Saturday, January 28, 2012

If You Can't Attack the Science, Attack the Person!

Hi Everybody!  It's me!  You might think you know me as an academic research scientist that is dedicated to training undergraduate and graduate students, helping science link real solutions to agricultural questions, and thinking of novel frontiers in genomics and other basic science.

You might also recognize me as the scientist that interacts with the public, teaching the science behind transgenic food (GMOs), climate change, evolution, vaccination, and other hot button issues that shouldn't be.  I'm glad to talk to people that disagree with me, and do it politely. Most of the time.

But my cover has been blown. See, according to one anti-transgenic advocate-- I'm a dupe for Pepsico.  Confused?  Me too until she explained.

(this is all public on Natural News comment thread, so I'm just reposting-- no violation of her privacy, and she'd appreciate me getting her message out in more places I'm sure)

While chiming in on the narrow-mindedness of labeling transgenic food (a topic in queue for this blog) I met with Ms. Lilia and used scientific evidence to provide a general debunking of transgenic food topics, where the reputation of this sound technology has been sullied by many.

She provides the same tired old articles in low-impact journals that were never repeated, or parrots the old distortions that she believes, but can be easily analyzed as not true.  So instead of addressing the science, she goes after me.  Worse, she goes after my institution, the University of Florida, and its 3000 faculty.


Oh No!  I've been found out!  First I'm practically Kevin Bacon's cousin and now this!
Our whole university is a dupe for Pepsico, brilliant on their behalf, as somehow Pepsi made the 
university decades before there was Pepsi! 

 This is pretty lame stuff. Calling my work bogus because of some contract?  I guess I'm particularly saddened because I feel great pride in being part of this faculty.  As a land-grant institution we take our mission of public education and service very seriously. It has been such a pleasure to work with farmers, students and other stakeholders in our State.  But alas, we are all shills for Pepsico.  We must be, heck, they licensed a product created by a UF scientist.  In fact, Pepsi probably hired him and forced him to create that product so that they could license it from us and pay royalties for decades to come.

Ms. Lilia continues on a separate thread:

Quite an indictment! Our University is run by Pepsico! 
We do have Pepsi vending machines... 

Here her evidence of Pepsi's deep influence on university science and technology is presented, noting that UF is "basically run by Pespsico" and that she does not believe that I have "no personal stake in (the GMO) argument."

I do take it personally.  She is impugning my integrity as a scientist, something I've trained for since the mid 1980's.  Plus it goes farther than that, personally.  I know that we have some nice transgenic tools in the lab that would be of great benefit to farmers and consumers, but they are DOA other than as research tools.  We could never afford to navigate the regulatory maze that would be required for commercializing a transgenic plant.  That is a tremendous personal disappointment.

Then it gets really fun to learn that everything that comes from my lab is essentially a fraud, as is everything that comes from UF research labs...

And you should check out the thread on Natural News where I describe to her  in scientific detail why it would be inappropriate to label transgenics without labeling any plant material generated through human intervention.  Please read- I make the sound scientific argument. 

So here a civil, polite and scientifically evidence driven discussion on my part, ends with the assertion that I'm a paid stooge for Pepsico, along with every other faculty member at UF.  She really thinks this.  What is scary is that she thinks this, but if you read the Natural News thread she clearly is intelligent, articulate and passionate.  She's one of the good ones!

The last thing I'll post is my reply to her direct allegation.  I hate to even pay credence to such things, but it is on a thread populated by anti-science goofballs, so perhaps a little gentle defense was in order... 

And I have absolutely no idea what that last comment means. Ya dig? 

To conclude, I thought I might list just a few examples of published research coming out of University of Pepsi.  It is a shame these are all frauds and based on Pepsi's approval, as they are performed by wonderful, caring people that have a mission as teachers, scholars, and stewards of society and our planet. We are people that have turned away from lucrative corporate opportunity, fight for every dollar, and work sixty hour weeks throughout our careers to remain competitive.  

-- Here is the UF Biofuels Plant.  Allegedly remediating plant waste to make renewable energy.  According to recent commentary, it likely really is just a way to make Diet Pepsi. 

-- My department's Organic and Sustainable Agriculture emphasis is one of the best in the nation. Strike that, the best.  Wonderful faculty, and rapidly growing with new students that care about sustainable ag and want it to be their career.  Too bad they are working for Pepsi, right? 

-- and efforts to assist small farms and promote local produce are just a facade, as Pepsi is pulling the strings...

I could go on and on, but I won't.  It is Saturday, going on noon, and I have the pleasure and privilege to be able to go to work today at a kick ass job that helps people.  I get to think about big ideas, new science, and how to be a better teacher. 

