Tuesday, August 31, 2010

Human microbiome project meeting (HMP2010) Day 1 wrap up w/ mea culpa

Well, Day 1 of the Human Microbiome Project meeting is over. And overall, I think it was quite good. So now for a Day 1 wrap up.

First, a bit about the meeting. The meeting is formally called the "Human Microbiome Research Conference" and more information about it can be found here. It is directly tied to the NIH "Human Microbiome Project", also known as the HMP, which has been in operation for a few years now. The HMP is one of a small number of NIH "Roadmap" initiatives (these are also known as NIH Common Fund Projects). These are cross cutting projects that are funded outside of the normal NIH departments/centers. The HMP started a few years ago and is focused on studies of the communities of microbes that live in and on humans. The HMP has so far funded a wide array of projects including some big scale and some smaller scale. This meeting is I think the first to try to cover the diversity of different projects funded by the HMP at once.

Day 1 covered a bit of introduction and then a diversity of HMP related and some not so related (but good) talks. The talks were perhaps a bit too reviewy for my liking, but I think actually, all of them were interesting. Some lessons I got from today include the following:

  1. The human microbiome is becoming a fascinating area of research with an ever growing set of data to look at
  2. The data for the HMP seems to be openly available, which is good. Reference genomes can be found here. Some rRNA data can be found here. Strains of microbes are available too. Not sure where the metagenome data.
  3. Ease of access and use of data is more important than just access to data; the HMP DACC is doing a decent job with helping access data.
  4. As important as access is metadata about samples. Not sure how much of this is available right now nor how easy the metadata is to make sense out of.
  5. As with most (all?) large scale, top down projects, there are multiple areas where improvements could be made in communication and engagement with the broader community. It seems like the HMP is working hard on this issue.
  6. There are some possible complicated issues around release of microbiome data and medical records from people
  7. There is still a big risk in overselling the potential benefits of microbiome research
  8. Correlations ≠ causation. Sorry I had to put that here. See #5 above.
  9. Analyzing and making sense of metagenomic data is still very very hard
  10. We desperately need more ecology driven studies of the microbiome
  11. To me, the HMP should really try to mimic the human genome project and focus on producing reference data (genomes, metagenomes, and rRNA) for everyone to use. Trying to do complex scientific/clinical studies in this project seems inappropriate. We all need the baseline to do the science.
  12. As with every meeting, the best stuff that happens is in between talks.
  13. Having the meeting room be something like 40 °C is probably not the best idea nor use of resources (hotel issue, not HMP issue).

Those are some of the lessons I am thinking about now, a few hours after the last talk. But if you want to get a "real time" feel for the talks, the best way to do this, if you weren't here, is to look at twitter posts about the meeting. If you do not know, the common practice these days is to use a code within twitter specific for the meeting called a hashtag. For this meeting the hashtag is #HMP2010 and you can find the tweets about the meeting easily by searching twitter for this code. There were other twitter posts about the meeting, but may be somewhat hard to find b/c they did not use this code. Such is life I suppose.

Anyway, if you want to see all the tweets from the first day of the meeting with this hash tag I have appended them at the bottom of this email. This includes anyone who may have reposted (aka retweeted) these tweets to their twitter feed.

As I have tweeted many meetings I guess I am used to various aspects of such activities but many out there clearly are not. Live tweeting a meeting is a rough thing in many ways, at least for me. I want to give people a feel for the meeting, as it happens. I want them to know what I actually think about talks, at least within some reasonable limits. But alas sometimes, hopefully not too often, I get things wrong. And sometimes I post something obnoxious. And sometimes I miss key points. To me, this is analogous to the conversations people have about talks all the time. Overall, I think mostly I do an OK job tweeting meetings. But occasionally I write something that does not sit right with others or myself. And alas, today has one such tweet (well, only one I know of right now).

It happened during Brice Birren's talk. Birren, from the Broad, was discussing a few different things including studies done by the Broad in which they have tried to compare and contrast and use rRNA PCR studies done at different centers associated with the HMP. Much of what he was discussing was technical details of the control experiments they did to assess how variable the results were between centers. I felt at the time that he was placing this work in enough of the context of other rRNA studies of the human microbiome. And I tweeted this feeling.
Birren presenting clustering of samples based on rRNA analysis - but could do much better referencing prior lit on this #HMP2010
Birren - given that they trust their PCR, now comparing many human samples - seems like they are way behind the field here #hmp2010
But in the end, after discussions at the bar later, I think I may have missed the point of his talk. I thought at the time that he was discussing solely new findings and new analysis tools that they developed. To me, I did not like that he did not spend much time discussing other analysis tools nor how their work compared to other studies of the human microbome. And that gnawed at me.

But in retrospect, I think perhaps he was focusing more specifically on the comparison across the centers. In that context, the way he laid out his talk and what other work he referenced makes more sense. I think perhaps he could have still placed things in a broader context but my comments in retrospect were a bit over the top and unnecessary. As I said above, I think it is useful to try and post what I am actually thinking at the time. I try to filter this if I know what I am thinking is rude, biased, obnoxious, etc; but I do post critiques if they seem relevant. But my filtering was a bit off here. Alas, now Bruce (if he reads twitter) probably wants to dump a beer on my head and people from Broad think I am a putz (well, some may have thought that before). I guess I may have to change the tuning on my filter a bit ... but I still will try and post what I think at the time. It is a fine balance I do not always do precisely ... off to sleep and in the AM - Day 2 plus time to make some in person apologies ...

Clarification to Overselling Microbiome Award to Marshall Protocol: Critique of some claims by supporters, not protocol per se

OK time for a bit of a clarification.

Recently I gave out a somewhat aggressive "Overselling the microbiome award" to supporters of what is called the Marshall Protocol. I have started this award because I feel that many working on microbiomes have been overselling the potential for these studies to lead to cures and treatments for all sorts of ailments. And certainly, some associated without the Marshall Protocol are making what I consider to be extremely overstated claims about this particular treatment.

