Wednesday, April 22, 2015

Precaution Potatoes! - Out of the EU and Organic Production

The discovery of transfer DNA (T-DNA) in sweet potato indicates horizontal transfer of genetic material from bacterium to plant.  The process is identical to that used in the generation of other transgenic plants, and transgenic plants bear the same bacterial DNA sequences used in the transfer process.

The sweet potato is thuslly out of compliance with European Union standards, and must not be cultivated on organic farms. We must follow the Precautionary Principle- right? 

Almost 50,000 angry petitioners stand up against sweet spuds! 

For decades anti-GMO groups have warned us against adding genes and T-DNA to genomes.  What do the critics say about T-DNA insertions?
  • ·        There are no long-term studies showing their effects or if products are safe.
  • ·         There is no way to guess at unintended consequences. Like causing Morgellon’s Disease and other infections.
  • ·         Sweet potatoes and foods with them must be labeled in the EU, as they contain a transgene.
  • ·         Sweet potatoes may no longer be grown in organic production, since organic cultivation specifically forbids transgenic plants.
  • ·         And right now Babes Against Biotech are feverishly unearthing every sweet potato grown in Hawaii and throwing them into a volcano.

Bummer.  These are radical adjustments, but are in keeping with the legal definitions and provisions as stipulated.  Just because the rules make no sense and are poorly conceived is no reason to stop following them now.  We have known this for a long time, and we need to enforce the rules, after all, it's for the children.

For me, it is sad because I love sweet potatoes, and don’t even get me going on how I can shove my face full of sweet potato fries.  Now that they are going to have to enter the rigorous deregulation process and may not be approved for 10 years, I’m going to stockpile.

And if you live in Benton County, Oregon—if you like your sweet potatoes, make sure you get out and vote, as your orange tasty spuds are now up for referendum.

Of course, my apologies to the sweet potato industry and I’m sorry that you are the new victim of stupid.   These are the rules that have been established by non-scientific minds, and it reinforces that we need to change the rules to something that makes sense. 

Monday, April 20, 2015

By 2030, 1 in 2 Children Will Have a Sweet Potato

Since the beginning of plant genetic engineering, one of the central criticisms has been that we never can predict the long-term effects of T-DNA integration.  T-DNA stands for "transfer DNA", and it is the little run of genes and stuff that is integrated into the DNA of the new host organism.  It is the piece of DNA that activists claim will unleash unforeseen devastation, and is the basis of all that's evil and wrong with the world, leading to disease, destruction and lost socks.

The recent sequencing of the sweet potato genome revealed that its collection of genetic material contains naturally-occurring T-DNA inserts.  Kyndt et al find that Mother "Monsanto" Nature has genetically engineered sweet potatoes, as they contain elements of horizontal gene transfer, making them naturally occurring GMOs.

Kyndt et al. find T-DNA in sweet potatoes-- but Monsanto didn't put it there, Mother Nature did.
Mother Nature is a Monsanto shill!

I'm not surprised.  A soil-borne plant pathogen that inserts its DNA into plants, probably has done that a few jillion times over plant history. Agrobacterium tumefaciens, or "Agro" is the bacterium that transfers a bit of its DNA to the plant in the hope of adding a few genes to make bacterial life more hospitable. It is the bacterium that is like the old college friend that shows up, moves in, but at least brings their own beer and bean bag chair.

Apparently at some point during domestication the a sweet potato plant became infected with Agro, and the integrated DNA has been passed along for generations. Today these bacterial artifacts are on the Thanksgiving Day table and have been a human staple for hundreds of years, and nobody has been harmed.

Or have they?

If you look at 1990-2010 USDA sweet potato production statistics in the USA, and compare them against MIT's finest scientist Dr. Stephanie Seneff's work, the results are clear.

Sweet potato production (blue line) and autism (bars).  Clearly the T-DNA in sweet potatoes is causing autism.  Or autism is causing sweet potatoes.  Glyphosate use (red line) might somehow also be related because it is involved in everything else.