.... and you know what?  Pepsi has nothing to do with it.  I don't even drink soda.  If I do, its Coke Zero. 

I was just blown away by such brainless allegations.  They illuminate the point that if you can't raise your argument, raise your voice or cast aspersions to misdirect the discussion. 

Wednesday, December 28, 2011

Science Denial in Political Candidates;The Importance of a Simple but Telling Question

Back in 2008 Republican presidential hopefuls gathered in an on-stage “debate”.  By debate I mean they did what all politicians do regardless of political party- they used the occasion to bend questions to fit their answers and stroke the expectations of smiling partisans counting down to that primary election.

The event was typical and boring.  Stock answers to non-issues and sidestepping issues that truly matter in our country.

But one web-submitted question resonated especially well with me and it should be a mandated question in all political debates from here on out…. “This is a yes-no question… Do you believe in evolution?”

The question should have been, “Do you accept the evidence for evolution,” because we don’t have to believe something when it has been substantiated with overwhelming evidence, but these are politicians, not scientists, so we’ll let it slide.

The question was posed to Senator John McCain, who enthusiastically said, “Yes.”

When asked to the rest of the stage with a show-of-hands, hands were slow to raise, and candidates looked back and forth at each other, thinking quickly of how their answer could be politically expedient.

Gov. Mike Huckabee was the first hand up, followed by Sen. Sam Brownback and Rep. Tom Tancredo.

This was a telling moment.  Here were three candidates willing to ignore evidence and brandish their ignorance in a show to placate a political base.  To me, grounds for immediate disqualification.

This year during the “debates” some pundit mentioned that such questions were useless in vetting a presidential candidate. I could not disagree more.  This is absolutely the best question to ask anyone seeking the highest office in the land, an office where they literally have their finger on the power to annihilate the planet. They also have to make many policy decisions that could benefit from objective scientific validation, and to turn a blind eye to science for political gains is detrimental to us all.

To deny that evolution happened over the last 3.6 billion years (and still happens and is ongoing) means that you have to be willing to ignore evidence.  Worse, you have to be willing to ignore evidence and accept what someone believes in the absence of evidence, but on the basis of faith.

So when an important decision needs to be made (like invade Iraq to take out Saddam Hussein in retribution for 9-11) who do we want to make that decision?  Do we want someone in power that will carefully consider and weigh all points of view, options, and evidence, and then make a decision based on the facts, or do we want someone that will default to the voice in his head, the voice he hears in prayers, the voices of his supporters, the voices of big business, the voices of his party, and/or the voices of contributors? 

Evolution is the basis of speciation and natural selection is the mechanism by which it happens.  That is not a subject of debate among the world’s scientists.  Fewer theories have more support from diverse scientists and avenues of inquiry.  To refuse to accept this evidence to placate the ignorant shows that a politician is either lying or stupid.

Anyone not accepting evolution as an established and supported theory that explains the diversity of life on earth should be immediately disqualified from holding the office of President of the USA.  The next decade will require hard decisions to be made on economic policy, energy policy, foreign policy, and many other areas.  We need leaders that are connected to science and quality information, that can make good decisions when provided with information, and accept reality over influences.

They could instead run for King of a planet that is flat, cooling and in the middle of the universe. 

Saturday, February 26, 2011

Never Cried Over Pasta

Until today.

It didn't even occur to me.  Today is Saturday and I finished work a bit early, around 4 pm, allowing me enough time to stop at the store and make dinner- not just put something together, but actually cook. Make real dinner.

I opted to make a big pot of pasta sauce with Italian sausage.

I malliardized the onions, added fresh garlic, then assembled the pasta sauce that my mom taught me how to make years ago.  Then it hit me.  She's gone.  The smell is here, the same thoughtful assembly of ingredients in the right proportions and right order was here, but she's gone.

My kitchen smelled like her kitchen and I crashed.

As a kid I learned how to cook from my mother.  She was really good, good at a gut instinct for what to add and in which proportions. I guess that is where I get it from.  When I was in Cub Scouts part of the badge requirement was to learn how to set a table and how to assist with serving a meal.  I learned that stuff from my parents. Dinner was a formal daily event, and it was always good.

The pasta sauce is not so much a recipe as an assembly. It comes from my mom's best friend's mother, a person I called grandma until she passed away, and for the most part of that time it was unclear why I got to have three grandmothers.  Why argue with that?  She was Greek, but knew how to cook Italian.

My mom borrowed that recipe and at one point showed me how to do it.  My house smells like her house, right now.

At some point I showed this to my nephew and will show it to my niece eventually.  This one is too good to lose.

I have not written anything because I've kept myself packed with business so that I can't think about the grieving process.  If I keep running I can't have the time to break down.

