 (76%)
  • Female: 8 (24%)
2013 - Future of Genomic Medicine VI - schedule from here
  • Welcome: Eric Topol
  • Patient / Family #1
  • Session 1:
    • Michael Snyder
    • William Gahl
    • Howard Jacob
    • Ali Torkamani
    • Gholson Lyon
    • Cinnamon Bloss
    • Misha Angrist
  • Session 2
    • Evan Eichler
    • Eric Schadt
    • Katrina Armstrong
    • George Weinstock
  • Session 3
    • Joe Ecker
    • Stephen Kingsmore
    • Stephen Quake
  • Session 4
    • Patient / Family #2
    • Siddhartha Mukherjee
    • Elaine Mardis
    • Daniel D. Von Hoff
    • Randy Scott
    • Susan Desmond Hellman
    • Elias Zerhouni
    • Janet Woodcock
  • Session 5
    • Peter Vesscher
    • David Goldstein
    • George Church
    • Jonathan Eisen
    • Atul Butte
    • AJ Jacobs
    • Neil Risch
    • Lonny Reisman
    • Daniel MacArthur
Speakers
  • Male: 26 (84%)
  • Female: 5 (16%)
2012 Future of Genomic Medicine V - schedule from here
  • Welcome
    • Chris Van Gorder, FACHE
    • Eric J. Topol, MD
  • Joseph Beery and Family
  • Moderators: Samuel Levy, PhD and Eric J. Topol, MD
    • Samuel Levy, PhD
    • Matthew J. Price, MD
    • Julie Johnson, PharmD
    • Michael R. Hayden MB, ChB, PhD
    • William E. Evans, PharmD
  • Moderators: Evan Eichler, PhD and Sarah Murray,
    • Evan Eichler, PhD
    • Christofer Toumazou, PhD
    • Siddharta Mukherjee, MD, PhD
    • Sarah Murray, PhD
  • Moderators Nicholas Schork, PhD and Bradley Patay, MD
    • Hakon Hakonarson, MD, PhD
    • Isaac Kohane , MD, PhD
    • John A. Todd, FRS, PhD
  • Moderators Eric J. Topol, MD and Nicholas Schork, PhD
    • Howard J. Jacob, PhD
    • Joseph G. Gleeson, MD
    • Stanley F. Nelson, MD
    • Lynn Jorde, PhD (note - originalled labelled as female - corrected thanks to comment from Bruce Rannala)
  • Eric J. Topol, MD
  • Moderators: Aravinda Chakravarti, PhD and Richard Klausner, 
    • Aravinda Chakravarti, PhD
    • Joseph Nadeau, PhD
    • Nicholas Schork, PhD
    • Hakon Hakonarson MD, PhD
  • Moderator Eric Topol
    • Matthew Herper
    • Daniel B. Vorhaus, JD, MA
    • Issam Zineh, PharmD, MPH
  • Moderators: Elaine Mardis, PhD and Jeffrey Trent, PhD
    • Richard D. Klausner, MD
    • Thomas J. Hudson, MD
    • Jeffrey M. Trent, PhD
    • Daniel D. Von Hoff, MD
    • Elaine R. Mardis, PhD
  • Moderators: Samuel Levy, PhD and Fred Gage, PhD
    • Fred H. Gage, PhD
    • Bruce D. Gelb, MD
    • Joseph C. Wu, MD, PhD
All speaker and session chair slots
  • Male: 44 (88%)  45 (90 %)
  • Female: 6 (12%) 5 (10 %)
Just speakers
  • Male: 31 32 (91.4%)
  • Female: 4  3 (8.6%)
2011 Future of Genomic Medicine IV - schedule from here
  • Session 1: Moderators: Sarah S. Murray, PhD and Eric J. Topol, MD
    • Hannah A. Valantine, MD
    • Geoff Ginsburg, MD, PhD
    • Steve Shak, MD
    • Cinnamon S. Bloss, PhD
    • Matthew J. Price, MD
  • Session 2: Moderators: Bradley Patay, MD and Nicholas J. Schork, PhD
    • Kevin Davies, PhD
    • Thomas Goetz, MPh
    • Melanie Swan, MBA
  • Session 3: Moderators: Samuel Levy, PhD and Nicholas J. Schork, PhD
    • Kári Stefánsson, MD
    • Aravinda Chakravarti, PhD
    • Howard J. Jacob, PhD
    • Sarah S. Murray, PhD
    • James R. Lupski, MD, PhD
    • Nicholas J. Schork, PhD
    • Stephen L. Hauser, MD
    • David R. Bentley, D.Phil, F.Med.Sci.
  • Keynote: Juan Enriquez, BA, MBA
  • Session 4: Moderators: Robert L. Strausberg, PhD and Samuel Levy, PhD
    • Robert L. Strausberg, PhD
    • Elaine R. Mardis, PhD
    • Thomas J. Kipps, MD, PhD
    • Samuel Levy, PhD
    • Daniel D. Von Hoff, MD
    • Dennis A. Carson, MD
  • Session 5: Moderators: Eric J. Topol, MD and Bradley Patay, MD
    • Eric J. Topol, MD
    • Amy Harmon
    • Misha Angrist, PhD
  • Session 6: Moderators: Sarah S. Murray, PhD and Samuel Levy, PhD
    • Hakon Hakonarson, MD, PhD
    • Mark McCarthy, MD, F.Med.Sci.
    • Karen Mohlke, PhD
    • Stephen S. Rich, PhD
    • Philippe Froguel, MD, PhD
    • Muredach P. Reilly, MB, MS
All speaker and session chair slots
  • Male: 35 (80%)
  • Female: 9 (20%)

How to keep up with microbial ecology and the built environment: microBEnet is your place

Tags
Just posting a wrap up of posts on microBEnet (where I blog frequently as do many other folks that work on something related to microbial ecology, the built environment, or the intersection of the two).  microBEnet is really becoming a central place to find out what is going on in the world of microbial ecology and the built environment.  And I love that we are getting more and more posts from outsiders about their work, their meetings, their ideas and more.  Anyway - here is a wrap up of the posts for the last month.  If you are interesting in joining microBEnet and writing posts about relevant topics, let me know.

Jenna Lang (staff scientist in my lab) -- meeting reports from a Planetary Protection meeting
My posts:
Alexander Sczyrba on the Critical Assessment of Metagenome Interpretation (CAMI)

Elisabeth Bik from Stanford roundups from Microbiome Digest
David Coil (a staff scientist at UC Davis in my lab)
Linsey Marr of Virginia Tech
Rachel Adams - post doc at UC Berkeley
Ben Kirkup of the  Naval Research Laboratory
Embryete Hyde from UCSD
Brent Stephens of the Illinois Institute of Technology

Calling attention to poor speaker gender ratio - even when it hurts

Tags
So I saw this Tweet earlier today


And that sounded very interesting. So I clicked on the link to check out the Plant Breeding for Food Security: The Global Impact of Plant Genetics in Rice Production A symposium honoring Dr. Gurdev Khush symposium.  And, then I went to the program.  And sadly I saw something there that was not to my liking.  The speakers were almost all male (men labelled in yellow, women in green)
  • Welcome to the Khush Symposium (Alan Bennett)
  • The Plant Breeding Center (Charles Brummer)
  • The Confucius Institute (Glenn Young)
  • Global food production – challenges and opportunities (Ken Cassman) Food production, technology and climate (David Lobell)
  • Panel – Impact of Gurdev Khush on plant genetics and food security Tomato genetics
    • (Dani Zamir)
    • (Pam Ronald)
    •  (Gary Toenniessen)
    •  (Gurdev Khush)
  • Lunch; The California Rice Industry (Kent McKenzie)
  • The rice theory of culture (Thomas Talhelm)
  • Recent advances in rice productivity and the future (David MacKill)
  • Hybrid rice technology contributions to global food security (Sant Virmani)
  • Super green rice (Qifa Zhang)
  • Tackling the wheat yield barrier (Matthew Reynolds)
  • African Orphan Crops – inspiration and execution (Howard Shapiro/Allen Van Deynze)
If this was a symposium outside UC Davis the first thing I would do would be to post about it.  To Twitter or my blog or both.  And to critique them.  Why?  Because there is a bad history in STEM fields of having meetings and conferences have under-representation of women as speakers.  And this has become a passion of mine and I write about it a lot.  But I hesitated.  Why?  Because this was from UC Davis and many of the people involved are friends / colleagues.  I did not want to anger them, or embarrass them.  And I don't think there is any intentional bias here by any means.  But, if I am going to critique people outside UC Davis, it seems like I should also apply the same standards to people inside UC Davis and to colleagues and friends.

So I posted to Twitter a response:

But that did not seem sufficient.  So I wrote up this post.  Underrepresentation of women as speakers is a serious issue in STEM fields.  And it is solvable (e.g., see Some suggestions for having diverse speakers at meetings by myself and the wonderful Ten Simple Rules to Achieve Conference Speaker Gender Balance by Jennifer Martin).

Now - do I know who the possible speakers were for this symposium?  No - I don't really know the field.  Is it possible that there just are no women in the field?  Sure.  But I would bet anything that is not the case here.  Having a meeting where the ratio of speakers is 16:1 male: female sets a bad example.  UC Davis and the organizers of this meeting can do better.  And though this will possibly hurt me in various ways (I already got grief from one person who I will not name for the Tweet), I think it is critical that we call out examples such as this.

And finally I note - I have taken on the issue of women at STEM conferences and meetings because, well, it is easy to identify cases where the numbers are anomalous and it is relatively easy to solve.  But it is also important that we consider other aspects of diversity of speakers (age, ethnicity, career stage, etc).  It is important to have diversity of speakers at meetings for many many reasons.  Speaking is a career building opportunity.  Speakers serve as role models for others.  Diverse points of view are important to have represented.  Bias - whether simplicity or explicit damages the whole practice of science.  And more.  Yes, we need to work on many aspects of diversity in STEM fields.  Improving the diversity of speakers at meetings is but one part of this.  But it is an important part and it is relatively easy to do.  So just do it.  And call attention to it.  Even if it hurts.



