TWiV 209 letters

TWiV 209

Raul Andino writes:

I was driving from Palo Alto to UCSF and listen to my favorite show (TWiV… well …. after the soccer south american show which is my real favorite…) and I heard the discussion on changing the scientific system…making some experiment to try to save science in this country. So, I want to say that you could count on me for this. I think that it is incredibly important. Probably, we can recruit additional people here at UCSF whom are also very concerned about it.

Let me know how can we help. Perhaps it would be a good idea to start a email discussion … follow by an informal meeting. Collecting ideas from people to enhance the proposal… I am naive on this (which is good and bad) and I imagine there are many very strong forces that may not want to see big changes on the system, but a small scale experiment may work (I like the idea of “retrospective” funding)

Vince: very nice programs! Thanks! I even listen when I on my bike riding the Santa Cruz mountains (nerd??)

Robin writes:

Overlooking the gun

Jon Yewdell needs to be informed that the government has nothing of its own. Everything it has has been taken from others under the threat of coercive violence to enforce compliance. Any time one talks about the government, one MUST keep one’s focus on the gun of enforcement.

Chris Suspect writes:
I am really enjoying the discussion with Jon Yewdell. At points he reminds of a right-wing political talk show host, not in the content or message obviously, but more in his verbal delivery. He’d make a great host for a show dedicated to science policy.

Jon writes:

Attached is the transcript for TwiV 131.

I did not include the concluding section where you answer emails on the air, but I finished the entire interview. (I won’t have time to add in the emails.)

Thanks for all the wonderful podcasts, I listen to TwiV and TwiP and sometimes Twim.

-Jon
(A postdoc in mathematical physics)

PS. I have followed Oncolytics Biotech very closely since I listened to Twiv 131 about a year ago, and it only looks more promising today.

Since that episode appeared the National Cancer Institute of Canada has announced funding for 4 roughly 100-patient randomized trials of Reolysin in 4 different types of cancer. The NCI in the USA is also funding two similarly-sized randomized trials.

The phase-3 interim data was expected out around early August 2012, but the trial design was changed. This change, which was announced in September, was made because the subset of patients with distal metastatic tumors but without local tumors were doing much better than the complement subset and also much better than expected given similar patient groups in studies for other drugs. The subset with local tumors (plus or minus mets) was also doing better than expected, but not as much so as the mets-only group. (Note that the data is still BLINDED, but the combined treatment+control group was doing better than expected.) I view this as a positive sign, since you may recall that on your episode Brad said that Reolysin was more effective on metastatic tumors than primaries.

Colm writes:

TWiVsters:

I’m writing to address a few of the points you’ve touched on recently. First, with regard to journal clubs and how to keep people interested/coming. Here at UAB we’re required to take a journal club every semester, most of which meet weekly. Mine in particular uses a setup where each student gives three types of presentations. First, the traditional ‘explain this paper, figure by figure with background, critique and Q&A. Second, a discussion format where the assigned student puts together slides with the figures and a brief introduction then leads a group discussion focusing on the overarching biological question posed by the paper, whether it was adequately addressed and future aims. The third is a more casual ‘bring in any article, newspaper clipping, MMWR report etc. you find interesting and say why in about 7-10 minutes.’ This is ideal for bringing up topics not suitable for our more molecular virology focused journal club, but still of interest to an individual or the group as a whole.

I think regularly presenting these different types of public speaking is a benefit, as one helps giving seminars, one is more teaching experience and the other helps you communicate science in a casual way. We also recently began presenting series’ of papers on single topics (animal models, short RNAs etc) to avoid jumping around vastly different fields every single week. I very much enjoy the way we have our journal club set up. Both of our faculty moderators listen to TwiV, but I swear I’m not just writing in to suck up.

Recently, you fielded a question about trying to get TwiV onto NPR, and the attendant difficulty. I think a more feasible approach would be going directly to what remains of College Radio. Many of these stations (WMUC at my alma mater, Maryland for example) are in some way overseen or advised by Journalism programs and air some form of educational or news programming, in between student driven free-form programming. And since many station have lost their FM licenses and moved completely streaming, it wouldn’t even have to broadcast. WKCR could have an entire TWiX substream. Another option would be reaching out to community based low-power FM stations either in developed or developing countries, but I’m not as familiar with them, maybe Alan would be that resource.

