Monday, July 27, 2015

How Pseudoscience Propagates

The paper published in Agricultural Sciences by Shiva Ayyadurai presents a hypothesis that transgenic soybeans are high in formaldehyde and deficient in glutathione.  The story is covered in the two previous blogs.  I reached out to Dr. Ayyadurai and suggested that he come to Florida, we grind some beans, and actually do the test. 

There has been no response, but he is certainly out playing up his findings as factual confirmation of formaldehyde in soy.  Read the headlines of the websites below:



That is not what the report claims, but it is what the authors want it to claim.  No data were presented on formaldehyde levels.



Again, overstating what the report says.  In both cases they emphasize "peer reviewed", showing the danger of predatory publishing. 


A credulous, scientifically-illiterate activist media basks in the joy of the conclusion-- even though it has no basis in reality.  The intent is to frighten people about good food. 

What does the senior author say?



The demand for immediate testing has been requested, along wtih his kind assistance as a collaborator and co-author.  We are collecting soybeans and corresponding controls to actually do the measurement he should have performed.  


This is absolutely an anti-GMO question. To make a claim that has no basis in empirical science, and fail to test a computational claim, by a guy that is a known anti-GMO activist (along with this anti-GMO activist wife, Fran Drescher), is deplorable. 

It is creating fear about good food, something he has plenty of access to.  It is elitist pandering to a credulous, activist movement that simply wants to create fear, and advance an agenda.

This instance underscores the damage of low-quality research finding ways into low-end journals. They have a patina of legitimacy and easy fool willing readers into overinterpretation.  This is going to only get worse.

For now, the offer to demonstrate the presence of his predicted formaldehyde in soy stands.  The work will be done by an independent lab, identified yesterday, that is blinded to the sample identification. Glutathione levels will be measured using commercial kits, using student help, so we can teach how science is used to deceive for political gains. 

The data will be open access and published in a real journal, with the hope to be a lovely example of how activists are invading our literature to push an agenda-- not to use the scientific method to find the truth.  



Thursday, July 23, 2015

GMO Formaldehyde Challenge!

Last week Dr. Shiva Ayyadurai published a systems biology paper in Agricultural Sciences.  The report left much to be desired, and was critically analyzed here.   The anti-GMO activist community exploded with the news that "GMOs are full of formaldehyde", of course not realizing that the paper represented a deeply flawed and testable conclusion, that was not tested. 

Nowhere in the existing literature, where tens of thousands of plant products have been analyzed, did anyone find actual measurements that match the predictions. When your computer prediction is wrong, then why publish it? 

Because it did exactly what it set out to do-- create fear and controversy around technology that folks like Ayyadurai and his spouse, the fabulous Fran Drescher, fail to appreciate. 

Fran and Shiva have been vigorously defending the work online, with Drescher even making the bold (tired) claim that scientists are all just working "4 monsanto".  She's even been so bold as to demand testing for formaldehye on all GM products based on hubby's computational synthesis. 


Which is not what the computer prediction found. 


A little agenda showing? 

Downside?  Changing safety protocols based on a crackpot computer program's output that does not match reality. 

Argument from authority.  Great to have degrees, too bad to see them misused to achieve unethical political gains-- scaring people from good, safe food with nonsense.


#ShowUporShutUp. I like it! 

Let's talk about #ShowUporShutUp.  It is really simple to measure formaldehyde levels quantitatively in plant extracts. I've started to build a collection of materials to actually do the test. 

I'll have probably a dozen soy/corn samples on hand in a week or so, both transgenic (GMO) and corresponding isolines. This way we can test the systems biology-driven hypothesis, potentially validating Ayyadurai's findings. 

I was hoping to just do this on my own to not waste lots of time. However, transparency and wider involvement would be a good thing.  

Therefore, I've invited Dr. Ayyadurai via Twitter to come to UF and do the extractions and analysis with me.  We can do this in a couple of days, no problem.  It probably should be video recorded just for transparency, and we can make a YouTube video afterwards.

Protocols and statistical methods will be determined mutually ahead of time, and results will be compared to those from an independent lab.  We'll make all raw data public. How cool is that? 

We do need to keep analysis pretty narrow to formaldehyde and glutathione, along with a few internal and spiked controls.  