But after talking to a supporter of the protocol here at the microbiome meeting I should clarify here that I was not actually critiquing the protocol itself. I was criticizing some of the claims of supporters of the protocol. In a way I erred in the same way that critiques of genomics have erred - where some have said genome sequencing is not useful because some promoters of genome sequencing oversell it. So I should have been more careful .. I should have focused on the claims about the protocol by some supporters. I stand by my criticism of many of these claims. The protocol seems to have no evidence that it works. And thus I did not like the claims that it cured all sorts of ailments.

But overselling the protocol by some supporters does not mean that the protocol does not work (though, again, there is no published evidence that it works). And overselling by some also does not mean that all supporters oversell it. It seems clearly that some of the supporters are sincerely interested in testing whether it works. In fact the person I talked to said they will work very hard to make sure that claims without evidence are removed from the Knowledge Base web site associated with the group supporting the protocol. I hope that is true. I am still skeptical about the activities of some supporters of the Marshall Protocol and whether the protocol can work. But at least some of the supporters really want to do clinical trials and use science to test the Protocol.

UPDATE 2019.  I was being WAY too nice with this post.  I was trying to engage the people behind the MP to help move them into doing real science.  And so I wrote this to give them a chance to shy away from some of the claims.  But in retrospect that was really just being too nice.  This was at least a the time, a scam. I have no idea if any evidence has been developed to support it since, but I sincerely doubt it.

Live from the Human Microbiome Meeting #HMP2010

For those interested, I and some others are posting live from the Human Microbiome Meeting in St. Louis

Perhaps the best place to find these posts is on Twitter using the hashtag #HMP2010 here

Will post a few more links here in a bit .. Listening to talks right now

Monday, August 30, 2010

Who owns UCDavis (& other University Names) in various Web Domains?

Well, this is awkward.  But apparently, some domain name registrars in China think I am the person to write to regarding UC Davis domain name issues.  Am I that high up in web searches somehow?  Perhaps I am if you do not use google, or maybe even if you do (I guess, perhaps most of the high hits to UC Davis are not people ... just web sites).  Anyway this is the email I just got:(If you are not the person who is in charge of this, please forward to the right person/ department, as this is urgent, thank you.) 

Dear CEO,
We are the department of registration service in China. we have something which needs to confirm with you. We formally received an application on  August 26h  2010. One company called "Napa International, Inc." is applying to register "ucdavis     " as Brand name and domain names as below:
After our initial checking, we found the Brand name and domain names being applied are as same as your company! So we need confirmation with your company. If the aforementioned company is your business partner or your subsidiary, please DO NOT reply us, we will approve the application automatically. If you don't have any relationship with this company, please contact us within 5 workdays. If over the deadline, we will approve the application  submitted by "Napa International, Inc " unconditionally.
Best Regards
Rensis Ho
Not sure if this is a scam of some sort or not so I figured I would post.  Anyone seen anything like this before?  If it is not a scam, does this mean they really think I am the CEO of some UC Davis brand?  

Another question is - if this is not a scam - can places register a domain name using someone else's trademark?  What is the protection for domain names outside the US?

Anyway - am forwarding this to people at UC Davis who I hope can answer the email ... but am wondering how much I can sell the UC Davis brand name for in various places ... could be a good fund raising opportunity

Saturday, August 28, 2010

Science Conference SPAM: ICEME2011 on all of engineering & metaengineering

Well this one really really takes the cake. I got an email today that I think I simply have to post the entire thing because of its awesomeness:
Dear J. Eisen: 
We invite you to submit a paper/abstract to The 2nd International Conference on Engineering and Meta-Engineering: ICEME 2011 (March 27th - 30th, 2011 - Orlando, Florida, USA): http://www.2011iiisconferences.org/ICEME. If you have any colleagues who might be interested in making a submission to the conference, please feel free to forward this e-mail to them. Below are the deadlines for ICEME 2011:
Papers/Abstracts Submission and Invited Session Proposals: September 22nd, 2010
Authors Notifications: November 22nd, 2010
Camera-ready, full papers: December 15th, 2010

Wednesday, August 25, 2010

Interesting take on peer review & openness from outside the sciences in @nytimes

I assume many supporters of open science may have seen this already but if not it is worth a look.  The New York Times had an interesting article on Monday by Patricia Cohen: For Scholars, Web Changes Sacred Rite of Peer Review.

The article starts off with a familiar refrain
For professors, publishing in elite journals is an unavoidable part of university life. The grueling process of subjecting work to the up-or-down judgment of credentialed scholarly peers has been a cornerstone of academic culture since at least the mid-20th century.
It follows with a very important discussion focusing on how the web can transform scholarly publishing.  For example:
... scholars have begun to challenge the monopoly that peer review has on admission to career-making journals and, as a consequence, to the charmed circle of tenured academe. They argue that in an era of digital media there is a better way to assess the quality of work. Instead of relying on a few experts selected by leading publications, they advocate using the Internet to expose scholarly thinking to the swift collective judgment of a much broader interested audience.
This likely will sound very familiar to those who have read my blog, those who follow the discussions on peer review, or those with a pulse in the scientific community.  But there is a catch that caught me off guard here and might surprise many of you.  This catch is highlighted by the fact that the article was in the Arts section of the Times.  You see, the article was about transformation in the humanities.  Seems as though there is an almost completely parallel universe there where peer review and publishing and sharing are all getting re-evaluated.

