Wednesday, February 24, 2021

Ten Years Ago- A Strawberry Genome

 One of the joys of publishing a scientific manuscript is the correspondence from the journal that the paper has finally been accepted.  Peer review and high journal standards are a slow and deliberate maze to navigate that stand in the way of sharing your prized work.

There is one monumental publication in the hundred plus I’ve authored where the research, writing and review processes became a delicate managerial dance between negotiation, combat, finesse, psychology, and arm twisting. This week we celebrate its 10 year birthday, with two sturdy gin and tonics for every piece of birthday cake.  

The publication of the woodland strawberry genome in February of 2011 was the culmination of efforts from at least 77 scientists.  It was a battle from the beginning, and story that few people know and the rest tried to forget. Somehow I became the manager of the project, so the successes and frustrations are still a little fresh even after a decade.

The genome sequenced was not that belonging to the big red commercial strawberry.  It was its relative, a tiny yellow-fruited cousin that shared similar genetic makeup.  It was a great choice to sequence.  In 2007 at the Plant-Animal Genome Meeting in San Diego, CA there were only several key species sequenced—things like rice, and the model plant Arabidopsis thaliana. Strawberry was a good choice to add to that rarified group. It was the red-fruited weirdo of the rose family, a group of plants containing apples, pears, peaches, blackberries and, well, roses. We knew the woodland strawberry’s simple genome was tiny, and likely didn’t contain much repetitive DNA, a problem that still confounds genome assembly efforts.

But as usual, politics wrecks everything. While there were many merits in obtaining strawberry sequence, there were vocal supporters of sequencing peaches and apples, tree crops with larger genomes that didn’t have the same lab value as the readily transformable and diminutive diploid strawberry. Other crops obtained funding and support from federal agencies and international bodies. We had a dumb little plant.

Six strawberry scientists huddled in the best privacy we could find at a conference, sitting on folding chairs behind a faux wall room divider in the lobby.  How would we do it?  How would we pay for it?  The best we could do is pass the hat, get the ball rolling, and see if we could recruit additional experts to make it happen.

The effort took off like cold molasses.  A few bucks here and there, some support from institutions like Virginia Tech and the University of Florida.  National strawberry organizations wanted nothing to do with it, despite a genomes immense value to breeding. Nor did the companies that would one day mine the data for every last nugget of value. It was frustrating. The deepest pockets that could make this a drop-in-the-bucket effort saw no value. Eventually they would contribute.

The beginning-beginning was gorgeous. I purified genomic DNA using an old-school technique, a cesium chloride gradient. The snotty threads of life were as white as unviolated snow, and that few micrograms of perfect starting material would seed the effort.

 To make a long story less long, that virgin DNA blob would be squeezed, interrogated and processed for information, trickling in a little at a time, all being assembled into longer threads as best could be done at the time. Eventually Roche/454 would join the effort, providing significant sequence at low cost, simply to prove they could do more than bacterial genomes. Additional experts joined the party, each lending their skills to unraveling part of the mystery. Soon, little stretches of information piled up, it became obvious that we were a few obligatory Venn diagrams away from submitting a draft genome sequence for publication.

The activities in that paragraph spanned 2008 and 2009, with bi-weekly phone calls that grew less and less enthusiastic with time. I can only thank my lucky stars that Zoom calls were still lost somewhere in the future.

As time went on the calls grew shorter and had fewer participants. Other genomes were being sequenced, had funding support, and were executed by teams of scientists whose full-time job was working on a genome. The diploid strawberry effort had no central funding source, so everything done was on donated time and materials.

It was really the efforts of Dr. Daniel J. Sargent that pushed this effort over the top. He undertook a massive campaign to understand the spatial relationships between DNA ‘markers’, little signatures that were present on the different stretches of DNA that were sequenced. That information allowed the pieces to be put together in the right order and orientation. That was the key, as Dan’s data allowed the piƱata to be built so that other scientists could beat it and pick up some candy.

Other prominent figures on the author team vanished. No contact, no participation. Gone.  Others played major roles and I felt were not appropriately credited.  Authorship order can be a delicate issue. Dr. Daniel J. Sargent should have been first author, as his efforts and ingenuity provided the data to elevate a skeletal work to near-publication form.

The original manuscript was written by a team, and it read like a string of personal spins on the data each felt was most important. The manuscript was probably 400% too long, and the few standing as an author team were divided on where to send it. While I wanted it anywhere and done fast, others demanded it be shopped to one of the prominent weekly science journals.

We sent it to Science, we sent it to Nature. Reject, reject. Another few months burned from revision and submission. At the time there were probably six or seven genomes published, including apple, so strawberry was looking like the really cool guy that got to the party right when everyone else was leaving.

Rejection, burnout, and being sick of a project that was becoming less and less significant scientifically led most of the team to disconnect.  The bi-weekly conference calls consisted of me and maybe another person talking about a chili recipe, if they were not cancelled altogether.

It needed one last push.  I started with an almost blank sheet and smashed the author team’s clunky manuscript into the tight template for Nature Genetics. It was the middle of 2010, three years after a tiny team of strawberry scientists decided to start the ball rolling.

The next months were a cycle of review and revise, review and revise. Tweak, crunch, edit, chop.  I remember those nights thinking that I should also punt this project as so many others clearly did. But there was maybe a light at the end of the tunnel, and after round after round of revision we were close.

I remember fielding at least a dozen calls with the Associate Editor, as she kept finding problems and generating requests from reviewers and other editors. I dreaded the conversations, as each request for more data, reformatting, additional experiments were going to sink the project. 

Somehow I navigated that maze with a skillful persuasion and dumb luck.  The work would eventually find acceptance at Nature Genetics, a decent journal where it fit quite nicely. The Editor relayed the good news that the work would be published in February of 2011.  It was November of 2010, so it seemed a million years away.

There were a few things that made this accomplishment unique, aspects that were largely unappreciated.

It was published in the same issue as the cacao genome, the 12th and 13th plant genomes sequenced.  Here in 2021 there are literally tens of thousands of plant genome sequences known. What took $350,000 and three years then can now almost be accomplished in a few days for a few thousand dollars.

It was assembled without a physical map. Knowing where genes or DNA sequences are located relative to one another helps put the little smudges of DNA sequence data in the right order and orientation. The strawberry genome did not have this guiding luxury as other crops did, and Dan Sargent’s efforts made it possible to assemble strictly from short reads. Later the panda genome would also be assembled from short reads with quite a bit more fanfare. Pandas are cute.  

There were no relevant reference maps.  Today genome assembly is less taxing because of the wealth of information that already exists.  It is easy to draw a map of the USA because everyone from settlers to satellites has already defined where the parts belong. The strawberry genome sequence was a pioneer.

It was done without a centralized funding source.  The work was done on a shoestring, digging in science’s couch cushions to capture enough scratch to push out more data.

Overall, it was a great experience to work with experts and learn a lot about how the tools of genome sequence assembly and analysis work.  Soon after I would move into university administration and forgot everything I knew. 

But I didn’t forget that phone call, the news that the work was finally accepted.

And I won’t forget the efforts of the scientists that really made it possible, as there were a few key players that carried the vast majority of the weight. You know who you are. Pat yourself on the back and celebrate, as your efforts allowed this seminal discovery to be translated to the commercial crop, and eventually influence genetic improvement efforts.  And that was our ultimately mission all along.



Tuesday, February 9, 2021

The Soul-Less Anti-Vaccination Movement

 I read the tweet and immediately was overcome with a vacant, empty feeling.  It was a cold and heartless castigation, aimed at hurting someone that was already down, someone experiencing monumental anguish.

Now, they were piling on. Cold, cold hearts. 

A radiation oncology resident named Dr. Sara Bertran Ponce was expecting a child.  She was 14 weeks into the pregnancy and all was well.  She received the COVID19 vaccine and proudly shared the experience in an interest to encourage others to do the same. The following quotation appeared on a story about the safety of the vaccines during pregnancy. 

Inspiring, courageous words of Dr. Ponce, guiding others to follow her expertise to protect others. 

Her twitter stream showed the words of a public advocate, someone dedicated to public health. 

And the #vaccineswork hashtag was certainly raising the blood pressure of many that see the COVID19 vaccines as a threat to their bankrupt movement. 

At that point Dr. Ponce placed herself officially on the radar of a hateful movement that silently stewed. Qualified physicians, clearly strong women professionals, worked to sway public opinion with their visible compliance with vaccination in a public health crisis. 

Six days later, she miscarried.

And the brutal punishment began.

