TWiV 280 letters

Paul Duprex writes:

As you may have heard, the Boston City Council is going to entertain an ordinance to ban BSL-4 research in the City of Boston. I can’t tell you how devastating such a ban would be, especially after going through the supplemental risk assessment process, having it blessed by 2 independent scientific groups (the NRC and the Blue Ribbon Panel), and having prevailed in Federal Court (and, we expect soon, the state court).

We need as many supporters as possible to come to the hearing, scheduled for April 16 @ 4:00 PM at the City Council. PLEASE MAKE EVERY EFFORT TO ATTEND. If you’d like to say a few words, please let me know.

Letter from ASM to members:

Dear ASM Member,

This email is to inform you of an event taking place in your region that could affect what microbiology research is allowed to be conducted in Boston.

In January 2014 a draft ordinance was introduced to the Boston City Council prohibiting activities involving biosafety level 4 (BSL-4) research within the city limits. The city council has scheduled its first public hearing on the proposed ordinance for Wednesday, April 16, 2014 at Boston City Hall. Members of the public are invited to attend and testify.

A copy of the proposed ordinance can be found online here and the notice of the public hearing is here. Any changes or updates can be found online on the Boston City Council Calendar of Meetings.

As background information you should be aware that In 2007, the ASM filed an Amicus brief with the Supreme Court of Massachusetts on a case involving a BSL-4 laboratory affirming the importance and safety of BSL-4 research laboratories. That same year, the Society also provided similar testimony before the U.S. House of Representatives.

We believe that scientists should be aware of events that can impact science in their region and have the opportunity to voice their opinions on actions that could affect them, directly or indirectly. We urge any members who are inclined to attend.

Sincerely,
Ronald Atlas, Chair
Public and Scientific Affairs Board (PSAB)
American Society for Microbiology

Saul Silverstein writes: [re paper on idiopathic pulmonary fibrosis associated with Herpesvirus saimiri]

He uses antibodies to human proteins to imply that HVS counterparts are expressed in these lesions, while conserved because of function this is not trustworthy. Similarly he makes quantitative measurements based on in situ hybridization intensities, not too hot. The only compelling data are those associated with PCR amplification and sequence analysis of the HVS DNA polymerase amplicon in Fig. 4, however, we are not shown these results.

Konrad writes:

Dear TWIV/TWIM-Team,

In TWIV episode #279 you discussed the publication of “negative results” (we really need a better term for this!) as well as the infrastructure that would be required and how to finance this. Don’t worry about that! This is more or less solved and can/should not only be applied to “negative results” but to all research data. For example figshare [1, 2] or Zenodo [3,4] are services that are designed to host scientific data and are basically free of charge (although figshare has some premium features like increased private storage and larger files sizes). At those platforms you even get a DOI for each item. You could even upload manuscripts that are not going to be submitted to a peer-reviewed journal to one of these platforms or send those manuscripts to preprint services like arXiv/bioRxiv. While you can host in principle anything on figshare or Zenodo, other publicly funded repositories are more appropriate for certain data types. For example short read sequencing data can be stored in the Sequence Read Archive (SRA) [5] or the European Nucleotide Archive (ENA) [6]. Those require beside the actual data also meta-data which improved the ability to search and find items.

I am aware that all these are just technical solutions. Besides those the different scientific communities have to develop a consensus where and how to host the data. This will be very important to increase the findability of such data.

Besides this comment, I would like to thank all of you for your educative and entertaining podcast series which I have followed since many years. Luckily/unfortunately I am commuting a lot and which gives me much time to listen to your and other podcasts. As a bioinformatician who is working in the field of infection biology and systems biology/medicine I highly appreciate the scientific input of your show.

Additionally, if you allow – I would like to place some self- advertisement by pointing you and the German speaking part of your audience to a related podcast. It is called Open Science Radio [7], was started by Matthias Fromm [8] and I joined it at the beginning of this year. We discuss biweekly – well we try to – different topics related to Open Science. The podcast is in German but we might have some interviews with English speaking scientist in the near future.

Keep on the great work – best wishes
Konrad

PS: The temperature in Würzburg, Germany, is currently 9.1°C (282.25 K), air pressure is at 1019 hPa, and it’s cloudy. The wind is
coming from north east and has a velocity of 3.6 km/h.

[1] http://figshare.com/
[2] http://figshare.com/features
[3] https://zenodo.org/
[4] https://zenodo.org/features
[5] http://www.ncbi.nlm.nih.gov/sra
[6] https://www.ebi.ac.uk/ena/
[7] http://www.openscienceradio.de/
[8] http://www.mfromm.de/


Dr. Konrad U. Förstner
Head of RNA-Seq Group
Core Unit Systems Medicine
University of Würzburg

Greg writes:

Hi!