This is yet another case of why we need more cross talk between the arts/humanities and the sciences.  For example, the article discusses how the journal Shakespeare Quarterly is becoming the first humanities journal to "open its reviewing to the World Wide Web." They even recently conducted an experiment in fully open review where four preprints were posted on the web and feedback was solicited.  The feedback was then used by editors to guide the revision of the preprints to become published articles.  Sounds a lot like Biology Direct.  Note however, that they are not talking about publishing the final articles in an open access manner (see discussion of this on BigThink here) - but more about engaging the broader audience in commentary before an article is published.

The article does suggest that perhaps the humanities are lagging a bit behind the sciences in experimenting with new forms of peer review but I think that is OK.  We desperately need new experiments and ideas in this arena.  Peer review, at least the way it operates right now, has many problems.  I think there must be many better ways to go about things.  And thus cross pollination across fields from arts and humanities to economics to physics to life sciences is a good thing.

Interestingly Cohen identifies what she considers to be the most daunting obstacle to opening up review:
peer-review publishing is the path to a job and tenure, and no would-be professor wants to be the academic canary in the coal mine.
I think this is the same main obstacle in the sciences.  That is, it is our system of promotion and tenure and hiring that is the main roadblock.

Finally, I note that though the article was focusing mostly on opening up peer review, it does have some interesting bits on openness in general. In particular, there is a great line at the end from Dan Cohen from George Mason
“There is an ethical imperative to share information,” said Mr. Cohen, who regularly posts his work online, where he said thousands read it. Engaging people in different disciplines and from outside academia has made his scholarship better, he said.
I could not agree more.  Seems like the arts and humanities and sciences actually have much much more in common that many might think.

For some related posts from the web see

Some recent web stuff on peer review in the sciences

New Stem Cell ruling trickle down effects: changes in NIH grant review/submission

Just got this email from UC Davis administration that I thought might be of interest

Dear UCD Research Community:
Pursuant to a court order issued on August 23, 2010, NIH is not accepting submissions of information about human embryonic stem cell lines for NIH review.
If you are currently preparing a proposal to NIH that includes stem cell research and NIH has not pulled the RFP, please continue preparing your proposal and Sponsored Programs will submit to Grants.gov.
Per the Council on Governmental Relations (COGR):
In a press briefing today August 24, 2010,  Francis Collins, Director of NIH, described the impact of the preliminary injunction prohibiting NIH from funding embryonic stem cell research under the NIH Guidelines on current and pending grants.    A NIH Guide notice will be issued shortly containing greater detail. 
In short, NIH consulted with the Department of Justice to make the following determination:
·                    Current grantees – those who have received their award already – may continue with their research;
·                    NIH will freeze the funds for the current grants due for annual renewal (non-competing renewals) by September 30, 2010;
·                    Grants in the review process – initial peer review or recommended for consideration by the advisory council – will be pulled from further consideration at this time.
We expect to receive additional information shortly, which we will share when received.

Overselling the microbiome award #2: The Marshall Protocol

Wow - until I started sniffing around actively, I never realized how much crap was out there in regard to the microbiome.  But there is so so much.  Certainly, the human microbiome (the microbes that live in and on people) is more important than people used to think.  The microbes in and on us show some interesting correlations relative to disease and health states.  And almost certainly changes in the microbiome likely cause some alterations in health state.  Recent studies on fecal transplants, for example, suggest even that altering the microbiome is both possible and could be helpful in some cases.  But we are really early in the work here.

But right now, for many health and disease states
(1) we don't know if the altered microbiome is a cause or an effect or not related at all and
(2) even if there were a causal relationship between microbes and various health/disease states, there will also be enormous complexities relating to history and genes that will be very hard to sort out
(3) even if we knew a causal relationship this would not mean we would know how to change the trajectory (e.g., what microbes are there) in a useful way

Because there is so much iffy stuff out there relating to the microbiome and because some are starting to use studies of the microbiome to indirectly lend credence to their crap, I have decided to start giving out an "Overselling the microbiome award". I gave out the first one a few days ago: Overselling the microbiome award: Stephen Barrie on pre and probiotics at the Huffington Post

Interesting, Barrie posted a comment on the blog trying to defend his post, but I was not convinced.  I think he did not understand my point about correlation vs. causation but am not sure.

Anyway, after I wrote the response to Barrie I looked around the web for others using the term microbiome in what seemed to be unsavory ways.  And I found a really painful one.  This is something called the "Marshall Protocol Knowledge Base."  This so called knowledge base is a web site set up to promote, you guessed it, the Marshall Protocol.  The Marshall Protocol is "a curative medical treatment for chronic inflammatory disease."  In turn this protocol is based on the Marshall Pathogenesis which is "A description for how chronic inflammatory diseases originate and develop."  It follows that this Marshall Pathogenesis "posits that chronic diseases (termed Th1 illnesses), are the result of infection by an intraphagocytic, metagenomic microbiota of chronic bacterial forms that are often referred to as the Th1 pathogens."  I have read the last sentence dozens of times and I still do not know what it means.  What is a metagenomic microbiota?  I just do not know.

Anyway, I am sure everyone will be shocked to find out that the Marshall Protocol Knowledge Base, the Marshall Protocol and the Marshall Parthogenesis are being promoted by someone named, well, Marshall (Trevor Marshall) who seems to be the head of the Autoimmunity Research Foundation which is the place promoting the Marshall Ps (I swear, I will not call it the Marshall Plan, I will not, I will not).

Based upon what appears to be little if any actual published research, the Marshall Protocol promotes the treatment of all sorts of ailments with in essence long term

high dose
cocktail of multiple antibiotics at apparently low dosage and a long term attempt to alter Vitamin D levels by treating in part with very high doses of a drug called olmesartan.  Among the ailments that this protocol is claimed to help are Crohn's, Type I diabetes, Multiple Sclerosis, Psoriasis, Rheumatoid Arthritis, Celiac Disease, and many many more.  (I note they say "The Phase II clinical trial conducted from 2002-2008 by the Autoimmunity Research Foundation has demonstrated applicability of this antibacterial therapy to a wide range of chronic Th1 immune illnesses " and then cite a powerpoint presentation).

