Tag: science

American Academy of Arts and Sciences – where men choose men to be cheered

So – I saw multiple posts by colleagues on Facebook and Twitter about gender skew in the newly elected members of the American Academy of Arts and Sciences. So I decided to take a look at the list. And it is indeed really skewed. Here is my analysis of gender ratio for mathematical and physical sciences and biological sciences.

Field Male Female
Math and Physical Sciences Totals 32 10
Math 5 1
Physics 6 1
Chemistry 7 1
Astronomy 3 4
Engineering 5 1
CS 5 2
Intersection 1 0
Biology Totals 31 8
Biochemistry 4 2
Cell and Development 7 1
Neuroscience 6 2
Ecovo 7 1
Medical 5 1
Intersection 2 1
More detail below:

CLASS I — Mathematical and Physical Sciences (41)

FOREIGN HONORARY MEMBERS (4)
SECTION 1 — Mathematics (6)
Pavel Etingof
Massachusetts Institute of Technology
Leslie Greengard
New York University/Simons Foundation
Janos Kollar
Princeton University
Bryna R. Kra
Northwestern University
Andrei Okounkov
Columbia University
Vladimir Rokhlin
Yale University
SECTION 2 — Physics (7)
Barbara V. Jacak
University of California, Berkeley
Christopher Jarzynski
University of Maryland
Hirosi Ooguri
California Institute of Technology
Roberto D. Peccei
University of California, Los Angeles
Robert J. Schoelkopf
Yale University
Steven R. White
University of California, Irvine
Foreign Honorary Member — Physics
Thibault Damour
Institut des Hautes Etudes Scientifiques
SECTION 3 — Chemistry (8)
Donald Hilvert
Eidgenössische Technische Hochschule Zürich, Zurich, Switzerland
Jeffery W. Kelly
Scripps Research Institute
Scott J. Miller
Yale University
Melanie S. Sanford
University of Michigan
Isiah M. Warner
Louisiana State University
Michael R. Wasielewski
Northwestern University
Foreign Honorary Members — Chemistry (2)
Hans-Joachim Freund
Fritz-Haber-Institut der Max-Planck-Gesellschaft
R. Benny Gerber
Hebrew University of Jerusalem/University of California, Irvine
SECTION 4 — Astronomy and Earth Sciences (7)
Andreas J. Albrecht
University of California, Davis
Joshua A. Frieman
Fermi National Accelerator Laboratory/University of Chicago
Jacqueline Hewitt
Massachusetts Institute of Technology
Chryssa Kouveliotou
George Washington University
Terry A. Plank
Columbia University
Lisa Tauxe
University of California, San Diego
Foreign Honorary Member — Astronomy and Earth Sciences
Thomas F. Stocker
University of Bern
SECTION 5 — Engineering Sciences and Technologies (6)
Donna Gail Blackmond
Scripps Research Institute
Gerald G. Fuller
Stanford University
Steve Granick
Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
Donald E. Ingber
Harvard University/ Boston Children’s Hospital
Robert B. Phillips
California Institute of Technology
Peter W. Voorhees
Northwestern University
SECTION 6 — Computer Sciences (6)
Jeffrey A. Dean
Google
Sanjay Ghemawat
Google Incorporated
Anna R. Karlin
University of Washington
Tom M. Mitchell
Carnegie Mellon University
Tal D. Rabin
IBM T.J. Watson Research Center
Scott J. Shenker
University of California, Berkeley
CLASS I INTERSECTION CANDIDATES (1)
Timothy P. Lodge
University of Minnesota

CLASS II — Biological Sciences (38)

FOREIGN HONORARY MEMBERS (6)
SECTION 1 — Biochemistry, Biophysics and Molecular Biology (6)
Richard H. Ebright
Rutgers University
Lila M. Gierasch
University of Massachusetts
Robert M. Glaeser
University of California, Berkeley/Lawrence Berkeley National Laboratory
Adrian R. Krainer
Cold Spring Harbor Laboratory
Lawrence A. Loeb
University of Washington
Eva Nogales
University of California, Berkeley
SECTION 2 — Cellular & Developmental Biology, Microbiology, and Immunology (8)
Keith W.T. Burridge
University of North Carolina at Chapel Hill
Mark W. Hochstrasser
Yale University
Michael J. Lichten
National Cancer Institute
Joachim Messing
Rutgers University
Carl F. Nathan
Weill Cornell Medical College
Anne M. Villeneuve
Stanford University
Foreign Honorary Members — Cellular & Developmental Biology, Microbiology, and Immunology (2)
Carl-Henrik Heldin
Ludwig Institute for Cancer Research/Uppsala University
Christof Niehrs
Institute of Molecular Biology
SECTION 3 — Neurosciences, Cognitive Sciences, and Behavioral Biology (8)
Michael S. Brainard
University of California, San Francisco
John Gabrieli
Massachusetts Institute of Technology
Alex L. Kolodkin
Johns Hopkins University School of Medicine
Kelsey C. Martin
University of California, Los Angeles
Bruce R. Rosen
Harvard Medical School/Massachusetts General Hospital
John L. R. Rubenstein
University of California, San Francisco
Foreign Honorary Members — Neurosciences, Cognitive Sciences, and Behavioral Biology(2)
Tamar Flash
Weizmann Institute of Science
Nancy Y. Ip
Hong Kong University of Science and Technology
SECTION 4 — Evolutionary and Population Biology, and Ecology (7)
Farooq Azam
University of California, San Diego
Andrew G. Clark
Cornell University
Douglas J. Emlen
University of Montana
Joel Grant Kingsolver
University of North Carolina at Chapel Hill
Mark Alan McPeek
Dartmouth College
Sarah P. Otto
University of British Columbia
Foreign Honorary Member — Evolutionary and Population Biology, and Ecology
Ary A. Hoffmann
University of Melbourne
SECTION 5 — Medical Sciences, Clinical Medicine, and Public Health (6)
John Michael Carethers
University of Michigan Medical School
James R. Downing
St. Jude Children’s Research Hospital
Gary Gilliland
Fred Hutchinson Cancer Research Center
Beatrice H. Hahn
University of Pennsylvania Perelman School of Medicine
Warren J. Leonard
National Institutes of Health
Ralph Weissleder
Harvard Medical School/ Massachusetts General Hospital
CLASS II INTERSECTION CANDIDATES (3)
Steven E. Jacobsen
University of California, Los Angeles
Yang Shi
Harvard Medical School/ Boston Children’s Hospital
Foreign Honorary Member — Intersection
Karen H. Vousden
Beatson Institute for Cancer Research, Glasgow, U.K.

Also these cross-field areas are not doing so well (not included in chart or table above).

