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 …

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Reorganization ramps up at UCD

By Cory Golden

August 18th, 2010

Enterprise staff writer

UC Davis leaders have OK’d in spirit a plan to cut up to $16 million in staff positions while rolling campus information technology, human resources and finance offices into a single shared services center.

An all-staff forum about the reorganization is set for Thursday at 10:30 a.m. in the UCD Conference Center Ballroom.

Chancellor Linda Katehi said last week that her goals for the effort, dubbed the “Organizational Excellence Initiative,” are to redirect money to academics, student services and other priorities while improving the service given to the campus.

For now, staff members are left with questions and union leaders have growing concerns.

Among them: how many jobs will be eliminated, how positions in the proposed new center willbe filled, how fast UCD will make the changes and how much money the campus will invest in technology intended to increase efficiency.

Some answers may come from a meeting of the chancellor’s cabinet Aug. 31.

At its last two-hour meeting, last week, the cabinet decided to move forward on the outlines of recommendations made by the Atlanta-based consulting firm ScottMadden, based on more than three months of on-site assessment.

About 6,500 finance, HR and IT employees would be affected by the first phase of the project, as drawn up by the consultant.

“On the amount of savings projected, what percentage of that is from staff positions?” asked a woman in the audience during a presentation Monday to employees of administrative units that would be part of the proposed center.

Answered Karen Hull, associate vice chancellor for human resources, “Those savings reflect staff positions.”

Just how many would be cut, she said she didn’t know.

“We don’t know that for a couple of reasons,” Hull said. “One is that we don’t know for sure whether the cabinet will support the recommendation that ScottMadden has made, so that’s one big variable.

“(It) would be very misleading to connect the (estimated savings) to actual positions,” she added. “There’s a lot of dynamic changes that occur. We have natural attrition every year. We have natural turnover. We have retirements. We will not be wanting to fill any of those positions while we are forming the shared service center.

“I know that it sounds alarming — and it is alarming. These are your jobs, but I think that when we get the picture painted in a more detailed manner it will be more clear as to what will be the potential job loss.”

The consultant found that, at a core cost of $54 million a year, the campus’ human resources, information technology and finance staffing exceeded those of similarly sized organizations.

Among its recommendations: creating a shared structure with one director, improving the use of technology for timekeeping, purchasing, accounting and other tasks, and simplifying policies and processes.

The report pegged one-time or recurring costs, much of it from computer software systems, at about $19.5 million. If UCD follows its suggested timeline, the report says the university should begin saving money in less than three years.

Under the proposed model, about 80 percent of faculty, staff and student questions would be handled through self-service, either through a web portal or interactive phone system.

In what’s likely to be a controversial recommendation, the consultant suggests that the campus create job descriptions for the shared services center, then have employees apply for those positions.

“They recommend kind of an open slate. Everyone has an opportunity, and you compete for those jobs,” Hull explained, adding that the administration may yet choose another way to staff the center.

Among existing problems the consultant’s report pinpointed: large amounts of the same or similar work being done by multiple departments, excessive reviews, delayed service and multiple IT help desks. It also found “manual data collection, transcription of data, high error rates and significant rework.”

One employee at UCD might process about 1,065 invoices per year, working on paper with a long approval process. At Johns Hopkins University, which uses a shared service center model and automated system, one employee can process 45,000, the report says.

Union leaders interviewed Tuesday wondered aloud if the reorganization was an attempt to weed out their members.

Dorie Decosta, president of UCD’s chapter of the Coalition of University Employees Local No. 7, said there was a “general feeling of unrest and discomfort” among staff.

The prospect of automation replacing personalized customer service “sounds like hogwash,” she said.

“You need that element of continuity and what UCD says it stands for: caring about students, caring about staff, caring about faculty.”

Wrote Susan McCormick, president of the University Professional and Technical Employees Local No. 6, in an e-mail message, “I am getting the feeling that UC is finding ways to eliminate the highest-paid employees. They are eliminating at the top of the pay scales, those at UC the longest and those with the most knowledge.”