Hope I gave you some novel ideas. Cheers.

Maria writes:

Hello TWIV!

First I must admit that I have not been the most faithful TWIV listener, but was amused to hear from my boss, Dr. Matthew Evans, that on TWIV one listener wrote in asking about how best to stay mentally sharp and ready for graduate school while training full time for the Olympics and that in response to this listener the TWIV crew stated that it would not be possible to simultaneously train at the Olympic level while earning a doctorate. Matt wrote in a response to TWIV, but I also felt compelled to enlighten everyone about being the ultimate student athlete after listening to the podcast myself!

I am a PhD candidate at Mount Sinai School of Medicine where I am studying Hepatitis C Virus entry in the lab of Dr. Matthew Evans. I just returned this September from London where I competed in the 2012 Olympic Games, representing our country the United States of America. I am currently beginning my 5th year here at MSSM and aside from a six month leave of absence spanning this past March-Aug (during this period of extra free time I finally got to read Vertical Farm, great read!) I have been a full time PhD student and part-time elite athlete. I have raced at the international level since high school and have competed all over the world at various competitions, most recently London for the Olympic Games. I am a race walker (RW), which for anyone who has never heard of this it is a discipline in track and field with the Olympic distance covering 20km. It is an endurance event, often contested on the roads where the athletes race around a 2km or 2.5km circuit. There are two rules that differentiate race walking from running, the first is you must maintain contact with the ground (therefore there is a double contact stage, as opposed to running where there is a mid flight stage). The second rule is that the front leg must straighten on contact as it becomes weight bearing and passes underneath the body (as opposed to running where the knee buckles and the quadriceps flex to catch one’s weight). I was never home schooled, I graduated from high school on time, and undergrad a semester early. At graduate school I have completed all my coursework on time and have even published my own first author paper. I did this while simultaneously earning and defending my indoor and outdoor nationals titles in which I have currently racked up 3 Indoor 3,000m RW and 3 Outdoor 20k (20,000m) RW titles. Last year I finished 30th at Worlds and this year 29th at the Olympic Games. I spend on average 2-3hrs a day training and cover 70miles a week while working a 10-12hr day in lab, 5 days a week with light work over the weekend.

I found it fitting how the next letter/comment that was addressed on the same episode (199) was regarding multitasking. In regard to those comments I couldn’t agree more. Yes, being a student athlete requires a lot of preplanning and careful time management. I can definitely atest to “multitasking” during periods of incubations. For example I may begin a transfer over night, then the next morning head into lab remove my blots and allow them to block while I go outside and complete training for 1-2hrs, then before showering I return to lab again add my primary antibody and then while it is incubating wash up and eat breakfast. Nearly everyone in my department has seen me come into lab on multiple occasions wearing spandex tights and my water bottle belt for training. I am at a huge advantage since MSSM is located right next to central park but I would be lying if I didn’t admit that the school’s proximity to a place for training was one of the reasons I chose MSSM. I also agree that multitasking in the sense of playing on one’s iphone, surfing the web or checking emails is unproductive multitasking. That is why there has been little time in my life for these activities.

In addition to my “multitasking”, planning, and jam packed busy days another huge factor contributing to my success was an understanding boss, Matt, supportive graduate school program, and an equally understanding and accommodating coach, Tim Seaman. There were plenty of times when I prioritized school over training like when I was studying for my qualifying exam. The reverse is also true when I would use my vacation time and attend a pre-training camp in Daegu, South Korea before Worlds requiring me to be absent from lab for 10 days straight. Matt could have very easily forbade me from taking the time off that I did to compete, which was always more than the allotted two weeks per year a graduate student is entitled to. Together everyone allowed me to reach my Olympic Dream, and I was never forced to give up on my academic pursuits.

