Wednesday, January 15, 2014

Massive Data Do Not Support Huber's Claims

Dr. Don Huber is traveling North America warning audiences of a mysterious organism that causes diseases in plants, humans and livestock.  He talks to famers and concerned food-oriented audiences.  He does NOT present to scientific conferences, as scientists and their professional organizations do not recognize his claims, and confront him with questions that cannot be answered without invoking hand-waving explanations and elaborate conspiracies.

I have a problem with anyone manipulating the gullible for personal or political gain, especially when they use fear to motivate action.  After seeing Huber scare the pants off an audience in Gainesville, FL, I have taken up the mantle of holding him accountable for his bad science and manipulating people for his twisted motivations.

Today it occurred to me how we know, conclusively, that there is no mystery organism.  No doubt. Evidence of absence in this case is tantamount to absence of evidence.  It is just that massive. 


Today's technologies have uncovered massive DNA/RNA sequence data from humans, plants and livestock, the organisms Huber claims are infected.  In all of the petabytes of public information, there has been no identification of any mystery microfungus.  If anyone were to discover a new organism by accident-- it would be a huge story.

Huber's mystery pathogen is fiction.  Here's why.

Since the mid-2000s we've seen the price of DNA sequencing drop incredibly.  The technology allows scientists to obtain massive genetic information from any organism.  Animal, plant, whatever.

When we sequence a plant or animal we routinely find sequence that does not fit into the genetic blueprint of the organism.  These sequences can be assembled separately and compared to databases.  They are the bacteria, viruses, fungi and other critters that represent the ecology of the sequenced organism.  In other words, when we take apart the airplane we find all the hijackers.

My lab did this on accident.  In our 2010 paper in Plant Genome we surprisingly identified a list of organisms resident to a greenhouse strawberry plant.  We found evidence of snails, probably from eggs on the plant!  We’re talking sensitive technology.  Most of all, we found evidence of bacteria and fungi that are not even problems, or thought event to be present, in Florida. They are all here, just not an issue for whatever reason.  That’s a great find.

Back to Huber.  Soybean, especially production soybean, has been massively studied and intensely sequenced.  Commercial corn, cotton, etc have been analyzed ad nauseum and there is more data in public databases than can be imagined.  In all of the data, in all of the reports, in all of the understanding of gene function and gene detection—

There has not been one report of a mystery organism.

There is no sequence that has been found that is assembled into a creature representing a new kingdom of virus-fungus or whatever the hell he’s talking about.

This absence of evidence cannot be ignored.  While typically absence of evidence is not compelling, in this case it can be clearly stated that in the massive accountings of DNA and transcriptome (RNA) data, there has been no reported evidence of a mystery organism.  If it was there, it would have been detected, the research would have been published and the scientists would be fighting about who would get to sniff the cork.

Huber has provided no organism (despite requests), no culture protocols, and no evidence that it exists.  There are no scientists confirming his allegations and after nine years the only suspect is a fuzzy electromicrograph of a cellular Bigfoot that is likely an artifact or familiar structure.

On the other hand, the massive sequencing of agronomic genomes shows no evidence that it exists, which by default says it does not. 


This simple fact provides question number eleven to the HuberWatch list. 

"If this mystery pathogen is such a prevalent problem leading to crop failures and human disease, why has it never been detected in the massive public collections of sequence data?"

If you get a chance to ask him about that one, please do.  Of course, there probably will be a computer conspiracy that cleansed all evidence from public servers.  You know the drill. 



Tuesday, January 7, 2014

These Ideas are the Thoughts of Folta and May Not Represent...


Illumination is here to help you separate the science from the junk.


The blog Illumination was originally prepared to present my personal thoughts of science and its interface with society.  Carl Sagan said it best; we live in a world filled with science and technology, where nobody knows anything about science and technology.  We live in a world filled with charlatans and scam artists, malevolent activists and dangerous pseudoscientists.  There is a place for scientists to help buffer the public, especially those most vulnerable, from these harmful forces.

I’m a scientist and I love to read, learn and then share science.  It is what I do. Full time. I don’t have a family, I don’t have hobbies and have yet to hit a mid-life crisis.  The world is filled with fascination and I’m so fortunate to contribute to it.

I like to use the current topics of public scientific discussion to teach about logical fallacy, critical thinking, evaluation of science, and skepticism in general.