ScottMadden’s contract calls for a fee of $350,000, plus up to $70,000 in expenses.

The proposed reorganization comes as UCD continues to grapple with an unprecedented $150 million in state budget cuts since 2008-09. It has cut 1,062 positions: 459 layoffs or employees who had hours cut, the rest through attrition or voluntary separation.

The campus has cut 30 percent of its administration’s core budget, compared to a 15.4 percent cut for academic units.

UCD faces another $38 million to $78 million shortfall depending on the outcome of state budget talks this year.

— Reach Cory Golden at cgolden@davisenterprise.net. Track him at http://twitter.com/cory_golden.

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Reports rap UCD research
By Cory Golden
August 15th, 2010

Enterprise staff writer
If UC Davis is to continue its climb in national status, it has its work cut out for it, according to a blunt assessment by an outside consultant.
While the campus has its share of advantages, including its broad research portfolio and location, it has been stymied by a risk-averse culture and a bottleneck in its research support structure, according to the Washington Advisory Group.
The advisory group, led by Eric Bloch, a former director of the National Science Foundation, interviewed more than 100 people on campus, from senior administrators to graduate students, over three days.
Many of the themes its 74-page assessment sounded were echoed in recently completed reports by two in-house “blue-ribbon” committees, one each on research and technology transfer. In an interview last week, Chancellor Linda Katehi said the campus would begin making changes in response to the three reports this academic year.
UCD ranked 36th among U.S. universities in the 2009 Academic Ranking of World Universities.
Despite state general fund cuts that could total more than $228 million since 2008, depending on the outcome of state budget talks, UCD “knows what it has to do,” the consultants write, to improve to a rank of between 20th and 30th. That group includes Northwestern University, UC Santa Barbara and the University of North Carolina, Chapel Hill.
Katehi has set a new goal of $1 billion in outside research support. UCD more than doubled such funding from $295 million in 2001 to a preliminary estimate of $679 million for 2009-10.
Claire Pomeroy, the chair of the blue-ribbon committee on research and dean of the School of Medicine, called it “a new era” for research.
“There’s a pent-up desire among the faculty and the staff and the students to really optimize how our research enterprise is functioning and a recognition that we have some work to do in that area,” she said.
“The statement that we made in the blue-ribbon report on research that UC Davis is ‘less than the sum of its parts’ reflects the idea that we have incredible excellence here, and if we can just bring it together and support the people and give them the administrative support and infrastructure support, then we can really propel this university up to the next level.”
Campus culture
To reach such heights, UCD will need to undergo a personality change, the advisory group writes:
“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.”
While collegiality can result in the interdisciplinary research that UCD touts, it “can also have negative consequences when events and behaviors are tolerated that in other similar institutions would cause friction and result in remedies. The prime example we heard about is tolerating decision-making delays that at times may have dire consequences.”
The university has been slower than its peers to embrace partnerships with industry, described by the consultant’s report as “frowned upon by former administrations as counter to what a university is all about.”
A lack of aggressiveness has sometime been costly in other ways, the advisory group writes. For instance, UCD “seems to have missed the opportunity to expand programs in human genetics, genomics and other ‘omics at a time of explosive growth in funding in these fields. This problem must be rectified swiftly.
“UCD and its accomplishments are not as well-known as they deserve to be, in large part because of some of the cultural traits discussed,” the report says.
Andrew Hargadon, chairman of the blue-ribbon committee on tech transfer and professor of technology management at the Graduate School of Management, said he did not think the campus suffered from “collegiality to the point of complacency.” However, he acknowledged “a long history of cultural conditioning” on the campus: feeling forever overshadowed by UC Berkeley and UCLA.
“We had such a huge growth of faculty in the last decade, and the increase of research dollars as a result,” Hargadon said. “When you look at the faculty we’ve got — they weren’t there in the ’50s and ’60s; they weren’t there when that identity was being shaped.
“They would very much like to have an impact, even if it comes at the cost of driving their agenda forward.”
Research support
The main target of the complaints that the advisory group heard: the Office of Research.
Those included “overstaffing, ineffective personnel and playing ‘lawyer games’ to be sure that no risks threaten the organization.”
The office is made up of three sections: sponsored programs, which submits thousand of grant applications; institutional review boards, which govern protocols for clinical trials; and technology transfer and business development, which handles applications for patents and royalties and acts as a broker between researchers and the corporate world.
Those interviewed by the advisory group said the sponsored research group is often “overbearing,” “dictatorial” and “prone to almost missing filing dates for proposals, thus jeopardizing the opportunity to participate in important competitions,” the report reads.