The dark slime of the internet oozed into social media space, adding insult to injury, and attacking a professional during a time when she needed love and compassion.  But that's what the internet does best, especially the horrible folks within corrupt movements. Your deep personal loss is their time to celebrate. 

Just a sample of the first few tweets around Dr. Ponce's account. The woman in scrubs is NOT her, but a doctored (ahem) photo of a pregnant physician that was added to the tweets. 

It is cold, ice-water-in-the-veins hate. No empathy, zero compassion.

This is the anti-vaccine movement. Self-appointed authorities, self-described experts, and cruel and heartless people. 

She has closed her account.  Good. She needs to heal. 

What can we do?  Share this story.  Show how awful this movement is.  Disgust is a very powerful motivator, and if we can get people to see what the anti-vaccine movement is about, perhaps we can garner their trust, then protect them, their children and their communities. 


Monday, February 1, 2021

Global News, Rachel Parent, and a Deliberate Hit Piece

 I remember going back to Chicago to visit my father just before Christmas in 2015.  The previous months had been brutal, and I was finally healing after activists deliberately misinterpreted my emails and the New York Times made false accusations that I traded grants for lobbying time. The personal and professional fallout was awful, but subsiding.

It was perfect timing for those seeking my demise to pile-on, to take another shot at a career academic researcher that has dedicated his time to research in indoor agriculture lighting and the genomics of small fruit flavor. His efforts to communicate the science behind biotechnology still were not appreciated by many.  

US Right to Know, a now irrelevant fossil of the anti-science crusade against biotechnology commissioned Allison Vuchnich of Global News Canada to drop the hammer in a carefully coordinated next phase of career assassination.  After all, I survived a their claims of malfeasance, quid-pro-quo payoffs, and colluding with companies to lie to the world about science.  They needed something totally toxic-- and a story from Vuchnich about my relentless attacks on a teenage girl would be just the ticket. 

I remember opening my laptop that snowy morning in Chicago and seeing the article. My heart almost stopped. Not again.  I was sick for three months after being hammered online, destroyed in my community, problems created at my university and home, threats and harassment, and almost quitting science altogether. 

Now the cycle would be re-ignited, skillfully. 

I never wrote about this or even explained it before, mostly because I was paralyzed by fear of more fallout at the time.  Today, Feb 1, 2021, five plus years after the article first presented its dirty smear, it was revived with full intent to harm.

Someone thanked me on Twitter.  She is a chef and would be working with high school students, and was kind enough to offer me thanks for my inspiration.  That's nice. 

Paul Thacker, a dirty player and gutter hitman journalist, responded. 

Tweet from 2/1/21

The awful defamatory article was still being wielded as a way to harm my ability to teach, communicate, and build public trust, now around issues like COVID19, climate, and genetic engineering.  

What did the article actually say, and how much of it was true?  Let's look at it in chunks.

1.  Catchy-Grabby Headline

No teenager was ever the target of a lobby.  A scientist (me) was concerned with the false information being provided by a website aimed at children and young adults. 

2.  Maliciously Taking Words Out of Context

During the Proposition 101 "GMO labeling" campaign in Oregon in 2014, a commercial ran that was a complete misrepresentation of science.  It was deceptive, it lied to the audience and was an anathema to science and reason. 

A friend of mine, who worked with extension in Colorado for the Monsanto company, asked me if I would be willing to write an Op-Ed or sign a petition with hundreds of other scientists, denouncing the disgraceful video.  

I said, "I'm glad to sign on to whatever you like, or write whatever you like... etc" a quote that is used out of contexts by scoundrels like Vuchnich to harm my reputation with a cherry picked sentence deliberately misinterpreted from my private email correspondence. 

Of course, Gary Ruskin, the guy that collected the emails and parsed out stories to reporters, was happy to celebrate Vuchnic's compliance with his mission. 

3. Allison, That's My Job. 

A big part of the role of scientists in the US Land Grant University system is to communicate science with the public.  I write articles, blog posts, blah blah blah. 

I never "defend GMO technology".  False. 

I teach about the strengths and limitations of technology as given by the peer-reviewed research.  To enemies of progress, I guess that could look like "defending" a technology, but it is simply sharing the science. 

And no, I did not "lobby" Congress.  It is illegal for me to lobby Congress.  I have been asked on multiple occasions to answer questions for Congressional Committees, and it is my obligation as a federally and state-funded scientist to do so. 

