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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!


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.

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.

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.


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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