Tonight the activists are working overtime, getting labels ready for sweet potatoes and trying to figure out how Monsanto built a time machine and did such evil deeds many thousands of years ago. At this rate, there will be more sweet potatoes, and if Dr. Seneff's logic is any indicator, there 1 in 2 children might have a sweet potato by 2030. 

T-DNA insertions are natural elements that dot plant genomes and potentially play roles in domestication.  It will be fun to hear how the realities of science continue to erode the arguments of scientifically broken movements.  How will they possibly distinguish Mother Nature's happy and benign T-DNA inserts from the deadly, poisonous ones introduced by humans? 

I'm excited to have a front seat for this discussion. 

Friday, April 17, 2015

Lazy or Plagiarism?

Did you ever read something and swear you have read it somewhere else before?  It happens to me now and then, particularly when something is so memorably awful that it burns a special place in my brain.

Here is one such instance.  A 2015 paper published by Hilbeck et al, co-authored by luminaries including Shiva, Hansen, Heinemann, Antoniou and others, is substantially lifted word for word from a 2013 website. 

Since its publication in January 2015, anti biotech activists have reminded us again and again, of the peer-reviewed journal that soundly declares no consensus on GMO crops. The paper, published in Environmental Sciences Europe, is a 'Discussion' paper, which means it is a non-peer reviewed opinion piece.

As a scientist, reviewer and editor I have a lot of problems with such work.  I do appreciate clearly marked Letters and Correspondence, and certainly welcome Opinions.  These can spark discussion and speculation, but are obviously distinguished as ideas representing a viewpoint that may not be supported by evidence.  After all, if they were actually supported by data, then such articles would constitute research reports. 

The part that bothers me is, that aside from an abstract, reference numbers and concluding paragraph, it is virtually word-for-word cut-n-paste from a website constructed in 2013.  Use of online plagiarism check tools indicate that there is 0% chance of the published work being original. 

However, the original statement on the ENSSER website was credited to the 2015 paper's lead author, so the journal-resident work is not a group of authors borrowing someone else's text.  Sort of. 

The pages below use yellow highlight to show how much of the 2015 ESE paper matches the website. 

The yellow highlight shows the direct matches between the 2015 published work and a 2013 website.  Such efforts would be considered an ethical breach in most universities, and certainly students have been reprimanded or excused for less.

Is it plagiarism?  That's tough call.  Certainly it falls under the definition of plagiarism in that it is a direct reprinting of text from an original published source.  The gray area comes because the lead author is the author of both pieces, and it remains to be debated if the ENSSER website is an "original source". 

"Verbatim copying of significant portions of text from a single source" is one of Springer, the publisher's, own criteria for plagiarism.

At the very least, it is supreme laziness, the desire to produce a political document that could be published in a journal, producing an air of scientific legitimacy on a position refuted by the broad scientific community. The fact that the author of the original work didn't take the time to simply re-write their own work is rather telling too. 

The journal is known for publishing scientifically flimsy political pieces. Here one is cut-n-pasted from a website, and that speaks very badly about the journal and the publisher. 

Sad.  I like Springer.  They've published lots of my work. 

It also is kind of unfortunate that it took a team of 15 authors to lift text from a website, then craft an Abstract and concluding paragraph.  Did all fifteen participate?  Sure did, according to the postscript on the article:

 "All authors contributed equally to the writing of the document" which I guess means that each one of them copied and pasted some text from the website? 

And you read it right--- the authors, some the most established activists in the field profiting directly from positions espoused in the manuscript, declare no competing interests.  Of course, the Springer website addresses that too, but nobody seems to care. 

Financial or other personal considerations from authors that could bias professional judgment and objectivity?  I guess when someone makes a living opposing accepted science, a paper they'd write saying that accepted science is junk might be a little conflicty.

I'm not the journal police.  I let the publisher know that this work pushed, if not crossed,  quite a few ethical lines. They've elected to not take action. That's fine. 