The problem is that many people do not agree with science.  When public figures speak of the science of climate change, GMOs, vaccination or other topics, some take offense, as scientific ideas collide with their worldviews.  There is retaliation against science and scientists that dare to present an evidence-based perspective.

Over the last several years I have found myself discussing transgenic crops and biotechnology, familiarly referred to as GMOs.  I’m glad to use this blog as a platform for information dissemination and discussion. I also occasionally write for Biofortified and Science 2.0. 

In 2013 I made a lot of people angry.  From activists to Hawaii to fans of Dr. Don M. Huber, many are not happy with my role in science communication, and more appropriately, scientific illumination of suspect concepts held dear by those with limited scientific acumen.  I have been effective in changing minds and sharing science.

Over the last few months, those who scream accusations of being unfairly attacked and silenced, are now attacking and trying to silence those of us that attempt to distill and communicate science.  Oh sweet irony.

In a world of aggressive science denial and internet-fueled self-empowerment, effective communicators can’t be tolerated.  The flying monkeys are out.  I've been hassled in many ways, some personally, some professionally.  There is a new push to hush me by contacting my university’s administration and complaining.   
So I’ll state it clearly here, again.  The thoughts presented here are my own, these are my personal statements and I stand by them.  They are not necessarily the viewpoints of the University of Florida or the Horticultural Sciences Department, so please don’t make that assumption.

If you have a problem with something I’ve said, let me know.  I’ve been wrong before and would love to discuss the issue or make a correction.  I learn something new every day.

The wrong way to handle this is to bother my boss and my boss’ boss, the governor or anyone else in an attempt to silence my level-headed, evidence-based discussion of biotechnology.

Sure, it might just work, as someone someday might ask me not to participate in hot-button discussions with lay audiences.  Universities are just like any other place and they don’t want hassles, unfounded bad press or anything to taint perception.  It takes a lot of time and resources to unravel a false accusation.

However, my university has stood by me solidly.  It is part of our mission as a Land Grant University to share science with the public. 

Let’s consider the irony.  The people that claim disdain for strong arm tactics by companies against farmers, silencing of critics and stifling of scientific information, are now using strong-arm tactics in an attempt to silence a public, independent scientist.

We live in challenging times where we need science to solve our most pressing problems. In order to maximize and hasten scientific impact we need the public to understand science, especially in hot-button areas.  We need everyone to learn the difference between real science and internet rants. 

2014 will be a great year for science and a great year for Illumination. I'm glad to have this little forum to provide a creative analysis of the current situation in biotech.  It is also wonderful to read the feedback, get the emails, both supportive and antagonistic. I learn a lot from the process. 


Friday, December 27, 2013

Demanding a Right to Know

In discussions around biotechnology and food labeling there have been three recent cases where people have demanded a right to know what's in their food, but then declined a kind offer to learn when I actually offered to help them.  The right to know is an empty mantra, three words that sound like they are pursuing freedom and information.  However, at their root there is no desire to know-- just a desire to believe.

*NOTE 1/4/2014 UPDATE BELOW*

Here I'll present Case 1.  Hofstra Debate Follow Up- The debate at Hofstra was quite one sided from my perspective. One side was about fear, Gish gallops and bad activist information, the other side was tethered with science. You can guess the side I was on.  One of the debaters was Bhavani Jaroff, a local chef, radio personality and food activist.  Her debate style was to discuss the most shocking activist statements, parroting garbage science and bad conclusions, following the party line with great precision. She stood firmly on Seralini's rat paper being retracted because of Monsanto, stood by the veracity of the data, and also used the widely debunked Aris and Leblanc "Bt in the umbilical cords and pregnant women" shock language.

I do appreciate Bhavani. While I found her critical evaluation of the literature as empty as the rest of the anti-GM movement's, I do like what she's all about at the core-- teaching people to eat better food and educating them about where food comes from.  That's something we agree on 100%.  The problem is that she's sold out to the vilification of biotechnology and is convinced that it is evil poison.

Plus, I had a great time talking to her before the event and at dinner afterwards.  She's obviously bright, but simply is a victim of cultural cognition-- in this case, if I'm going to believe that eating healthy is important, then I have to be opposed to biotechnology, no matter what the scientific evidence says.

