Ted writes:
Hi Vincent,
I wanted to thank you again for featuring my paper in TWIV 386 and having me on to discuss the research, I had a great time doing so! Since the taping I realized that during our discussion I forgot to mention one thing that I wanted to pass along to your listeners. That is: how much of a pleasure it was to publish through eLife (and not just because they decided to publish my work). Kartik Chandran mentioned this during his TWIEvo 5 episode and I wanted to join him in praising the publication process through this journal.
Several aspects of the process were more streamlined than those of other journals. That said, the initial submission process is SO MUCH easier and more streamlined than other journals that I felt they should be praised for it specifically ! I can’t overstate how nice it was to upload a simple compiled PDF file for review, as opposed to spending an entire afternoon (or longer) figuring out which file/figure is being rejected by the online submission compiler and then determining the reason behind the failure. I understand that each journal has their own formatting requirements, but why is it necessary to worry about that prior to review?! In my opinion, it’s an entirely pointless waste of time to have to deal with this until the manuscript has been accepted and those issues become relevant (especially if the manuscript is rejected). The publishing process would be much less of a headache if every journal had a similar system.
Best,
~Ted Diehl
—
William Diehl
Postdoctoral Fellow
Program in Molecular Medicine
UMass Medical School
william.diehl@umassmed.edu
Mehul writes:
Vincent,
I was recently made aware of your blog post on the paper discussing the possibility of Dengue virus antibodies enhancing Zika virus infection. With utmost respect for you and the your efforts on science communication, I was a bit disappointed by your (blog) commentary that was posted regarding this “paper”. First, and most importantly, this paper did not go through a formal peer-review process. Instead, it was simply published online and it was only screened for offensive and/or non-scientific content (see below). One would not immediately know this simply by looking at the paper. I find this process a bit disturbing. Second, the authors used the highly cell culture and neuroadapted strain of ZIKV- MR766. While it is the prototype strain, scientists have to be careful to consider the ZIKV strain and temper their conclusions appropriately. Third, and probably the most “offensive”, there are several controls that are missing in this paper that make the findings difficult to interpret. Figure 1 C and D lack a negative control- where are their controls with mock-infected cell lysates? Figure 2- Without a positive control for ZIKV neutralization, the results are uninterpretable. How do we know that their assay was working correctly on that given day? In a later figure, the authors show ZIKV neutralization using Dengue virus sera, but a non-specific negative control is needed to appropriately interpret these findings. Figure 3- Again, the authors did not include a non-specific negative control sera? In the last figure, the authors measure ADE by PCR, which I feel is not appropriate (and you pointed out as well in your blog post).
This also raises a serious ethical and scientific concern- Does this data exist in the scientific knowledge space if the work has not rigorously evaluated through a formal peer-review process? Is this not one of the most integral aspects to rigorously evaluating one’s findings? What happens if this paper goes through the peer-review process and it is rejected for publication? Would we be made aware of the reviewers’ comments? I strongly disagree with research, especially of this importance and magnitude, being published through a server before it has ever gone through the peer-review process. This can have damaging consequences if the findings from this research are incorrect and not representative of the current epidemic ZIKV strains.
Sincerely,
Mehul Suthar
********
From their website:
bioRxiv (pronounced “bio-archive”) is a free online archive and distribution service for unpublished preprints in the life sciences. It is operated by Cold Spring Harbor Laboratory, a not-for-profit research and educational institution. By posting preprints on bioRxiv, authors are able to make their findings immediately available to the scientific community and receive feedback on draft manuscripts before they are submitted to journals. Articles are not peer-reviewed, edited, or typeset before being posted online. However, all articles undergo a basic screening process for offensive and/or non-scientific content and are checked for plagiarism. No endorsement of an article’s methods, assumptions, conclusions, or scientific quality by Cold Spring Harbor Laboratory is implied by its appearance in bioRxiv. An article may be posted prior to, or concurrently with, submission to a journal but should not be posted if it has already been published.
Authors may submit a revised version of an article to bioRxiv at any time (prior to publication in a journal). Once posted on bioRxiv, articles are citable and therefore cannot be removed.
Steve writes:
Hi Vincent and team,
Just thought you ought to see this. I checked out the Offit book on the Amazon.UK site, and was quite sickened by what I found. The Offit book has just two reviews, both accusing him of making a fortune from ‘Big Pharma’, against which there are dozens of antivaxxer books, all with four or five star reviews. Anyone who looks for a book about vaccines on Amazon will *only* see that the ‘vaccines bad’ view is the orthodox one. Rubbing it in even further: one of the two reviews criticising the Offit book says we need someone to write a book with a ‘balanced’ view!
The flat Earthers are way ahead of the scientists in getting their message to the public. One thing that could at least give the public a chance of seeing a balance, would be to try and get people who really know the science, to write proper reviews of both Offit’s book AND all the many ‘recommended’ charlatan books. (I don’t really understand why these are allowed: they all ought to be contrary to advertising standards and be withdrawn as a danger to public health.). Surely you could get the TWiX community to start an, Amazon balancing, review writing campaign: at the very least by getting the Offit book, that you all seem to admire, an overwhelming number of 5* reviews on both sides of the Atlantic.