TOTAL: 213

FELLOWS: 176
FOREIGN HONORARY MEMBERS: 37

INTERCLASS CANDIDATES (10)

FOREIGN HONORARY MEMBERS (5)
Benjamin F. Cravatt
The Scripps Research Institute
Robert L. Goldstone
Indiana University
Larry L. Jacoby
Washington University in St. Louis
Jay D. Keasling
University of California, Berkeley/LBNL
Gordon D. Logan
Vanderbilt University
Foreign Honorary Members (5)
Edwin Cameron
Constitutional Court of South Africa
Fergus I.M. Craik
Rotman Research Institute/University of Toronto
Menachem Magidor
Hebrew University of Jerusalem
Mikhail Borisovich Piotrovsky
State Hermitage Museum/St. Petersburg State University
Shimon Ullman
Weizmann Institute of Science

EMERGING FIELD CANDIDATE (1)

Robert J. Full
University of California, Berkeley

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

——–

Rule #1: Don’t ever emulate @lifesciadvisors – #everydaysexism

//storify.com/phylogenomics/sexism-by-lifesciedtiors/embed?template=slideshow//storify.com/phylogenomics/sexism-by-lifesciedtiors.js?template=slideshow[View the story “Sexism by @LifeSciAdvisors” on Storify]
——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Does #AAAS care about #Ebola anymore? Nope. And probably never did. #ClosedAccess

In October I wrote a blog post criticizing AAAS (and ASM) for trying to give themselves a pat on the back for making a few papers about Ebola freely available: The Tree of Life: No #AAAS and ASM you do not deserve good PR for freeing up a few papers on Ebola.  The whole thing was a publicity stunt.  And AAAS in particular tried to play up how they were doing this for the benefit of humanity.

So today I decided to check back and look into whether AAAS was making new papers on Ebola freely available. So I searched for the word Ebola in the title or Abstract 

The most recent seemed interesting:

Lessons from Ebola: Improving infectious disease surveillance to inform outbreak management 

  • Mark E. J. Woolhouse, 
  • Andrew Rambaut, 
  • and Paul Kellam

Sci Transl Med 30 September 2015: 307rv5. [DOI:10.1126/scitranslmed.aab0191]

Surely AAAS must still care enough about Ebola to make new papers freely available right? Nope. $20 to rent for a day

How about #2:
Ebola vaccines face daunting path to approval 

  • Jon Cohen and

    •  

  • Martin Enserink

Science 18 September 2015: 1272–1273. [DOI:10.1126/science.349.6254.1272]

Seems useful and worth reading if one works on Ebola.  Free right?  Nope: $20/day

How about #3:

Why infectious disease research needs community ecology 

  • Pieter T. J. Johnson, 
  • Jacobus C. de Roode, 
  • and Andy Fenton

Science 4 September 2015: 1259504 [DOI:10.1126/science.1259504]

Seems peripherally relevant to Ebola but I would not mind if more Ebola workers read this.  Free right?  Nope.  Guess how much? $20/day
And so on.  A few in the first 10 were, at least for now freely available.  But overall it seems, AAAS and Science have decided Ebola is no longer important.  So much for helping the world.
——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Removing my name from the author list of #closedaccess "Unified Microbiome Initiative" paper in Science

//storify.com/phylogenomics/removing-my-name-from-the-author-list-of-closedacc/embed?border=false//storify.com/phylogenomics/removing-my-name-from-the-author-list-of-closedacc.js?border=false[View the story “Removing my name from the author list of #closedaccess “Unified Microbiome Initiative” paper in Science” on Storify]
——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

AAAS – Blocking Access to the Scientific Literature Even When They Say It Is "Free"

Today, I wanted to show someone a PDF of a paper of mine that I co-authored in 1999.  The paper was, I think, kind of cool.  It reported the sequencing and analysis of the genome of Deinococcus radiodurans, an incredibly radiation resistant bacterium.  Alas, I did not have a copy on me, and the only electornic device I had with me was my phone.  The person I wanted to show the paper to had their computer, a device with a strange little red trackball and running some sort of Windows operating system, so I looked at it and panicked and said “Maybe you should drive” (as in, maybe they should be the one controlling the computer).

So this person, who shall remain anonymous mostly because of the ancientness of their computer, did the kind of obvious thing, and opened a web browser (don’t even ask which one) and typed in “Pubmed.Com”.  OK – that would work.  I might have preferred going to Google Scholar, but I use Pubmed about as frequently.  And though I do not have a Windows machine or the weird web broswser they used, I have recreated what happened next.

A nice Pubmed window.  And I said, type in “Deinococcus Eisen.” and seven papers showed up.

And so I said “Scroll Down” and “Near the Bottom” and there was the paper “White et al” from 1999.   I was happy to see it said “Free Article” since I could not remember if AAAS had made this article available or not. So I said “Click on that one”.

And we looked around for a minute and at the same time we both realized, there in the upper right corner was a link to Science “Full text”.  And I thought – cool – the text is available just at Science not at Pubmed.  And my colleague clicked on this.

And here is where is got annoying.  A new page comes up from this link:

So – the paper is not actually readily available, one has to register in order to see it.  What a pain.  And my colleague just stopped there and said “I do not want to do this right now” and I said “Understood”.  And we stopped and I never showed him the paper (we could have tried other routes but we both had other things to do).  When I got home this evening I decided to look in more detail at the registration and clicked on the link:

Hmm.  So to register it seems I have to sign up for emails from AAAS and all sorts of other crap.  And I have two choices for email neither of which is “I do not want any FU#*(#@ email from AAAS”.  Great.  So I filled out some parts and scrolled to the bottom to see the Privacy Policy option.    And so I clicked on the link.  And the section on Uses of This Information is pretty annoying:

The information collected may be used by AAAS for the purpose of operating and improving the Science Website, fostering a positive user experience, and delivering the products and services that we offer. We may also use the information we gather to inform you of other products or services available from the Science Website or to contact you about your opinion of current products and services or potential new products and services that may be offered. 

We may use your contact information in order to send you e-mail, postal mail, or other communications regarding updates at the Science Website, such as Job Alerts, newsletters, new opportunities, and additional listings which may be of interest to you. We may also use it to send you information about third-party products and services that match your interests and preferences, if you opt in for this communication. We do not release any of your contact information to third parties unless we have your permission. The nature and frequency of these messages will vary depending upon the information we have about you. In addition, at the time of registration for certain services, such as Science Careers Job Alerts, or free partial access to any of the Science websites, you have the option to elect to receive additional communications, information, newsletters, and promotions relating to topics that may be of special interest to you. 

We may share information, such as your IP address, with third parties as might be required for technical purposes, such as facilitating user discovery and access via web search engines.

Well they say they will not share information unless I opt in, but the only way to get access to this paper is to opt in.  Great.   And it gets more explicit under the email policies section:

Users of free online services provided by AAAS±such as free partial access to Science, Science Signaling, or Science Translational Medicine, access to ScienceNOW or SAGE KE, e-mail alerting services or Science Careers services±are agreeing that AAAS may contact them by e-mail in exchange for these free services. Users can also opt in for third-party informational e-mails. Users who do not wish to receive e-mail may cancel their online services by following the unsubscribe instructions at the bottom of any e-mail message from AAAS.

So, actually, there is no opt in policy for those wanting free access to papers.  If you want access, you agree to be contacted.  So – I used a email address I have never used for anything else (so I can track who AAAS sells my name to) and sucked it up and registered.  And I checked the box for agreeing to the Privacy Policy even though I felt icky doing it.  Seemed like I should consult with a lawyer before doing that given how long it was.  Certainly not easy access.  And for the form I had to fill out I tried to not fill out anything under “Discipline” but the site would not let me.  I tried to not fill out anything under Lab Products but the site would not let me either.  And so I filled something out and then amazingly, when I submitted the form, I got sent another page where I had to keep filling out information.

