Thursday, December 30, 2010

Scintillating Dinner Conversations...

... on a tiny, tiny keyboard... that don't involve me.

This is the frustrating reality of life in the smartphone era- a syndrome I refer to as Hyper-Connectivity Addiction.  The syndrome presents itself as a constellation of symptoms, ranging from inappropriate use of electronic communication devices, prioritization of electronic interaction over personal interaction, and etiquette-busting rudeness with no sense of time or place for use of personal electronics.

Over the last year, going out to dinner with others frequently turns from a time to share conversation and time together into a time where I watch someone play with a phone.  Whether it is texting, talking, or checking their fairy-tale football team, the time at the table previously filled with witty banter, personal interaction and news exchange has transformed into the prime venue to catch up on trivial electronic business with the rest of the world.

Now, it could just be that I'm boring and bring nothing to the table, leading those I'm with to seek distraction.  I fully admit that possibility.

However, I really think that there's a time and a place for technology.  I am trying to train my 12 and 16 year old nieces on how to have a conversation.  I'd like to hear about their schoolwork, their days, etc.  Two of my nephews are 20 and 22.  We were disconnected for 7 years and they grew into really cool guys.  I look forward to the limited time I have with them, but invariably have to share it with the rest of the world via iPhone.

Again, maybe I'm just boring.  Or smell.  Or both.


Good times at dinner, watching family electronically 
interact with the rest of the world. 
(Taken with a smart phone)

And I do verbally request that phones be put away, usually met by rolling eyeballs and a few minutes of phone-free time.

My wife will tell me that all I do is talk on the phone during dinner all the time, which I wholeheartedly disagree.  It is one of my pet peeves, right up there with throwing out food and sock puppets.  I usually use the time in a restaurant or other philosophically phone-free zone as an opportunity to leave my phone charging in the car. I am rarely guilty of this atrocity.

On rare occasions, maybe once every two months, I am expecting a call that must be prioritized.  If it coincides with a meal (at home or away) I mention that I may have to take a call.  When the call comes, I excuse myself from the table and go to a lobby or non-intrusive area to take the call.  I minimize the time away from the table as best I can.

Maybe I sound like gramps here, but the day that a solar flare takes out the goddamn SmartPhone satellite I'm going to rejoice.  I'm taking my wife, dad, nieces and nephews out for dinner and we'll talk with no interruptions. Again, it could just be me.  I don't get enough time with my wife, dad or family and really do appreciate those fleeting times.

It is a question of priority, unplugging, just for a bit.  The world will be just fine-- even if people can pry themselves out of the cloud for 45 minutes.

The table is a great place to connect-- but with the person across the table rather than the person across the country.

Sunday, December 26, 2010

The Strawberry Genome: The Story Behind the Story

Today we have witnessed something that many of us thought we'd never see- the completed publication of the strawberry genome.  The story appeared today in Nature Genetics.

But what is the story behind the story?  As someone that was there from the beginning, I think it is helpful to recap the highlights and lowlights that did not reach the journal article. It adds much more texture to the news release and gives a much better understanding of the process of getting from crazy idea to final publication.

When next-generation sequencing came into vogue, there was immediate buzz about sequencing strawberry.  It was late 2005.  Arabidopsis and rice were fully sequenced, others were in progress and other plants were in line for genome sequencing.  At the time we solicited various government agencies for the funds to use the new 454 sequencer at the University of Florida.  We were one of the first places with the platform, so we dreamed of using it in a revolutionary way.  The tiny strawberry genome was an obvious target.  We asked for around $100,000 to start the process, soliciting mostly through earmarks and initiatives that UF put forward to the State of Florida.  Heck, it costs $200K to improve an intersection, so half of that to get an accounting of the nuts and bolts of an economically important crop plant should be of some priority.

Funds never materialized.  However, the opportunity to apply for funds from DOE-JGI came to the table.  The funding solicitation was broken down to two levels, genomes over and under 200 Mb.  Since strawberry was estimated to be just around 200Mb, it seemed to be a no brainer for the under 200 Mb solicitation.  Dr. Tom Davis from University of New Hampshire submitted the letter of intent for the January 13, 2006 deadline, days before the Plant Animal Genome meeting in San Diego.

At the Rosaceae Executive Committee annual meeting on Jan. 15 Tom announced that he had submitted the letter. The news was not well received.  The broader Rosaceae community had discussed sequencing a plant species, but interest swirled around peach and apple, mostly peach.  Those organisms, while possessing larger genomes, had good physical maps and substantial Sanger sequencing support. After a rather pointy discussion, Tom was convinced to withdraw his strawberry sequencing proposal, differing to the eventual DOE-JGI support of peach.

