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Tuesday, 19 September 2017 17:45

TWiV 459 Letters

Written by

Peter writes:

Good Morning,

I’m a fan of your show, though I admit I haven’t listened in a while.  You probably saw the news:..

Tuesday, 19 September 2017 17:18

TWiV 458 Letters

Written by

Anthony writes:

When I was looking for Fenner’s papers Online, I could not find any.  As luck would have it, someone soon after handed me a copy of the 1957 – 1958 Harvey lectures — one by Frank Fenner.  I put a PDF here:

Tuesday, 05 September 2017 20:05

TWiV 457 Letters

Written by

Ed Grow writes:

Hi Vincent and the TWiV gang-

On TwiV 447 Pete asks several questions about ERVs, and I’ll try to answer them focusing on HERV biology but drawing on examples from other organisms.

If it were feasible to remove, say, 1 – 5% of the ERV base pairs from a sexually reproducing organism: Would you expect that organism to be able to reproduce with an unmodified partner?

Saturday, 26 August 2017 19:32

TWiV 456 Letters

Written by

Jennie writes:

Hi TWiVers,

I have a follow up to Episode 455, in which you mentioned the film Unrest. The film is not yet available, but it opens in select US cities on September 22nd, including in New York at the IFC Center. The film will also air on PBS Independent Lens in January 2018.

Sunday, 20 August 2017 19:30

TWiV 455 Letters

Written by

Steve writes:

Interesting paper on Viral DNA, the type that makes you sick, well, sort of.

Hello my industrious TwivMasters,

The link that you find below is a paper from U Washington which discusses the creation of an actual code, written in in the language of nucleotides, for a computer virus, dressed up and disguised as a DNA molecule. If this whole concept doesn’t mess with your head then you are obviously not thinking deeply enough.

Saturday, 12 August 2017 19:28

TWiV 454 Letters

Written by

Hannah writes:

Dear TWiV hosts,

This email has nothing to do with virology, but I wanted to respond to Dickson’s pick from TWiV 447. I share his fascination with tiny creatures, and his pick immediately brought to mind this Discover Magazine article about the third smallest insect, a beautiful parasitoid wasp.

Monday, 31 July 2017 08:45

TWiV 452 Letters

Written by

Nathan writes:

Dear TWIV team,

Thank you for featuring our paper on TWIV 451. I thought that you did a wonderful job of describing our experiments and findings as well as navigating through our jargon. After hearing non-mosquito folks talk about our paper, I now recognize how strange some of our approaches must seem and I should improve my writing for a broader audience. Your discussions were very helpful, so thank you.

In response, I thought that y’all might appreciate some additional details. These experiments were very difficult and tedious. Our initial goal was to construct a model natural transmission cycle using multiple rounds of mosquito and bird infection. The first issue was getting individual mosquitoes to infect birds without wasting any 1 to 2 days old chicks with mosquitoes incapable of transmitting West Nile virus. If the chicks do not get infected, we cannot reuse them because they are either too old to become infected and it throws off the timing of our experiments. Hence the development of using the filter paper to test for transmission without sacrificing the mosquito. Compounding the issue was that our Culex mosquitoes did not feed well alone, they needed to get into a feeding frenzy with their friends. Many other mosquitoes, like Aedes aegypti, have no issue feeding alone in the lab. It might even be that our particular Culex colonies are picky. To overcome this, we sprayed our transmitting mosquito with fluorescent powder and put her into a 64 oz ice cream carton with mosquitoes that were unexposed to the virus. Then we restrained the chick, placed it on the carton, and waited for the pink mosquito to get fat with blood.

The real hard part was orchestrating the timing of hatching chicks and mosquitoes to be of a particular age and screening the exposed animals for West Nile virus as close to the transmission day as possible. Sometimes this would require collecting filter paper, extracting RNA, and screening for virus from >500 mosquitoes starting at 5am, marking mosquitoes pink powder and combining into cartons in the evening, and transmission experiments going past midnight. I owed my lab lots of beers, to say the least! This was a ton of work to have the main objective not quite work out, mainly because of the mosquito death issue. The consolation prize was using the filter paper saliva collection method to track West Nile virus populations over time – which turned out to be quite surprising.

The discovery of unique virus populations spit out by individual mosquitoes over time is a nice extension of our previous work examining the random bottlenecks that West Nile virus must overcome within the mosquito before transmission. See our graphical abstract in the attached paper for an overview:

http://www.sciencedirect.com/science/article/pii/S1931312816300944

In summary, only a few randomly selected viruses make it into and out of the major barriers for transmission: the midgut and salivary glands. It’s the constant bottlenecks at these sites that, in my opinion, contributes to the unique virus populations in the saliva.

Considering how much y’all appreciate semantics, I should comment about the quasispecies theory. Quasispecies is not synonymous with genetic diversity, as it is often used. Rather, quasispecies is a form of mutation-selection balance where the entire mutant spectrum behaves as a single unit and collectively determines fitness (i.e. group selection). It is quite difficult to demonstrate that this form of selection is actually happening during infection, thus it is still very much a theory and not absolute. We did not mention quasispecies in our paper because we did not investigate how the virus behaves as a group, only how drift and selection act to reorganize virus populations.