UPDATE 3/25 11:29 AM

The meeting organizers have responded on Twitter

Storify of some responses here


Treponema are not "ancient" but absence from some human's guts is very interesting

Tags
So I saw some Tweets today that caught my attention, discussion news stories about "ancient" bacteria being missing from some human's gut microbiomes:





These refer to a sadly inappropriate headline in Science



What is wrong with this?  Well, there are no "ancient" bacteria around today.  They are all modern.  I am not even sure what they were trying to say.  Just a really bad evolution argument I guess.  I pondered giving Science a Twisted Tree of Life Award which I give out for exactly this kind of thing -  but decided first to dig into the science here and gloss over the bad evolution headline.

And it turns out - what the news story is about is in fact interesting - a new paper out in Nature Communications:  Subsistence strategies in traditional societies distinguish gut microbiomes.

The paper is freely available and has some really interesting material in it.  They key to me - at least related to this "ancient" bacteria claim is the following part of their abstract:
As observed in previous studies, we find that Treponema are characteristic of traditional gut microbiomes. Moreover, through genome reconstruction (2.2–2.5 MB, coverage depth × 26–513) and functional potential characterization, we discover these Treponema are diverse, fall outside of pathogenic clades and are similar to Treponema succinifaciens, a known carbohydrate metabolizer in swine. Gut Treponema are found in non-human primates and all traditional peoples studied to date, suggesting they are symbionts lost in urban-industrialized societies.
And then some further detail in the paper:
Although Spirochaetes have been previously reported from the gut microbiome of non-human primates and ancient human populations, they have only been observed in high abundance among extant human populations with non-Western lifestyles, such as a traditional community in Burkina Faso and a hunter-gatherer community in Tanzania. As such, they may represent a part of the human ancestral gut microbiome that has been lost through the adoption of industrial agriculture and/or other lifestyle changes. 
So they don't go into the full detail here but what I think they are saying is that they infer that human ancestors had Spirochaetes (based on the finding of it in non human primates and some human populations).  And thus they further infer that human populations (e.g., the people they studied in Oklahoma) that do not have these Spirochaetes have "lost" them.

I note - I think this terminology of "loss" they are using is not quite right here in a way.  Saying that these Spirochaetes have been lost implies to me that they are heritable.  But they do not in fact show that.  It could be that these are related to diet or environment in some way - something shared by some human populations and non human primates, for example.  And thus the absence from some "Westernized" populations could be more of an environmental thing than a "loss" in the past.


In a similar way, we could say that Westernized humans have "lost" the ability to be skinny (since obesity is high in many such populations).  Non human primates have such abilities and so do some non Westernized populations.  But "losing skinnyness" does not seem quite right since we do not know exactly why obesity is higher in Westernized populations.  I think it would be better in such cases to say something like "do not show an ancestral trait" (the ancestral trait here being skinnyness) and to not use "lost" until we know more about what is going on.  Similarly, I think saying some human populations have "lost" these Spirochaetes is not quite right.

Nevertheless, the absence (or at least, low levels) of these Spirochaetes from some human populations is certainly interesting.  And given that the presence of such Spirochaetes does appear to be an ancestral trait, the absence is even more interesting.  And thus this paper here, which details some of the genomic features of these "missing" Spirochaetes is definitely worth paying attention to.

In addition, I note - the findings in this paper serve as an additional justification for projects to generate genomic data from across the phylogenetic diversity of microbes.  Consider for example their Figure 6 and 7 which show that the most closely related Treponema species and the ones with the most similar genomes to these human Spirochaetes are those from Treponema succinifaciens and Treponema brennabornese.



Both of those genomes were generated by the Genomic Encyclopedia of Bacteria and Archaea project which I coordinated with the DOE-JGI and DSMZ.  See the paper on one of them: Complete genome sequence of Treponema succinifaciens type strain (6091T) and the posted data on the other.

We argued that we needed to sequence reference genomes from across the tree of life because this would help inform studies of uncultured microbes from diverse ecosystems.  Little did I know that one of the key ecosystems we would help inform would be the human gut.

Certainly more needs to be done in regard to these Spirochaetes.  Why are they at low levels or missing from some Westernized populations?  What do they do in other populations?  Would they be helpful if they were reintroduced to populations that do not have them?  So many questions actually.  But despite the misleading news article headline, this paper seems to me on first glace at least to in fact be quite interesting.

I made a Sorify of some comments

The ChuckNorrisMicrobiome will get you, and you, and you ...

Tags

Overselling the microbiome award: Dr. Raphael Kellman at MindBodyGreen

Tags

Well this article by Dr. Raphael Kellman has just lots of overstatements about the microbiome: Why The Microbiome Is Your Key To Glowing Skin & Healthy Weight

For example, he writes:
Have you and your boyfriend or girlfriend ever gone out for a feast of delightfully unhealthy proportions only to then find yourselves picking fights with one another once you're back home and digesting?  Fueling your body with unhealthy bacteria, and then feeding it with more unhealthy bacteria, is a sure-fire way to destabilize your mind-body connection. Instead, focus on supporting the positive bacteria in your belly with fermented foods like yogurt, sauerkraut, and kefir and watch your spirits soar.
This implies that somehow the microbome has some role in such situations and in mediating the relationships between two people.  And it implies that that can be fixed with fermneted foods.  And this is without any shred of evidence ...

Then there is a discussion that makes the microbome sound like the master controller of all that is human:
Our bodies are cohesive entities, yes, but within each there are several languages spoken. 
The microbiome works like a translator for all of these systems, deciphering and decoding so that one process can communicate with the other for more efficiency and effectiveness (helping our systems to work as a team instead of independently alongside one another).
And then there is evidence free claims about fatigue and the microbiome
I've found that this kind of unexplained fatigue is often linked to a lack of diversity in the microbiome and can be remedied, despite what conventional medicine says
Whenever someone critiques "conventional" medicine and then presents no evidence for their claims, one should be wary, very wary.

And it ends with

Your inner ecology, your microbiome, is influential on your physical health, and that shows through glowing skin, a balanced weight and a youthful essence.  
So - if you want to be youthful and glowing and have good sex and relationships and get rid of your fatigue and fix your automimmune disorders and obesity and connect all of your systems together, all you have to do is fix your microbiome.  Simple.  Oh and how do you do that?  Why funny you asked, because I am selling this new book on the Microbiome Diet to solve all your problems.  Ridiculous.  And dangerous.

And thus I am giving out an Overselling the Microbome award to Dr. Kellman.

Some silly microbome ideas from @DeepakChopra and @rudytanzi

Tags
Well, just got to reading this: Big Idea 2015: Medicine, Wellbeing, and the Microbiome | Deepak Chopra MD. Yes, it was from December 2014 but I could not get up to reading it then because I saw some of the comments online about it and it seemed off.  But anyway I caught up to it today.  It has many inaccurate and misleading statements about microbes and microbiomes I just felt like I had to post something.  Some of the problemmatic parts are below with comments.

Let's start gently.  As with many other stories on the microbiome, this article quotes the oft cited "fact" of a 10:1 ratio of microbial cells to human cells.
By some estimates the body has between 35 and 100 trillion cells with only 1 in 10 belonging to tissues and organs and the rest belonging to the microbiome.
This has been refusted by a great article in the Boston Globe by Peter Andrey Smith in September 2014 (long before this was published): Is your body mostly microbes? Actually, we have no idea.  Yes, I and many others cited this 10:1 ratio before the Globe.  But seeing it cited in this from December 2014 suggests Chopra and Tanzi aren't really paying attention to microbiome science.

The next comment I find a bit off is the follwing:
Our personal human genome also determines the composition of our microbiome, which in turn can influence metabolism and propensity for weight gain.
Sure.  Our genes influence out microbiome.  But "determines the composition" is way to strong a statement.

But the things that got to me most were many of the comments supposedly about evolution.  I list some of them below:
  • This varying ecosystem isn't populated by foreign invaders and pathogens but by colonies closely connected to human evolution.
    • I don't even know what this is supposed to mean.  These are not "colonies" first of all.  And second, what does "connected to human evolution" even mean?  And wouldn't pathogens be connected to human evolution?
  • The microbiome interfaces between the human body and the outside world in complex ways, but the gist is that human DNA has evolved in cooperation with microbial DNA. This fact is more important than the interactions that cause diseases created by invading bacteria and viruses.
    • Re "human DNA has evolved in cooperation with microbial DNA".  Well, sure.  Some of the microbes we live with are mutualists. But most likely only a limited number of mutualistic interactions are going on.  This sounds like a Gaia type of model, with no evidence.  
    • And then "This fact is more important than the interactions that cause diseases created by invading bacteria and viruses."  Really?  More important than the plague?  Than malaria? Aids?  Cholera.  TB? Worms? And more.  This sounds really silly.
  • Mitochondria actually have their own genomes inherited from the mother without change.
    • Umm - no mitochondria mutate and change, well, all the time.
  • Some of the most archaic microorganisms on Earth survive today in our microbiome.
    • This is without any justification.  First of all - what does "most archaic" mean?  And second, if it means what I think it means (organisms that have features like those from billions of years ago) - well - no - the human microbiome does not have a lot of such organisms.  This is just complete hooey.  
  • It would appear that the genome and the microbiome cross-talk, a conversation that has been continuing for billions of years with no signs of stopping.
    • What does this even mean?  In what way has the human microbiome been interacting with the human genome for billions of years.  In what way have human ancestors been interacting with microbiomes for billions of years?