It was a blow to those of us that hoped that a strawberry/peach combo platter would be possible, but the broader feeling was that we would not get both, we'd get neither.  Who knows?  I'm from the camp that if you have a compelling scientific argument you have to ask if you are going to get.  There's also some merit in thinking big- and an opportunity to get two for the price of one seemed legit to me, and certainly to Tom. Oh well.

Time went on.  It was clear that there was going to be little/no support for strawberry sequencing.

At PAG in San Diego, 2008, Vladimir Shulaev and Richard Veilleux from Virginia Tech attended the Rosaceae Executive Committee meeting.   Vladimir announced that Virginia Tech had thrown support behind the idea of genome sequencing- both some financial support as well as technical and facility support.  This was the seed that was needed.  The discussion had a pure "pass-the-hat" flavor to it.  Nobody had big funds, but Vlad and Richard had a big idea.  That proved to eliminate the first major barrier to a complete sequence.

After that meeting Vladimir, Janet Slovin, Tom Davis, Todd Michael and I met in a corner of the conference hall and talked about where to get the rest of the funds needed.  We wrote a quick grant proposal to the North American Strawberry Growers Association, asking for $8000.  We brainstormed on other options.

Months later, the NASGA grant was declined, but other funds were coming in.  Most of all, Roche 454 was giving an excellent break on reagents. It was important for them that we succeeded.

Many other pools of funds materialized, including money from IASMA (italy), the USDA (J. Slovin), Virginia Tech, Driscoll's Strawberry Associates, Plant and Food Research (New Zealand), and the Dean for Research at UF.  Our strawberry breeding program pitched in as well.  Of course, many labs donated time and expertise.  The value of this contribution can not be understated, as literally thousands of human hours were committed to this project with no guarantee of reward.

Sequencing proceeded almost exclusively at Virginia Tech, with some paired ends being done at Roche 454. The runs were being performed as funds would come in and substantial coverage was brewing.  Weekly conference calls would tell us of increasing coverage.

There were skeptics.  Many in genomics, including some friends, predicted failure.  They told us that there was no way that a draft sequence could be obtained without a physical map, and especially with a purely short-read based approach.  Time would prove them incorrect.

Soon after new people joined the consortium, including many experts in genome annotation.  Mark Borodovsky, Paul Burns, Todd Mockler, Keithanne Mockaitis and others all came aboard, sequencing mRNA libraries that my lab put together from various tissues, then annotating the genome accordingly.

Assembly was facilitated by Steven Salzberg's lab at U Maryland.  Art Delcher really advanced this project forward, as Newbler itself was not providing ample collapse of contigs.  Finally advanced assemblies were reported during our conference calls.  Scaffolds were getting larger.

The genome browser came online with expert input from Ross Crowhurst at Plant and Food Research.  PFR had a huge role, with experts like Andy Allan and Roger Hellens contributing.  The final version is at www.strawberrygenome.org

The scaffolds were anchored to the genetic linkage map by Dan Sargent at East Malling Research in the UK. This exercise was a massive undertaking and involved input from Jasper Rees' lab.  This was really important because it provided organization of the scaffolds that placed them into pseudochromosomes.

Functional annotation was performed with the expert care of Pankaj Jaiswal and his lab.  Aaron Liston assembled a chloroplast and ran some excellent phylogenetic analyses with Allan Dickerman.  These data suggest a rethinking of how poplar clusters with other taxa.

The last year was a grind.  Every 4pm we'd have a conference call with fewer and fewer members.  Even pivotal people, there from the beginning, were losing interest or were consumed with other priorities.  Things were uninteresting and heading towards collapse.  All of us were burned out and bored.

I tried to stir some momentum and interest with daily email updates, but even this futile effort ended in about a week.  It was sad that we had all of the data in one place.  No more sequencing was being done, annotation and predictions were complete and the genome browser was up and running to those with credentials.

Talk about frustration.  We had the genome sequence in a pile, but the report was a disorganized mess of fragmented ideas looking for codification.

Luckily some enthusiasm was found at PAG 2010.  Vladimir presented the genome work at a major symposium.  It looked awfully sweet on the big screen and many of us felt a sense of prime time.  It was energizing.