4.  Scientific Independence, Damn Right. 

I was objectively answering questions about technology and teaching communication skills to many groups, and I don't have a budget for travel costs.  So BIO picked up the tab on a couple of trips, maybe two. There was nothing hidden. 

I was not given an "unrestricted grant" for "research and outreach projects." The company made a donation to a science communication program I ran, and sadly provided the check with a boilerplate letter that would be gold for folks seeking to defame a scientist by misinterpreting what actually was happen vs. what they wanted to happen. 

I never had any research support from Monsanto. They don't care about my research. 

The threats called into the university and my office were real. We found ourselves communicating with the Domestic Terrorism Task Force and establishing police presence near my office. The online environment was filled with hate and promises of retaliation. 

For my safety, the university moved the funds from the science communication program to a campus food pantry.  The $25,000 was never used for teaching science. 

Science communication is so critical in mitigating problems like COVID19, climate change, vaccination, etc. I teach that. Companies like Monsanto (back when it existed) and others want farmers and scientists to be better communicators about the technologies they use. That's why they made the donation (along with many others). 

5. I Vehemently Deny False Claims. Still Do.

The ad was in the Global News story.  Sorry. 

I'm a scientist that teaches science. No, I don't care about companies and my first allegiance is to the evidence, my students, the public, and to sharing science. It has always been that way.

6. Distortion, Distortion, Distortion

In 2013 I was contacted by a woman named Mary Beth (something) from some communications/PR company I can't remember, asking me to write an article about the impacts of misplaced activism and I was glad to oblige.  That's my job as a scientist, to bust fake news and show its impacts. 

This was on the heels of the horrible paper by Seralini et al., the paper that was filled with problems and made claims about seed and cancer that have not been reproduced to this day, nine years later. 

That paper shut down seed technology in Kenya and had other wide impacts.  Damn right I was excited to teach the evidence and show the impacts of damaging disinformation. 

Again, Vuchnich frames this as a nefarious conspiracy.  It was actually a scientist stepping into a public discussion to educate others about science. 

7.  The Anatomy of their "Attack Video"

I remember this day.  I left Gainesville, FL at 5 AM and landed in a Washington DC snowstorm, getting in before flight cancellations hit.  I took the metro into the city center to the Biotechnology Industry Organization headquarters for a 9AM meeting (I can't remember what for), but it was cancelled because of the blizzard.  

With cancelled meetings, an evening flight, and a day to kill in front of me, I called the company coordinating GMO Answers and asked if I could swing by to maybe answer a few questions on video, something that we had discussed previously. 

I took a cab ride through the snow over to Ketchum Communications. They had a skeleton crew working that day due to the blizzard, but we put together an impromptu background of someone's cubicle and jammed it with fake plants from around the office. This is the actual stupid anatomy of Vuchnich's implication of a sophisticated well-orchestrated attack on a teenage girl.  

I answered a few of the questions submitted to GMO Answers on video. One of the questions was about tactfully responding to Rachel Parent, at the time maybe 14.  She was framed as a vocal proponent of food labeling and a champion against biotech.  

Many were disturbed that she was so young, so wrong, and had such visibility. Clearly someone was giving her bad information, and they wanted someone with experience in nuanced communication to help address how we'd counter her claims with grace and class. That's what I do. 

I was happy to answer.  Here is the video that was described as "targeting" and "degrading".  What do you think?  A polished biotech stooge attacking a Canadian teenager would at least fix his tie.

8. Facts Don't Matter.

Looking back, it was kind of fun to see that truthiness was alive and well in 2014.  The information on her site was not scientifically sound, it still scientifically isn't.  Kids Right to Know is targeting kids and young adults with false information. I take that very seriously. As a university educator, I get to clean up that mess, and it is unfair to poison young minds with fake science.

It is particularly egregious because Rachel's family runs health food franchises around Canada, a relatively large company called Nutrition House.  The bad scientific information is actually not just lying about science, but it is a marketing campaign, a way to scare customers into purchasing from the family empire and related businesses.  

She considered my video "almost degrading", but apparently not degrading, because absolutely no degrading took place. I was pretty damn nice in recognizing her strengths and talents. But that message was twisted in Vuchnich's article, which makes sense, as I emphasized critical thinking and the importance of young women to be involved in STEM disciplines. That is quite offensive to those that fail to embrace science. 