During the debate there was a point where one side gets to ask questions to the other.  She held up Seralini and Aris and Leblanc as evidence to support her position. I asked her two questions, both about the papers, their data, methods and interpretations.  She had no clue, and obviously had not read the papers she presented as evidence, or at least did not evaluate the statistics and controls with any scientific resolution.

I felt pretty bad making her feel like a deer in the headlights with hard science questions, but if you're going to use that trash as evidence, then you have to be able to defend your position.  I would never have been so pointy about it at a dinner conversation, but this was a debate where hearts and minds could be swayed, so I was compelled to expose the empty analysis of an ardent anti-GM local hero.

Afterwards I did follow up with her with a kind email.  Certainly I respected so much about what she (here it comes) brought to the table. Is she just missing key information and want to know, or is she subscribing to and ideology with all of its scientifically bankrupt claims?

She certainly is intelligent enough to confront science if it is offered, and I do think she'll flip like Lynas in a heartbeat once brought to learn the evidence. But it is not going to be that simple.

I post the offer letter here, sorry for the small type, but I summarize below.

 A kind offer to explain the science, and a reminder that Ms. Jaroff and I were really on the same side of a very important issue- food and nutrition.


I offered to explain the science and walk her through the papers that were the foundation of the evidence in her presentation.  My offer was sincere.  From the little bit I knew about Bhavani I completely anticipated resounding cooperation, that she'd be thrilled to have time to discuss how a scientist reviews literature and determines that it is flawed. 

The email I got blew me away.  It started with how we'd have to "agree to disagree because I love the work of Jeffrey Smith and Vandana Shiva".  She then noted how science is not always right and cited margarine and DDT. She also reminded me that she can't understand why someone would want to block another's right to know. 

There you have it.  It frames my argument perfectly. I'm all for people having a right to know.  But if you want to know, you have to want to know facts.  You have to demand to know reality.  You have to desire to learn science.

I do not want people to have a right to know, if they opt to be deceived.  To know something wrong and promote it, is worse than knowing nothing at all.

As a scientist and humanitarian, I'll do my best to stop someone from sticking their head into a wood chipper, no matter how much it is their right to do it.

A right to know must go hand in hand with a desire to learn.  If you choose to only know the bad information, the lies and the distortions presented by Smith and Shiva, then a science-based right to know is meaningless.  If you don't want to know the science, if you want to 'agree to disagree' that science is better than activists belief, then what good is a right to know?

In other words, why do you want a right to know, when you already know everything?


** Update **

In fairness, I did receive an email from Bhavani on Dec 31 or so asking about the Gene IV issue.  I was glad to explain.  It is a good point that runs contrary to her original position and certainly says that my blog here may have overstepped the situation.  I'll always be happy to explain the science going forward, and hopefully this one question will be the basis of many more.







Saturday, December 7, 2013

Someone Forgot to Tell Me...

When does the crazy misinformation machine stop?

According to this thread over on AgTalk, I'm in the process of being censured, that is, that I'm in the process of receiving a strong formal criticism and reprimand for information stated.  So far, nobody bothered to tell me!


Censured? I think they have it backwards. I'm being heavily supported to moving up in our institution. 


As the caption above states, I've been interviewing for the Chairman position of the Horticultural Sciences Department, 50-some faculty over locations all over our state, the #2 hort crops state in the country. I've had support throughout my department and upper administration.  In fact, I had to be convinced to do it.  I've actually been in the job for a year, but only as an interim appointment. 

The post also claims that I interrupted and badgered Huber, that ultimately he told me off and the audience applauded.

Just wait. Let's let this continue to stew for a bit.  I just listened to the audio, it is amazing how I didn't interrupt.  All you hear are the unabated ramblings of Huber. Video does too, and soon we'll see what actually happened.

The take-home message is that here's a post again meant to harm reputations and draw suspicion, as well as support the claims of Huber's mystery pathogen. 

Let's revisit this one in a year.  Shall we? 

Wednesday, November 20, 2013

The Sincerest Form of Flattery

When they are trying to tear you down in cartoons, while distorting the scientific message and lauding the deception of a phony, you know you are doing something right.

When Huber publishes his groundbreaking story on the new pathogen I'll happily apologize for my skepticism, but I don't think I'll receive the same courtesy. 