Your special TWIV episode with Ian Lipkin and Thomas Briese on MERS coronavirus in dromedary camels reminded me of one of my favorite Frank Zappa songs, an instrumental at the end of the 1969 Hot Rats album called “It must be a camel.”[1]

Speaking of Frank Zappa, a press release went around recently about a microbe that has supposedly made the leap from a human opportunistic pathogen to an obligate endophyte [2]. Two of the authors were quoted as saying “this bacteria is so unconventional in its behavior, and its new habitat is so unexpected that we thought of Frank Zappa.” So my question for TWIM is: is their evidence for this amazing transformation convincing?

1. http://www.last.fm/music/Frank+Zappa/_/It+Must+Be+a+Camel

2. http://mbe.oxfordjournals.org/content/ear

Jon writes:

Dear TVIWmeisters,

On episode 274 you advocated safe-sex or no-sex in reference to avoiding HPV infection.

It is important to note that condoms, even if correctly used, do not eliminate the risk of HPV infection, since it is transmissible from vaginal fluids to parts of the skin not covered by condoms.

I would provide more definitive references, but they seem to mostly be stuck behind a paywall, the great knowledge-censoring condom of our time. (I am sure Alan will infer what human organ most resembles the for-profit journal system.)

Incidentally, HPV causes cancer in males as well as females, most notably head & neck cancer.

Oh, for more FU, a few episodes back there were some remarks made about injecting herpes virus into humans. This is exactly what Amgen has done with its T-vec oncolytic cancer virus, which appears to be well on its way to approval in melanoma, given its most recent interim phase 3 data release. It is important to note, however, that Amgen has made a genetic deletion which eliminates the neurotropism of their virus.

-Jon

PS. Dixon and the anti-abstinence crowd might find it amusing that my uncle, who practiced family medicine, once testified in front of the Texas state legislature that “just say no” had done about as much to prevent teenage pregnancy and illegal drug use as “have a nice day” did for depression.

Martin writes:

Dear TWIV

I am honored that you have chosen me to be the denialist kook to periodically beat up on!

Here is something a little bit more substantial for you to chew on (and spit out!)

The reason I need a response is that we HIV/AIDS dissidents, of which there are tens of thousands around the world and growing, are split down the middle. Half think Duesberg is right– the virus exists but is harmless. The other half, led by The Perth Group, think the virus does not even exist!

I don’t honestly know which is correct and I would like to get to the bottom of it.

The sticking point that I don’t understand is molecular cloning. I get that you can split the DNA chain into pieces,  get a phage or bacteria to multiply each piece so that it can be read, then piece it together like a puzzle. But the source of material that the clone comes from is not purified, containing all sorts of cellular debris, etc. It can yield hundreds of different clones.

How do you know which one is HIV?

Here is a clear explanation of the Perth position published in the British Medical Journal in 2003. Brian Foley is a research scientist at Los Alamos National Lab.

From: http://www.rethinking.org/bmj/response_34575.html

Francois writes:

Hello from France,

Small presentation : I’ve missed a scientist career 10 years ago to … find a job ! And find some use for my microbiology training & work on raw milk cheese “microbiota” ( … way cooler term than microflora by the way).

If you can find some in the US, try it when coming back from turista prone country … empirically it makes miracles. Of course in the US it may be classified as massive destruction weapon :).

If you’ve not already speak of it.

Here an article about “Effective Messages in Vaccine Promotion”
http://www.livescience.com/43794-vaccination-rates-messages.html

Pre article
http://pediatrics.aappublications.org/content/early/2014/02/25/peds.2013-2365.abstract?sid=4c82b05f-5ad9-4ab5-b91e-b187e90

To make it short :

Ask parents with reservations about vaccines if they will vaccinate their children against MMR … vaccination 70% chance.
Then explain them that the link between MMR vaccination & autism was bogus … and chance drops to 45% !!!!

With this kind of reaction in some of the most developed country … humanity will go DODO in no time. That an astonishing level of stupid !

François

Yong writes:

Dear editor

I’m a Chinese student majoring in veterinary. Last day I read a paper which talking about monoclonal antibodies. I found a question in the productive process of these MAbs.

The paper (Yixin Chen,et al. Broad Cross-Protection against H5N1 Avian Influenza Virus Infection by Means of Monoclonal Antibodies that Map to Conserved Viral Epitopes.2009) has described as followed:

Generation of H5 MAbs: Five representative H5N1 strains were chosen as immunogens from these major genetic clades/subclades on the basis of phylogenetic analysis. Preparation of anti-H5 MAbs followed standard hybridoma technology, as previously described [25]. Six-week-old female BALB/c mice were injected subcutaneously with 5 ×10 7TCID 50/mL of formalin-inactivated A/Ck/HK/YU22/2002 (clade 8) and then, at twice weekly intervals, with successive equivalent infective doses of inactivated A/Dk/VNM/S654/2005 (clade 1), A/Dk/IDN/MS/ 2004 (clade 2.1), A/BH Goose/QH/15C/2005 (clade 2.2), and, finally, A/Dk/VNM/568/2005 (clade 2.3) [26]. Fusion was performed 6 weeks after the final immunization.