I think it makes a better point if it is left exactly where it is.  

It shows that there is an activist movement masquerading as a scientifically-vetted enterprise.  It shows their laziness, and a certain kind of irresponsible bravado, as authors hijack a journal and then don't even bother to populate that published opinion space with original work. 

But what do we expect?  Integrity?  Accuracy?  Sound science? 


This is just another great reminder that the movement comes first, facts, evidence and science are a remote consideration.  It also gives me a teaching tool and will be incorporated into our classes, as we train our scientists on how not to prepare a scientific work.

Sunday, April 12, 2015

Who Are the Real Shills?

I hear it almost every single day.  Because I talk or write about science, and promote ideas consistent with the scientific literature, I must be somehow receiving compensation to share such views.  After all, what kind of sick bastard would spend their personal time communicating facts to the public?  There must be something hidden!

These are the brilliant speculations that fuel the #Science14 public records request, the endless accusations of being a Monsanto lackey, and the distrust in scientists in general.  If we are talking about cool scientific ideas, then there must be some secret money trail encouraging that discussion. 

It is one of the most small-minded assertions I've ever heard, but coming from small minds it makes perfect sense.  There are a lot of people making big bucks by promoting bad ideas. They have been doing it for centuries.  Swindles are financially lucrative, because "there's a sucker born every minute", and many modern-day charlatans are cashing in on building fear and/or exploiting the credulous. 

It is the muck where Food Babes and Health Rangers are spawned. 

This discussion prompted me to think about the question, "What is a shill, and how would I know if I am one?"  For the purposes of this discussion we'll go with the idea that a "shill" is a "paid shill" someone receiving compensation for perpetuating false ideas. 

There are fundamentally two criteria.  

1. You must espouse a position that is not consistent with evidence.  Either out of ignorance, self-deception or knowingly false statements, claims are made. Claims continue to be supported after correction from sources with authority. 

2.  Compensation is received to make the claim. Some sort of compensation, financial, career motivation, etc is provided in direct exchange for the statements made.

Who are the real paid shills? 

This table sums it up pretty well! 

Who really benefits from the perpetuation of false ideas? As they say, "Follow the money!"

The table above spells it out pretty clearly.  There are many that promote scientific ideas and are well compensated to do so. These are the folks in companies, PR firms, advertisers, and others that make a living promoting scientific ideas-- especially if their efforts benefit a company or themselves. 

The second column are those that promote science and evidence strictly because it is the right thing to do.  These are scientists, volunteer science communicators, teachers, physicians, and their national organizations. The science shared is not source-dependent, as it changes based typically on evidence emerging in the peer-reviewed literature. 

The third column are the people that make a living selling information that is inconsistent with the scientific consensus, generating false or wild claims that result in increased visibility and financial gain.  Many of these folks promulgate bad information for a living-- it is what pays the bills. 

The fourth column is the most curious.  These are people, mostly professionals, that for some reason have adopted non-scientific reasoning and perhaps have a personal agenda or other motivation to espouse a non-scientific viewpoint. 

So who is the real shill? 

Column three! -- and these are the all stars of the anti-vaccination, anti-climate, and anti-GMO movements.  They get rich off of selling bad ideas. 

It reminds us of how the internet just aids in the dispersal of modern day snake oil, perpetuating bad information to the gullible for substantial financial gains.  Those are the shills-- those that enthusiastically promote a false idea for serious financial gain. 

Saturday, April 11, 2015

Bad Advice from the Well Meaning

I have a friend here in Gainesville, FL that I'll refer to as Annie. Annie goes to her temple, then squeezes out some yoga, talks of peace and love, smokes like a fiend, and then tells you how evil medicine is after she rips a bongload.  She's a sweetie that I would do anything for, as her kindness towards others allows me to approach her softly on issues where her science leaves much to be desired. 