We'd do extractions and separations together here, along with a colleague who specializes in such things.  The three of us would publish the results together, all three authors, and would report about how the results support, or do not support the hypothesis, "GMO crops have higher levels of formaldehyde, and lower levels of glutathione".  

All samples will be blind to researchers, and coded by a third party. We'll do formaldehyde using published protocols and glutathione using a commercially-available kit I'll buy this week.  All materials will be screened for transgenes/lack of transgenes using PCR, along with appropriate controls. 

In addition, I'll cover the cost of taking a subset of the materials, chosen by Dr. Ayyadurai, and sent to independent analysis. We will include formaldehyde-spiked samples as positive controls. 

I'm usually not so rude, but since Ms. Drescher used the term, how about #ShowUporShutUp?  

Or as it should be put, let's do the experiment. Let's agree to the materials to be used, and quantitative methods.  Let's agree on an independent lab to validate results. 

If it actually hyper-accumulates formaldehyde, then that Science paper will look pretty good on my CV.  

What do you say Shiva?  Let's do it.  Plus you'll have a good time down here in G-ville.  We'll welcome you with open arms and a kind spirit of finding the Truth through collaborative, transparent research. Show me I'm wrong, that would be just fine. Let's do it.



Tuesday, July 21, 2015

Independent Big Ag Research - Lose/Lose!

Critics of agricultural biotechnology claim that there is no transparency and no independent evaluation of transgenic crop products.  Of course, there are many, many cases where academic labs are recruited to perform independent analyses.  

When independent results do not match the company results, the project is DOA, at least temporarily. 

When the independent results do match, and those scientists report them, they are admonished as shills of Big Ag.  The implication is that companies do not fund research, they fund the manufacturing of favorable results.



Damned if you do, damned if you don't. 

This came about because I found a website listing USA public universities and the funds donated to them by ag companies.  This is all public record.  The surrounding text said that university results could not be trusted because of financial influence. Who else should pay for the company's research? 

The bottom line is simple, independent research is valued because scientists have specific skills, along with the tenacity and courage to tell the truth. A company potentially commercializing a product does not want something released that will come back to haunt them later-- remember, these are money-grubbing, evil corporations, bent on keeping shareholders happy and they can't endure expensive lawsuits and bad PR.

The people that make such allegations come from a place I don't understand.  I could not fake data, lie in a paper, or publish something I knew was wrong.  That stuff stays in print a long time. 

But we're dealing with people who brandish an agenda, we know they feel like victims, and that being untruthful is an acceptable part of fighting their battle. 

All together, it is a perfect storm of nonsense and hypocrisy, and the losers are the people that need good technology the most. 



Sunday, July 19, 2015

Munich is Not by Florida; Soy is Not High in Formaldehyde

If you developed a computer program that integrated internet data to predict the location of Munich, and the program told you it was squarely in the Gulf of Mexico, right off Florida, it does not mean that Munich is in the Gulf of Mexico, right off of Florida. 

It means that your program, your assumptions, or your input data are wrong. These things are quite testable. 

When you decide to not challenge those data, but instead publish a map showing that Munich is squarely in the Gulf of Mexico, opposing all other data and the claims of millions of rather dry Germans, it does not mean that you are brilliant.  It means you have absolutely no clue, or more likely, have some reason you want a major German metropolis to be a two-hour boat ride from Tampa.  

When you are the map publisher that actually prints the deceptive map, what does that say about your integrity as a reliable information source?  



If your computer algorithm predicts a major European city is closer to The Everglades than the Alps,  you might reconsider your program, the input data, or your competence as a programmer. By all means, don't publish the map, or lots of well meaning drunks will drown looking for Oktoberfest.


New "Research"


I looked at this steaming deuce of a paper last week and hoped that it would just be ignored.  But alas, a dozen emails later, and a few "Ha-toldya" twitter comments and now I actually have to waste time noting why the paper is just about as awful as they get.  Biased, conflicted authors want an outcome and develop a computer algorithm to produce it, and it does not disappoint.  