Results:A panel of 52 broadly cross-reactive H5 specific MAbs were generated and characterized

My question is that why this measure can produce so many different kinds of antibodies? Do those viruses recombine and if so, why can they after been inactivated?

Thank you for your patience.

Yours Yong

Randy writes:

Hello TWIV hosts.

The current conditions in Phoenix… 16 Celsius, 33% humidity, winds SE at 4 mph, barometer 29.95 Hg mercury.

Last year my wife and I found a stray dog that appeared to be ill. We took him to the vet, who diagnosed him with canine distemper. Over the course of the next several days/weeks it progressed to the neurologic state. He had several seizures over a one week period. After the seizures ceased, he began making a very slow but progressive recovery. In the months since, his myoclonus and ataxia have improved from severe to slight. Aside from his inability to jump, there are almost no outward appearances of any physical deficiency. He eats, drinks, sleeps, and plays like any healthy dog.

Here’s where the story gets interesting. Nasal, ocular, blood, and fecal tests are negative but (bi-monthly) urine based RT-PCR tests have been positive for several months. The CT bounces between 34 and 35, but most recently has been in the 35′s. We’ve consulted numerous vets but can’t seem to get consensus on several issues. This led me into the world of virology. I must say, I’m fascinated beyond words. Had I known this world existed, I would have become a virologist instead of going into finance. I’m studying Virology 101 as well as Columbia University’s Virology W3310 on iTunesU.

Here are my unanswered questions… in no particular order.

1. What are the possible outcomes of an animal infected with this virus? Certainly death is one, viral clearance is another, what about carrier status (persistent infection)? Does a very low viral load imply carrier status, or simply shedding? I’m told dogs can shed for a year. Speaking of shedding, does the term mean infective virus, or harmless viral particles that have been dispatched by the immune system? We’ve been told the virus can ‘hide’ in the CNS (or other cells) and come back months or even years after tests show he’s negative. Is this true? If so, won’t antibodies make this a non-event, or will the virus have mutated to a point where the adaptive immune system will no longer recognize it… which we’re told is a possibility?

2. Since the virus is still active, albeit at a very low viral load, cell damage is still occurring. How does the rate of this cell damage compare to natural cell death? The reason I ask is because I’m concerned about long term damage and/or the body’s inability to cope with this rate of damage.

3. Interferons are truly amazing. Currently, he’s on alpha/beta. I’ve read great things about feline recombinant interferon Omega. My concern about human alpha/beta is the likelihood he has an immunity to interferon. The vet prescribed giving them 5 days a week versus 7 days a week to prevent immunity but this doesn’t sound correct to me. Does reduced frequency of exposure really prevent or minimize immunity? If he has developed an immunity, what alternatives to interferon exist? There appear to be quite a few “immune system boosters” on the market but many seem pseudo-scientific and some really look like snake-oil? What’s your opinion of anything which claims to “boost the immune system”?

4. Is every infected cell considered an inclusion body? I see references to “infected cells” and also “inclusion bodies” but don’t understand the difference, if any. If there is a difference, do cytotoxic t-cells target inclusion bodies?

5. Once cleared from the body, if indeed this is a possible outcome, is there cause for concern over future virus related complications? Wikipedia states “Life-threatening signs usually include those due to the degeneration of the nervous system. Dogs that have been infected with distemper tend to suffer a progressive deterioration of mental abilities and motor skills. With time, the dog can acquire more severe seizures, paralysis, reduction in sight and incoordination. These dogs are usually humanely euthanized, due to the immense pain and suffering they face”. This seems counter-intuitive. How can a virus that’s no longer present cause progressive deterioration and impede the body’s natural ability to heal itself?

Also, I love the casual conversation format of the podcast. If it were a lecture, it wouldn’t be nearly as enjoyable. May I suggest the addition of a story arc? Many TV shows have a story that spans several episodes or even a season or more. This is referred to as an ‘arc’. The arc is generally not the focus of any episode. In fact, sometimes only a very small amount of time per episode is used to advance the story. Isn’t the life cycle of a virus a story? In the case of a typical CDV infection the story begins with initial infection in the respiratory system, then viremia, then sometimes neuro, then death or clearance. I think it would be very interesting and informative to listeners to take a given virus and describe its life cycle, how it moves from one stage to another, and how much of an impact its ‘life’ may or may not have on the host. What I mean by ‘impact’ is how some infected dogs are asymptomatic/subclinical and others succumb to the virus in less than a week.

Thanks for a great podcast.

Stephen writes:

Funny coincidence in that I was listening to twiv 274 on my work commute today and later in the day I ran across this related slashdot post.

http://science.slashdot.org/story/14/03/04/1920211/pro-vaccination-efforts-may-be-scaring-wary-parents-from-shots

Stephen writes:

I wouldn’t be so crass as to mention a few writing errors, such as “an infected amoebae.” Or “giant viruses, which typically infect amoebae,” instead of “are cultured in amoebae.”

