TWiV 289 letters

Robin writes:

Yet another multiple sclerosis treatment:

A letter writer’s sister has multiple sclerosis.

Polyclonal vegetables should not be harmful, and might even be beneficial:

<a href=”http://m.youtube.com/watch?v=KLjgBLwH3Wc“>Minding Your Mitochondria: Dr. Terry Wahls at TEDxIowaCity</a>

Mortality in biology:

Remember, nucleotide based life is geared to promote and perpetuate nucleotides. The fitness or otherwise of the genotype is based on the interactions of its associated phenotype with the milieu, the phenotype in effect being the interface.

The cells (and virions), organisms, social groups, nations and empires are emergent phenomena associated with the phenotype. In spite of all their varied scales, they all feed back to the genotypes. Some of our DNA sequences go back as far as the Last Universal Common Ancestor. From the perspective of nucleotide chemistry, that’s where the action is. All the rest is supporting and ancillary stuff, some of which is quite important at our scale. Natural phenomena may have a long reach at scales that are barely comprehensible to us.

And for Dr. Dickson:

The Oldest Living Things in the World, photographer Rachel Sussman interviewed by Ira Flatow:

Science Friday

<a href=”http://www.wnyc.org/story/scifri-documenting-the-oldest-living-things-in-the-world/“>SciFri: Documenting the Oldest Living Things in the World</a>

Connor writes:

Dear Vincent, Rich, Alan, Kathy, Dickson & guests,

I just want to take this opportunity to thank you all for such a fun and informative blog and podcast. I too have experienced a ‘TWiV bump’ of sorts recently in that as of last week I have passed my Ph.D. viva and as of February I am a postdoc at the MRC Centre for Virus Research in Glasgow. While I cannot prove it, I am convinced that reading the blog, listening to the podcasts and being allowed to be a part of two TWiVs, shaped my personal and intellectual development as such to help me complete my Ph.D and pursue a research career in virology. As part of the first ‘generation TWiV’ I would like to thank you again and long may it continue to inspire the generations of scientists to come!

Kind regards,

Connor Bamford

Raihan writes:

Hey Twivvers,

This is a comic i found online, just wanted to share….

This is funny, you must check it out! :D

To vaccinate, or not to vaccinate. That is the incredibly stupid question.

http://9gag.com/gag/aM1WRQV?ref=9g.m

Regards

Jon writes:

I thought you might like this article on Slate:

A Brief, Terrifying History of Viruses Escaping From Labs

http://www.slate.com/articles/technology/future_tense/2014/04/how_dangerous_viruses_could_escape_from_laboratories.html

Robin writes:

How long can viruses survive?

Crystallised viruses placed in a vacuum and protected from electromagnetic radiation should last indefinitely. But even eukaryotic cells can be deep frozen.

However VIABILITY is related to the ecosystem in which the entity lives. A human cubicle serf from a metropolitan area taken in a time machine back to a time and place before the first Rhipidistia clambered ashore would be non-viable. The same would be true for most if not nearly all of today’s Tetrapoda.

Any biological entity in nature evolves pari passu with its ecosystem. Isolate it from its ecosystem, and the mutual influences on shaping evolution cease. Even if the isolate is allowed to reproduce, its evolution will be shaped by the altered influences. If not allowed, its functionality will be frozen in time.

A virus that is viable after prolonged isolation has dependencies for which the ecosystem has not changed sufficiently over that time. This could be related to the virus bringing along a lot of its own tools and equipment.

The Four Laws of Thermodynamics are about energy:

0th: Connected systems will come into equilibrium.

1st: It can’t be destroyed.

2nd: It turns to trash.

3rd: It can’t be cleaned up after it is trashed.

However, matter in the presence of energy gradients is disturbed by energy flows. Some of the resulting in random configurations may follow dynamic reconfigurations impelled by energy flows. The dynamic configurations that best enhance the dissipation of energy gradients are selected for, and even more so when those configurations can direct more matter into like configurations. Hence, chemical, biochemical and biological evolution.

http://www.intothecool.com

Feeding on viruses

Prokaryotic biomass (grams of carbon) = 5×10^17

Viral biomass = 5% of prokaryotic biomass = 1×10^15

The ecosystems must do something equivalent to eating to recycle that viral biomass.

Articles that are subject reviews usually have a very high information density.

It is said that if you copy from one source it is plagiarism, ten sources a topical discussion, a hundred sources a subject synopsis, and a thousand sources a comprehensive literature review.