Yes, the microbiome is important.  But this "essay" is filled with nebulous pseudoscientific comments about the microbiome all, apparently, to sell an upcoming book and related activities

"In an upcoming book we are co-authoring, Super Genes, we will present the latest findings as well as a lifestyle program devoted to what we call Self-Directed Biological Transformation"

Right now, I don't think Chopra and Tanzi show any evidence they really understand the microbiome .. doesn't bode well for their book and lifestyle program.

Horizontal gene transfer into humans? I am not convinced. Full text of my comments to reporters here

Tags
Some news stories about a new paper claiming evidence for horizontal gene transfer into humans and other chordates. I got asked by many reporters about it and some used some of my email comments in their articles.

See for example

 Here is the full text of my responses:

"got asked by another reporter to comment on this

so - have seen the paper 
it is interesting .. but I am not overwhelmed by what they present in the paper itself. For example, the HAS story seems really incomplete as presented (e.g., the Figure showing the tree does not have all the HAS1, HAS2, HAS3 genes even though they imply they studied that). "
I have been looking through the supplemental information. I find it impossible to judge the quality of this paper without being able to see the alignments they used for each phylogenetic tree. I cannot find alignments for the trees even after going to their Figshare site with the trees. I therefore think there is not much to say about the paper until being able to see those. 
Without seeing the alignments I offer multiple alternative hypothesis for their findings
  1. They have identified genes for which they are unable to produce reasonable alingnments. Alignments are central to phylogenetic analysis and if their alignments are poor quality then the trees will show all sorts of anomalies that have nothing to do with phylogenetic history. By scanning through 1000s of genes and flagging those with unusual patterns they may be selectively identifying genes for which producing good alignments between species is tough. I note - clustalw is a bit notorious for not producing idea alignments in some cases.
  2. I do not buy their arguments for why gene loss is not a possible explanation. They need to present more detail on how many gene losses would be required for each gene family under consideration and then present some evidence for why that # of gene losses is less likely than HGT.
  3. They have not even considered as far as I can tell, the possibility of divergent evolution (as opposed to gene loss) in many taxa which could lead to them being unable to identify homologs in some species
  4. I am not convinced by the arguments against long branch attraction as an explanation for some of the tree patterns.
  5. Related to alignments they need to show which regions of alignments they excluded from phylo
  6. Convergent evolution could also explain some of the patterns they observe.
  7. I could go on. I am NOT saying that HGT into chordates is impossible. It seems plausible. But it is up to them to exclude other MORE plausible alternatives and I just do not think they have done that.
Reporter: asking if it was OK to quote me

Yes it is OK to quote from me. I would like to reiterate - I am not saying they are wrong. Just that I would like to see (1) all the data (e.g., alignments) that unreels their conclusions and (2) them do more to exclude other possibilities.
Reporter asking what other analyses could they do
So - I don't want to be difficult, but it is their job to figure out how to do such tests before claiming they have strong evidence for HGT. 
In general, this is pretty typical of claims of HGT. Many researchers show evidence that is consistent with the occurence of HGT (which they did here) but few actually explicitly test alternative hypotheses such as gene loss, bad alignments, convergence, divergence, contamination, random noise, and more. I think their work is certainly interesting, but they just have not tested all of these alternatives. And I personally have grown a bit tired of pointing out how people can do better controls for their papers.
Reporter asking about initial impressions:
I see little here that is particularly convincing evidence for HGT ...
My follow up email
Note - I am not saying that this is a bad paper -- just that I am not overwhelmed by their evidence and especially by what they put in the paper. 
For example, the HAS1 gene story seems incomplete.  Figure 3 seems to show just HAS1 but in the text the say they show the same thing for all HAS genes.  And the tree they show shows a tiny subset of all the available sequences (e.g., HAS1 HAS2 HAS3 and fungal and bacterial homologs).  They claim that they now have proof that HAS1 was transferred near the base of chordates but I just don't see how they tested alternative hypotheses ...

Some related links:
Also here are some presentations from many years ago with some discussion of HGT




Probiotics for athletes? Possible someday, but right now - I (and others) don't think so

Tags
Nice article in Outside Magazine by David Despain: Should You Be Taking Probiotics? | Performance Plate | OutsideOnline.com.  The article has comments from me, Peter Turnbaugh and Ellen Silbergeld.  The article discusses some of the overhyped claims about probiotics and athletic performance and even mentions my Overselling the Microbiome award.  I like in particular the following paragraph:

The biggest issue scientists currently have with probiotics, however, doesn’t have to do with athletes. Instead, it has to do with the initial hypothesis that we need them in the first place, says Ellen Silbergeld, a professor of Johns Hopkins Bloomberg School of Public Health. Because there’s still no real understanding of what makes “healthy” or “poor” microbiomes, there’s no real understanding of how or if we should cultivate them.

Today's gender biased meeting-GlycoCom2015-sponsored by @generalelectric @ualberta #YAMMM

Tags

Got pointed to this via a Tweet:
The Tweet pointed to this meeting: Home - Glycomics Official Website of GlycoCom Conference 2015 in Banff, Alberta, Canada.  Lame.  14:1 ratio of men: women speakers.  Just completewly lame.

Confirmed Speakers

  • Richard Cummings, Emory University School of Medicine
  • Paul DeAngelis, University of Oklahoma and Caisson Biotech LLC
  • Donald Jarvis, University of Wyoming and GlycoBac LLC
  • Nicole Koropatkin, University of Michigan Medical School
  • Mario Feldman, Washington University, St. Louis and VaxAlta Inc.
  • Gordon Lauc, University of Zagreb
  • Todd Lowary, Alberta Glycomics Centre and University of Alberta
  • John Magnani, GlycoMimetics Inc.
  • Glenn Prestwich, University of Utah and GlycoMira Therapeutics Inc.
  • Peter Seeberger, Max Plank Institute
  • Tadashi Suzuki, RIKEN Global Research Cluster
  • Ajit Varki, University of California, San Diego
  • David Vocadlo, Simon Fraser University and Alectos Therapeutics Inc.
  • Michael Wacker, GlycoVaxyn AG
  • Robert Woods, Complex Carbohydrate Research Center & Glycosensors & Diagnostics, LLC
The University of Alberta and GE and the other sponsors should be embarassed by this.  

My microbiome talk at #FOGM15 - the perils (and fun I guess) of redoing one's talk at the last minute

Tags
Just got back from the Future of Genomic Medicine 2015 meeting where I gave a talk about microbiomes.  My original plan was to talk about the need for evolutionary and ecological approaches to microbiome studies but I changed my mind a few days before the meeting and decided to switch to talking more about citizen microbiology.  I did this because the meeting has a lot of people who think about digital and wearable technology and public engagement in the audience and it just seemed like a good chance to introduce them to the growing personal/citizen microbiology movement.

To help prep for my talk I emailed some colleagues who work on Citizen Microbiology (including a few in my lab like Jenna Lang and David Coil) and asked them if they had any slides I could pilfer.  And then I started drafting an outline of my talk (I draft all my talks by hand with pen and paper). Here are my handwritten notes










 I realized I would not likely be able to focus enough at home to work on the talk so I kind of waited until heading down to San Diego on Wednesday (talk was on Friday).

I got in pretty late and worked a little on my talk before going to bed.  I also emailed the organizers of the meeting to say I was changing the topic of my talk a bit and asked if they could change the online program which they did.  Eric Topol in response to my saying I wanted to talk about citizen microbiology and personal microbiomes very wisely suggested that I talk about my vision for the future of microbiome research.  I (lamely) had been so focused on Citizen Microbiology that I had not been thinking much about the bigger picture.  But once he suggested this notion my talk really congealed (in my head and on paper at least).  It is interesting to me how one simple suggestion from someone with vision and perspective can transform one's thought process so much ...

Anyway, the next day I headed over to the meeting venue (by the beach - life is rough in San Diego).  I got there in time to hear Francis Collins' talk.  I spent the day sitting outside in the outdoor tent viewing area, pondering my talk and listening to the talks of others. Lots and lots of interesting things presented there.  More about this later I hope.  Anyway - that evening I worked on my talk some more, headed down to the hotel bar for a bit and then worked on my talk some more.  And eventually went to sleep.  Friday I spent much of the AM working on my talk in the outdoor tent (while listening to the talks though this time not watching them on the screen since I was a bit too far away from it).  And voila - only 30 minutes before the PM session was to begin I finished the prep.  I do not like to do this normally but I just felt like my talk would be much better if I re-conceived it and I had to make all new slides pretty much for the whole talk (other than the few I pilfered from colleagues).

I note - I was talking after Marty Blaser and figured I would not have to introduce the human microbiome at all and also that he would give an overview of the risks that come from disturbing the microbiome.  Anyway, I gave my talk, and recorded the slideshow with Camtasia.  Below are my slides, the video slideshow, and a Storify of the Tweets others posted during my talk.
As is frequently the case, afterwards I felt I was too rushed and that it was not the best talk I have ever given. But that being said, I like the general outline and some of the concepts and figured I should share, warts and all. My biggest regret after talks which I have rushed a bit in preparing is that I usually do not do a great job in mentioning who did all the work I refer to. I try to put people's pictures and names on all slides and references but I don't always get this done in time and I worry I screwed this up for a few topics here. Oh well, life goes on ...

Here is a slideshow with Audio (which I recorded via Camtasia)



Here is the Slideshare posting of my slides



Today's YAMMM - The British Society for Plant Pathology

Tags
Well, this is not the most egregious example of a mostly male meeting but it still has some issues: The BSPP - The British Society for Plant Pathology 2015 meeting.  Nine speakers.  Seven male.  And this in a field with plenty of excellent female researchers.

Cassava brown streak disease
(1) James Legg - IITA Tanzania
(2) Stephan Winter - Leibniz Institute DSMZ Germany
(3) Maruthi Gowda - Natural Resources Institute, University of Greenwich

Late blight
(1) Bill Fry - Cornell University
(2) Sophien Kamoun - Sainsbury Lab, Norwich
(3) Jonathan Jones - Sainsbury Lab, Norwich

Rice blast
(1) Sarah Gurr - University of Exeter
(2) Lauren Ryder - University of Exeter
(3) Thomas Kroj - INRA, Montpellier, France

But the weirdest part --  it says
"This year, the BSPP President, Prof. Gary Foster, has only chosen a few invited speakers on specific diseases, and wishes the remainder of the talks to be selected from offered papers."