Todd Mockler, Todd Michael and Tom Davis met.  Later that night we had a strategy-n-pizza meeting with all of those present in the consortium.  Many of us met in person for the first time.  Our decision was that we'd assemble a "writing team", a small group to put the massive outline and verbose rantings of thirty eggheads into a publishable format.  Tom, Tia-Lynn, Richard, Aaron, Todd, Andy, Mark, Herman, Lee, Dan, and I attacked this charge. We worked fast and with purpose, submitting a pre-submission inquiry to Nature in February of 2010.

Our solicitation was declined about two weeks later.  We formatted for Nature Genetics. The slow re-submission was due to additional data coming in, and we finally submitted in June.  Reviews were back in August. High quality, appropriately critical reviews led us to reshape to a stronger version of the work and then resubmit in September, 2010.

Final acceptance didn't come until late November.  Most people, even those close to the project, don't know that we were down to the wire for addressing editorial concerns toward publication.  I have no finger nails left.  Even this last week there were serious concerns if it would be published because some of our data were not accessible online.

The work found needed final touches by an outstanding team of re-writers and proofers.  Some of those in the consortium somehow mustered up another awesome critical read. We had no warning- and a 24 hour deadline. A good paper got a final makeover.  Richard,  Keithanne, Tom D., Janet, Aaron, Todd Mockler, Lee, Herman and others gave volumes of excellent suggestions. It was a relief to see the point when every error was found at least by two independent parties, suggesting that all was in order.  The "final" galleys were returned to Nature Genetics and were a turbulent sea of yellow-highlighted adjustments.

I'll also pat myself on the back for at least a few sleepless nights near the end where my desire to see this complete gave me intense focus and drive. I wanted it done, flawlessly.

While it is beautiful to see it in print, it is more a testament to the thousands of person-hours on conference calls, Vlad and Richard's vision and persuasion in the beginning, a mega-talented team, generous funding from non-traditional sources and an expert, supportive editorial job at Nature Genetics, among many things of course.

Most of all I gained a new respect for people I already admired.  It was a joy to work on a common project, but also to endure the ups and downs together. And I apologize to those that were not acknowledged here. Add a note in the comments if you would please.

It was quite a journey, and a journey only to the beginning.  Now the real fun begins...

Wednesday, October 6, 2010

Natural News. Shame On You.

Natural News is a website devoted to, well, insanity.  While appearing to be folksy yet alternative, they give the worst possible medical advice (cure any cancer for $5.15 a day) and promote a non-scientific point of view, invoking every logical fallacy possible.  They draw conclusions that can't be supported and promote the most un-critical thinking I've ever seen.


I read a recent post and now I"m mad.   The post "Bill Gates Says Vaccines Can Reduce World Populations" is a lie right off the top.  In a recent TED talk Bill Gates said:


"The world today has 6.8 billion people... that's headed up to about 9 billion. Now if we do a really great job on new vaccines, health care, reproductive health services, we could lower that by perhaps 10 or 15 percent."


 Of course what Gates is saying is that population is an issue, especially in the developing world, and that steps need to be taken to ensure the health of people there.  If families believe that their children will survive, they will stop having huge families.  Vaccines ensure that they will be healthy and reproductive counseling will help with family planning.


Natural News author Mike Adams sees this a different way.  Clearly the plan is to use vaccines to drive the population down. According to Adams, vaccines will be implemented to kill people slowly by inducing degenerative disease, reducing fertility (or he means fecundity) while causing miscarriages, or sensitizing a population to pandemic viruses.  To Adams, vaccines are deadly poisons that are now being aimed at reducing populations.


Shame on Adams.  Not only is his propaganda dangerous, it makes an implicit accusation that Gates is interested in genocide.  The Gates foundation is currently engaged in an expensive and almost impossible feat of eliminating polio using vaccines, much like how smallpox was eliminated.  They are traveling to remote areas, knocking on doors one by one, and administering vaccines to stop this disease where it still flourishes. Seems like that approach worked pretty well here.  Not many people walking around with polio.


Adams sees this as part of that genocidal plan.  Clearly eliminating polio is not Gates' plan, but rather it is to cause degenerative disease, reduce fertility, cause abortions and increase sensitivity to disease.


Of course Adams does not say that "health care" is part of Gates' plan for world domination and genocide in developing countries.  That would make him look like a fool.  Yet vaccines are singled out in that sentence in classic distortion of Gates' real intent.


Shame on Natural News.  The Gates Foundation is doing enormous good for developing countries, much more than the Natural News does.  To attack the motivations of the people that are driving and bankrolling these unprecedented efforts is truly shameful.

