Viruses

mailboxTWiM regularly receives listener email with corrections, comments, suggestions for show topics, requests for clarification, and additional information. A selection of these is archived on this page.

TWiM 47 Letters

Maureen writes:

I love all your series (TWIM,TWIV, and TWIP) and learn immensely from them. I am a Clinical Research Nurse and work at NIH in the National Institute of Allergy and Infectious Disease (NIAID) unit that houses the KPCR  patients that you may have recently read about.

http://www.washingtonpost.com/national/health-science/superbug-stalked-nih-hospital-last-year-killing-six/2012/08/22/5be18b1a-ec66-11e1-9ddc-340d5efb1e9c_story.html

I'd like to hear a discussion about this isolate as you educate everyone so thoroughly. Our hospital has worked diligently to track and eliminate this organism from our hospital and we've just about succeeded but I'd still like to be better informed about KPCR. Thanks.

http://stm.sciencemag.org/content/4/148/148ra116.full

P.S. Please Please Please start a TWIB!! We work with so much that I still need to be educated about various bacteria.

Thanks immensely for all the education you give us.

Jim writes:

Hi Vincent and Friends,

Thank you very much for the informative and often imaginative discussions that take place in TWiM. It's a real pleasure to listen to such a quality, fun, easily accessible (and free!) source of microbial material. I'm sure you are often thanked for taking the effort to put it out there, but I wanted to add my voice. As a cell and molecular biology student it offers some wonderful connections and points of interest to my education.

My question relates to a recently published book by Trudy M. Wassenaar that I have been reading, titled "Bacteria: The Benign, the Bad, and the Beautiful." Has anyone read this book, and if so what are their thoughts on it? I would recommend it to those with a broad interest, or who need an introduction, like students such Pokies as myself. It offers an incredibly interesting and diverse description of bacteria and is easy to understand. I actually picked it up because it was recommended by the google+ "Microbiology" account (https://plus.google.com/u/0/109102265263486263584/posts).

Thanks again, and warm regards.

Steve writes:

TWiM Audio File with Interactive Transcription

Here is a link to a partial, video I created from the TWiM 06 audio file: http://www.youtube.com/watch?v=JtOXD_X6g_w. I created a video file from the audio file so that I could use the YouTube captioning tool to import an interactive transcript -- minutes five (5) through twelve (12). I created the time-coded transcript using an online tool called Subtitle-Horse, (http://subtitle-horse.com).

If you click the interactive transcript button on the button-bar (Like, Dislike, Add to, etc) just below the video player, you can see how the transcript works. The transcript is indexed, time coded to the audio.

Potential Benefit of Interactive Transcription

The time-coded transcript text could be parsed and placed in a database for easy query. Then all included audio/video files are text searchable and associated to the segment of the source audio/video clip.

Collaborative Transcription

On TWiV a number of people have completed or are working on transcripts. In my experience, transcription is a time intensive process. To lighten individual time commitment, it would be nice to get several people to work collaboratively to transcribe one TWiV audio/video. Although far from perfect, the subtitle-horse online transcription tool could be used for this.

Volunteer to Help Transcribe

As a first step, if interested, I’d be interested in coordinating a collaborative transcription of a TWiV session with one to three others.

TWiM 46 Letters

Jeff writes:

Hello TWIMers -  In TWIM 26  I heard the listener email asking if you would consider offering continuing education credit for your podcasts, and you understandably cited the work that would you need to do (such as writing learning objectives, tests etc) as a real barrier to that.  I was wondering if you would consider "contracting" that kind of work out to some of your listeners; being a teacher of a microbiology class at a community college, I spend a large amount of time coming up with learning objectives, tests etc  anyhow, and it would help me to generate fresh material for my students from your podcasts.  I wouldn't be surprised if there were others in your listening base who might feel the same.  This still would add work for you, so I understand if its a no-go.

