Sunday, February 19, 2017

Imagine - Standing Up for Science

I'm going to catch a lot of grief for today's post. There was a very nice pro-science rally in Boston today.  Lots of people! That's good. 

If there is something that scientists should be excited and fighting for it is gene editing. The USA will potentially regulate it to death.  We have a choice to influence its regulation with the FDA. The FDA public comment period on the use of gene editing has been up for a month.  There are a total of 162 comments now.  The vast majority look like this:

Help me understand the disconnect. How is it that we can get 1000 people to march with a sign for an afternoon, but we can't get 10 to write a thoughtful, evidence-based note about enabling technology?

Pseudoscience is running rampant in the space.  Why doesn't anyone want to stand up for science?  

What am I missing here?   

Saturday, February 18, 2017

Massive Consumption of Soy Milk and Herbicides for Five Weeks Might Make Your Sperm Weird

In the ongoing war on glyphosate, Carey Gillam posted a link on Twitter highlighting a newly-published article.  The article comes from a team of Brazilian scientists that fed developing male rats massive amounts of soymilk, and then massive amounts of soy milk spiked with gigantic doses of herbicide (not just glyphosate).  They then analyzed factors potentially related to reproductive toxicity.

Did they really see it?  What did it take for it to be seen?  When people draw conclusions without actually reading the papers, the interpretations can be deceptive.

The referenced work is Nardi et al. 2017. The paper seems a little odd out of the box.  As a scientist, I don't know the rationale of pounding animals with massive doses of chemistry just to see what happens. It almost seems a little like it was done to secure the headline that Gillam and others seek.  

To make this relevant, I'm ~100 kg. To achieve the amounts used in this this experiment I'd have to drink a liter of soy milk and just under a half-cup of herbicide a day, for 35 days.

There is minimal mention of the copious literature on soy products as endocrine disruptors, which is well established. Here's a good review. Here animals are basically fed a potent dose of plant-based estrogens and then hit with lots of herbicide. I'd be surprised if they didn't observe something!

The Introduction talks about soy milk a bit, and the whole second paragraph is about glyphosate and how awful it is.  They cite papers from Seralini (insert grain of salt here) and some from authors on the current author team.  This is interesting, because in the intro they write: 

First, "innumerous"?  The dictionary says that this means "incapable of being counted" and that must mean that the authors are not capable of counting them. However, they can be counted. There are many papers that show interaction with hormone-based processes, but typically at high levels or within cells in a dish.  These are important studies because they lay the groundwork for toxicity assessments, and in general show that the cells don't like to be bathed in herbicides, including the soapy chemicals in the formulation. 

They imply that effects have been observed at relevant levels, yet the paper they cite does not reinforce this interpretation. Dallegrage et al 2007 say:
Dams were treated orally with water or 50, 150 or 450 mg/kg glyphosate during pregnancy (21-23 days) and lactation (21 days). These doses do not correspond to human exposure levels
So they are putting in a half a gram per kg body weight in some cases.  That's 50 grams (about ten nickles) of pure glyphosate every day for 35 days.  Hmmm. They do not cite any of the many reports that show no effect on endocrine processes, such as this one

The animals were fed 10 ml/kg a day of soy milk, or soy milk containing 50 or 100 mg/kg (ppm) glyphosate as Roundup.  Not glyphosate.  The complete herbicide.  You can buy reagent-grade glyphosate, my lab does all the time. Not sure why they didn't do that.

To make this relevant, I'm ~100 kg. In this experiment I'd have to drink a liter of soy milk a day, and just under a half-cup of herbicide, for 23 days.  I would guess that my dude parts might not be working great after that treatment. The other thing to note is that animals were fed ad librium meaning they ate what they wanted.  Frankly, you give me a liter of soy milk and a gutful of Roundup delivered by a tube down my throat into my stomach, I might not be eating much.  Controls got saline solution.  There was no glyphosate only treatment. The authors note that there was no difference in body weight after the close of the experiment. 

As a reviewer, I don't have a problem with the experimental design or data in general. I would have used glyphosate, not Roundup because you can't rule out the likely effects of the herbcide's co-formulants.  It is a small number of animals, but they discuss the results based on those numbers and this all seems reliable. 

The problem is how they present the data and their interpretations.  Here is one of the figures:  

The authors do in fact deliver 50 and 100 mg/kg glyphosate, but they do this as the Roundup herbicide.  How do they know the effects are from glyphosate and not from feeding rats large amounts of surfactants for 35 days?  Glyphosate is available as a reagent, and when used has no effect in tissue-culture cells.  When applied to cells as Roundup, it does. The surfactants are soapy chemicals that allow the herbicide to penetrate cells. This stuff could certainly affect animal physiology. 