“Proximal to the microphone”.

Proximal, like distal, implies directionality, “upstream” or “nearer to the center/source”. More like a vector than a scalar quantity. In this case it would refer to some point between the microphone itself and the sound system to which the microphone is connected. “More proximate to the microphone” would be “nearer to the microphone”.

Anne writes:

Dear TWiV Team:

Wondering if you saw the article in the NYTimes last week, “Watching Proteins Do the Jitterbug”.  The article included links to wonderful animations of cell contents and structure, and protein packing.

http://www.nytimes.com/2014/04/10/science/watch-proteins-do-the-jitterbug.html?ref=science&_r=0

(Here is the narrated version of “Inner Life of a Cell”:  <http://www.youtube.com/watch?v=FzcTgrxMzZk>).

This sent me down the rabbit hole of you tube videos on related topics, and I also found these videos.

I did a quick search on the TWiV site to see if these had been submitted before, but didn’t explicitly find these, so here you go (but feel free to omit if these are already listed).

Flu Attack!  How a Virus Invades Your Body

https://www.youtube.com/watch?v=Rpj0emEGShQ&app=desktop

Deadly Dengue Virus video

https://www.youtube.com/watch?v=z0SduiVTsi0

Regards,

Anne

CN writes:

Greetings Professors,

Multiple times has the discussion come on the topic of “what is not working in science.” The funding, the publishing and the way science is done. Often when I talk to my fellow researchers, I get mixed opinions. So I put up a online questionnaire to see what people have to tell. The sad part is the response has been very low. So I thought, If TWiV could give me some boost through announcement, that had be a great way of finding what others have to say.

The link to questionnaire is http://varuncnmicro.blogspot.in/2014/04/research-poll.html.

With some preliminary polling, I wrote what I could gather

http://varuncnmicro.blogspot.in/2014/04/bloggers-desk-whats-wrong-with-our.html

If I could get sufficient response from all around, I want to put the results out there in the web. And sorry for the self promotion.

Thank you for all the free, super quality education on the microscopic life. It just keeps getting better and better and better…

TWiX fan

Kevin writes:

Hello TWiVers,

I’d like to chime in on the discussion from the last e-mail episode (280) about the “what is life” arc. Rich’s pick of the week was an article saying that defining life is “futile and unnecessary,” and Vincent said he disagreed and that there actually was a clear definition of life and that it’s useful to have. I think both the article and Vincent are partially right.

The definition of life, like most of our definitions, is a model of reality; it doesn’t describe reality itself. All definitions break down at the edges – most textbook definitions of life would exclude viruses, but it’s absurd to put viruses in the “non-living” category. Alternative definitions like Rich’s from the same episode that “living things can convert energy into heat” would seem to include things like stars that we do not consider living. To take a less complicated example that illustrates the same point, try to come up with a clear definition of “chair.” What you’ll find is that most definitions are too specific and exclude things that are legitimately chairs, or too broad and include things like tables.

However, this is not to say that trying to come up with a definition and arguing about it is not a useful exercise. We use definitions because they help us bring order to our fundamentally chaotic experience. Without definitions, everything we encountered would be a completely unique instance and we’d never relate anything to anything else. However, like experimental models, the danger is when we forget that the model is a model, and believe that it describes reality more accurately than it does.

For the definition of “Life” perhaps, this is somewhat pedantic, but I see it happening in my own field of immunology all the time. Cells are defined by certain cell-surface proteins, and then someone finds a new subset that falls outside the definition (or falls inside only due to cell-surface expression), and conclusions are drawn and rigidly held due solely to the original definition, which was made up in the first place.

Cheers!

Kevin

emmunity.org

Michael writes:

Esteemed doctors,

I want to thank you for mentioning my microbiology history blog, Amboceptor, as a “Pick of the Week” a couple months ago. And also thank Alan Dove for being one of the blog’s first followers.

They say that if you want people to start reading your website, the best way is to have started writing it seven years ago.  Nonetheless, it seems like I have a new twitter follower every couple of days, and it’s gratifying to be able to converse with established members of the science writing community.

Although I’m trained as a virologist, it’s often hard to write about virology from a historical point of view, because our knowledge of the subject has developed  so recently that even a paper from the 1950s is hard to understand. So unfortunately, the majority of the posts on Amboceptor would appeal more to TWIM than to  TWIV. For example…

How long does typhoid last in ice cream?

The care and feeding of typhoid carriers

Taiwau bozu: The bald geisha plague of 1901

But this week’s post (Yellow fever stops at the Miami airport) was particularly inspired by things I heard on TWIV, in particular Dickson’s discussions of West Nile virus. Vincent may also be interested in a post from January, in which I try to comprehend some experiments on polio survival in the housefly stomach, from the University of Michigan in the 1940s.

Look at the polio fly

Thanks for all your podcasts, from a longtime listener.

John writes:

Hey Vinny and the Capsids,

I wanted to comment on the Mother Jones vaccination rate article from TWiV 278.

The map of state vaccination laws is at best misleading.

Compare Oregon and Massachusetts.  The map says both are “medium” difficulty, requiring a note from your doctor if you don’t want to

vaccinate your kids.

The doctor’s notes in these states are very different.

In Massachusetts the doctor must say that vaccination would endanger your child’s health.  The medical exemption must be renewed every

In Oregon the doctor must say that you heard about the benefits of vaccines and still chose not to vaccinate your child.  Before this year you didn’t need a doctor’s note or counseling.

Sounds like Oregon makes it easy to opt out.

Now let me put the opposite spin on it.

Alan’s statement that Massachusetts does not allow religious exemptions from vaccination (TWiV 268 at 1:34:00) is not correct.

State law allows parents to claim a religious exemption without a doctor’s advice.  (MGL 76-15, linked below.)

If he lived in Oregon he would have to listen to medical advice before claiming a religious exemption.  (SB 132, linked below.)

Now it sounds like Oregon makes it harder to opt out.

Here is the reason for the difference.

If a state allows a religious exemption, anybody can claim it.  The state is not allowed to judge the merits of a religious objection.

In Oregon many parents claimed religious objections that were really medical objections in disguise.  Vaccination rates fell low enough to cause a public health problem.  In response the state required parents to hear why their medical objections were unfounded.

In Massachusetts there is no public health problem.  Vaccination rates are high and state rules bar the few unvaccinated children from school during a disease outbreak.  (105 CMR 220, linked below.)

Only two states do not allow religious exemptions: Mississippi and West Virginia.  These are religious states, but no mainstream American religion opposes vaccination in general.

Complicating this discussion is the existence of multiple overlapping vaccination programs.  In Massachusetts town boards of health can order mandatory vaccination if they provide free vaccine.  There is no religious exemption in this law, only a medical exemption.  (MGL 111-181, 183.)

A more interesting story from Mother Jones is from 2013, explaining that the main reason for missed vaccination is much more mundane than religion or McCarthyism.  Even in America getting children, parents, doctors, vaccines, and money to the same place at the same time is a difficult logistical task.

References:

2013 Mother Jones story:

http://www.motherjones.com/environment/2013/05/vaccines-whooping-cough

Out of date CDC survey of state vaccination laws, including the fuzzy “religious” vs. “philosophical” distinction:

http://www2a.cdc.gov/nip/schoolsurv/schImmRqmt.asp

Massachusetts vaccination laws, including sections cited above:

http://www.lawlib.state.ma.us/subject/about/vaccination.html

Oregon school vaccination law, “SB 132″:

https://public.health.oregon.gov/preventionwellness/vaccinesimmunization/ruleslaws/Pages/index.aspx

Kristopher writes:

Hey Twiv team or Vincent whoever reads this… So I got into a debate with my teacher today who told me interferon has no side effects – obviously wrong. She also claims to use low dose oral interferon for influenza prophylaxis, and I can only find one study (paid for by the pharma company who sells the lozenges) that shows it isn’t all that great. do you know of any studies that really discredit this particular therapy? I really don’t see it working… Maybe you guys can give me insight on whether it would work or not.

Your faithful follower,

Kristopher

P.S. this was the article “Low-dose oral interferon alpha as prophylaxis against viral respiratory illness: a double-blind, parallel controlled trial during an influenza pandemic year”

Fernando writes:

Hi Vince and friends,

Your occasional comments about tighter research funding and decreasing support for fundamental science agree with my observations of my own field, computer science, as well as with my experience during my academic foray into computational biology before moving back to industry over six years ago.

I just came across a recent PNAS article http://www.pnas.org/content/early/2014/04/09/1404402111.full.pdf that I think describes the situation well and makes some interesting recommendations that match some of what you’ve said in the podcast. I feel you could have written this quote:

“Overvaluing translational research is detracting from an equivalent appreciation of fundamental research of broad applicability, without obvious connections to medicine. Many surprising discoveries, powerful research tools, and important medical benefits have arisen from efforts to decipher complex biological phenomena in model organisms. In a climate that discourages such work by emphasizing short-term goals, scientific progress will inevitably be slowed, and revolutionary findings will be deferred.”

Please consider this as a listener pick.

Lisa writes:

Long time listener, first time writer!

In episode 278, Andrew wrote in about island biogeography with ideas about how it could relate to viral ecology. I just love that people are thinking about these kinds of ideas. I’d like to take a moment to help flesh out some of the background of the ideas that you all were discussing. Andrew hypothesized that larger animals may host a greater number of viral species than smaller animals. Alan responded that there are a limited number of niches in an organism. Presumably there are similar numbers of tissue types in mammals ranging from mice to elephants, so despite the vast difference in biomass, the number of niches remains roughly constant. However, in organisms with vastly different physiology, the number of niches may vary greatly, such as a sponge versus a mouse. Alan’s response harkens back to Gause’s classic experiments with Paramecium in which he demonstrated that the number of species (or phenotypes with different resource use) that can coexist within an environment is limited to the number of resources, i.e. niches, available in that environment. If there is only one resource, then the fitter of the two species will competitively exclude the other. There are also examples of cross-feeding where two phenotypes can coexist on one resource: one phenotype uses the single provided resource, and the other uses the waste from the first phenotype.

This competitive exclusion principle holds true at equilibrium in a well-mixed environment; that is, when the environment is constant. In nature, Darwin’s finches appear to follow this rule, but by and large it is difficult to find other cases so tidy. The classic example of this is the paradox of the plankton: a variety of species of plankton can coexist within a community on a limited set of shared resources (nutrients from seawater + sunlight). Several explanations have been put forth to account for the coexistence among competitors in nature, such as niche partitioning, spatial heterogeneity and disturbance.

Bottom line: nature is complicated and does not necessarily follow the rules we observe in the controlled laboratory environments, but that does not mean that we cannot glean important knowledge from lab experiments, which allow us to isolate specific mechanisms and test them directly.

So back to Andrew’s question, yes, the number of viral species is limited to the number of niches in theory, but in practice I think that we cannot simply assume that just because mice and elephants have the same number of tissue niches that they also harbor the same diversity of viruses. Perhaps the larger size of an elephant will allow for greater spatial heterogeneity, for instance. The jury is still out. I’d be curious to see some cross-species comparisons of microbiome diversity in general (bacteria will also face limitation in the number of niches), but I’m not as familiar with that field.

Vincent also gave a great example of a retrovirus using  a surface protein to inhibit other viruses from attaching. This is a perfect case of interference competition where one species directly prevents its competitor from accessing a shared resource. Another form of competition that viruses could experience is exploitation competition, which occurs when a virus (or anything else for that matter) exhausts a shared resource before its competitor.

Vincent mentioned (somewhat dismissively!) that a few studies have been done in the lab. I’m working on one such study for my dissertation work. I’m currently a fifth year graduate student (almost done!) using an experimental evolution approach in bacteriophage to study competition as a key driver of diversification and specifically the evolution of novel resource use. When viruses evolve to utilize a novel resource, they are evolving to infect a new species. We found that novel host use is more likely to be selected for when there is competition for resources present (Bono et al. 2013). We’ve also been looking at how the strength of competition affects the ability of multiple phenotypes to coexist and how gene flow affects adaptation to a novel host. I suspect that by the time I defend I will have counted hundreds of thousands of plaques!

I have been looking forns could coexist. This presented a conundrum: why didn’t the new, fitter strain win out? They found that during coinfections, the old strain actually has higher fitness. Thi work on how my work relates to viruses in nature. I happened to hear a relevant talk at the Jacques Monod Conference series entitled from Emerging to Pandemic Viruses: the interplay of host ecology and viral evolution, which you advertised on this very podcast. (Great meeting by the way) Gael Thébaud presented work from his group (Péréfarres et al. 2014) that examined competition between two viruses in nature. They observed that when a second viral strain invaded an island, both the old and new strais allowed both the old and new strains to coexist. Pretty cool, huh?

Thank you for all your hard work on these podcasts. They have really helped expand my background and understanding in virology and microbiology and make the hours of pipetting go by. The weather here is a perfect 74 degrees F (23 degrees C) under blue skies but very high pollen here in beautiful Chapel Hill, NC.

Cheers,

Lisa

Citation for my work (a little shameless advertisement): Bono et al. 2013. Competition and the origins of novelty: experimental evolution of niche-width expansion in a virus. Biol. Lett. 23 vol. 9 no. 1 Open access!

Citation for Gael Thébaud’s work: Péréfarres, Thébaud et al. 2014. Frequency-dependent assistance as a way out of competitive exclusion between two strains of an emerging virus. Proc. R. Soc. B 22vol. 281 no. 1781

Curt writes:

Hello TWiV team!

I would like to begin with a thank you to Vincent, as the Virology II course comes to a close on Coursera. The experience was as entertaining as it was educational. I’m hopeful we’ll see even more microbiology on there soon.

I was recently pondering the inability to grow human norovirus in cell culture that you mentioned in the course, and, well, I hope this train of thought makes sense. Caliciviruses seem to be primarily at home in aquatic environments, but what keeps the virions from scattering hopelessly in environments such as the open ocean with whales? Worse yet, according to an article in Applied Environmental Microbiology (http://aem.asm.org/content/73/2/581.short ), murine norovirus is inactivated by room temperature water pressures of about 400 MPa (readily achieved at less than a meter in seawater) in roughly 5 minutes. What’s a virus to do?

I’m operating on the assumption that formed virions take a small portion of cytoplasm when they form. Consider that Noro and other Caliciviruses may benefit from producing virulence by replicating in cells with reduced electrolyte loads secondary to diarrheal disease. The lower tonicity plasma/cytoplasm in the virion may represent a lower density than the surrounding seawater, allowing the virion to stay near the surface, where it’s more apt to endure and get picked up by an unsuspecting mammal. To elaborate, pure water is about 1000 kg/m^3, sea water is 1025 kg/m^3 at the surface, and typical plasma is also 1025 kg/m^3 from what I’ve read. The more virulent strains would create more of an electrolyte imbalance. Presuming all electrolytes are shed with near equality, this leaves our virion with a more water-like, less-dense cytoplasm. Perhaps this also lends a structural stability to the virion, which may help explain why the virus fails in cell culture, which requires an isotonic setting for the cells to persist.

I hope that wasn’t too silly. Thanks for your time and effort in doing this show, guys and gal. Pondering the microcosms with you helps the late night driving. If appreciation could be cashed in, you would want for nothing.

Stephen writes:

Here’s an interesting story. Cast: a bearded dragon, a cricket colony, an iridovirus, an insect behavioral biologist and Donald B. Stoltz, who works on viruses and parasitoids

<http://www.cbc.ca/quirks/2014/04/26/2014-04-26-3/>

Nele writes:

Hi everybody,

You are listening to Nele from Hamburg, Germany and what, she thinks, was very interesting about Vincent´s interview.

I am a student of Infection Biology at the University of Luebeck in Germany and spent  4 month in Ann Arbor, Michigan to work there which was not that long ago… Maybe Kathy remembers me :)

I really enjoy listening to the podcast because, beside all the really important and interesting informations about virology – which I think is awesome! -, I also get to hear you guy talk about less important stuff like the weather and interact with each other… In my opinion, people who I met in the US have an especially friendly, funny, positive and open-minded way of talking to each other and I am missing that a little bit since I am back home.

Anyway…

What I actually want to do with this email, is comment on Vincent´s dreams/plans for the future…if you should ever go through with the vision of building a company that tries to interact with the society and communicate science, please let me know!

I am very interested in that and know from experience how important it is, because my mother always taught me how bad vaccination is, which of course is not true, but that was the way she thought without ever really explaining it to me. Unfortunately as a child you think everything is true that your parents tell you.

Now I am 27 years old and of course vaccinated, because I learned that parents are not always right, even so I love my mom :)

But Germany is, in general, a country where the rate of people who get vaccinated goes down, because the politics had some problems to communicate well with the public during the problems with the swine flu in 2009. At that time, there were different vaccines available for the public and for the people who worked for the government, and nobody understood why. Everybody thought that the government employees got the good and pure vaccines and the public got the cheap vaccines, which wasn´t true, but nobody explained that to the public. So now a lot of people in Germany mistrust vaccinations.

I think we should really learn from that and communicate better in the future!

And there is so much other science stuff out there that is fascinating and great and mind blowing, but people who don´t work in the field have trouble understanding it and what consequences it might have for them — because we use all these complicated terms and talk to each other in a language that is difficult to understand for poeple who have nothing to do with science. I think thats really sad.

So in 2018 or 2019, when I have my PhD in virology- which I am sure of :) – I would love to work for you, Vincent, if you are really going forward with your dream, which I think is awesome and a really good contribution to society! (evenso I know this email is a looonnngggg shot, because you might don´t realize your dream and even if, you probably won´t remember me… but that´s okay… I will keep track of your career and write you again, if it happens :) )

I also volunteer in a science association that tries to communicate science to the public, but as you know, you often only reach the people who are already interested in science anyway. It is still a lot of fun and I always get reminded how difficult it is to explain science simple because the systems always get more complex. But I like the challenge!

I hope to hear from Vincent some day :)

Have a nice day everyone!

Nele

James writes:

Dear TWiV team.

OK, I have written far too much recently (I type ‘TW’ and you pop up in my address field) but here goes, one last time for a while- I promise.

On TWiV 282 you mention the large intake of PhD students and job availability. Vincent in-particular spoke about ‘staff scientists’. I left the biological field after graduation to work in the most tenuous, farthest fringe of science. I have two key points in relation to the discussion one reflective of my experience, one of my current workplace:-

**NOTE: Some of this will be from a UK or European perspective, but I suspect not totally irrelevant.**

1. The number of post-doc positions not being sufficient is easily seen in my work. Until recently (last decade or so), those doing my job and directly under me would be high school leavers (UK). Now they are invariably those with Masters, PhD’s, even multiples thereof despite the low pay and zero progression in most cases (for those working on the scale below me almost invariably significantly less than £19k). What I have also experienced, upon setting short-listing tasks and questions for these is the quality. While this partly is a reflection of the salary, it isn’t in all cases a few are excellent. I have seen people who have gained scientific masters and PhD’s from numerous countries yet they have not attained the most basic of laboratory skills. Possessing biochemical science higher qualifications but are simply unable to calculate or make a simple solution- at all, never mind accurately do this in practice; with no more success focusing a simple slide on a light microscope. This brings me to wonder- just how did they attain their PhD position! (I know there is variability between institutions- but come-on! These are post doc’s and skills I gained across the scientific disciplines, before I even started my undergraduate biology degree)

2. The proposed ‘staff scientist’ position sounds like a perfect idea. Having always been commended for my ability, particularly in cross liking with other disciplines and with a meticulous, quick accurate ability to pick up practical science procedures to the highest of standards and in considering the data. The fact I have previously built high end scientific equipment additionally helps with my understanding on a technical level. But not being in a position to take the short contracts (I wouldn’t like eviction!) that would be my main pathway into science and less than enough experience for direct PhD entry and unable to afford gaining a masters first or do expensive volunteer work, alas it is my fate (i’m slowly learning to live with it although those in my work questioning why I am do ‘only this job’ doesn’t help).

The compromise of giving up a ‘potential track’ and career progression would be counter balanced by a secure income and more beneficial to working in a completely unchallenging environment for those in various similar situations. The staff scientist can also do something unique- concentrate on lab work. Not on the next grant, not on the next position, not the looming end of contract. So the researcher knows the day to day benchwork is going on safe and un-compromised. In addition to the continuity provided to researchers and the department, the finance invested by the university would not be ‘lost’- staff scientists would be less likely to take their knowledge elsewhere- they amass more instead, becoming a pool of information to draw upon. A early career scientist is encouraged to move to get the next position at the end of a contract (and all the work involved in doing so in the last few months), a staff scientist would have less impetus to.

Summary

I would concur on introducing staff scientists and/or reducing the PhD positions. But does this experience not question the methods by which those are selected in the first place? From your valuable perspectives, knowledge and hear-say has there become a initial layer of natural selection, rather than the best skilled for the positions?

A staff scientist would be a wealth of knowledge for a department, with no general factor to leave one institution to go to another in contrast to an early career scientists. That is of course in addition to the number of post-doc positions compared to those who completed a PhD. I wonder if valuable scientists are lost as a result in favour of those who can ‘ride the storm’? (I am working on being concise in the future)

Thanks for TWiX, as always.

Joseph writes:

Esteemed TWiV Panel,

I was pleased to hear you read a letter from my old labmate and good friend Nathan on TWiV 282.  I have very fond memories of Jacob Bronowski’s excellent show from my childhood, and was recently reminded of it by this interesting commentary in the New York Times:

http://opinionator.blogs.nytimes.com/2014/02/02/the-dangers-of-certainty/, which contains an embedded video of the last few minutes of the Bronowski series.

Intellectual modesty and self-criticism are indeed essential features of good science that can benefit wider fields of human endeavor.

Thanks again for the excellent work,

Joe

PS—it’s a lovely Sunday afternoon here in New York.  Who cares about the temperature? The dew point is a delightful 1* C (34*F).

Joseph

Jacob writes:

Hi all,

I just wanted to add my two cents to the “negative results” thing.

I’m currently listening to TWiV 279 (in which there were several listener emails about this) while doing DNA extractions using a procedure that I developed that would not have been possible without other people publishing things that didn’t work.

When publishing a method development paper, people include a lot of information about things that didn’t work, because they compare several different procedures for doing something and one (or more) of the options are more successful than the others. The results for all of the options are published alongside the ones that did work. Even in a “normal” paper, there are a lot of results for things that didn’t work if you read the methods and results. They just make the story of the actual results more interesting. I must admit at this point that I usually read the methods section of a paper first (after the abstract) to see if their methods and controls look legit before I read the rest. Sadly, some papers don’t make it through.

More broadly, if you use appropriate positive and negative controls (which you should be doing anyway) it should be possible to differentiate between the procedure failing and the result being negative. If you can’t do this, you probably need to re-design your experiment.

On the topic of having a database of things that didn’t work, this might be problematic, seeing as though we don’t even have a database of things that DID work at this stage.

On the discussion from a listener comment in this episode about successful vaccines preventing replication I think that, after listening to the Salk interview yesterday, there would be a good argument for saying that OPV is unsuccessful in that it cannot eradicate the disease, but it is successful in preventing poliovirus replication in the gut, where IPV is not.  The question is not if they are “successful” but it if they are “fit for purpose” for what they are needed for.

On the general bashing/support of peer review, peer review is not designed to ensure that your results are correct. It is meant to ensure that the conclusions you have come to are consistent with the data presented.

As an aside, does Vincent pay attention to things shared to him on social media for TWiV picks and comments? I shared something (with some exposition) on either Facebook or Google+ (I can’t remember which) a while back (quite a while back) but I haven’t heard of it on audio.

Currently in Sydney, Australia it is 18.6°C and cloudy.

Thanks,

Jacob

Duncan writes:

Hi guys,

I don’t know if this article by a mathematician in Cambridge (England) has crossed your path yet, but it is absolutely worth reading. The author does some outstanding investigative journalism into the pricing strategies that large publishers have been practicing. Perhaps if enough people read this work then it will help to break the cartel formed by major publishers at the moment, and push forward competitive pricing, rather than the shielded-by-confidentiality-clause type of unfair market that exists today (or, better yet, a move towards all journals being open access – the publishers add almost nothing in a post-web world, and yet wield so much power).

The article is here:

http://gowers.wordpress.com/2014/04/24/elsevier-journals-some-facts

p.s. Love the show, and keep up the good work,

-Dunk

Alice writes:

Dear TWIVvers,

I was quite interested in the e-mail from Randy, which you read on TWIV #280.  He became interested in virology after taking care of a stray dog who had canine distemper.

I fell into it the same way.  About four years ago, I stumbled on a Facebook group that was trying to find homes for dogs in the hell hole otherwise known as the Miami-Dade Animal Shelter.  There was a pitiful dog, covered with (healed) scars, who was a pit bull/ lab mix. They were going to kill him if nobody claimed him that day.  Something about him touched me, and I told the group I’d adopt him, but since I live in Laurel, MD (where it is partly cloudy and 63 degrees F), one of the group who lived in Fort Lauderdale offered to board the dog at her vet’s until I could pick him up.

I named him Jude.  Jude had apparently been a bait dog for dog fights (hence the scars).  I flew down to Florida to pick him up, but when I got there, I was told he was spiking fever and they determined it was distemper.

The vet explained to me what distemper was, that it was a virus and so there was no antibiotic for it, and that he could treat the symptoms until it “went neurologic”, but if that happened, he would recommend that Jude be euthanized.  I agreed to that.  Jude was there for a couple of weeks, and since he had barely escaped getting killed in the “shelter,” I was going to try to keep him alive to beat this, no expense spared.

We were all optimistic.  But it was all for naught.  One day I got the call that he was stumbling around like he was “drunk” and suffering seizures.  I tearfully told them to go ahead and let him pass.

I had already begun reading everything I could find about distemper and other viruses, and I now have a particular interest in the morbilliviruses.  I no longer snicker in *GONE WITH THE WIND* when they show that Captain Hamilton (spoiler alert!) died of “pneumonia following an attack of measles”, which I used to think was just some routine childhood disease that only goofy Charles Hamilton could die of.  I now know how extremely deadly that family of viruses can be.   PLEASE have Paul, the canine distemper guy on.  I think that would be a fabulous podcast, and maybe he can talk about the other viruses in the family.   I’m especially interested in the morbilliviruses that are killing dolphins and other cetaceans.

I’ve taken Vincent’s courses, bought The Book, I read The Blog, and listen to The Podcast.  Like Randy, I wish I had found these little buggers 40 years ago — I would have chucked law school.  I did manage to get a nursing degree recently; there’s that.

I do have a question out of all this.  Someone suggested that the distemper shot that Jude received when he left animal control might have made his illness worse, if he already had the disease.   I assume it’s a live virus vaccination, so might it have made things worse for him?   (This is a totally academic question; of course he would not have been released without getting the shot.)

Love the show,

~Alice

Steven writes:

Dear TWiV gunners:

First, the term “gunners” is a term often used in medical school to refer to an individual that makes a habit of going above and beyond. It is a part of their personality. It is a complement.

Second: I last wrote regarding the “Cyclospora epidemic” in Iowa and Nebraska (I’m from Iowa”. You’ll be happy to know we all survived and are waiting for the next “epidemic”.

The real subject of my e-mail is episode 282 and the discussion about Tamiflu and the subsequent discussion about research, funding, etc. I found much with which to agree in this discussion. A point I would make is that one does not get to translational research until one has done good basic/bench research and I agree that not everything needs to have clinical application. As a practicing physician who also has a strong interest in science beyond medicine I think we have not done as good a job educating the public, physicians and policy makers as well as university administration about how science functions. There unfortunately is the reality of commercial funding/influence in science which can be especially apparent in pharmaceutical research. I don’t have the answer…more public funding?? A coalition of universities?? An international approach?? Some other arrangement??

Thanks for a great podcast and keep up the good work!

Just posted but forgot two items:

1. Garrison Keillor was the Commencement Speaker at my graduation from Luther College. He is, as you will recall, the author and creator of “A Prairie Home Companion” with its chapter of “Lake Wo-Be-Gone”. Just a tidbit of trivia.

2. A pick of the day/week if you would consider: “How to Think Like Sherlock Holmes” by Mria Konnikova. This is required reading for every student who comes through my practice. and is a well written book geared to the motivated amateur and easily readable by the professional in any number of disciplines. The ideas broad applicability and I can say that I am a better physician since reading it.

Again, thanks for a great podcast!

Meika writes:

Hello professors!

This morning I was thinking that someone needed to tell Vincent that the state located between Washington and California is OreGUN, not OreGONE.  Rhymes with sun…. Oregon.  Just a helpful hint.

Once in a while a virus related article will come through my horse channels, and I wanted to pass it along to you.

Thanks for my weekly science dose… and now I have to run off and feed the horses. (really)

http://www.thehorse.com/articles/33847/bornavirus-antibodies-detected-in-horses-in-iceland

Johnye writes:

Another great website for introducing children to science.

http://richannel.org/

Johnye Ballenger, MD

Cambridge, MA

Ricardo writes:

Hello Vincent and all the TWIV members.

Listening as usual and getting richer and richer (intellectually) by the episode.

This time I’m writing to send a listener pick.

Gabriel G. Martins, the head of the Advanced Microscopy Unit at Instituto Gulbenkian de Ciência won the first prize on Nikon Small World in Motion Competition 2013 using a SPIM/DSLM/OPT microscope that he build for about $ 4200.

Then he published it in Nature Methods. “OpenSpinMicroscopy: an open-source integrated microscopy platform”

Also he and his colleges also created a DIY web page so everyone can build one.

https://sites.google.com/site/openspinmicroscopy/

http://www.nikonsmallworld.com/galleries/swim/2013-small-world-in-motion-competition

http://www.igc.gulbenkian.pt

My best regards and keep Twiving, You are doing it very well.

Ricardo Magalhaes, Ph.D.

Associate Professor of Microbiology

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

Faculty of Health Sciences of Fernando Pessoa University

Portugal

Chris writes:

Hello Professors,

For your consideration for a pick of the week.

Gut Check: The Microbiome Game

http://phylogenomics.wordpress.com/gut-check-the-microbiome-game/

Thanks,

Chris

Long time TWIV, TWIM, TWIP listener and Epidemiology PhD student