In a separate vein: quite a while ago I was doing dishes and listening to a TWIM.  As I was using a sponge to wipe off the counter a ridiculous question popped into my head (as opposed to my toe, I guess): are there strains of bacteria that can provide a protective commensal role on environmental surfaces?  A counter top is nothing like a biological surface, as only the latter should have organic material to eat on it, but still, is there any evidence in any situation that something like this happens?  Please read  the following sentence with extra emphasis: I am not fishing for an excuse to get out of doing the dishes, and I regularly boil our kitchen sponges and use bleach to Pokies clean the counters.

Keep up the great work!

Velma writes:

Dear TWIM-team,

Greetings from a longtime listener and fan of all three TWI-podcasts. I'm a biotechnology Masters student at the University of Helsinki, Finland, but I earn my living as a part-time driver in the world's most northern metro. Your podcasts help me pass the dull hours at work so that I feel like I'm doing something to advance my studies as well.

I've been thinking of writing for quite a while. Now that I'm finally doing it, I have a rather general suggestion and a link. The suggestion is, I'd like to hear more about the archaea - maybe even an entire episode dedicated to them. They seem like such a mystery. At least at my home university, they're almost always just mentioned as an aside, while the bacteria get all the attention. The one time they were actually discussed on a course, I learned that they are not just extremophiles, but actually all around us, just like bacteria. This made the fact that there are no pathogenic archeae seem even more curious to me.

As for the link, it's for the Earth Microbiome Project: http://www.earthmicrobiome.org/

I just ran across it today, and don't remember this project being mentioned on TWIM before. I think the idea is awesome, not to mention really ambitious, maybe even overly so. What do you think, is creating even a rough map of the microbiome of our entire planet an attainable goal? And would it be a useful resource for research?

Thanks for the inspiring and informative podcasts,

Velma

TWiM 45 Letters

Elitza writes:

Dear TWiM Team,

I just finished listening to the TWiM 35 on LPS in Vibrio (among other topics). Dr. Elio Schaechter mentioned a field in Microbiology that I think is of great interest to the scientific community and should definitely be covered in a podcast. The topic is: Outer Membrane Biogenesis in Gram-negative bacteria. For decades people have been hypothesizing and trying to find an evolutionary link that would answer the following questions: how did a second membrane in bacteria come about and was the last universal common ancestor (LUCA) a single or double-membraned organism. These questions are extremely difficult to address and rely heavily on bioinformatics and phylogenetic analysis.

I'm the first author of the paper that I'm suggesting here as a resource for a potential podcast. I've read extensive amounts of scientific literature before the paper was finalized and published in Cell to realize that currently, there are no favored hypotheses and the very few hypotheses that exist are highly controversial. In our paper we structurally characterize (using electron cryo-tomography) the process of endospore formation. The process is typically thought of as exclusive to Gram-positive bacteria members of the phylum Firmicutes, however, we imaged a Gram-negative organism (Acetonema longum) that is also able to sporulate! Through our structural studies, phylogenetic profiling and biochemical analysis we showed that A. longum possesses a true outer membrane. Not only that, after sporulation, the spore is surrounded by two membranes both of which originated from the inner membrane of the mother cell. Upon outgrowth, the second membrane of the spore becomes the outer membrane of the bacterium and therefore is remodeled from and inner into and outer membrane. These are fascinating new results that may provide us with a missing link between Gram-positive and Gram-negative bacteria and give insights into how an outer membrane may have evolved.

Here are a couple of links to the paper I'm suggesting and a commentary by Dr. W. Vollmer on this work:

http://www.ncbi.nlm.nih.gov/pubmed/21884938

http://www.ncbi.nlm.nih.gov/pubmed/22173345

Thanks!

 

Fabio writes:

Dear Prof. Schmidt, I listened the podcast in Microbiology that you recently contributed together with Vincent Racaniello, Joseph John and Elio Schaechter. You made a very nice summary and commentary of the International Symposium on Staphylococci held last August in Lyon.

Furthermore, I would like to thank you for all your nice words about the symposium that we organized and on our recent opinion paper titled “Inferring reasons for the failure of S. aureus vaccines in clinical trials” and published in Frontiers Cell. Inf. Microbio.