This is where I got bored.  The Results are what you would expect by feeding animals tons of phytoestrogens and herbcide. The Discussion attempts to tie the results to previous work, mostly by citing in vitro experiments, and a lot of self-citation and Seralini citation.  The authors draw the conclusions:

Despite the sample limitations in this study, the results presented here show enough evidence that glyphosate impairs male reproductive system by affecting innumerous components in a prepubertal exposure.

To the best of our knowledge, this study demonstrate f(ic) or the first time a relevant endocrine disruption of a soy milk rich diet during prepubertal period. Sexual development is more affected in groups receiving soy milk supplemented with glyphosate.

My conclusion:  Innumerous?  Really? When you poison pubescent, developing male rats with isoflavones (a type of phytoestrogen) you screw up their development. Then when you add massive doses of herbicide every day for 35 days you can find differences in testosterone and sperm morphology. It shows that sick animals fed herbicides show physiological differences. Duh. 

But the authors don't prefer the conservative interpretation that I would draw.  This sensational conclusion omits the fact that these were rats hammered with herbcides and soymilk, yet makes it seem like relevant doses from normal exposure.  

That conclusion would not be acceptable if I was a reviewer or editor. 

But it is a great conclusion for Gillam, paid by the anti-GMO industry, who can now cherry pick the scare out of the article to make it seem like food-based exposures of glyphosate are dangerous. 

Same old, same old.  Actually, one huge outcome is how surprisingly small the differences are after such chemically-invasive treatments for 35 days. 

Are these people that should be trusted with information about food and farming technologies?  The tweet above is deceptive, especially when you understand the paper and what was actually tested. 

Friday, February 10, 2017

Science Marching? Stand Up for Science Today!

A few weeks ago when the internets exploded with news of a March for Science in DC, I wrote that I would not be joining. My feeling is that such things are important, but not for me. I’m using other channels on a daily basis to help broaden the understanding of science issues and improve trust in scientists. I’ve been doing that for years.
This sentiment brought me angry emails and hostile tweets. Not many, but a enough to realize that my inflammatory statements like, “Not the most effective use of my time in supporting science” are not always well received with a group poised to descend on the nation’s capital.
My point is a simple one. Protests and marches are fine, but are rather empty if we don’t follow up with sustained commitment to standing up for science.
So as you start to put ink to poster board for that April 22 march, know that science needs your help now. Right now. Actually yesterday. Your comments are needed in support of sensible Gene Editing regulations in crops. Or against it. The FDA is in the middle of a public comment periodYour voice needs to be there.

Support Gene Editing
Gene editing (or genome editing) techniques allow scientists to install precise changes in genetic sequence, conferring a new trait. The techniques are not classical genetic engineering (familiarly “GMO”), which installs new genetic material and associated regulatory regions— frequently with other non-native goodies as well. Gene editing uses precisely guided enzymes that digest DNA to install precise changes to genetic sequence, typically by removing a few little bits of information that disrupt the function of the gene. It is like cellular surgery, precise, effective and testable.
These technologies have been used with astounding success in medicine and animal agriculture. Gene edited cells have brought infants into remission from leukemia and produced cattle that don’t grow horns, or don’t catch tuberculosis. The applications in these areas are endless.
Gene editing can also be used to tweak genes in crops, particularly those that lead to unwanted characteristics. Genes affecting post-harvest decay, undesirable flavors, susceptibility to disease—these all are intuitive targets for gene editing. It is happening everywhere from the developing world to multinational seed companies, universities to small businesses. Most importantly, the plant products produced by this technology are identical to those obtained by traditional breeding.
Request Realistic Regulation
Traditionally bred (plant sex) and gene edited crops cannot be discerned from one another using any available technology. Therefore, there is no reason to regulate them differently. Based on these findings, Sweden has indicated it will not regulate gene edited products, and the USDA/FDA appears to be leaning in that same direction.
However, the anti-biotech interests have started a campaign to malign this technology. They want to defeat it, keep it our of our crop-improvement toolbox. Their fear is that companies might use it and make money, even if it could help the environment or the poor. They don’t want this technology just regulated, they want it stopped.
The FDA has opened a Public Comment Period. As of 12:45 pm EST on 2/9/2017 there are 36 comments, all firmly opposed to this revolutionary technology and none of them espousing a sound scientific rationale for their objections. Some of them are sadly hilarious.
Public comment ends on April 19, but do it now. Try to stay within the framework of the questions they would like answered, as described here.
Where are the protesters and science marchers? It’s stand up for science time! This technology will inevitably revolutionize agricultural genetics. Can you please stand up, be counted, and comment?
It does not matter if you want to mention the need for testing, the need for some regulation. I agree and that’s great. The point is that this technology should not be hampered by the same strangling regulatory system that burdens new crop variety development with standard genetic engineering approaches.
The ball is in your court. Stand up for science, study this issue and make your voice heard!
And if you add the hashtag #standupforscience in your post, we’ll know that you are responding as part of a commitment to driving policy with evidence and reason. That is the spirit of the proposed march in Washington DC!