And even though I was not subscribing to the journal I had to agree to some subscription policy.  So I clikced on that and got to another policy.  This including a Copyright warning:

Copyright Notice
Although there is no charge for the use of some portions of the materials contained on the Science websites (“Websites”), all the materials are protected under copyright and other laws of the United States, and, under international conventions, similar laws abroad. Please respect the copyrights and related rights of the authors and publishers of the Websites.

And then many many limitations on use

Limitations on Use by (and to) Registered Users
The contents of the Websites as available through the Free Service, may only be accessed, viewed or otherwise used by a Registered User. A Registered User is permitted to view, browse and/or download for temporary copying purposes only the contents of the Websites, provided these uses are for noncommercial personal purposes, and further provided that the Registered User maintains all copyright and any other notices, on all copies. Registered Users are not, however, permitted to store in electronic or any other form, any significant portion of the Websites. Except as provided by law or by this Agreement, the contents of the Websites may not be further reproduced, distributed, transmitted, modified, adapted, performed, displayed (including adaptations/displays such as by “framing”), published or sold in whole or in part, without the prior written permission from AAAS. 

Any use which is commercial and/or non-personal is strictly prohibited, and may subject the Registered User making such uses to immediate revocation of access to this Free Service, as well as any other applicable civil or criminal penalties. Similarly, sharing a Registered User password with a non-Registered User or otherwise making this Free Service available to third parties is strictly prohibited, and may subject the Registered User participating in such activities to immediate revocation of access to this Free Service; and, the Registered User and any third party, to any other applicable civil or criminal penalties. 

In the case of an authorized site license, a Registered User shall cause any employee, agent or other third party which the Registered User allows to use the Free Service materials to abide by all of the terms and conditions of this Agreement. In all other cases, only the Registered User is permitted to access the Free Service materials.

Well, this is getting pretty complicated and there was a lot of other stuff there.   But I checked the box.  I felt even ickier with this one and thought I really should consult a lawyer.  But I did not.  And I submitted this form.

And finally I had it.  It took about an hour.  This may seem minor to many out there but it seems inappropriate to me.  This paper represented hundreds of thousands if not millions of dollars of work funded by the Department of Energy and was published in 1999.  The goal of the work was to share knowledge.  And this is a major roadblock to sharing that knowledge.  Plus, all the restrictions on use and reuse mean that anyone wanting to share the knowledge with others also is restricted.  The agreements imply that I should not use anything from the paper in a talk or a class or in any way.  There is no mention of Fair Use or any other hint that it would be OK to share the material for educational or scholarly purposes. And who knows what crap I am going to get sent to the email address I used for this registration.

So – why are there all these restrictions?  I presume, to make AAAS money in some way.  Is that a bad thing?  Well, in principle I am all for publishers making money.  I subscribe to many newspapers.  I subscribe to many magazines.  I buy lots and lots of books.  I pay for music and movies and other works.  I don’t download anything illegally.  So why not just accept that people should pay for scientific papers?  Well, because this paper, and 1000s and 1000s of others are different than all the other works I list above.  Owen White and I (with some help from some others) wrote this paper.  AAAS and Science did little except handle the peer review and do some copy editing.  They just simply do not deserve the rights they are claiming to this article and to all the others.  And as a society supposedly for the “advancement of science” it seemed to me that they should make it easier to access the old literature. They could certainly make all papers published more than 12 months ago freely and openly available and deposit them in Pubmed Central.  It would be incredible beneficial to science and to scientists.  But they do not.  Is this in the interest of the “advancement of science”?   Unquestionably no.  But I guess they have decided it is in the interest of the “advancement of Science” where the journal and money for the society is the goal and the advancement of science is lost in the ether.

In the end, I deeply regret having ever published in Science.  15 years after publishing this paper I would definitely say it would have been better to have published in another journal – one that makes papers more openly and freely available.  I cannot change the past.  But I will not support AAAS or its activities in the present or the future unless they change policies and practices.

Some related posts:

UPDATE 1. 8/18 – 5 PM. Been Storifying some of the discussion

//storify.com/phylogenomics/aaas-blocking-access-to-free-papers/embed?border=false//storify.com/phylogenomics/aaas-blocking-access-to-free-papers.js?border=false[View the story “#AAAS Blocking Access to Free Papers” on Storify]

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

——–

Overselling the microbiome award – many – for stories about placental vs. oral microbiomes

A few days ago on Twitter I was pointed to a news story about the human microbiome:

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I looked at the article and definitely agreed with Ed. So I responded

//platform.twitter.com/widgets.js And then a mini conversation happened

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And I pondered writing up an “overselling the microbiome award” but I got caught up in other things. And then today some people (including Jens Walter) pointed me to this New York Times article about the same topic: Study Sees Bigger Role for Placenta in Newborns’ Health – NYTimes.com. And I decided I had to write something up because too many news stories were not doing a great job with the science here.

So here goes. First, the Science news (UPDATE – NOTE this is the news part of Science magazine, not ScienceNewsOrg) story Ed Yong pointed to originally and the parts I have problems with.

  • Sentence 1: Researchers have discovered a small community of bacteria living in a most unlikely place: the placenta, the organ that nourishes a developing fetus through the umbilical cord.  No – not really.  They did not discover this.  They did a more detailed characterization of the community.
  • Sentence 2: The finding overturns the conventional wisdom that the placenta is sterile.  No – the study is another piece of evidence that argues against the “conventional wisdom”
  • Sentence 3 is OK.
  • Sentence 4.  Medical experts have long assumed that any bacteria found in the organ must have been picked up when it passed through the vagina after delivery.  Sure – some “experts” have assumed this.  But there has been growing evidence for many years that this is a bad assumption.  

I could go on and on.  Actually though I won’t.  Becuase every news story can have some limitations.  I don’t like inaccurate statements but it is a part of life I guess.  But the part that drives me batty in this story is the inclusion of a discussion about oral health.  Here are the two paragraphs that are the crux of my concern (with bold emphasizing the worst parts).

Surprisingly, the mix of bacteria in the placenta looked more like the microbiome in an adult human’s mouth than the vaginal, skin, gut, or other body microbiomes, Aagaard’s team reports today in Science Translational Medicine. The researchers think the microbes may get to the placenta from the mother’s mouth through her bloodstream, perhaps when she brushes her teeth and dislodges them into the blood. That possibility is intriguing, because there’s a well-known correlation between gum disease and preterm birth. Indeed, the array of bacteria in the placenta differed in women who gave birth early, before 37 weeks. 

“This reemphasizes the importance of oral health” during pregnancy, Aagaard says. In fact, women may need to pay attention to their teeth even before they may become pregnant, because the placenta develops early in pregnancy, she says. That may be a challenge for low-income women who can’t afford dental care, Aagaard adds. The team also found a correlation between the composition of the placental microbiome and urinary tract infections, which suggests that such illnesses or antibiotics taken to treat them could alter the microbiome in unhealthy ways.