Yes, this is often not the case, I would estimate that at least 90% of my Olympic teammates were full time professional athletes, and of the other 10% I do not know another single person simultaneously earning a PhD. While rare, it is not impossible. I think this would be a great comment for you guys to address, after all a good number of listeners are probably undergraduates and it is important for them to realize that they do not have to choose a less demanding career path if they want to stay active in sports. It is possible to train at an elite level AND pursue your academic studies.

Thanks for taking the time to read my letter, for more info about my recent Olympic journey visit my website: www.mariamichta.com  or check out the attachment to see what an Olympic PhD candidate looks like! I look forward to listening regularly again to both TWIV and TWIM.

Zachary writes:

After watching your iTunes U lecture, reading your textbook for class, and more recently, listen to your podcast on local meteorology and virology, I came across TWiV 190 (I’m a little behind). In it, you put out the call for computer-ready volunteers. I’m a senior at Sarah Lawrence College, and I’m looking into starting a virology club on campus. If there’s anything left that you can put a volunteer to, I’d be more than happy to volunteer in any way I’d be useful. Come September, I’ll also hopefully have the membership of a small virology club to offer as well.

Thanks for the education,

-Zachary

Adam writes:

Ask and ye shall receive, or in this case subscribe to citation alerts and you shall be found by cool papers.

On a recent episode you resolved to discuss more bug papers. Not long afterwards this paper landed in my inbox, a drama seemingly perfect for TWiV: Among the cast are the industrious honey bee, Apis mellifera, whose colonies are beset by an insidious parasite, Varroa destructor, carrying a devastating curse on its lips (or mandibles I suppose). The mites unwittingly transmit Deformed Wing Virus (DWV) to the developing larvae, leaving them crippled as adults. Enter doctors Desai, Eu, Whyard, and Currie from the University of Manitoba, Canada. In this study they test the ability of a DWV-dsRNA construct, delivered orally, to protect bees from the effects of DWV.

At risk of spoiling the ending, it appears to work, the vaccinated bees form healthy wings – but the paper left me with unanswered questions, which I address to the Racaniello media empire:

Does this study actually demonstrate the effectiveness of dsRNA as a vaccine against DWV?

The authors posit that an RNA interference response is occurring to limit viral replication upon later infection. I imagine that the RNAi response occurs in the first cells encountered by dsRNA – the cells of the gut – rendering them non permissive to DWV – effectively quarantining the gut.  Assuming that DWV infection is naturally transmitted by the bite of the Varroa mite, local immunity in the GI track wouldn’t protect bees bitten later in life from infection – unless siRNAs had been distributed systemically. The authors conclude from the lowered viral load and absence of wing deformity in dsRNA-fed bees, that siRNAs are being actively distributed.

Could the lowered viral load and preserved wings instead be the result of gut-localized RNAi stifling viral infection long enough for the wings to complete their development?

For example, having only 1% of gut cells remaining permissive after dsRNA treatment would be equivalent to reducing the inoculation dose by 10^-1

RNA isn’t a super stable molecule, how would you expect to deliver dsRNA laced sugar solution to colonies of bees in the field? Are there chaperone proteins that stabilize RNA at environmental temperatures?

Further, if the larvae are the vulnerable stage, dsRNA would need to be consumed by workers, regurgitated, possibly stored as honey, and then consumed by larvae all without being digested or degraded.

Desai, S. D., Eu, Y.-J., Whyard, S. and Currie, R. W. (2012), Reduction in deformed wing virus infection in larval and adult honey bees (Apis mellifera L.) by double-stranded RNA ingestion. Insect Molecular Biology, 21: 446–455. doi: 10.1111/j.1365-2583.2012.01150.x

Thanks again for a great podcast,

Adam

Melbourne, Australia, where it is currently 11C and overcast.

Todd writes:

I remember one TWIV that talked about how dry conditions cause mosquitos to tend to bite humans more.  Are the current drought conditions in Texas maybe a factor here?

