TWiV regularly receives listener email with corrections, comments, suggestions for show topics, requests for clarification, and additional information. A selection of these is archived on this page.
In case this didn’t make the news in the city, I thought you might be interested in this report of Hantavirus in the Adirondacks. It looks like a wooden lean-to was the “scene of the crime” again!
Dear Cast of Thousands:
Normally you speak far enough over my head that I just sit back and absorb information at the feet of the Masters. Occasionally, I admit, I fall into an information-overload-induced coma – fortunately not while driving. Your episode involving the Wired article on rabies, however, fell well under my head as I had actually (and accidentally) read it the week before. I really wish that you had read the article more carefully because you stumbled over a number of important points.
There may have been some antivirals involved but I believe that the article mentioned the ketamine was the primary coma-inducing agent and was also believed to exhibit some anti-viral properties. I may have that a little off but it’s close.
More importantly, the coma was induced because of the observation that most of the neural damage was caused by over-stimulation of the neurons which, in turn, causes neural death. I believe that it is called excito-toxicity. The drugs used to generate the coma were chosen for their ability to decrease neural activity. The idea was to reduce neural activity long enough to allow the neurons to survive until the immune response kicked in.
Most importantly and related to the second point, the girl was not fine afterwards. She has had to go through months of physio-therapy just to be able to walk and talk again. A year afterward she is functioning well but will probably never be 100%. The coma-therapy probably did reduce neural death but it didn’t eliminate it. For this type of therapy to be more effective in the future and, thus, reduce recovery time (and, let’s face it, death), better neural receptor agonist will have to be selected, ones that more specifically target the excito-toxicity that rabies induces.
Anyway, you probably received a great many e-mails on the subject but, just in case this one proved helpful in some way, I thought that I had better send it. Thanks to all of you for the podcast and I look forward to the next 100.
I heard a recent TWIV episode this week in which it was mentioned that about twenty cases of Hand, Foot, and Mouth disease are confirmed in Canada per year. Including my 1 1/2 year old son’s case, I am aware of five cases affecting the very young that occurred in Houston, TX in May 2012. There have likely been many more cases in the area. To reduce the spread of this disease, it is important that parents isolate their children for two full weeks after they are back to feeling normal. My son, Holden, did not seem to be experiencing discomfort while eating but very cold fluids did help his appetite.
BTW, I have been listening to your show for a few weeks now on my Android phone using DoubleTwist Pro paired to Bluetooth headphones. I listen while playing with my son in the water for about an hour shortly before his bed time. Both my son and his several week old sister were home births facilitated by the well known nurse midwife Jackie Griggs.
It is too bad that the U.S. insurance companies will not cover what is the standard method for child birth in the Nordic countries. Over 1/3 of all U.S. hospital births result in Cesarean births with over 50% of induced hospital births resulting in Cesareans. In contrast, over 98% of all home births involving midwives do not require transport to a hospital. The U.S. lags behind many of the most prosperous countries in the world in limiting infant mortality rates and our medical system that incorporates some of the worst aspects of capitalist and socialist systems is a factor in the issue.
Enough ranting – please keep making science entertaining!
Does this apply to any situations you have seen?
I shall begin, my friends, with the definition of a pseudoscience. A pseudoscience consists of a nomenclature, with a self-adjusting arrangement, by which all positive evidence, or such as favors its doctrines, is admitted, and all negative evidence, or such as tells against it, is excluded. It is invariably connected with some lucrative practical application. Its professors and practitioners are usually shrewd people; they are very serious with the public, but wink and laugh a good deal among themselves. The believing multitude consists of women of both sexes, feeble-minded inquirers, poetical optimists, people who always get cheated in buying horses, philanthropists who insist on hurrying up the millennium, and others of this class, with here and there a clergyman, less frequently a lawyer, very rarely a physician, and almost never a horse-jockey or a member of the detective police.
Oliver Wendell Holmes, Sr.
“Autocrat of the Breakfast Table” 1858
Dear TWiV Team,
Love your show. Keep up the great work. I was just listening to episode 192 and would like to second the request for a bioinformatics 101-type episode. You might consider getting someone(s) from the Broad Institute, specifically the Viral Genomics group on the show. (I’d highly recommend Matt Henn, though he appears to have just left his position as Director of Viral Genomics at the Broad, which might rule him out. I saw a talk by him and really enjoyed it; he’s a microbiology guy, and thus more understandable than some bioinformatics types.) I think that the Institute is a very neat model for scientific collaboration, particularly between more traditional scientists and computer geeks. I’d love to hear a discussion about how the Broad is set up, its advantages and disadvantages, etc as well as to get insight on the great bioinformatics work they do.
My name is Greg, I’m an undergraduate at the University of Manchester, I’m a big fan of your Podcasts and over the last few months I have set up one of my own – The Life Sciences Podcast, it covers a range of things biological/medical related. As my podcast is in association with my University they’ve asked me to get some listener feedback, I was wondering if you’ve ever carried out a listener survey? Or have any advice on getting useful feedback from listeners?
Any advice would be greatly appreciated!
Different animal species have different kinds of placenta (and different levels of interaction of fetal-maternal tissue/blood). Are trophoblast cells from other species also resistant to viral infection? Can the conditioned medium of human trophoblast cells interfere with animal viruses infection of human cells (or human viruses infection of animal cells)?
[answer from Carolyn Coyne]
We have never directly tested non-human placentas for their infectivity or ability to transmit viral resistant to recipient cells (via conditioned medium). Presumably, many would have a similar mechanism(s) of resistance to those that we study in the human placenta. The cluster of placental-specific microRNAs that we have been studying (and which confer viral resistance) are specific to primates, but it is very possible (and perhaps likely) that other animals have specific miRNAs with similar functions. I will note that in vivo, the mouse placenta seems to be rather impermeable to most viruses (studies on mCMV rely on microinjection of the virus directly into the placenta), but there are not many studies that have investigated this question specifically.
In terms of animal viruses, we have not specifically tested these. However, given that the mechanism of viral resistance induced in recipient cells seems to be rather non-specific and far-reaching (autophagy primarily, but perhaps others), I would anticipate that many viruses of animal origin would also be susceptible to the antiviral effects of the placental conditioned medium.
Greetings from North Carolina,
I am a PhD student studying Norovirus in the Food Science department at NC State University. Norovirus as you probably know is a difficult virus to research in that there is no culture system available for it. I recently read a paper from a group at Baylor describing a new way to culture enteric viruses. The system works by creating a lab grown “intestinal epithelium” from stem cells. The paper shows that the concept works for Rotavirus. Perhaps this is a first step towards a functioning Norovirus culture system? I thought perhaps you would enjoy the read and maybe entertain the idea of discussing this on a future episode.
Thank you for TWiM and TWiV..I am a big fan of both !!!
primary paper in mBio http://mbio.asm.org/content/3/4/e00159-12.long
Your most recent TWIV in Nebraska made me want to add a few verses to that old kids’ song…
“There’s a virus in the alga in the paramecium on the speck on the flea on the wart on the frog on the bump on the log in the hole in the bottom of the sea.”
Just thinking and thought it might amuse you guys, too.
Jim writes (re TWiV 200 video):
Will we finally see a naked Racaniello?
Congratulations on surpassing 200 episodes!
I’ve been a rabid fan of TWi(V/P/M) since I first stumbled upon TWiP. I look forward to every new episode- they’ve helped me get through my days as a small electronics technician and have made multiple road trips bearable. This series of podcasts awoke a latent interest in microbiology- time to make something for TWiV! I’ve attached a picture of some simple plaques I’ve printed on my DIY 3D printer.
Thanks for all the hard work and time you folks put into these podcasts. I look forward to more! Let me know where to send these plaques and I’ll send them on their way!
[Claudio's photo is the episode art for TWiV 203]
I’ve been working on a transcript for episode 131: A REOstat for cancer.
I hope I’m not duplicating anyone else’s efforts.
Thanks for the wonderful podcasts, I listen to them while I do all manner of stupid things, like cooking, cleaning, ect. I must admit, my apartment got a lot cleaner after I found TWiV and TWIP.
(A postdoc in mathematical physics)
This may be a bit random, but here it goes: A friend of mine (a virologist) absolutely adores your podcast. She’s done me a great favour and I’d love to say thanks with a little gift. I was thinking of a magazine subscription, but am not sure what to go for. I want something on the ‘geekiness level’ of twiv (so a bit more geeky than National Geographic or New Scientist) that is affordable for a ‘normal’ person. She’s relocating to the States this week, so maybe you guys have some magazines that would be perfect, but that I’m not aware of.
Do you have any suggestions for me?
Many thanks and kind regards,
I’m a 4th year PhD student at Yale University in the Environmental Engineering Department working in an environmental microbiology lab. The weather in New Haven these days is scorching hot with the occasional summer thunderstorm- a great deal for my adviser who can be assured that I spend the majority of my time inside our building as my home lacks air conditioning.
I’d like to comment on your amazing podcasts- I am a regular listener to Twiv and Twim- I especially enjoy your coverage of the human microbiome (get Jo Handelsman on Twim more often!) and the talks about influenza transmission. My PhD work centers on the influence of the human occupant on the indoor air microbiome and, thus, these topics are at my dear heart.
In Twiv 191, you talked about influenza transmission via the airborne route, droplets and contact. The question about virus inactivation in air was raised and remained unanswered at that point. I’d like to take this opportunity and hint to a great modeling work by Lindsey Marr of Virginia Tech that combines dynamics of influenza virus containing aerosols (influenced by temperature, humidity, as well as varying air exchange rates in the room) with virus inactivation parameters to estimate removal rates from air. Her results indicate that virus inactivation is important for virus removal from air and largely dependent upon humidity (virus inactivation and humidity are positively correlated). The modeled air exchange rate (AER) parameters (1 or 10 in the paper) are very reasonable for mechanically ventilated building as often found in the US. But having some experience in measuring air exchange rates in public buildings and schools, 1 air exchange per hour sometimes is (sadly) high in those common spaces and may partially explain why we catch a cold in places such as classrooms and waiting rooms. Removal by deposition, air exchange and inactivation should be kept in mind when the infectivity of influenza is discussed especially under the recent focus by the academic community.
As Lindsey shows the importance of humidity on virus inactivation, she had also mentioned (not sure if that is listed in this paper) that protein content in saliva influences survival rates of viruses (high and low content are good for survival). Did you know that infants and adults have different saliva compositions with regards to protein and salt content?!? Isn’t that mighty cool?!?! So, again, another parameter is added. In summary, one has to look on a much broader scale and might have to take many more factors into account than previously shown when accurately estimating disease transmission via the airborne route.
The paper is published in PlosOne and thus accessible to all listeners. Here is the link:http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0021481
I also attach the paper saving you some time.
Great podcast! Keep up the viral work!
Yale University, Environmental Engineering
I am glad you had a chance to get a glimpse of the BSL4 world. You might remember that I have been trying for 1 1/2 years to get you to see the Galveston National Laboratory, a facility with an actual ACTIVE program and a number of very experienced PIs that currently work in the BSL4.
I wish we would have had the chance first especially for TWIV 200.