I have read and reread the paper (which I note – is not open access – making it hard to the public to actually dig into the paper if they wanted to).  And I see no evidence presented anywhere of the importance of oral health or any causal connection between oral health and the placental microbiome or risks to pregnancies. The claims made about this here in this news story are irresponsible.  Yes, there have been some other studies about dental health and birth issues.  But nothing in this paper.  And to imply otherwise is misleading at best.  And then to go on with “That may be a challenge for low-income women who can’t afford dental care” is really not appropriate.  And to then go on about UTIs and how treating them may “alter the microbiome in unhealthy ways” is also misleading and not supported.  
Where is the critical evaluation of such claims?  Certainly the paper is very interesting.  Among the findings of interest to me: (1) that low amounts of DNA from diverse microbes is found even in the placentas from healthy pregnancies and (2) that in their analysis these microbes were most similar to those from the mouth.  But how we get from those findings (and some others) to “the importance of oral health during pregnancy” and “such illnesses or antibiotics could alter the microbiome in unhelathy ways” is, well, not in the realm of scientific research.  This is in the realm of speculation.  And speculation is fine -IF YOU TELL PEOPLE YOU ARE SPECULATING.  If you don’t tell people you are speculating I have another term for it – it is called misleading.  I assume the researchers and reporter did not intend to be misleading but that is the end result of excessive speculation without making it clear what one is doing.

Now this brings me to other articles about this study.  There are many out there.  And most seem to have eaten up this oral health connection without questioning it.  For example, consider the artilce in the New York Times yesterday:Study Sees Bigger Role for Placenta in Newborns’ Health – NYTimes.com by Denise Grady.  Some issues I have with this article:

  • Let’s start with the title “Study Sees Bigger Role for Placenta in Newborns’ Health.”  Well, no – there was nothing in this study that showed any evidence about a new connection between the placenta and newborns’ health.  
  • NYTimes: “During pregnancy, the authors of the new study suspect, the wrong mix of bacteria in the placenta may contribute to premature births.” Sure – they suspect it.  Would have been good to point out they have no evidence for this.
  • NYTimes: Although the research is preliminary, it may help explain why periodontal disease and urinary infections in pregnant women are linked to an increased risk of premature birth.  Again, may help explain – sure.  But it also may have no connection whatsoever.  There is no evidence presented in the paper connecting periodontal disease and UTIs and the placental microbiome.  So this is pure speculation.  And it should have been met with some discussion of all the other ways that periodontal disease and UTIs could lead to risk of premature birth.  Like leading to increased inflammation in the mother.  Or affecting blood flow in the mother.  Or other things.  There is actually a TON of research in this area.  Below are some of the factors that affect preterm labor, as listed by the Mayo Clinic – are we now discounting the years and years of work on this and going whole hog into proposing a new cause without any evidence?
    • Previous preterm labor or premature birth, particularly in the most recent pregnancy or in more than one previous pregnancy
    • Pregnancy with twins, triplets or other multiples
    • Certain problems with the uterus, cervix or placenta
    • Smoking cigarettes, drinking alcohol or using illicit drugs
    • Certain infections, particularly of the genital tract
    • Some chronic conditions, such as high blood pressure and diabetes
    • Being underweight or overweight before pregnancy, or gaining too little or too much weight during pregnancy
    • Stressful life events, such as the death of a loved one
    • Domestic violence or any form of abuse during pregnancy
    • Multiple miscarriages
    • Red blood cell deficiency (anemia), particularly during early pregnancy
    • Too much amniotic fluid (polyhydramnios)
    • Pregnancy complications, such as preeclampsia
    • Vaginal bleeding during pregnancy
    • Presence of a fetal birth defect
    • Little or no prenatal care
    • An interval of less than six months since the last pregnancy
    • Also, having a short cervical length or the presence of fetal fibronectin — a substance that acts like a glue between the fetal sac and the lining of the uterus — in your vaginal discharge might be linked to an increased risk of preterm labor. 
  • I note – the authors even say in their paper “Although this study is not able to address the relationship between periodontal disease and the placental microbiome, we, as a community of obstetricians, have appreciated for decades the association between periodontal disease and preterm birth”. Clearly the paper received more scrutiny that the quotes and the news stories. 
  • NYTimes: The new study suggests that babies may acquire an important part of their normal gut bacteria from the placenta. No.  Nothing in this study showed any connection between what is in the placenta and what is in the babies guts.  None.
  • NYTimes: If further research confirms the findings, that may be reassuring news for women who have had cesareans. Some researchers have suggested that babies born by cesarean miss out on helpful bacteria that they would normally be exposed to in the birth canal.  Again – there is no evidence that babies pick up microbes from the placenta.  So speculating that this may reassure women who have C- sections is way way way too premature.
  • NYTimes: “I think women can be reassured that they have not doomed their infant’s microbiome for the rest of its life,  said Dr. Kjersti Aagaard.  Wow. Now we have gone from “if further research confirms” to just flat out reassuring women who have had C-sections that there are no effects on the microbiome.
  • NYTimes: “It didn’t make a whole lot of sense to us,” she said. “It’s not like babies are hanging out in the vagina. They come shooting out pretty fast.” Also, she said, they emerge covered in a waxy substance called vernix, which most likely helps keep bacteria from latching on. Wow.  So babies come shooting out of the vegina and therefore cannot get microbes from the vagina.  This despite the massive amounts of evidence that they in fact do get microbes from the vagina and that C-section born babies get a different community (see for example this).  (UPDATE 5/26 – see UPDATE below with some comments / papers about C-sections vs. vaginal birth and how my use of “massive” here may be an overstatement itself).
I could go on and on.  But I won’t.  I am pleased the reporter talked to Martin Blaser who puts some damping on the speculation:

Dr. Martin J. Blaser, director of the human microbiome program at NYU Langone Medical Center, and the author of a recently published book, “Missing Microbes,” said that Dr. Aagaard’s study was important, but preliminary, and that it did not provide information that could be used in treating pregnant women. 

Thank you Martin.  But even with this, these articles leave me very frustrated.  The best I can do I guess is give out an award or two. So, for their reporting on the topic I am giving Denise Grady of the New York Times and Jocelyn Kaiser of Science News an Overselling the Microbiome award since they oversell the potential connection between oral health and infant health as mediated by the placenta.  And I am also giving this award to  Kjersti Aagaard, the first author of the paper, for her comments on the topic.

For more examples of “Overselling the Microbiome” awards see my page here.