Being in Gainesville, FL I can avoid pictures, I can avoid the topic.  I live 1154 miles away so I can't see her home or think about the places she'd go or the things she'd do.

But I can't hide from the wonderful aromas and the thoughts and memories they carry with them.

I've been blindsided into grief by a steaming pot of simmering tomato goo.  This will be a long process.

Friday, January 21, 2011

Pinball Repair Master Adrift in the Age of Modern Marketing

Florida State Highway 33 is a desolate ribbon of asphalt that connects Polk City to Groveland, two places that are little more than speed bumps and never destinations.   It is an artery we must transit when moving between Gainesville and the USDA labs in Winter Haven, FL, as they do a lot of analytical chemistry in association with our projects.  There are no gas stations, mini marts or scenic stops, just mile after mile of pine and palm, broken up only by a toothless goon here and there, occasionally one rolling a tire.

About six miles out of Polk City and 21 miles before Groveland there is a sign hammered into a naked spot on a tree.  It is about eighteen inches wide and twelve inches tall.  It is unpainted wood and features black block letters that say PINBALL REPAIR, followed by a phone number.

Now, what are the odds....   you see where I'm going.

Imagine the almost infinite alignment that needs to happen here.  First, someone has to own a pinball machine.  Next, it has to be broken.  Next, they have to want to repair it.  Next, they could find nobody to do the work.  Next, they have to be driving north on Florida State Road 33 from Polk City to Groveland, during the day.  Finally, they have to actually spy this rather innocuous sign, then be quick with a pen to jot down the phone number.

WTF?  I think you'd be more likely to find Bigfoot walking arm-in-arm with Jimmy Hoffa in the middle of Disneyland, or the Cubs winning the Super Bowl.

Sadly I picture a sixty-something unkept guy, perhaps missing a limb, sitting near an old rotary dial phone in his home near the modest suburbs of (ahhem) Polk City.  Every morning he dons the coveralls, sits down at his work desk by 9AM, on time, every day, waiting for a service call.  He sits among boxes of flippers, bumpers, plungers and tilt lights, maybe rolling a heavy shiny silver ball across his desk over and over to keep what's left of his sanity.

But the call never comes.  Perhaps once in the middle of the night the phone exploded into its song, leaving him only to find a wrong number.

He might wonder what is wrong.  Is his advertising network not connecting with its market?  Maybe he needs  to modernize his marketing strategy, perhaps a note in the church bulletin or maybe he needs to thumb it up to Groveland and put ads under windshield wipers at the DQ.  Clearly the net he has cast is not reaching his potential clientele in broken-pinball-machine space.

To me it speaks to the ambitions of the human spirit and how well-intended ideas die from poor execution.  Next time I'm down there I'm going to get that number and make the phone call.  Stand by for details.

Saturday, January 8, 2011

The Cause of Mysterious Bird/Fish Deaths Revealed!

Over the last week there have been numerous reports of widespread avian and fish death.  Apparently large swarms of birds and huge schools of fish give up the ghost for no known reason.  Or so it is thought.

The genius think tank over at Natural News has it all figured out.  In his January 4th column Mike Adams applies his usual less-than-rigorous approach to resolve this mystery.  The column speculates based on zero evidence:

For all we know, these 100,000 dead fish are downstream from a field of GMO corn that mutated into something even more deadly than the GMOs we already know. This may not be so far-fetched, actually:Monsanto has a corporate office in Arkansas(in Stuttgart, Arkansas) that's not too many miles from the Arkansas River.

Let me get this straight.  His hypothesis is that there was a mutation in GMO corn that was specific to the transgene, not the 40,000 other genes, and then this corn was magically transported into water and killed fish, because the Monsanto office is a few miles away.

Is it just me, or does this reek of intellectual emptiness?

Adams makes his usual allegations and conclusions without any evidence supporting them.  In other words, making shit up.  Only the scientifically bankrupt could make such leaps.  In typical Natural News/Anti-GMO fashion, the ignorant choose to dismiss real causes and facts to promote an agenda that feels groovy but is scientifically baseless.  This misdirection leads us away from real causes and eventual, scientific solutions.

Yo Mike, what are the "deadly GMOs we already know"?  From the peer-reviewed literature please. Oh, that's right, you can't find it there because BigFarma owns all the journals and scientists, leaving websites and opinions to do the scholarly heavy lifting.

Sadly, the article was also picked up by Google News.  That's how I found it.  The problem is that Natural News isn't about news at all, it is a website dedicated to promoting the naturalistic fallacy.  There is no science, no rigor, no review, just the opinions of a few whack jobs that make money by promoting junk and junk science.

Of course, maybe if the fish and birds were wearing Kinoki Foot Pads or energy bracelets this stuff would not happen.

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...