Thursday, February 9, 2017

Harvard Public Health- Sadly Vilifying Conventional Ag?

A month or so ago Cleveland Clinic physician Daniel Niedes posted an inflammatory column in the local news about the dangers of vaccines, including their links to autism, etc.  The article was widely disseminated in social media under the mantle of the Cleveland Clinic, using its reputation and name to promote blatantly false claims that imperil public health. 

Turns out that a rogue physician that somehow drank the pseudo-science Kool-Aid decided to spew scientifically false and dangerous opinion has vetted fact from the prestigious institution.  He was apparently reprimanded and the school took a strong, scientific stance regarding the use of vaccines as an important tool in public health.

Not to be outdone, Harvard Public Health has a similar problem. Apparently an Adjunct Professor in Denmark associated with Harvard Public Health is exploiting the reputation and name of this prestigious institution to promote an agenda, and using a EU Parliament document as the vehicle.  

This is the familiar vilification of conventional agriculture. 

The faith and credit of Harvard Public Health being exploited to promote a personal agenda against conventional agriculture. 

As always, I'm fine with organic production methods and am very happy that farmers can make a buck using them. I'm excited to see people thinking about minimizing inputs and producing using alternative methods.  That's awesome.  But don't tell me that the food is more nutritious or safer.  The data do not support  that conclusion.  Minor differences are seen for different nutrients in either direction, under different conditions, and with different plant lines. 

The main claim is that "Three long-term birth cohort studies in the U.S. suggest that pesticides are harming children’s brains." 

The associated report is from the EU Parliament.  I breezed through it, mostly focusing on major syntheses.  The conclusions are rather telling. 


So apparently this was evidence enough to satisfy Harvard Public Health of the glaring dangers of conventional agriculture.  I'm crossing them off of my liver transplant list. 

Other conclusions note associations between eating organic produce and conventional, but those are really hard to interpret.  Folks that choose organic have higher incomes, tend not to smoke, have healthier relationships with alcohol, get exercise, and stay away from consistent consumption of processed foods.  Those factors can cloud interpretations, and certainly do not mean that conventionally-farmed produce is bad.

The only thing I could find in the document that was consistent with the author's claims was a citation that organophosphates (and some other old-school insecticides) have an occupational association with some cancers, like non-Hodgkin's Lymphoma.  I don't think anyone questions those associations. 

They also cite a study of California farm workers and show that women with higher levels of the pesticides in their urine associate with children exhibiting different neurological issues, scattered across deficiencies in reflexes to ADHD. The authors note that there the wide range of study designs and endpoints clouds clear interpretation and conclusions. The conclusions would not be surprising-- but again these are occupational exposures (and we should do everything possible to limit them!).

Later they delve into pesticides specifically, but again it is a set of loose connections that are not surprising. It is important to note that there is minimal residue on crops, and these levels are monitored. 

In defiance of that reality, the online document with Harvard Public Health posts a link to the Environmental Working Group for information about pesticide levels on food.  Ugh. 

EWG provides a non-scientific, zero-tolerance, and artificially alarming synthesis of numbers gathered by the USDA explicitly to ensure that pesticide residues are below unacceptable levels, and far-far below levels of biological significance. 

The Harvard Public Health website also says, "Organic foods are produced virtually without pesticides."  Not true. Plants make their own protection, and certain non-synthetic pesticides are allowed.  Few have been tested for effects on human health (not that anything is anticipated), and some do have environmental impacts. 

The numbers that they produce annually remind us that we live in a time of abundance, with the safest food supply in human history. That's what I get out of it.

There is a lot more in the EU Parliament report, but mostly a recapitulation of what we know already.  Insecticides kill insects and can have human physiological effects if used improperly.  But like everything, the dose makes the poison. 

Harvard Public Health would be well guided to vet the claims made in such articles on their behalf.  These soft-science claims end up affecting a reputation.  Ask Cleveland Clinic.  They had to remove home homeopathy kits from their gift shop after the Niedes vaccine debacle. 

Saturday, February 4, 2017

Talking Biotech #68 - Brassica oleraceae, the Dog of the Plant World

Today's podcast is about Brassica oleracea a species with many forms.  Broccoli, cauliflower, brussels sprouts, cabbage, kale and kohlrabi are all members of the species.  That's right, these very different forms have almost exactly the same genetics, with minor differences.  The differences were all installed by domestication.  Humans found a trait that they liked, and over the course of years they had a distinct form of the plant. 