The blue-ribbon committee on research, in its own 20-page reported submitted Thursday, writes that its members are “greatly concerned that UC Davis, including its research administration, has become overly bureaucratic and risk-averse, and is too narrowly focused on compliance with rules and constraints. This risks frustrating creative researchers and reducing the level of scholarly creativity and productivity.”
Said Pomeroy, “We need to find the right balance between, of course, emphasizing safety and research quality and research compliance with being at the cutting edge of discovery. I think there has been a desire to minimize risk, sometimes at the expense of efficiently processing some of the research applications.”
Additions like expanded use of technology can help speed the process, she said.
The 12-page report by the tech transfer committee recommends creating a new office that would concentrate decision-making authority for technology licensing and industry research agreements. It also urges the establishment of standards for transparency, timeliness and accountability of patenting, licensing and processing industry research agreements.
The advisory group also found that area sorely lacking: “We did not get the impression that UCD has taken this general subject of intellectual property rights and technology transfer very seriously.”
UCD doesn’t have a long tradition of spinning off businesses, Hargadon said. That means that while there are faculty who have started a business, they aren’t great in number. So those who aspire to do so must lean on the tech transfer office for help.
“There’s no hard and fast rules on tech transfer. There’s no clear value with any intellectual property,” he said. “There’s a lot of clear-cut ways to go wrong, in terms of the legality of contracts and conflicts of interest, but there’s not clear-cut ways to go right.
“It would have taken a lot of strong leadership and vision to get the process to one where the university could make bold bets and make a claim that a particular patent would have more impact if it got out than if it got out with some sort of onerous revenue obligation associated with it. As a result, the office, without that sort of leadership vision, ended up weighing compliance and weighing risk mitigation higher than was really good for the system.
“Basically, we spent more time trying to stay out of trouble than trying to launch companies.”
Increased workload
The doubling of research funding has meant a greater workload for staff. That money has increasingly come from the federal government, which has steadily imposed more stringent regulations and reporting guidelines.
At the same time, the office’s staff has been trimmed from about 90 to about 75, said outgoing Vice Chancellor for Research Barry Klein.
He said of his staff, “These are very good people working very hard for the university, but very good people working hard doesn’t mean there aren’t ways to make our organization better; there are.
“If you look across the country at organizations that have these sort of hot-button service roles as we have, they are always subject to criticism. It’s impossible to be perfect,” Klein added.
“The faculty are like thoroughbreds. They want to win the race. It’s a mad dash to the finish line, but that causes a lot of tension and getting things in at the last minute and quickly, so there’s always this dynamic tension with the research office.”
Klein said being less “risk-averse” will increase the risk of violations and fines, but his staff would oblige.
“The people in my office don’t make the rules, they implement the campus culture,” he said. “And if it’s a culture that’s emerging now where you’re putting more things back to individual responsibility — having less oversight of details and assuming the departments and colleges and individuals will follow the rules — staff will move in that direction as well.”
One of the longest-serving vice chancellors for research in the UC system, Klein was due to step down in June 2009 but he said he stayed on to smooth the transition for the new chancellor, who arrived last August. His return to the physics department, announced last December, was a joint decision with Katehi.
“I was ready for a change and it was good for her to bring in some fresh blood,” Klein said.
Other findings
Among the other findings in the advisory group’s report, UCD:
** Lacks a five-year strategic financial plan;
** Needs a new strategy for technology transfer and business development;
** Suffers high student-faculty ratios in some areas;
** Should invest in technology on par with peer institutions;
** Needs a well-organized campaign to make itself and its faculty more visible if it’s to become a household name; and
n Faces a space crunch, including a lack of Biosafety Level 3 and 4 containment facilities, and should build them elsewhere if the community is opposed.
The advisory group also found that school- and college-level strategic plans were “meaningful and well-documented” but that “an institution as complex and broad as Davis requires a five- or 10-year strategy, plan and budget. No such interlinking documents exist today.”
Katehi recently unveiled a vision statement for the campus. Next, units will set out plans to meet those newly stated goals and, sometime next year, UCD will begin funding those priorities, the chancellor said.
The advisory group found it worrying that it received different financial information about research depending on who provided it.
“One wonders: What are the numbers that are at the chancellor’s disposal?” the report asks.
The advisory group also received complaints of “bloated” administration generally, despite recent cuts. UCD is rolling out a new effort this month to further reduce and reorganize its administration.
UCD paid the Washington Advisory Group $226,000, plus up to $30,000 in expenses.