I could go on and on.  But it seems clear to me that they are both making mistaken claims about what we know about the effect of microbes on health as well as making almost absurd claims about how one treatment system can cure a series of diseases by fixing ones microbial content.  Note I am NOT saying microbes have no connection to these ailments - studies are supporting the microbial diversity in people with these ailments is different than in people w/o the ailments.  Nor am I saying that Vitamin D is unimportant.  In fact, it is becoming clear that Vitamin D is much MORE important than people realized.  But importance alas, is different that saying we know exactly WTF is going on.  And certainly the treatment outlined by the MP folks here is not as far as I can tell supported by any evidence of effectiveness not is it obvious how it connects to scientific knowledge about microbes and vitamin D.

Fortunately, others have taken on the MP folks here and have written about how it appears to be a scam of sorts, and a potentially dangerous one at that.  See for example:
I know, there are lots of medical scams out there.  But this is the first one I have seen discussing metagenomics and the microbiome. And for that, I am giving the Marshall Protocol and the folks behind it, my second "Overselling the microbiome award".

UPDATE 7/18/2012 - some stories worth looking at

UPDATE November 2019. 
  • See Buyer Beware: “Miracle Cures” for Sarcoidosis - see last sentence below in particular.
    • "Trevor Marshall came up with a treatment for chronic inflammatory diseases like sarcoidosis that consists of five seemingly simple steps. The first of these steps is to take a minimum of 40mg of olmesartan every 4-6 hours, which is a very high dosage. Olmesartan is not a drug that is commonly administered to treat sarcoidosis – in fact, it is used to treat high blood pressure, which is not one of the more prominent symptoms in sarcoidosis. Marshall protocol also requires limiting one’s Vitamin D intake, which means avoiding foods that are rich in Vitamin D as well as sun exposure. Vitamin D irregularity is common in sarcoidosis, but it is certainly not the root of the problem. However, Marshall Protocol bases its treatment on the belief that sarcoidosis is caused by an excess of Vitamin D paired with infection. We do not know what exactly causes sarcoidosis, but we do know that it is characterized by the formation of granulomas, not infection or Vitamin D irregularities. Focusing solely on these symptoms in treatment of sarcoidosis is missing the mark. Marshall Protocol is an expensive treatment, and there is no real evidence on its efficacy and we cannot be sure that it is harmless."
  • And also see Disciplinary Action against  Susan J. Shlifer, M.D.
    • "USE OF HIGH RISK AND INEFFICACIOUS MARSHALL PROTOCOL 2.11 The "Marshall Protocol" implemented by Respondent in her treatment of patients is not supported by placebo controlled clinical trials or animal experiments. Developed by a non-physician, this protocol is contrary to the standard of care for treatment of anti-inflammatory and autoimmune diseases in the following aspects."

Tuesday, August 24, 2010

When Universities Grow in the Wrong Places

A bit of a rambling post here but here goes anyway ...

Well, normally I have avoided digging in to UC Davis too much here on my blog.  Mostly because it does not really fit with the themes of evolution, open access, microbiology, genomics, etc.  Plus, overall, I really really like Davis and UC Davis.  The town is very pleasant - simple - but very nice.  I lived on my bike in the Washington DC area, taking my life into my own hands, and now living in bike town USA is great.  In fact, I even have a blog about life in Davis.  And UC Davis is overall a great place to be for me, especially with its strengths in evolution and ecology, population biology, and various aspects of microbiology.

But alas, now all is perfect here in blissville. And one thing that drives me crazy is the mind numbing complexity of the bureaucracy.  I note, I moved to Davis from The Institute for Genomic Research (TIGR), a small non profit research institute that helped lead the genomics revolution.  And mostly I have suffered annoyances of the crazy giant complex system here in silence (except for with a few colleagues here and there).  However, I have been planning to start to discuss some of these issues in public more.  And just as I was thinking about this, it seems that others are also discussing some issues with the need to reform some UC Davis admin activities.

You see, last year we got a new Chancellor (the name they use here for the head of the University).  The new Chancellor is Linda Katehi.  I have met her a few times and overall I am very impressed.  Perhaps the thing that impresses me most is that in times of somewhat bad financial struggles she has decided to take on the bloat in the administrative side of things as one of her first activities.  And it seems this is not all talk.  For example our great local newspaper, the Davis Enterprise has been running a series of articles, most by Cory Golden, on some reports and announcements from UC Davis suggesting that Katehi really will be trying to change things around here.  Alas, the Davis Enterprise is not available for free on the web for all to read.  If you want to get some really insightful stories about UC and UC Davis, you should subscribe.  It is not much and if you have any connection to Davis it is worth the money.

Fortunately for me, and perhaps for you, the Davis Enterprise has agreed to let me post extensive quotes from their articles especially as they relate to UC Davis.  I will delay a bit in posting to try and respect their need for subscribers (unlike with scientific publications, which should all be open and freely available, I do not feel that way about private enterprises like newspapers).  Anyway - I am posting below two stories by Cory Golden of relevance to the UC Davis attempts to change the way things are done here.  One is about reorganization of some administrative functions.  And one is about an outside evaluating group that just wrote a report on some of the challenges for research at UC Davis.  A third is about a campus "vision" statement put out by Katehi.

The main gist is, that UC Davis has enormous potential that is being impeded by some bureaucratic complexities and inefficiencies.  Some good quotes include:
Those included “overstaffing, ineffective personnel and playing 'lawyer games' to be sure that no risks threaten the organization.”
“Over many decades Davis has developed a culture that permeates its institutions and people, one that can best be described as risk-averse, modest and insular.”
And Katehi seems like she is going to try and fix many of them.  No - the plans are not exactly what I would do.  But more on that later.  The direction things are moving is very appealing to me.  I was not inspired by the previous leadership of UC Davis.  I am much more hopeful now and am awaiting these changes very impatiently.