A very disappointed,
A recent BBC Health Check program included a segment about rabies which notes that vaccines derived from dog rabies may only be effective for people bitten by a rabid dog, but not a bat! I've attached the program and it's the first segment which is only about four minutes long. A Dr Behrens (link to some of his advice) from the London School of Tropical Medicine and Hygiene is the speaker and source of the comment. Are there multiple vaccines for rabies? This complicates things....
Mattias Schnell responds:
All USA bat rabies is covered by the current rabies vaccine but its different for bat derived rabies in other regions.
Two thing are important to know:
1) When people talk about rabies they normally mean classical rabies virus (RABV) and this is still the most important member of the genus Lyssavirus. Almost all death of humans is caused by RABV transmitted by dogs.
Big problem in developing countries (South America, India, Africa, China, Asia in general). In Europe and USA we do have rarely rabies transmitted by domestic animals because we do vaccinate that problem is gone.
We still have a large rabies problems in wild animals (skunks, raccoons, foxes) but if somebody get bitten by a rabid animals we do postexposure treatment, which is 100% efficient if applied correctly. About 30,000 people do receive postexposure treatment in the USA every year (that is not cheap). We do have about 3 cases of rabies in the US every year but they were imported (people who traveled an got infected) or they got infected by bats. This brings us to the bat topic. All bat derived rabies virus in the USA is classical RABV so postexposure will work. However, people might not realize that the have been bitten by bats (small teeth). So the problem in the US is more that people do not realize they were exposed or do not know that bats are transmitting rabies virus.
2) Bats are very likely the natural host of lyssaviruses. Bats seem not to be as sensitive to rabies virus and a lot have actually antibodies. That doesn't mean they dont get rabies it but it is probably not 100% lethal. Make sense if you think how close they live together. Also important, there are bat derived lyssaviruses, which are antigenetically different from RABV so the vaccine doesn't protect. This is the case for the to African lyssaviruses mokola and Lagos bat. So for these viruses there is no vaccine even it would be easy to make one.
Hope that help - a bit more info is in the powerpoint file. As usual things are simplified and not everybody probably would agree with me....
All the best
Matthias J. Schnell, Ph.D.
Professor Department of Microbiology and Immunology
Director Jefferson Vaccine Center
Jefferson Medical College
Hi Twiv crew,
The Texas Wild Child was mentioned on 192 (listening now). Did you see the August Wired?
The article describes a therapy for rabies victims and its controversy. How did I miss this? 6 survivors (of 41 attempts) since 2004? Not including the Wild Child.
I would love to hear your thoughts, especially since this was an article I could easily follow, not a research paper.
Thanks for all you do!
Interesting short article on Fox News about Vampire bat bites conferring resistance to Rabies. What are your thoughts on the subject?
Great show - thanks for all your hard work. - Micki / Simon Lab / UMD
PS - have you thought about doing a show about Rhabdovirus that would include a plant rhabdovirus scientist? Maybe Andy Jackson or Michael Goodin. Just a thought . . . . . . .
Rabies seems to be in the news these days. There is also a new cultural history of Rabies, entitled "Rabid" by Bill Wasik and Monica Murphy. I'm listening to it on audible and it's fascinating. Regards, John
Dear TWIV hosts,
I caved in when my 4 y.o. daughter asked me for an iTouch last year. I resisted for as long as father could. But, in the end, I gave up and bought her one.
Few months later, she cracked the screen, lost interest in it and asked me for an ipad, instead. Initially I laughed at her request, but, since I caught her mother looking for an iPad ad in the weeks preceding mother's day...guess what? Yes, you're right, I caved in again and bought them both the latest generation iPad.
I noticed there was nothing wrong with the iTouch, except for the cracked screen. So, I decided to fix it myself. A few attempts later and the broken iPod was good as new. "What am I going to do with this?" I thought, realizing that the whole world was ahead of me with regards to popular electronic gadgetry.
"Play games", said my daughter.
"Listen to podcasts", suggested my creative wife.
"How do you do that?", I asked.
That question has thrown me to an entire new world. From then on, it was just a matter of hours until I found your program. [ks: don’t read next line?! ad: Definitely read the next line, then act regretful when you get to the parenthetical part.] And I truly fell in love with it (please, please, please, don't say that out loud on the program! I've got a reputation to maintain!)
I'm a virologist as well. I started studying baculoviruses when I was an undergrad back in Brazil and eventually got a BSc degree from the University of Brasilia. Soon after, I went to Japan to study more about "baculos" and pursue my postgrad degrees (MSc and PhD) at Nagoya University. In 2003, once I could safely display the "mission accomplished" banner, I sailed away to the uncharted waters of New Zealand for a short postdoc position at the University of Otago in Dunedin. A place I now call home.
After my post-doc experience, I became interested in the field of Science Communication and documentary filmmaking and was fortunate enough to have stumbled across a a postgrad course at the University of Otago, which combined these two topics. For my final project, I decided to combine my virus research expertise and tell the story of the Auckland Island Pigs. Here's a link to the movie:
The movie, posted by co-director Adam Thompson, talks about the pigs being commercially exploited as promising xenotransplantation tools for the treatment of type 1 diabetes. Long story short, a couple of hundred years of complete isolation " made" the pigs germ-free. At least, that's what the charismatic mayor of the city where the pigs are now kept and the biotech company tells us all. But the truth is far from it. The pigs have very low copies of PERVs (porcine endogenous retroviruses) integrated in the pigs genetic make-up
I would like to invite you, dear TWIV hosts, to watch the short movie (for some feedback) and perhaps discuss about PERVs in the future. In addition, I would love to know your thoughts regarding xenotransplantion and viruses, in general. That would mean the world to me, as, even after having finished this movie, I still can't reach a verdict. Do we abandon this live-saving technology due to its potential risks of pandemic proportions or embrace it and utilise it in large-scale xenotransplantations world-wide?
Please keep up with the outstanding work you guys are doing with the program. Your ideas and comments are truly inspirational!
PS: Really sorry about the animations in the pig movie. We received no money for this project and had to be creative with explanatory animations.
PPS: http://www.youtube.com/watch?v=ChIeTB-XHsM is another movie I made. It only touches the issue of varroa-mites as carriers of honeybee viruses.
Cris Felipe-Alves, PhD
Virus Research Unit
Microbiology & Immunology Dept
University of Otago
Matt Evans writes:
Hi Vince and gang,
Last week you had a letter from an Olympic athlete who wanted to know how he could stay in touch with science while training. I was amused when Rich said there is no way you could work for your phd and train for the Olympics at the same time because that is exactly what my student, Maria Michta, just did. She was the only female race walker from the US to compete in London. Now she is back in lab as a full time student. Training was balanced carefully with lab work over the last few years, but being right next to Central Park made it a lot easier. She even had a first author paper while training.
Not bad huh!
I’m doing an EPQ (independent research qualification taken at end of high school) on the eradication of polio, and whether the current attempt is worthwhile or not. I have a vague memory of it being mentioned in TWIV that it is advantageous for attenuated poliovirus to regain virulence, but haven’t been able to find anything on this anywhere. Could you give me any further information, or direct me to where I can find it?
P.S. TWIV is fantastic; it was what inspired me to choose a virology based topic for my EPQ and to apply for university courses which include virology - prior to listening I had very little interest in it.
Good afternoon! I know you're busy, but I hope this email finds its way to you. I've been listening to your podcasts for quite some time now. I really admire your innovation and ingenuity in regards to educating the general public about viruses.
I've been interested in virology and host-pathogen interactions for quite some time, especially those of newly emerging viruses. This led me to pursue my MS in Entomology last fall. I have one year to go, and I'm beginning to look at PhD programs in virology in order to combine the two skill sets. Viruses like Ebola, Hendra, and Nipah are especially intriguing to me, and I'd really love to work with newly emerging pathogens. However, as I search for PhD programs, I'm finding that the number of researchers working in this area is low. It seems that the majority of this work goes on in level 4 laboratories (of course) by researchers, rather than professors. I was curious to know if you could recommend any programs to me that might be a good fit, or, if you could tell me whether working with another virus for my PhD would affect my ability to land a job with level 4 agents later in my career.
Any advice would be great! Although I've almost completed my Master's degree, I still feel like a nascent scientist with a lot to learn. You, Rich, and Alan help tremendously though!
Have a great day, and I look forward to hearing from you.
Still going through old podcasts and still don't understand virus, but I do know a little physics.
On using the supercritical CO2 to create a dry virus may allow viable virus particles to survive. The killing of enveloped virus on drying may have to do with the surface tension of water changing the physical structure of the virus particle and drying under supercritical conditions the surface tension of the gas/liquid interface goes to zero.
To see how an open gel type structure can be dried without destruction -- just a common example that shows the principles. If the virus didn't change upon drying, it is small enough that the time it would take to rehydrate from the gas phase at 100% RH at lung temperatures and lightly hydrophilic surfaces could be so fast that no structural collapse would occur on rehydration.
Someone else probably already answered this physics type question.
It was mentioned in TWiV 178 that Puerto Rico doesn’t currently have other mosquito-borne viruses like yellow fever or malaria. Can this be attributed to anything other than luck? Do any countries undertake efforts to curtail the spread of viral vectors (by controlling used tire trade or otherwise)?
This question is in response to episode #182.
You three discussed the benefits of immunizing in the skin rather than the muscle. This may be a naïve question, but wouldn’t injecting vaccine directly into the blood stream be better than both skin and muscle? Is this an issue of medical “difficulty” and patient compliance?
Dearest TWiV hosts (reservoir?) I’ll try to be as brief as possible, though typing that rather than simply doing it is probably not helping there… ANYWAY my name is Bronwyn, I’m a 2nd yr biomed undergrad studying on Australia’s Sunshine Coast and though only newly infected, i’m immensely fond of your show! I love the break down/discussion of papers and new research which saves me drowning in the great sea of articles that is; scholar/pubmed/scidirect/etc/etc/etc. And as an undergrad wanting to get into research; #184 on the broken science system (and more importantly how to work towards fixing it + just survive in the meantime) was BRILLIANT, i clicked download on the Casadevall and Fang papers as soon as i had played it out, which meant that they had just finished by the time i finished playing it through the second time over. I’d been getting despondent over the dog-eat/poison/cripple/render-otherwise-harmless world that science research seemed to have manifest itself as, a model one would have expected from a somewhat business-like paradigm, not the province of a collaborative pursuit of understanding so that we, as a biologically social species, might go about interacting with the world in a more intelligent way. But enough ranting; essentially i love your work guys, and incidentally its about 20’C and a bit overcast here and there, which is really quite cold for us -winter just started.
But now to get to the reason why I’m spamming your already inundated inbox: earlier this term in a micro class my lecturer was talking about plant viruses and i couldn’t help noticing they, for the most part, have RNA genomes rather than DNA… i was curious and asked but she was unaware of any reason why and couldn’t find any explanation when she researched it a bit later, either could i… any ideas??? Is this possibly a quirk of nature arising from a/an RNA-containing evolutionary forbearer/s or does anyone know of there being some sort of selection preference for RNA genomes in plant viruses?
