HMS Beagle set sail on 27 December:
The Royal Society added 4 new photos.
Concerning the comments on TWiV #473, I already knew that confirming that a case of Dengue was a first infection could be done. I also knew that it should be done if one wanted to gauge the severity of an initial infection. Whether that indeed is being done or if self-reporting is being relied on — that I don’t know. I did an admittedly all too quick skim of Google results. I expected / hoped that there would be clear statements of the step(s) taken to confirm that severe first time infections really were that. This I did not see.
I’ve actually been thinking of this for a while. Perhaps you might remember my neighbor whose family became sick while on a trip home to India. (I asked him if it was the Flu and he replied , “No. It was viral.”) The topic of Dengue came up in the conversation. I mentioned how the first time Dengue was relatively mild. He the said “That’s not true. My sister only had Dengue once and she never was so sick in her life.” I didn’t argue with him, but I did wonder to myself how his sister could be sure that this indeed was an initial infection.
For everybody, a passing slight digestive upset, a headache, muscle ache or perhaps just some out of sorts feeling is common. This generally is just thought of as some effect of an unpleasant commute, boring meeting, long day at work, something eaten, etc. How often is this actually an invasion by a pathogen that the immune system manages to suppress quickly?
It’s been a while since I have written to TWiV, but as always it was great listening to all the “in depth” discussion on various issues concerning life as a scientist, especially in response to Raihan’s email and pressures / frustrations of publishing (Amy also added to this a bit). Personally having gone through the grind of a graduate school and a postdoc, I can totally understand this predicament and frustration. Circumstantially, I have unfortunately worked in labs where publishing only in a CNS (Cell, Nature or Science) journals was the holy grail and pretty much the sole criterion for measuring your intellect. However personally, I was always befuddled by this rationale that for science to be good and impactful, I need to make sure it has a CNS publication “TAG” too. Btw the TAG in biology also manifests a stop codon (geeky?:)). Sorry I digressed but in any case, this was a common discussion point amongst a lot of my fellow colleagues especially during my postdoc days but like me, they were also burdened with the same responsibility and outcome i.e. to keep slogging for the elusive manuscripts in one of these damn top tier journals. And to this day, this is something that continues to puzzle me since how can where and not “WHAT” be more intriguing in science?
In my humble opinion, highly reputable journals like JBC, PNAS, JCB etc do publish amazing scientific stories and CNS journals at times do publish some really crappy ones (there, I said it J). Having suffered through this personally, I have at times had difficulty even reproducing Figure 1a, forget about the whole premise of the publication from the CNS journals (Nature in particular for some reason). For e.g., on one occasion, we even made a KO mice based on the results of a publication (my postdoc lab at Genentech was apparently very well-funded), just to find out that the observed genotype to phenotype effect, was totally false as the involved gene had nothing to do with it. That made the “bleeding” so to say, excessive. It made me wonder as to why does one need to be “elitist” so to say when it comes to publishing high quality work. And to make matters worse, why are scientists measured on those metrics? Clearly the system isn’t working. No one really regulates or validates what gets reported in a journal article anyway, so to make life and death situation based on where the work was published seems a bit foolish. Isn’t the true scientific merit based in the impactful nature of the discovery rather than the impact factor of the journal where it is submitted for publication? And unfortunately to make matters worse, a lot of scientists, either under the pressure of gaining tenure or addicted to glory points, are also to be blamed for the sustenance of this culture. If the reported science is fundamentally solid and can be reproduced for the most part, then that is a fantastic outcome as far as I am concerned. And to that point, Rich, I am glad you had a clean mindset of publishing relevance rather than rushing after namesake glory.
Overall I do realize that the difficulty in getting funding for “exploratory” science is probably getting harder and it helps to get support from PIs who are giants in the field, but the amount of stuff that gets reported in CNS articles at times seems obscene. Why should one have to answer all the relevant questions? Isn’t the fact that the reported work has generated more curiosity equally important? And to make things worse, this professional line of work doesn’t at all pay you well. One probably spends close to 8-10 years of their prime being a grad student and postdoc (I am talking more about the biomedical sciences) and even at the end of it, there generally isn’t a very well laid path forward. And especially if you wish to venture into the biotech industry, it becomes even harder coming from academia. A lot of times the jobs demand some “on the job” experience and without having been exposed to that facet of a research enterprise, how can one do justice? Due to all these reasons and an absolute lack of mentoring (unfortunately that has been my experience up until I started working in a startup), I feel science can be a very lonely endeavor. Everything seems positive when experiments work, but in a profession where 90% or more of the efforts fail (although one mostly learns from those), I think this whole charade of glory chasing through publication in “high impact” journals seems depressing, counterproductive and somewhat outrageous.
But it’s not all gloom and there certainly is the upside of being engaged in doing something that is both invigorating and rewarding in a very tangible way. Overall based on my experience all I will say is, that being in research will surely test your patience and resolve, but if you have the passion and the fight in your heart, you will overcome the limitations. For me, a life outside research would be a life without curiosity and fun of discovering the unknown. Personally, exploring the unknown is the biggest driver for me and I hope when I am done, I would have made some intriguing and hopefully interesting discoveries that can invigorate an idea, and maybe an individual.