Best wishes,

Fabio

Fabio Bagnoli, PhD

Project Leader

Novartis Vaccines & Diagnostics


Alice writes:

Hey TWIM-MERs -- this is from a wildlife rehab newsletter, thought you might be interested:

MRSA in Wildlife

One of the most notorious and hard-to-treat bacteria in humans has been found in wildlife, according to a new study in the Journal of Wildlife Diseases. Researchers isolated methicillin-resistant Staphylococcus aureus (MRSA) in two rabbits and a shorebird. Wild animals may act as an environmental reservoir for the disease from which humans could get infected.

Molecular typing of the isolates showed that the shorebird carried a hospital-associated strain of MRSA, while the rabbits had community-associated strains. The rabbits' MRSA also was resistant to tetracycline, which is common in farm animals.

Perhaps most troubling of all was that one of the pigeons carried a Staphylococcus bacterium that, while still sensitive to methicillin, was resistant to the antibiotic vancomycin. "Vancomycin is used as a last resort in MRSA infections," says study co-author Shylo Wardyn, “and vancomycin-resistant staph strains are rare in humans.” Abstract: http://www.jwildlifedis.org/content/48/4/1069.abstractlink

Peter writes:

Happy Halloween greetings Twim Team.

For a slightly microbiology themed Halloween costume I constructed a Plague Doctor mask.

You can see its construction on the instructables site:

http://www.instructables.com/id/Plague-doctor-mask-for-Halloween-1/


Michael writes:

Hello, TWiM!

News Article: http://www.guardian.co.uk/environment/2012/oct/15/pacific-iron-fertilisation-geoengineering

Comment:  I feel like this issue is quite broad and interesting and was hoping that ocean geoengineering might be worth discussing.  It's my understanding that scientists are wary of such approaches, to say the least, but this event seems to demonstrate a certain necessity for the international community to come to terms with geoengineering and sort out strategies and methods.  As a layman, I'd be very interested in what you guys have to say!

Quick excerpt from the beginning of the article:

"A controversial American businessman dumped around 100 tonnes of iron sulphate into the Pacific Ocean as part of a geoengineering scheme off the west coast of Canada in July, a Guardian investigation can reveal.

...

Satellite images appear to confirm the claim by Californian Russ George that the iron has spawned an artificial plankton bloom as large as 10,000 square kilometres. The intention is for the plankton to absorb carbon dioxide and then sink to the ocean bed – a geoengineering technique known as ocean fertilisation that he hopes will net lucrative carbon credits.

George is the former chief executive of Planktos Inc, whose previous failed efforts to conduct large-scale commercial dumps near the Galapagos and Canary Islands led to his vessels being barred from ports by the Spanish and Ecuadorean governments. The US Environmental Protection Agency warned him that flying a US flag for his Galapagos project would violate US laws, and his activities are credited in part to the passing of international moratoria at the United Nations limiting ocean fertilisation experiments

Scientists are debating whether iron fertilisation can lock carbon into the deep ocean over the long term, and have raised concerns that it can irreparably harm ocean ecosystems, produce toxic tides and lifeless waters, and worsen ocean acidification and global warming."

Thank you for the great podcasts,

Michael

 

Øystein writes:

Dear TWiMmians,

I just found the latest edition of Clinical Microbiology and Infection and read about a concept that is new to me: culturomics.

Maybe you'll be as intrigued as me by this concept. It contrasts well wil all the high-throughput-genomics hype these days. It might be a good article to put on the show (some day?).

Here are the links, I am happy to forward pdf's of the articles to you if needed.