Also; I was watching a video: ‘MIT World’ talk on Global Pandemics (Nov 17 2009) given by Hidde Ploegh (Prof. Biol MIT) available from itunesU (or http://video.mit.edu/watch/global-pandemics-9508/), it’s a soap-box-talk-night-sort-of-thingy… ANYWAY Hidde briefly discusses the FDA-approved method of flu vaccines production, pointing out the fact that not all flu strains grow equally well in eggs, which limits the strains covered by an American-made vaccine to those that perform sufficiently in chicken eggs. Is this a serious limiting factor in the vaccine quality or merely something that needs to be kept in mind when making a vaccine? In Europe flu strains are grown in cell cultures, this would eradicate the problem of allergic reaction is caused by chicken proteins, is there any other reason why an allergic reaction would occur in response to a vaccine? and it’s 1hr 5 minutes long...; maybe HP part is 15 minutes long then there’s Q&A, according to the introduction][I listened to about 20 minutes of it, didn’t get to any juicy parts]
If you’ve time i recommend watching the talk, there’s a great dismissal of an ‘evil drug company flu vaccine hiding’ conspiracy theory and a criticism of the economic priorities of funds allocations in research and of the concern (paranoia?) the US seems to have over biodefense (despite the lack of reasonable threat assessments) @38:56 - 42:07. Just think; this was 3 years before the NSABB censored the Kawaoka and Fouchier research! But my favourite part (if it’s not the fact that he’s wearing bright red pants) is the final word he gives on the moral obligation of vaccination and the dangerous selfishness of people who rely on herd immunity; it’s a serious problem i think; -here in oz there is a massive anti-vaccination sentiment, rooted in a distrust of science/medicine/drug companies and fear of vaccination side-effects like autism from a measles vaccine (jeez looks like a symptom of the winner-takes-all-system with its pressure to publish giving rise to bad science and fraud - A retraction does not and cannot undo the damage done by bad science). This attitude seems to be concentrated in more alternative towns like Byron. Paul Corben (director of NSW North Coast Public Health) said there had been TWICE the level of disease in Byron Bay as had occurred in Ballina, a town pretty well adjacent to it (this info is taken from the ABC TV show Catalyst Episode 9 of 2012). Is regional social psychology also a big factor in American vaccination rates? Do public health systems attempt to address this? I mean wouldn’t unvaccinated people, when concentrated into small geographic areas be so much more dangerous than if they were dispersed as the statistics for the unvaccinated: vaccinated ratio make it appear??
I don’t expect this to be read on air or anything, I’d just really appreciate any answers/info/links/TWiV episode suggestions. i’m still working my way through the back catalogue (just finished 2008) in addition to listening to current episodes as they’re released so i do not doubt that some of this would be addressed therein. I’m especially curious in regards to the apparent plant preference for RNA…
oh dear… Short-message-fail: that was so much longer than the paragraph i had originally intended, well my apologies and many magnitudes of thanks from down under!
T. Jack Morris responds:
I can think of no fundamental reason for this to be the case other than an accident of evolution. Here is the rationale. It turns out there are no true dsDNA viruses. There are pararetros like Cauliflower mosaic and ssDNA viruses like geminiviruses, so it is not because plant cells could not support true DNA virus replication. It is not likely a cell to cell movement restriction because there are plenty of viruses of papilloma size that infect plants. It could have something to do with the nature of plant meristems where cell division is primarily restricted. It is a question worth considering, perhaps at the TWIV. I am copying a colleague with whom I have had this discussion.
Just a quick comment on the podcast covering journal retractions and other "scientific" errors. A comment was made that the problems seems to be in the first rate journals which have the most retractions -- at least the ones we hear about. However, if you want to find a lot of papers that should be retracted, the second, and third tier journals have even more junk, advocacy science and false information, but most of it isn't worth anyones time to bother proving false or pointing out the errors.
To complicate the problem in the second and third tier journals, you have advocacy groups of various types (ranging from environmental groups to anti-global warming groups) playing a bootstrapping game to create scientific "facts" with great "truthiness" that can be cited in first tier journals. For an example of this bootstrapping, a friend of mine in academia was charged with the task of tracing the source of a scientific "fact" about damage from the aquaculture industry on the environment that found it way in proposed regulations and into law suits. It turns out that an activist group created a damage estimate out of a "consensus" feel among other activists and got it past the reviewers in a third rate journal, after adding a lot of caveats about this estimate just being a SWAG (scientific wild ass guess) with no data. The activist group then got another publication in a similar area in a second rate journal referencing the first article, without the caveats, which was then referenced in a first rate journal by a related activist group with a common funding source. Being in a first rate journal, it was now a proven scientific "fact" and used by regulators being lobbied by the activists groups. The industry was then facing a scientific "fact" with great truthiness, which didn't match with their unpublished observations.
With the high frequency of manure in the second and third rate journals, it may be a good training exercise for starting graduate students to plow through some of these journals and pick a paper to reproduce the most suspicious parts or demonstrate error in their methods or analysis. They would end up learning a lot about everything from good lab work to ways of analyzing the data. It may be a good way to sharpen the thinking of grad students and reinforce the message that all you read is not true. It would also force the students to go through a lot of articles looking for particularly bad one for their class project and read them all very critically. A year later, when they are writing a paper, have them visualize how their class mates would cut it apart and you may get better first drafts.
If you want, I could provide several examples from the environmental literature, especially aquaculture, where truthiness rather than true "facts" dominate the literature.
I am a semi-retired retreaded physic/thermodynamics/engineering type who spent 3 decades solving environments and aquaculture problems (heavy into using microbiology to destroy hazardous materials or convert waste products -- it is all about the bugs and bug habitat), who is slowly working my way through old twig podcasts with great delight. Keep up the excellent work educating senior citizens about the fascinating world of virology. I have a great interest and little knowledge about phages in the real world, where they seem to often be the "keystone" species -- not the lions and sharks discussed in ecology classes.
Huntington Beach, CA
This article in Ars Technica on disrupting the publishing model of papers in biological science might interest you and your fans.
Keep up your valuable and entertainlng podcasts!
Neva in Buda
Dear TWiV Doctors,
You will probably get a thousand emails about this, but there was an article in Nature about curing Ebola virus in monkeys. Here's the link:
The June issue of ASM's Microbe magazine had a feature article on virus-induced obesity that had so many holes I had to break out my pen and write all over it. I followed the references to the 2005 paper that the article seemed to be based on, and as much as I believe in the possibility of an infectious factor in obesity, my BS meter just kept going off here. Looking past the incredible number of variables that weren't even considered in data collection, questionable sample handling, missing context, and leaps in logic, I couldn't get past two fundamental issues. One is the author's apparent belief in a causal connection between the initial detection of this virus in 1978 and an epidemic of obesity that seemed to begin around the same time (detection and emergence of a virus are two quite different things). The other is the glaring conflict of interest evident in his founding of a company that makes assays to detect this virus for consumers. The company's website skips scientific caution and flat out states that Ad-36 causes obesity. (The author is also the editor of the journal in which the 2005 paper was published... how awkward is that for peer reviewers?)
I'm coming off of three recent influences on the importance of keeping a skeptical mindset and using critical thinking as a verb -- the dogged insistence of Mike Osterholm's statements during the NSABB brouhaha, reading The Panic Virus, and then reading A Demon Haunted World by Carl Sagan. It seems like freight trains of misinformed, truthy opinion can leave the station before anyone figures out what's happening, and by then all any rational person can do is stick to their evidence-based guns and let the situation run its course. (I'm not saying Osterholm is being truthy like Jenny McCarthy, but I've wondered whether he thinks that someone in the biowarfare labs in Iraq are just waiting to get their hands on Fouchier's paper.)
My husband teases me because I don't mind writing a letter about something on which I have an informed opinion, whether it's about a product, customer service, a news article, etc. He has a point; sometimes it's better to just let it go. There are limitations to all experiments. But when you all come across papers like this that make you just cringe, what do you do? Is it better to let it slide, write a critique, or just talk about it on TWiV? :-) As I move into a healthcare career I'm concerned about these issues not only for the sake of science but for the sake of public health policy, grant funding, and what new damage could be done with the combination of the media and outspoken narcissists or misanthropes. I now not only see microbes everywhere I go but also the subtext of human behavior. Gray hairs may be soon to follow (just kidding).
Thanks and keep having fun!
Thought you might find this useful....
I noticed that you sometimes do on-air internet searches and end up with commercial results. Switch to DuckDuckGo.com to regain your integrity. It is also more efficient. The URL "ddg.gg" gets you right there. Once you are ready to "Quack" for something, try "bang searching." Examples of bang searching would be "!amazon Racaniello" or "!cdc dengue".
Hello TWiV Doctors,
My listener Pick of the Week suggestion is 3.091x: Introduction to Solid State Chemistry from MITx(edx). This is the online version of the MIT freshman class 3.091: Intro to Solid State Chemistry. It begins October 15th, 2012. It's free, there are no prerequisites, and if you successfully complete the course, you get a certificate of completion from MITx.
I realize this is not biochem, but I think it is still relevant for TWiV listeners. I took(and completed!) the first MITx online class, 6.002x: Circuits and Electronics, and I will tell you that they do not water down their classes just because they put them online. It was MIT hard, and it was a brutal process getting through it.
Some of us were saddened to learn that the excellent lecturer Dr. Donald Sadoway would not be the instructor. However, in a bonus for TWiV listeners, Dr. Michael Cima will be the instructor. It's a bonus for TWiV listeners because his speciality is more medical than Dr. Sadoway. Specifically in nano-technologies for medical monitoring and drug delivery. Here's a video where he runs down what his is working on:
In addition, edx is offering PH207x: Quantitative Methods in Clinical & Public Health Research, through the Harvard School of Public Health. 5 other courses are offered through a combination of MIT, Harvard and UC Berkeley. You can see all of them at edx.org.
I am writing to you this time because I have just read a short report in “El Pais” (the highest-circulation daily newspaper in our country) referring to the fact that five “exotic” mosquitos are establishing a permanent home in Southern Europe. This is not really new, since global warming seems to be driving tropical species to Northern latitudes. What I found interesting and probably attractive for you and the audience of your podcast is a series of maps which are produced by the European Centre for Disease Prevention and Control (http://ecdc.europa.eu/en/Pages/home.aspx). They show a detailed distribution of different species of mosquitoes (and also ticks) by provinces within Europe, and apparently are periodically updated.
It is particularly interesting the one that shows the actual distribution of the tiger mosquito (Aedes albopictus), a vector for dengue, yellow fever, West Nile, Chikungunya virus, and others. In fact, there have been recent outbreaks of West Nile virus infections in Greece, and Chikungunya virus in Italy, for example.
If you check the map you will see that specifically, the tiger mosquito appears to be recently introduced and probably expanding in Italy, Southern France, NE of Spain, the Balkans and the Russian Black sea coast.
The link is:
Thank you very much again for your wonderful show. I am not sure if this e-mail will be read before episode 200, but in any case let me congratulate you all for this achievement, and wish a very long live to TWiV!
