Tag: Harvard

From 1988 to 2015 – how Jennifer Doudna shaped my career (and now science and society)

Well, yesterday was really fun.

In college, I switched from being an East Asian Studies major to being a Biology major in my sophomore year but had no idea what aspect of biology I might focus on.

Then I took a course that changed my life. The course was taught by a PhD student at Harvard and it was a kind of supervised reading class. The course was a full year class with weekly meetings to discuss various papers and news stories and such.  The topic was “The Origin of Life: Catalysis in Evolution” and it covered things like chemical evolution, catalytic RNA, the RNA world, introns, Lamarck vs. Darwin, and more.   The course syllabus is posted below:

 
This course changed my life in multiple ways.

First, in the course I learned how to critically read scientific papers. A very important skill. And also I got introduced to the world of catalytic RNA and also the world of “Cairnsian Mutation” which became the topic of my grad. school applications, my NSF predoctoral fellowship application, and the first two years of my PhD work. And I also got introduced to the work of Norm Pace.

This led me to seek out ways to combine my interest in ecology and evolution with molecular biology, which in turn led me to joining the lab of Colleen Cavanaugh and starting work on culture independent DNA studies of microbes.

Anyway, I could go on and on. But this course was transformative. Over the years I had heard about the student who had taught the course and her work, but had not actually seen her in person until yesterday.

The course instructor was Jennifer Doudna. And yesterday I got to see her talk about her work on CRIPSR and CAS9 systems. She has already won a large number of prizes for her work on this, and likely more to come. I cannot say I am surprised. Though I had many teachers at Harvard who were famous, and some of whom were also great teachers and researchers, I can say without a doubt that the one who impressed me most was Doudna. Her passion for science, for biology, for teaching, for being critical while reading articles, and for just wild things that organisms do, was contagious. So cool to see what she is doing now.

Anyway – I made a Storify of the Tweets (mostly mine) from her talk. Check them out below:

UPDATE – found my term paper from the class . posting it here.
//storify.com/phylogenomics/jennifer-doudna-talk-on-crispr-cas9-at-ucdavis/embed?border=false//storify.com/phylogenomics/jennifer-doudna-talk-on-crispr-cas9-at-ucdavis.js?border=false[View the story “Jennifer Doudna talk on CRISPR CAS9 at #UCDavis” on Storify]
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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Harvard, hope and hype: the sad reason behind overselling diabetes stem cell work – raising money

Earlier in the week I got all fired up – not in a good way – about a press release and news stories relating to a new paper from Doug Melton on a insulin producing STEM cell study

//platform.twitter.com/widgets.js With a little more discussion I just got more angry

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//platform.twitter.com/widgets.js I was angry both about the overselling of the implications of the paper and the fact that the paper was not published in an open manner. This was despite the stated goals of HHMI which funds some of the Melton Lab work.

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I was especially upset that much of the press coverage was reporting on an imminent cure for type I diabetes when this was clearly not imminent. Although I note – some coverage was OK. Like these:

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//platform.twitter.com/widgets.js Another good piece of news – HHMI got Doug Melton to post a copy of the paper on a web site

//platform.twitter.com/widgets.js Although this was kind of hidden

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//platform.twitter.com/widgets.js Another good thing – Paul Knoepfler, a colleague of mine at UC Davis wrote a blog post for his excellent STEM cell blog about the Harvard study and the hype.

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//platform.twitter.com/widgets.js But the hype was still spreading …

//platform.twitter.com/widgets.js So I felt like there was a continued need to say something about this

//platform.twitter.com/widgets.js I even changed a talk I was giving on Sunday to include a discussion of this paper and the hype as, well, a bad thing
  

And I thought, and kind of hoped, that this might just go away. And then, many people forwarded me this email from Harvard sent out as part of a fundraising campaign. Most of the people who sent it to me sent it in happiness with the possibility of a cure for type 1 diabetes. Here is the email:

Of for $&*#*# sake.  Really.  So now Harvard was going to use this as a fundraising tool.  And they would oversell it even more:

“A giant breakthrough in making that possible” with “that” referring to “finding a cure”.  And then they say “these cells can replace or augment daily insulin injections” without saying that this WAS NOT IN HUMANS.  THIS WAS IN MOUSE.  $*#($#) DECEPTIVE LYING SCHMUCKS.

