Tag: microbiology

Can food safety be fun? Not sure, but this video is OK. #microbes

Continuing with my running theme of microbe-related music videos here is another one. It has good and bad parts. But then again, don’t we all …

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Microbial music: Christine Lavin and the Amoeba Hop

Always searching for science-art-music combinations.  Especially ones that focus on some aspect of science I work on, like microbes. And, well, though this recording is less than ideal, and you need to wait a minute and a half or so, once you get to the song it is worth it.

The song is “The Amoeba Hop” and the singer is the brilliant Christine Lavin.

I have had this song in my head on and off for years and wanted to post about it for a while.  I finally remembered to Google it tonight after reading a tweet about combining music and biology.  I used to listen to Lavin all the time in college and even went to a show of hers in 1989 in Ft. Collins, CO with my brother and my friend Saul Jacobson.  As a side note – we saw Lavin at some music hall type of place the the night after seeing Killdozer at a VFW post.  As a second side note – the Killdozer show was crazy (and I even found someone else who wrote about it here).

Anyway – not only did I find the video posted above but I discovered she wrote a book in 2002 based on the song – and the book even got a review in the New York Times.   Gonna probably have to get that book at some point …

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Most unusual use of #microbes of the week: fermented fashion

Fermented clothing on mannequin from
http://bioalloy.org/o/projects/micro-be.html

Well, this is certainly unusual: The Genteel | Fermented Fashion.  I found out about this from a Tweet from Irene Kim

Anyway the article describes the “Micro’be'” project for which more details are available here.  Some interesting details at that site include a description

Imagine a fabric that grows…a garment that forms itself without a single stitch!
The fashion that starts with a bottle of wine…
Micro’be’ fermented fashion investigates the practical and cultural biosynthesis of clothing – to explore the possible forms and cultural implications of futuristic dress-making and textile technologies.
Instead of lifeless weaving machines producing the textile, living microbes will ferment a garment.
A fermented garment will not only rupture the meaning of traditional interactions with body and clothing; but also raise questions around the contentious nature of the living materials themselves.
This project redefines the production of woven materials.
By combining art and science knowledge and with a little inventiveness, the ultimate goal will be to produce a bacterial fermented seamless garment that forms without a single stitch. 

So – in essence they are trying to grow clothing as a side product of wine fermentation.  Not sure what it is like to wear such clothing – or to be around someone wearing it – but it is a fun idea.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Pics from the Redrum hotel in DC where we stayed for #SAMG12

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Kimberly-Clark’s deceptive self serving PR regarding germs in the workplace #BadReportingToo

First I saw of this story was here: Study: Bacteria fills office break rooms – Local News – Houston, TX – msnbc.com

Something sounded off with this.  I think it was the fact that it involved “Cleaning products company Kimberly-Clark” that raised some alarm bells.  The involvement of Charles Gerba also left me a bit queasy as I have seen his name associated with a few recent “studies” which are basically germaphobia funded by cleaning product companies.

After looking around a bit I got discouraged at the whole thing and put it out of my head for a few hours.  And then David Coil, a post doc in my lab, sent me a link to the press release behind this story.  And boy is it a doozy.

The PR basically makes the following dubious statements or implications
* All bacteria are bad.  The whole PR references a study that they imply is about detecting bacteria in various locations.  And when they detect high levels they conclude this is bad.  For example in the title “Where the Germs Are: New Study Finds Office Kitchens and Break Rooms are Crawling with Bacteria“.  Or in the text: “If you thought the restroom was the epicenter of workplace germs you don’t want to know about office break rooms and kitchens” “office germ “hot-spots,”” “Office workers are potentially being exposed to illness-causing bacteria right in their own lunchrooms” and much more.  Uggh.  Not all bacteria are bad.  Gerba and Kimberly-Clark must know this yet they purposefully mislead.

* Presence of ATP means presence of bacteria (and see above – this must imply presence of bad bacteria).  Wow.  Not sure what to say here.  But they use a test for ATP which they say  “ATP is present in all animal, vegetable, bacteria, yeast and mold cells. Detection of ATP indicates the presence of contamination by any of these sources. Everyday objects with an ATP reading of 300 or higher are considered to have a high risk for illness transmission.”  No citation given. And sounds highly dubious to go from ATP – > risk for illness.  Sounds completely dubious actually.

* That it is OK to make claims in Press Releases without presenting evidence behind the claims.  The PR tries to make this all seem very scientific.  Well, where is the paper behind this?  They claim “The findings are from a study carried out by Kimberly-Clark Professional* and is believed to be one of the most detailed and comprehensive studies ever conducted on identifying workplace hotspots where germs can lurk.”  Where is the actual data?  Where are the methods described?  Yuck.

Alas – despite the fact that the Press Release is at best a self serving piece of dubious scientific quality – the press has run with the story sucking up everything Gerba and Kimberly Clark are saying.  Ugg.  Here are some examples, many of which really do a poor job on the science and the conflicts of interest inherent in an unpublished study from a cleaning products company

I am getting sick and tired of crap like this.  Kimberly-Clark may make some useful products.  I don’t really know.  But deceptive press releases like this suggest that their dedication to science is, well, low.  They need to clean up their act.
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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Meta-Omics and Phylogenetics Journal Clubs

If you’re looking to catch up on your reading, come to journal club!

The Meta-omics journal club is run weekly on Tuesdays, from 11-12 in 5202 GBSF (organized by the Facciotti Lab, papers are sent around via an e-mail list).

There is also a bi-weekly Phylogenetics journal club run by the Center for Population Biology, 4-5pm every other Friday in Storer 5343 (The Treehouse). Regardless of journal club, there is always a 5pm Happy Hour at CPB every Friday – although be warned there are always are a substantial number of vertebrate biologists in attendence.

Hmm … City of Davis definition of microorganism needs work

From City of Davis Guide to Composting

MICROORGANISM microscopic plants and animals.They exist in soil for the purpose of breaking down organic matter into basic mineral elements.They include bacteria, fungi, actinomycetes, algae, protozoa, yeast, germs, ground pearls, and nematodes.

Gonna have to get them to work on this …

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Interesting 2011 pub on origin of multicellularity in cyanobacteria

Just a quick one here.  There is an (openaccess) publication I thought people might find interesting: The origin of multicellularity in cyanobacteria.  Schirrmeister BE, Antonelli A, Bagheri HC. BMC Evol Biol. 2011 Feb 14;11:45.

In particular it has some very nice figures on phylogeny of cyanobacteria and the evolution of phenotypes in the group.

Figure 1. Phylogenetic tree of 1,254 cyanobacterial species. 
Figure 4. Phylogenetic tree of a cyanobacterial subset. 

Some of the same authors also have a paper on the need for better phylogenetic sampling of genome data in the group:

Evolution of cyanobacterial morphotypes: Taxa required for improved phylogenomic approaches. Schirrmeister BE, Anisimova M, Antonelli A, Bagheri HC. Commun Integr Biol. 2011 Jul;4(4):424-7. Epub 2011 Jul 1.

Though I note, I am a bit annoyed and surprised they did not cite my “Phylogeny driven genomic encyclopedia” paper in this pub …

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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First "Guardians of microbial diversity" award to Rob Dunn #microbiology #GMDs

For this I am awarding him the first of what will be many “Guardians of Microbial Diversity” awards here (we can just call these the GMDs). Not only will he get an award – I am going to send him a GMD gift from the various GMD doodads I am putting together.
Congratulations Rob.  Now off to design some more diverse GMD doodads. 
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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Draft post cleanup #8: Don’t let a hospital kill you – CNN.com

Yet another post in my “draft blog post cleanup” series.  Here is #8 from 5-1-2008
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Saw an interesting article today on CNN.Com: Don’t let a hospital kill you – CNN.com.  It has some useful suggestions for how to protect yourself from infection in a hospital.  In many cases we have an excessive fear of germs which can be a bad thing.  But in hospitals, staying clean is almost certainly a good idea …

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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