I did like “Chantal Abergel and Jean-Michel Claverie, a wife-and-husband team”!

<http://www.nytimes.com/2014/03/04/science/out-of-siberian-ice-a-virus-revived.html?ref=science&_r=0>

Marc writes:

Hello Team TWiV,

Its Mark F. in San Jose, CA again. We’re in the midst of a pacific storm bringing needed rain. Weekly listening to TWiV has made me aware of how large weather fronts occasionally cross the continent, changing character as they move. Last week CA’s rain became your snow.

I am transplanted from the East Coast. I was an undergrad at MIT and believe my tenure overlapped with Vincent’s when he post-doced, to create a verb, in David Baltimore’s Lab. Question to Vincent: were you in Cambridge for the blizzard in January 1979 when the Charles River froze? I walked across the Charles River from Cambridge to Boston, near the Harvard Bridge, a few times.

On to serious stuff…

In an economics blog I read, the author quoted an LA Times story of Claverie’s recent discovery, reported in PNAS this week, of another giant virus discovery. The article, in my opinion, is alarmist, and seems to me written as link bait. Here is the URL: http://www.latimes.com/science/sciencenow/la-sci-sn-giant-virus-revived-20140302,0,4662287.story#axzz2uwHSgh00

I have two requests of the TWiV-ome:

1. discuss Claverie’s new paper, “Thirty-thousand-year-old distant relative of giant icosahedral DNA viruses with a pandoravirus morphology” that is hidden behind a paywall, at http://www.pnas.org/content/early/2014/02/26/1320670111

2. post the LA Times article as a Listener Pick of the Week, BUT with a twist. TWiV listeners should read and dissect it paragraph by paragraph noting the subtle intermixing of relevant and irrelevant facts to stir things up. One example: describing HIV’s physical size and implying that Claverie’s new discovery could be more lethal to humans because it is physically larger. He makes a parallel argument in terms of the number of base pairs in each virus. There are many other constructions to discover.

All the best.

Jennie writes:

Greetings to everyone at TWiV,

On Episode 274, you asked if there were any listeners left from the XMRV days. Hi! I discovered the show during the early days of XMRV, back to Episode 76, and I have been a weekly listener ever since. I guess I’m just n=1, but I continue to enjoy the podcast every week, and you have helped me become a better science consumer.

Please bring on Dr. Silverman to talk about his paper tracking down how the XMRV finding went wrong. He showed great integrity in conducting such a thorough check of his own work, and I am very glad it was published because it’s important to have a full and accurate record of what happened. It is all too easy for the story to be revised in the telling. I’ve written about one example of this from 2013: here and here.

While the role of XMRV in ME/CFS has been settled, the ramifications and impacts of the issue continue. The story is still being written, both in a forthcoming book from Dr. Mikovits and in the political controversies of research funding and creation of a new case definition. The ME/CFS landscape is still experiencing the aftershocks of the XMRV controversy.

Thanks for all you do with the show, including presenting science in a way that this former lawyer can understand!

Cheers,
Jennie

Keith writes:

Dear TWIVologicians,

In the discussion on TWIV #274, the question arose of how long RNA might be capable of surviving in aged samples.

You may find of interest the link below for a study suggesting the recovery of 750 year old RNAs. The described RT-PCR products were 123-137 nt in length. The bulk of the biochemical work consisted of an analyses of sRNA with an average length of 20 nt. The conclusion of the authors was “This evidence leads us to conclude that we have detected a genuine instance of BSMV from a ,750-year-old archaeological sample of barley, which is the oldest authenticated instance of an ancient virus, and the first archaeological virus genome that has been sequenced.”.

A complete ancient RNA genome: identification, reconstruction and evolutionary history of archaeological Barley Stripe Mosaic Virus

http://www.nature.com/srep/2014/140206/srep04003/full/srep04003.html

———————————————————-
Keith L. Perry, Associate Professor
Department of Plant Pathology and Plant-Microbe Biology
Cornell University

Ericka writes:

Hello Twiv team!

I just stumbled upon twiv this past week and I have fallen in love with the podcasts! I have been listening to them while I do bench work in my labs.

I am currently an undergraduate in Microbiology at the University of Florida, but my heart lies in virology. My main reason for emailing was to thank you all for such informative and entertaining podcasts. I have learned so much through twiv and twim this past week!

Rich, in twiv 265 you mentioned my PI, Dr. Stephanie Karst and her work! I thought it was so awesome to hear such great praise about my PI in the podcast! We just recently put out a publication (my first!) and I wanted to share it. http://mbio.asm.org/content/5/2/e01032-13

The weather here in Gainesville is beautiful, 69°F, sunny, with 54% humidity.