— Reach Cory Golden at cgolden@davisenterprise.net. Track him at http://twitter.com/cory_golden

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Katehi details campus vision
By Cory Golden
July 30th, 2010

Enterprise staff writer
UC Davis Chancellor Linda Katehi and other campus leaders have crafted a “Vision of Excellence,” 10 months in the making, to guide the campus for the next 10 years.
The 17-page document combines many of the themes Katehi has sounded since her arrival last year, about the campus’ readiness for greater national and international prominence, with long-standing notions of UCD’s land-grant identity.
Released last week, the vision statement received a warm response from faculty, staff and student leaders reached for comment for its positive tenor, even against a backdrop of ongoing financial turmoil.
“To transform our university, we must chart a new course of action, an equally transformative vision to guide our actions and define our future,” Katehi writes in the document. It lays out goals like “foster a vibrant community of learning and scholarship” and “champion health, education, access and opportunity.” The document also describes how progress toward each goal will be assessed.
Bob Powell, chair of the Academic Senate, said the vision statement spells out change in ways both big and small.
“Before, it was about collaboration and now it’s about leadership,” he said. “It’s one thing to say you’re going to develop joint or international programs to enhance UC Davis, but this, to me, is a step above anything we were talking about before.”
Powell read one line aloud: “UC Davis will provide an efficient, professional administrative organization that is committed to serving and advancing the university’s academic mission.”
“From the outside, people would say, ‘Isn’t that obvious?’ Well, I’ve been here 26 years and it’s never been obvious,” he said. “To have that as an explicit statement is really important.”
Powell said he believed the document would go a long way toward building “grassroots support” when it falls to the colleges, schools and divisions to flesh out corresponding goals and plans to realize them.
An example of the document’s approach is its emphasis on increasing UCD’s international reach.
UCD will seek to increase the number of faculty, scholars and students from abroad and the number of students and faculty who pursue academic experiences overseas, the document says.
To accomplish those goals it will evaluate its needs in attracting, retaining and supporting international students; develop joint, collaborative international graduate programs; launch academic and clinical health research projects that tackle global challenges; strengthen and expand international alumni and global business ties; and provide the technological tools, cultural programs and student services to expand international dialogue.
Linda Bisson, professor of viticulture and enology and past chair of the Academic Senate, said the “solid” document is important for what it includes — and what it does not.
“It is different than what we’re used to because it has metrics,” Bisson said. “Typically, these kinds of vision statements are kind of just platitudes stuck together.
“This is going to sound weird,” she added, “but the change of focus that I see is that we’re not apologizing for who and what we are. Previously, things like this have read like we’re apologizing for not being (UC) Berkeley, the jewel of the UC crown.
“But this says, this is our value internationally: We’re problem-solvers — we’re a different kind of animal than Berkeley. It says we are very strong and proud of what we do — and that we’re not going to chase esoteric things when there are real things to be addressed.”
Though talk of breakthrough discoveries and spinning off research into new businesses can sometimes leave those in the humanities left wondering where they fit in, Margaret Ferguson, a professor of English and former chair of her department, said in an e-mail message that she felt that was not the case here.
“Im thrilled to say that this vision statement does speak to many of the questions that preoccupy those of us in the humanities, arts and humanistic social sciences,” she said. “These areas are mentioned early on as among the comprehensive research universitys ‘core disciplines,’ and the vision statement includes among its goals some that will particularly excite those students and faculty whose work focuses on deepening and expanding our understanding of past cultures as well as on creating new ideas for the future.”
She said she also was happy to see the goal of increasing need- and merit-based financial aid for both undergraduate and graduate students — which is “especially important for humanities graduate students, who are rarely supported by federal grants.”
Dan Wilson, chair of the Academic Federation, praised the vision statement’s emphasis on collaboration across disciplines, its promise of incentivizing success and its commitment to UCD’s land-grant role in improving the fates of the state and region.
Money, of course, remains the $228 million question mark. That may yet be the size of state cuts, dating back to July 1, 2008, depending on the outcome of the stalled state budget.
Bruno Nachtergaele, chair of the mathematics department, said in an e-mail message that he and many of his colleagues felt the document took into account their goals while also showing “the personal vision and commitment of the chancellor.”
“The recession we all suffer through is a hurdle, but not one that will stop her from promoting this vision and the long-term project of making UC Davis into the best university it can be,” Nachtergaele said.
Chair Peter Blando said in an e-mail message that the Staff Assembly was “extremely pleased to see a positive campus vision that takes us beyond the near daily concern over our job security and the university budget.
“While both are important,” he added, “staff morale is helped by providing any positive vision of the campus.”
Jack Zwald, president of the Associated Students of UC Davis, said he liked what he read, too, but was left wondering how Katehi would manage to increase the size of the university’s endowment while expanding programs. Likewise, he had questions about how UCD will be able to expand need- and merit-based aid to students.
“I think they’re going to give it a shot, but do I think it’s going to get done? I’m not overly optimistic it’s going to happen,” he said.
Wilson said the chancellor was right not to set the university’s sights lower because of the financial crisis.
“We don’t want to crawl into a shell — we want to move forward as a university,” he said.
To read the full document, see http://vision.ucdavis.edu.
— Reach Cory Golden at cgolden@davisenterprise.net. Track him at http://twitter.com/cory_golden