UPDATE: Some other news stories where the headline alone is painful

UPDATE 2: Some articles that discussed placental microbes before this story came out

and many more

UPDATE 3: Paper on placental – mother – infant connection not even mentioned

Just found this paper from a Google Scholar search:  Probiotics Modulate Host-Microbe Interaction in the Placenta and Fetal Gut: A Randomized, Double-Blind, Placebo-Controlled Trial.  Seems like it is of direct relevance.  Abstract is below;

Abstract
Background: Early host-microbe interaction provides important maturational stimuli for the developing immune system. The role of prenatal microbial contact remains elusive. Objectives: Our aim was to investigate whether microbes in placenta or amniotic fluid affect fetal innate immune gene expression during late pregnancy and whether innate immune gene expression profiles in the placenta and the fetal gut may be modulated by dietary supplementation with specific probiotics. Methods: Altogether 43 pregnant women were randomized to receive (1) Bifidobacterium lactis, (2) B. lactis in combination with Lactobacillus rhamnosus GG (LGG) or (3) placebo for 14 days before elective cesarian section at full term in a double-blind clinical trial. Bacteria in amniotic fluid and placenta were detected by quantitative (q)PCR. The expression of Toll-like receptor (TLR)-related genes in the placenta and meconium samples was assessed by qPCR. Gene expression patterns in meconium were interpreted to reflect immune physiology in the fetal gut. Results: The study was completed by 29 mother-infant pairs. Bacterial DNA was detected in all placenta samples. Microbial DNA in amniotic fluid and placenta was associated with changes in TLR-related gene expression in the fetal intestine. Maternal probiotic supplementation significantly modulated the expression of TLR-related genes both in the placenta and in the fetal gut. Conclusions: Microbial contact in utero is associated with changes in fetal intestinal innate immune gene expression profile. Fetal and placental immune physiology may be modulated by maternal dietary intervention using specific probiotics.

This paper was not mentioned or cited as far as I can tell in the current study.

UPDATE 4: This paper also seems relevant

Microbial contact during pregnancy, intestinal colonization and human disease.  Abstract:

Interaction with colonizing intestinal bacteria is essential for healthy intestinal and immunological development in infancy. Advances in understanding early host–microbe interactions indicate that this early microbial programming begins in utero and is substantially modulated by mode of birth, perinatal antibiotics and breastfeeding. Furthermore, it has become evident that this stepwise microbial colonization process, as well as immune and metabolic programming by the microbiota, might have a long-lasting influence on the risk of not only gastrointestinal disease, but also allergic, autoimmune and metabolic disease, in later life. Modulating early host–microbe interaction by maternal probiotic intervention during pregnancy and breastfeeding offers a promising novel tool to reduce the risk of disease. In this Review, we describe the current body of knowledge regarding perinatal microbial contact, initial intestinal colonization and its association with human disease, as well as means of modulating early host–microbe interaction to reduce the risk of disease in the child.

UPDATE 5 – more misleading quotes

  • From Time’s misleadingly named article “The New Way to Predict When Pregnant Women Will Deliver“: “By focusing on oral health, we may actually be optimizing the health of the pregnancy and limiting the risk of pre-term birth,” says Aagaard. After paying so much attention to the more obvious ways to make a pregnancy healthy, it may be time to consider the less obvious – and less visible ones
  • That quote is just so inappropriate … uggh

UPDATE 6: May 24.  Some  Made a Storify with some of the Tweets related to this post.

//storify.com/phylogenomics/overselling-the-microbiome-in-placenta-story/embed?border=false&template=slideshow//storify.com/phylogenomics/overselling-the-microbiome-in-placenta-story.js?border=false&template=slideshow[View the story “Overselling the microbiome in placenta story” on Storify]

UPDATE 7: May 26 – some other papers of relevance to birth mode and infant microbiomes and placentas

A key question to me I guess is the following – how do differences between the microflora in babies born by C-Section vs. vaginal birth arise if the microbes in placentas have a big role in colonizing infants?  Perhaps the differences between C-section babies and vaginal birth babies are small — I do not know — need to dig into this more.
——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

"Scientific Pride and Prejudice" in the @nytimes makes claims about sciences not using evidence correctly; alas no evidence presented

Well, I guess I can say I was not pleased to see this tweet from Carl Zimmer.

//platform.twitter.com/widgets.js It is not that I have a problem with what Carl wrote. It is just that, then I went and read the article he referred to: Scientific Pride and Prejudice in the New York Times By Michael Suk-Young Chwe. And it just did not make me happy. I reread it. Again and again. And I was still unhappy.

What bugs me about this article? Well, alas, a lot. The general gist of the article is that “natural” scientists are not aware enough of how their own preconceptions might bias their work. And furthermore that literary criticism is the place to look for such self-awareness. Well, interesting idea I guess but alas, the irony is, this essay presents no evidence that literary criticism does better with evidence than natural science. Below are some of the lines / comments in the article that I am skeptical of:

  • “Scientists now worry that many published scientific results are simply not true.”
  • “Scientists, eager to make striking new claims, focus only on evidence that supports their preconceptions. Psychologists call this “confirmation bias. We seek out information that confirms what we already believe. ”
    • This statement is misleading. Confirmation bias according to all definitions I could find is something more subtle. For example Oxford Dictionaries defines it as “the tendency to interpret new evidence as confirmation of one’s existing beliefs or theories.” That is, it is a tendency – a leaning – a bias of sorts.
    • I would very much like to see evidence behind the much more extreme claim of this author that scientists focus “only on evidence that supports their preconceptions”. 
    • In my readings of actual research on confirmation bias I can find no evidence to this claim. For example see the following paper Confirmation bias: a ubiquitous phenomenon in many guises. which states:
    • As the term is used in this article and, I believe, generally by psychologists, confirmation bias connotes a less explicit, less consciously one-sided case-building process. It refers usually to unwitting selectivity in the acquisition and use of evidence. The line between deliberate selectivity in the use of evidence and unwitting molding of facts to fit hypotheses or beliefs is a difficult one to draw in practice, but the distinction is meaningful conceptually, and confirmation bias has more to do with the latter than with the former.

    • “Despite the popular belief that anything goes in literary criticism, the field has real standards of scholarly validity”
      • This is a red herring to me. I can find no evidence that their there is a popular belief that “anything goes” in literary criticism. So the author here sets a very low bar and then basically any presentation of standards is supposed to impress us.
    • “Rather, “the important thing is to be aware of one’s own bias.”
      • The author then goes on to discuss how those in the humanities are aware of the issues of confirmation bias and rather than trying to get rid of it, they just deal with it, as implied in the quote.
      • The author then writes “To deal with the problem of selective use of data, the scientific community must become self-aware and realize that it has a problem. In literary criticism, the question of how one’s arguments are influenced by one’s prejudgments has been a central methodological issue for decades.“
      • Again, this implies that scientists have not been thinking about this at all which is just wrong.
    • And then the author uses the Arsenic-life story as an example of how scientists suffer from “confirmation bias.”  If you do not know about the arsenic life story see here.  What is the evidence that this was “confirmation bias“?.  I think more likely this was a case of purposeful misleading, overhyping, and bad science.  
    • Then the author gives as an example of how science actually is prone to confirmation bias by presenting a discussion of Robert Millikan’s notebooks in relation to a classic “oil drop” experiment.  Apparently, these notebooks show that the experiments got better and better over time and closer to the truth.  And in the notebooks Millikan annotated them with things like “Best yet – Beauty – Publish”.  And then the author concludes this means “In other words, Millikan excluded the data that seemed erroneous and included data that he liked, embracing his own confirmation bias.”  I don’t see evidence that this is confirmation bias.  I think better examples of confirmation bias would be cases where we have now concluded the research conclusions were wrong.  But instead, Millikan was and still is as far as I know, considered to have been correct.  He won the Nobel Prize in 1923 for his work.  Yes, there has been some criticism of his work but as far as I can tell, there is no evidence that he had confirmation bias. 
    • I am going to skip commenting on the game theory claims in this article.
    • Then the author writes “Perhaps because of its self-awareness about what Austen would call the “whims and caprices” of human reasoning, the field of psychology has been most aggressive in dealing with doubts about the validity of its research.”  Again – what is the evidence for this? Is there any evidence that the field of psychology is somehow different?
    I could go on and on.  But I won’t.  I will just say one thing.  I find it disappointing and incredibly ironic that an article that makes claims about how some fields deal better with evidence and conformation bias than other fields does not present any actual evidence to back up its claims.  And many of the claims pretty clearly run counter to available evidence.