P.S.: Oh! I almost forgot. It is very hot in Madrid, few clouds, and temperature about 100ºF (37ºC approx.).
Centro de Biologia Molecular Severo Ochoa (CSIC-UAM)
Hey TWiV team,
I'm a first-year bioinformatics student doing my PhD in a virology lab. I visited the NEIDL (the BSL4 the Boston University built) a few weeks ago, and really enjoyed it. During the visit, the director of the center explained that the building has remained unused for more than two years after it was built because local community groups sued Boston University for building what they claimed was a "bioweapons lab". This is just another example of the importance of educating the public about the true purpose of science –pursuing knowledge.
Anyway, save me a seat for the anniversary episode at the NEIDL in September. I discovered your podcast a few months ago and you've been a constant motivation for me to explore the virology world. I especially enjoyed the Lassa episode (back in #9) and the incredible story of my compatriot, Jordi Casals, since I'm currently working with Lassa and other hemorrhagic fever viruses.
The invincible Vincent & crew,
Here is the weather in °C:
(at the very top of the page (above the ad banner) on the right side is the switch : °F°C.
In the location box below the ad banner you can type in the city & state or the zip code to get your location. I have it set for my location.
Kenneth Stedman writes:
As a TWiV "bump" I am starting a collaboration with Adam Abate at UCSF based on our TWiV chat.
Just a quick email to say that I recently found TWiV and enjoy it greatly. I will try to branch out into TWiM and TWiP when I can, as well as making my way through the back issues - I've no idea how you've got the time to do all of them!
I've only recently gotten into the sciences and will be starting a physical therapy degree in September. During a preparatory health science course in basic biology and chemistry which I took over the past year, I've found myself much more fascinated by the small-scale physiology and microbiology side of things than the large-scale anatomy, leading me to find TWiV. I am contemplating pursuing some sort of research route after I graduate (e.g. into muscle or bone physiology), although it's still very early days of course. I was wondering if you or any of the team had ever come across anyone who started out with a larger scale focus in biology and "zoomed in" toward something only distantly related, perhaps even someone from a physical therapy background? Coming into the sciences after having only really studied the humanities feels a bit like being presented with an enormous buffet after having gotten by on oatmeal all my life!
Many thanks to you and the team for putting out a great show every week.
David in the UK
I am responding to your navigation of the Reforming Science in I&I papers on the show. I was a bit disappointed at how you covered them. At times the hour sounded like a list, rather than a discussion. It's a lot better that than not having talked about it at all, so for that thanks.
Are there training fellowships for women academics who might be coming back after family leave in North America? Wellcome has these in the UK. Maybe this is a way to address one of the leaky pipelines?
Remember that you have a great deal of influence with what you have created with your podcasts. Look at what happened on the flu papers: TWIV had an effect some would argue a huge impact! Look at what you have already achieved with respect to changing some ordinary peoples' view of scientists! People are listening, people are looking to you guys to help come up with other ways to reform, not to tell us what we already know (that changes will be hard to achieve and unlikely). I don't think it's helpful to say that many suggestions from the reforming science papers won't work: maybe instead like Rich said, let's come up with new innovative ideas for solutions rather than saying change is unlikely.
I've been faithfully listening to the TWi-fecta for quite some time now and I enjoy them all thoroughly (though I don't know that I'll ever be able to catch up on all the old episodes of TWiV). I hope you won't mind another self-serving, advice-seeking question.
I always listen with great interest to your answers to students as I am just finishing my undergraduate degree in microbiology. However, I've noticed that all of the questions directed to you are in regards to continuing on in academia.
It's taken me a few semesters of laboratory placements, a well timed discussion by your pannel of experts, and a few months of reflection but I've decided that I might not have the drive to continue on in academia. I would be just as happy to be a technician of some sort as a post doctorate fellow, which is not at all how my peers feel.
I intend to work in one of my professors' labs in the spring to determine if I am cut out to be a grad student or not but in the meantime I have much to think about.
I've found that in Canada, and abroad, all that is really promoted in universities seems to be research and development as nothing else is ever discussed. I'm beginning to feel like there IS nothing else. While I consider all of those involved in the TrWi-fecta to be at the top rung of the academic ladder I also believe that you've had much experience with the wide variety of microbiology based occupations. In your opinion, what can I expect to find outside of academia?
Thank you again for all of your effort on these podcasts. They fill my days :)
A note of gratitude to you and your crew for generously “interrogating” my recent paper on the experimental evolution of vaccinia virus.
BTW, it was evolutionary biologist Leigh Van Valen (not Richard Dawkins) who proposed and coined the Red Queen Hypothesis in 1973. Leigh was a true character and early advocate of open access publishing. His original manuscript on the Red Queen was published in Evolutionary Theory, a journal he created and self-published at the University of Chicago; still available free and now online at leighvanvalen.com, along with some interesting stories about this unconventional and brilliant scientist who recently passed away.
Count me as a new listener and fan of TWiV!
Best wishes, Nels
Nels Elde | Ph.D.
Mario R. Capecchi Endowed Chair of Genetics
Department of Human Genetics
University of Utah Salt Lake City, UT
Marian writes (re Red Queen’s hypothesis):
“Originally proposed by Leigh Van Valen (1973), the metaphor of an evolutionary arms race has been found appropriate for the descriptions of biological processes with dynamics similar to arms races. Van Valen proposed the Red Queen’s Hypothesis as an explanatory tangent to his proposed “Law of Extinction” (also 1973), which he derived from observation of constant probabilities of extinction within families of organisms across geological time. Put differently, Van Valen found that the ability of a family of organisms to survive does not improve over time, and that the lack of correlation between age and extinction is suggestive of a random process. The Red Queen’s Hypothesis as formulated by Van Valen provides a conceptual underpinning to discussions of evolutionary arms races, even though a direct test of the hypothesis remains elusive, particularly at the macroevolutionary level. This concept remains similar to that of a system obeying a self-organized criticality.”
Dear TWiV crew,
I was listening to TWiV 198 and the Red Queen hypothesis of antagonistic coevolution was brought up. I thought I should make a correction regarding the originator of the Red Queen hypothesis. You attributed it to Richard Dawkins, however, the term “Red Queen hypothesis” was actually coined by the evolutionary biologist Leigh Van Valen in 1973*.
*Van Valen, L. 1973. “A new evolutionary law” Evolutionary Theory 1: 1-30. Link to full text here: http://dl.dropbox.com/u/18310184/evolutionary-theory/vol-01/Vol.1%2CNo.1%2C1-30%2CL.%20Van%20Valen%2C%20A%20new%20evolutionary%20law..pdf
You can read more about Van Valen in this obituary here:http://articles.chicagotribune.com/2010-10-24/features/ct-met-obit-van-valen-20101024_1_extinction-journals-modern-biology
Love the show, keep up the good work
P.S. I listened to the end so I know that I shouldn’t be hanging out for a show this week.
Loved the recent episode (TWiV 198) in which you discussed Nels Elde’s paper investigating ‘genomic accordions’ of poxviruses. Elde describes in his paper a mechanism of transient gene family expansion that allows poxviruses to rapidly generate variation in genes whose products interact with host proteins, thereby overcoming host defenses. He goes on to refer to this evolutionary game of cat-and-mouse between viral and host proteins as a classical Red Queen conflict.
In the episode there was some musing about the term ‘Red Queen Hypothesis’ and it was decided that the term was coined by Prof. Richard Dawkins in his book of the same name. ‘The Red Queen’ was indeed the title of a popular science book, of the general flavor that Dawkins writes, however it was authored by Matt Ridley and entitled ‘The Red Queen: Sex and the Evolution of Human Nature’ (an excellent read and available from $7.99 on Amazon).
The Red Queen Hypothesis itself was first proposed by yet another great scientist and communicator Prof Leigh Van Valen (University of Chicago). In his 1973 paper ‘A New Evolutionary Law’ Van Valen used the analogy of Lewis Carrol’s Red Queen – forever running just to say put – to explain a self-perpetuating fluctuation in fitness between two or more evolutionary units (species or genes) arising from mutually incompatible optima.
I have to thank you for making this mistake, as it has led me to actually read Van Valen’s paper in full – which I had not done before, despite having cited it in a number of undergrad essays. There is something really enjoyable about reading old papers where the authors wax philosophical (sic) on their topic, and it is a nice change from the dense, ultra-concise papers that are standard these days. Whether this was because they had less data to cram into figures, fewer authors, or the journals were less pressed for space back then I do not know. Maybe all of the above in this case seeing as this article was the first, in the first edition, of a journal that Van Valen founded.
Probably because I have more pressing uni work I should be doing I spent quite a bit of time reading about Prof Van Valen, who died in 2010. He was a pretty amazing guy who wrote on many subjects, taught and was beloved by his students, contributed several original ideas to his fields, founded journals, and even wrote explicit songs about dinosaurs.
I would like to nominate Leigh Van Valen as a pick of the week – by way of his memorial site at Leighvanvalen.com.
A few choice links: Sex among the Dinosaurs –http://dl.dropbox.com/u/18310184/songs/sex%20among%20the%20dinosaurs.pdf A New Evolutionary Law (Van Valen, 1973)- http://dl.dropbox.com/u/18310184/evolutionary-theory/vol-01/Vol.1%2CNo.1%2C1-30%2CL.%20Van%20Valen%2C%20A%20new%20evolutionary%20law..pdf
Kind Regards, Adam
Melbourne, Australia (18C with a chance of rain)
PS: If nothing else, go check out the Acknowledgements section of Van Valen’s ‘A New Evolutionary Law’ (1973).
Dear TWiV Doctors,
I have a question about the paper discussed last week on the Emergence of Fatal Avian Influenza in New England Harbor Seals.
What I cannot figure out is if they were looking for an Influenza virus from the start. I mean, I assume if you sample a bunch (5 in this case) of seals, you are going to get a bunch of viruses. Did they report the detection of any other viruses in the seals? I listened to your segment again and read the paper on mBio. The paper says this:
Nucleic acids extracted from lung, trachea, liver, kidney, thoracic lymph node, mesenteric lymph node, spleen, skin lesion, and oral mucosa were tested by PCR for the presence of a wide range of pathogens, including herpesviruses, poxviruses, adenoviruses, polyomaviruses, caliciviruses, paramyxoviruses, astroviruses, enteroviruses, flaviviruses, rhabdoviruses, orbiviruses, and influenza viruses.
They looked for a wide range of pathogens, but I can’t find something that says we found ONLY H3N8 Influenza. Am I reading it wrong? It just seems odd that they found nothing else. However, I’m not a scientist, so maybe I’ve misunderstood.
Simon Anthony replies:
Thanks for the question! Your listener is quite right, we did find other viruses in those animals. I have a strong interest in the ecology of co-infection, so was very keen to see what other viruses might be present. We also found herpesviruses and adenoviruses in addition to the influenza, though none of these viruses were found in all five animals, and none could be linked to the observed pathology. Interestingly, we found three different adenoviruses. Two of them were known seal adenoviruses, and one was actually an avian adenovirus!! So it would seem that avian influenza was not the only avian viruses that spilled over. In addition we performed deep-sequencing and identified some novel picornaviruses. We’re working those up now, but would love to chat more about them with you at some point.