It is also interesting that the kind hearts of they anti-GM movement now have me planned for a dart board and claim I'm all for hurting children.  Plus, the sophisticated use the word, "retard"

The scientifically illiterate hate Folta, but they loves them some Shiva! One of them is lying to you.


Once again a reminder that if you can't legitimately question the science, attack the scientist.  My request to Dr. Huber was simple and from a kind place of assistance.  It is unfortunate that the anti-GM movement found it offensive that I'd point out that the emperor literally wears no lab coat. 

Monday, November 18, 2013

Huber's Takedown- A Group Effort!

Over the last few days the emails have been coming in.  Notes of thanks and congratulations have arrived from all over the state, the nation and the world for publicly exposing Don Huber and his magic organism as fiction.  To recap, I saw him speak live, asked him to share the organism so we could sequence it, and then watched him pirouette through painfully awkward nonsense.  When I get some time I'll post the live audio here.

I'm quite uncomfortable here.  Not for throwing someone under the bus for spreading misinformation, rather, that this was just the most recent salvo in an ongoing call-out of Dr. Huber and his mystery pathogen.  The story really starts long ago with efforts over on Biofortified.

The criticism against Huber has been rich at Biofortified.org.  My recent foray is simply an extension of previous efforts. 


Anastasia Bodnar blogged about this almost three years ago.  Karl Haro Von Mogel spoke with Huber for two hours by phone, two years ago.  When encouraged to release the pathogen for wider science study, Huber claimed that the manuscript was in the works and would be published soon.

When I learned that Huber was coming here to Gainesville, FL to spread his nonsense I wanted a good plan.  If I came out salty and swinging I'd alienate the audience, and audience already skeptical of biotech and certainly accepting of Huber's trash science.

I contacted Anastasia and Karl about what questions I should ask.  Certainly I had ideas, but wanted to get their expert opinions.  Karl reminded me of asking Huber to release the organism.

That's where I thought to extend an offer to sequence it. Rather than getting something from him, I'd collaborate with him, and instantly solve this important "crisis".  It then went on to the petition to ask Huber to release the organism on change.org.

The fact is, there is no secret mystery pathogen.  Huber's out on the circuit fooling any room full of concerned citizens he can find.

That's sad, sick and wrong.  It is not the way we do science, not the way we represent science, and we never should twist science to suit some political end.

Without Anastasia, Karl, and Biofortified the stage would have not been set for that crushing takedown of pseudoscience. I just was in the right place at the right time to tip it in.

This illumination of Huber's sham is only in the first phase.  Watch for the next shoe to drop this week...

Wednesday, November 13, 2013

A Generous Offer to Dr. Huber -Turned Down

This is the beginning of the end of this particular sad tale of fear mongering and misinformation.

Anti-GMO darling Dr. Don M Huber is on a tour of the Sunshine State, giving two talks in Tallahassee and one in Gainesville.  In Tallahassee he got a rock-star's welcome with coverage on the news describing how dangerous GMO food is, and a meeting with politicians.  On my calendar November 12 had a big red circle on it for some time. Huber was in town tonight to tell his story of poison food and deadly new organisms.  I went with one of my favorite organic & sustainable extension/research faculty and had a GREAT time.

I never saw Huber's whole shtick.  It starts out about the failures of biotech and the crisis and danger from glyphosate.  A lot more on the details of his talk later.  Seriously, it was a science abortion.

A significant portion of the presentation addressed his mystery organism.  He allegedly has identified this novel not-quite-a-virus, not-quite-a-fungus plant-animal kingdom-hopping pathogen in 2005, according to his slide.  He attributes this organism to widespread plant harm, problems (like abortion) in cattle and a slide of disorders in humans.  The audience was amazed, a new infectious agent, probably made in the Monsanto dungeon.


The kicky title "Failed Promises; Flawed Science; Interactions of Glyphosate and GMOs on Soil, Plant, Animal & Human Health" a presentation by Dr. Don Huber at the Civic Media Center in Gainesville!


At the end of the talk I was identified in the room by Marty from Florida Organic Growers as someone in favor of biotech and we had a good smile and a certainly civil introduction.  Marty and others don't realize that I support all kinds of low-input ag and defend organic all the time. Still, all very nice.

He asked me if I had any questions for Dr. Huber.  "I have a lot of questions," I said, "But I want to start out with a kind offer."