So does this mean Prof. Gary Foster just picked all speakers?  If so, perhaps Prof. Gary Foster needs to do a little thinking about his possible biases ...




Another day, another microbiome journal ... alas not as "open access" as claimed

Tags
Just got this email
Dear Doctor Jonathan Eisen,

I would like to invite you to consider submitting a paper to our recently launched Open Access journal Microbiome Science and Medicine (http://www.degruyter.com/view/j/micsm).
As can be seen from the titles of articles published in our first volume, MICSM reflects the full breadth of research in the diverse areas of microbiome-related science, from molecules to ecosystems:
Newton ILG, Sheehan KB, Lee FJ, Horton MA, Hicks RD "Invertebrate systems for hypothesis-driven microbiome research"
Amato KR "Co-evolution in context: The importance of studying gut microbiomes in wild animals"
Nelson DR, Tu ZJ, Lefebvre PA "Heterococcus sp. DN1 draft genome: focus on cold tolerance and lipid production"
Rudlaff RM, Waters CM "What is the role of cyclic di-GMP signaling within the human gut microbiome?"
Fang Y, Chia N, Mazur M, Pettigrew J, Schook LB, White BA "Genetically identical co-housed pigs as models for dietary studies of gut microbiomes"
MICSM is a broad-spectrum platform for the rapid publication of works of broad significance, originality and relevance in all areas related to the study of microbiomes, their components, and their roles in health and disease. We solicit research and review articles, as well as communications and vision papers. The manuscripts submitted in response to this invitation will be processed with the highest priority and all accepted papers will be immediately available on-line.

Authors are offered a variety of benefits:
– transparent, comprehensive and fast peer review;
– language assistance for authors from non-English speaking regions;
– convenient, web-based manuscript submission and tracking system;
– efficient route to fast-track publication and full advantage of De Gruyter Open's e-technology;
– no publication charge in the first two annual volumes.

I look forward to your manuscript!
Please forward this invitation to any interested colleagues and associates.
Seemed right up my alley - an open access microbiome journal.  Alas, when I clicked on the journal link and then browsed around I found out that articles will be published using some pretty restrictive conditions. Some key parts of the text from this page is below:

1. License
The non-commercial use of the article will be governed by the Creative Commons Attribution-NonCommercial-NoDerivs license as currently displayed on http://creativecommons.org/licenses/by-nc-nd/3.0/., except that sections 2 through 8 below will apply in this respect and prevail over all conflicting provisions of such license model. Without prejudice to the foregoing, the author hereby grants the Journal Owner the exclusive license for commercial use of the article (for U.S. government employees: to the extent transferable) according to section 2 below, and sections 4 through 9 below, throughout the world, in any form, in any language, for the full term of copyright, effective upon acceptance for publication.
Other than being, well, painfully legalesy, this is just too restrictive for me and does not really seem like "open access".  The no derivatives part drives me batty.  Also they write:

9. Scope of the Commercial License
The exclusive right and license granted under this agreement to the Journal Owner for commercial use is as follows:
 to prepare, reproduce, manufacture, publish, distribute, exhibit, advertise, promote, license and sub-license printed and electronic copies of the article, through the Internet and other means of data transmission now known or later to be developed; the foregoing will include abstracts, bibliographic information, illustrations, pictures, indexes and subject headings and other proprietary materials contained in the article,
 to exercise, license, and sub-license others to exercise subsidiary and other rights in the article, including the right to photocopy, scan or reproduce copies thereof, to reproduce excerpts from the article in other works, and to reproduce copies of the article as part of compilations with other works, including collections of materials made for use in classes for instructional purposes, customized works, electronic databases, document delivery, and other information services, and publish, distribute, exhibit and license the same.
Where this agreement refers to a license granted to Journal Owner in this agreement as exclusive, the author commits not only to refrain from granting such license to a third party but also to refrain from exercising the right that is the subject of such license otherwise than by performing this agreement.
Well, no thanks.  Too many restrictions and not open access in my view.  If I had to choose a "microbiome" journal to publish in, I would choose "Microbiome" an actually open access journal, where papers have the following info on them:
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
Go Microbiome ...

الاشتراك في: الرسائل (Atom)

Total Pageviews

Popular Posts

الاثنين، 30 مارس 2015

Painful, kind of hilarious, typesetting error in a #PLOSOne paper from my lab - should I try to get it fixed?

Saw this tweet:

So I went and found the paper.

Wu D, Jospin G, Eisen JA (2013) Systematic Identification of Gene Families for Use as “Markers” for Phylogenetic and Phylogeny-Driven Ecological Studies of Bacteria and Archaea and Their Major Subgroups. PLoS ONE 8(10): e77033. doi:10.1371/journal.pone.0077033

And discovered what he was pointing to

Then I looked at the Pubmed Central version of the paper and it was the same.  So I wnet and found the arXiv version of the paper and it looked correct.



So apparently, PLOS One somehow replaced "nonmember" with



Brutal.  And even worse, this may have been there all along and I missed it.  So I responded:

And then Michael Hall pointed out another mistake.



Aaargh.  And funny too.  So now the question I guess is - should I fix it? And if so, how do I do that?

مرسلة بواسطة في ليست هناك تعليقات:
التسميات: ,

الأحد، 29 مارس 2015

Calling attention to meetings with skewed speaker gender ratios, even when it hurts, part 2


A few weeks ago I gave a talk at the Future of Genomic Medicine 2015 (aka #FOGM15) meeting.  The talk seemed to go over well.  I talked right after Martin Blaser in a session on "The Microbiome".  I posted my slides and then a video of my talk as well as notes from the meeting: see My microbiome talk at #FOGM15 - the perils (and fun I guess) of redoing one's talk at the last minute.  And I met some really interesting people at the meeting and enjoyed most of the talks I went to.

But alas, one thing stuck in my head from this meeting.  One single Tweet from someone out there threw me for a loop:

And this let to a bit of soul searching on my part.  Some of the conversations on Twitter are captured in this Storify:


Which I guess culminated in a post to the organizers of the meeting


Then, when I left the meeting I went to say goodbye to the organizers.  And, well, one of them did not take too kindly to the critique of the meeting, saying that they were doing a better job than other healthcare meetings.  I disagreed and said I thought they could do much better, but I had no numbers to cite at the time and the conversation ended there.

So on the way to the airport I started digging around for some numbers and I found some great resources - especially this from Rock Health.

And for the last few weeks I have continued to fester wondering - well - should I post more about this?  Should I dig into the gender ratio of the FOGM meetings in more detail?  Well, why do it?  Because I think it is important to know how meetings perform in terms of diversity.  Why not do it?  Well, I like Eric Topol and the other organizers.  And the meeting has many strong points.  But, as I wrote a few days ago - sometimes one needs to call attention to meeting gender ratio issues, even when it hurts.  

So then I decided to dig a little deeper and look at past versions of the "Future of Genomic Medicine".  And, well, when I did this, things just do not look so good (detailed analysis is at the end of the post). (Note - for the numbers i counted all presenting slots - session chairs, keynotes, welcomes, etc.  The numbers are not much different if one counts just "talks").



If one compares these meetings to the ones catalogued by Rock Health, the FOGM meetings are at the low end.  Not the worst certainly.  But definitely not something to be proud of.  And certainly something that could be improved upon enormously.  So I repeat the Tweet I posted during the meeting, and I stand by it, even if it means I am unlikely to be invited back and even if it means pissing off some big shots in the world of genomics ...


If you are running a meeting, please consider the ways in which bias may creep into the speaker and session chair slots.  If speakers come from invitations, perhaps the invitation list is biased.  Perhaps certain types of people are more likely to say no to invitations.  Perhaps the timing of the meeting (e.g., on weekend) may lead certain types of people to not be able to participate.  Perhaps the meeting does not provide enough travel funds or child care or the right kind of schedule.  There are so many things that can lead to bias - from explicit bias against certain groups to very subtle implicit biases.  Consider inviting people from diverse career stages, which can open up speaking slots to more women and underrepresented minorities.  Consider providing child care.  Consider asking people why they say no to invitations to try and understand what is going on if many people say no.  Consider asking for help in finding speakers covering the diversity in the field.

If you do all these things, and the meeting still does not have diverse speakers, well, try some other things.  Keep trying to figure it out.  There are resources out there that can help.  Read things like Some suggestions for having diverse speakers at meetings (by me) and Ten Simple Rules to Achieve Conference Speaker Gender Balance (by Jenny Martin) and Increasing Diversity at Your Conference by Ashe Dryden (which is just completely awesome) and How To Create A More Diverse Tech Conference ... and Would I attend my own conference? - O'Reilly Radar by Sarah Milstein.

Why is this important?  Well, speaking at a meeting is important for people's careers.  It helps in merit and promotion and tenure cases.  It helps get their work recognized and known.  Speaking at a meeting is also good practice for speaking at other meetings.  Having diverse speakers also is important in terms of providing role models to attendees.  And having diverse speakers helps a meeting not just be about the same old, white, men talking about their ideas.  Or, in other words, it makes a meeting more, well, diverse.  And almost certainly more interesting.  And so on.  Diversity of speakers at meetings is important for 100s of reasons.  And don't just focus on one aspect of diversity.  I post a lot about women speakers because, well, it is easy to make a reasonable guess as to whether a person is male or female.  But there are MANY other aspects of diversity to consider (see Increasing Diversity at Your Conference by Ashe Dryden (which I referenced above and which really is awesome).