How to Scare Parents

If you wanted to design an experimental outcome that was scare parents and influence  political decisions, it might be effective to find something dangerous in their food.  What plant metabolite would you suggest?  Of the tens of thousands that occur in plants, nobody is going to freak out if you over-produce eugenol (the stuff that smells like clove oil) or ascorbic acid (vitamin C).  You need something scary, something evil-- formaldehyde! 

Formaldehyde!  Of course!  This takes us back to the famously debunked fake data in the Stunning Corn Comparison, where they claim to have found formaldehyde and glyphosate levels through the roof!  So this new prediction validates and verifies that fake data in the soil test chart.


Systems Biology

Let's visit the paper by Ayyadurai and Deonikar, published in Agricultural Sciences, a journal I've never heard of, and a journal with no actual impact factor.  The publisher is Scientific Research, which is on the 2014 list of predatory publishers

The work, entitled,  "Do GMOs Accumulate Formaldehyde and Disrupt Molecular Systems Equilibria? Systems Biology May Provide Answers" was recently published, and one look is all you need to see agenda and bias, and a new dookie in the collection of peer-reviewed (by what peer I don't possibly know) journal papers that will be held up as conclusive evidence against agricultural biotechnology. 

How does systems biology work?  It is a computational approach where a series of inputs, usually data from published work that are matched in silico to generate new hypotheses. It is a way to make predictions based on integrating existing data, and then statistically deriving a likelihood that the predictions may be correct.  The predictions can then be tested and the systems approach validated. 

Now when a systems model does not match what we know, it says that the model is wrong. If the model puts Munich in the Gulf of Mexico, it says STOP, rethink the input data, assumptions or the algorithm itself.   If I'm the scientist, I don't publish that flawed model, I go back to the drawing board, look at my inputs and assumptions and start over. 

But It Says Formaldehyde.... 

This outcome is likely exactly what the authors wanted to see, and allowed them to publish a verbose, poorly-written, goofy paper that serves an important political purpose to advance at least one of the author's interests.  More on that later. 

The bottom line is, corn is probably the most biochemically dissected plants in terms of composition. Soy too. There is no evidence ever published or otherwise reported in a legit place that shows a difference in formaldehyde between GM and non-GM varieties of anything. These authors could have tested their prediction, and maybe they did, but there is no evidence of formaldehyde ever reported.  

Munich is not in the Gulf of Mexico. 

Brief Scholarly Review

The paper would have been rejected out of hand because the writing is awful, the conclusions overstep the data, and the data come from inputs that are not reported and apparently do not come from peer-reviewed sources.

1.  The writing is pure rhetoric, the first line stating that safety is a "contentious issue" when safety of transgenic crops has been well established for two decades. Constantly referring to "GMOs" is meaningless.  It is not a scientifically precise term, and any transgenic organism should be studied on the merits of the gene and the organism it is in.  Are GMO microbes making insulin equivalent to cotton making Bt proteins?  No.

2.  It is unclear what data were used for input and where they came from.  They cite "pubmed/google searches" and list their search terms in Appendix A. 

3.  What organisms, what were the transgenes, what tissues and what conditions were used in the input data?  Not terribly clear. My guess is that they actually used the numbers from the Stunning Corn Comparison.  

4.  I want a sandwich, so I'm not going to keep going.  Bottom line is, they make a computational prediction and it is WRONG.  There are no data that support their conclusion, nor do they attempt to present any. 


What is the Purpose of this Work? 

First, what do we know about International Center for Integrative Systems?  Certainly sounds impressive!  Turns out it is a 501(c)3 non-profit organization, surprise, started by the lead author.  They have a variety of projects, including one that seeks to define standards for raw and organic food.  A little poking around the website and the agenda is showing.  


The International Center for Integrative Systems may have a little conflict of interest, as they also promote foods that are not GMO. 

The International Center for Integrative Systems seems like a well-financed woo factory. Read this. Yep, no conflict of interest in outcomes that harm safe technology and can bring in the donations! 

The lead author is Shiva Ayyadurai, a guy that claims to have invented email and has a rather checkered history.  He's married to actress Fran Drescher (aka Bobbi Flekman) a staunch anti-GMO activist who has appeared in many venues stating her anti-GMO beliefs. (Note. I always liked Fran Drescher. She survived a rather nasty bout with cancer, she always was great in interviews, and while I never was a fan of her on prime-time television, I did feel bad when she was ill, but she's off-the-rails goofy now)

Could this simply be someone tied to the anti-GMO movement putting something appearing scientific and complicated with no sound biological conclusions into the public science space?  

Ding! Circle gets the square. 


Should Scientists Point Out These Journals/Publishers? 

When predatory publishers, or journals with such lax standards allow such things to pollute peer-reviewed space, shouldn't there be some repercussions?  They are confusing the legitimate dialog, getting used by activists to put faux data with strong conclusions into an important conversation. 

I think it is time that we make visible the publishers that manufacture the map placing Munich in the Gulf of Mexico, without ever asking someone to take a look first. 

Going forward, can we all agree never to publish in Agricultural Sciences or any of the journals from the publisher Scientific Research?  If they have to tell us it is scientific research, it probably isn't.   








Thursday, July 9, 2015

Repeat a Lie Often Enough...

It was Nazi guy and photographic sour-puss Joe Goebbels that might have said, “If you tell a lie big enough and keep repeating it, people will eventually come to believe it."  Nobody really knows for sure that it was The Goebbler, and ironically this quotation has been ascribed to everyone from Hitler to Martha Stewart. 

It does encapsulate the phenomenon spawned by the 2011, long-debunked paper by Aris and LeBlanc, claiming to detect the BT protein (presumably from transgenic crops, but that control was never done) in fetuses and pregnant mothers. There have been a number of brilliant discussions of why this work is not credible, posted here, here, here. here and here.  I even discussed it here

One of them is from New Zealand and the other from a French dude, two classes typically not immediately disqualified as corporate lackeys. 

But those facts don't get in the way of GMO Free USA, a group that latches on to any report it can manipulate, regardless of its authenticity or scientific rigor. 

Despite all of the well-constructed criticisms, they still promote the work as conclusive evidence of transgenic crop harm. Isn't that deceptive?  



Why hasn't further research been done?  Because the first research was trash. No reputable scientist would waste their time and wreck their reputation chasing this nonsense. 


Again, this is the attempt to persuade the middle, frighten mothers away from perfectly safe food by using such imagery and (now well-debunked) claims.  

That should mean something.  If Aris and LeBlanc's claims were real, they would have published the follow up in 2012, maybe two more in 2013, and by now would have a complete dossier of how these proteins moved from corn to fetus, and how the corn consumed was different than the BT used on organic crops.  We'd know if there were biological consequences too. Other research groups would repeat and expand the study from the crop science and human health side. 

But when the first work was incredibly flawed and over-interpreted, its death on the science vine is precisely consistent with the typical resting place for work that should have been more carefully reviewed and never published.  The paper could have been published, but should have said, "No clear evidence of Bt using this method."  That's what the data presented tell us. 

Since it was published as an alarmist, over-interpreted work, it now is dead to scientists, but alive and screaming in activist circles, where people believe first, and ask hard science questions, well, never.  


And what does the internet say?  On sensationalist websites science takes a back seat to vivid imagery of poisoned babies, where the intention is to frighten mothers away from perfectly safe food.  


It pains me to write another blog on this antiquated, long-debunked nonsense.  However, it keeps popping up, just like every election cycle when some group of brainstems feels it necessary to introduce a bill to teach creationism and our 6000 year-old planet in science class. 

Some fantasies last a long time.  Worse, they still are used to trick others.  Goebbels knew that propaganda was an important tool, that continued repetition of a falsehood had the potential to cement the lie in common vernacular.  GMO Free USA and others know that. Dr. Chuck Benbrook even reported the "umbilical cord" findings in a testimony to the Pennsylvanian House of Representatives Ag Committee on October 6, 2014. 

Why do people still believe it?  It reinforces what they want to believe, that safe biotechnology, used for almost 20 years now, is somehow harming us.  They exploit the vivid imagery of poisoned babies to emotionally propagate that falsehood, and hopefully scare mothers, with often limited food resources, away from safe and affordable food. 

Shame. 

Monday, June 29, 2015

High Roads

Over the last few years you'll find that a substantial number of my twitter posts are followed by the objections of a certain veterinarian from from Long Beach, CA.  I'm not naming her here because I don't want anyone searching for her professional or business information to find this page. This is an appeal to others to take a high road in dealing with her, and if possible, to not engage with her. 

Why is it a problem?  

She comments on my blog posts. She slams me on her blog. She systematically checks all of my tweets and chimes in on a large number of them, using fallacy to negate key points. She has dug for, and has broadcasted personal financial information, obtainable because I am a public scientist, then she claims I'm paid by Monsanto and not a public scientist.  She's endlessly tries to tarnish my reputation as an independent voice of science, as an expert in genomics and someone that can faithfully interpret the literature for the general public.  

I'm comfortable to make these statements because her words are proudly part of her public persona, placed daily into various venues for all to see. She uses her real name and defends her positions, which is admirable. You can scroll backwards through her timelines and bask in the vitriol. I keep a file of several hundred screen shots of angry and defamatory posts she's made about me and other scientists. 



A little sample of the nasty comments I've saved over the years. 
I'd rather keep it all private for now.


One side of me would love to post the whole set of screenshots.  I've been told that her comments cross lines and are legally actionable. I've asked her nicely if she could refrain from commenting on just about every post, and that does nothing. It just keeps coming. 

Still, I sit on my little treasure of anger nuggets. They really should never see the light of day, but it is an ace in the hole in case she ever starts creeping me out with facts about my wife's business again. 

*****

When I visited Long Beach, CA in 2014 I invited her to lunch. It was mega weird, but we ultimately had a nice chat, and it was a positive visit. I toured her clinic and answered all of her questions. My point was a simple one-- to try to build a personal connection with this person that finds it necessary to endlessly chastise me and harm my reputation.  Maybe if she saw a real person, and understood how damaging false claims are to a public scientist's reputation, they might stop.

That's what this discussion needs.  Fewer all-caps, softer tone, evidence-based content... and buying someone a breakfast burrito.


Even if it doesn't work. 

And before you scramble into the bowels of the internet and shove my own words in my face, yes, I know that I have been less-than-cordial on a few occasions.  That's partially why I'm writing this. It hurts me to be like that, and I do tend to apologize when I cross that line. I know how much it hurts, and I understand that it is not how we should treat each other. 

Most of all, as stewards of science and purveyors of evidence, we must follow the truth, and do not need to operate like that.

*****

About six months ago I got an email from someone with an attached screencap.  I don't remember what it was, but it was some dirt about her that someone scrounged from somewhere on the web, and he/she was so excited to blow it up in a public forum in an act of retaliation.  True, false, manufactured, whatever, it was not important.  That's not the way to correct this situation.  I suggested that their quest to smear her end immediately, and it did, as far as I'm aware. 

I'm glad.  I know what it is like to have people trying to damage my reputation, and I don't wish that on anyone. Even cranky people.

I have a list of people that have tried to get me in hot water at my university. I also have false and defamatory statements made by Dr. Don M. Huber in a certified letter to my superiors.  I have a letter from another sorta-academic that reported a simple misunderstanding right to my boss, complete with legal threats. Ultimately it was a simple explanation, something relatively minor, and I was quick to deliver an appropriate apology. 

I know what it is like to have people spread bad information about me and try to harm me professionally. 

That said, I'm disappointed in the fact that her business website has now become the target of those that disagree with her about non-business issues.  Her business facebook page has become a wall for an agriculture debate.  I even posted something there about how she treats me, and when I realized it was her business page, I deleted the comments. 

If you are reading this and you are disappointed in her approach, please take the high road.  Refrain from angry retaliation in social media- especially in ways that would harm her business or her professional reputation. I have no reason to doubt that she's probably good at what she does, and people that care for animals automatically get points in my book. 

The best alternative is to block her from commenting.  I didn't do that because I wanted to monitor what she was saying about me and others.  However, at this point I've blocked her from Twitter, I will not reverse that action. 

She has not been blocked from my blogs because I am critical of the blogs that remove my comments.  However, I think a policy change is probably going to happen soon, probably right after she chimes in after this posting about what an asshole I am. 

And I did invent, and she inspired, the hashtag #blockthewhackjob, and have used it on her at least a few times.  I'll own that, but I won't use it again. 