As always, thanks to all you folks for being so generous with your time and effort. It is always special to listen to these podcasts and learn,
Neeraj Kapoor, Ph.D.
Finally killed for good: https://arstechnica.com/tech-policy/2017/11/eff-destroys-the-podcasting-patent-one-last-time/
I hope you are all well and the weather everywhere is good. I am following up on the discussion over capping the number of NIH grants per investigator from episode 467 that Alan and I have continued on Twitter. Let’s start with the fact that, ultimately, funding of investigator initiated proposals is decided by their peers and that these ever-changing committees of scientists known as ‘study sections’ are NOT composed primarily of old, established investigators. In fact, the study sections I have been on have been the complete opposite and in my experience were not at all biased when evaluating applications from big labs. The NIAID paylines also favor young investigators, their applications have to be in the top 13% to obtain funding whereas for everyone else this percentile drops to 9%.
Importantly, the reports on which Alan has based his opinion, that big labs do not produce the most impactful papers, have several flaws. One such major flaw is that they only consider the NIH (or equivalent) funding of each lab in their analysis. Therefore, labs that have other sources of funding, HHMI being the most prominent, are misplaced on the graph and thus skew the results. Furthermore, in the PLoS One study the data are plotted on a log scale which diminishes differences.
What I have not heard being mentioned in this debate is a recent shift in the NIH funding from investigator initiated proposals to multi-million dollar ‘pet’ projects selected by administrators. I think this is a problem as it reduces funding that allows investigators, young and established, to pursue what they think is important.
Ultimately, increasing this latter pool of money is key and I wonder why we turn on successful big labs, whose funding is actually a tiny fraction of the total NIH budget, rather than consider the NIH budget itself and work on ways to increase the part devoted to investigator initiated research. There is no point funding young investigators without a plan to continue their funding once they are not ‘young’ anymore. There has to be competition and track records matter. This is not a perfect system, but it is the one most based on merit I have experienced. It is what allowed for my own success while not being a ‘rich’, evil, privileged white male head of a big lab. And I am in no way a ‘cherry picked’ example.
Sad to relate, I only learned of this yesterday.
The Web Site does show some events for this week.
If this was mentioned in TWiV 461, I’m sorry for an unnecessary email. (I’m just up to 87 minutes.) If it was not mentioned, was the choice of paper covered serendipitous? Yes, I know that the text readability checker — and Gerard Manley Hopkins — would say that 5 syllables is way too many.
My name is Or and I am a BA student in Biotechnology from the Technion in Israel, and I’m on my way to becoming a Virologist.
First of all, I wanted to say that I’m a fan of TWIV and of Professor Vincent Racaniello’s Virology lectures on YouTube. I’ve watched them prior to the Virology course I am taking now and I found them to be a very thorough guide into the world of Viruses as they greatly prepared me.
I want to ask of you if you could do an episode about examples on the positive effect Viruses have on nature.
In a recent lecture during my Virology course we discussed a few examples of traits that viruses grant their hosts, like the well-known case of Cholera and its toxin. All examples were negative, so when asked if anyone knew of anything else I pointed out a positive example from Professor Racaniello’s Lecture, about Yellowstone’s plant Dichanthelium languinosum and its virus-infected fungus. I would like to have a batter arsenal of examples (even if there are only a handful) for the positive effect Viruses have on nature (beside, of course, evolution).
I’ve found an ASM entry from 2015, that said:
“Mammalian viruses can also provide immunity against bacterial pathogens. Gamma-herpesviruses boost mouse resistance to Listeria monocytogenes, an important human gastrointestinal pathogen, and to Yersinia pestis, otherwise known as plague. Humans are often infected with their own gamma-herpesviruses, and it is conceivable that these could provide similar benefits.” (https://www.asm.org/index.php/asm-newsroom2/press-releases/93495-viruses-you-ve-heard-the-bad-here-s-the-good)
However, my search yielded nothing more that was of relevance to my query.
Thus, I would like to ask you: could you make an episode on the subject. It would be very educational for many people.
Thank you for taking the time to read my email, and I look forward to future episodes of TWIV.
G’day TWiV team,
My question relates to TWiV 457:
I really enjoy learning the origin of words. It helps me remember the disease pathogenesis and brings meaning to the scramble of the Latin binomial.
What is the etymology of Myxomatosis. Growing up in rural Australia I always thought the scientific name for myxo was ‘Myxomesothelioma’. Is this just some misspoken version of the actual disease name or does it have an actual base in science?
Hopefully, you can reassure me since I’ve been telling people for years that its Myxomesothelioma. Whoops.
Thanks for the show,
I work a very mundane lab job and listening to TWiV helps to keep my mind moving while I work.
Hello TWiV team,
I’m months behind in listening to TWiV/TWiP/TwiEVO but the dispiriting political news of late has encouraged me to focus on constructive conversations that can help keep my focus on curiosity and learning.