Anyway - if you are organizing a meeting, make sure to think about these issues.  And do something about them.  And if you are invited to a meeting, look at the speaker list (if it is available) and consider saying no to speaking if the meeting has diversity issues (see a post of mine about doing this here: Turning down an endowed lectureship because their gender ratio is too skewed towards males #WomenInSTEM).

And if you are considering attending a meeting, consider diversity of speakers when deciding whether or not to attend.  Meetings with high diversity of speakers should be supported.  Meetings with poor diversity relative to possible candidate speakers (e.g., who is in the field) should be avoided, shunned, and called out.  We need to force change upon some fields and the only way will be to call out the bad apples.  Mind you, it is not possible to know WHY a meeting has a skew in terms of diversity of speakers.  Thus one additional thing to consider is whether something is a consistent pattern.  For example see my post about meetings from the National Academy of Sciences Sackler Colloquia - Apparently, the National Academy of Sciences thinks only one sex is qualified to talk about alternatives to sex #YAMMM. Sadly it seems to me that the FOGM meetings have a consistent pattern of poor representation of women among the presenters.  Unless the organizers commit to changing this, I think people should not attend this meeting in the future.


Detailed analyses of these meetings are below.

People I have identified as males are labelled in yellow.  People I have identified as females are in green.  I realize that this is an imperfect thing to do.  I may make mistakes in my inferences.  And dividing people into two categories is not representative of the true diversity in the human population.  But I still think this is a useful, informative thing to try to do.

2015 FOGM (schedule is from the one sent around to participants on 3/4/15)
  • Welcome
    • Eric Topol
    • Pateint #1 - Eunice Lee and Nilesh Dharajiya
    • Francis Collins
  • Session 1
    • Moderator Ali Torkamani
    • Diana Bianchi
    • Evan Muse
    • Stephen Quake
    • David Hoon
  • Session 2
    • Moderator Ali Torkamani
    • Mark McCarthy
    • Christopher Austin
    • George Yancopoulos
  • Session 3
    • Moderators Nathan Wineinger and Andrew Su
    • Atul Butte
    • Eric Schadt
    • Andrew Su
    • Joe Pickrell
  • Welcome Day 2
    • Patient #2
    • Eric Topol
  • Session 4: 
    • Moderator Ali Torkamani
    • Cristian Tomasetti
    • Nazneen Rahman
    • Roni Ziegler
  • Session 5
    • Moderators Kristin Baldwin and Fyodor Urnov
    • J. Keith Joung
    • Fyodor Urnov
    • TBD
    • Kristin Baldwin
  • Session 5
    • Moderator Kristian Andersen
    • Martin Blaser
    • Jonathan Eisen
    • Stephen Steinhubl
  • Session 6
    • Moderator David Goldstein  (he did not show up)
    • Elizabeth Worthey
    • Ali Torkamani
    • Seth Mnookin
    • Virginia Hughes
All speaker and session chair slots
  • Male: 30 (81%)
  • Female: 7 (19%)
Just speakers
  • Male: 23
  • Female: 6
2014 - Future of Genomic Medicine VII -  schedule from here
  • Welcome
    • Chris Van Gorder, FACHE
    • Eric J. Topol, MD
    • Patient / Family #1
  • Session 1
    • Frank McCormick
    • Bert Vogelstein
    • Elaine Mardis
    • Robert Nussbaum
    • Sarah Jane Dawson
    • Michael Pellini
  • Session 2
    • J. Craig Venter
    • Eric Topol 
    • Al Gore
    • Heidi Rehm
    • Muin Khoury
  • Session 3
    • Moderator Katrina Kelner
    • Leonid Kruglyak
    • Carl Zimmer
    • Magdalena Skipper
    • Chris Gunter
  • Session 4
    • Patient / Family #2
    • Athur Beaudet
    • Jay Shendure
    • Howard Jacob
    • Hakon Hakonarson
    • David Epstein
    • Nir Birzalai
    • Ali Torkamani
    • Jeffrey Hammerbacher
  • Session 5
    • Michael Specter
    • Jessica Richman
    • Andrew Feinberg
    • Russ Altman
    • Anne Wojcicki
    • Harry Greenspun
    • Zubin Damania
Speakers
  • Male: 25 (76%)
  • Female: 8 (24%)
2013 - Future of Genomic Medicine VI - schedule from here
  • Welcome: Eric Topol
  • Patient / Family #1
  • Session 1:
    • Michael Snyder
    • William Gahl
    • Howard Jacob
    • Ali Torkamani
    • Gholson Lyon
    • Cinnamon Bloss
    • Misha Angrist
  • Session 2
    • Evan Eichler
    • Eric Schadt
    • Katrina Armstrong
    • George Weinstock
  • Session 3
    • Joe Ecker
    • Stephen Kingsmore
    • Stephen Quake
  • Session 4
    • Patient / Family #2
    • Siddhartha Mukherjee
    • Elaine Mardis
    • Daniel D. Von Hoff
    • Randy Scott
    • Susan Desmond Hellman
    • Elias Zerhouni
    • Janet Woodcock
  • Session 5
    • Peter Vesscher
    • David Goldstein
    • George Church
    • Jonathan Eisen
    • Atul Butte
    • AJ Jacobs
    • Neil Risch
    • Lonny Reisman
    • Daniel MacArthur
Speakers
  • Male: 26 (84%)
  • Female: 5 (16%)
2012 Future of Genomic Medicine V - schedule from here
  • Welcome
    • Chris Van Gorder, FACHE
    • Eric J. Topol, MD
  • Joseph Beery and Family
  • Moderators: Samuel Levy, PhD and Eric J. Topol, MD
    • Samuel Levy, PhD
    • Matthew J. Price, MD
    • Julie Johnson, PharmD
    • Michael R. Hayden MB, ChB, PhD
    • William E. Evans, PharmD
  • Moderators: Evan Eichler, PhD and Sarah Murray,
    • Evan Eichler, PhD
    • Christofer Toumazou, PhD
    • Siddharta Mukherjee, MD, PhD
    • Sarah Murray, PhD
  • Moderators Nicholas Schork, PhD and Bradley Patay, MD
    • Hakon Hakonarson, MD, PhD
    • Isaac Kohane , MD, PhD
    • John A. Todd, FRS, PhD
  • Moderators Eric J. Topol, MD and Nicholas Schork, PhD
    • Howard J. Jacob, PhD
    • Joseph G. Gleeson, MD
    • Stanley F. Nelson, MD
    • Lynn Jorde, PhD (note - originalled labelled as female - corrected thanks to comment from Bruce Rannala)
  • Eric J. Topol, MD
  • Moderators: Aravinda Chakravarti, PhD and Richard Klausner, 
    • Aravinda Chakravarti, PhD
    • Joseph Nadeau, PhD
    • Nicholas Schork, PhD
    • Hakon Hakonarson MD, PhD
  • Moderator Eric Topol
    • Matthew Herper
    • Daniel B. Vorhaus, JD, MA
    • Issam Zineh, PharmD, MPH
  • Moderators: Elaine Mardis, PhD and Jeffrey Trent, PhD
    • Richard D. Klausner, MD
    • Thomas J. Hudson, MD
    • Jeffrey M. Trent, PhD
    • Daniel D. Von Hoff, MD
    • Elaine R. Mardis, PhD
  • Moderators: Samuel Levy, PhD and Fred Gage, PhD
    • Fred H. Gage, PhD
    • Bruce D. Gelb, MD
    • Joseph C. Wu, MD, PhD
All speaker and session chair slots
  • Male: 44 (88%)  45 (90 %)
  • Female: 6 (12%) 5 (10 %)
Just speakers
  • Male: 31 32 (91.4%)
  • Female: 4  3 (8.6%)
2011 Future of Genomic Medicine IV - schedule from here
  • Session 1: Moderators: Sarah S. Murray, PhD and Eric J. Topol, MD
    • Hannah A. Valantine, MD
    • Geoff Ginsburg, MD, PhD
    • Steve Shak, MD
    • Cinnamon S. Bloss, PhD
    • Matthew J. Price, MD
  • Session 2: Moderators: Bradley Patay, MD and Nicholas J. Schork, PhD
    • Kevin Davies, PhD
    • Thomas Goetz, MPh
    • Melanie Swan, MBA
  • Session 3: Moderators: Samuel Levy, PhD and Nicholas J. Schork, PhD
    • Kári Stefánsson, MD
    • Aravinda Chakravarti, PhD
    • Howard J. Jacob, PhD
    • Sarah S. Murray, PhD
    • James R. Lupski, MD, PhD
    • Nicholas J. Schork, PhD
    • Stephen L. Hauser, MD
    • David R. Bentley, D.Phil, F.Med.Sci.
  • Keynote: Juan Enriquez, BA, MBA
  • Session 4: Moderators: Robert L. Strausberg, PhD and Samuel Levy, PhD
    • Robert L. Strausberg, PhD
    • Elaine R. Mardis, PhD
    • Thomas J. Kipps, MD, PhD
    • Samuel Levy, PhD
    • Daniel D. Von Hoff, MD
    • Dennis A. Carson, MD
  • Session 5: Moderators: Eric J. Topol, MD and Bradley Patay, MD
    • Eric J. Topol, MD
    • Amy Harmon
    • Misha Angrist, PhD
  • Session 6: Moderators: Sarah S. Murray, PhD and Samuel Levy, PhD
    • Hakon Hakonarson, MD, PhD
    • Mark McCarthy, MD, F.Med.Sci.
    • Karen Mohlke, PhD
    • Stephen S. Rich, PhD
    • Philippe Froguel, MD, PhD
    • Muredach P. Reilly, MB, MS
All speaker and session chair slots
  • Male: 35 (80%)
  • Female: 9 (20%)

مرسلة بواسطة في ليست هناك تعليقات:
التسميات: , , , , ,

السبت، 28 مارس 2015

How to keep up with microbial ecology and the built environment: microBEnet is your place

Just posting a wrap up of posts on microBEnet (where I blog frequently as do many other folks that work on something related to microbial ecology, the built environment, or the intersection of the two).  microBEnet is really becoming a central place to find out what is going on in the world of microbial ecology and the built environment.  And I love that we are getting more and more posts from outsiders about their work, their meetings, their ideas and more.  Anyway - here is a wrap up of the posts for the last month.  If you are interesting in joining microBEnet and writing posts about relevant topics, let me know.