Hope all is well over the road! S.
New ‘Heartland’ Virus Discovered in Sick Missouri Farmers
I’m a fan of your pod casts and thought you might be interested in the article if you haven’t heard of it yet.
Could you please discuss the relationship between HPV vaccine and GB, also it would be interesting to know what causes GB and its relationship to Polyradiculoneuritis (coonhound paralysis) and MS. Do these diseases have any viral relationship, thanks. i listen to the show while gardening.
Hey TWIV team!
I have been listening to your podcast for only a few months but listen with rapt attention on my way to work each morning. I was shown the podcast by my professor in my intro Virology class during my last semester of my undergrad in Cell and Molecular Biology. I have recently graduated and decided not to immediately re-enter academia for several reasons. The first being I have no idea what type of degree I am going to pursue (MD PhD or hopefully both). Also and largely I am training as an Elite trampolinist with my sights set on the 2016 Olympics in Rio. Unfortunately that means I plan to put the vast amount of my focus in effort in that venue of my life for the next four years and after I retire would like find a school with a good program without worrying where I will be training. Since, that could put me out of school until 2016 I am terrified I will lose my edge for applying for school when the time comes. I am trying to stay sharp with your podcasts and reading articles that pique my interest, but I don't think it will be enough. My most recent idea is to take the GRE this year and then apply for a masters program in either the biochemistry department or the biology department which includes cell biology, molecular biology, immunology, and virology research areas at a local university. I flip-flop between the two departments because I've heard on your show the importance of chemistry education for virology and that my research adviser previously advised me to not educate myself in solely one discipline. My questions to the TWIV team are whether this is a good plan considering my goals and which department you would most recommend for me? Thank you so much and keep putting out the viral podcasts!
p.s. make sure you watch trampoline in the Olympics, we can reach heights of almost 30 feet!!! Or get excited and take a peek on youtube by searching Olympic trampoline!
In episode 191, the subject of working smart and not long came up. When Rich mentioned multitasking, I couldn't help but think of the lifehacker article on the subject.
It goes on to explain why multitasking (as most people do it) reduces your over all productivity. It's a great read, and is changing the way I work.
Here is another article on the same subject:
Great TWIV 197, it is really nice to learn how science was. Fascinating to see how laborious was to do things that nowadays are only "kitology".
Keep up the great podcast.
After watching Mark’s science pick from TWiV 196 (a Youtube channel dedicated to interesting and entertaining videos shot with a slow motion camera), I felt I had to share a link that I came across the other day.
While standard slow motion cameras record at about 5,000-10,000 frames per second, this technology, which is dubbed femto-photography (developed at MIT), captures light at one trillion frames per second. Because of the incredibly small amount of light that is captured with each frame, the videos they shown computationally reconstructed from “millions and millions” of events with “very clever synchronization”. In one resulting video, we’re able to watch a ~1mm long packet of photons travel and scatter as it hits a surface. A proof-of-concept demonstration also shows that the technology can be used to ‘see around walls’ through light reflection and more clever computation, which could be beneficial in biomedical imaging.
Thank you for the podcast. I’ve been interested in viruses and working in virology labs for several years now and TWiV always gives me something new to think about.
Dear TWiV crew,
After many episodes of listening I thought some active participation was in order, especially after meeting Dr. Racaniello over drinks at the Brocach Irish Pub during ASV in Madison. First, thanks to the entire TWiV crew for your service to the scientific and lay communities. I think that an enhanced science presence in the classroom (particularly early on) could really be transformative on many levels: more inquisitive minds, more kids amazed at the complexity of life, more logic-based thinking... The point I'm trying to get to is that TWiV is an awesome vehicle to disseminate science, and having done many hours of outreach in classrooms, it's very empowering to see how many people can be reached. So many thanks, and also a sincere offer to help out the TWiV cause in any way possible.
And now tidbits from the random thought generator of my mind:
tidbit 1) In a TWiV covering an influenza virus in bats there as some question as to the cycle of transmission and whether the virus could have come from insects. This was considered unlikely because insects do not harbor orthomyxovirus viruses, but in fact, this is not true. There is a family of influenza-like orthomyxoviruses (e.g., Thogoto virus, Dhori virus) that are tick-borne infections of rodents (http://viralzone.expasy.org/all_by_species/79.html). Interestingly, selection in insects has resulted in the glycoprotein of these viruses being more similar to baculoviruses than influenza viruses.
tidbit 2) We had discussed an enhanced multimedia interface for ASV. I think that CROI does this really well (http://retroconference.org/static/webcasts/2012/), and the fact that all the talks are free and online hasn't stopped people from going to CROI.
tidbit 3) Although I hope this is of general interest to the entire TWiV crew, I thought that Rich in particular would find this interesting, and perhaps might result in a TWiV bump for new faculty Nels Edle (lead author) and Harmit (senior author, and my mentor):
Elde et al. Poxviruses Deploy Genomic Accordions to Adapt Rapidly against Host Antiviral Defenses (https://www.cell.com/abstract/S0092-8674%2812%2900870-7)
I hope this finds you all well, and thanks again for TWiV.
Patrick (its 26 C and absolutely beautiful in Seattle)
Patrick S. Mitchell
Division of Basic Sciences
Fred Hutchinson Cancer Research Center
Molecular and Cellular Biology Graduate Program
University of Washington
Your delightful podcast has helped to steer my interests towards virology and immunology. I studied Mathematics as an undergraduate, and realized that my calling was in medicine while completing the Teach for America program in New Orleans. I will be starting medical school next month at the University of Pennsylvania, and I'm looking for particular directions of research that might be most appropriate for my quantitative background. I'm particularly interested in HIV/AIDS, but very flexible given that I'm just starting out in the biomedical research world. Any suggestions of papers, books, people, or journals that I could seek out would be incredibly helpful as I try to understand where my skills as a "Math guy" would be most useful.
Thank you for sharing your conversations with the world -- your work has had a measurable positive impact on my life!
Dear TWIV Doctors,
I was just listening to the Twiv#190 where Dr. Racaniello was talking about making TWIV accessible to more people especially in the developing world where people do not have regular access to internet. I think Radio can be a very effective way of spreading scientific knowledge not only in parts of Asia and Africa but also right here in the United States. Have you explored the possibility of using local radio stations such as NPR in United States for increasing the audience base of Twiv and the other two podcasts. I am not sure how much the radio station administrators will be interested, but it is definitely an idea worth exploring further. May be TWIV/TWIP/TWIM already has a listener who knows more about making it happen.
As always, love the podcasts. Please keep them coming.
Rohit K Jangra, PhD DVM MVSc
Postdoctoral Fellow, Kartik Chandran Lab
Wanted to make sure you didn't miss this news item:
"Vaccine Storage 14 mins - This five part digest starts with Greek IT, but the fourth item concerns the very smart idea of using cell phone tower power systems in developing countries to reliably run refrigerators used to store vaccines. A web site with details is here. To download the audio file go to the link, find the title "Greek IT Upgrade, Bullet-Proof Cars in Mexico, Hajj Facial Recognition Tech, Keeping Vaccines Cold, and Rebuilding Tatooine," right click "WTPpodcast368.mp3" and select "Save Link As."
[here’s a direct link to the podcast from PRI’s The World (#358); the story is at 14 minutes into the podcast- you can use the fast forward button; this eliminates the need for the somewhat more complicated instructions and the Vaccine Storage link at the start that leads to adding an RSS feed and not the audio:
Thanks as always for an excellent podcast (as well as TWIM and TWIP). I especially loved the "how to read a study" helpful hints segments, as it was really nice to hear that learning to read studies is a skill that takes practice and education. And to know that I will have to struggle with reading studies for a while before I'll be able to really parse them.
[TWiV #169, or excerpt, “How to read a scientific paper;” right click here to download]
Anyway, I recently read a Young Adult book called "The Way We Fall" by Megan Crewe. It's a story about an island in Eastern Canada (if I remember correctly) where a viral pandemic hits. The fatality rate is high, and the island gets quarantined. I don't know how accurate the science is, but I thought it was a fun read. Amazon says this is part one of a trilogy, so I guess there's more, but at the time I finished it, it felt like an actual ending. Not great literature, but a fun, gripping (and quick) read.
Keep up the great podcasting! I love listening and learning.
An online bulletin board community dedicated to photomacrography, amateur microscopy, and photomicrography.
Oh, it's 9PM and still 32 degrees C.
I am going through the old podcasts, when I have time. Number forty one covered ISA — a salmonid virus with a billion dollar class damages history. When someone mentioned vaccines development, a comments was made about how can you vaccinate salmon.
Most salmon are already vaccinated for bacterial diseases using automatic machines, where the salmon smolt are lined up, given a shot and released. When you have hundreds of millions of fish to deal with, the machines are fast.
To give you an idea of what has happened to antibiotic consumption over time in Norway salmon farms as vaccines for bacterial pathogens have developed (there is a similar graph showing the increase before vaccines, but I couldn’t find it):
Notes: Use of antibiotics (yellow line) and amount of fish produced (blue columns). The numbers on the left side are the tonnes of fish; the numbers on the right side are the tonnes of antibiotics.
Sources: NMD & Directorate for fisheries, as cited in Ministry of Fisheries (2002).
Virus in the wild fish stock are also a significant issue, but as an old marine biologist once told me: nothing ever dies in the ocean, it is eaten alive before it is actually dead. That makes wild virus hard to study, but the source in aquaculture net pens is from the wild.
Don’t believe all the nonsense being spread by the anti-aquaculture activists and the commercial fishermen who don’t like competition. For example, the red pigments used in the diets are the same chemicals that make wild salmon red and the same as found in “red yeast” or red algae sold in health food stores and found in pepper meal. The color added label was politically added by the Alaska commercial fishermen, who were getting economically killed by the quality control possible with farmed fish (no sitting around on the deck for hours before processing).
Omega 3 fatty acids are a required dietary component in salmon feed and they end up with these fats in their tissue, just like wild salmon. One dinner of farmed salmon — or high fat wild salmon species — equals 10 or so of those fish oil pills and tastes a lot better.
I still haven’t run across an episode on shrimp virus that are resulting in consumers paying an extra billion+ dollars per year in their shrimp cost to cover virus losses.
Love your podcast,
Thanks so much all these brilliant podcasts, especially episode 184 (Reforming Science). Crowd-funding for science is an interesting grassroots mechanism to obtain support for small projects; you’re probably familiar with Petridish already but I wanted to highlight this project http://www.petridish.org/projects/targeting-mosquito-spit-to-limit-virus-transmission. Only 28d to hit the funding target! Would be great if you could mention it on TWiV.
ps- no conflicts of interest to declare.
Hi Vincent et al,
In case you haven’t seen this yet:
Merck has known for a decade that its mumps vaccine is “far less effective” than it tells the government, and it falsified test results and sold millions of doses of “questionable efficacy,” flooding and monopolizing the market, a primary caregiver claims in a federal antitrust class action.
Alabama-based Chatom Primary Care sued Merck on Monday, the week after the unsealing of a False Claims Act complaint two relators filed in 2010.