A further point, which I hesitate to make, but which I must, is that there is a distinct sarcastic and superior tone in the majority of work that I’ve read and heard from what might be called the ‘skeptic’ community, and that tone even comes across in the voices and comments of some of your own team on occasion. Some of the links that you provide for the balanced view are actually to some of the most sarcastic and superior writers and publicists–certainly those you refer to on this side of the Atlantic.
I know that it is incredibly frustrating trying to reason with people who are too ignorant to know how ignorant they are, and who you know will never read any link to authentic information, but it is much better not to say or write anything at all, if it can’t be done in measured tones that don’t sound superior and patronising. I’m a ‘skeptic’ (I don’t believe anything.), but I honestly can’t bear to read many of the people who think they are doing a great job of putting down ‘Bad Science’: Most of the time they are just making things worse by alienating undecided people with their superior or typical ‘doctor-who-thinks-he-could-do-stand-up-comedy-with-lots-of-stories-about-quaint-patients-they’ve-had’ tones [These seem to be a large percentage of UK doctors.].
Lobby groups like the ‘Science Media Centre’, and ‘Sense About Science’, are, in effect, little more than a recruiting service for the conspiracy theory industry: which, by all accounts, is now very big and profitable. Even I don’t believe anything from SMC or SAS without careful checking, because they are not just promoting science sense: they are promoting science with regard to promoting British business, and do spin the ‘facts’ accordingly. [As David Tuller will tell you: They also promote some establishment-popular science *beliefs* which are not yet supported by evidence. Some of their associates were familiar to environmentalists as media climate change contrarians, before ‘Spiked’ gave way to SMS]
I’m pleased to say that I think that Nina Martin came over as an encouragingly down to Earth person to be going forward as a science communicator and teacher of science communication. If she can also pull off a sensible interview with Andrew Wakefield despite getting targeted for abuse by the diehard conspiracy industry trolls, it will be a great thing to hear. But I do think there are an awful lot of ‘science champions’ who need to be listening carefully to the likes of Nina, and Kathy too, I think, because most of the ‘science guys’ really aren’t doing us any favours.
Sorry to have to say this, but I’ve even seen factual inaccuracies on some of the outspoken skeptics’ blogs, and when I’ve written comments with links to the correct case or data, they’ve just been deleted without acknowledgement. I detect far too much ego and testosterone, for the good of effective science communication.
Anyhow, I hope I can at least expect to see a few good positive reviews of Offit’s book on Amazon before long.
Keep it up despite the criticism: the last few podcasts have been especially good. 🙂
Steve
Bedfordshire
England
Weather typical changeable English ‘Spring’
Dylan writes:
Dear Twi-umvirate,
I really enjoyed your latest episode featuring Nina Martin. It was interesting to hear from a scientist who has seen Vaxxed and can make more directed comments on its claims. During your discussion the topic of the Tribeca Film Festival came up again and Alan(?) made a comment about Robert De Niro not being an anti-vaccer. While I think this is true, I wanted to draw your attention to an interview he did on Today a few weeks ago (see link below). Although he does talk about a need to have safe vaccines, he also mentions that he thinks it was a mistake to remove Vaxxed from the film festival because “it’s a conversation that needs to happen.” Unfortunately some of his other comments seem more biased towards the anti-vaccers. I was left with the sense, correct or not, that he does believe vaccines can be responsible for autism. In my mind this interview undoes a lot of the good that was originally done when he pulled the film.
After discovering TWiV a couple of years ago I have now transitioned to listening to the entire TWi family to get me through my daily commute. Thank you all for your tireless work to educate the public.
https://www.youtube.com/watch?v=FJ7iPn39i08
Sincerely,
Dylan
Tischler Lab
Microbiology, Immunology, and Cancer Biology PhD Program
University of Minnesota – Twin Cities
Stephen writes:
Saw this and thought it would be a good listener pick.
I have a total of about 5 hours of commute time a week. If each twiv episode could be 5 hours that would be great. I really don’t understand people complaining about twiv being too long.
https://boingboing.net/2016/04/13/animated-3d-printable-virus-t.html
William writes:
Thought you would enjoy these if you haven’t seen them already:
http://qz.com/662037/a-molecular-biologists-delightful-trading-cards-of-deadly-viruses/
William F. Ettinger, Ph.D.
Professor
Biology Department
Gonzaga University
Norma+Maurice:
Hello Twivsters!
Thanks for your wonderful podcast, I look forward to every episode. I saw these cool virtual virus trading cards and thought others might like them too.
Virus trading cards
APRIL 11 2016
cheers
Tom writes:
Dear Dr. Racaniello,
In case you haven’t seen these: virus trading cards. They’re a bit of a techie tour de force, but there is something beautiful and something unsettling about them.
-Tom
Tom
Nullius in Verba
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