Jenna Lang (staff scientist in my lab) -- meeting reports from a Planetary Protection meeting
My posts:
Alexander Sczyrba on the Critical Assessment of Metagenome Interpretation (CAMI)

Elisabeth Bik from Stanford roundups from Microbiome Digest
David Coil (a staff scientist at UC Davis in my lab)
Linsey Marr of Virginia Tech
Rachel Adams - post doc at UC Berkeley
Ben Kirkup of the  Naval Research Laboratory
Embryete Hyde from UCSD
Brent Stephens of the Illinois Institute of Technology
مرسلة بواسطة في ليست هناك تعليقات:
التسميات: , , , , ,

الأربعاء، 25 مارس 2015

Calling attention to poor speaker gender ratio - even when it hurts

So I saw this Tweet earlier today


And that sounded very interesting. So I clicked on the link to check out the Plant Breeding for Food Security: The Global Impact of Plant Genetics in Rice Production A symposium honoring Dr. Gurdev Khush symposium.  And, then I went to the program.  And sadly I saw something there that was not to my liking.  The speakers were almost all male (men labelled in yellow, women in green)
  • Welcome to the Khush Symposium (Alan Bennett)
  • The Plant Breeding Center (Charles Brummer)
  • The Confucius Institute (Glenn Young)
  • Global food production – challenges and opportunities (Ken Cassman) Food production, technology and climate (David Lobell)
  • Panel – Impact of Gurdev Khush on plant genetics and food security Tomato genetics
    • (Dani Zamir)
    • (Pam Ronald)
    •  (Gary Toenniessen)
    •  (Gurdev Khush)
  • Lunch; The California Rice Industry (Kent McKenzie)
  • The rice theory of culture (Thomas Talhelm)
  • Recent advances in rice productivity and the future (David MacKill)
  • Hybrid rice technology contributions to global food security (Sant Virmani)
  • Super green rice (Qifa Zhang)
  • Tackling the wheat yield barrier (Matthew Reynolds)
  • African Orphan Crops – inspiration and execution (Howard Shapiro/Allen Van Deynze)
If this was a symposium outside UC Davis the first thing I would do would be to post about it.  To Twitter or my blog or both.  And to critique them.  Why?  Because there is a bad history in STEM fields of having meetings and conferences have under-representation of women as speakers.  And this has become a passion of mine and I write about it a lot.  But I hesitated.  Why?  Because this was from UC Davis and many of the people involved are friends / colleagues.  I did not want to anger them, or embarrass them.  And I don't think there is any intentional bias here by any means.  But, if I am going to critique people outside UC Davis, it seems like I should also apply the same standards to people inside UC Davis and to colleagues and friends.

So I posted to Twitter a response:

But that did not seem sufficient.  So I wrote up this post.  Underrepresentation of women as speakers is a serious issue in STEM fields.  And it is solvable (e.g., see Some suggestions for having diverse speakers at meetings by myself and the wonderful Ten Simple Rules to Achieve Conference Speaker Gender Balance by Jennifer Martin).

Now - do I know who the possible speakers were for this symposium?  No - I don't really know the field.  Is it possible that there just are no women in the field?  Sure.  But I would bet anything that is not the case here.  Having a meeting where the ratio of speakers is 16:1 male: female sets a bad example.  UC Davis and the organizers of this meeting can do better.  And though this will possibly hurt me in various ways (I already got grief from one person who I will not name for the Tweet), I think it is critical that we call out examples such as this.

And finally I note - I have taken on the issue of women at STEM conferences and meetings because, well, it is easy to identify cases where the numbers are anomalous and it is relatively easy to solve.  But it is also important that we consider other aspects of diversity of speakers (age, ethnicity, career stage, etc).  It is important to have diversity of speakers at meetings for many many reasons.  Speaking is a career building opportunity.  Speakers serve as role models for others.  Diverse points of view are important to have represented.  Bias - whether simplicity or explicit damages the whole practice of science.  And more.  Yes, we need to work on many aspects of diversity in STEM fields.  Improving the diversity of speakers at meetings is but one part of this.  But it is an important part and it is relatively easy to do.  So just do it.  And call attention to it.  Even if it hurts.



UPDATE 3/25 11:29 AM

The meeting organizers have responded on Twitter

Storify of some responses here


مرسلة بواسطة في ليست هناك تعليقات:
التسميات: , , , ,

Treponema are not "ancient" but absence from some human's guts is very interesting

So I saw some Tweets today that caught my attention, discussion news stories about "ancient" bacteria being missing from some human's gut microbiomes:





These refer to a sadly inappropriate headline in Science



What is wrong with this?  Well, there are no "ancient" bacteria around today.  They are all modern.  I am not even sure what they were trying to say.  Just a really bad evolution argument I guess.  I pondered giving Science a Twisted Tree of Life Award which I give out for exactly this kind of thing -  but decided first to dig into the science here and gloss over the bad evolution headline.

And it turns out - what the news story is about is in fact interesting - a new paper out in Nature Communications:  Subsistence strategies in traditional societies distinguish gut microbiomes.

The paper is freely available and has some really interesting material in it.  They key to me - at least related to this "ancient" bacteria claim is the following part of their abstract:
As observed in previous studies, we find that Treponema are characteristic of traditional gut microbiomes. Moreover, through genome reconstruction (2.2–2.5 MB, coverage depth × 26–513) and functional potential characterization, we discover these Treponema are diverse, fall outside of pathogenic clades and are similar to Treponema succinifaciens, a known carbohydrate metabolizer in swine. Gut Treponema are found in non-human primates and all traditional peoples studied to date, suggesting they are symbionts lost in urban-industrialized societies.
And then some further detail in the paper:
Although Spirochaetes have been previously reported from the gut microbiome of non-human primates and ancient human populations, they have only been observed in high abundance among extant human populations with non-Western lifestyles, such as a traditional community in Burkina Faso and a hunter-gatherer community in Tanzania. As such, they may represent a part of the human ancestral gut microbiome that has been lost through the adoption of industrial agriculture and/or other lifestyle changes. 
So they don't go into the full detail here but what I think they are saying is that they infer that human ancestors had Spirochaetes (based on the finding of it in non human primates and some human populations).  And thus they further infer that human populations (e.g., the people they studied in Oklahoma) that do not have these Spirochaetes have "lost" them.

I note - I think this terminology of "loss" they are using is not quite right here in a way.  Saying that these Spirochaetes have been lost implies to me that they are heritable.  But they do not in fact show that.  It could be that these are related to diet or environment in some way - something shared by some human populations and non human primates, for example.  And thus the absence from some "Westernized" populations could be more of an environmental thing than a "loss" in the past.


In a similar way, we could say that Westernized humans have "lost" the ability to be skinny (since obesity is high in many such populations).  Non human primates have such abilities and so do some non Westernized populations.  But "losing skinnyness" does not seem quite right since we do not know exactly why obesity is higher in Westernized populations.  I think it would be better in such cases to say something like "do not show an ancestral trait" (the ancestral trait here being skinnyness) and to not use "lost" until we know more about what is going on.  Similarly, I think saying some human populations have "lost" these Spirochaetes is not quite right.

Nevertheless, the absence (or at least, low levels) of these Spirochaetes from some human populations is certainly interesting.  And given that the presence of such Spirochaetes does appear to be an ancestral trait, the absence is even more interesting.  And thus this paper here, which details some of the genomic features of these "missing" Spirochaetes is definitely worth paying attention to.

In addition, I note - the findings in this paper serve as an additional justification for projects to generate genomic data from across the phylogenetic diversity of microbes.  Consider for example their Figure 6 and 7 which show that the most closely related Treponema species and the ones with the most similar genomes to these human Spirochaetes are those from Treponema succinifaciens and Treponema brennabornese.



Both of those genomes were generated by the Genomic Encyclopedia of Bacteria and Archaea project which I coordinated with the DOE-JGI and DSMZ.  See the paper on one of them: Complete genome sequence of Treponema succinifaciens type strain (6091T) and the posted data on the other.

We argued that we needed to sequence reference genomes from across the tree of life because this would help inform studies of uncultured microbes from diverse ecosystems.  Little did I know that one of the key ecosystems we would help inform would be the human gut.

Certainly more needs to be done in regard to these Spirochaetes.  Why are they at low levels or missing from some Westernized populations?  What do they do in other populations?  Would they be helpful if they were reintroduced to populations that do not have them?  So many questions actually.  But despite the misleading news article headline, this paper seems to me on first glace at least to in fact be quite interesting.

I made a Sorify of some comments
مرسلة بواسطة في ليست هناك تعليقات:
التسميات: , , ,

الأحد، 22 مارس 2015

The ChuckNorrisMicrobiome will get you, and you, and you ...

Some Saturday fun ...



مرسلة بواسطة في ليست هناك تعليقات:
التسميات: , ,

السبت، 14 مارس 2015

Overselling the microbiome award: Dr. Raphael Kellman at MindBodyGreen


Well this article by Dr. Raphael Kellman has just lots of overstatements about the microbiome: Why The Microbiome Is Your Key To Glowing Skin & Healthy Weight

For example, he writes:
Have you and your boyfriend or girlfriend ever gone out for a feast of delightfully unhealthy proportions only to then find yourselves picking fights with one another once you're back home and digesting?  Fueling your body with unhealthy bacteria, and then feeding it with more unhealthy bacteria, is a sure-fire way to destabilize your mind-body connection. Instead, focus on supporting the positive bacteria in your belly with fermented foods like yogurt, sauerkraut, and kefir and watch your spirits soar.
This implies that somehow the microbome has some role in such situations and in mediating the relationships between two people.  And it implies that that can be fixed with fermneted foods.  And this is without any shred of evidence ...