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:

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

ResearchBlogging.org

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

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”.

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.

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

ResearchBlogging.org

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.

doi:10.1371/journal.pgen.1001050.g001


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

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:

  • 7/31/10: The Human Genome Project: 10 Years Later, Progress but Still a Puzzle – WNYC. Interesting piece by Sarah Kate Kramer discussing the limited clinical value of the HGP.  Includes some criticisms of personalized genomic medicine. 
  • 7/29/10: Spiegel interview with Craig Venter with the headline “We have learned nothing from the genome”.  Has lots of interesting tidbits.  Love the Venter line “Well, nobody likes to be beaten — by superior intelligence, planning and technology. That gets people upset.”  But I note Craig emphasizes the basic science value of human genome data.
  • 7/6/10: Public Radio mini story about Mike Mandel’s article on the failure of the human genome project.
  • 6/12/10: Nick Wade’s NY Times article on “A decade later, genetic map yields few new cures“.  In this Wade discusses many of the issues with both the sequencing of the human genome and some of the spinoff projects (and also butchers some evolutionary biology for which I gave him a twisted tree of life award). 
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.

——————–
UPDATE

Also see

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:

Testing, testing – why we need more testing like this in genomic informatics & annotation methods

Just got an announcement regarding this challenge:

Automated Function Prediction SIG 2011 featuring the CAFA Challenge: Critical Assessment of Function Annotations | Automated Function Prediction 2011 July 15-16 2011, Vienna, Austria

Here is a description:

CAFA is a community-driven effort. We call upon computational function prediction groups to predict the function of a set of proteins whose true function is sequestered. At the meeting, we will reveal the functions, and discuss the predictions. The CAFA challenge goals are to foster a discussion between annotators, predictors and experimentalists about methodology as quality of functional predictions, as well as the methodology of assessing those predictions. Registration for CAFA starts July 15, 2010 and the CAFA challenge will take place September 15, 2010 through January 15, 2011.See here for more details on how you can enroll in CAFA.

This is near and dear to my heart as I have been working on methods to predict gene function from sequence for some 15 years now.  My first paper on this was in 1995 in which I showed that for genes in multigene families, phylogenetic trees of the gene family could help in predicting functions of uncharacterized members of the gene family.  More specifically, I suggested that the position of an uncharacterized gene in a gene tree relative to characterized genes could be used to predict its function.  I did this for one family in particular – the SNF2 family – but argued that it could be applied to other families.  (I think perhaps it was the first time someone had made this specific argument about using trees to predict function, but am not sure)