Culturomics: a new approach to study the human microbiome

http://onlinelibrary.wiley.com/doi/10.1111/1469-0691.12032/abstract

and

Microbial culturomics: paradigm shift in the human gut microbiome study

http://onlinelibrary.wiley.com/doi/10.1111/1469-0691.12023/abstract

And again, thank you for three great show to walk, commute, run, bike and do housework to:)

All the best,

Øystein

Registrar in clinical microbiology

Vestfold municipal hospital, Tønsberg

Norway

TWiM 44 Letters

Jeff writes:

Hi All - I am getting to the part of my Micro class where I have students analyze antibiograms and noticed a blog pointing to the attached paper. Forgive me if this topic (antibiogram data changing as a function of when samples are taken from a patient) has already been covered or commented on, but just in case, take a look. I particulary enjoy data tables showing "time to unreliability" and boy, things sure change fast in the ICU! I would be interested to hear a program about the "ecology of antibiotic resistance" in hospitals/clinics. I can think of reasons why resistance might vary depending on location within a hospital, but not being a clinical person I have no idea what the real reasons are. Forgive me if this too has been already featured.... teaching 5 classes and then coming home two young children keeps me chronically behind.

Love the program, thank you so much!

Here is the link - I don't know if it is copyright protected or not....

http://www.ccih.med.br/m/aluno/mod/biblioteca_virtual/revistas_2012/ICHE/Junho/0589.pdf

Jeff
Georgia Perimeter College

Katie writes:

Dear TWIM Doctors,

Thank you so much for your wonderful podcast.  I enjoy the entire TWI series, and I am thrilled that I finally have something to contribute!

In TWIM #43, a really interesting paper on bacterial caveolae was discussed. While this was amazing work, I do have to point out that being chock full of membrane vesicles is not unheard of in bacteria.  The photosynthetic purple nonsulfur bacteria (PNSB) Rhodobacter sphaeroides forms membrane vesicles in the cytoplasm to house its photosynthetic apparatus.  I have attached a paper with EM images (see Fig. 2 of the Adams and Hunter paper) showing how full these bacteria are with vesicles.  Beautiful studies by investigators such as Dr. Neil Hunter are beginning to uncover how these vesicles are formed, but there is still a lot that is not understood including what happens to these vesicles during division.  Another PNSB, Rhodopseudomonas palustris doesn’t form vesicles, but it does form lamellar membranes in the cytoplasm. If you look at the EM images in the second paper I attached, you can see that they have just a splash of cytoplasm. Considering how crowded the bacterial cytoplasm is already, it is really amazing!

Keep up the great work, and I look forward to the next podcast.

Cheers,
Katie

[she sent:
http://www.sciencedirect.com/science/article/pii/S0005272812001703

http://www.ncbi.nlm.nih.gov/pubmed/6343353 ]

Ayush writes:

Hello TWiM team,

I enjoy listening to you all every week. I apologize that my comment here is about not-so-recent TWiM (#30) about Burkholderia pseudomallei.  Some of you may know that that Melioidosis was perhaps described (Tapanuli fever) as a bioterror agent by Sir Arthur Conan Doyle in 'The Dying Detective'.  In this story, Sherlock Holmes was sent an unknown bacterium in mail to get him killed. Here is a paper describing Holmes' encounter with the bioweapon.

Please keep up the great work. I would strongly recommend TWiM as a must-listen for every microbiologist.

Alice writes:

Soil bacteria as source of drug resistance genes - does this have implications for nosocomial infection via contamination followed by gene swapping?

Glenn writes:

TWim podcast #11

I am wondering about the comment that was mentioned about the cutting board being the most dangerous tool in the kitchen. What is the best way to clean the cutting board? Also if one was to only use quick frozen chicken and cook it without pre-thawing. Will this keep one from acquiring the transfer of microbes from chickens to human by touch. I am assuming that by cooking all meats it kills all microbes.

Thanks,

Glenn

Glenn writes:

first I am really enjoying listening to TWiM and as a non-scientist you make the information about the micro world understandable. My question is related to TWiM podcast #16. I have several health issues that require me to take ibuprofen for pain and inflammation. How much concern should I have about the depletion of change in my gut and its ability to function properly.

thank you,

Glenn

TWiM 43 Letters

Jake writes:

Hello Vincent,
I've been listening to your TWiM podcast now for a few weeks as I am a student at SDSU taking a microbial genetics class with stanley maloy.  It be be another few months until I've caught up to the current episodes.  I saw this recent article on phage use in cleaning up achne and thought you'd like to hear about it.

http://www.genengnews.com/gen-news-highlights/zapping-zits-with-viruses/81247383/

cheers
Jake

Franco writes:

The article by Frits R. Mooi et al. linked on the episode “The sound of whooping cough” is contradicted by a study published on the current issue of EID: Schmidtke AJ, Boney KO, Martin SW, Skoff TH, Tondella ML, Tatti KM. Population diversity among Bordetella pertussis isolates, United States, 1935–2009. Emerg Infect Dis  Volume 18, Number 8—August 2012 http://dx.doi.org/10.3201/eid1808.120082.

I would greatly appreciate a comment on this point.

Best regards
Dr. Franco Giovanetti
www.aslcn2.it
http://medicinadeiviaggi.blogspot.it


John writes:

Dear TWIMmers,

I just finished listening to TWIM #39 (yes, I'm behind) and I had a question about the paper Michael reviewed.  Let me spell out how I understood the discussion, and then maybe you can tell me if I've misunderstood something, or if my question even makes sense.

Michael was talking about the question of how mutations arise and are selected for in nature.  The idea supported by Darwin (though long before anyone knew about DNA) was that mutations were in some sense driven by stress, right?  And then, there was this famous experiment which showed that mutants were present in the population before selection pressure was applied--a bunch of microbes were put on a plate with some antibiotic, and a small fraction of them were mutants that had resistance genes.  In this case, there was no pressure on the microbes to adapt the the antibiotic until they were put in a situation where they died unless they had the resistance genes.  Is this right so far?

Then, there was a second experiment, which used less powerful selection--the microbes were put on a plate where the only source of carbon was lactose, which the normal population of these microbes couldn't use for carbon.  And at first, these didn't grow much, but over time, even in an environment where the normal microbes couldn't grow Buy Viagra at all and so selection shouldn't have been able to bring anything new about, some microbes arose that could grow under these conditions.  Again, have I understood the basic idea?

Now, this is where I got a little confused.  From Michael's explanation, what I got was the idea that a bacterial cell can mutate in place even when it's not dividing.  That is, even in these bacteria that were sitting there unable to divide because they couldn't get any carbon from their environment, mutations could arise over time, and this led to a population of microbes that started out without the ability to grow with no carbon sources other than lactose, and then a few mutations arose that allowed some growth.  Is this right?  Is this kind of mutation important in eukaryotic cells, say in cancer or cellular senescence?

An alternative seems to be that the bacteria started out with a huge diversity of mutations already present, many of which gave them some small ability to get carbon from the lactose.  Then, over time, it seems like those would do all the dividing, and you'd get something like classic selection, with the bacteria that could reproduce faster leaving more copies of themselves which themselves could mutate to get better at reproducing.  Was there something observable in the experiment that ruled this out?

Anyway, thanks for answering my amateur questions.  I'm a computer scientist with no biology background, so I apologize if I'm making some dumb mistakes somewhere.

I wanted to also point out a really fun quote I ran across awhile back.  It's in a very old book (_Mutual Aid: A Factor in Evolution_ by Petr Kropotkin)--I think it was published in 1902.  It was a kind of argument against social Darwinism from a Russian naturalist and anarchist, combining observations on history and nature both.

> Mutual aid is met with even amidst the lowest animals, and we must be prepared to learn some day, from the students of microscopical pond-life, facts of unconscious mutual support, even from the life of micro-organisms.

Reading this, the words "biofilms" and "quorum sensing" popped immediately into my head.  Along with all the other kinds of mutualism between microbes.

Thanks again for your wonderful podcasts,

--John

TWiM 42 Letters

Sarah writes:

Hi Twimologists!

I just found this wonderfully instructive paper on concepts of bacterial ecology that are relevant to the antimicrobial resistance problem (doi: 10.1086/340245,link). The author mentioned the existence of genes conferring resistance to metallic ions like copper, which reminded me of the discussion about copper surfaces from TWiM episode 1. I hate to ask because it involves chemistry which we ALL took ages ago, but could you comment on this? (Dr. Maloy?)

A lot of papers about copper resistance in bacteria came out before Y2K, such as the above paper's reference # 47. But this paper just talks about metabolism of ionic copper, which is different than metallic or solid state copper (if I remember right). However, a 2004 paper (link) in BMC Microbiology suggests that metallic copper releases copper ions which are transferred into bacterial cells when a bacterial suspension is incubated in a copper vessel.

So, is it futile to celebrate the antimicrobial properties of copper surfaces, or is metallic copper reliably antibacterial by brute force, able to overcome any resistance gene that lets bacteria metabolize copper ions?

Thanks!
Sarah, BS, BSN, RN, Infection Preventionist

Peter writes:

I am not sure if the BBC programme Horizon is available in America but I found  the recent edition on combating antibiotic resistant bacteria was very interesting.
Of particular note were the interviews with Dr David Harper of AmpliPhi BioSciences in England on the development of bacteriophages to fight bacterial infections and Professor Viagra 100mg Bonnie  Bassler of Princeton University who is investigating  using antagonists to bacterial quorum sensing compounds to moderate their pathological effects.

http://www.ampliphibio.com/index.php/about/about_us

http://molbio.princeton.edu/faculty/molbio-faculty/31-bassler

I think that these scientists would make good guests for TWiM.

Behzad writes:

It is always a delight hear Vincent chairing these informal and incredibly informative podcast discussions of microbiology.  The world should be eternally grateful for what he is achieving and making so accessible both through smart phone streaming and on the web.  He engages his panelists enthusiastically as they discuss a wide range of topics important to understanding the diversity of microbes and their to understanding infection, ecology and even climate!

Hearing Elio is particularly rewarding as he is, dare I say, even more articulate than Vincent as he explains his topics clearly in terms that non-experts can understand and, importantly, puts these into historical context.

I do hope that this message is communicated to the shows sponsor, ASM.

Keep up the great work!

Steve writes:

Hi,
Of course, I immensely enjoy the podcasts. Thanks for making front-line science so accessible and informative. This is something America, society needs -- a more intimate, clear-eyed look at science and scientists in action.

Are there transcripts available for the TWIM podcasts? If not, is this something planned or in process? If not, I would help transcribe and index the text to the audio/video files.

Regards,

Steve

Abhinav writes:

Why do only a few bacteria out of billions act as endophytes by entering tissues of plants?

TWiM 4 Letters

Aric writes:

I just stumbled upon your podcasts last week and wanted to say that I enjoy them all (TWiV, TWiP, and TWiM). While listening to episode one of TWiM I began to think about the significance of finding human DNA in a bacterial genome. While this discovery is certainly very exciting I do have one question, doesn't the nature of LINEs make this discovery somewhat less remarkable? They are reverse transcriptases, which are built to copy and insert themselves into host DNA. I think this discovery may be due to the fact that LINE elements are very mobile sequences, and N. gonorrhoeae may be the 'victim' in this case. What are your thoughts on this? And would you feel different if the DNA found in the bacterial genome contained a gene for a membrane protein (or other random human gene) instead of a LINE?

-Aric

Allie writes:

TWIV, TWIP, and now - of all things TWIM? it just doesn't get any better. As an adult 'back to schooler' and beginning-again science learner, I can't believe my luck at beginning my ed adventure into science and beyond, during the era of the "Axis of unsee-able"  - the TW's. Once I listen to a TW discussion, the book (especially those dratted ch's on microbe-human interactions and all the replication stuff - aarrggh) comes alive. Here I was last week wishing you TW guys had a microbiology podcast, and poof - my prayers are answered! I thought my ears would pop out of my head as I listened along to TWIM #1, and actually understood stuff! This makes learning fun! You guys have a somehow magical combination of hard-core geek-ism, humor, loopbacks to clarify things for the "LlL's" (less learned listeners), and way too cool: all the heavy hitters seem to be gettin' together to chit chat - thanks a 10(-)7th mol or something like that (clearly more to learn!) Let's vote you folks along with  Sal Khan as "egalitarian educators" of the year(s)..

(by the way the piece of human DNA stuck in there on Ng thing was really "eerie", as Sal Khan of Khan Academy would probably say. And, the copper thing - why can't microbes eventually get around that, like they get around everything else eventually  - temp, salinity, pH, penicillin? Years from now I'll realize this was a dumb question, but for now it has Viagra me wondering).

Thanks

Allison

Kenneth writes:

Hi Vince, was just about to download TWiV when I saw that you have actually released the first episode to TWiM on the microbeworld website and I just can't stop jubilating. I strongly hope this podcast would be successful as TWiV and TWiP and I appreciate your help very much Vincent..You really helping some of us and I just cant thank you enough.

I pray for long life, happiness and good health for you, your family and all your friends helping you out to bring such an imparting tool in our lives and you all will be blessed anytime someone listens to any of your wonderful podcasts. This is just a thank you message and my questions will be following next.

All the best and goodluck.

Best Regards,

Ken (BioCrowd) in case you've forgotten me.

Stephen writes:

Here's a couple of ideas for signing off the show: "Another TWIM is added to the culture." "Another TWIM enters the culture." - Stephen

Atila writes:

Dear twimers,

First of all, congratulations to professor Racaniello and Racaniello Media Corporation for this new initiative. I am a regular TWiV and TWiP listener from Brazil, and just when I had listened to all episodes, you release this new podcast. Now I can only expect This Week in Vertebrates, or This Week in Plants. Until then, let me make my first TWiM question:

Many times I have heard the explanation that the smell that comes after the rain is caused by antibiotics produced by actinomycetes and other bacteria in a silent war for space. But I have never seen a decent reference to support this. People always say it but do not cite any source. Is it true, and do you have a good source for this?

Thank you all for making another fantastic podcast. I hope you inspire other researchers to do the same, or else Racaniello corp. will end up having 10 or more podcasts, and this is monopoly! Best, Atila Iamarino

p.s. thanks also for introducing Futures in Biotech, its a great podcast too and I am impressed. I'm listening to old episodes, from 2006 to 2008 and many of the discussions are about research that I have only heard last year. I'm anxious to get to the new episodes and know what will be published in 2015.

TWiM 39 Letters

Merry writes:

Writing the sprint event for the Microbial Olympics published recently by Nature Reviews Microbiology was surely my most fun writing assignment ever! The idea for this feature article originated with Dr. Andrew Jermy, Senior Editor at NRM in London back when the city was just starting to hum with preparations for the summer Olympics. He invited Forest Rohwer and myself to cover one of the events. Fortunately he offered us the sprint, which was a perfect opportunity for my favorite entrants, the phage, to win. He also enticed me by clearly stating his intent, that this was to be a fun piece for the reader (and the authors alike). Because my name happens to be first on the article, rumors have been going around that this was my idea. Actually, this was but the latest of a series of innovative features he has put together. I look forward to the next one.

Merry Youle

James writes:

Hello twim,

I just wanted to write to you guys and say thanks for highlighting our nature reviews article (Microbial Olympics). I'm glad our approach of writing a pieces that could be appreciated by experts and laypersons alike was successful and as its my first outing into the publication world I'm thrilled it has received such positive feedback! Thanks again!

Sincerely

James Gurney

Jim writes:

Another wonderful TWIM.  
Jo Handlesman's credentials are more impressive by the week.  

Will apologize for my low brow humor in the letter you read.

Taking a dump is used to say having a bowel movement. Hence "dump data" would be data derived from the study of bowel movements.
73

Stanley writes:

So, maybe it was because I was irritated from sitting in a traffic jam in LA, or maybe (like Elio) I was just being an old curmudgeon. As I was parked on the freeway listening to TWiM and looking forward to accelerating through Elio and Michaels autobahn through the recent General Meeting of the American Society of Microbiology, their comments made me feel stuck in an intellectual roadblock.

Elio made a good point that when a field gets started it begins with a lot of ideas, then goes through a period of accumulating a lot of data, before finally maturing into a robust blend of ideas, data, and broad insights that lead to interesting, testable predictions. But research on the microbiome is not just stuck in the boring burial in data phase. The field began with learning about a small number of cases to learn "who is there" and trying to guess from the sequences "what are they doing", work that was important to build the foundation of microbiome studies. And, it is true that there is a lot of that still going on in labs around the world. But the research has also progressed to other broader questions like how does the microbiome change after treatment with antibiotics and how long does it take to recover, how does diet influence the microbiome, is a person's microbiome stable or does it change over time, do certain microbes in the microbiome seem to protect against particular diseases -- questions that both make us think about the role of microbes in our health and illness, and data that leads to testable predictions that can lead to new therapeutics and treatments. For example, probiotics have been around for a long time, but we didn't understand how they work (and in some cases didn't even have good evidence that the really do work). Likewise for age old treatments like fecal transplants.

In short, this is a very exciting time for the microbiome and, if you're willing to listen and think, a fun time to be in the audience learning about the new Generic Viagra discoveries. If you'd like to hear from some of the people who spoke at the ASM as well as some perspectives on the future of this work, check out the ASM Life interviews from the General Meeting (http://www.microbeworld.org/index.php?option=com_content&view=article&id=1204).

Thanks for the cerebral distraction from the bumper in front of me. --> Stanley


Joe writes:
I wanted to follow up to an email the I sent to you all a while ago about evolution and entropy and my sense of paradox  regarding the ever increasing complexity of biologic systems and their concentration of energy in spite of the overriding  natural continual dispersal of energy captured in the idea of Entropy.

Let me first say that one of my gifts as  a scientist and engineer is an ability (and willingness) to ask fuzzy questions about bigger concepts at the boundaries of my knowledge looking for unexpected insights. Usually these questions are not quite so fuzzy that I mistake 2 for 3 as in the laws of thermodynamics, I guess I just like Gibbs Free Energy more than Entropy! That effort to identify what we don't know that we don't know is what has always excited me about science, the chance to think an entirely new thought that reveals something new about nature. How cool is that!

I appreciated that Michael and the rest of the crew tried to tackle the question in the spirit that it was offered and his answer essentially pointing out that nature arrives at complexity through massively large numbers of trial was useful after I thought about if for a while. Yet I must say that it still did not quite get at the core of my question. I was surprised by the email responses to my question that you later read. Particularly by the person who all but accused me of being an evil Creationist! I will just say that since it is not an issue that I care about I suspect the assertion says more about his world view than my own. The phrase "evolution driven by random chance" has never seemed to capture the awesome  sense of inevitability and thoroughness that I see in evolution. To me that phrase seems equivalent to calling it "magic".

Since then, I have come across a much more complete answer to what underlies this drive to complexity in Ray Kurzweil's book The Singularity Is Near, which I recommend as an interesting read whether you agree with his thesis or not. On page 85, he references research done by Stephen Wolfram on Cellular Automatons. This is a mathematical study that describes how complex non repetitive patterns can be generated from digital systems with a few very simple rules. In particular there is a category called class 4 automata that appear to characterize the evolution of biological systems. I have picked up  Wolfram's book A New Kind of Science and even though I am but a few pages in, it appears to be a very promising brain stretcher. Assuming I don't injure my back lifting it, I will let you know if it addresses my questions about the underlying drivers in evolution.

In closing let me say that I appreciate all the great work you all are doing in all 3 podcasts. I value the dialog, spontaneity  and asides and believe that you all capture the emotional enthusiasm that make science such a great life's work.

Joe
EH&S Manager

Peter writes:

Greetings TWiM team

I saw these instructions on instructables.com for culturing bioluminescent bacteria from fresh sea fish and thought they may be of interest.

http://www.instructables.com/id/Bioluminescent-Bacterial-Lightbulb-Water-Polluti/?ALLSTEPS

For those not familiar with it Instructables is a very eclectic DIY site where people can publish instructions for various projects they have done.

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