“Dallas in state of emergency after West Nile virus” http://www.bbc.co.uk/news/world-us-canada-19276240

BTW, BBC has better coverage of America’s news than any American news chain.  That sucks. 🙁

Robert writes:

Drs. Et al

A. Love M,P, and V.  Each teaches and entertains.

B. Could an episode of each show be a dictionary of terms to exPlain the science a little better for those of us who aren’t in the field? I who am a horticulturalist, understand parasitism better than microbes or viruses or phage.

C. Please relate more of those historic stories which give more life to the discovery of tric, giardia , or bubonic plague.

Forever indebted to all hosts and hostesses on each show. Thank you

Alice writes:

Professor Racaniello:  FYI, from the NWRA wildlife rehabilitator’s newsletter.

• New Human Phlebovirus Discovered in MO
  Two farmers in northwestern Missouri became ill with fever, fatigue, diarrhea, and loss of appetite that led to severe illness following a tick bite, including hospitalization for two weeks and a month and a half for full recovery. The virus is unique as it has not been found elsewhere and is the first phlebovirus found to cause illness in humans in the Western Hemisphere. While the virus is thought to be transmitted by ticks, this has not been confirmed and it could be transmitted by mosquitoes or sandflies. Article: http://thechart.blogs.cnn.com/2012/08/30/new-virus-found-in-missouri-ticks-suspected/. New England Journal of Medicine article abstract: http://www.nejm.org/doi/full/10.1056/NEJMoa1203378.
•  Record Number of Human West Nile Virus Cases
  Thus far in 2012 [as of August 21], 47 states have reported West Nile virus [WNV] infections in people, birds, or mosquitoes. A total of 1,118 cases of West Nile virus disease in people, including 41 deaths, have been reported to the CDC. Of these, 629 (56%) were classified as neuro-invasive disease (such as meningitis or encephalitis), and 489 (44%) were classified as non-neuro-invasive disease. The 1,118 cases reported thus far in 2012 are the highest number of West Nile virus disease cases reported to CDC since West Nile virus first was detected in the US in 1999. Over 75 percent of the cases have been reported from five states (TX, MS, LA, OK, and SD), and almost half of all cases have been reported from TX. Details:http://www.cdc.gov/ncidod/dvbid/westnile/index.htm.
• Birds to humans: Usutu Virus in Germany
  Originating from Africa during the summer of 2011, Usutu virus is the cause of mass die-offs in blackbirds (Turdus merula) in southwest Germany. Again this summer [2012] thousands of blackbirds have died. Usutu virus was found in Culex pipiens mosquitoes in Germany and the virus may be transmitted to humans through a mosquito bite. The virus first appeared in Europe in the Vienna area in 2001 and included some deaths in great gray owls (Strix nebulosa) in addition to the blackbirds; in 2009, two immunocompromised Italians became infected. The first human case of Usutu virus infection in Germany has been confirmed. The affected man, from Gross-Gerau (Hesse), indicated he has experienced no symptoms of illness. More details: http://www.promedmail.org, click on Search to the right, enter Usutu virus.

Jim writes:

Vincent,

I’m working through some British podcasts, two of which concern evidence-based medicine. It seems that most work in this area is in Britain, Canada and Australia. These are the podcasts:

Evidenced Based Medicine, a 43 minute lecture, and Future of Evidenced Based Medicine, a 30 minute lecture, both by Professor Paul Glasziou. The Evidence Based Medicine Journal mentioned in one has a lot of rss feeds that I like and the Mendeley service has a virology group.  Should virology, microbiology and parasitism be a part of this concept, or have a similar program? A good power point presentation notes, as does another of these podcasts, that over 30,000 clinical trials are started each year which must affect every bio-medical field. This is the first time I’ve seen how big the research field has become. Is this a major reason that grants are more difficult to obtain? Is the upward trend in number of trials likely to continue, or is the system beginning to break down, or evolving into something else?

TWIV 197 with Prof Marcus was terrific, well done and just right on target.  I hope you can capture any other senior researchers who had seminal roles. Thank you.

Regards,

Jim

Smithfield, VA

Sheri writes:

Hi Vincent et al.,

I am writing to ask if you would address the recombination potential for live attenuated influenza viruses in the FluMist vaccine.  I enjoyed TWiV 191 (When two rights make a wrong) but was left wondering why recombination of attenuated flu viruses wasn’t considered to be a risk.

Thanks in advance.

All the best,

Sheri

PS – I am a second year PhD student in the University of Maine Oceanography program conducting research on persistent virus infections in marine phytoplankton and virus-mediated gene and carbon flow among marine trophic levels.  I am working in Willie Wilson’s Marine Virology lab at Bigelow Laboratory.

Thanks for transforming my long commutes from a chore into a cherished part of the day (my time to listen to TWiV).

Peter Palese replies:

This issue has been discussed (at length) before FDA approval, but there were NO concerns raised by the FDA during the hearing.

Additional points:

1) The HA and NA on the vaccine strain are those of co-circulating human strains (or at least those from strains circulating a year or two earlier). Thus nothing “new” would be introduced into the human population, were those HA/NAs to escape.

2) The non-HA/NA genes of Flumist – in essence – all contain attenuation markers (ts, ca etc.) and thus would make the circulating wt strains less fit when “reassorted” into them

3) The M gene of Flumist has an interfering activity and thus reassortment is actually pretty difficult when a ca strain is involved. (Julie Youngner from Pittsburgh has/had a patent on this “therapeutic” effect of Flumist; when Flumist is given to a patient this patient appears to be protected against a superinfecting wt influenza virus for at least a week or two).

Frank writes:

Dear Wise Men,

In chorus with your many listeners, THANK YOU and know that we depend upon your continued TW(xx)ing.  I was lucky to have stumbled upon TWIV in the single digit era and have not missed my weekly “TWIV inoculation” since.  After forty years of building technical materials companies in many markets, I am trying to turn my energy towards societal goals, but you guys make it very hard to stay out of the commercial implications of the weekly microbiome revelations. Oh, to be 30 years old again!

I have just finished Vincent’s pick from #192, Microbes and Evolution, and a paper referenced in the Rowher chapter (#9, Phage) which describes the broad presence in phage of exotoxin genes common in pathogenic bacteria. I can just imagine bacteria paraphrasing Flip Wilson who said, “The Devil (virus) Made Me Do It”.  (http://onlinelibrary.wiley.com/doi/10.1111/j.1574-6968.2006.00345.x/full)

I would like to suggest that you consider an episode dedicated to a paper such as this and the topic of virus as the ultimate and continuing force behind evolution, sustainability and life.

Thanks again to all of you for giving your time to share your knowledge in such an accessible style and vehicle.

Best Regards,

Frank

NY, NY

Len writes:

I would like to hear you discuss this on TWiV:

Flu shot linked to higher incidence of flu in pandemic year
http://www.cbc.ca/news/health/story/2012/09/10/flu-shot-pandemic.html

It’s about work presented at an ICAAC poster session by Dr. Danuta Skowronski et al.

They say it might be related to the dengue fever phenomenon that you’ve discussed before (antibodies to one serotype increase the risk of serious disease from a different serotype). In their experiment they gave influenza to ferrets – but don’t worry, it wasn’t H5N1, it was only the 2009 H1N1 pandemic strain. 🙂

Shinai writes:

Hi guys of the TWiV, my name is Shinai, i’m biomedical (virologist) and illustrator in Brazil. I like a lot of your work, I can say that every week I’m always watching the news from you. I love science (virology am passionate about) and I am one of those who believe that viruses were the first “living”, and viral symbiosis in humans …. which today is already a fact, but some years ago I called crazy because of it.

Well, I’m creating paper models (papercraft) for science and did a bacteriophage and an HSV-1 that serve to decorate or to help in education. I wonder if you’d like to put my designs on TWiV page. It will be an honor for me to have my papercrafts and graphics on the page of yours and still allow each virologist might have a virus on your preferred model home …. contributing to the advancement of science.

Thanks

Shinai

Visit Thera Biomedical Illustration to see the models papercrafts: http://www.facebook.com/pages/Thera-Biomedical-Illustration/323802371047905

Jim writes:

Hi TWIVers,

Thanks for pointing out the use of paper flicks in session 198; new concept for me. I see how the accordion concept was conceived.  Paper flicks will allow multiple poster presentations at conferences by a researcher involved with several topics. It looks like the start of another mini-industry.