Anyway - thanks to the Davis Enterprise for allowing me to post here.  And please consider subscribing to the paper.  That way you will get stories as they come out ...

Bad omics word of the day: waveomics

Let's just cut to the chase.  The Bad Omics Word of the Day is Waveomics.  Suggested to me by SeaSaver.

On the one hand, I really like that people in biology related fields are putting out preprints in places like Nature Precedings.  On the other hand, this one is a bit painful from the omics terminology point of view: Waveomics: bringing experimental data to online collaboration : Nature Precedings

Well, the term is really just, well, awful.  Here is a key phrase about it:
A Robot is introduced here, waveomics, which provides the first example of allowing experimental data from multiple sources to be queried and shared in the Google Wave environment.
The concept is not so bad in principle - the author Neil Swainston (who has done some cool things - check out his blog and his slideshare presentations and his Academia.Edu page for some detail) was trying to design tools for streaming genomics data in Google Wave.  So this is not a critique of Neil or his work, just of the word waveomics.

Thankfully, in many ways, Google Wave is going extinct.  I guess we should wave good bye to waveomics too. 

Monday, August 23, 2010

Twisted Tree of Life Award: NPR on the Evolution of Crying

Well, normally I really like NPR science stories. But this one dug into my anti adaptationism feelings. Adaptationism is, in essence, the practice of saying something must be adaptive (i.e., beneficial), simply because it is there in an organism. Such cases are also referred to as "just so stories" - a play on the old Kipling "Just So Stories".  That is, in essence, people who claim something is adaptive just because it is there are in essence telling you something is this way because it is just so.   I am actually not sure of the whole history of using the just-so analogy to refer to adaptationist stories - I know Stephen Jay Gould discussed this a lot in his books and lectures, but not sure who first did it. 

Anyway - NPR has an adaptationistic doozy from Morning Edition: 
Teary-Eyed Evolution: Crying Serves A Purpose : NPR

Basically, it seems the gist of the argument here is the following line:
Scientists who study evolution say crying probably conferred some benefit and did something to advance our species — because it's stayed with us.
Wow - that is like straight out of the adaptationist playbook.  The problem with this argument is that many things exist and persist in organisms even when they are not adaptive.  There are many reasons why this can happen from constraints (e.g., if bones were not adaptive in humans it would be pretty hard to get rid of them) to  invisibility to selection (e.g., some features that only show up after reproductive age may not really influence fitness) and so on.

In essence the NPR story is one of the worst examples of adaptationism in the good science press I have seen in a while.  Sure this shows up all over the place.  But rarely this bad at NPR.  The story ends with an even worse line than the rest
Maybe that's another reason evolution kept humans weeping: Tears help reveal the truth. And that's because along with the tears, we've evolved a very sophisticated ability to interpret them.
Yes that is right.  Crying has been maintained in humans because we also evolved another adaptive feature - the ability to interpret tears.  So the logic here is that crying is adaptive because it is needed for another adaptive trait for which there is no evidence it is adaptive.

So for their story on crying and for in essence inventing some just so stories to explain why they think it is adaptive, NPR is the recipient of my Twisted Tree of Life Award.  Previous recipients are

See also these things for some stuff on evolution of crying:

Saturday, August 21, 2010

More (you know you wanted it) on fecal transplants and the microbiome

Image from
I Heart Guts blog
There is an interesting mini review in the Journal of Clinical Gastroenterology's September issue that may be of interest to some out there. It is entitled "Fecal Bacteriotherapy, Fecal Transplant, and the Microbiome" by Martin Floch and well, the title is indicative of the article.

Yes, the fecal transplant meme is here to stay. Sure, the cognoscenti already knew about fecal transplants. Perhaps they had read Tara Smith's discussion of it in her Aetiology blog in 2007. Perhaps they had pondered it when they read the article from my lab on intestinal transplants. Perhaps they had seenthis discussion on MSNBC, or various other stories out there such asthis or this post from Angry by Choice. Or, maybe you just learned about it from Bora's Carnival of Poop.

But the meme on fecal transplants really spread and many may have first heard about fecal transplants from Carl Zimmer's New York Times article a month or so ago "How microbes defend and define us"

In the article Zimmer discussed how Dr. Alexander Khoruts used a fecal transplant to treat a woman with a persistent and severe Clostridium infection. And Zimmer discusses how, thought such transplants had been done before, this was the first time that the microbial community was carefully surveyed before and after. (Note, my favorite part of the article is this part, where my friend Janet Jansson describes her reaction:
Two weeks after the transplant, the scientists analyzed the microbes again. Her husband’s microbes had taken over. “That community was able to function and cure her disease in a matter of days,” said Janet Jansson, a microbial ecologist at Lawrence Berkeley National Laboratory and a co-author of the paper. “I didn’t expect it to work. The project blew me away.”
Anyway Zimmer's article, as with many of his, garnered a lot of response and got many people discussing the poop on fecal transplants.

Well, this issue of the Journal of Clinical Gastroenterology may now be the biggest pile of information about fecal transplants around. That is because, in addition to this little review mentioned above, there are in fact three articles in this issue relating to fecal transplant. Alas, most of you out there will probably only be able to read the review since the other articles are behind a pay wall.

But the review is good. And I think this is not the last you will hear about this. (Though I note that, even though I think fecal transplants have some major potential, they seem to be being oversold a bit by many as some cure all -- fodder for a future "Overselling the Microbiome Award" I am sure).