Then last week she posts this on her Facebook page:

Don't get a shot-- take a shot!  A glass of plant goo is claimed to exceed vaccination in protection against the influenza virus.

She's crossed a line here.  I simply posted, "You make my science hurt" because any time I inject science onto any of her postings I get to deal with the usual patchouli-soaked retorts that make me lose faith in humanity. 

I have to deal with this one a little more aggressively. Folks are welcome to down as much plant juice as they can stomach-- but let's not tell outright lies that can harm, or kill, others. 

The flu is no joke.  Many are stricken every year, and this disease kills three times more in the USA in the average year than die from Ebola virus.  Worse, approximately 100 of those are pediatric deaths.

Hospitalization events due to do flu are additional costs to an overburdened health care system.

These can be prevented for the most part with a flu vaccine. 

Of course, juice drinkers will tell you that the flu vaccine is just a conspiracy by Big Pharma to make a quick buck and inject people with poison.  

It is another case where I have to figure out how to softly communicate critical science to someone that will not want to hear it.   I'll talk to her today.  Let's see how it goes... 

Monday, April 6, 2015

The Value of the Farmer's Voice

U.S. farmers make up approximately 1.5% of the population. They are the most credible source of information about production details, the inputs used, and the challenges faced.  However, they are not active in social media. 

Of course, there are notable exceptions, one featured here today.

On the other hand there is Moms Across America, a group of anti-farmer, anti-vaccination, anti-biotech affluent Californians that have a strong social media presence.  They don't know about farms and farming, yet they write about how detrimental farming is, they certainly don't like the major seed companies, and they even promote false or flimsy data. 

So Kansas farmer Mary Mertz reached out.  The following note was re-posted in the Food and Farm Discussion Lab on Facebook, after its original post was posted as a comment on the MAA site. 

Mary Mertz reaches out to Moms Across America.  Her heartfelt honesty is what is needed to build trust with the average consumer. 

This is a textbook example of how to make progress in this area. 
  • The message drips with credibility and honesty. 
  • It is kind, and emphasizes the values Mary and MAA share. 
  • While it would be appropriate to slam MAA as the dim bulbs they are, Mary is not critical of them, she discusses what she does in the interest of educating them. 
  • It does not attempt to change MAA (which will never happen), but instead it puts an honest and warm message into MAA-space where the unsure can hear an alternative, real message.
Farmers hold a huge amount of power in this discussion and are among the least likely to use it.  Their increasing participation can influence the hearts and minds of the people in the middle, those that do not have firm understanding, and the people that typically capitulate to the fear and lies promulgated by MAA and their cohorts. 

The American farmer will be the most impacted by bad public policy that restricts traited seeds, targets the products from them, or limits safe chemicals used for their production.  Farmers have the most to lose- yet the most power to influence the situation. It is great to see them reaching out more and more to a public that needs to understand where food comes from.  

Saturday, April 4, 2015

Glyphosate: Deadly Microbial Poison or Life Enhancer?

The recent flap on glyphosate has been fun to watch.  It is an ag chemical that is used on some transgenic crops that contain a gene allowing them to grow through herbicide treatment, where weeds die. This technology has been extremely helpful for farmers. 

Because the folks opposed to ag biotech have had zero luck tying the process of gene transfer or the genes themselves to any health issues, they have retreated to hammering glyphosate.  After all, it is the chemical that makes the trait valuable. Plus it kills weed pests, so it can be lumped in with the ever-evil pesticides.

Plus, herbicides by definition kill herbs, and herbs cure every disease in the world, ever. Big pharma just won't let that happen.

Therefore, glyphosate has become the new popular target for the anti-GMO movement. 

Of course, nobody points out that glyphosate is used extensively in non-GMO applications, such as a harvest aid in grains, clearing rows of weeds in tree-crop orchards, or heavy use by municipalities.  It is safe, cheap and works well. 

They also fail to point out that there is none, or next to none, on food.  It is sprayed on GM crops weeks before they flower, and most of it is long-gone by the time plant parts used as food are harvested.  Oops. 