Brassica oleracea is the species of plants that have many derived forms, all a product of human selection. In this case, can we say that any of these crop plants are "natural"? 

This week's discussion is led by Dr. J. Chris Pires and his students from the University of Missouri. 

It is a lot like the story of dogs, where they all descend from a common grey-wolf ancestor. 

Today's podcast is with Dr. J. Chris Pires and his graduate students Makenzie Mabry and R. Shawn Abrahams. 

Monday, January 30, 2017

We Speak Labanese Here

I'm proud that my laboratory has always welcomed exceptional scientists from all over the world. We have benefited from the expertise of international experts that  brought their time, talents and friendship to make beautiful contributions to our scientific mission. 

Scientists: Strive for Proper Application of Outrage

It is heartwarming to see a little discontent inside scientific community.  To those of us with careers in the discipline, the daily assault on reason is part of the experience, and the scourge of fake news and evidence denial are well known.  We’ve watched it for decades with the frustration that empirical evidence and inconvenient truths were cast aside in policy discourse and public discussion, propagated by a complicit media.  Willful ignorance has spawned a hot planet, expensive ballot initiatives for warning labels on safe food, calls to teach about a 6,000 year old planet in science class, and outbreaks of diseases long believed to be defeated. And that’s the tip of a melting iceberg.

Scientists, nice to see you raise a fist, but think before you fight.

Scientists themselves have even ventured into the public discussion only to be falsely maligned everywhere from crank websites, to conspiracy radio shows, to the Old Gray Lady herself.  The outrage from the broader community is typically gooey and short lived, if it even happens at all.  It is about what we’d expect from non-confrontational nerds engrossed in more important pursuits.

But now a new attack on science appears to be well underway, and some long overdue mental magma is finally pumping in the community’s normally molten core of soft serve.  

Recent Presidential mandates drew quite a reaction from the scientific community, some appropriate, but some overstepped.  That’s a major problem.

USDA Bungle
The big screw up happened upon the notice from the USDA.  The internet exploded with news that the Agricultural Research Service (the USDA research arm) was suspending publication of any “public facing documents”. 

Scientists interpreted this as a broad swipe at suppressing the flow of data.  I did it too.  I retweeted and shared the rage!

I was inundated with tweets and emails, asking about the gagged silencing of USDA employees. As the internet’s network inflamed the story, USDA scientists in the Agricultural Research Service were apparently blindfolded and bound, loaded into unused Amtrak trains (which is most of them), and relocated to Area 51.

Oops. We just royally effed up.  We over-interpreted the message, which ultimately was nothing.

Bad move, scientists.  We are so poised to react, that our outrage was misspent.  Most of all, it made us look bad to those that wish to discredit our normally measured reactions.

March on Washington? 

Everyone from internet science sleuths to Bill Nye are calling for a Science March on Washington, a chance to show solidarity among those that value the scientific method and embrace the truths that science gives us. Good for them. 

Not me. The best way I can support science and scientists it to create durable work and actively create the change I want to see.  This is a long game, not an expensive afternoon in DC. The cure is investment of our non-existent time in public-impact pursuits. 

For me to get to DC, stay a night, and uber around will cost me at least $500, and that’s if I bivouac with other smelly scientists and dine on stale peeps and trail mix.

What if we invested that same money on a microscope for a local classroom and then spent the day showing kids how to use it?  That’s the way we create the change.  Rather than coming off as whining complainers for 20 seconds on CNN, let’s be the proactive teachers we are, and then use social media networks to tell the world about what proactive teachers we are.

The Science March should be a website showing the beautiful things we did specifically in response to the anti-science movement. 

Again, it is nice to see a little rage bubbling from within the lab coat.  The challenge now is to channel the energy properly.  At this point we need to be sure that our efforts are appropriate and consistent with the evidence.  Then let’s avoid knee-jerk reactions and implement effective and visible means to protest, flooding social media with overwhelming acts of good.

We have the cred.  Others might be trying to take it.  Let’s not make it easy for them.

In Conclusion

In research we are taught to challenge evidence presented, even from trusted sources.  We claim to guard against self-deception, and over-interpreting data.  We portray ourselves as responding in measured, calculated ways that maximize impact of our actions.

I’m just suggesting a little self check here and watch out for jerky knees.

Like I said in the opening, we’ve lived in the midst of science denial for a long time and are poised to fight back against coordinated encroachment from a demonstratedly science-soft administration. Let's not jump the gun and look bad doing it. 

Let's not create a stir, let's invest that energy and create change.