I will end with this line from the review which raises some other issues about fecal transplants:
Probably one of the major problems is to define how this therapy can become socially accepted. (Can you imagine the Food & Drug Administration discussion?)
Floch, M. (2010). Fecal Bacteriotherapy, Fecal Transplant, and the Microbiome Journal of Clinical Gastroenterology, 44 (8), 529-530 DOI: 10.1097/MCG.0b013e3181e1d6e2

Grehan, M., Borody, T., Leis, S., Campbell, J., Mitchell, H., & Wettstein, A. (2010). Durable Alteration of the Colonic Microbiota by the Administration of Donor Fecal Flora Journal of Clinical Gastroenterology, 44 (8), 551-561 DOI: 10.1097/MCG.0b013e3181e5d06b

Khoruts, A., Dicksved, J., Jansson, J., & Sadowsky, M. (2009). Changes in the Composition of the Human Fecal Microbiome After Bacteriotherapy for Recurrent Clostridium Difficile-associated Diarrhea Journal of Clinical Gastroenterology DOI: 10.1097/MCG.0b013e3181c87e02

Yoon, S., & Brandt, L. (2010). Treatment of Refractory/Recurrent C. difficile-associated Disease by Donated Stool Transplanted Via Colonoscopy Journal of Clinical Gastroenterology, 44 (8), 562-566 DOI: 10.1097/MCG.0b013e3181dac035

Wednesday, August 18, 2010

Overselling the microbiome award: Stephen Barrie on pre and probiotics at the Huffington Post

Yes, I think the microbes that live in and on people are important, interesting, cool, and worthy of lots and lots of attention. However, I am getting sicker and sicker of the ways in which the effects of these microbes are, well oversold. So today I am starting a new series here on the Tree of Life - the "Overselling the Microbiome and Probiotics Award."

And, we have a winner today. The winner is Stephen Barrie who has posted something at the paragon of high quality science - the Huffington Post (for more on the dubious science at Huffington Post, a good place to look is Bora's Blog Around the Clock). Well, Barrie really takes the cake on this one

Stephen Barrie, ND: The Keys to Maintaining a Healthy Gut

He starts off OK - referring to the number of microbes in the human ecosystem and even quoting Jeroen Raes, who does some great work.

Then he mentions how
"These bacteria have a profound influence on human physiology, your immune system, your nutrition, and are crucial for human life."
OK I can go with this -- maybe an exaggeration but still within reasonable confines. Then the woppers begin
"The health of your body and mind is largely tied to the health of your gut".
Wow- that is one serious jump - from these microbes have a profound influence to the gut driving health of body and MIND.

Then he goes back to some OK territory again, discussing some functions known for gut microbes, like vitamin production, preventing infection, etc. But just after this he switches to the woppers again claiming that out of balance microbes can cause allergies, inflammatory bowel disease, eczema, arthritis, irritable bowel disease, obesity, autism and personality changes including paranoia, hostility, aggression and so on. Completely ludicrous actually. What we know about these issues is that researchers have found that microbial populations may be altered in people with these maladies. But that does not mean the alteration in the microbes caused these maladies. It could be that other factors cause both the malady and the microbial alteration or the malady itself could lead to altered microbial populations.

But wait, it gets a bit better. Now that he has established that microbes cause all these problems, he tells us how to
"avoid one of the emerging causes of both obesity and food allergies? Lower your risk of inflammatory bowel disease, irritable bowel disease, eczema, colon cancer (15) strengthen your immune system? All this while reducing any levels of paranoia or hostility (and retaining your Jon Stewart sense of humor)."
The recipe for prevention is as follows:
  • Eat a low fat diet rich in vegetables, fruits and complex carbohydrates
  • Limit consumption of animal protein
  • Reduce sugar consumption
  • Increase pre-biotic and probiotic intake
  • Consume enough soluble and insoluble fiber to maintain a daily bowel movement. A slow bowel transit time leads to increased exposure of your body to toxic bowel contents.
  • Reduce dietary sulfate consumption.
Again, I am all for more research into the microbiome.  And I think microbes that live with us must have all sorts of positive and negative effects on our health.  And yes, I understand why "probiotics" and "prebiotics" are getting lots of hype.  But because Barrie has gone from what must be a gut feeling (sorry) to making medical claims without evidence and prescribing treatments to cure ailments that probably don't exist, he is the recipient of my first "Overselling the microbiome award".

Thursday, August 12, 2010

If a picture=1000 words, what is sound worth? #burrowingowls

Well, my brother Matt is visiting and he has in one fell swoop opened my ears to a whole new world.  We went for a walk on this trail near my house in Davis, CA where a massive number of burrowing owls live.  I have spent the last few months, on and off, trying to take some good pictures of these amazing owls.  Here is a slideshow of some of my favorites.

Anyway, while going on this walk, Matt brought an extensive collection of giant strange looking sound equipment.

 You see, he is a sound engineer in his spare time and this is, well, what he does. And when we found some owls he told us to mosey on down the trail so he could record. And here are some of his recordings - completely changing my view of these owls.

Burrowing Owls by mattglenn

He has more detail about this on this blog.

Tuesday, August 10, 2010

Bad omics word of the day: adversomics h/t @jennifergardy @mentalindigest

Well, I guess the bad omics blogger in me is back. The bad omics word of the day today is adversomics. First pointed out to me by Jim C at from MentalIndigestion and now reintroduced to me by Jennifer Gardy.

This one is so awful I had to write it up. The first I know of it is here in an article by Gregory Poland et al. entitled "Adversomics: The Emerging Field of Vaccine Adverse Event Immunogenetics". And now in a new article by the same authors: Application of pharmacogenomics to vaccines where they say
Another area of importance is genetically determined vaccine-associated adverse events, which we have called ‘adversomics'
I note this is the same group that brought us a previous bad omics word of the day winner in "vaccinomics". So they are double winners. Hooray for them.

Quick blog post: interesting piece on the evolution of ecology by Simon Levin

There is a very interesting piece in the Chronicle of Higher Education by Simon Levin on the "Evolution of Ecology."