And of course, with regard to experts like me, if you're Rachel, "... their opinion doesn't matter."  

9. More Distortion of a Non Event. 

I remember this morning.  It was a Sunday and I was at my home computer working.  I took a break and was perusing the web, and I discovered the website Kids (sic) Right to Know. I was deeply disturbed by what I found.  The information was wrong, and it targeted children and young adults. 

Just off the cuff I fired off an email to the folks that ran the GMO Answers website.  I told them that if they were to assemble a website to counter this blather, to provide real scientific information to that age group, I would help.  I deeply care about youth science education. 

This was not a nefarious cabal as portrayed. 

10. Extrapolation from Private Meaningless Private Correspondence.

After floating that original idea in the email, I quickly forgot about the whole thing. It was never mentioned again.  I guess I put it on their radar and was happy to help if it was of interest, but obviously it wasn't so nothing ever happened. 

Frankly, I forgot all about it.  I never even thought about it again until it surfaced in Vuchnic's hit piece a couple of years later. 

And Parent's family purchased the domain name last time I checked. As of today it seems to be available, and I have no interest in it. 

Rachel's family actually owned/owns the domain. 

11. I Have a Duty to Correct Disinformation.   

False claims that misinform children are extremely disturbing.  It is my job, it is all of the educated world's job, to correct that kind of disinformation. Parent should not be disappointed that a professor did that, she should be disappointed if he/she didn't. The false information on the website should be discredited as appropriate. The bogus claims have not aged well. 

12. Evidence, Schmemividence 

Parent disagrees with scientific research and Health Canada. She apparently argued at the time that there were health risks, a claim that is not reflected in over 30 years of research, 25 years of use in the animal/human food supply, and wider international adoption than ever. 

I said the technologies were "very safe and very effective".  Usually I avoid the imprecise weenie word "very" so that is a strange sentence for me. 

But five years after the article one of us is still right, and one of us is still horribly wrong. 

12.  Fallout from the Article.  Notice how much of it is coming from the people that provided my emails and inspired the article, and how Rachel retweets their filth.  It is their strategy. 

13.  Her Website is Still Wrong. 

Years later the website (accessed 2/1/21) still makes claims about bans in most countries, crops "doused" and "saturated' with herbicides, and other false claims. The lower image above is a field of wheat, which is not genetically engineered. 

Kids' Right to Know?   Or sadly, Disinformation for Kids? 

14. Conclusion.

Allison Vuchnich's article used quotations out of context, distortion of information, and disinformation in an attempt to harm my reputation and my career.  Today the attack piece on Global News stands as a forever-accessible defamation, guided by the hand of US Right to Know, and executed by another sucker journalist that saw a juicy story rather than the much more interesting actual truth.

The problem is that I have to ride this slander wave to the grave.  I teach in the classroom, and every semester have to point to articles like Vuchnich's, telling students about the dangers of speaking up for science-- then imploring them to do it.  I have to be preemptive in showing the disinformation to keep their trust as their teacher.

I have stepped into COVID19 discussions, eager to see a pandemic end, and stop the pain of families suffering from preventable loss of loved ones. 

And anti-vaxers will post Vuchnic's article adjacent to my presentations and posts, using her distortion to steal the trust I have earned as a scientist and scholar, showing that I cannot be trusted.  

And  a scientific voice is diminished in a pandemic. Congrats Allison.  

Her article was a gift to thugs like Ruskin and Thacker that will use it forever, especially when I'm educating kids. 

The good news is that this article has not aged well.  The claims I made back then are just as valid today as they were then.  Efforts to frame biotech as a dangerous technology have dissolved with the advent of biotech vaccines and slick cures for insidious human disease. 

And somewhere deep in my heart I somehow think that Parent and Vuchnich might be big enough to apologize. Even if they did, the problems they caused for me personally and professionally can never go away. 

But it is not about me. Their part in the war on science and reason will have long-lasting impacts on many, especially those that rely on biotechnology or wish to adopt it in their operations. Time should not be kind to them. 

This is what happens when you speak about science in a volatile climate where the internet affords easy assassination of those that present science that some find offensive. My hope is that this synopsis shows the anatomy of defamation.  

A Canadian teenager was not the target.  It was an American scientist.