STOP HERE.  ALL OF THIS CONVERSATION IS ON VIDEO AND AUDIO RECORDING.  EVERYTHING HERE CAN BE VERIFIED. 

Here's what happened.

"I offer to sequence the genome of the pathogen and identify what it is," I said.  "If Dr. Huber could kindly give me a small amount of the culture we could identify this new life form before Christmas."

I'm not bluffing here. We could do that.  I could pay to have the libraries made and get several lanes of Illumina sequencing done in a few weeks. We'd get several hundred million 'reads' (small bits of data) that could be computationally assembled into a whole genome of his novel organism, if it actually existed.  If it was real, we could have 300-fold coverage of its sequence.  Completely do-able, and I'd pay for it.

"So can you send me cultures?" I asked.

What do you think his answer was?  After a ten minute talk about the organism and how it is killing cattle and causing problems he said he would not send it.

I said, "Don, you say this is a crisis, that a new pathogen is causing disease in humans and plants, and you won't release it to the broader scientific community for eight years?"


It's tough to read this blurry slide, but my hands were shaking so hard from the blatant abuse of science and deliberate confusing correlation with causation, this is the best I have. I was livid.  he also blamed GMO and glyphosate as the causal agents of Morgellan's, as "agrobacterium has been identified in the muscles of the affected"  Ugh. 


He assured me that he had an international team working on it.  When pressed for collaborator names he said he could not reveal them because they would be threatened.

I said, "But I can solve this mystery in a month. People are dying, kids are suffering... Let's solve this mystery."

He went on to say that if he relinquished the new pathogen that I'd be threatened and others would be too.  I told him to meet me in a parking lot and hand me an unmarked tube, that I'd take the heat, that I am not afraid.  If I was threatened, we'd blow the roof off of the conspiracy.

He shifted gears.

"You can culture it yourself very easily," he said.

At this point people in the Huber-friendly audience were getting annoyed with his evasive nature. "Why can't you just give it to him?" one person asked.

I asked him to send me the culture protocols and instructions on how to isolate it.  He then said that I could probably not isolate it, that it is probably a prion.

THIS WENT ON AND ON FOR 15 MIN.  He's not sharing his finding with the broader scientific community. Period. 

I was frustrated and all he did was deflect and misdirect. I offered again and again to sequence the organism.  He went back and forth about whether it was even an organism, he said at one point that "it has no DNA", said at another point that I could never culture it.  It was 100% obfuscation.

Clearly the audience was seeing through his garbage at this point.  I wish there were 1000 people there to see his slimy gymnastics. One farmer in attendance afterwards said, "If someone is at that put up or shut up point and they keep making excuses of why they can't put up, you know something isn't right."

To add insult to injury I talked to Huber afterwards and asked him about the replication of the "Stunning Corn Comparison" that he finked out on with Vlieger and Ho, after I pressed them for an independent replicate.

"Go do it yourself!" he said as his handler walked him out the door.
****

The best part is that a room of interested and passionate people got to contrast how garbage science and real science behave in real time.  I offer to do the work, my efforts are blocked with threats of threats, alleged technical impasses, and restricted distribution of the materials-- materials he says cause disease and death.

****

In the early 1980's a new disease called GRID was infecting many people, primarily IV drug users and men in the gay community.  Scientists sprung to action to identify the source of this horrible pathogen. A few years later after hundreds of international efforts set out to identify the causal agent, the Human Immunodeficiency Virus was identified and published in Science by two independent groups. 1983.  A couple of years, 30 years ago when we didn't have nearly the tools we have today.

Within a few years we knew HIV's epidemiology, the structure of the virus, the way it spread and evaded the immune system.

This is how science works.

Huber has a pathogen he says causes massive human disease and plant death.  He will not release it to the wider scientific community for further tests, even after eight years of no publications or any signs of progress.

But he'll jet set around the nation scaring people into believing his story. This should speak volumes.  It did tonight, and in a room not usually warm to biotechnology.

What I saw him do tonight was scare people for two hours with frightening slides, no controls, speculation, outright bogus claims, flawed logic and straight-up fear.  Concerned heads around me nodded in acceptance, taking his authority as a credible source of information. I was so mad watching him misrepresent science and flat out spread misinformation to an interested audience.

It stops here. I want to shine light on his false claims and starting with his pathogen is step one.  I'm really angry about the distortion of science and the use of science to build fear.  Here comes the science hammer.