This was an excellent episode, especially the discussion of plaque assays. I still haven’t taken Dr. Racaniello’s Virology course (hopefully remedied in the new year). So I was pleased to hear the discussion of the techniques and Dr. Despommier’s questions, some of which were the same ones I had. As a former student and science teacher, I appreciate the questions, and the team’s willingness to answer them.
Thanks again for all the work you do to bring science to the rest of us. It is much appreciated!
P.S. I went looking for some of the ‘movies’ showing viral action in a plaque assay, and unfortunately, most of the links don’t work (http://www.virology.ws/2010/02/03/now-playing-viral-plaque-formation/ , at least in Safari on my iPad). I did find the more recent Virus Watch episode on YouTube where Dr. Racaniello described plaque assays and which included one of the films.
Story spotted while browsing:
“The U.S. Environmental Protection Agency (EPA) has approved the use of a
common bacterium to kill wild mosquitoes that transmit viruses such as
dengue, yellow fever and Zika, Nature’s news team has learned. On November
3rd, the agency told biotechnology start-up MosquitoMate that it could
release the bacterium Wolbachia pipientis into the environment as a tool
against the Asian tiger mosquito (Aedes albopictus). Lab-reared mosquitoes
will deliver the bacterium to wild mosquito populations. The decision —
which the EPA has not formally announced — allows the company, which is
based in Lexington, Kentucky, to release the bacteria-infected mosquitoes
in 20 U.S. states and Washington DC.
MosquitoMate will rear the Wolbachia-infected A. albopictus mosquitoes in
its laboratories, and then sort males from females. Then the laboratory
males, which don’t bite, will be released at treatment sites. When these
males mate with wild females, which do not carry the same strain of
Wolbachia, the resulting fertilized eggs don’t hatch because the paternal
chromosomes do not form properly. The company says that over time, as more
of the Wolbachia-infected males are released and breed with the wild
partners, the pest population of A. albopictus mosquitoes dwindles. Other
insects, including other species of mosquito, are not harmed by the
practice, says Stephen Dobson, an entomologist at the University of
Kentucky in Lexington and founder of MosquitoMate.”
P.S. While watching TWiV 466 “The Capsid Club” I was intrigued (as I have been in the past) with Vincent’s comment to the audience, something like “How many of you work with double-stranded RNA viruses?”. I guess that someone choosing to work with a given virus or family of viruses had to choose it on the basis of practical considerations (RNA viruses mutate more frequently, is there a model host in which the virus will propagate, etc.), funding considerations, “popularity”, how crowded the field is, etc. etc.
Might this make an interesting future TWiV episode or sub-episode?
Dear Vincent and other TWIV hosts,
Thank you for your fantastic podcast(s).
I recently ran across a short story by Ted Chiang who is a multiple award winning american sci-fi writer. The story is very short (it doesn’t take that much time to read it) and has been included in The Best American Short Stories, 2016.
Hi, I am a physician and a writer who is interested in writing a science fiction thriller about bioterrorism. One thing that worries me is that advances in synthetic biology may permit the reconstruction of a virus such as smallpox, which can then be weaponized by simply introducing a suicidal vector (like a suicide bomber) into the population. I note that the genome of the smallpox virus is in the public domain, and while synthesis of a full genome may not be immediately possible, one can imagine that some sort of piece meal approach, may be possible presently (horsepox was recently reconstructed), One can readily imagine that a “from scratch” synthesis could be possible within decades.
I do not want to give anyone any ideas, but it seems to me that the best defense against such a threat, would be a public appreciation.
Can you comment on what precautions are in place to prevent this from happening?
Please let me know if you plan on addressing this on your show.
I came across this pick through a Facebook post by ASV on Sunday, December 10, 2017. From the first glance, it looked like a virology crossword puzzle. I paused for a second before opening the link and thought: wow, this is very cool! After taking a careful look at the link, it turns out that these are crossword puzzles created by Dr. Kevin Maringer, a lecturer of microbiology at the University of Surrey. It seems that he creates them based on the lecture material to quiz the knowledge of his students, what a great teaching tool! Here is a sample: http://www.armoredpenguin.com/crossword/bin/crossword.cgi?cmd=solve&filefrag=2017.12/0913/09133111.694.html
I was curious to know how he generates them. It turns out that there is an online tool called Armored Penguin, which will do it for you if you can come up with the words and associated clues. Here is a link to the puzzle maker: http://www.armoredpenguin.com/crossword/
I have a suggestion for TWiV. For the book contest episodes, how about instead of asking the interested participants to simply send an email, ask them to solve a puzzle based on the topics discussed in that episode? I know that this will come with the additional burden of creating and grading the puzzles, but you are the professors and this is what you do, right? 🙂
I always felt that just sending an empty message to win a precious book by random chance is not fair. Perhaps, the TWiV crew can run these puzzle contests once in a while, which should add a lot of fun to the process and draw the winners out of those genuinely interested TWiV fans.
I can’t thank you enough for all that you do to enlighten us.
Also, kudos to Dr. Kevin for turning virology quizzes into fun!
Greetings TWiV team.
I have a listener pick of the week, an article from Gizmodo.com where reporter Jennings Brown interviews some of last few people still using Iron Lungs and talks about their experiences and the difficulties they have maintaining their ageing machines in working order: