TWiV 278 letters

Stephen writes:

Dear Twivers,

First, I wanted to say that despite Vincent’s dire warnings of doom and gloom, the most recent podcast on his background was fascinating. I only wish the other regular hosts could have been there so I could have heard their reactions.

Second, the etsy store Watty’s Wall Stuff recently came to my attention:

https://www.etsy.com/shop/aliciawatkins?section_id=11480156&ref=shopsection_leftnav_5

It includes many cross stitched microbes. In addition to selling completed items, she has kits and patterns for anyone who wants to make their own T4 phage or anything else in her collection.

Thanks for all the great work,
Stephen

Jon writes:

http://www.thisiscolossal.com/2014/03/cross-stitched-germs-and-microbes/

Jon, KS

Atila writes:

Dear prof. Raniello and other twiveiros (portuguese for twivers),

It’s been a long and busy time since I last wrote to TWiV, but I’m still listening from here. It is a nice 27ºF here in New Haven, CT, where I’m postdocing for this year. Or a rainy 21ºC back in São Paulo. I’ve been moved to send an email by the recurrent discussion on Open Access and high impact periodicals, and would like to share my inexperienced opinion.

Now that we use search engines like PubMed or my personal favorite Google Scholar, the title of the article is much more evident than where it was published. How many citations they receive also seems to be one of the sorting criteria in Google Scholar results. And people read each time less of an entire journal to find relevant research.

Meanwhile, journals like Nature and Science still publish very important research. But they “have been publishing a decreasing proportion of these top cited papers”, as Lariviere et al. pointed out last year (http://arxiv.org/abs/1304.6460). This means that they still have a very high Impact Factor, but are not keeping pace with the diversification of journals. Things probably will get worse with the adoption of article level metrics so prized by PLoS and others, as the fraction of highly cited articles that sustains the high IF is very small.

Not surprisingly, I’ve been hearing and reading more and more from top journal editors about how much grant money or professional influence they provide. Please see this Nature editorial full of testimonials on how a publication at their journal led people to get a job position or win a grant or clinical trial proposal. Which is to say that their actual relevance is sustained much more by committees and grant review panels than for scientific reasons.

I think what Clay Shirky wrote about scribes, music industry and others in the book “Here Comes Everybody” can be applied here. When some business models collapse or change too fast, as is the case of scientific publications, the first reactions from institutions that profit from the old model it is to try to stop things from changing. By giving so much importance to where the articles were published instead of what they contain we’re just helping this.

Thank you all for the great discussions. And for the first true international virology meeting.

Best,
Atila

Tim writes:

Twivers,

I started listening to your program when the XMRV debacle started. I guess I was in the category of what Alan at the time at the time “a bunch of crazies”. Eventually I found my way to listening to TWIM also. Not being a microbiologist (but being a scientist), I appreciate that you try to find subjects that sometimes are applicable to the public. I really enjoyed episode 271 on viruses that may have crossed kingdoms. I’m curious about a phenomenon I seem to have noticed, and was mentioned in episode 271. It seems to me that the press releases concerning the publication of research papers has moved into the realm of hype and unfounded claims of new discoveries. Have you noticed this also? Any speculations as to why? Is the competition for research money (and thus income to the research institution”) just so great that this is the result? If I was one of the authors who had put so much time and effort into producing this paper only to see it being touted with unfounded claims, I would be upset.

For a Listener pick of the week, I want to nominate Alan Dove’s recent attempts to explain the scientific thinking/method to the general public on his website, “The Turbid Plaque”. Nice work, Alan.

Tim

Suzanne writes:

I will agree with you that “real” isn’t the best word to use. I don’t know what is. It’s always annoyed me when people use the word real to talk about any one section of the population. I know what they mean but we need a better word.

On the other hand, I do agree with Alan Dove that the people he’s trying to reach who really need a primer on how science works aren’t listening to your podcast. That’s ok. Your podcast is great outreach to a lot of the non science community population and the info you share does get filtered out even further than us. I don’t think the science media is a complete echo chamber. Also, plenty of us could use a refresher or a follow up course on basic science and those videos are useful for that. So there is overlap. But it wouldn’t surprise me if there is a much larger audience that just needs to know how science works before they can even listen to someone like me talking about what I hear you say and really get much out if it.

Johyne writes:

Greetings from chilly, – 5 degrees C, Boston, MA.

Special thanks to Prof. Despommier’s for his pick this week: Ronny Tertnes’ artistic images of “Liquids Colliding”. (Can’t help but think there are physics majors who could translate the images into equally amazing graphs and equations.)

http://news.yahoo.com/photos/amazing-macro-views-of-snowflakes-slideshow/

At the Yahoo News site, I came across “Macro Views of Snowflakes”, taken by photographer, Valeriya Zvereva. Seemed most apt given the current weather pattern here in the NE, and thought I would share. Now to listen to this week’s TWIV.

Stay warm. Johnye

Johnye Ballenger, M. D., FAAP
West Cambridge Pediatric and Adolescent Medicine
Cambridge, Massachusetts

Ricardo writes:

http://www.motherjones.com/environment/2014/02/vaccine-exemptions-states-pertussis-map

Bill writes:

Folks,

I discovered the twiv podcast about 18 months ago and have since given up trying to keep current and listen to all of the previous podcasts , so please forgive me if this has been already mentioned. Dr John Janovy jr taught parasitology and the University of Nebraska-Lincoln for 40+ years and is now retired. Dr Janovy has written a number of books dealing with various topics but I think that his nonfiction works dealing with the training of young minds to be scientists are very good. Everything from his early material (Keith County Journal, Return to Keith County,Yellowlegs etc) to more recent works (Dunwoody Pond,Pieces of the Plains,etc ) are very good reading. Since I am a physician I tend to work in the realm of applied science rather than in the pure science arena (Dr Janovy obviously failed in converting me) but I still understand the importance of formulating clear questions and getting people to think rationally and realistically about things.

Again please forgive me if this material has been previously mentioned.

Disclaimer-although I currently practice in north central Pennsylvania I am a Nebraska native and my perspective maybe somewhat biased.

I very much enjoy the twiv podcasts and have learned much from listening to them. I will continue my efforts (which I fear are futile) to get caught up and then remain current.

Sincerely, Bill

Mauricio writes:

Dear TWIV team,

How are you enjoying the winter? Here in Frederick (MD) life has been slightly challenging, mostly because every time we have some snow or ice they close Fort Detrick where NCI-Frederick main labs are located. Yesterday we had a nasty winter storm but right now is wonderful 0 C with a thermal sensation of -4 C and 24 km/h winds.

I had a blast (like most of the time) listening at podcast 267 where you discussed the paper by Shushan Harutyunyan about viral uncoating, where they used Fluorescence Correlation Spectroscopy to learn if there is any directional uncoating. During my last year and a half of my Ph.D. I used FCS to measure the number of multiple copies of packaged RNA by a plant virus capsid protein (all in vitro work) and I got hired at NCI to keep doing FCS experiments to study HIV-1 gag/RNA interactions. Anyway, I want to point out that the work done by Harutyunyan is brilliant and extremely challenging. What I like most about the podcast was the way you explained FCS and what is a autocorrelation function, specially why it goes from 1 to zero. I would like to point out three more things; i) You can know the exact number of molecules in your confocal volume and from this information you can “count” the number of molecules interacting, ii) you can follow chemical reaction (or binding events) at different time scales from microseconds to several minute-long, and iii) you have to work in a very dilute regime so there are between 1 to 10 fluorescently labeled molecules in the confocal volume (~ 1 femtoliter). Working in this dilute regime is what gives FCS a great power when looking at in vitro viral assembly. Most techniques required very high concentrations to determine the size of a molecule and most of the times they cannot discriminate between different kind of molecules present in the same sample. For example, it is thought that in the cell just a couple of HIV-1 gag molecules interact with the virus genomic RNA (Paul Bieniasz lab), there is no other technique that could study the strength of these interaction under such diluted conditions. Of course there are a lot of artifacts which limits your system, but those are very technical details. I hope this technique comes back because it is extremely useful both in in vitro and in cell work.

You all did a great you explaining something that is very obvious for a spectroscopist but not for other scientist.

Cheers

Mauricio

HIV Drug Resistance Program
National Cancer Institute
Frederick National Laboratory for Cancer

Christoph writes:

Hi Vincent, et al.
Christophe here again.
I have been thinking of making some sort of t-shirt / sticker idea for you guys as a thank you for the crazy amount of work you all do with the TWiV/TWiM/TWiP podcasts and i really like the Mice lie, monkeys exaggerate bit you guys keep saying.

Anyway here is a first effort. Hope you like it. Feel free to use it anyway you like or not at all.

ps. The grey shape is in the background is a silhouette of the polio virus – no idea how accurate it is – i am just a web designer after all. Maybe i should do a Pox version for Rich and Trichinella for Dickson – not sure what Alan and Kathy would like.

Christophe

Stephen writes:

Thought you might find these graphics about vaccine exemptions interesting.

http://www.motherjones.com/environment/2014/02/vaccine-exemptions-states-pertussis-map

steve

Marion writes:

Everybody complains about the weather, but nobody does anything about it.
Well, it appears that we ARE changing the weather, by changing the climate

transcytosis:

transcytosis of secretory IgA has been known about and understood for a long time.

Reasons for flu vaccination:
another important reason for flu vaccination is to reduce transmission by asymptomatic carriers.

Andrew writes:

Dear TWIV comrades,

I am currently a student at Penn State Behrend (PSB) of Erie, PA in the undergraduate fields of Biology and Chemistry. I stumbled upon TWIV, TWIM, and TWIP while I was attending Jamestown Community College (JCC) to obtain my A.S. Biotechnology. I thought this podcast was perfect to listen to while driving, so I could reinforce the main ideas and details that I learned in some of my classes (i.e. Virology, Cancer Biology, Cell and Molecular Biology, Immunology, and Genetics). Since the day of discovering the triad (TWIV, TWIP, and TWIM), I have graduated JCC, transferred to PSB, and now have a 50 minute drive to school each day. The drive makes a excellent time to catch up on the episodes I missed and I usually listen to one each day. I had enough with introducing myself, and onward to my response and questions.

First, I have a response to the discussion of GMOs in TWIV 272 and the cause to health effect they cause. Since I am a man of science and biotechnology, I don’t agree with the conjecture that GMOs are causing a dramatic increase in food related illnesses, cancer in particular, just by observing an increase in instances of these types of diseases and the coincidence of using GMOs as food. These types of disease are theorized to be related to diet and habitual practices (e.g. smoking), and certainly cannot be inferred to be a caused by mutant recombinant DNA inserted into the genome of an organism. With this said, there is one type of carcinogen that is used in the food growing industry that may be responsible for high rate cancer incidences, if indeed the cause is in the industry; chemicals like herbicides and pesticides are two examples used when growing GMO crops. It is known that some pesticides used are carcinogenic, as told in the literature “Pesticides and Cancer” by Ditch J. et al (http://www.ncbi.nlm.nih.gov/pubmed/9498903), and I wouldn’t doubt that there are herbicides involved in causing cancer too. It is truly a “Silent Spring” related issue. Now, the advances that Bonning BC et al made it possible to create areas of land where the crop has a higher fitness without the use of toxic chemicals to which the crop is resistant or immune. Theoretically, assuming no drawbacks are found and cancer instances are due to the carcinogens introduced into the environment from growing monocultures, if other studies like this are done and they are applied, the use for these chemicals will be eliminated; therefore, the theoretical drop of cancer instances. Overall, this is a excellent study, and I applaud the authors and investigators.

Now for the theory and questions:

During my studies at PSB, I was required to take a survey course on ecology. While taking this course, I realized the importance of ecology to, and the application the theories discussed, other biological disciplines, so I am taking a 400 level population biology course and reviewed the major theories from that class. During the period of time that I was reviewing this material, I made a connection between the material and TWIV, particular one of the episodes about sequencing bat viruses. In the class we discussed the theory of Island Biogeography and its 5 important postulates:

“1) The closer the island to another land mass, the higher the probability of colonization.
2) The older the island, the more likely it will be colonized.
3) The larger the island, the more species are likely to be established.
4) Geographic isolation reduces gene flow between populations.
5) Over time, colonial populations become genetically divergent from their parent population due to natural selection, mutation, and/or genetic drift.” (http://www.ucmp.berkeley.edu/fosrec/Filson.html)

Also, this theory is illustrated by the a graph relating the probability or rate of colonization is influenced by the relative distance from the mainland and probability and rate of extinction is influenced by the size of the island with the species richness of the population (Figure 1 attached). The illustration relates postulate 1 and 3 in respect to species richness.

Now, if we state that an “island” is an organism (e.g. a bat), then in theory the size of organism, or size of island, influences the species richness of the microbes housed inside of the organism according to postulate 3. This means that theoretically bigger organisms will then house a richer range and more of those microbes, like viruses, assuming contact between the “mainland” (the rest of the population) remains constant. In addition to the size of the organism, during an inf! ection viruses replicate in great numbers, and in theory this creates interspecific and intraspecific competition between viruses and different strains (e.g. Influenza strains) respectively; therefore, bigger organisms will house more viruses.

Since, all the background information is said, my questions are:

1) Has there been a study or studies to compare the quantity the richness of viruses, or microbes, in a particular organism to members of the same population, but with significant different sizes?
2) Has has there been a study to observe the interspecific and/or intraspecific competition between viruses?

The podcast that I was listening when I made this connection, I believe, was TWIV 258, but I am not 100% sure.

Thanks for taking your time to read, critique, and answer the questions in my emai! l, and sorry for the explanations, if they are not needed.

Happy TWIV(P or M)-ing,
Andrew

“We are healthy only to the extent that our ideas are humane.”
-Kurt Vonnegut, Breakfast of Champions

Curt writes:

Hello again, TWiV team!

In the face of the mounting problem of antimicrobial resistance, some quick research revealed phage therapy as a possible alternative to antimicrobial compounds. I’m certain you guys have to have heard of this, and some studies have shown promise against resistant infections (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC90351/). My question is: why don’t we seem to be putting more effort into developing bacteriophages as a viable, regular-use antimicrobial therapy?

PS: In taking your Coursera Virology I course, I noticed that you mentioned that viral glycoproteins are visible on the cell surface before the virion buds off (if that’s how the virus escapes the cell, as opposed to lysis). Wouldn’t that make a persistently infected cell vulnerable to an ‘antiviral’ lytic virus by engineering a virus that binds to the target virus’ entry proteins while the virion is still budding. The idea would be, for example, to use the influenza (not persistent, I know) HA to enter the persistently infected cell, replicate, and destroy the cell, thereby preventing further Influenza proliferation. Has anyone tried this before? I hope my explanation isn’t as convoluted as it feels.

Thanks for your time and hard work, guys and gals, it is appreciated.
-Curt

[see TWiM 53 and 6 for more on bacteriophage therapy]

James writes:

Dear TWIV team.

Thanks for a fantastic series of podcasts that keep my mental stimulation into science going while I work in a less stimulating environment!

In episode 272 one of your picks concerned the over reliance on statistical data. While I share some of the concerns- such as the difficultly that can be perceived in attempting to get published without a p-value (or three!), I do wonder if some of the concern addressed both in the article and in discussion is the age old horror of statistics. While myself I feel very confident with statistics (you might even use the word ‘like’) I found most of those around me when I was studying in the biological sciences and even those asked to teach at undergraduate level in some subjects- don’t enjoy the subject at all. Further more, inappropriate use of an inappropriate statistical tests can result in ‘desired results’. There are however very few situations where you can select the statistical analysis to apply. If you are doing it correctly there are usually only a few, or one test, that can be truly selected. This however (as is usually the case) is not often fully understood and leads to even elite publications selecting to publish articles applying the wrong statistical test.

I think the problem is going to remain. While I enjoyed and understood statistics naturally, I was taught well by lecturers who [begrudgingly] had to teach it- but did this well. Largely I suspect because they worked in areas where IT could not be used (too cold) and so to get results ‘on the fly’ they had to apply preliminary tests by hand, so having a full understanding of the subject beyond most of us. My cohort still hated the aspect of the course, and I helped many of them. My partner in another discipline during undergraduate studies however was less lucky and despite the unit of study being almost exact, the tuition was not as easy to follow. I had to decipher simple questions just so I could begin to help her (and others on her course). The problem being non-specialist teaching. Follow this with stories I have heard of statistics departments in universities instead of being co-operative charging departments four figure sums just to spend an hour to look-over already worked figures to ensure accuracy. How can we hope to resolve the chicken-egg situation.

The larger question of whether P-values and statistics should be important takes me back to when, as part of my dissertation research, I went to a collaborating vaccine-development lab at university for the western blotting stage. A member of staff there was talking about their career path. They started studies in ecology but hated the ‘wishy-washy’ results. Eventually moving to disease and virology because they can run tests and get ‘results’.

London is a very clear, bright and sunny today at acceptable 10oC, 49% humidity, and I can currently see right across the city. Much warmer than my ‘home’ where it is 6oC but feeling like -2oC (so the internet tells me).

Thanks

Marshall writes:

I don’t have a question at the moment, just a listener pick of the week. I don’t know if you’ve seen it yet, but I just came across this on imgur. The caption says it all:
http://imgur.com/gallery/S8QQRI4

Anyways, been listening since the very beginning. I really appreciate all that you good Drs are doing for us laypeople.

Keep up the good work!

Steve writes:

Here is a nice list of many of the flu vaccine myths all in one place for the This Week in Vaccinations segment of TWIV.

http://io9.com/lets-just-debunk-every-flu-vaccine-myth-in-one-fell-sw-1454237689

steve