Anyways, thank you again for presenting our paper. I’d be happy to address any follow-up questions.

Cheers,

Nate

P.S. I live in San Diego, so I won’t upset you with the weather details. Trust me, it’s nice.

********************

Nathan D. Grubaugh, Ph.D., M.S.  

Post Doctoral Fellow

Andersen Lab

The Scripps Research Institute

Greg Ebel writes:

Dear TWiV hosts,

Thanks so much for the nice discussion of our recent paper on TWiV.  You all do such a great service to our field through this podcast, and although I’ve never really thought to thank you for it, it’s now high time . . . so, really, thanks a lot.

The phenomenon about group feeding in mosquitoes is pretty strange, and it may be that someone understands it somewhere, but I don’t.  It does make for some experimental headaches, though.  I’m sure that Nate has emailed you a lot (he’s a huge fan) to answer and clarify, but if any questions remain don’t hesitate to contact me.

Best,

Greg

Gregory D. Ebel

Professor, Department of Microbiology Immunology and Pathology

Director, Arthropod-Borne and Infectious Diseases Laboratory

College of Veterinary Medicine and Biomedical Sciences

Colorado State University

Paul writes:

Dear TWiVians

A quick message to correct (as you predicted we would) your musings on the origin of the style of map used to produce the wonderful Roman roads graphic in one of the week’s picks.

The origin is, of course, the London Tube map and not that of the New York underground. The London map was designed by Harry Beck and first printed in the UK in 1931. A brilliant, original piece of graphical design that has been co-opted around the world for a wide range of network representations.

The New York underground version was produced in 1955 by George Salomon and was the official NYC map from 1958 to 1967. Salomon was a German immigrant and proposed route names and colours that mirrored those of the Berlin U-Bahn. He knew of Beck’s London map from time spent in London and adapted the same modernist style.

A cool morning here in Brisbane of 6degC but warming up to a sunny 26degC later in the day. Might go for a wander around the university lake.

Cheers

Paul

Professor Paul R Young | Head of School |

School of Chemistry and Molecular Biosciences (SCMB) | The University of Queensland | Brisbane | Queensland | Australia |

Australian Infectious Diseases Research Centre (AID) | The University of Queensland | Brisbane | Queensland | Australia |

Maureen writes:

I am a clinical research nurse with NIAID at the NIH. I work with infectious disease patients of many types and we run the Special Studies Unit where the Ebola virus patients were treated. The director has put out an article in his blog on some findings from the research done from the Ebola patients. I thought you might be interested in the paper. Thanks for all the informative podcasts that you present each week and for the summaries now of the papers you are presenting. The intelligent discussion among all of you is such an inspiration. It is 95 degrees (35 C) and sunny now in Bethesda, Maryland.

Ebola Virus: Lessons from a Unique Survivor

Steve writes:

https://www.healthrising.org/blog/2017/05/23/doctors-hyde-amy-browns-m-e-enterovirus-story/

Hi Vincent,

I wonder if you might be able to discuss this idea of a ‘newly discovered branch to the enterovirus tree’, and if Byron Hyde’s theorising is likely to stand up in the case of M.E.

He weaves a rather flowery story/case history, here, but I have little doubt, from my own experience of what passes for ‘diagnostic procedure’ in the UK, that the majority of cases of ‘CFS’ really are just patients who used up their ‘three strikes and you’re a hypochondriac’ allocation of tests or consultants, and were simply never taken seriously again–until an acute crisis like a minor stroke happens, as in my own case.

Here the case history develops around what should have been an easily diagnosed case of ‘hand, foot, and mouth’ disease, but I’d be interested if you could fill us in with an up to date, state of the knowledge on enteroviruses and the diseases they may cause, on TWiV.

I’ve been interested in your case histories as enthusiastically described by Daniel, on TWiP, and, the way he describes his working collaborations with what seems to be a diagnostic team, which is a marked contrast to the process of serial short interviews with solo ‘consultants’ whose relevance has only been guessed at, at widely separated intervals of months, that passes for a diagnostic effort here in the UK. With our system it seems to me that diagnosing any non-obvious illness can only ever happen by sheer fluke. Dr Hyde’s example of the ‘diagnostic’ process applied to the poor patient ‘Amy’, in the above account, is, I’m sorry to say, very familiar.

The ‘closing of ranks’ by the UK professionals that Dr Hyde experienced when he tried to advise them of the more appropriate diagnosis for ‘Amy’, you should be already familiar with, as it closely parallels, and partly stems from, the same culture that David Tuller has been investigating over the PACE trial, and the closing of ranks against anyone who dares to question it.

All the best; and many thanks for the continuing free education on all things microbiological that you and your colleagues are providing to the World.

Anthony writes:

And perhaps monitor the winds and clouds for microbes, too?

FWIW

AO

# # #

https://www.nytimes.com/2017/06/13/science/world-view-stratollite-balloon-kfc-sandwich-space-stratosphere.html

“…

Ultimately, stratollites could prove a boon to atmospheric and astronomical research, serving as platforms for long-term observations. Downward-looking radar could provide data to generate earlier and more precise storm warnings. Other stratollites could serve as internet relays over remote parts of the world.

Kenneth Howard, a research meteorologist at the National Oceanic and Atmospheric Administration, said that although computer models that predict hurricanes and tornadoes have improved, “they’re data-starved.”

Ground-based weather radar is blocked by mountains. The curvature of the Earth limits the area that a radar station can monitor. And there is no radar coverage at all for weather over vast stretches of the oceans.

Mr. Howard envisioned stratollites loitering over Tornado Alley, the slice of the Central United States where the storms strike most often. Weather models can point out two or three days in advance where storms could spawn tornadoes. A stratollite could then be sent to that location to quickly spot tornadoes as they begin to spin and perhaps give people a half-hour or more of warning to seek shelter. (Current warning times are less than 10 minutes on average, Mr. Howard said.)

Mr. Howard said the agency hoped to fly several demonstrations of radar and other weather instruments on World View stratollites in the coming

…”

Connor writes:

Hi all,

Thought you and your listeners might appreciate the virology colouring book that we at the CVR produced as part of the MRC Festival of Medical Research.

Follow this link: http://www.gla.ac.uk/researchinstitutes/iii/cvr/public%20engagement/colour/

It is free to download and distribute. There is also a competition running to win a hardcopy of the book.

Enjoy!

Torma writes:

Dear World of Virology Professors!

First thing first, I would like to express my huge appreciation for your great work and for the really stimulating and informative podcasts. I write from the oven hot Budapest where is curently 34 °C or 93.2 °F, all blue sky, no cloud, no sign of redeeming rain… During the previous podcast there was a conversation about the Japanese term for ladybug and about the urge for the more pronounced presence of women at scientific events. Speaking of urges I cant help to share with you the hungarian word for ladybug. It is spelled „katicabogár” more specifically „hétpettyes katicabogár” ( the seven speckled, which brings one’s good luck). The first part “Katica” is nick/ pet name for Kathy or Kate and the second part “bogár” means bug, so it also has a feminine character to it in Hungarian. With being said that that, big shout out for all the dedicated Women Scientists for their great contribution for building the Tower of Science higher and higher. Btw Prof. Spindler, great video about the pipette washer and the “AstroKate interview”  was just over the top! Thank you all for making science soo Cool!

I wish you all the best!

Tomra Ferenc from the Research Center of Sport and Natural Sciences

Ps:. I was really impressed with Prof. Despommier’ pronunciation of ‘Budapest’. It almost sounded native! Probably a heritage from Miklós Müller.

Seweryn writes:

Dear weekly virtual bus companions,

In the most recent TWiV episode 447, there was a discussion about science communication, including an example of new ways of engaging with the public through “tea and science” sessions. Here in Australia (as well as the UK and possibly other places?) there has been something similar going on for a few years… but in a pub (they say that many great ideas come from discussions over a drink or two, right?) It’s called Pint of Science and has sessions held around the country about a wide variety of topics. Check them out, and keep up the wonderful work.

https://pintofscience.com.au/about/

Regards,

Seweryn

Seweryn Bialasiewicz, PhD  | Senior Supervising Scientist

QPID Queensland Paediatric Infectious Diseases Laboratory

CCHR Centre for Children’s Health Research | Children’s Health Queensland Hospital & Health Service

CHRC Child Health Research Centre | The University of Queensland

Kasey writes:

Hello,

I wrote in a few weeks ago regarding the gender parity paper that was discussed with interest in the gender parity of TWiV. I wanted to follow up because after hearing it read, I realized I broke rule#1 of giving feedback, which is that you should always start by describing the things you like. I must’ve been in a rush so I’ll try to remedy that now. I’m a big fan of the show and love being able to listen to descriptions of interesting virology papers while walking my dog in the morning. Listening to your podcast really helps to motivate me to try to do more science communication. I’m an Assistant Professor at Georgia College & State University (a public liberal arts college in central Georgia) and am trained as a molecular virologist. I mostly studied adenovirus although I worked on an adenovirus-vectored malaria vaccine during my postdoc. I teach the Molecular Virology course here and just used the Principles of Virology textbook and loved it. I also like supplementing it with some of these podcasts and Vincent’s blog posts. I started and am the current faculty advisor for our GC STEM club, which hosts monthly Science Cafes during the Fall and Spring semesters. I’ve facilitated a couple of them so far – one on vaccines and another one on Zika (we did that one trivia style). I also do some radio interviews on our local NPR station about the upcoming Science Cafes. And we have Times Talks every week in our library where a NY Times article is picked and we facilitate a discussion with students regarding that topic. I’ve done a couple of those on CRISPR technologies and issues with the anti-vaxx movement.

I also want to clarify a couple things. Sometimes I try to be succinct, but end up not explaining my ideas thoroughly enough and misunderstandings occur. A) I didn’t mean to suggest that Vincent only knew male virologists. It was more that if you’re picking from a limited pool of colleagues and compound that by the small sample size, it is reasonable to expect gender disparity without sexism being a cause. And B) I did not mean to suggest that any of the current hosts should stop being hosts. I love everyone’s contributions. I understand not wanting more than 5 hosts, but I didn’t want to suggest ways to achieve more gender parity since you all would know the logistics better. I think you ended up coming up with some great ideas. It does seem like a lot of work so I can see why several people have turned you down. I myself would love to be a host if I had more time: case in point, it’s taken me a few weeks just to write this follow up email and it’s during the summer. The timing also coincides with the first real day of my “vacation” (I used quotes because I still have several work-related items I want to accomplish during my “vacation”).

I’m actually on Long Island visiting family for my vacation so the weather is a beautiful 28˚C and partly cloudy. Much more pleasant than Georgia this time of year.

Thank you everyone for all that you do. Keep up the good work!

Kasey Karen, Ph.D.

Assistant Professor of Biology

Biological & Environmental Sciences Department

Georgia College & State University

Stig writes:

Hello Professors

At the moment it is hot for Danish standards, and my guess would be that it is around 20 degrees C, and mostly clear skies. I am still not using a weather app, so that is about as precise as I can be.

Unfortunately I can’t really enjoy it seeing as I have my master thesis to hand in at the end of August, feels like I am working around the clock.

I just finished reading “Ignorance” by Stuart Firestein as recommended by someone from TWiV, I don’t remember who, sorry !

This is my 3rd e-mail to the TWiV podcast, but this is the first time not trying to win a book.

I listen to TWiV when I can, while working at the bench and usually while pipetting and it seems that I almost have lot of stuff to e-mail in about but I never get it done. So now was the time to do so …. agin.

I would like to hear your opinion on the matter of sci-hub. I have included some links outlining what it is and how it works. I hope you will take the time to discuss it among you. I don’t think that it have been discussed in any of the TWi(X) podcasts, if so I apologise. As I have “only “ been listening to TWiV and TWiM, TWiEVO and sometimes TWiP for a little over a year now (I think).

https://en.wikipedia.org/wiki/Sci-Hub / https://torrentfreak.com/sci-hub-ordered-to-pay-15-million-in-piracy-damages-170623/ / http://sci-hub.io/

If you want to get a bit further into it, the level1techs news/podcast talks about it as well: https://www.youtube.com/watch?v=Hqo0341Z8W453:28

Thank you for a fantastic podcast, keep scienceing !

Finally I would like to make a pick of the week. And I think Vincent, your son might like it, being in cyber security. If you are like me and value online privacy I can recommend this podcast.

Security now! With Steve Gibson @ www.grc.com

Oh, one more pick, if Vincent can have two picks, so can the listeners. 

“The Gene: An Intimate History” by Siddhartha Mukherjee an Indian MD. I am reading it now, just about halfway through – I find it really interesting.

Best regards

Ricardo writes:

Hello TWIV Friends.

Long time no writing, but I’m listening.

Here I send a link for a listeners pick.

It is a movie from Last Week Tonight with John Oliver about Vaccines.

He uses several communication techniques to pass the message, and ends with a very nice touch.

https://youtu.be/7VG_s2PCH_c

My best regards my friend and keep the beautiful work.

Ricardo Magalhães

Universidade Fernando Pessoa

Portugal

Monday, 24 July 2017 09:23

TWiV 451 Letters

Written by

Jane Flint writes:

https://en.wikipedia.org/wiki/Tube_map

With respect to schematic subway maps (TWiV 450), goes back to 1930’s in London.

Great discussion with Ben,

Jane

Sasha Trubetskoy writes:

Hi guys, thanks for sharing my Roman subway map.

I think the name you’re looking for is Harry Beck, designer of the London Underground map. He was actually an electrical engineer by training, and came up with the idea of representing a transit system as if it were an electrical circuit. In 1932 he published an early version of the now-ubiquitous map, which was immediately rejected by the London Underground’s Publicity Department. However, due to Beck’s persistence, a small print run was allowed and the map was released at a few select stations. Riders loved the simple design and demanded more–the Publicity Department conceded, and ordered 700,000 copies. Other cities would copy Beck’s idea, and the rest is history.

Johnye writes:

Learned Scientists.

A couple of months ago I discovered Jennife Khan’s TED talk on CRISPR gene drives. During the conversation around 00:23:23 brought to mind the activity of the a gene drive. A some point, when appropriate and pertinent, could the group discuss CRISPR gene drive as a tool for use in maybe vaccine production or other uses in research?

Jennifer Khan’s talk was most engaging.

https://www.ted.com/talks/jennifer_kahn_gene_editing_can_now_change_an_entire_species_forever

Thanks from 27 C, fairly sunny, but officially partly cloudy, Boston.

Johnye

Vr: check out TWiP 100 where we talked about a cas9 mediated driver gene in mosquitoes http://www.microbe.tv/twip/twip-100/

Wiki on gene drive

Shallee writes:

Dear TWIVumvirate;

Humid and warm in New Hampshire. 26 deg C (78 F).

Thank you so much for TWIV 449 and 450 about RNAi. I am hard-pressed to keep up with all these ‘new-fangled’ RNAs. Dr. tenOever talks fast, but his parenthetical explanations were excellent. At one point, I wanted one of Rich Condit’s interruptions to slow down and recap, but I guess he was away!

I also wanted to thank Prof. Young for the letter about predatory publishing.  I received an invitation to write a book chapter this summer and I considered paying the page costs out of my faculty development funds or my pocket because it was about past research that is no longer grant-funded. One of the editors listed was someone I knew and respected and Wisconsin-Madison’s icon was on their webpage! Fortunately, I googled the book series before I accepted the invitation or started writing. I found a blogger that had blogged about it being a bit of a scam.

But, I still wasn’t sure that I made the correct choice.  Even if it was a minimal impact publication, I figured my promotion committee might not care. So, it was a great service for Prof. Young to write.

There is a list of predatory publishers no longer quite current, but amazingly extensive: http://beallslist.weebly.com/

Thank you again for serving so many different constituencies from undergrads up to older scientists trying to keep up with new findings!

Shallee Page (a male FWIW)

———————————–

Shallee T. Page

Assoc. Prof. of Chemistry

Franklin Pierce U.

Jess writes:

Hiya TWiV Team!

It’s a balmy 26C with 83% humidity and 16kmh winds at 7pm in Rhode Island.

I just wanted to express how excited I was to hear from Ben tenOever in episode 450.  While I have meant to read more of his publications and listen to past TWiV appearance(s?), I will admit I was only first introduced to his work via his ABSA International conference presentation last year in Grapevine, TX.  

His talk was one that I remember distinctly because it instilled so much excitement and curiosity in me regarding engineering suicidal viruses in the lab. On several occasions I scanned the audience to possibly connect with another soul who was as wowed as I was by the research so that we could silently agree that his work was “SO COOL.” Alas, I did not find my nerdy soul sister or brother in the moment but it did not take away from the experience.

No matter how much I learn about molecular biology, genetic engineering, virology etc. I’m constantly impressed by what we know and by what we don’t know!

It was also nice to have my worlds collide between Dr. tenOever as a TWiV fan and guest AND as a participant at the ABSA conference where biosafety experts from around the world gather annually.

Speaking of the ABSA conference, the year before I met Dr. Ian Crozier who is an MD and ebola survivor who gave an amazing and compassionate presentation regarding the West African outbreak and the subsequent medical community/volunteer response.  He’s a phenomenal speaker and would probably be a great guest for the show someday if you could get him.

In any event, kudos as always for presenting really cool science.

Take Care,

Jess

Steve writes:

http://www.promedmail.org/direct.php?id=20170517.5041381

Hi Vincent et al,

Just came across this case of a virus infecting a fungus, and enabling–for now–survival of European Chestnut, after‎ the fungus made its way to the US and wiped out most of the American Chestnuts, before finding its way to Europe and meeting the virus.

(If I’ve read it right, that is!)

Sounds very much a ‘TWiV story’.

All the best,

Steve

Luton

England

Beautiful blue sky morning getting under way here.

Average Jane writes:

Dear twiv scientists, professors & science communicators: you are, I suspect, the sort of experts to address a question like this.

Let’s say you are an average Jane, average education, who lives in a world of fake news.

You want to use critical thinking, especially on issues of science that directly affect you and your family.

What steps can you take to think critically when you see opposing views like the example below?

it could be any example, I just chose this for illustration.

————————————–

Do We Dare To Eat Lectins?

http://www.huffingtonpost.com/entry/do-we-dare-to-eat-lectins_us_5935c6a7e4b0cca4f42d9c83?section=us_healthy-living

—————————————————————————————–

versus:

——————————————————————————————–

Dr. Gundry: Lectins are the Root Cause of Inflammation and Disease

https://www.youtube.com/watch?v=luna9RQsL1E

——————————————————————

best regards,

average Jane

https://theskepticalcardiologist.com/tag/vital-reds/

Johannes writes:

Dear Prof. Racaniello, dear hosts of TWiV,

I am  a relative regular listener and enjoy your discussions, may it be on virology or on more general science related topics.

Even the political ones.

Doing my PhD in molecular toxicology, I enjoy following you to broaden my scientific horizon.

Viruses are to me just complex nanoparticles, naturally occurring and sometimes of the kind that make you sick.

In the  episode ‘TWiV 449: The sound of non-silencing’ you discussed the problem of predatory journals,

Going through the  literature my B.Sc. intern used, I recognized that educating young scientist is an important thing to fight off predatory journals.

I spend quite a lot of time myself tracking down some of the cited literature of which I didn’t know the publisher.

While doing that, I realized it is not easy for a scientist in training to differentiate an open-source journal propagating open access for the sake of society from a predatory journal.

What I found on my search, and what I would like to share with you is a neat website:

http://thinkchecksubmit.org/

It is a website providing a process called Think. Check. Submit., basically a check list containing useful tips and tricks helping to identify predatory journals.

Since you are all experienced members of the scientific community, I would like to hear your opinion on this website and also how to educate scientists in training to watch out for predatory journals.

I assume we as a scientific  community will never be capable of fully preventing this parasitic form of publishing.

But it is our duty to give the predatory journals a hard time to be successful.

Best regards,

Johannes

P.s.: Please revive Urban Agriculture podcast! I enjoyed it a lot!