Then there is a discussion that makes the microbome sound like the master controller of all that is human:
Our bodies are cohesive entities, yes, but within each there are several languages spoken. 
The microbiome works like a translator for all of these systems, deciphering and decoding so that one process can communicate with the other for more efficiency and effectiveness (helping our systems to work as a team instead of independently alongside one another).
And then there is evidence free claims about fatigue and the microbiome
I've found that this kind of unexplained fatigue is often linked to a lack of diversity in the microbiome and can be remedied, despite what conventional medicine says
Whenever someone critiques "conventional" medicine and then presents no evidence for their claims, one should be wary, very wary.

And it ends with

Your inner ecology, your microbiome, is influential on your physical health, and that shows through glowing skin, a balanced weight and a youthful essence.  
So - if you want to be youthful and glowing and have good sex and relationships and get rid of your fatigue and fix your automimmune disorders and obesity and connect all of your systems together, all you have to do is fix your microbiome.  Simple.  Oh and how do you do that?  Why funny you asked, because I am selling this new book on the Microbiome Diet to solve all your problems.  Ridiculous.  And dangerous.

And thus I am giving out an Overselling the Microbome award to Dr. Kellman.

مرسلة بواسطة في ليست هناك تعليقات:
التسميات: , ,

Some silly microbome ideas from @DeepakChopra and @rudytanzi

Well, just got to reading this: Big Idea 2015: Medicine, Wellbeing, and the Microbiome | Deepak Chopra MD. Yes, it was from December 2014 but I could not get up to reading it then because I saw some of the comments online about it and it seemed off.  But anyway I caught up to it today.  It has many inaccurate and misleading statements about microbes and microbiomes I just felt like I had to post something.  Some of the problemmatic parts are below with comments.

Let's start gently.  As with many other stories on the microbiome, this article quotes the oft cited "fact" of a 10:1 ratio of microbial cells to human cells.
By some estimates the body has between 35 and 100 trillion cells with only 1 in 10 belonging to tissues and organs and the rest belonging to the microbiome.
This has been refusted by a great article in the Boston Globe by Peter Andrey Smith in September 2014 (long before this was published): Is your body mostly microbes? Actually, we have no idea.  Yes, I and many others cited this 10:1 ratio before the Globe.  But seeing it cited in this from December 2014 suggests Chopra and Tanzi aren't really paying attention to microbiome science.

The next comment I find a bit off is the follwing:
Our personal human genome also determines the composition of our microbiome, which in turn can influence metabolism and propensity for weight gain.
Sure.  Our genes influence out microbiome.  But "determines the composition" is way to strong a statement.

But the things that got to me most were many of the comments supposedly about evolution.  I list some of them below:
  • This varying ecosystem isn't populated by foreign invaders and pathogens but by colonies closely connected to human evolution.
    • I don't even know what this is supposed to mean.  These are not "colonies" first of all.  And second, what does "connected to human evolution" even mean?  And wouldn't pathogens be connected to human evolution?
  • The microbiome interfaces between the human body and the outside world in complex ways, but the gist is that human DNA has evolved in cooperation with microbial DNA. This fact is more important than the interactions that cause diseases created by invading bacteria and viruses.
    • Re "human DNA has evolved in cooperation with microbial DNA".  Well, sure.  Some of the microbes we live with are mutualists. But most likely only a limited number of mutualistic interactions are going on.  This sounds like a Gaia type of model, with no evidence.  
    • And then "This fact is more important than the interactions that cause diseases created by invading bacteria and viruses."  Really?  More important than the plague?  Than malaria? Aids?  Cholera.  TB? Worms? And more.  This sounds really silly.
  • Mitochondria actually have their own genomes inherited from the mother without change.
    • Umm - no mitochondria mutate and change, well, all the time.
  • Some of the most archaic microorganisms on Earth survive today in our microbiome.
    • This is without any justification.  First of all - what does "most archaic" mean?  And second, if it means what I think it means (organisms that have features like those from billions of years ago) - well - no - the human microbiome does not have a lot of such organisms.  This is just complete hooey.  
  • It would appear that the genome and the microbiome cross-talk, a conversation that has been continuing for billions of years with no signs of stopping.
    • What does this even mean?  In what way has the human microbiome been interacting with the human genome for billions of years.  In what way have human ancestors been interacting with microbiomes for billions of years?

Yes, the microbiome is important.  But this "essay" is filled with nebulous pseudoscientific comments about the microbiome all, apparently, to sell an upcoming book and related activities

"In an upcoming book we are co-authoring, Super Genes, we will present the latest findings as well as a lifestyle program devoted to what we call Self-Directed Biological Transformation"

Right now, I don't think Chopra and Tanzi show any evidence they really understand the microbiome .. doesn't bode well for their book and lifestyle program.
مرسلة بواسطة في ليست هناك تعليقات:
التسميات: , ,

الخميس، 12 مارس 2015

Horizontal gene transfer into humans? I am not convinced. Full text of my comments to reporters here

Some news stories about a new paper claiming evidence for horizontal gene transfer into humans and other chordates. I got asked by many reporters about it and some used some of my email comments in their articles.

See for example

 Here is the full text of my responses:

"got asked by another reporter to comment on this

so - have seen the paper 
it is interesting .. but I am not overwhelmed by what they present in the paper itself. For example, the HAS story seems really incomplete as presented (e.g., the Figure showing the tree does not have all the HAS1, HAS2, HAS3 genes even though they imply they studied that). "
I have been looking through the supplemental information. I find it impossible to judge the quality of this paper without being able to see the alignments they used for each phylogenetic tree. I cannot find alignments for the trees even after going to their Figshare site with the trees. I therefore think there is not much to say about the paper until being able to see those. 
Without seeing the alignments I offer multiple alternative hypothesis for their findings
  1. They have identified genes for which they are unable to produce reasonable alingnments. Alignments are central to phylogenetic analysis and if their alignments are poor quality then the trees will show all sorts of anomalies that have nothing to do with phylogenetic history. By scanning through 1000s of genes and flagging those with unusual patterns they may be selectively identifying genes for which producing good alignments between species is tough. I note - clustalw is a bit notorious for not producing idea alignments in some cases.
  2. I do not buy their arguments for why gene loss is not a possible explanation. They need to present more detail on how many gene losses would be required for each gene family under consideration and then present some evidence for why that # of gene losses is less likely than HGT.
  3. They have not even considered as far as I can tell, the possibility of divergent evolution (as opposed to gene loss) in many taxa which could lead to them being unable to identify homologs in some species
  4. I am not convinced by the arguments against long branch attraction as an explanation for some of the tree patterns.
  5. Related to alignments they need to show which regions of alignments they excluded from phylo
  6. Convergent evolution could also explain some of the patterns they observe.
  7. I could go on. I am NOT saying that HGT into chordates is impossible. It seems plausible. But it is up to them to exclude other MORE plausible alternatives and I just do not think they have done that.
Reporter: asking if it was OK to quote me

Yes it is OK to quote from me. I would like to reiterate - I am not saying they are wrong. Just that I would like to see (1) all the data (e.g., alignments) that unreels their conclusions and (2) them do more to exclude other possibilities.
Reporter asking what other analyses could they do
So - I don't want to be difficult, but it is their job to figure out how to do such tests before claiming they have strong evidence for HGT. 
In general, this is pretty typical of claims of HGT. Many researchers show evidence that is consistent with the occurence of HGT (which they did here) but few actually explicitly test alternative hypotheses such as gene loss, bad alignments, convergence, divergence, contamination, random noise, and more. I think their work is certainly interesting, but they just have not tested all of these alternatives. And I personally have grown a bit tired of pointing out how people can do better controls for their papers.
Reporter asking about initial impressions:
I see little here that is particularly convincing evidence for HGT ...
My follow up email
Note - I am not saying that this is a bad paper -- just that I am not overwhelmed by their evidence and especially by what they put in the paper. 
For example, the HAS1 gene story seems incomplete.  Figure 3 seems to show just HAS1 but in the text the say they show the same thing for all HAS genes.  And the tree they show shows a tiny subset of all the available sequences (e.g., HAS1 HAS2 HAS3 and fungal and bacterial homologs).  They claim that they now have proof that HAS1 was transferred near the base of chordates but I just don't see how they tested alternative hypotheses ...

Some related links:
Also here are some presentations from many years ago with some discussion of HGT




مرسلة بواسطة في ليست هناك تعليقات:
التسميات: , , , , , ,

الأربعاء، 11 مارس 2015

Probiotics for athletes? Possible someday, but right now - I (and others) don't think so

Nice article in Outside Magazine by David Despain: Should You Be Taking Probiotics? | Performance Plate | OutsideOnline.com.  The article has comments from me, Peter Turnbaugh and Ellen Silbergeld.  The article discusses some of the overhyped claims about probiotics and athletic performance and even mentions my Overselling the Microbiome award.  I like in particular the following paragraph:

The biggest issue scientists currently have with probiotics, however, doesn’t have to do with athletes. Instead, it has to do with the initial hypothesis that we need them in the first place, says Ellen Silbergeld, a professor of Johns Hopkins Bloomberg School of Public Health. Because there’s still no real understanding of what makes “healthy” or “poor” microbiomes, there’s no real understanding of how or if we should cultivate them.

مرسلة بواسطة في ليست هناك تعليقات:

الاثنين، 9 مارس 2015

Today's gender biased meeting-GlycoCom2015-sponsored by @generalelectric @ualberta #YAMMM


Got pointed to this via a Tweet:
The Tweet pointed to this meeting: Home - Glycomics Official Website of GlycoCom Conference 2015 in Banff, Alberta, Canada.  Lame.  14:1 ratio of men: women speakers.  Just completewly lame.