Your mention of Khan Academy reminded me to sent this link for an interesting Bozeman site that has some 70 video segments dealing with biology. I don’t know how one teacher could put so much together, but it’s the best collection I’ve seen. Here’s the 10:30 video on viral replication so you can see how well it is done. For some reason it is one that shows a distorted picture, though the time-line mini shots are readily seen and a strange ad at the beginning was clear.

Regards,

Jim

Smithfield, VA

Shamus writes:

Hello Dr Racaniello et al.,

I saw this paper and thought I would pass it along. The authors present data for the inclusion of viruses in the tree of life. Since the question of whether viruses are living or not is a common topic of dicussion on TWiV, I thought it was worth sharing.

I really enjoy all the TWi-podcasts and appreciate all your efforts!

Cheers,

Shamus

Postdoctoral Research Associate

Southeastern Cooperative Wildlife Disease Study

Department of Population Health

College of Veterinary Medicine University of Georgia

Athens, Georgia

[sent http://www.biomedcentral.com/1471-2148/12/156/abstract ]

Magda writes:

Hello TWiV Team

I’m a student from Poland, this year I am beginning my master in biotechnology.

First of all I would like to thank you for this podcast. I haven’t been attending to any virology course yet, so most of my knowledge about viruses since now is from TWiV and my own “researches”. When I started listening to TWiV I had to check many things which I didn’t understand but with every next episode it was easier and now I can say that I learned a lot and found viruses really fascinating.

I’ve recently read an interesting article on sciencedaily about the possible theory of viral evolution.

http://www.sciencedaily.com/releases/2012/09/120913123520.htm

“A new study of giant viruses supports the idea that viruses are ancient living organisms and not inanimate molecular remnants run amok, as some scientists have argued. The study may reshape the universal family tree, adding a fourth major branch to the three that most scientists agree represent the fundamental domains of life.”

Researchers looked for evidence of past events in the three-dimensional, structural domains of proteins, rather than comparing genetic sequences, which are unstable and change rapidly over time.

“The new analysis adds to the evidence that giant viruses were originally much more complex than they are today and experienced a dramatic reduction in their genomes over time. This reduction likely explains their eventual adoption of a parasitic lifestyle. They suggest that giant viruses are more like their original ancestors than smaller viruses with pared down genomes.”

I would like to know what is your opinion on this subject.

I’ve already heard in one of the episodes, that you believe that viruses are not living organisms but just chemical molecules. I’ve been thinking about this for a long time and I do not understand why do we have to call something  “alive” or “inanimate”. Isn’t there something between? Why do we have to describe something as black or white, what about gray? And why isn’t there such a problem with parasites, which also can not live on their own, but need another living organism.

I know you are getting lots of e-mails but I hope to hear from you soon.

Waiting for the next episode

Magda

PS. I’m one of those who listen to TWiV till the end 🙂

Hans writes:

Dear Twivers,

please see attached an interesting publication regarding giant viruses and their consideration as a distinct and ancient form of life.

I personally disagree with the authors to consider viruses as a distinct form of life. But according to the authors’ conclusion, giant viruses have played an important part as messengers for gene transfer and contributed to the biodiversity.  This is a very interesting aspect, and keeps the brain thinking.

Manuscript:

A. Nasir, KM Kim, and G Caetano-Anolles. 2012. BMC Evolutionary Biology. 12: 156.

I really enjoy your podcast, really great work, and I do recommend it to my students to listen to it. I am based in Melbourne, Australia, and teach and research at the Dept. of Microbiology, Monash University. Melbourne has actually four seasons, and now we are heading towards summer time. Let me know if one of you goes to “Down Under” some time, would be nice to catch up. We have definitely “nice” viruses here, such as Hendra.