Johannes P. Schimming | PhD Student | Division of Toxicology | Leiden Academic Centre for Drug Research (LACDR) | Leiden University

Steve writes:

https://www.change.org/p/salt-river-pima-maricopa-indian-reservation-stop-the-monkey-farm-from-breeding-monkeys-to-use-the-babies-for-scientific-experiments

Hi Vincent and team,

As an environmentalist/conservationist and lifetime science enthusiast, I find I am all too often faced with impossible choices like the one presented by this position. For most of my friends it is an easy choice: more and more research is showing that even creatures once thought to be non-sentient are showing surprising empathy and care for one another; monkeys are right at the top of the ‘almost human scale’; experimenting on them is torture without any doubt. I, certainly could not do it, even for mice (I noted that even Vincent seemed to balk on realising recently, that a mouse had been pinned down alive for four days whilst a cell of its leg was observed under a microscope.).

Do I sign: or not?

Regrettably,

Steve Hawkins

Luton

Beds

England.

Anthony writes:

“…

Retraction Watch (RW): Rigor Mortis begins with the story of the 2012 Nature paper by C. Glenn Begley and Lee Ellis that is now famous for sounding the alarm about reproducibility in basic cancer research. But as you document, this is not a problem that began in 2012. When did scientists first start realizing there was a problem?

…”

http://retractionwatch.com/2017/04/04/failure-essential-part-science-qa-author-new-book-reproducibility/

# # #

I’ve just started to read this with great interest.   

The book does have what might be considered an unflattering comment concerning Stuart Firestein.

FWIW

Neil writes:

These Smart Girls Are Here To Debunk Anti-Vaxxer Nonsense

http://digg.com/video/vaccines-song-hamilton

John writes:

Hi Vincent, Dickson, Alan, Rich, and Kathy,

I offer a listener pick of John Sever’s reddit “ask me anything” about the Rotary Club and polio eradication…

https://www.reddit.com/r/IAmA/comments/6if2wr/i_am_dr_john_sever_vice_chair_of_rotarys/

Thanks and regards,

John in Limerick

Monday, 17 July 2017 08:22

TWiV 450 Letters

Written by

Hitoshi writes:

The correct pronunciation for “Tentomushi” is like ten-toe mushi, not ten-two (10-2) mushi.

Paul writes:

Twivoli:

An Excessive heat warning covers SE PA for tomorrow but presently 32C with 50% and 27m/h winds.

Thanks for episode 449.

One question and one comment.

Question:

The article discussed the method a mammalian virus used to suppress RNAi suppression.  It implied that RNAi could be common in mammals but routinely suppressed by mammalian viruses.  In any event it definitely identified a fairly straightforward RNAi suppression mechanism available to RNA viruses. So, why wouldn’t such a suppression mechanism be common in plant and invertebrate viruses that face RNAi as their primary barrier to success.

Comment:

Ockham’s Razor originally referenced  primarily that “Entities [i.e. hypothetical entities] must not be multiplied beyond necessity”; this is different from a general bias in favor of simpler hypotheses. For example, the Razor would prefer a more complex hypothesis that hypothesized one enzyme to a simpler hypothesis that required two.

Great content.

Chris Sullivan writes:

Dear TWiV Hosts,

I am glad that you are dedicating back-to-back episodes to cover the exciting topic of RNA silencing and antiviral defense in vertebrates, something my lab thinks about. As you mentioned us in the previous episode TWIV#449 for possible comment, I thought I would briefly respond. This paper by Qiu et al., similar to recent work from Cullen and Ding labs, clearly demonstrates siRNAs matching viral sequence can arise in mammalian cells at least at some level in the right context. It also provides further genetic evidence consistent with an antiviral activity of RNAi. I think a picture is emerging in the field as a whole that there are at least some hallmarks of antiviral RNAi in mammals. The debate now moves from “do these hallmarks ever exist?” to “how meaningful are they?”.

Although the issue of whether RNAi is a relevant mammalian antiviral response still remains unresolved, I think all parties can agree that some hallmarks of antiviral RNAi exist but are more context dependent and limited in mammals. Whatever your favorite take on the larger issue of antiviral mammalian RNAi, I think most would also agree that RNAi is clearly different between mammals and invertebrates. Whether due to differences in the effectiveness of mammalian versus invertebrate VSRs, or more likely in my opinion, due to the differences between mammalian and invertebrate host biology, viral derived siRNAs are of lower abundance and likely less importance in mammalian cells infected with WT virus. Further, our own published and unpublished work, combined with work from numerous labs (including the Pfeffer, Cullen, and Sousa labs) shows that there are clashes between the effectors of the protein-based mammalian antiviral response (e.g., RNase L, PKR, IFN) and multiple components of the RNAi machinery. Thus, it remains unclear to me how much antiviral RNAi matters in mammals where the protein based response appears to have superseded and even counters components of RNAi.

It has been fun to watch the science unfold around this issue over the years. Yes, the dialog has been heated at times, but as long as this is kept to debate about the data and its interpretation, this is what makes science work. I commend all parties for the strife they have endured to stand up for their perspectives when, as too often happens, it would be easier and less risky to just ignore those papers you don’t agree with. Antiviral mammalian RNAi is an important issue, and I am glad the discussion continues. This is good for science and gets us closer to true understanding.

As always, thanks to all of you for what you do. Listening to you is one of the enjoyable parts of my job.