Friday, August 13, 2010

Climate Conspiracy, Part II

Today's blog follows up on the Climate Conspiracy blog posted last week.  It was based on two conversations I had with a clear climate denialist.  The first entry details a discussion where the other party has direct evidence of bias in funding for climate research... that is, until I call him on it.

Today I'll provide another example.  It is interesting to note the climate denialists follow the same exact scheme as those that deny evolution or the safety of GMO food.  There always is a conspiracy, chocked full of secrets.  There are threats and intimidation, nameless figures and warped senses of victimization.

This is the second part of my discussion with James McGaha.  Again, we had a very nice conversation where I did a lot more listening than talking.  It was a private conversation, he had no idea that I'd write here about it (neither did I), but it is a good case for understanding science denialism.

During the conversation he told me that he knew someone, that must remain nameless, that has concrete evidence that will "blow the lid off of the global warming nonsense".  This alleged figure is a scientist and has this data, data that will contradict the findings of thousands of independent laboratories worldwide, upending data generated over the last three decades.

"Why doesn't he publish it, say in Science or Nature", I said.  Certainly concrete evidence that refutes a well established scientific consensus would be publishable in the best journals.

McGaha claimed that he would publish it, but is afraid of the intimidation that will come to him if he published work that does not agree with the scientific consensus.

Of course I vehemently disagreed, as top-tier journals are where you place the best data that overturn accepted paradigms.  I then had a stellar idea.

"Ask him to write up his data into a paper for Science, then send it to me.  I'll submit it with my name on it," I said.   "I'm a scientist, I can submit that work, then I'll deal with the intimidation (said with mocking sarcasm)."

It was the perfect plan. If this scientist has the data and is just afraid, then give it to a scientist that isn't.  Then when I show up in a shallow grave with a jumbo thermometer up my heiney and a Gore-Lieberman sticker across my forehead, then they can show the world how evil the conspiracy is.  If his conclusive work gets published, then he has accomplished the mission, we change the name on the report from mine to his, and he gets a Nobel Prize, or at the very least a lifetime of interviews on Fox News

Of course, my offer fell on deaf ears, probably because there is no shadowy scientist and equally vacant solid data.

It is a lot like those that cry foul in discussions of evolution.  There always are some alleged scientists that are not allowed to publish their data that prove creation or that the earth is 6000 years old.  They are afraid of intimidation or losing status or their job.  They claim a great conspiracy to suppress the real data.

In the end, there's science and there's non-science.  If we have real data, we publish it.  Real data stand up to scrutiny and are reproducible.  Real data always win.  That's why every nut living in denial of real science has to resort to the conspiracy and intimidation story, because as long as the real data are suppressed and hidden, then they don't have to ever be tested, reproduced or independently verified.

So that was my conversation with a science denialist.  We concluded by me saying, "Science is a put-up-or-shut-up business. If you have the data, show the data, confirm and retest the data, and change the way we think.... that is the way science works."

Wednesday, August 4, 2010

The Climate Conspiracy

A panel convened at The Amazing Meeting 8 (TAM8) to discuss the skeptical coverage of climate change.

Panelist James McGaha made a number of statements that I really disagreed with.  He's a self described climate skeptic, as any good scientist should be, only he demonstrates his patent ignorance toward the scientific method and the critical consideration of evidence.

During his time on a panel, clearly as a representative of the camp that anthropogenic global warming (AGW) is a figment of the imagination and a liberal conspiracy, he espoused several positions that demonstrated his clear departure from the scientific method.

Multiple times he stated, "Science is wrong".   He framed this in several ways, all of which will be more comprehensively disclosed once the TAM8 videos become available.

Science is not wrong.  Science is a tool to answer questions in an objective and powerful way.  Science is not wrong.  Science just disagrees with his non-scientific conclusions, so it must be faulty.

He also claimed that federal funding agencies do not fund or publish work that is contrary to the status quo on AGW.  He said that legitimate work that contradicts AGW is unpublished.

After his talk I stood in line to talk to him.  I asked specifics, especially about the funding for those that have data supporting a non-AGW position.  He told me that is was the NSF, JPL and NASA.  I could not disagree more, as NSF especially prefers to fund quality work that expands our understanding. The work that runs counter to the consensus is considered very favorably.

I sent him an email last week and asked for a few minutes of his time.  He graciously agreed to call me.

He called and the first thing he asked was, "Are you a believer in AGW or a skeptic".

My answer was that I accept the scientific consensus and I am a skeptic.  We were off to a unproductive start.

