Sunday, January 11, 2015

Horizontal Transfer of GMO DNA

To the critical science reader, the claims by the anti-GMO world are a goldmine of intellectual turds.  Over the last few weeks I've been blown away by the junk that is accepted and promoted by folks like (we don't know their actual name, just their fake sock puppet name) GMO USA.  Unfortunately I've been behind on a dozen writing assignments and can't very well put fun discussions like this into the public space without feeling a bit guilty.  However, I could not let this one go! 

To the rocket surgeons over at GMO USA, the work by Oraby et al (2014) is quite compelling. However, to anyone with even a high-school level understanding of the science, these data are just awful, and the conclusions unacceptable. The title says "Horizontal Gene Transfer" when the authors don't even test for it!

The manuscript was published in the African Journal of Biotechnology, a journal with an impact factor of 0.5 or so.  The lead author, Hanaa Oraby, has some publications here and there, so there's evidence of actual scientific training, but his work is rarely cited with a total of 109 citations since first publications in 1989.

This is important because the claim is that the authors have publishable evidence that the Cauliflower Mosaic Virus 35S promoter, the molecular switch that drives expression of a transgene at a high level in some transgenic constructs, is detectable in brain, blood and liver.  They claim that this is due to horizontal gene transfer, meaning a stable integration into genomes in these cell types.

They start with 19 experimental and 10 control rats, feed the former a GM diet from weaning and the latter a non-GM diet.  They sacrifice the animals at 30, 60 and 90 days,and prep DNA from the blood, liver and brain.  They then use PCR to detect evidence of DNA from the CaMV35S promoter using primer pairs designed against the DNA sequence.  PCR is the sensitive detection method used to amplify specific DNA fragments.  


The results show that after 40 cycles of PCR on 100 ng starting template that the authors can amplify evidence of the CaMV35S promoter in a fraction of their experimental rat parts, but not controls. 

Strengths of the work
1.  The authors actually sequenced the product to show that it is not just a spurious artifact. 
2.  The authors use non-GM fed rats as a control.

Major Weakness!
The two smaller primer pairs are "nested", meaning the sequences are found within the sequence of the large fragment.  However, the authors detect the large fragment, but in the same samples do not detect the small fragment!  They say that the short fragments are not taken up as well as the large ones.  That might be the case, but the small fragment is part of the large fragment-- so when the large one is detected, you'd have to detect the small one!   This point strongly suggests the authors are measuring false positives. 

Weaknesses
1. Figure 1 does not show a negative control
2. The authors start with 100 ng of template!  This is a huge amount to start with. It increases the likelihood of contamination and false positives. 
3. The authors rely on 40 cycles of PCR to amplify their targets.  The use of this many cycles cannot be reliable, as a bona fide molecular target would amplify in 30.  Anyone that does quantitative real-time PCR knows that signals occurring after 35-40 cycles are evidence of contamination or artifacts.
4. The authors do not provide positive controls for PCR in their assays, which would be helpful.  A quantitative measurement would be good too.
5.  The "transfer efficiency" says that DNA was detected in 1-4% of samples, yet they authors present some level of detection in 100% of agarose gel samples. 
6. The values in Figure 6 depict "mean of GMtransfer" but shows no units and the values are based on 6, 6, and 7 rats.  Not sure what these numbers mean or how they were derived. 
7. When they report that positives were detected in "33, 37, or 52%" of samples from 30, 60, and 90 days, these are based on six rats, six rats and seven rats respectively.  They must be referring to positive samples, not positive rats (three samples per rat) to get these values, so rats with a "positive" in one sample were negative in others. Again, more evidence that they are measuring noise. 

Conclusions:

When you have to rely on 40 cycles of PCR on 100 ng of starting template as your detection method, results are difficult to trust. Even with negative (non-GM consuming) controls, "detecting" a positive in 1-4% of samples after 40 cycles is not strong evidence of "horizontal gene transfer". 

Something concrete would go the extra step.  Prepare DNA from nuclei so that it eliminates fragments that might just be circulating in blood, as the authors cite that DNA can be found in the bloodstream (brains and livers have blood too).  Then amplify at fewer than 30 cycles using a nanogram of template, and show independent replicates and that multiple primer pairs targeted to the same DNA template amplify it as well.  That would be a start. 