Confirmed Speakers

  • Richard Cummings, Emory University School of Medicine
  • Paul DeAngelis, University of Oklahoma and Caisson Biotech LLC
  • Donald Jarvis, University of Wyoming and GlycoBac LLC
  • Nicole Koropatkin, University of Michigan Medical School
  • Mario Feldman, Washington University, St. Louis and VaxAlta Inc.
  • Gordon Lauc, University of Zagreb
  • Todd Lowary, Alberta Glycomics Centre and University of Alberta
  • John Magnani, GlycoMimetics Inc.
  • Glenn Prestwich, University of Utah and GlycoMira Therapeutics Inc.
  • Peter Seeberger, Max Plank Institute
  • Tadashi Suzuki, RIKEN Global Research Cluster
  • Ajit Varki, University of California, San Diego
  • David Vocadlo, Simon Fraser University and Alectos Therapeutics Inc.
  • Michael Wacker, GlycoVaxyn AG
  • Robert Woods, Complex Carbohydrate Research Center & Glycosensors & Diagnostics, LLC
The University of Alberta and GE and the other sponsors should be embarassed by this.  
مرسلة بواسطة في ليست هناك تعليقات:
التسميات: , ,

السبت، 7 مارس 2015

My microbiome talk at #FOGM15 - the perils (and fun I guess) of redoing one's talk at the last minute

Just got back from the Future of Genomic Medicine 2015 meeting where I gave a talk about microbiomes.  My original plan was to talk about the need for evolutionary and ecological approaches to microbiome studies but I changed my mind a few days before the meeting and decided to switch to talking more about citizen microbiology.  I did this because the meeting has a lot of people who think about digital and wearable technology and public engagement in the audience and it just seemed like a good chance to introduce them to the growing personal/citizen microbiology movement.

To help prep for my talk I emailed some colleagues who work on Citizen Microbiology (including a few in my lab like Jenna Lang and David Coil) and asked them if they had any slides I could pilfer.  And then I started drafting an outline of my talk (I draft all my talks by hand with pen and paper). Here are my handwritten notes










 I realized I would not likely be able to focus enough at home to work on the talk so I kind of waited until heading down to San Diego on Wednesday (talk was on Friday).

I got in pretty late and worked a little on my talk before going to bed.  I also emailed the organizers of the meeting to say I was changing the topic of my talk a bit and asked if they could change the online program which they did.  Eric Topol in response to my saying I wanted to talk about citizen microbiology and personal microbiomes very wisely suggested that I talk about my vision for the future of microbiome research.  I (lamely) had been so focused on Citizen Microbiology that I had not been thinking much about the bigger picture.  But once he suggested this notion my talk really congealed (in my head and on paper at least).  It is interesting to me how one simple suggestion from someone with vision and perspective can transform one's thought process so much ...

Anyway, the next day I headed over to the meeting venue (by the beach - life is rough in San Diego).  I got there in time to hear Francis Collins' talk.  I spent the day sitting outside in the outdoor tent viewing area, pondering my talk and listening to the talks of others. Lots and lots of interesting things presented there.  More about this later I hope.  Anyway - that evening I worked on my talk some more, headed down to the hotel bar for a bit and then worked on my talk some more.  And eventually went to sleep.  Friday I spent much of the AM working on my talk in the outdoor tent (while listening to the talks though this time not watching them on the screen since I was a bit too far away from it).  And voila - only 30 minutes before the PM session was to begin I finished the prep.  I do not like to do this normally but I just felt like my talk would be much better if I re-conceived it and I had to make all new slides pretty much for the whole talk (other than the few I pilfered from colleagues).

I note - I was talking after Marty Blaser and figured I would not have to introduce the human microbiome at all and also that he would give an overview of the risks that come from disturbing the microbiome.  Anyway, I gave my talk, and recorded the slideshow with Camtasia.  Below are my slides, the video slideshow, and a Storify of the Tweets others posted during my talk.
As is frequently the case, afterwards I felt I was too rushed and that it was not the best talk I have ever given. But that being said, I like the general outline and some of the concepts and figured I should share, warts and all. My biggest regret after talks which I have rushed a bit in preparing is that I usually do not do a great job in mentioning who did all the work I refer to. I try to put people's pictures and names on all slides and references but I don't always get this done in time and I worry I screwed this up for a few topics here. Oh well, life goes on ...

Here is a slideshow with Audio (which I recorded via Camtasia)



Here is the Slideshare posting of my slides



مرسلة بواسطة في ليست هناك تعليقات:
التسميات: , , , , ,

الخميس، 5 مارس 2015

Today's YAMMM - The British Society for Plant Pathology

Well, this is not the most egregious example of a mostly male meeting but it still has some issues: The BSPP - The British Society for Plant Pathology 2015 meeting.  Nine speakers.  Seven male.  And this in a field with plenty of excellent female researchers.

Cassava brown streak disease
(1) James Legg - IITA Tanzania
(2) Stephan Winter - Leibniz Institute DSMZ Germany
(3) Maruthi Gowda - Natural Resources Institute, University of Greenwich

Late blight
(1) Bill Fry - Cornell University
(2) Sophien Kamoun - Sainsbury Lab, Norwich
(3) Jonathan Jones - Sainsbury Lab, Norwich

Rice blast
(1) Sarah Gurr - University of Exeter
(2) Lauren Ryder - University of Exeter
(3) Thomas Kroj - INRA, Montpellier, France

But the weirdest part --  it says
"This year, the BSPP President, Prof. Gary Foster, has only chosen a few invited speakers on specific diseases, and wishes the remainder of the talks to be selected from offered papers."

So does this mean Prof. Gary Foster just picked all speakers?  If so, perhaps Prof. Gary Foster needs to do a little thinking about his possible biases ...




مرسلة بواسطة في ليست هناك تعليقات:
التسميات: , ,

الثلاثاء، 3 مارس 2015

Another day, another microbiome journal ... alas not as "open access" as claimed

Just got this email
Dear Doctor Jonathan Eisen,

I would like to invite you to consider submitting a paper to our recently launched Open Access journal Microbiome Science and Medicine (http://www.degruyter.com/view/j/micsm).
As can be seen from the titles of articles published in our first volume, MICSM reflects the full breadth of research in the diverse areas of microbiome-related science, from molecules to ecosystems:
Newton ILG, Sheehan KB, Lee FJ, Horton MA, Hicks RD "Invertebrate systems for hypothesis-driven microbiome research"
Amato KR "Co-evolution in context: The importance of studying gut microbiomes in wild animals"
Nelson DR, Tu ZJ, Lefebvre PA "Heterococcus sp. DN1 draft genome: focus on cold tolerance and lipid production"
Rudlaff RM, Waters CM "What is the role of cyclic di-GMP signaling within the human gut microbiome?"
Fang Y, Chia N, Mazur M, Pettigrew J, Schook LB, White BA "Genetically identical co-housed pigs as models for dietary studies of gut microbiomes"
MICSM is a broad-spectrum platform for the rapid publication of works of broad significance, originality and relevance in all areas related to the study of microbiomes, their components, and their roles in health and disease. We solicit research and review articles, as well as communications and vision papers. The manuscripts submitted in response to this invitation will be processed with the highest priority and all accepted papers will be immediately available on-line.

Authors are offered a variety of benefits:
– transparent, comprehensive and fast peer review;
– language assistance for authors from non-English speaking regions;
– convenient, web-based manuscript submission and tracking system;
– efficient route to fast-track publication and full advantage of De Gruyter Open's e-technology;
– no publication charge in the first two annual volumes.

I look forward to your manuscript!
Please forward this invitation to any interested colleagues and associates.
Seemed right up my alley - an open access microbiome journal.  Alas, when I clicked on the journal link and then browsed around I found out that articles will be published using some pretty restrictive conditions. Some key parts of the text from this page is below:

1. License
The non-commercial use of the article will be governed by the Creative Commons Attribution-NonCommercial-NoDerivs license as currently displayed on http://creativecommons.org/licenses/by-nc-nd/3.0/., except that sections 2 through 8 below will apply in this respect and prevail over all conflicting provisions of such license model. Without prejudice to the foregoing, the author hereby grants the Journal Owner the exclusive license for commercial use of the article (for U.S. government employees: to the extent transferable) according to section 2 below, and sections 4 through 9 below, throughout the world, in any form, in any language, for the full term of copyright, effective upon acceptance for publication.
Other than being, well, painfully legalesy, this is just too restrictive for me and does not really seem like "open access".  The no derivatives part drives me batty.  Also they write:

9. Scope of the Commercial License
The exclusive right and license granted under this agreement to the Journal Owner for commercial use is as follows:
 to prepare, reproduce, manufacture, publish, distribute, exhibit, advertise, promote, license and sub-license printed and electronic copies of the article, through the Internet and other means of data transmission now known or later to be developed; the foregoing will include abstracts, bibliographic information, illustrations, pictures, indexes and subject headings and other proprietary materials contained in the article,
 to exercise, license, and sub-license others to exercise subsidiary and other rights in the article, including the right to photocopy, scan or reproduce copies thereof, to reproduce excerpts from the article in other works, and to reproduce copies of the article as part of compilations with other works, including collections of materials made for use in classes for instructional purposes, customized works, electronic databases, document delivery, and other information services, and publish, distribute, exhibit and license the same.
Where this agreement refers to a license granted to Journal Owner in this agreement as exclusive, the author commits not only to refrain from granting such license to a third party but also to refrain from exercising the right that is the subject of such license otherwise than by performing this agreement.
Well, no thanks.  Too many restrictions and not open access in my view.  If I had to choose a "microbiome" journal to publish in, I would choose "Microbiome" an actually open access journal, where papers have the following info on them:
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
Go Microbiome ...

مرسلة بواسطة في ليست هناك تعليقات:
التسميات: ,
الاشتراك في: الرسائل (Atom)