Cheers and all the best,

Hans

———————–

Assoc Prof Hans Netter

Dept. of Microbiology

Monash University, Vic 3800

Australia

Sarah writes:

Hi TWiV team,

A terrific blog I follow had this post today about avoiding what they called predatory open access journals. I thought you all and the TWiV/ TWiP/ TWiM audience might find this heads up useful. It is a disappointing development for the field, but I suppose from an economic perspective it shows that predatory entrepreneurial creativity is alive, well, and continuing to expand its range!

Best wishes,

Sarah

Renato writes:

Hi Vincent et al!

Again, thank you for your wonderful podcasts! I wrote you a little while back suggesting that you could hire someone to transcript the shows and let the text online, so that Google can index it. It occurred to me that some listeners might want to do that, so you could crowdsource the effort.

I want to try to explain to you a few concepts in computer science, because I wonder if there are natural processes that work in analogous fashion. I am not an expert in any of this, but I do study it.

Let’s pretend a computer program has two instructions: “go to the folder X in the hard drive” and “erase everything at the current folder”. Notice that this is a legitimate” program, that is, if I want to delete everything at folder X, I run this program. The actual program that is run by the computer consists of a series of numbers, which codify the steps to be actually performed. Let’s say that this particular program is codified the numbers “01 02”. That is, 01 means, “go to folder X”, and 02 means “delete everything in the current folder”.

If I wanted to do some harm, I could devise a way to start the execution of this program at step 02, instead of at its start point. This would make the computer execute the instruction “delete everything in the current folder” wherever it currently is – which may or may not be the folder X.

There is, however, an even more ingenious way to use the program list. To understand it, please notice that computers don’t need spaces between numbers, so the listing “01<space>02” is stored in the computer as the list “0102”. Then, I could force the computer to start execution at the second digit, that is, I can make the computer execute the program “102” instead of “0102”!

Now, what does this “102” listing codifies? It could be that the number “10” is an instruction understood by the computer – for instance, it could mean “flash the screen once”. Also, what does it happens when the computer reaches the number “2” instead of “02”? Does it automatically insert the leading zero? Does it stay put, waiting for the next digit?

I ask these questions to you because I imagine some transcription processes might face analogous situations. What happens if, because of some ribosomal error, a gene starts to be transcribed not on its first codon, but from some middle one? What if the mRNA loses a base somewhere? How frequent is such stuff? We can measure DNA replication errors because we can observe mutation, but can we observe transcription “malfunction”? Can we make it happen more frequently?

Also, are there viruses that hijack cell functions not in a “per gene” basis, but in a “dirtier” manner, by starting transcription of already encoded “stuff” in our genes that is “shifted” from their “correct” positions? For instance, say that the sequence AGA AGA AGA encodes a protein needed for the cell membrane. Say that the sequence GAA GAA – which is encoded by the same sequence as before, but “shifted” one letter – encodes a protein which is part of a virus capsid. Wouldn’t it make sense for the virus to use our genome as a library – but reading the books using a different “index” than our own?

I am sorry for the long email, and grateful for your attention.

– From a very hot and dry São Paulo (34 Celsius, 61 days without rain),

Renato.

Étienne writes:

Hello professors,

I’ve been a long time listener of your great podcasts. Since you traded a few of your favorite quotes about science at the end of TWIV 199 I decided to share one of my favorites. It’s from Isaac Asimov and goes as follows:  “If knowledge can create problems, it is not through ignorance that we can solve them.” I think it’s a valuable quote to keep in mind when science and politics come at a cross-road.

Étienne

Québec, Canada

Ebrahim writes:

Dear TWIV team

I have a problem that I want to investigate in twiv-o !

I am a graduate student that just finished my Master’s degree program in infectious diseases from Heidelberg university, Germany, basically working on viruses! I did my thesis on oncolytic viruses, and also have experience in virus-host interactions. I became stuck to “Virology” and willing to proceed further doing also my Phd in “Virology”. Now I feel myself “lost in space” going through announcements for scholarships and open positions here and there, sometimes with hope of getting a position and others with desperation, when it comes to applying for a scholarship I think I face a problem with writing!, I don’t know how to write a good research proposal, I faced the problem earlier when I was writing my thesis that I am too slow and don’t know how to start and when to stop writing!. My question is, are there standard ways for writing in science that I shall follow as well as everyone, or it is just like art and related to personal attitudes and styles? I would appreciate any help in this regard and keep up the good work.