I then formalized this idea with a few papers (e.g., here and here) describing a “phylogenomic” approach to predicting function (alas, this is when I invented my first omics word).  And for many years since, I continued to work on functional prediction methods and continue to do so.  When I was at TIGR for eight years I did this both in my own research and helped others with their functional predictions.  I firmly believe that evolutionary approached approaches are critical in such functional prediction and have laid this out in a series of talks and papers (e.g., see this more recent one).

Anyway, enough about me.  I can argue all I want about how brilliant I am and about how evolutionary methods are the best approach.  But arguing is alas not science.  What we need are tests and experiments.  And that is where things like CAFA come in.  In CAFA one can test how well various functional prediction methods work.  And the people involved in CAFA (including organizers  Iddo FriedbergMichal Linial, and Predrag Radivojac and others such as Amos Bairoch, Sean Mooney, Patricia Babbitt, Steven Brenner, Christine Orengo and Burkhard RoshRost)) are to be commended for putting this together because we do not have a lot of these activities and need more in all aspects of genomics (and metagenomics too).  Others have discussed doing tests of functional prediction methods before, but I am not sure if any have happened per se.

Have a favorite functional prediction method?  Enter it in the competition or give a talk on it.  And if you are feeling inspired, organize a similar activity in your area of science – testing is a good thing.

See also Iddo Friedberg’s post about this

What is not getting any love at this #metagenomics meeting

Well, Here I am for day 2 in Snowbird at a meeting/workshop discussing the potential for “Terrabase metagenomics”. The main point of the meeting is to discuss whether there would be value in massive massive Metagenomic sequencing in one way or another. I note I have enjoyed this meeting so far greatly – nice and small with some really good people.

Yesterday i gave a talk on microbial evolution and a few others talked about other topics (Rob Knight talked about microbiomes, Jeroen Raes discussed multiple Metagenomic projects, and Rachel Mackelprang discussed permafrost metagenomics). I will write more i hope soon about the science side of this meeting. But that is not what I am here to write about today. I am going to tell you what topics were not getting any love so far at this meetings. And this is not a completely snarky thing here – what people complain about does give some feel for what people are thinking about. In no particular order, here are some examples.

  • The human microbiome project (well, some parts of it)
  • The CAMERA metagenomics DB (significant disappointment in their progress )
  • NCBI (or specifically the short read archive)
  • Bureaucracy (and how it impedes science)
  • Lack of support for informatics
  • Lack of air (we are at 8000+ feet)
  • Large meetings
  • Jet lag
  • IRBs
  • Lack of RAM (many Metagenomic analyses require massive amounts RAM)
  • Bad alcohol (as in drinks)
  • Plants and animals (this is a meeting focusing on microbes)
  • Lack of cooperation among funding agencies
  • Pathogens (most people here are interested in either human commensals or environmental organisms)
  • Difficulty in founding joint projects between US and Europe
  • Projects that don’t collect metadata
  • Software tools that don’t work with each other