"Roundup Herbicide" is a deadly poison that kills .... wait, what's this?  It makes bacteria survive better?

But let's play along.  Computer scientist Stephanie Seneff claims that it is responsible for half of autism cases. Web quack Joe Mercola claims that glyphosate causes celiac disease.  Retired scientist and hobby micro-cryptozoologist Dr. Don M. Huber says it pretty much causes everything else, including cancer, morgellian's, fibromyalgia, Alzheimer's, Parkinson's, and a list of a dozen other diseases. 

When pressed, none of these experts have a clue about how it works to cause the problems they claim. In science, disease-causing agents have well-defined mechanisms of action, in other words, when something causes a problem, we learn exactly how it causes the problem.  

Despite the claims of glyphosate-related ills, nobody can demonstrate any hard connection to the diseases in question. However, these folks boldly assert, without data, that clearly it is because glyphosate interferes with the microbiome, at least that's the conclusion drawn by Samsel and Seneff (2013), without doing any actual experiments to support that conclusion.

So the chemical you don't really consume causes all these human ailments by destroying internal microbes. 

So what does the new paper by Kurenbach et al, 2015 really say?  Glyphosate not only doesn't kill bacteria, it actually helps them survive. 

The group tested several bacterial strains for their response to antibiotics, in the presence of several weed control chemicals, including glyphosate. In short, when you grow cells in weed killers, they survive antibiotics better. 

Statistically meaningful differences in sensitivity were observed in many cases, as in the presence of weed control chemicals they survived ampicillin, tetracycline, chloramphenicol, ciprofloxafin or kanamycin treatments better.  

The authors then test the mechanism, which is a great next step. They hypothesize that the herbicides might increase the expression of an efflux pump, a kind of molecule that actively removes compounds from the cell.  Cells have mechanisms like to this to sequester and remove toxic compounds. Efflux pumps give oncologists fits, because they pump out chemotherapeutic chemicals. 

The authors use two indirect methods to test the efflux pump hypothesis, first showing that the promoter of the gene (the gene's on/off switch and volume knob) is activated by the herbicide.  This shows that the first step in production of the efflux carrier is active. The second test uses a chemical inhibitor of the pump to test if it changes the sensitivity to some of the compounds. 

The results are consistent with the hypothesis that herbicides activate mechanisms that facilitate removal of compounds like herbicides or antibiotics from the cell. 

The work seems technically solid and there's no real question there. 

The problem comes in how the authors chose to frame these data in the context of antibiotic resistance and its relationship to herbicides. This is where their agenda starts to show. 

If I was asked to review the work I would have noted the good experiments and statistical treatment.  However, I would have suggested that statements like:

"The magnitude of the induced response may undermine antibiotic therapy and substantially increase the probability of spontaneous mutation to higher levels of resistance. The combination of high use of both herbicides and antibiotics in proximity to farm animals and important insects, such as honeybees, might also compromise their therapeutic effects and drive greater use of antibiotics."

be a little toned down. Clearly they include the "honeybee" pathos (where I'm not sure how much antibiotic is used in bee hives, maybe there is).  At best, it is tempting to speculate that there could be enhanced resistance, but the herbicide levels tested are not likely to be encountered on food.  Even amounts used in the commercial formulations would have be directly in bacterial contact to make these experimental concentrations relevant. 

For instance, the glyphosate concentrations used are 31 times higher than the maximum amount allowed as food residue, and even those maximum residual levels are rarely encountered. 

The paper gets high marks for its methods, but the relevance to clinical antibiotic therapies is a stretch. 

Most of all, it shows that these chemicals have little effect, or minimal effect on bacterial growth at reasonably high levels.  This conclusion contrasts greatly with the conclusions of Seneff, Smith and others that claim the tiny amounts that might be present on foods derived from glyphosate-treated crops have profound effects on intestinal bacterial populations, and directly underlie human disease. 

This is a case where some good data are over-interpreted to support a conclusion, and that's a science no-no.  Stronger reviewers and a more rigorous editor would have asked the authors to adjust the language to fit the data, and fit the relevance to the concentrations used and where they may be encountered in food. 

Other than that, another good in-vitro study that has marginal direct relevance to antibiotic resistance.  It does frame a compelling hypothesis, and now we'll see if the authors follow up and expand these findings to actual biological circumstances, or if this one ends up as another one-off lab study with no relevance to the reaching speculation it makes. 

Wednesday, April 1, 2015

Science as a "Marketing Arm" of Big Ag

The most hilarious part about US-RTK is that they are so clueless on science that they'll actually print the stuff like you find here.  Go ahead and read it.  After you compose yourself from laughing, come back and continue reading. 

Their claim is that the GMO Answers website is a PR tool.  I suppose at some level it is, as the technology, traits, seeds and users of agricultural biotech have been defamed and smeared by activists for two decades without a whole lot of push back.  Here the science is related to the public, which I guess defines public relations. 

However, Truth does not need "PR"-- it just needs to be communicated effectively. 

That is what does.

For almost twenty years the non-scientific arguments, blatant untruths, and half-cocked evidence were allowed to tarnish the reputation of technology that has performed safely and effectively.  These efforts have led to calls for horribly-conceived, non-scientific and expensive changes in public policy (like labeling). The worst part is that new technologies that can help the farmer, the consumer, the needy and the environment are slow to develop. 

The organizations that fund GMOAnswers are tied to the ag biotech companies, so the unsophisticated thinker will automatically assume that the companies dictate what information is presented. 

But this is the difference between science and non-science. In the world of anti-biotech activism you can make up stats, skew numbers, conflate false parameters and generate false associations in the interest of fooling a reader.  That's common practice. 

Science must play by rules.  No matter what the ag biotech companies want, no matter what the communications firms desire, the facts are the facts, and the evidence rules.  Period.

If I read anything on GMO that was not true, I would tell them, not ask them, to correct it.  Period.  If they failed to do it, they would be the subject of a very pointy blog here at Illumination, and widespread criticism from the broader scientific community. 

So let's analyze the conspiratorial and paranoid USRTK rant.  Once again, they go after public scientists and promote nonsense, the old formula to keep the supporters happy and the cash flowing. 

Ironically, they get funding based on their support for non-scientific ideas, whereas the independent experts they criticize get nothing (except hassles). 

Click to enlargenate.  The thesis- activists like USRTK are not exactly happy that scientists have a place to speak the truth, and to share science with a curious public. It is sad to see them go after a resource that connects independent scientists with people that want answers. 

Click to embiggen.  This part shows a lot of the careful deceptive wording and reliance on low-quality "science", as well as their desire to discredit truly independent public scientists (like me!)

Perhaps my favorite comment by Stacy Malkan is that GMO does not address the "peer-reviewed statement" that 300 scientists claim "no consensus".   I hope they do eventually, heck, I might even ask the question on GMO Answers.   

First, they are still about 2,000 behind the Creationists that state there is no consensus on evolution, and waaaaay behind the climate change folks that say there's no evidence of global warming.  

Just because two reviewers for a journal known to publish soft work print an opinion (the article cited presents no new data), does not make it scientifically valid. 

To the casual reader or person concerned about ag biotech, there is one way to correctly interpret the USRTK claims:

GMOAnswers is an effective portal to obtain hard scientific information about the topic, a lot of it coming from independent experts.  This kind of information drops their stock.  As more people learn the science, and develop disgust for heavy-handed activist tactics, their credibility and influence continues to drop toward irrelevance. 

The avalanche of irony is that here is an organization getting paid to distort science, which is exactly what they accuse others of doing.  How can you sort it out?  Start with the hard science and compare it to what is presented at USRTK and GMO Answers. One of them isn't being exactly truthful.