Best!

Beverly writes:

I just listened to your interview with Dr. Lipkin and I have a couple of questions and comments.

I read the paper itself but I don’t understand the thing about the 9 patients and 9 controls that tested positive. I’m not sure if it was not fully explained or I just don’t know enough to understand. I know for sure that my brain fog from CFS has been pretty bad lately. I got the impression that it was kind of waved off as some type of contamination or false positive.

I noticed in the press conference that when Dr. Lipkin was asked about XMRV being a lab created contaminant that was supposedly created by passaging of prostate cancer tissue on nude mice, he dodged the question by discussing how scientists are working to come up with some guidelines on hybrid viruses that are being deliberately created. I’m sure that is very needed but the question was about viruses that are being created accidentally. It seems to me that there is an important story here about accidentally lab created viruses and/or natural hybrids and chimeras contaminating labs, reagents and other products. Dr. Mikovitz did talk about the amount of effort that the Ruscetti lab went to in order to make sure their lab was clean.

One incident in this soap opera sticks in my mind. One of the labs that got negative results admitted later that they had thrown out the results when a control had tested positive. Turns out that they used their lab personnel as controls and they were sure they were negative because they got regular blood tests. That person may in fact have been exposed to XMRV and be positive. Or it could just be more contamination….

I think the lab contamination issue would make a good topic for a show. If you have already had one, please send me the link.

I have an MPH in Biostatistics so I know a little about experimental design and things that can go wrong and how easy it is to come to false conclusions. I enjoyed the discussion near the end with Dr. Lipkin about Koch’s postulates and the respiratory disease study that went wrong. I’m eager to hear the program when his new paper on this comes out.

Thank you,
Beverly
Austin, TX

Amy writes:

Dear Dr.s twiv,

I am a huge twiv, twip and twim fan and was finally compelled to write after listening to twiv #181 since I am currently reading the book The family who couldn’t sleep by D.T. Max, a book about a family who has an inherited prion disease called fatal familia insomnia. The author goes into the history of prion diseases and the discovery that they are not viruses or bacteria but a protein. I am about half way through the book and love it. I also have on my nook the book The wild life of our bodies by Rob Dunn. He talks about what lives on or in us and is a big fan of Dickson’s vertical farm idea.

I also have to say that my son likes to listen when we do errands in the car and once commented that i listen to the most interesting podcasts. He really got a kick out of the viruses in video games episode and also the zinc finger inspired by the NCIS episode (it’s called toxic by the way).

I am a __ year old woman who always has loved science since a small child but did not have a chance to go to college, but i try to learn as much as possible on my own. I have tried lots of science podcasts and these are my favorites of all.

amy

Jim writes:

These podcasts might be of interest to listeners of TWIV, TWIM and TWIP, especially students.

The ENCODE podcast is almost an hour, by one of the British authors of the work.

myIDP (Individual Development Plan) you know about, but the 7 minute podcast will explain it to student listeners.

Experiment Reproduction 56 mins – “Brian Nosek of the University of Virginia talks with EconTalk host Russ Roberts about how incentives in academic life create a tension between truth-seeking and professional advancement. Nosek argues that these incentives create a subconscious bias toward making research decisions in favor of novel results that may not be true, particularly in empirical and experimental work in the social sciences. In the second half of the conversation, Nosek details some practical innovations occurring in the field of psychology, to replicate established results and to publicize unpublished results that are not sufficiently exciting to merit publication but that nevertheless advance understanding and knowledge. These include the Open Science Framework and PsychFileDrawer.”

Regards,

Jim
Smithfield, VA

Mark writes:

Hey TWiV-ome,

Here is a way for listeners and hosts to inoculate against “mathematics-phobia” — the USA’s first Museum of Mathematics. It is opening in Manhattan on 12/12/12. Outreach to generate interest among youth is a key part of their activity. More information is on their web www.momath.org.

Ciao.