Have a great week!

Neil writes:

Hi Twiv team
Saw this article today and couldn’t resist sending it on. You needn’t read this on the show if it feels too much like the proverbial dead horse.

Neil

http://www.businessweek.com/articles/2014-03-10/vaccines-are-safe-for-infants-but-dont-tell-their-parents

———————————————————–

Neil Parkin, Ph.D.
Data First Consulting, Inc

Cheryl writes:

Hello to all!
I enjoy all the “twi” (twiv, twim and twip.) I am a high school social studies teacher and science enthusiast and felt compelled to enter the fray over what constitutes outreach to those who are not members of the “science ghetto.” – By the way, glorious imagery, though I hope the modern connotation of ghetto (a run down, crime ridden and hopeless place) is not implied!- Hopefully, I do not further muddy the waters….

I have found it my experience that all outreach, all attempts at education have benefit. From sharing a children’s book on the wonders of the world with small children (my family & friends know that if I watch a child, a science book or even worse an experiment will be on the schedule) to discussing the impact scientific knowledge had to our ancestors, to showing science shows in school, to sharing my love of science with students, to discussing the importance of science with parents during parent teacher conferences (& convincing the religious that a science education is not blasphemous) all makes an impact. [It's a run on sentence I know, my English colleagues are having the vapors!]

While I bemoan as loud (if not louder, I’m not known for being reticent) the woeful state of understanding of basic scientific principles and theories (evolution- this could be an entire email diatribe, you really don’t want me to get started on that!) I’ve found that slogging through the bog of ignorance IS possible. No single method of outreach is going to completely erase the problem, but if every scientist, and every enthusiast take every opportunity – how about grad students at malls and state fairs explaining and showing the difference between viruses and bacteria, or antibiotic resistance, etc…- we can, over time positively and significantly impact science ignorance and illiteracy. As to those who willingly stay ignorant for religious reasons, well, you don’t want to get me started on that diatribe either!

Thank You all for the yeoman’s work you do on these podcasts. You are making a difference!

Cheryl

Bill writes:

See if Dickson et al like this:

https://www.youtube.com/watch?v=8YEdHjGMeho

Mauricio writes:

Dear all,

I’m catching up with past TWIV episodes and decided to stop in the middle of 271 and write this e-mail. I read the mBio paper on the jump of a plant virus to a honeybee and given that my Ph.D. work focused in another plant virus I was not surprised this could happen. I have to admit that because of my background I was inclined to believe the collection of facts reported in this paper and it wasn’t until I listened to your podcast that I realized that they had no negative controls. I think the whole story might fall apart once that negative controls are done. I guess that I assumed that although not mentioned they carried out negative controls so I accepted the validity of their experiments, however after your discussion it seems like indeed they did not have negative controls. I have lately been doing RT-qPCR and the first set of experiments I did was to do RT-qPCR to my blanks, cell and supernatants that did not contain my sample and I was surprised by the amount of signal I was getting from negative control cell samples. It took me a lot of work to optimize a more stringent PCR protocol to be able to separate the background signal from the real one and I have to say that I’m a little bit insulted by this paper. Doing negative controls is crucial to validate your point so I think that someone at the editor board of mBio is ought to take a look at the comments from the reviewers because I can’t believe no one asked about negative controls. Perhaps that is the reason why this article was not published in Science, Nature or PNAS.

It is well known that Nodaviruses like FHV or NoV can replicate in plant, insect and animal cells, however I don’t think they actually cause a disease in all three of them, so how can they be sure that TRV is actually replicating and causing a disease? One last thing… purifying plant viruses from plants is extremely simple compared to mammalian viruses so I was surprised they did not look for TRV in plants.

Anyway, the bottom line is that when I read this paper I assumed that they did a lot of controls which were not mentioned and that has made me think that I need to re-evaluate how I read scientific articles.

Cheers.

Mauricio

Mauricio Comas-García, Ph.D.
————————————————————-
————————————————————-
HIV Drug Resistance Program
National Cancer Institute

Craig writes:

Dear twiv team,

In your twiv 274 you read an email regarding my recent paper demonstrating that commonly used disinfectants do not kill HPV. You discussed how someone may potentially be infected from a fomite. While we feel that the common person probably does not have anything to worry about, however there are certain situations where there is concern. Many OB/GYN labs use reusable devices for examinations. These devices cannot be autoclaved and are treated usually with a glutaraldehyde based disinfectant. Our study showed that even after a 48 hour exposure, much longer than recommended for OB/GYN equipment, did not inactivate the virus. Additionally, about 20% of individuals with anogenital HPV infections at any one time have HPV on their fingertips and the active ingredient in the sanitizer does nothing to the virus. While the study does not in anyway suggest an ubiquitous risk of fomite transmitted HPV infection, it does suggest the possibility under certain circumstances that it could be possible.

Your show is great! Keep up the great work.

Craig

Craig Meyers, Ph.D.
Distinguished Professor
Department of Microbiology and Immunology H107
The Penn State College of Medicine

Joseph writes:

Vincent, et al.

Many podcasts ago you were gracious enough to read my poorly structured question about why life would form in such glorious complexity given the drive for disorder in the universe described in the SECOND law of thermodynamics. At the time you all were unable to shed much light on my conundrum, however you did ultimately provide a great answer through one of your weekly picks on TWIV, the magazine Quanta which you recommended. As a dutiful listener I went to the site to check it out and was amazed that the first article I found addressed exactly the issue in question. A great article that provides a real insight into why life is so prolific.

Life does not violate the second law of thermodynamics, but until recently, physicists were unable to use thermodynamics to explain why it should arise in the first place. …

From the standpoint of physics, there is one essential difference between living things and inanimate clumps of carbon atoms: The former tend to be much better at capturing energy from their environment and dissipating that energy as heat. Jeremy England, a 31-year-old assistant professor at the Massachusetts Institute of Technology, has derived a mathematical formula that he believes explains this capacity. The formula, based on established physics, indicates that when a group of atoms is driven by an external source of energy (like the sun or chemical fuel) and surrounded by a heat bath (like the ocean or atmosphere), it will often gradually restructure itself in order to dissipate increasingly more energy. This could mean that under certain conditions, matter inexorably acquires the key physical attribute associated with life.

https://www.simonsfoundation.org/quanta/20140122-a-new-physics-theory-of-life/

Great science is when someone can state the question in a way that leads in a solvable direction. I should have been asking under what conditions is life thermodynamically favored over nonliving systems. The answer then becomes when there is a good source of energy as food and good waste heat dump. This allows the high efficiency of organized living process to out compete other systems. Seems like a nice way to describe the driving force behind evolution. As always love the shows.

“Good-bye and thanks for all the fish.”

Joe
EH&S Manager, LSG

Lance writes:

Hi TWiV team,

I really enjoyed Vincent and Rich’s episode this week with Eugene Koonin. I did find Eugene Koonin a little difficult to understand, and I had to keep skipping back, but it was still an excellent episode. I have a question. You mentioned there are an estimated one million gene families. Does this refer only to viral gene families, or is it the number of gene families in all organisms?

Can I offer you a listener pick of the week? It is Myles Power’s you tube channel, here’s the link:
http://www.youtube.com/user/powerm1985

And Facebook:
https://www.facebook.com/powerm1985

Recently Myles (not his real name I don’t think) has made a series of videos debunking the 2009 HIV/AIDS denialist film “House of Numbers.” In return for his efforts he has had several notices under the digital millennium copyright act (DMCA) claiming he is infringing copyright by showing segments of “House of Numbers” for the purpose of criticism. In other words, the HIV denialist argument is so poor they have resorted to trying to silence a vocal critic by getting his YouTube channel shut down. Fortunately they failed. Those responsible for the DMCA notices are Journalist Liam Scheff and businessman Martin Penny (who runs a business that supplies the British National Health Service, worryingly). I know your policy has been not to discuss this issue on TWiV because the science is so resoundingly settled, and I agree with that. But I did not realise quite how harmful the HIV denial movement was until I came across this article recently from JAIDS in 2008 (http://www.ncbi.nlm.nih.gov/pubmed/19186354) which estimates that 330 000 people died because of delayed antiretroviral roll out due to the HIV denialist movement in South Africa. That said, this movement is not susceptible to reason. Look at the recent email from your listener Martin. I believe I am right in saying he has been listening a long time, owns a copy of your book, and emails regularly over this issue. Clearly his view has not changed from several years of exposure to good, broad science (and exceedingly well explained if I may say so) on TWiV.

But Myles has been given a hard time and some support from TWiV listeners I am sure would be appreciated, although I am a little late on the uptake with this. This story has been followed by Ben Goldacre and Abbie Smith (ERV) amongst others. He also has lots of great videos on science!

[Please feel free to redact the above if you don't want to get into the debate. All of the above is publicly available on the internet, mostly on Myles' YouTube channel, Facebook page and blog.]

The weather in Bangalore is unseasonably, and pleasantly, cool at 27C. We have even had a little bit of rain recently!

Maria writes:

I enjoyed this episode on twiv. It was a really fascinating discussion and i hope you will expand the evolutive implications of viruses.
I understand that it’s time to replace the introductory phrase on twiv. What about:”… the kind that shaped and still are shaping (your) life”?

I really appreciate your contagious passion in virology.

Best regards from a virocentric listener.

Maria

Jing writes:

Dear Twiv hosts,
In the episode twiv275, Dr. Koonin mentioned that viruses are the most abundant biological entities on the planet earth. As I was reaching the end of an hour long jogging, instantly I wondered if there’s any life form that can feed on these tiny particles. After all a virus is a little ball of tasty proteins and nucleotides, some of the enveloped ones even brings along fat. Let me know what you think,
Jing

Cynthia writes:

http://www.notonlyquilts.com/2012/06/periodic-table-quilt.html

I wish I could craft like this, but it is not one of my talents.

Cindy Fuller, Ph.D.

Assistant Professor
Biology Department
Henderson State University
Arkadelphia, AR 71999

Greg writes:

The recent special episode on MERS coronavirus in camels was excellent, just like all episodes of TWIV. Keep up the good work.

I want to respond to a point that Dr. Lipkin made regarding King Saud University’s intellectual property rights in MERS coronavirus. I agree with Dr. Lipkin that it is important that the University make its virus isolates freely available to researchers for study, but I cannot agree with his statement that “it doesn’t make any sense to try to maintain it as intellectual property, because it doesn’t have much value in that respect.” Elsewhere in the podcast, Dr. Lipkin expresses his hope that someone will develop a camel vaccine against this virus to prevent the sorts of outbreaks in camels that lead to human infections.

It takes a lot of upfront capital investment to develop a vaccine and obtain regulatory clearance to mass manufacture it and bring it to market. Without intellectual property protections, no entity with the infrastructure to bring a vaccine to market will find it worthwhile to make the necessary investments. There is a balance to be struck between freedom of scientists to study these isolates and King Saud University’s IP rights, but Dr. Lipkin goes too far when says that these IP rights “[don't] have much value.”

Best regards,
Greg in St. Louis

Claire writes:

Hi Vincent and pals,
First, thanks for all your work, I am always impressed with your dedication and the effort you put into TWIV/TWIM/TWIP.
I recently moved from an tech position in a freshwater and marine ecology lab to another tech job in a human immunology lab. The contract basis of the work in the previous job made it so there was not much time (or encouragement) to read literature and the lab didn’t have a journal club. (We mostly did microscopy, I bet I’ve seen more Chironomids than Dickson!)

I’ve done some reading related to the projects I’m working on in the new lab but it is sometimes difficult to get through papers where it seems like every other word is unfamiliar, even if the topic is interesting. (Although I have to admit there are times when I don’t even understand it enough to know if I AM interested!)

Does the TWIV team have any “How to Read a Paper” tips? Where do you begin when you are just getting started with a topic? Should I stick with reviews? Turn back to my text books from college for more brushing up on acronyms?

Also, any ideas for how my microscopy/insect/other invert ID skills might transfer to my new position or a future career?

Thanks!

Claire in Seattle where, regardless of time or season, it is probably 10 degrees C and overcast.

Mark writes:

Dear Twiv team,

I thought you might like to see this cross stitch art work of a variety of pathogens, to add to the growing number of picks on the art of microbes.

https://www.etsy.com/uk/shop/aliciawatkins?section_id=11480156&page=1

I didn’t see a polio virus for Vincent, but you could order one from the artist.

I’m not sure of the accuracy of some of them (the bird flu one looks strange to me).

Whilst writing this, I also found this site too.

http://www.giantmicrobes.com/us/

Still no polio though.

Mark Page

Principal Scientist
Division of Virology
National Institute of Biological Standards & Control
UK

Agnes writes:

Good afternoon,

I am a biology student in Germany and we just finished a molecular genetics course with introduction to virology. As I find virology very interesting I am also currently following your virology 2014 course on youtube. However, I have a question that so far I cannot find an answer to.

I read in one of the textbooks that when particular phage enters bacteria and integrates into its genome in lysogenic cycle, no other phages are able to infect that bacteria. My question is, why? Do they modify receptors of bacteria? I know that in human case this does not happen (influenza virus case for example and antigenic shift). So why does it happen in bacteria?

Thank you for your time!
Agnes
Germany

Ricardo writes:

Hello Twivome (I like this one) have you seen this?

Ricardo Magalhães

http://nextbigfuture.com/2014/03/virus-decoys-nano-scale-virus-traps.html

Neal writes:

Dear Vincent and TWiV colleagues,

I enjoy the podcasts when I get a chance to listen. They are both informative and entertaining. Nevertheless, I do want to comment on a non-virological statement made in a podcast from last month.

In TWiV episode 266, you commented (at about 25-26 min.) that the testing for breast and ovarian cancer-related genes BRCA 1 and 2 by 23andMe was a positive aspect (“actionable”) of their direct-to-consumer business. I am not a supporter of 23andMe, their business model, their testing methods, and their largely irresponsible approach to providing information of potential medical relevance.
Specifically with respect to testing for BRCA 1 and 2, some months ago I came across a summary (see link below) of a consumer genetics conference in which Ellen Matloff, Director of the Cancer Genetics Counseling Center of the Yale Cancer Center, expressed her view that the 23andMe reports on BRCA testing were “criminal.” The relevant paragraph is quoted verbatim below:

“In a session on the pros and cons of consumer testing, Ellen Matloff, Director of the Cancer Genetic Counseling Center at Yale Cancer Center, presented a GAO report from 2006 highlighting issues with direct to consumer tests. Matloff called some practices “criminal” (specifically the 23andMe recommendations included in the report for patients with positive BRCA findings), and questioned the practice of ever providing genetics results without counseling.”
http://www.bio-itworld.com/2013/9/30/a-field-maturing-2013-consumer-genetics-conference.html

I wrote to Ellen to learn a bit more about the sources of her dissatisfaction. In her e-mail reply to me, she noted that the 23andMe BRCA-related analyses and reports had multiple problems, including: 1) using panels of SNPs for which there is no consensus (presumably with respect to interpretive significance), 2) advertising to and testing for children with respect to adult-onset diseases (which is contrary to the consensus in the field), 3) providing 23andMe customers testing positive for cancer-associated BRCA alleles with the American Cancer Society guidelines addressing breast surveillance for the average American woman, and 4) in a couple of cases from the Yale Cancer Genetics Counseling Center, patients testing positive (according to 23andMe) for cancer-related BRCA alleles received reports assigning them ‘average’ or ‘low risk’ for breast and/or ovarian cancer.

Below are two additional links that address some of the complexities associated with BRCA testing. Although 23andMe may be temporarily prevented from disseminating test information that could be interpreted as medically-relevant, these articles provide more reasons why such direct-to-consumer testing is potentially problematic for disease-associated alleles at loci such as BRCA 1 and 2 in the absence of expert genetic counseling services (at least for some consumers).
—-
http://www.kevinmd.com/blog/2013/12/problems-brca-test-23andme.html
http://www.kevinmd.com/blog/2013/06/tested-brca-mutation-4-booby-traps-watch.html
—-
Best regards,

Neil Greenspan

———-
Neil Greenspan, M.D., Ph.D.
Professor of Pathology
Director, Histocompatibility
and Immunogenetics Laboratory
University Hospitals Case Medical Center
Case Western Reserve University

Aine writes:

Dear Twiv team,

Thank you all so very much for such wonderful podcasts. You have no idea how happy you have made me since I discovered Twiv. I am a research scientist in Queen Mary Medical School London and I’ve researched HIV for many years. I’ve always been embarrassed about how little I know of other viruses. Your podcasts are fantastic! I mostly listen to them when I’m out jogging. They are very inspirational and keep up to date. They’ve even helped inspired me to start a new research direction. Because running is the only real time I have totally to myself its a perfect time to listen to you – lots and lots of fun. Even more keeps me motivated while running.

The main reason I’m getting in touch with you now is that next week (26th March) I’ll be giving a seminar on viruses in my local school The Archery Academy to children 11-12 years old. They have regular seminars after school called Bright Ideas. Do you have ideas of anything particularly exciting I could present to them? I’m going to talk about HIV, swine flu, SARs, chicken pox, small pox, viruses that cause common colds, transmission and vaccines.

I’ll also announce a competition for the best Minecraft virus produced by the children (end date 26th April). I don’t really know what the uptake will be but I think there is unlikely to be more than 20 entries. I will be directing them to Twiv 101 for some ideas. Would the Twiv team be willing to judge this competition? If this is too much..no worries I can find another solution.

Keep up the fantastic work!
Áine

Raihan writes:

This is toooo awesome. Cheap, DIY microscope made from paper (primarily), which users can assemble themselves. It can be used for diagnostics, especially to be sent to places where it’ll be difficult to send large bulky microscopes to.

Judging from the diseases listed, I would guess that this should be more applicable for TWiP than TWiV but like what you always remind Prof Despommier, ‘We don’t do picks on TWiP’

Enough of me talking, I’ll let the video speak for itself.

http://youtu.be/h8cF5QPPmWU

Love the show. Greetings form Singapore

Jerald writes:

Hi TWIV,

I am compelled to send thanks to you all and to offer up a website chock full o’ information.

I am a Virology 2 Coursera student. I have enjoyed the course immensely. I recently discovered a link from TWIV that is something I have been looking for for a long time. I never would have found it unless I became connected to your course and of course, TWIV itself!

The link I recommend is : http://www.davincipress.com/professional.html.

On this website is a free biochemistry textbook that is in PDF form and which contains links to all course lecutres as Youtube videos delivered by professor Kevin Ahern at Oregon State University, where, of course Linus Pauling supplanted himself as a two time Nobel Prize winner so many years ago.

Thank you all again. Keep up the great podcasts.

Neil writes:

SO many places this could go… “viral video”, for example.

Heard about this while listening to my OTHER favorite podcast, Wait Wait Don’t Tell me, after a short bit about the 30,000 year old virus that was “revived” (ha ha)

Full circle.

Enjoy:

http://www.youtube.com/watch?v=kYf_Sl8W3qY

———————————————————–

Neil Parkin, Ph.D.
Data First Consulting, Inc