See The Evolution of Ecology - The Chronicle Review - The Chronicle of Higher Education

In it Simon, who I consider both a friend and colleague and who has been an inspiration to me for much of my work, discusses the history of the concept and the field of ecology. He repeats a key phrase he has used elsewhere:
Ecology, the unifying science in integrating knowledge of life on our planet, has become the essential science in learning how to preserve it.
I like this phrase and plan to use it a bit here and there, with attribution of course.

Levin also discusses how Darwin's Voyage of the Beagle helped launch the field of ecology because it
defined a new and synthetic way of looking at nature—in which the patterns characteristic of particular regions found explanation in a unifying, dynamic framework
It was only after Voyage of the Beagle and Wallace's work and others that the term "oekologie" came into being.

I particularly like the end where he connects ecology to study of other complex adaptive systems like economic ones and medical ones.

The article is really really really worth a read.

Monday, August 09, 2010

Lack of neutrality in bacteria and where pseudogenes go when they die


Pseudogenes, which are in essence regions of the genome that used to be genes but no longer able to produce a functional unit, have long been considered to be models of the genetic equivalent of Switzerland's neutrality. With this assumption of neutrality in hand, researchers have used studies of pseudogenes to better understand what happens to DNA when it is not visible to any form of natural selection. That is, pseudogenes have been thought to be neither harmful (as in, they are not under negative selection) or helpful (i.e., they are not under positive selection).

And from this assumption we have supposedly learned about mutation rates and patterns (because if they are neutral then the changes in pseudogenes should be reflective of mutational processes, not selection) as well as all sorts of other features of genome evolution.

Over the years, some have challenged the assumption of neutrality of pseudogenes (e.g., see here) like many have questioned whether Switzerland is really neutral. But overall, the feeling that pseudogenes were mostly neutral seems to have stuck. However, that may change a bit with a new paper from Chih-Horng Chu and Howard Ochman in PLoS Genetics (PLoS Genetics: The Extinction Dynamics of Bacterial Pseudogenes).

In their paper they report: (this is their authors summary)
Pseudogenes have traditionally been viewed as evolving in a strictly neutral manner. In bacteria, however, pseudogenes are deleted rapidly from genomes, suggesting that their presence is somehow deleterious. The distribution of pseudogenes among sequenced strains of Salmonella indicates that removal of many of these apparently functionless regions is attributable to their deleterious effects in cell fitness, suggesting that a sizeable fraction of pseudogenes are under selection.
Basically, what they did was the following

1. Compare Salmonella genomes. Identify putative pseudogenes and trace their evolution onto a phylogeny of the species.

Figure 1. Distribution of pseudogenes among Salmonellagenomes.
The phylogenetic tree was inferred from 2,898 single-copy genes shared by all fiveS. enterica subsp. enterica strains and the outgroup S. enterica subsp. arizonae.

2. Carry out a variety of analyses of the pseudogenes such as
  • looking at ratios of Ka/Ks (this is in essence a ratio of amino acid changes - aka non synonymous substitutions to "silent" synonymous changes which occur when the DNA sequence changes but the same amino acid is encoded).
  • examining the types and frequencies of gene inactivating mutations
3. Then they looked at the "ages" of pseudogenes - with age being estimated by the position in the tree in which the pseudogenes appear to have arise.

4. Finally the examined the age class distribution of pseudogenes as well as whether there were other differences between pseudogenes of different ages. And what they found was inconsistent with a neutral model. Instead, what they conclude is that something is making it advantageous to delete pseudogenes more rapidly than one might expect.

What explains this? After testing multiple possibilities the authors conclude that their is some negative selection against pseudogenes (or I guess positive selection for deletion of pseudogenes).

They conclude by suggesting this is likely to be pervasive across all bacteria and even in archaea. And furthermore make a connection to possible selection on intron size in eukaryotes. Anyway - the paper seems quite interesting and worth a read. Still pondering what it all means, so I would welcome comments.

Kuo, C., & Ochman, H. (2010). The Extinction Dynamics of Bacterial Pseudogenes PLoS Genetics, 6 (8) DOI: 10.1371/journal.pgen.1001050

Friday, August 06, 2010

Starting to like Academia.Edu, except for annoying emails re: who is searching for me

Well, I am continuing to play around with Academia.Edu. I created a profile there for myself and am also building one for my father Howard Eisen as part of my campaign to "Free my father's publications." Academia.Edu has some nice features. I think I still like Mendeley more, but am reserving judgement.

That being said, the default setting at Academia.Edu for email updates is really annoying --- I keep getting messages like

Hi Jonathan,

Someone just searched for you on Google, and found your page on Academia.edu.

To see the search query they used, what rank you are on Google for this query, and what country the search came from, follow the link below

Link removed by me


The Academia.edu team


To ensure that your Academia.edu page appears high up on Google, link to it from the website of your department, college, university or blog. 88% of people on Academia.edu who link to their page like this appear #1 on Google for searches for their name + university, e.g. 'Richard Price Oxford'.

First of all, getting emails like this should be Opt In not Opt Out. Second, I find this to be a bit too earnest an attempt to manipulate google rankings to help out Academia.Edu. (I note, while creating this post, I did a search for myself and Academia.Edu and got the links above and then I got an email again, telling me someone searched for me. I know. It was me. I mean, I guess link trading is a real thing, but telling me to add a link do that my Academia.Edu profile might move up in searches is I guess annoying to me.

Anyway - still playing with Academia.Edu. Still liking much of it. But if you search for me on the web and go to Academia.Edu I am sorry but I will not know as I will be disabling email messages from them.

Ooh - Science Quiz Show for the Explorit Museum in #DavisCA #ScienceIsFun

Quick link here --- for those in the Davis area interested in science in any way you might want to check out the upcoming Explorit quiz / game show/ challenge. October 7 2010 at Freeborn Hall.