And they end this email with “make a gift today.”  How about this Harvard.  I will make donations to anyone but you until you stop marketing in hope and hype and start being responsible.

UPDATE 10/16/14 8 AM PST

Some of the overhyped statements relating to this story:

Harvard Press Story: “We are now just one preclinical step away from the finish line,” said Melton

Rawstory: Stem-cell cure for Type 1 diabetes ‘on par with discovery of antibiotics’

Telegraph: Cure for Type 1 diabetes iminent

Times of India: Type 1 diabetes cure within reach after breakthrough that could spell end of insulin injections for millions

BBC: Giant Leap to Type 1 Diabetes Cure

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Harvard Club of Sacramento outing to Yolo Basin #Birds #Birds #MoreBirds

Had a good outing today with the Harvard Club of Sacramento to Yolo Basin.  Some pics and notes are below.

Coots

Geese way way up high

Turkey vulture

Turkey vulture

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American bittern .. a bit out of focus

Bittern again

Great egret

Great egret

Black phoebe

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Harvard Crimson changes its mind – supports PLoS One

Well, the folks at the Harvard Crimson have apparently changed their mind. In a new Editorial, two writers from the Crimson discuss PLoS One and open peer review. Unlike the previous Crimson editorial (see my blogs about it here and here), the two writers of this one now come out clearly in support of the PLoS One idea as well as some PLoS ideals.

For example, the liken the battle between Open Access and Closed Access publishing to the battle over democracy

Democracy has reached a new frontier, and we’re not talking about the Berlin Wall. It’s a new decade and a new millennium, and yet another wall is crumbling—this time, not between countries, but in the domain of scientific research.

Perhaps most importantly, they end the editorial with

Initiatives such as PLoS ONE will help promote free and unfettered scientific study, supplementing and revolutionizing an oligarchic academic process. It is both ignorant and regressive to reject this democratization.

Although they did not address the previous highly ignorant editorial in their own newspaper, Yifei Chen and Patrick Jean Baptiste deserve kudos for a well written, well thought out editorial on a key topic for the whole endeavor of science.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Harvard Crimson Editorial Update

OK – so I am biased here but those interested in Open Access should check out my brother’s letter to the Harvard Crimson that was published today. He wrote it in response to the lame editorial the Crimson wrote about PLoS One. Some of my favorite quotes from his letter

They did not, however, respond to your repellent effort to rally the forces of elitism to derail a project whose primary aim is to rapidly bring scientific knowledge to everyone.

….

Once they see PLoS One, we are confident that consumers of scientific papers will discover what employers have long ago: If you’re looking for the imprimatur of greatness, try Nature or Harvard—but if you want the real thing, try PLoS One or Berkeley.

Of course, I disagree with the use of Berkeley in this context. Yes it is a public school. But come one – to use Berkeley as the “anti”elitist school of the world is a big stretch. So if you want the real thing, try U. C. Davis, not Berkeley.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Harvard Crimson PLoS One "Commentary"

Well, the newspaper of Harvard has posted an editorial about what they call “Science in Print.” The editorial is disappointingly a confusing mashup of ideas, facts, and flasehoods regarding PLoS One. The Crimson folks criticize online science journals under the idea that none of them are peer reviewed. They take issue in particular with PLoS One because they think it is to have no peer review at all. Fortunately, Chris Surridge, Pedro Betrao, and others have already posted messages to the comments section online about this correcting many of the mistakes in the editorial.

What is most disappointing to me about my undergraduate institution’s newspaper’s actions is that they seem to have written this editorial without even taking the time to read anything about the system they were criticizing. In doing some google searches I cannot even figure out where they got some of the misinformation they cite regarding PLoS One.

I completely understand people being uncomfortable with some aspects of the PLoS One system. Any change is scary to scientists and to supporters of science. But the experiment PLoS One is carrying out is not about replacing peer review entirely. It is about modifying the peer review system slightly (basically – papers will be reviewed for techincal quality only and not things like novelty) and also about adding a better evaluation system for scientific publications. I confess, I am not sure it is the perfect idea. But the world is a very very different place than it was when the current scientific publishing paradigm was established. We need to try some new ways of publishing if science is to take advantage of the internet driven, blogging, podcasting, mashup, [insert favorite technojargon here], world.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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