Chris

Monday, 10 July 2017 09:20

TWiV 449 Letters

Written by

Jens writes:

I may be wrong, but I think Occam’s Razor is not about preferring a simpler hypothesis over a more complex one in general (because Nature is complicated) but it is more about  skipping unnecessary steps in a thinking process that either way would yield the same result. For instance, if you ask the question “Who made the universe”, the answer could be “Nobody” or “God”. But if you chose “God” as an answer then the logical follow-up question would be “Who then made God?”. If your answer then is: “Nobody, God always existed”, then Occam’s razor would demand to skip that entire step because you could have answered “Nobody, the universe always existed”…

Best,

Jens

PS:

Anybody coming to ICV in Singapore?

Kaine writes:

My name is Kaine and I manage communications for the Department of Biochemistry at the University of Wisconsin–Madison. I came across your cool TWiV podcast on gender disparity at virology conferences that was based on a paper by one of our faculty members, Ann Palmenberg. It was a great listen! I wanted to also let you know about a recent press release that happened on the paper. I’m sending it because I saw that you linked to the actual paper on your site but could include this more general audience-friendly read if you wanted as well.

https://biochem.wisc.edu/news/2017/news-palmenberg-virology-conference-gender-disparity-2017-06-26

http://www.microbe.tv/twiv/twiv-446/

Do let me know if you have any questions.

Thanks!

Kaine Korzekwa

Marketing Specialist

Department of Biochemistry

University of Wisconsin–Madison

Stephen writes:

Another article about how science education is changing.

The Traditional Lecture Is Dead. I Would Know—I’m a Professor | WIRED

https://www.wired.com/2017/05/the-mechanical-universe/

Paul writes:

Dear TWiVters

Another great episode last week – episode 447 and the un-impacted pachyderm.

One reader’s email on the wave of predatory journals that are currently being inflicted upon us, stimulated a robust discussion – I agreed with all of your comments. Like so many of my colleagues, I’m inundated every day by offers of guaranteed publication in a bright new journal, requesting my services as an editor on same or having my abstract accepted for oral presentation at a new, must attend meeting at which a bevy of Nobel laureates will be in attendance. An early morning task before I head off to work, is rapidly deleting them all without so much as a second thought.

But what you didn’t talk about was the worrying trend in predatory behaviour by well established and respected journals – perhaps a consequence of their traditional business model faltering as the new OMICS wave bears down.

One such journal scoped interest in a special edition on dengue with a colleague of mine – a highly respected leader in the field. My laboratory has worked in Dengue research for the last 30 years and we were asked to contribute, as were a number of leading groups around the world. We were tasked with providing relatively short, state-of-the art reviews on selected topics – up to 2,500 words. We all dutifully put in the effort to produce a collection of reviews that I believe provide a comprehensive, yet concise overview of the dengue viruses, the diseases they cause, diagnostics available and control strategies under development.

The privilege of putting in all of this effort? A bill to each of us, varying between US$5,500 and more than US$8,000 as “page charges”. The subsequent email traffic between the contributors and the journal became a little heated – with the journal ultimately agreeing to a 10% discount. Nevertheless, the dent to my budget was still significant!

A different sort of predatory behaviour, but this experience has burnt all of us and I’m writing this email as a cautionary tale to others who may be tempted by invitations from highly respected journals to contribute to their bottom line. Just be aware that there is likely to be a sting in the tail of that invitation.

Keep up the great work – it’s the middle of winter here in Australia and the family were out today in T-shirts strolling along the Brisbane River boardwalk in a “balmy” 22degC. Crazy!

Regards

Paul

PS The journal is The Journal of Infectious Diseases – you may not want to mention the name.

Professor Paul R Young | Head of School |

School of Chemistry and Molecular Biosciences (SCMB) | The University of Queensland | Brisbane | Queensland | Australia |

Australian Infectious Diseases Research Centre (AID) | The University of Queensland | Brisbane | Queensland | Australia |

Matt writes:

Hello TWIV council,

My name is Matt and I’m writing from UW Madison. It feels like the first day of summer here in Wisconsin (whether that be the temperature in the 60s, the beautiful sunny sky, or the fact that finals are over, I’m not sure.) I have to express my jealousy that Vincent’s students get one week to study for exams. Like Kathy’s students, we have a single day. But I survive, and I finished my last final yesterday, which was virology, so I thought it was fitting to listen to the most recent episode of twiv. (By the way, my professors are excellent, and eagerly awaiting the arrival of ASV.)

I have actually been listening to TWIV since last summer. I want to study immunology in grad school. Unfortunately I had a hard time finding an immunology podcast, but instead stumbled onto TWIV. I started listening back then and would tune in every so often, but could not really understand what was going until I got part way through my virology course this semester. I have to echo a recent emailer’s sentiments about really enjoying when you sit down and talk with a panel of scientists. It’s really awesome to see how they got into science, and get such a wide ranging discussion about their various research projects. I especially enjoyed your discussion with the ZEST team here on campus.

I’ve learned a lot from your podcast, and I actually have a summer research abroad project involving HIV that I’m very excited about. I’ve always thought viruses were cool, but now I actually know something about how they work!

Keep up the great work, and if you know any immunologists that would be great podcasters as well, you should push this toward starting a TWII: This week in Immunology.