Those relators, Stephen Krahling and Joan Wlochowski, were Merck virologists who claim in their unsealed complaint that they “witnessed firsthand the improper testing and data falsification in which Merck engaged to artificially inflate the vaccine’s efficacy findings.”
All the best
Hi Vincent and Co hosts
I just thought you should know, since I guess this is deliberate, that what you are doing is working.
So far you have got me to learn more about science, specifically biology, and virology, than I ever thought I would. To the point of working my way up to Kevin Ahern’s bb450/550 molecular biology course on itunes u. Of course I had to start with basic chemistry, so as to understand things like swartzchild radius etc. From there I went to basic biology, as well as all of your virology lectures. I then took a bit of a break, to grow some bacteria and phage, then to use the phage to create plaques. (I wish I had saved the instructions, as it seems the pages have gone away. Though I am sure I can find them on the Internet somewhere.) Right now I’m round 2/3 of the way through the molecular biology course, as mentioned above.
I am sure that you will have had a similar effect on some small percentage of your listeners. It’s taken several years, more or less since episode 1 of twiv, to get here. However 99 percent of what you say, I now understand, including gell electrophoresis, western blot, 16s subunits etc. Etc. This makes listening to twiv much less infuriating, as now I rarely have to look things up, except for things relating to the papers you discuss.
I guess I should give some details of my background, I studied electrical and electronic engineering. I am an engineer working on water and wastewater treatment. In doing this I’ve done some work in laboratories, testing samples of water. I’ve also spent many an hour staring down a microscope, identifying the various types of bacteria, and protozoa that actually do the ‘work’ of treating sewage. Not to mention trying to identify, and find ways to make life difficult for, foam forming filamentous bacteria. (if you can imagine a 1.5 million gallon aeration tank at sewage works, with such foam. Then a strong wind, blowing bus size chunks of foam about…. Well you get some idea of my feelings towards filamentous bacteria). So I wasn’t unaware of biology, but treated it like a car, I could in effect check the oil, water, and simple stuff, anything heavy duty, I would leave to the laboratory.
I hope you don’t mind me blaming you, as it were. I think this an interesting topic, and I’m enjoying learning about it. I guess that was your intention, to spread interest in a topic you clearly love.
If I get the chance, then I will be taking some sort of biology course, with the view to ending up in virology. Though I’m quite settled in my current career, who knows what opportunities the future might hold.
I guess you can file this particular listener, and under the heading “mission accomplished”
Thanks for taking the time to produce the pod casts that you do. I thought I should pass on my story, so you can see just how good a job you are doing.
Please excuse the brevity of the email, but I typed it on my phone.
I think I have removed all the auto correct blunders, but if any got through, I can only hope they are funny
Dear Professors Racaniello et al,
Thank you for the TWIV, TWIP and TWIM podcasts – I find them immensely interesting, even though my wife forbids me to listen to them during meals – her loss, really!
I am a computer science graduate student at Universidade de São Paulo, Brazil, and I would like to make a suggestion to you.
Recently you discussed an episode of a podcast named “Futures in Biotech”, which I listen to regularly, along with some other podcasts which are “syndicated” in twit.tv.
They have a very interesting podcast about computer security, called ”Security Now”. (Hey, that is my pick of the week – a show about viruses that make you poor:http://twit.tv/show/security-now).
The host of “Security Now” does something which I believe you should also do: he pays to have his podcasts transcribed and then publishes the transcription online. By doing this, the contents of his shows can be indexed by Google and other search engines. If your podcasts also had this, I believe many people would discover you by accident, by simply googling virii-, parasite- and microbial-related keywords.
Again, thank you all!
[we began be re-reading part of Deena's email from TWiV 193]
Hello TWIV Crew,
I must first apologize it has been a long time since I have listened to the podcast but I promise to get caught up. I am seeking guidance from you as fellow scientists here. On a matter of personal and professional development I was curious as to the most effective and sanity preserving ways you deal with pseudo-science and or the complete lack of acceptance of science and evidence based medicine by some people. A little background I am entering graduate school going for a PhD and when I try to have discussions with my non-science friends or acquaintances I get hear a lot of science bashing and evidence based medicine bashing. I know this has been experienced by you all in the show many times, XMRV and chronic fatigue being an obvious example. On a personal level I have experienced it myself but in a strange way, a sort of reversal of the normal paradigm. I have ADHD (Attention Deficit Hyperactive Dissorder), I know its a controversial issue but I have it, and have been prescribed by my physician for some 15+ years now a medication to help me focus. It's worked for me wonderfully, I did well in High School, excelled in sports, have had great work success, got my B.S. in Biology, preformed independent research as an Undergraduate with great success and now I am going to be working on my PhD. Yet I have people out there that are telling me, I don't have a disease I don't need to be medicated (despite the fact that it works and I am successful), I just need more "fresh air" and to exercise and eat right and get more vitamin D and see posters like "Childhood is not a disease, don't medicate children" I try to have rational, science and evidence based conversations with these people but I am just a crony of western medicine or am only treating the symptoms not the cause, etc. I worry that a child who is in my situation may not get the help I got.
I just don't know how to deal with people like that who refuse to accept evidence or only accept anecdote when it works for what they believe (not that anecdote is ever a good argument). I am a man of truth, that's why I love science. It upsets me when people don't want to hear evidence or don't accept the scientific method. I tell them questioning is good but you have to also examine evidence not anecdote. I truly want to educate people and greatly enjoy it but am saddened by people who refuse to learn, and worry that people like that could run our country and in turn try to control my life based on unscientific beliefs. Rarely someone is honest enough to tell me they didn't know something and that I taught them something and changed their mind (and it felt really good, hence why I want to be in an academic setting). How have you learned to deal with people like that refuse to learn. I don't want to give up on them but is that necessary? Should I just pick my battles? I know your podcast has been extremely successful in educating people, especially outside the academic setting, do you feel like the battle for knowledge and education is being won? Sometimes I actually become saddened that people are not willing to learn, or accept evidence, but I don't want to let that ruin my career of seeking truth.
I thank you for reading this I know you are all very busy. I don't expect this to be read on air (if you do feel free to trim it as you see fit) but do sincerely hope for a response of some kind time permitting via email hopefully maybe a few words from each of you since you all may have different opinions, or strategies that have helped you all to success as scientists.
P.S. My girlfriend and I both went to see Vincents talk at the University of Washington when he was here a while back. Being a Plant Biologist myself and only part time Virology enthusiast it was a bit out of my area but love to support your cause!
Welcome to the great state of Wisconsin! I hope you enjoy your stay. I suggest in your free time that you try some fresh cheese curds from a local creamer and maybe some fried ones too. I'm sure that those from the area can let you know where to get the best curds.
Next, thank you for all the hard work you do. As a senior in high school who is passionately in love with viruses, Twiv never ceases to bring joy and an education regarding the world of viruses. It has also provided entertainment while sewing my prom dress and another dress. Twivers aren't just lovers of science but also creative!
On a final note, a question. As being a senior, I'll be applying for college and undergraduate positions at college labs. I was wondering if you fine men have any suggestions for the whole process? Should I inform these scientists that even though I have had no opportunity lab experience I have tried to become familar with the world of virology through Twiv and reading books such as the The Great Influenza?
Thank you, Angela
Dear Vincent Racaniello and TWIV host-ers with the most-ers,
Vincent: To ring your recollection bells: We met shortly in Dublin during the Society for General Microbiology's Spring Conference and since it was just before your panel interview of Wendy Barclay, my PhD supervisor, and Ron Fouchier, of ferret transmission fame, we discussed the H5N1 influenza virus controversy. At the time I promised to send you an email to request that you and the TWIV team discuss ways that scientists increase serendipitous encounters with new ideas.
Of course there are many ways to learn about new techniques or cellular pathways that might relate to ones research, including reading papers and attending conferences, but I am interested in the activities in between: The once-a-month kind of activities, where you get to interact with other people on your level who are abnormally excited by the nitty-gritty details of molecular biology/virology/epidemiology or immunology.
What drove me to write today is because I was trawling through the literature trying to find a journal article that would entice enough people to attend our voluntary journal club and hopefully stimulate an interesting discussion. We do alright for a department of about 35 Post Docs and PhD Students, we provide pizza and drinks and usually keep about ten participants entertained for an hour. Our Journal Club is run in the traditional way: There is a presenter, who reads an original research article thoroughly and uses powerpoint slides to present the figures as he or she explains them, we ask questions during the presentation and have a general discussion at the end, but there is a little voice inside me that says "this could be better". Therefore, I would like to ask you, the TWIV-hosts and your listeners to share your experiences of Journal Clubs or other brainstorming/ discussion/ mixers that you have tried and what you have found that makes the experience that little bit extra-special.
Thanks in advance for your input,
Final year PhD candidate, looking for a new research home
P.S. Please keep the podcasts coming, I'm totally addicted. I have compared TWIV to other's, such as Cell and the Naked Scientists, which are good, but your focus, linked with the breadth and depth of knowledge that your hosts bring to the table leads to the best story telling around.
Do you plan to do any promotion of an #asv2012 hashtag for the meeting in Madison this year? I remember some limited tweeting from Minneapolis last year (in between melting into the sidewalk) but I think TWiV would be a great way to promote it ahead of time, along with using it when you tweet about the TWiV episode to be recorded there. After the discomfort with livetweeting the morning sessions last year it may not be encouraged, but I think ASV could be moving faster in the social media realm.
As you said on twitter, there was a specially designed app for ASM this year, and I know Society for Neuroscience has one too. ASV as far as I can tell doesn't even have a twitter account and only the barest of Facebooks. With all of the focus on H5N1 (loved the discussion) this seems like the perfect time to expand ASV's reach on the Internet.
Maybe I'll apply to run their social media presence once I finish my PhD. Someday.
Richard Compans writes:
No sampling of lymph nodes was done in the case of the in vitro cell migration experiments using excised ear tissue, from which we observed the emigration of DCs.
For the skin immmunization on the dorsal surface of the mouse, we examined the inguinal lymph nodes at intervals post-immunization. We think that several factors may have contributed to our lack of detection of cells containing labeled viral antigen in these lymph nodes: retention of some of the antigen at the immunization site, problems with insufficient labeling, timing or quantitation, or possibly the processing of antigen. We don't anticipate that any novel mechanism is involved.
Additional work is underway using improved procedures for labelling of the antigen, which we hope will resolve this question.
Richard W. Compans
Professor of Microbiology and Immunology
Emory University, School of Medicine
I was listening to TWIV on my drive to work today. Just want to let you know that there is at least one paper (by Chris Upton, David Esteban and coworkers) describing the sequence of a vaccinia virus strain derived from a person who experienced complications from smallpox vaccine. Here is the link:
Love the show.