    UPDATE 9:20 AM 2/2/2014: Storify of discussions on Twitter

    //storify.com/phylogenomics/discussion-of-scientific-pride-and-prejudice-and-m/embed//storify.com/phylogenomics/discussion-of-scientific-pride-and-prejudice-and-m.js[View the story “Discussion of “Scientific Pride and Prejudice” and my response to it” on Storify]
    ——–
    This is from the “Tree of Life Blog”
    of Jonathan Eisen, an evolutionary biologist and Open Access advocate
    at the University of California, Davis. For short updates, follow me on Twitter.

    ——–

    I f$*#@#ing love science but really f$*#Ing hate travel much of the time

    Well, have already written a bit about my fun trip to DC on Twitter and Facebook but thought I would sum it up here too. Last week I had to go to DC for a meeting relating to a Department of Homeland Security grant we have in my lab (it was the annual meeting of the program).  Of course the point of the whole trip was to present about our work.  And for the record – here are the slides for my talk I gave on Wednesday.

    But alas, going to give talks is not just about the Science is it? It unfortunately is also about the travel. And boy do I hate travel most of the time these days. Here is a tale of my trip …. I was supposed to go on Monday but had to delay going until Tuesday due to illnesses in the family. So I called United and changed my flight and called the Westin in Alexandria and changed my hotel reservation and emailed the meeting organizers and let them know.

    All seemed good. Then Tuesday AM I got an email from United saying my flight had been cancelled and I had been rebooked on another flight. After calling up United and finding out that the seat upgrade using my miles / Premier status was not available I at least confirmed that I would be getting in to DC not too late. And so after lingering at home I headed to the airport and got on the flight from SMF to Houston.

    I got to Houston, walked around for a while and eventually made my way to the connection to DC. I went to board and the machine gave the ticket agent an error message saying “Passenger is not ticketed for this flight” or something like that. Great. And I had to leave the line, go to the desk and wait a bit until someone helped me. There I found out that United had somehow cancelled the entire rest of my flight and thus I was not only no longer booked on a flight to DC I had no return flight either. After a painful but brief delay somehow they put me on the connection and I got to DC.

    It was after getting the error message that I ended up engaging some social media to express my frustration and I tweeted about United. And eventually the United Twitter handler got back to me and helped me confirm that I did now have a return flight.

    Anyway – I moved on past the United issue and got in a cab in DC and headed to the Westin Alexandria. I got there and checked in. Sadly I found out there was no food available anywhere at the hotel (it was only 10:50 PM or so). So I decided to just go up to my room and crash. I went up to my room and – well – was seriously in for a shock. My room was a meeting room of some sort overrun with meeting tables and with a small, rollaway bed smushed up against the wall.

    Oh my God. You have got to be kidding me. I have serious trouble sleeping when I travel and am not exactly the smallest guy in the world.  A rollaway bed in the middle of a conference room? Uggh.  So I called up the front desk and asked

    “Is this some sort of mistake. Is there supposed to be a bedroom connected to this room?“

    And the person from the desk said “No. That is your room.”

    And I said “Well, I can’t sleep on that bed“

    And he said “Sorry – we are fully booked – that is all we have.”

    And I said, again “Listen, I called yesterday and confirmed my room and told you I was coming late and this is not acceptable. I want a normal bedroom with a normal bed. Nothing fancy.  Just a bedroom.“

    And he said “OK.  I have another room.”

    So I said “Can someone bring up the key?“

    And he said “No. There is no one else here.“

    So I said “OK I will come back down.”

    So I got my stuff and went back down and really wanted to ask “Well, why is there a room now if you told me the room with the rollaway bed was the last room” but I held my tongue.  And after a computer malfunction that led to a 5-10 minute wait he gave me a new room key.

    And I was off again.  Once there, I opened the door to the room and I knew before even getting into it why they did not give it to me at first.  It reeked of cigarette smoke.  Like someone had a cigarette testing party in the room.  Drowning in smoke smell.  I took a pic of the air vents to represent the smell … for what that was worth.  So I immediately went to the phone and called the desk again.

    Me: “Hey it’s the guy who you just gave a new room to. This room is even worse.  Unbearable cigarette smell here.  Is this a smoking room?”

    “No we don’t have smoking rooms.”

    Me: “So did the cleaning crew mark this room as having been smoked in and you gave it to me even though it has not been cleaned yet without telling me?“

    Answer “No.”

    Me “I need a different room.”

    Him: “Ok – let me look.  (click click click).  OK I have another room“

    Me: “Can someone bring the key up?“

    Answer: “I don’t think so.”

    Me: “OK I will come back down.”

    So down I went and finally got a third room.

    And this one was OK.  Meanwhile I was also positing details of the debacle to Twitter and Facebook.  And enjoying (in a theater of the absurd kind of way) some of the responses I got from miscellaneous people and also the communications with the Westin Twitter handler.  Here below is a Storify of some of the communications around both the United issue and the Westin issue.

    //storify.com/phylogenomics/i-f-ing-love-science-but-f-ing-hate-travel-much-of.js[View the story “I f#ing love science but f#ing hate travel much of the time” on Storify]

    But perhaps the most entertaining part were the DM messages from the @Westin person. Here is the thread – copied and pasted from Twitter

    • @Westin: 1/2 We do apologize for the inconvenience. We spoke to the hotel and was informed that you have been shifted to another room 
    • @Westin: 2/2 with a king bed. Please let us or the front desk know if you need any further assistance. 
    • Me: Third try … Why wouldn’t the cleaning crew inform them of the smoky room? It was awful
    • Me: And why would they give me a room with a rollaway as the only bed without saying anything? 
    • Me: I would like to formally request a free night in exchange for this absurdity 
    • @Westin: 1/3 We truly apologize for the inconveniences.Your booking was made through a group rate & that was originally the room type booked for you. 
    • @Westin: 2/3 Unfortunately, we are unable to grant you that request as hotel has accommodated by shifting rooms for you to a king bed. We spoke to 
    • @Westin: 3/3 the hotel regarding the strong smell next door as there are no smoking rooms at the hotel. Someone will reach out to you in the morning. 
    • Me: ????- are you saying they booked me a room with a rollaway bed? 
    • Me: Are you saying the room did not smell of smoke ??? 
    • @Westin: We understand your frustration & do apologize again for the inconvenience. The management team will reach out to you in the morning to
    • @Westin: further follow up on your concerns as they are in the best position to address situations. Please feel free to let us know if you require 
    • @Westin: any additional assistance from our team
    I spent a few hours working on my talk and then finally got a little bit of sleep.  In the morning I ordered room service.  An espresso, and eggs and toast.  I asked for fried eggs and got scrambled.  I did not want meat but got some.  I asked for water and got none.  But I never mentioned this to the hotel.  Seemed kind of pointless. 

    And then I had an email exchange with a representative of the Westin Alexandria that ended up being somewhat interesting.

    Westin

    Good Morning Mr. Eisen,

    I have received your feedback from our corporate office in regards to your check-in experience last night.

    First of all, please allow me to apologize on behalf of my team and the hotel for the inconvenience you went through last night. Our hotel was closed to sold out last night so there were some challenges in the room assignment with the preference of each of our guest.

    I also meant to touch base with your directly this morning but I have noticed you have already departed the hotel.

    I will go ahead and take care of your night for the inconvenience you went through and it will also be my pleasure to recognize you as a loyal SPG member by giving you a credit of 5,000 SPG Points.

    If there is anything further I can assist you with, please feel free to contact me directly. I hope you will choose us again for your future travel plan in Alexandria. When you do so, please let me know so I can review your accommodation.

    Once again, my sincere apologies for the inconvenience.

    Be Well,
    Thomas

    THOMAS
    POTEAU
    Director of Operations
    THE WESTIN ALEXANDRIA
    400 Courthouse Square, Alexandria, Virginia  22314 

    Me

    Thanks for the email. 

    I appreciate what you have done.  I would very much like to know of you can give me some explanation of what happened – like why was I sent to a room with a rollaway bed with no warning or explanation.  And whether the second room I was sent to was empty because of the smoke smell and if so why I was sent there? 

    Thanks 

    Jonathan Eisen 

    Westin:

    Mr Eisen,

    In a sold out situation like last night, we review the last arrivals and room assignment and with your SPG status, my front desk supervisor upgraded you to our hospitality suite. Yes this is a room which doesn’t have a permanent bed so we put a rollaway in this room, however this is a much larger room (suite) than our Traditional King. Most of our guests usually don’t mind the situation and actually enjoy the larger room. Since our rollaway beds are heavenly beds like any of our beds, the size of the bed is the only difference and most of the time acceptable with our guests.

    That being said, yes, we should have been proactive and contact you to verify the accommodation, informed you during the registration of the situation and being accommodating in taking care of your rate knowing it was an inconvenience for you. My apologies for that, I have addressed it with my team this morning.

    As far as the smoking room, again when we only have a couple of rooms available, it becomes much more challenging. The room had been treated for smoke for the last 2 days by the housekeeping team and was turn back to market due to our occupancy level. When our system assigned you that room, the agent didn’t know that room had smoking issue since it was back in his system as an available room.

    I personally walked this room this morning and confirm the smell was still very much a discomfort. I have removed the room from our inventory for further treatment.

    Once again, I am sorry for the inconvenience and hope you will come back to stay with us again in the near future so I can personally make sure we provide you with the service levels Westin offers.

    Be Well
    Thomas

    THOMAS
    POTEAU
    Director of Operations
    THE WESTIN ALEXANDRIA

    Me

    Thanks very much for the further explanation.  I note – IF someone had said that that was a heavenly bed I might have tried it, but I have extensive experience with rollaway beds because I have two kids.  And the rollaways are almost always unusably by me.  So perhaps when you inform the people what to do they should say “We only have a rollaway bed BUT it is comfortable and is a Heavenly bed.  That might have made everything fine … but without that knowledge I just thought I got screwed … 

    Jonathan

    Westin

    Thank you. I agree and I will certainly take on the feedback and share with my team so we can better explain it to our guest.

    THOMAS
    POTEAU
    Director of Operations
    THE WESTIN ALEXANDRIA

    So then – finally it seemed resolved.  Not only would my room be free but perhaps they learned something and would do a better job next time.  And finally I got to give my talk.

    //storify.com/phylogenomics/dhs-talk.js[View the story “DHS talk” on Storify]
    I note – the return trip was OK.  United let me change my flight to an earlier one.  I got home in time to read to my kids before they went to sleep.  And other than being exhausted and still a little peeved, I think it went OK.

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

    ——–

    Guest post: Kevin Carpenter on his new microbial photo exhibit at the Exploratorium in SF #SoCool

    Special guest post from Kevin Carpenter who has microbe photos featured at the Exploratorium.

    One of my colleagues who does research on the microbes that live in the hindguts of lower termites once remarked that interesting organisms can be found in the most unusual of places. And the lower termite hindgut, by almost anyone’s estimation, is certainly an unusual place. It is also a fascinating place for anyone interested in biology, ecology, evolution, biochemistry, or beautiful natural forms and patterns.

    Since my undergraduate days in the early 90s, I have had a deep interest in the tree of life, especially eukaryote phylogeny. After a Ph.D. in Plant Biology at U.C. Davis, I headed off to the University of British Columbia to work in Patrick Keeling’s lab to pursue these interests. Anyone who has this peculiar obsession (actually, I think it’s peculiar not to have this obsession!) knows that the eukaryote tree comprises mostly protists, and they arguably encompass greater structural, cell biological, biochemical, (and certainly evolutionary!) diversity than all plants, animals, and fungi combined.

    In Patrick’s lab I developed methods for SEM and TEM imaging of these microbes to investigate their phenotypic character evolution, functional morphology, and symbioses with bacteria in the light of molecular phylogenetic data. In addition to a number of publications (with more to come) and talks in Russia, Germany, Norway, etc. my electron micrographs have been featured on numerous journal covers, textbooks, and invited artistic presentations in Canada and Germany.

    On 17 April 2013, a collection of 11 of my scanning electron micrographs of lower termite hindgut protists and their bacterial symbionts will go on permanent exhibit at the Exploratorium museum as they open their new $300 million dollar location on Pier 15 in San Francisco. This is a large (12′ x 4′) installation in the East Gallery (overlooking the bay):

    The waterfront location, the architecture, the exhibits, and sustainable technology (rooftop solar panels, etc) are all amazing, and I encourage anyone with any interest in science/biology, art, experimentation, tinkering, and beautiful views to come out for a visit. For more information on the exhibit, the organisms, additional images and other resources (including a blog!), please visit my website at: KevinJCarpenter.com

    As for the organisms…

    The hindgut of wood-feeding lower termites–comprising approximately 1000 species (out of a total of several thousand species of termites)–is densely packed with symbiotic protozoa (protists), many of which engulf and enzymatically degrade wood fragments making their way to the termite hindgut. Far from being parasites, numerous studies have shown this to be a mutualsitic symbiosis, by demonstrating that the termites will starve and die if deprived of their protist symbionts. The symbiosis between lower termites and their hindgut protists is one of the longest-studied and best-known examples of microbial symbiosis, dating back nearly a century and a half to the work by Joseph Leidy and others.

    The protists are anaerobic flagellates belonging to Parabasalia or Oxymonadida–members of the Excavate eukaryotic supergroup (also including euglenids, trypanosomes, Giardia, and heterolobosean amoebas). There are numerous odd, interesting, beautiful, and instructive things about these protists.