Tuesday, August 03, 2010

Human genome project oversold? sure but lets not undersell basic science

Well, the piling on the human genome project continues, it seems at an accelerating pace.  I think most of this comes from the fact that we are in the range of the 10 year anniversary right now.   Here are some examples of recent stories suggesting the human genome project (or projects, if you count the public effort and Craig Venter's effort as separate) have had little benefit:
These are but a small sampling of the many many blogs, articles, and other reports that either directly state or suggest that much of the money spent on the human genome project was a waste.

Certainly, contrary to the suggestion of some of these articles, there have been some practical benefits that have come directly or indirectly from human genome sequencing.  But equally certainly, these critiques have a segment of truth to them in that the practical benefits have been few and far between.

Normally, one would not expect too many direct practical benefit to come from this kind of science project.  But alas, the problem here is that many of the key players (e.g., Eric Lander, Francis Collins, Craig Venter) in the sequencing of the human genome(s) oversold the potential benefits that could come from the sequencing.  In a way, it was their job to oversell the sequencing, since each was a cheerleader in ways for getting others to do a lot of work.

Many people knew at the time that this overselling was going on.  It was talked about extensively at various genome conferences and even occasionally in the press and scientific literature (boy do I wish I had had a blog then, because I was one of those people at conferences practically begging people to not oversell the benefits of the project - I now even give out an "overselling genomics award" on my blog ).  The cautionary voices were mainly saying that there was no need to oversell the project and that we should stick to the benefits of "knowing" ourselves and not guess about how it will lead to immediate cures for diseases.  And many said "If you oversell this now, it will come back to bite you"

And thus it is not surprising to me that there is somewhat of a backlash now.  But there is a very dark side to the backlash that has potential to hurt science for many years to come.  If there is a need in the future for large scale science / medical projects, I can guarantee that some critics will step up and say things like "Well the war on cancer failed.  And the human genome project failed.  Why should we trust you now?"

The problem here is that the human genome project should never have been sold as a means to a series of practical ends.  It should have been sold as a massive basic science project, much like going to the moon or building a giant linear accelerator.  That is, the human genome project was, and still really is, about knowledge.  It is about knowing ourselves.  It has enormous potential benefits in all sorts of areas, like human medicine.  It should greatly aid and abet studies of human biology and genetics and disease.  But given that benefits that come from such studies are impossible to predict, the human genome project should have been presented in a different way.  We need to discuss more in public why basic science is important even if one cannot predict what the benefits are.

In many ways, this is very much like the "war on cancer" which some have argued failed because we still have cancer killing a lot of people.  But this is off base because in fact the war on cancer has provided us with an incredible baseline of information about the biology of cancer.  We need to do a better job in all of these cases of defending the need for knowledge, and discussing how fighting cancer and curing diseases is not the same as building a big bridge or road.

The best person discussing this issue for the last ten or so years in my opinion has been Harold Varmus, who was once the head of NIH and is now the new director of the National Cancer Institute.  I have heard him repeatedly defending the "war on cancer" in terms of its basic science benefits.  For example see his comments on Science Friday 1/30/2009 and 7/16/2010.  There just have not been too many people doing a good job of this with genomics.  Venter and Collins have been OK here and there.  But we need more.

On a related note, we probably should have more discussion about how the money spent on the genome project and the war on cancer pales in comparison to money we spend on other things (e.g., interest on the national dept, wars, etc) but perhaps that is a side discussion.

Most importantly, we need to bring out to the public more of a discussion of the benefits from basic science. Here are some useful resources if you want to try and help:

I also encourage people to look at the National Academy of Sciences report A New Biology for the 21st Century: Ensuring the United States Leads the Coming Biology Revolution.  I note, I was one of the coauthors.  You can download the PDF of the whole document after giving your email address.
I am going to start a new series here on this blog called "Benefits of basic science" where I will be discussing these issues.  I encourage others out there to also bring more to the forefront discussions of the need for basic science.


Also see

Monday, August 02, 2010

Twisted tree of life award #6: Scientific American Origins piece for dissing microbes

There is an interesting series of mini articles in the August 2010 Scientific American tracing the origins of various concepts and things: Origins: Going Back to Where the Story Really Starts: Scientific American

Not open access mind you, but if you have a subscription it is worth checking out. They track the origins of the following:

  • swiss cheese
  • paternal child care
  • computer viruses
  • animation
  • sexual reproduction
  • malaria
  • fireworks
  • barbed wire
  • hand washing in hospitals
  • human morality
  • electric cars
  • the influenza virus
  • wheeled vehicles
  • black holes
  • zero
  • biodiversity
  • noodles
Many of the discussions are interesting.  Some are a bit trite.  But that is not what I am here to report on.  I am here to complain about one aspects of the article series: too much emphasis on humans and multicellular organisms as "higher" creatures.  There are various subtle phrases here and there that I did not like too much but the parts that really grate on me are the two below:
  • In the article on biodiversity Melinda Moyer discusses the remarkable possibility that single celled creatures might have in fact had some diversity in them "Today we think of biodiversity in terms of multicellular life, but flowering plants and animals didn't arrive until relatively recently" she writes.  And ends with "It is no comfort to know that the worst catastrophe would still preserve some biodiversity -- even if only for the lowly cell."
  • In the mini article on sex, Brendan Borrell writes "The truth is, nobody really knows why people -- and other animals, plants and fungi -- prefer sex to, say, budding."  This of course leaves out all the other eukaryotes that are not plants, animals and fungi that have sex.  
And though these are certainly subtle small issues, I feel that Scientific American should do better.  So for directly and indirectly dissing the microbes on the planet - I am giving them my coveted Twisted Tree of Life Award #6.  Previous winners are listed below:

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