I mostly listened for 45 minutes.  He told me that the NSF was a major dupe of the AGW system, funding only work that agreed with the consensus on AGW.   I told him that I was interlaced reasonably well with NSF and would like to know which funding initiatives were showing such bias.  I told him that I could investigate this with the Program Managers (the people that make decisions and ultimately write the checks) from the appropriate sub-disciplines at NSF.  I was going to be in Arlington at NSF headquarters, so it would be easy to knock on some doors.

He then says, "Well it was not NSF as much as JPL and NASA".  The story changes.

... more in the next blog.  It gets weirder, but more backpedaling.

Thursday, March 25, 2010

Pale Blue Dot Revisited

I was talking to a friend this morning.  She speaks to the vastness of space and our insignificant position relative to the universe and everything.  I thought of the Sagan's "pale blue dot".

 The tiny blue dot in the center of the bright band on the right is Earth. You ain't so cool.

The picture was taken from the Voyager spacecraft as it left our solar system in 1990.  Scientists turned the camera back toward the sun and captured an image.  The image shows our planet, our home, the place where everyone that every human that has ever lived, modestly presented as a dim tiny fleck- a pale blue dot.  This single pixel shows our position we were all there in that photo, all of us captured on that single spot of light.

It is humbling and maybe tragic, as it shows how minor we are in the true grand scale.

Sunday, November 1, 2009

Lipozene and the Obesity Research Institute

NOTE:  After knee surgery last week I've been subjected to a lot of television watching, fertile grounds for scams and claims that demand skeptical dissection.  There will be a few reports along this line over the coming weeks.

Lipozene. The commercials claim rapid weight loss.  They appear highly clinical and are quite persuasive. Lipozene is packaged and pitched with an implicit claim of miracle weight loss drug status. The product and the clinical claims come from the Obesity Research Institute. The Obesity Research Institute LLC is a Los Angeles based company founded in 2003 that has sold several ill-fated products such as fiber-thin and Propylene.  A quick search of the scholarly literature shows no formal published research results from the Obesity Research Institute, so this appears to be a company and not a place actively engaged in scientific research.


I was particularly drawn into the commercial when I read the blue italic print under the Lipozene name.  It says, Amorphophallus konjac, which just happens to be one of my favorite plants.  So Lipozene is just a derivative of A. konjac, actually the ground up corum (bulb). The bulb has high levels of glucomannan, a carbohydrate that swells massively when wet.  It is used as a gelling agent in some Asian cuisine. This explains the role of this compound in Lipozene.

As a diet compound glucomannans have been shown to be mildly effective in weight loss.  The most compelling data come from 1984 and the International Journal of Obesity (8(4):289-93) where Walsh and colleagues gave 1 g of glucomannan or a placebo in a double blinds study.  Over eight weeks the glucomannan group lost significantly more weight (5.5 lbs over 8 weeks).

The red flag for me is that this paper is from 1984 and there is no evidence of a successful replication or expansion of the study.  This was a dead end.  In the field of weight loss, we'd expect more labs to pile on to these findings and do their own trials.  In reality, they probably did, and didn't see the same results.  Independent replication is the Achilles Heel  of flawed or just plain wrong studies.

Other studies, mostly by Dr. Dan Gallaher's lab at the University of Minnesota, do show a positive effect of glucomannan in lowering blood lipid profiles, increasing their presence in the feces. Serum cholesterol decreases. His work spans many similar compounds and I absolutely trust these data.

But these are the best tests. Recent evidence tests glucomannan and outside of small, uncontrolled studies there is little treatment effect in weight loss.  It does appear to promote relief from constipation, lowers blood lipid profiles and probably can be regarded as safe. The mild effects in weight loss probably stem from the swelling of the compound in the gut, leading to an increased feeling of satiety in those that use it.

The problem for me comes from the fact that this is a ground up plant bulb and it can be purchased for a much lower price than from Lipozene.  Google "glucomannan" and you'll find hundreds of vendors.  Also, check for complaints against Lipozene and the Obesity Research Institute.  I won't go into detail here, but a quick check shows a history of lawsuits and unauthorized charges, at least as evidenced by the web results.

So the Obesity Research Institute straddles the scientific fence with this claim.  With a foot in reality and the other in hyperbole, they stretch the science to sell a familiar plant compound as a magic bullet for weight loss.  Testimonies abound on the web, for and against the product.  The science tells a different story.  Clearly some positive effects, but not a consistent record of promoting weight loss over placebo in well-constructed studies.