Dear hosts (of podcasts, viruses, and more),
I have just finished listening to the excellent Twiv 183 and I can't help make a certain observation. In this episode, but also generally, it would seem that the Twiv crew may suffer from a case of bioinformatics-o-phobia. I wouldn't be too concerned as I expect that this affliction is very common, in fact I have attacks from time to time. Since Twiv is so successful at teaching many of the other aspects and techniques of virology, why not confront bioinformatics head on? It would be a blast to invite a bioinformatician or computer scientist onto Twiv to talk about some exciting virology related computational work, and really delve into the details of bioinformatics methodology. I've heard awesome explanations of cutting edge molecular techniques on Twiv, but when difficult bioinformatics gets mentioned in a paper on I'm often left wondering what's going on "under the hood".
Anyway, keep up the great work,
p.s. I thought this was a cool random example of bioinformatics at the cutting edge of virology...it was the first result that caught my eye after searching for "influenza" and "bioinformatics"
Schanen, B. C., A. S. De Groot, L. Moise, M. Ardito, E. McClaine, W. Martin, V. Wittman, W. L. Warren, and D. R. Drake 3rd. 2011. Coupling sensitive in vitro and in silico techniques to assess cross-reactive CD4(+) T cells against the swine-origin H1N1 influenza virus. Vaccine. 29:3299-3309. doi: 10.1016/j.vaccine.2011.02.019.
Hi Vince, et al,
Just listened to TWIV 183. As usual it was fabulous. Am also a big fan of TWIP and TWIM.
I do think it would help to get a participant to interpret the bioinformatics which seems to be increasingly present in the more recent articles.
Was delighted to have DDD present again.
I've been listening to a lot of TWIV, TWIM and TWIP recently. I'm learning a lot and being reminded of a lot.
You touch on insect biology a number of times. But I wonder if you, or maybe a listener knows, of the Racaniello and friends of entomology.
I'm thinking someone should create something very like TWIV, wide ranging but academic, not restricted to agricultural pest management or the global fight against the "bugs are icky" meme, fun but information dense. Of course, my imaginary podcast does not exclude the topics covered in the TWI family.
There must be tons of research going on in insect biodiversity, ecology, phylogenetics, genetics, genomics, (am I being redundant?) systematics, behavior (eg. mimicry), species descriptions, biomechanics (eg. Berkeley IB department), etc. And, of course, the multi-layered symbioses you folks have mentioned. Interspersed with the history of entomology (Darwin was a beetle collector), and descriptions of the orders and particularly interesting species, I think this could be a wonderful resource, with a nearly endless list of potential topics and papers to discuss.
Regarding audience, I would venture that the participants in bugguide.net represent a fair number: http://en.wikipedia.org/wiki/BugGuide ("BugGuide had over 809 million hits in 2010").
In TWIV 46*, you discussed Israel Acute Paralysis Virus in response to an e-mail. At about 34:40, you both chuckled about the idea of putting a radio tracking collar on honey bees.
I remembered posting about just such an experiment several years ago on my animal communication site.
The photo shows a radar transponder on a honey bee <http://acp.eugraph.com/news/news05/riley.html>. That was a 2005 Nature paper, and technology has advanced since then (a couple of examples below, gleaned from a quick Google search).
* I'm listening to the Virology 101 podcasts in order.
A quick email in response to TWiV 181 in which Kathy used APOD as her pick of the week. Rich asked how he could get this as his desktop wallpaper. I have it on my windows 7 desktop, but not as the wallpaper. As seen in the attached images I have APOD at the bottom of the screen in a panel, and shown progressively larger if one wanted to have it alone. A program called rainmeter (http://rainmeter.net/cms/) can display a number of skins/themes. This particular theme, called omnimo (http://omnimo.info/), is designed to look like windows phone 7/windows 8.
As ever, thank you for keeping me informed and entertained.
sent by Lance via Twitter:
Matt Frieman writes:
A handy temperature chart for TWIV
Hello TWIV Tertulia.
On TWIV 174 a Google engenier asked for a test that would help him to figure out the respiratory infections on his house. I just found out a test named xTAG RVPv1 and xTAG RVP FAST that are able to qualitatively identify several respiratory virus. Probably expensive, but it is information.
Congratulations on your growing numbers and keep up the wonderful work.
Ricardo Magalhaes, Ph.D.
Associate Professor of Microbiology
Faculty of Health Sciences of Fernando Pessoa University
(And Alan and Dickson and Rich.)
First off all, I'm sorry for this email because it is a request.
I have already write You about this but I'm really struggling with it.
I can't find a source of information (help) to prepare laboratory classes for undergrad virology students. Our lab is a teaching lab and the coolest thing I can do, is to find plaques with bacteriophages and that only take two 90 min classes (in 18).
Can you help me here?
My best regards.
Ricardo Magalhaes, Ph.D.
Associate Professor of Microbiology
Faculty of Health Sciences of Fernando Pessoa University
I love TWiV I learned about it from my Virology professor and always listen to it in my car now and at the gym. I was just wondering if you guys would consider making an iphone app so we can listen to it on the road without having to plan it (kind of like the Science Friday one) and maybe a facebook page too get people interested in science! I am the only science major in my family of political science buffs and I am always wanting to get my Dad into listening to these (he listens to NPR since forever) but now NPR has an iphone app which makes things really easy. Just some thoughts... plus I really love your podcasts on oncolytic viral therapy! I recently learned about RNAi therapy ( in regards to diseases) this summer and thought that was a very interesting subject as well.
Thanks for all the podcasts and you guys are really funny, especially when you guys first got your iphone I cracked up! I just recently got one too hehe! Keep up the great work :)
Might be nice at some point to have a renewed discussion on the 'incurable wound' revisited, with the possibilities of rabies virus therapy?
I believe Drs. Willoughby and Glaser could be great candidates for an interesting chat on same.
Also, with the advent of World Rabies Day on 28 Sept, would be ideal to have a mention of a rabies topic that week before, if possible.
Houston rabies case poses new questions about age-old illness
Hello Microbiology Crew,
As always the TWiV /TWiP and TWiM has kept itself on the top of my priority list. An i must say keep it up. And all i can say it has kept getting better and better. I have a couple of questions and a few suggestions.
My first question is that is there any chemical that that attacks the geometry of the virus. I couldn't find any, but did find that the viral geometry once disrupted will cause interruptions in assembly of at least most of the viral machinery. Please enlighten this area. My second question is could you elaborate about DEAD box proteins. This group of proteins has really been difficult to digest intellectually.
I have a suggestion. Since you interview various scientists on the show which really has given all the audience a great peak into current science, it would be fantastic if you could get Stanley Prusiner and Irwin W. Sherman on the show, and talk about their current research. Also i request you to have occasional virology 101. I feel it has now reached near extinction.
I also have a listener pick of the week, if you would like. If you consider Matt Ridley's Genome as master piece which was picked previously in the show, then i guess his other book "Agile gene" is a step next to master piece. And thats my pick.
Once again thank you for this highly entertaining education prog
Hi TWiV team (+audience),
I enjoyed your discussion of polydna viruses and Michael Strand's work. At one point in the discussion, someone (I can't remember who, now) asked how such a complicated relationship could have evolved in a non-integrating virus-host relationship. I think this is a very interesting question, and wanted to point out some interesting examples of wasp-virus commensalism, which it turns out seems to be quite common. While the polydna viruses are certainly the extreme example--barely viruses at all anymore, really--there are several examples of other relationships where the virus maintains a lot more independence.
There are probably many more examples of this than I am aware of (this is not what I work on), but the first example that comes to my mind should be of unusual interest to Rich, if he is not already aware of it. A colleague of his at the University of Florida (Pauline Lawrence, Dept. of Entomology) discovered an entomopoxvirus in the venom of the parasitoid wasp Diachasmimorpha longicaudata. Unless I am mistaking, it is required for wasp development--appears to suppress the immune response of the host (fruit fly, Anastrepha suspensa). Unlike the polydna viruses, this is a legit virus--replicates to high titer in the fruit fly and contains all its own genes. It seems that the wasp acquires the virus during development in the fruit fly, presumably by consuming infected hemolymph (insect blood). Adult male wasps are positive for the virus, too; but only at very low titer in all body segments. How the female concentrates the virus into her poison gland remains a mystery. The virus appears to be perfectly self sufficient in the fruit fly--you can passage it in fruit fly larvae, but it seems to lack any ability to transmit from one to the next without the wasp. Super cool--maybe a virus on its way to integration?
Unless I am mistaking, Pauline has discovered additional viruses in the venom of the same wasp--a rhabdovirus and maybe some more. As molecular biology tools become increasingly available to the entomology community, I expect that we will will see a lot of these type of symbiotic relationships in the venoms of hymenoptera (wasps, ants, bees)--would be interesting to see if it is only the solitary parasitoids or if social hymenoptera also maintain them. The presence of this sort of relationship across such unrelated virus types suggests that there is actually a very large ecological niche for viruses in this capacity, so maybe it is not so surprising that we see the polydna virus story emerging the way it is.
Thought you might think this was interesting--my apologies if you are already familiar. As I said, this is not what I work on, so my apologies in advance to important work in the field which I have undoubtedly failed to mention. I believe Pauline is mostly retired now, but I am sure she would be happy to discuss it with you, Rich, if you offered her some Satchel's.
Thanks for all the work you do--TWiV is undoubtedly the best podcast out there and has made me a much better graduate student (must have used at least 5 things I learned from TWiV in my qualifying exam).
Dear TWiV crew,
You guys occasionally talk about the flaws of the publication and grant review process, so I was wondering what your thoughts were on the recent commentary in Nature regarding an investigation done by AMGEN (http://www.nature.com/nature/journal/v483/n7391/full/483531a.html). They tried to reproduce the results of 53 "landmark" papers in cancer research and were only able to do so for six, even after contacting the labs where the studies were done as well as, in some cases, using their reagents or even physically conducting the experiments in the original labs. Although, as you have mentioned, the severity of this problem is different for different fields (cancer research, due to its clinical applications, being perhaps one of the worse ones), my guess would be that it exists to some degree everywhere. Ideally, as with the XMRV story, misleading results are resolved, but the Nature commentary shows that this is not always the case. And while in many cases such a study could cause some dead ends in the lab, other cases exist where misleading results make their way into clinical trials, large sums of money are wasted, and patients receive treatments that do not work.
I was wondering what your thoughts were on this problem in general and if you had any guesses as to how prevalent it is in virology specifically. You've remarked on supplemental data. Especially with Science and Nature, which would like to squeeze in as many articles as possible, the supplement has become a way to have very short main bodies of articles with frequent references to supplemental figures that make the papers unreadable. However, having the supplemental information means that you can publish all the data that is generated, which would allow for others to see any existing inconsistencies and more accurately judge how reliable the study is. As Bagley and Ellis remark, this would mean the stories would become less perfect, but most people who work in biological sciences already know that biology is sloppy and rarely as clean cut as we would like it to be. Any thoughts on how the pressure for complete, perfect stories could be lifted given the existing competition for grants?
As always, thanks a lot for all your efforts to make science accessible to people outside your field. The casual conversational style that the these podcasts have make them a pleasure to listen to after a long day of focusing on small technical details in dryly written formal texts.