The authors show some weak bands on a gel that represent only a fraction of the samples analyzed.   They apparently used 19 experimental animals and made three samples from each.  It was not clear if the samples showing positive for one primer set also showed confirmatory positives for separate set.  In fact, it appears that it is not the case, as there are only three positives for blood and more for others, when using different primer pairs.

The results were also from a single experiment, so any trace contamination would not be flagged by an inability to replicate in subsequent trials.

Overall:

I get asked to review for the African Journal of Biotechnology all the time and never accept an assignment.  If they are willing to publish single replicates from cherry-picked data sets, then it is not a place that I need to invest my time.  These data are hardly compelling and my feeling is that if a comparable number of controls were used they'd see the same data there as well, even though the "data" are hardly reliable.  Size and sequence indicate they are amplifying and sequencing their target, but where there is zero evidence presented that it comes from horizontal gene transfer. To get that, they'd need to demonstrate that it is actually integrated, which is not impossible using similar techniques.

That would be a real story, and would be in Science or Nature, not the African Journal of Biotechnology

Wednesday, January 7, 2015

What Shiva Can Teach Us About Science Communication

We can learn a lot about people from not just what they say, but how they choose to say it.  Communication scholars claim that something like 75% of meaning comes from non-verbal cues. Non-verbal cues are not just gestures, they come from our rate, volume, proximity and our willingness to absorb feedback.  Many suggest that the non-verbals communicate true intention, and that these signals may not always match the words.    

When we critically evaluate the non-verbal performance of Dr.Vandana Shiva on China’s CCTV, (beginning at 23:00 min) we learn a lot about the person. This video is a MUST WATCH.  Portrayed by her supporters as a kind-hearted and gentle defender of the downtrodden and the environment, we see her true colors. It is not just her words, but the way she chooses to say them. We can analyze her communication style and rhetoric and draw some important conclusions.


If you want to learn how NOT to discuss biotech, watch Shiva closely.
Nobody learns anything from an angry steamroller. 


The discussion was about biotechnology, particularly the interface between biotech and China’s policies. China is a massive importer of GM soy and corn.  However, activists have made amazing headway in tarnishing the reputation of a technology that Chinese scientists are poised to dominate. Anecdotally, there are literally thousands of potential products, from disease-resistant rice to improved corn, that Chinese laboratories are set to release.

Back to Shiva.  The host was aware of the limited time for the conversation and she asked specific questions.  Rather than answer the questions directly, Shiva took the opportunity to grandstand, speaking loudly and angrily over the host while other guests sat quietly. She blatantly ignored the host's requests for order and was abrasive and disrespectful.

Aspects to Note

She dominates a conversation.  There is an angry arrogance that comes off from the first moments at 27:20.  From 27:50 to 28:50 she loudly ignores the host and and attempts to control the flow of what is designed to be a discussion.  The host even had to reign her in, stating, "We're not having a shouting competition Ms. Shiva..."

The camera actually pulled off of her to a wide shot of the stage to at least take the focus away from her domineering. 

She does not answer the question.   The host even asks her to specifically answer a question about if we need to carefully consider all forms of genetic improvement.  Shiva goes into a rant on long-laid-to-rest claims about antibiotic resistance and viral promoters, never answering the question.

Emphasis on fear building.   Note the hard emphasis on “toxin” when discussing Bt.  Of course, we know that this protein is not toxic to non-targets, including most insects, but for her agenda she must install fear by manufacturing risk using key buzzwords.  She also claims that there is no testing or regulation, which is patently false. 

She plays to the myth and conspiracy.  Not only does she lay on the monarch butterfly canard, she claims that independent scientists are "being silenced".  She raises Pusztai and Seralini as examples of scientists that were silenced, ignoring of course that nobody else has replicated their work, and the scientific community notes those authors as less than credible.   
  
CONCLUSIONS

What can we learn about Shiva?   She’s a hard-line activist that is not afraid to distort facts, play to old myths and rely on conspiratorial thinking.  She will raise her voice when she can’t elevate her argument.   She avoids the questions, and comes off as an agenda-driven politician more than a knowledgeable scientist.  That’s not surprising, because she actually is a politician and not a knowledgeable scientist.

What can we learn as biotech communicators?    Soft is persuasive.  To win hearts and minds we can’t come off as hard and angry.   We must always respect the forum.  It is important to actually end a sentence, and speak directly to the question. 


Most of all, it is not only the  words that have meaning.  It is also how the words are presented.  As scientists, our ideas flow better if we are a kind conduit.  

Saturday, December 20, 2014

Sony, KJU, and a Coward's Way Out

Next week another movie I don't want to see was going to premier.  The Interview was a comedy about journalists interviewing Kim Jong Un, the leader of North Korea... and then they were given the job to assassinate him.  The huge advertising campaign suggests that the film's script and humor are rather simple and targeted to eighteen year old dudes.

As we all know by now, alleged North Korean hackers cyber-attacked Sony and made terrorist threats to anyone showing or seeing the movie.  

Theaters pulled the film, Sony ceased promotion.  Way to go, morons.  You just bent to threats and further empowered anyone not appreciating artful criticism.

Art pokes fun at international leaders. Remember the scenes from good movies like Naked Gun?  Ayatollahs, Sadam Hussein, Ronald Reagan, Mikhail Gorbachev, Fidel Castro-- all sitting around a table arguing, portrayed in a less-than-lovey way. 

Yep, and here's how Sony and Kim Jong Un played these cards wrong


Where Sony Went Bad

Sony, or any company, never should capitulate to a terrorist threat.  They should have made a strong statement about the value of art, the value of motion pictures as political speech, and what we can learn from communicating through satire.  They should have said, "In response to North Korea's threats we will show the film for free, everyone may download it, use it as you wish-- we support freedom of expression and political dissent." 

Where Kim Jong Un Goofed

KJU shows poor discretion in earning some easy political capital.  The first bad move was hitching his trailer to Dennis Rodman.  There's an ambassador of all things delinquent.  KJU could have made this into political gold.  Instead of inspiring a hacker attack, what if he asked to attend a screening in downtown Hollywood, attending with Seth Rogen and James Franco, the film's two main stars?  He could have had a good time, bought the big tub of popcorn and Snowcaps, joked about how it costs a year's pay in North Korea, and had some fun at his own expense. A softer KJU would be tougher to criticize and criticism would be less effective.  

Synthesis.

Here a major corporation and a world leader could have made different decisions to change the political tenor of this dust-up, caused by a lame movie that would be forgotten by Ground Hog Day. Instead we have escalated poor relations to uber crappy and KJU found a new cellar in his public perception. Two lessons.  1. Don't be a dick.  2. Never give in to terrorism

If it was a movie that made fun of President Obama or George W. Bush Sony would have never pulled it.  If it was an American Flag on the ground at the Metropolitan Museum of Art or a picture of Jesus painted with a dog dookie they would have defended the artist and the need for free expression.

Here they fold like a house of cards.  I say it all the time, never make a decision based on fear






Tuesday, December 16, 2014

Never Met a "Merv" I Didn't Like

The folks over at Safe Affordable Food retweeted one of my recent articles on the cost of activism.

A guy named Merv was not very happy about that, nor very congenial. 

I was nice. 


Friday, December 12, 2014

The Value of Vani

Can she be an ally?

I’ve been extremely critical of Vani Hari, aka “The Food Babe”.   She freely demonstrates, without humility, her complete disregard for science and evidence when vilifying food, chemistry and farming. She has amassed a substantial group of venomous followers that subscribe to her leadership. 

As we attempt to illuminate products, technology and method to feed a growing population, Hari’s shameful resistance to reality needs to be met.  We've done that, and I'm proud of the push back from Steven Novella, Kavin Senapathy, John Coupland, David Gorski, The Chow Babe and the Food Hunk.  Well done. 

But when scientists take the time to show her errors, she lashes back with a string of lies and allegations that are truly curious.  She’s stated in her recent writings that I’m just a pawn doing the bidding of corporate ag, which of course, is supported by zero evidence.

It turns into two groups.  One that manufactures the trash, and another that points a finger at manufactured trash.  Do we ever change anything? 


What if the charismatic Hari could be convinced to teach the science of food and farming?
Could she be a powerful ally? 


Conflict and debate are time consuming and they don’t change true believers. Can we shift Vani Hari herself?  Instead of working against her, can we look at what she does well, and maybe help her come to science?

Let’s say some good things about her.  She’s clearly gifted at communicating a message that resonates.  She has a huge following that hangs on her every word.  She does a good presentation live, and can connect with an audience. 

What if Hari were to take a long look in the mirror and decide that while scaring people into boycotts and book buying pays the bills, the legacy associated with it is embarrassing.  Time will frown on Hari, and it already is happening.  While adored by internet fans, scientists, physicians, the food industry, farmers and science fans see her clearly as the empty information vessel she truly is. 

I’d welcome her change.  I’d be glad to help her with that change. Can we as a scientific community reach out to Vani and welcome her into our fold?  She’s got a lot of learning to do, but we’re good teachers.

Recently I’ve given a number of talks and interviews where I’ve been described as the “guy that stood up to the Food Babe”.  While standing up for science is important, I’d rather be described as the guy that changed her mind because I took the time to teach the facts.   

We know that we’re not going to change hearts and minds pounding people with the science fist.  We need to share our ideas, revise her way of thinking, and educate her about science. 

She’s wrong, but I don’t think she’s stupid.  She bought into her own mistakes and was picked up by the momentum.  Can we #reachouttovani and build trust, teach science, and motivate her to work with us to shape the future of food?


Monday, December 8, 2014

Vani Hari (Food Babe) and Silencing Critics


When you can't discuss things scientifically, just do your best to make sure critics can't be heard. 


This is the level of Hari's continued assault on science and reason in the food theater. After a rather pointy article in NPR's The Salt blog, she now throws herself on the sword, a victim of Big Food and Evil Scientists. Like me!

On her website about the "attacks" she refers to me loosely...



  • The bottom line is that the time ended and there was no public Q&A.  There was no way that the 300 students she just misinformed could question her claims.  I have posted a letter from the organizers that invited her, stating that she did not answer questions except for a small group that convened to meet her by the stage.  That's true.  However, students left without the opportunity to challenge her claims.  That is not a question.

  • Of course, she ties me in with Monsanto.  Blatantly false.  But since when does she need evidence before making a claim?

  • Students had to get to the next classes?   At 8:30 pm?

  • And yes, the "whisked away in a limo" comment was originally stated, based on what someone told me about her as we were walking back from the event.  I learned that it was not true, and that comment was removed immediately.


So I decided to comment on her blog.  Of course, I knew it would be taken down,  Comments that don't stroke her warmly are eliminated by her crack team of censors. I did put up a rather soft and forward-thinking defense of my position.



Luckily someone took screenshots of this, because it was deleted within an hour. She can tell the world about my non-existent relationship with Monsanto, but then blocks and deletes critics that hold her accountable for actual facts. 

That is a very soft note on her site... but it has been removed. 


No matter what anyone says about Hari, it is absolutely clear that she has no room for honest discussion, reasonable criticism or scholarly defense of her positions.   Her position is to control the flow.  Keep it one sided.  Eliminate corrections or criticisms. Discredit those that attempt to adjust her.

She did address the allegations of censorship:


You can see from my comment above just how vulgar I was.  Her continued censorship is about protecting the Food Babe brand for future efforts in Food Terrorism and continued profits.

This is not about education or teaching people to be better eaters. It is about her being a victim and scientists being bullies and corporate hoodlums. Time will show that she's an empty vessel that could learn from those of us that study these topics, but she instead chooses to be a fear monger.  

Just like The Salt article claims.






Sunday, December 7, 2014

Status of the Strategic Shampoo Reserve

I hate waste. I like clean hair.

I also travel.  A lot.

I started to think about the little bottle of shampoo that I'd get in a hotel.  I'd use a little goob of it, but then would think about where the rest of the bottle would go next. Certainly they don't have people spending time on refilling them....

My guess was that they went in the garbage, an assumption confirmed by discussions with housekeeping.  So I decided that I was going to cut my soap-suds footprint by taking the little bottles home and using them there.

Now a new first-world problem.... I accrue close to one-hundred little bottles.

So I decided to marry them into a common container, a strategic shampoo reserve.  Here the many fragrances and colors combine into a delightful mixture that feels weird, smells awful, and doesn't work well.


An addition of Citron Essence hotel shampoo to the strategic shampoo reserve.


I'm glad to report that as of 12/7/2014 the reserve stands at about 120 ml, and with a spring of dense travel will probably reach close to 500 ml soon.

I'm also thinking that conditioner, mouthwash and hand moisturizer might have occasionally found their way into the mix too. 

So if you are on a plane or in an elevator and smell citrus, hemp, basil, passion fruit, almond oil, green tea, avocado extract, saddlewood, musk and saskatoon berry mixed together in a twisted produce cocktail that's more like daiquiri vomit than an attractive essence of nature, look for me.  You might be smelling my head.