    First, they are endemic to termite hindguts and are found nowhere else. Most of the protist species are found only in association with a single species of termite. The termites pass their hindgut biota from adult to newly hatched nymphs and moulting adult termites (which lose their hindgut contents) via specialized feeding behaviors. It is thought that termites evolved social behavior and caste differentiation from their cockroach ancestors partly to pass hindgut protists between individuals.

    Second, many of the protist species and lineages have attained large size (up to 300 microns in length), and enormous structural complexity. Some of the protists are estimated to bear up to 50,000 flagella, each associated with specialized proteinaceous structures (kinetosomes, parabasal fibers) inside the cell. Hence, these are likely among the most structurally complex cells known to science. This is in marked contrast to other symbiotic protist lineages such as microsporidia, apicomplexans, and the coral reef symbiont Cyanidioschyzon, all of which have undergone extreme structural reduction. When looking at these termite gut protists in all of their great structural complexity, dwarfing their numerous bacterial surface symbionts, it is is kind of mind-boggling in a sense to realize that this is a unicellular organism!

    Third, the cell biology of these organisms is so different from what is taught in undergraduate cell biology (which is really mammalian, or at best, metazoan cell biology), that it may (hopefully) cause one to reflect on how truly diverse and unknown our biosphere really is. As one example of this, in parabasalid protists, mitochondria have become drastically reduced structurally (loss of cristae), functionally (loss of oxidative metabolism/Krebs cycle), and genomically, and their only known function is the conversion of pyruvate to acetate, with the production of hydrogen gas as a waste product. Hence, these relict mitochondria are called hydrogensomes. The oxymonads are among the least understood group of eukaryotes, and for many species it is unknown what they eat (some of the smaller species apparently do not eat wood), how they reproduce, or how they metabolize their food. Some even have a non-canonical genetic code.

    The sitution becomes even more complex when we consider the bacteria in lower termite hindgut systems. In light of their importance in the human and other gut microbiomes, it is no surprise that the termite gut is swarming with innumerable bacteria, many of which are likely found only in one species of termite. What is surprising is that an estimated 90% of all bacterial cells in these systems live either on the surface of, or inside of a protist, and are not free-swimming. One study estimates that the large protist Pseudotrichonympha harbors about 100,000 bacterial cells. Microscopy reveals specialized attachment structures that help the bacteria anchor to the protist surface. Our research shows that the large protist Barbulanympha has not only vast numbers of rod-shaped bacteria on its cell surface and interior, but also bacteria surrounding extruded strands of cytoplasm. This is possibly a mechanism to increase the area available for exchange of nutrients.

    Recent research on bacteria symbiotic with termite gut protists suggests that they are important in nitrogen metabolism–both in nitrogen fixation and synthesis of vitamins and amino acids. They are thought to transfer these compounds to their host protist (and to the termite) in return for sugars derived from breakdown of wood.

    Just as the protists are generally endemic to a single species of termite, in many cases, bacteria found in symbiotic association with the protists are endemic to a single species of protist. Given this close, three-way association between termite, protist, and bacteria, it is perhaps not surprising that evidence of triplex speciation has been found in these organisms: both the bacteria and their protist hosts speciate in tandem in response to termite speciation events. This is one of only a handful of putative cases of triplex speciation.

    The symbiosis between termites and protists is actually also present in a species of wood-feeding cockroach–Cryptocercus punctulatus. C. punctulatus is actually more closely related to termites than to other cockroaches (cockroaches are paraphyletic). It is believed that symbiotic protists were present in the hindgut of the ancestor of C. punctulatus and modern termites, which likely lived over 100 million years ago.

    Thus, I consider these termite hindgut systems to be among the most unusual, beautiful, and instructive natural laboratories in evolution and ecology known to science. Nature indeed seems to enjoy tinkering, and in that spirit, I think this is well suited to representation in a place like the Exploratorium!

    A few references (copied straight out of one of my manuscripts!) for those interested:

    Brune, A. & Ohkuma, M. (2011). Role of the termite gut microbiota in symbiotic digestion. In Biology of Termites: A Modern Synthesis, Bignell, D. E., Roisin, Y. and Lo, N. (Eds.), pp. 439-475. London: Springer.

    Carpenter, K.J., Chow, L. & Keeling, P.J. (2009). Morphology, phylogeny, and diversity of Trichonympha (Parabasalia: Hypermastigida) of the wood-feeding cockroach Cryptocercus punctulatus. J Eukaryot Microbiol 56(4), 305-313.

    Carpenter, K.J., Horak, A., Chow, L. & Keeling, P.J. (2011). Symbiosis, Morphology, and Phylogeny of Hoplonymphidae (Parabasalia) of the Wood-Feeding Roach Cryptocercus punctulatus. Journal of Eukaryotic Microbiology 58(5), 426-436.

    Carpenter, K.J., Horak, A. & Keeling, P.J. (2010). Phylogenetic position and morphology of spirotrichosomidae (parabasalia): new evidence from Leptospironympha of Cryptocercus punctulatus. Protist 161(1), 122-132.

    Carpenter, K.J. & Keeling, P.J. (2007). Morphology and phylogenetic position of Eucomonympha imla (Parabasalia: Hypermastigida). J Eukaryot Microbiol 54(4), 325-332.

    Carpenter, K.J., Waller, R.F. & Keeling, P.J. (2008). Surface morphology of Saccinobaculus (Oxymonadida): implications for character evolution and function in oxymonads. Protist 159(2), 209-221.

    Hongoh, Y., Sharma, V.K., Prakash, T., Noda, S., Taylor, T.D., Kudo, T., Sakaki, Y., Toyoda, A., Hattori, M. & Ohkuma, M. (2008a). Complete genome of the uncultured Termite Group 1 bacteria in a single host protist cell. Proc Natl Acad Sci U S A 105(14), 5555-5560.

    Hongoh, Y., Sharma, V.K., Prakash, T., Noda, S., Toh, H., Taylor, T.D., Kudo, T., Sakaki, Y., Toyoda, A., Hattori, M. & Ohkuma, M. (2008b). Genome of an endosymbiont coupling N2 fixation to cellulolysis within protist cells in termite gut. Science 322(5904), 1108-1109.

    Ohkuma, M. & Brune, A. (2011). Diversity, structure, and evolution of the termite gut microbial community. In Biology of Termites: A Modern Synthesis, Bignell, D. E., Roisin, Y. and Lo, N. (Eds.), pp. 413-438. London: Springer.

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

    ——–

    Amazing opportunity: California Science and Technology Policy Fellowship

    This is a great opportunity for anyone who wants to mix science and technology with policy: California Science and Technology Policy Fellowship.  This Fellowship is basically a modified version of the well known AAAS Fellowships.  But it is better because, well, it is in California.  The first PhD student to finish from my lab did this a few years ago and is now working at the White House.  More information about the program is available here: PROGRAM DESCRIPTION.

    To be eligible one must possess a PhD or equivalent degree or an MS in an engineering discipline plus at least three years post degree work experience.

    Instructions for applying are available here.  Some FAQs about eligibility and the program are here. 

    Previous Fellows are listed here:

    Applications are due Feb 28, 2013.
    ——–
    This is from the “Tree of Life Blog”
    of Jonathan Eisen, an evolutionary biologist and Open Access advocate
    at the University of California, Davis. For short updates, follow me on Twitter.

    ——–