Just as a followup, because there were so many groans about Netter's cadaver... Its common for the intended anonymity for cadavers to not work out. In Dr Netter's case, I recall that he specifically wanted the anatomy class to know that it was his body. When I did gross anatomy, my cadaver was still wearing his hospital wristband! It's a very interesting phenomenon, as the first year of medical progresses: Medical students, who spend inordinate amounts of time in the anatomy lab, go from being squeamish to being very non-chalant around dead bodies.
Again thanks and keep it coming. I especially like the revisit of basic parasitology with Dickson. I hope you don't run out of parasites of minor medical importance anytime soon.
I read in the BBC's April-June "Focus on Africa" magazine an article by freelance journalist Alice Klein an article about health issues in Zambia. Klein notes that medical professionals in Africa are accusing NGOs of bending to financial incentives when they institute new vaccine programs with newly created vaccines. (Rotavirus was the example used in the article.) The African doctors argue that pushing newly-created vaccines creates neglect of vaccination for "basic" diseases such as measles. I had been under the impression that the profit margin for newly created vaccinations was relatively (?) small--ie., not large enough to influence such funding allocations or disrupt existing vaccination programs. Your (financially disinterested) thoughts? Have you also been hearing Developing World anecdotes about short-changing older, well-proven vaccines in favor of flashier, costlier new ones?
lay-reader in Goodrich, TX
NIH recently offered two presentations that your post-doc and younger listeners might appreciate. They are from the NIH. One deals with "Using Linked-In Effectively: Seventh in the "How to" Series" while the other is about "Careers in Science Writing: Sixth in the 'How To' Series." Both sounded pretty useful. The video version of the Linked-In talk includes visual demos of computer screens so the video version of that one is more useful. Alan might like to comment on the science writer talk. Both talks are professionally oriented and detailed enough to be useful to job hunters, job suppliers, and anyone interested in improving communication skills.
Science writer advocates might also appreciate this item I put in my blog:
Professional Listening - Conversations Network seeks people to listen to podcasts and write summaries of them for which it pays $5 each. The link will produce the application processes which consists of producing a short and long summary of a sample podcast, with photo, biography of the speaker, and resources, exactly what is seen for each entry at this typical page. Once accepted you have to produce two reviews under the eye of a mentor who will get your payments for that work, but payment will go to you starting with the third product. You need a Paypal account where payments are made. It can take a month until you get your first payment and they may be bundled, rather than one-at-a-time. You will be paid to learn!
Once again, thank you very much for your excellent podcast and your service to the community of researchers and educators in the biology field (and specifically in virology). It has been a while since my last e-mail. Don’t worry! You haven’t lost a fan. I haven’t missed a podcast since TWiV 113, when I learnt about your show. Your recent podcasts TWiV 173 and 183 discussing about bats harboring influenza and paramyxovirus, respectively, brought back to my attention a paper published last year in PLoS Pathogens, where using deep sequencing techniques, authors reported finding Ebolavirus-like filovirus sequences in bats from caves located in Asturias, Northern Spain. http://www.plospathogens.org/article/info%3Adoi%2F10.1371%2Fjournal.ppat.1002304
As a native of that part of the country I was surprised and interested on the whole story. Of course, there was no evidence of infection or disease, and there were just (only) sequences, but anyway, I found it very interesting and intriguing. I wonder if this kind of search for filovirus has been carried out in other countries outside of Africa (maybe in the U.S.?).
On a related issue, I recently learnt about a huge virus hunting project known as “Global Viral Forecasting Initiative” (http://www.gvfi.org/). Do you have any information about it? Perhaps, it would be nice to have one of their leaders talking about it in your show…
Thank you very much again for your efforts to promote science in general and virology in particular… and long life to TWiV!
Centro de Biologia Molecular Severo Ochoa (CSIC-UAM)
Just in case you haven't seen this. Sort of timely, after your immunology podcast. Perhaps your son, the game player, can evaluate?
I thought you might like to look at Michael Specter's piece in the March 12, 2012 issue of The New Yorker entitled "The Deadliest Virus." It might seem out of date at this point, but it's featured on The New Yorker web site's new Health section. This kind of article could get cited in classrooms, etc. (The article's behind a paywall, but the issue is in libraries.)
I'm not qualified to do a point-by-point analysis, but I saw a number of errors--or at least questionable statements.
Of course, some of these points could be called picky. I don't expect a response; I just wanted to bring this to your attention.
No mention that the 1918 flu was an avian flu. The opening discussion could be read as contrasting avian flu with the 1918 flu.
Definition of "pandemic," point two: "it would have to kill them [humans]" See http://www.virology.ws/2009/05/23/who-will-redefine-pandemic/ for example.
I'm not so clear on point three: "it would have to spread easily." How important is "easy" spread in defining pandemic?
Description of the annual meeting of the European Scientific Working Group: were the scientists "astonished" at Fouchier's presentation? Had it been carried out in secret up to that point?
Description of Fouchier's work as "simply transferring avian influenza from one ferret to another had made it highly contagious." My understanding from TWIV's discussion of the now-published paper is that there was a *lot* of genetic work done on the virus, and that the issue was whether the virus could spread from ferret to ferret at all.
"...they had altered the genetic sequence of the virus in a variety of ways. That had no effect." My understanding from TWIV's discussion of the now-published paper is that the genetic work was what made the virus transmissible.
"When Fouchier examined the flu cells..." Maybe he meant "the cells infected by the flu virus," but I think it's just a mistake.
"There were only five genetic changes in two of the viruses' eight genes." 8 RNA segments, 11 genes, correct?
"Fouchier's achievement was to place all five mutations together in one virus, which meant that nature could do precisely what he had done in the lab." The first part of the sentence contradicts the first point I made for this page. And is the second part of the sentence true? Can we assume that any lab-built genetic construct could arise naturally? Of course, in this case, the intent of the research was to investigate what genetic changes would be needed for transmission.
"...a dangerous form of life, manipulated and enhanced by man, had become lethal." Lethal to *ferrets*.
Michael T. Osterholm is characterized as "one of the nation's leading experts on influenza and bioterrorism," and is quoted extensively.
Re: the 1970s H1N1, "Most virologists familiar with the outbreak are convinced that it came from a sample that was frozen in a lab and then released accidentally." I've never heard this. It is true?
"The labs in Rotterdam and Wisconsin where the H5N1 ferret work was conducted were both BSL-3 facilities." My understanding from TWIV's discussion of the now-published paper is that the work with the actual genetically manipulated H5N1 was in BSL-4. Did I get that wrong?
"Fouchier's virus, which now sits in a vault within his securely guarded underground laboratory in Rotterdam, has fundamentally altered the scope of the biological sciences." Seems like hyperbole to me.
Osterholm: "Those researchers have all of our lives at the ends of their fingers."
"worldwide pandemic" is redundant.
"Fouchier hoped to characterize the properties that make the virus so much deadlier than others." Deadlier to what?
"Once you create a virus that could kill millions of people." Is there evidence that this is true?
Thomas Inglesby"s quote seems to contain some assumptions:
"turn a lethal virus into a lethal and highly contagious virus" Lethal to what? Contagious in what?
"publish how they did it so others can copy it." Well, other virologists with the proper facilities and expertise and institutional approval could copy the work. Isn't that the core of scientific publishing? (There's an important point here. What kind of lab is actually required to replicate this kind of work? What would it cost? How much eduction and training would a staff need? What size staff? Could all the equipment and reagents be acquired secretly? I suspect the mention of "garage" is bogus.)
"As biology has become more accessible, the balance between freedom and protection has become harder to maintain." What does "biology has become more accessible" mean? Is scientific publication about "freedom"? Does suppression of publication equal "protection"?
While a slippery-slope argument can easily be ridiculed, both of these statements seem to me to be at least partly aimed at biology eduction.
"It is not clear when or where the research will continue." If The New Yorker had delayed publication for a month or two, this would have become clear.
The whole discussion of Rob Carlson's blog post on home meth labs and e-mail hacking seems irrelevant or barely relevant.
Hi, I’m Sizun Jiang, a graduate from Wisconsin-Madison and waiting to enter grad school in the Harvard Virology Program. I am currently residing in Singapore (where the weather is 29C and 84% humidity, but usually it is 33C and a gazillion humidity).
I have always been a great fan of viruses, and have always been interested in using molecular virology as a tool to understand ourselves better. Interestingly, although I have yet to actually had the chance to work on or with viruses, I have been lucky enough to have had a great education from established virologists like Paul Ahlquist, Ann Palmenburg, Rob Kalejta and Thomas German. Sadly, I never had the chance for any interactions with Yoshi Kawaoka :(
Ever since discovering your podcast 2 years back while researching for virology programs for grad school, I AM ADDICTED! It is hands down the best podcast I know! It is a great source of information for anyone on viruses, and always a great way to keep up to date with current information both with-in and with-out the virology world, while learning about scientific writing, ethics, biosafety, etc, with a healthy dose of humor mixed in! I love leeching off all the great information from Vince, Rich, Alan and Dick. Although the latter may be more for anecdotes :P Oh I jest.
Twiv is a great companion for me when I go for long runs, giving me a comprehensive workout both physically and mentally. I have always wanted to write in to Twiv, but have yet to come across anything interesting to share, or anything fun to contribute. That changes today!
Here is a great listeners’ pick for you guys:
It’s a little game called plague inc, which I just came across and was hooked on. Of course my first reaction was: I gotta share it with Twiv! In the game, you play the role of viruses, bacteria, prions, etc as you try to mutate your strain to infect and wipeout the whole world, starting from patient zero! Think of it as epidemiology for pathogens. I highly recommend trying this out on an ipad, although you can play with it on the iphone too!
All in all, keep up the awesome work! I look forward to many more episodes of great fun and great learning from Twiv.
Dear Vincent & team,
I thoroughly enjoyed your podcast on reforming science - very thought provoking. There was, in my view, one thing missing from the discussion (and from the articles) though it's of a slightly different nature and not such a systemic problem. That is: improving management and leadership in science. This is a problem in common with the only other field I have direct experience of, the field of clinical medicine. In both areas, at least until relatively recently and still persisting in many quarters, exists the dogma that being good at something also means you will be good at managing other people doing that same thing. This is most definitely no so in my experience, and I have seen some truly appalling efforts at trying to manage and motivate a group of people. This is something that most scientists have no formal training in, and nor as far as I can tell does it play much role in promotion or the awarding of funding. You can have the best ideas in the world but if you can't work effectively with other people they aren't much use. Paying more attention to the role of management and leadership in science would lead to greater productivity in my view.
Thanks again for a great show,
Hello Vince, and co-hosts (I'm never quite sure who will be on the podcast, you swap things about quite often, this is likely a good thing)
The weather here in Weston super Mare, England. It is cloudy and 11 C, though it will get warmer and brighter later in the day.
It's just a quick note, I'm sure you have already heard of the genome compiler project. I've just found out about it from Twit, they have an interview with the creators, it is twit live special 126 (from twit.tv).
I haven't yet decided if I like the idea, but it seems like the beginning of something big. I guess time will tell. I can see that this is something that the human race needs, but I'm not sure if the potential to do bad things outweighs the benefit.
I must get to work, unfortunately, however I'll have the latest episode of twiv to listen to, while on the way.
Thanks again for the podcasts, keep up the good work.