Thanks for all you do,

Matt

Anthony writes:

“Poets are always taking the weather so personally. They’re always sticking their emotions in things that have no emotions.”—J.D. Salinger

Posted on Facebook by PEN America

https://www.facebook.com/PENamerican/photos/a.10150192424389058.272779.38234604057/10154087397529058/?type=3&theater

Josephine writes:

Hello Twivologists,

Greetings from southern Alberta where the weather is a glorious 27°C with clear blue skies and a light breeze. And yes, I know Dave the sheep shearer – I introduced him to the Twix podcasts! Truly, my favorite podcasts!

I wanted to let you and your listeners know about the 2017 Rabies in the Americas Conference which is being held in Calgary, Alberta, Canada, 22-26 October 2017. This is an annual conference and this year it is Canada’s honour to host the event. Attendees come, not just from the Americas, but from all over the world. There will be simultaneous translations of all presentations into English, French, Spanish and Portuguese. More information regarding the conference can be found at www.ritaconference.org for those interested in attending and/or presenting.

Thank you for such a wonderful family of podcasts.  I no longer listen to them on my commute to work as I have retired from working in the rabies diagnostic lab,  but now y’all accompany me on my daily walks.

Cheers,

Josephine Kush

Anthony writes:

It appears that all that needs to be done is to claim that the research will lead to a better understanding of Autism or Alzheimer’s.

https://www.alnmag.com/news/2017/05/mouse-vocalizations-provide-insight-autism

This study actually is very important, but I need to wonder about the relevance to Autism.  My understanding is that mouse vocalizations are calls (instinctual), not language.  

The invoking of a key to a cure for Autism or Alzheimer’s is all but de rigueur in animal studies — the more baseless the better.

Way back in the mid-’70s, I heard Juan Cortes (a Psychology professor at Georgetown University) say that the funds used in most studies claiming to help children with cognitive impairment would be better spent by taking the kids out for ice cream.

FWIW

Jay writes:

Hello everybody, just writing to let you all know how much I enjoy your podcast and to say thank you. I look forward to each new episode as they are very entertaining and full of in-depth leading edge science discussion.

My background is in aerospace engineering so I have to work hard to understand the subject matter at times, but I thoroughly enjoy doing my homework on terms and concepts I don’t understand.  You do an excellent job in combining high level information with molecular level details, and your recent addition of overview and summary discussions are a real bonus for me.

I discovered your TWIV podcast in a roundabout kind of way as historically I have shied away from microbiology and virology. A year and a half ago I was presented the opportunity to enroll in a gene therapy clinical trial for hemophilia B, and in researching the trial I Google searched on Dr. Katherine High who was the senior author of the study.    Vincent knows where this is going…

I found a very informative video interview with Dr. High, done by none other than Vincent Racaniello! This led me quickly to Vincent’s online Virology lectures which I have watched and continue to rewatch. From there it was a short jump to becoming an avid TWIV listener, and since then TWIM and TWIP too!

As for the gene therapy trial, with my confidence bolstered by listening to the very impressive Dr. High and my newfound understanding of gene therapy, I joined the trial. Since then, the AAV vectors have done their job, and I am now a happy host to a bunch of Padua mutant FIX genes. My hepatocytes have been diligently producing hyperactive factor IX protein for over a year now and without even one traumatic bleed in that time, I consider myself functionally cured (for now, and hopefully for years to come).

I distinctly remember watching a scene from a just-released Star Trek movie back in 1986 (the dark dark dark days for hemophilia) and being put off by Dr. McCoy giving a pill to a hospital patient, instantly curing her of kidney failure – how unbelievable I thought, and how I wished that could happen to me.

Well, thirty years later, after a one half hour intravenous injection of a clear liquid – it did.

The medical science you all do is very real, and has a very real effect on real people. For your dedication and perseverance I thank you and your many listeners.

Bye for now, and I look forward to many future episodes of This Week in Virology, the kind that make you sick – or in my case the kind that make you better!

Jay

Cambridge, Ontario

Currently 17 degrees Celsius with CAVOK skies – sunny and just a few fair weather cumulus floating by.

Neva writes:

Super TWIVs,

A wonderful example of science communication.

MIchael Summers, the author of Exoplanets: Diamond Worlds, Super Earths, Pulsar Planets, and the New Search for Life Beyond Our Solar System, is interviewed by Father Robert Ballecer on the TWIT.TV network program Triangulation.

https://www.youtube.com/watch?v=7zgQN3N_TuU

Dr Summers entertainingly shares his delight in his field and is careful to say what is known and what is speculation.

A fun interview and …..SPACE! PLANETS!

Another Pick:    A virus coloring book contest.

“At the MRC-University of Glasgow Centre for Virus Research (CVR) we know that, like viruses, creativity is contagious. To help spread the fun, we have designed our very own colouring book! Illustrated and written by CVR scientists, we hope this book gives you a bit of welcome relief from the daily stresses of life, while inspiring you with interesting facts about viruses and the incredible research underway at our centre in Glasgow.

Created with the support of the Medical Research Council, we hope you enjoy learning about the tiny pathogens that never cease to amaze us.

To mark the MRC Festival of Medical Research (17 – 25th June), we are running a competition to allow 10 people to win a FREE hard copy of the book!”

http://www.gla.ac.uk/researchinstitutes/iii/cvr/public%20engagement/colour/

Keep it coming with your own team entertaining science communication.

Best to you,

Neva from Buda

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