My request is that we take a high road.  No matter how much it hurts, let's do it.  Don't try to harm her business.  Don't argue with her.  

Replace #blockthewhackjob with #highroad 

It is disappointing to see where this has gone and I'm sorry for my lapses.  I have to remember that the folks we need to convince are not the people like her.  They are the folks in the middle that are also repulsed by her message and approach.  Why would we adopt that? 

Let's let the science do the talking, take the high road, and move forward.  Block, ignore, whatever -- but don't get down to that level.  Let's lead by example.  Who knows, she might be our best future convert. 






Saturday, June 27, 2015

Celebrating a Failure, That Really Was a Success

You miss 100% of the shots you don't take. -- Wayne Gretzky



Back in 2012, the activist group Take the Flour Back was settled on destroying a science experiment.  The trial was set on an English hillside near Rothamstead Research Institute, rows of wheat specially genetically engineered to produce a natural plant compound (E-beta-farnesene) that faithfully repelled aphids in lab experiments.  Certainly plants protect themselves with natural compounds from insect pests, and engineering in a compound that repels pests but has no effect on humans would be a great innovation. Such approaches have been tremendous environmental successes in corn and cotton.

After pleading on You Tube, scientists convinced the activists to not destroy the crop, and to let the trial progress to completion. Public pressure was palpable, and the to-be vandals saw the potential backlash of their actions. 

The trial would proceed, and would-be crop crushers went back to hackeysack and glassblowing. 

Turn the clock ahead two years. The data are in, the experiment is over.  The results show that the approach does not produce a significant reduction in aphids in a field setting. 

What does the media say? 


The anti-GMO media empire is dancing in the streets, as a solution to limit insecticides has not provided sufficient data of efficacy. 

In these media outlets the trial is called a "failure" and a "waste".  My Twitter feed also erupted with posts rubbing my biotech friendly nose in the outcome of the trials. True to form, it exhibits that these folks know absolutely nothing about how science works.


Time to celebrate!  A couple of incoherent caveman rants seem to bask in the excitement that a public test of an insecticide alternative did not produce desired results. 


Actually, the experiment was an outstanding success

Why?  It answered the question.  A hypothesis was tested, and the data did not support it.  That is how science works.  It only is a failure if the data were noisy or the experimental design was bad.  Ask Seralini how that works. 

Experimental trails are not failures if the outcomes are reliable.  The only failed experiments are those that are never done, or those that are done poorly so they must be repeated.  A solid answer is a good outcome, even if it does not support the hypothesis. It just means the method needs to improve, or it suffers from insurmountable technical drawbacks.  

It could also mean that the complexity of the problem was under thought. That happens to me all the time. In my lab, a surprise negative outcome is a good thing, as it means there's more thinking to be done.   

The aphid-resistant wheat is a major win for the research group, as it says that they now need to rethink the approach, that the methods were insufficient to translate what was seen in the lab to a field setting.  That's good to know. 

Off to Plan B. 

Notice how scientists and activists interpret a negative result.  The writer at Daily Mail referred to Rothamstead's words glossing over the reality. 


This is how science works.  We take baby steps, demonstrate that a concept works in the lab, then take it to the field.  Field experiments subject even the best experimental system to a new level of noise and variables, real-life inputs that challenge the models obtained from controlled environment studies. 

It was not a failure.  Solid results are solid results, and sadly these did not support a hypothesis that the plant could produce the repellent. 

But wait!  I seem to recall the endless screams that experiments just generate fake data and that scientists can't be trusted.  They get the results they want, and that independent research is just a corporate proxy.  Where are those voices now? 

Congratulations to the scientists at Rothamstead Research Institute. The experiment turned out to be several experiments in one.  Outside of your original proposal we learned:

1.  That scientists can speak to a concerned public and change the discourse.

2.  That the public needs more help in understanding how science works.

3.  That activists are so set against a technology that a negative outcome by a public lab (not a company) is celebrated, even though the purpose was to limit environmental impact of farming. 

I applaud your efforts, and this is one small step for a lab, one giant leap for science. On to Plan B.  Somewhere around Plan F we'll have a solution, but we'll have to go through B, C, D, and E first. Congratulations and thank you for defining the first step.