Author: Jonathan Eisen

I am an evolutionary biologist and a Professor at U. C. Davis. (see my lab site here). My research focuses on the origin of novelty (how new processes and functions originate). To study this I focus on sequencing and analyzing genomes of organisms, especially microbes and using phylogenomic analysis

Absence of women from Middle East policy debates

For those who think about the underrepresentation of women in science meetings – this may be of interest: The mysterious absence of women from Middle East policy debates – The Washington Post.  65 percent of the events in Washington DC relating to the Middle East had no female speakers.  Disheartening and something that needs to be dealt with.

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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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Bactopets(c)

There is growing evidence supporting that having pets in the home from a young age can have profound effects on our long-term health. Dozens of recent studies have linked the microbes associated with doggie and kitty cat friendly households to the health of a building’s occupants, including a significantly decreased risk of asthma, allergies, and an overall less resilient microbiome. With such knowledge, parents now face a predicament that is sure to tug on the heartstrings. Parents shouldn’t have to sacrifice the long-term health of their child just because they don’t have the time or money to care for a furry, four-legged, divine carrier of microbes. Now, they don’t have to!

Introducing Bactopets©, a collection of stuffed animals that have the same microbiome as the real animal! Forgo all of the cleaning, pooper-scoopering, and shredded furniture with the same benefits as having a real cat or dog. Bactopets© are inoculated with a Slo-Release Microbial Technology™ to insure maximal effectiveness. We made Bactopets© to be extremely soft and adorable so they are guaranteed to improve your child’s microbiome because your child will be unable to resist the urge to rub it in on their face, snuggle with it (good for maximal microbial respiratory entry), and possibly even suckle on it. Bactopets© are odorless so you can even sneak this as a gift to your child without your germophobic spouse finding out.

Collect them all!

BactoLab© reflects the microbiome of a Labrador retriever who has been swimming in a stagnant pond, rolled on an unidentifiable carcass, chewed on numerous neighborhood sticks, and sniffed dozens of doggie butts. BactoLab© is now available in brown, black, and golden colors.

BactoTabby© reflects the microbiome of a tabby cat who has hunted several mice and birds, dug in a dirty litter box, and explored the most cobwebbed corners of the neighborhood.

BactoPetPlus© is a deluxe version of the aforementioned products with the addition of real pet dander for even greater long-term health benefits.

BactoSpray© is an inoculated dog or cat microbe solution that you can simply spray on your child’s favorite stuffed animal and around your home. BactoSpray© is also available in a more discrete packaging under the guise of “probiotic” to blend in well with your germophobic spouse’s collect of kombucha and yogurt.

 

 

So so so cool: Tangible Interactive Microbiology for Informal Science Education

This is so cool: Tangible Interactive Microbiology for Informal Science Education.

Abstract:

We present an interactive platform that enables human users to interface with microbiological living cells through a touch-screen, thereby generating a tangible interactive experience with the microscopic world that is hidden to most people. Euglena gracilis, single-celled phototactic microorganisms, are imaged and optically stimulated via a microscope setup equipped with a projector and a touch- screen display. Users can directly interact with these organisms by drawing patterns onto the screen, which displays the real-time magnified view of the microfluidic chamber with the motile euglena cells. The drawings are directly projected onto the chamber, thereby influencing the swimming motion of the cells. We discuss the architecture of the system and provide exploratory user testing results in a facilitated setting, which shows engaging nature of our system for children and the general public. In conclusion, our tangible interactive microscope allows artistic expression and scientific exploration with the ease of “child’s play.”

And check out this video.

I would post a picture here but they discourage it.  So you will just have to go look for yourself.  The PDF is free, at least for now.

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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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Today in microbes and art: Bioart and Bacteria – The Artwork of Anna Dumitriu

I could spend a lot of time on this website: Bioart and Bacteria – The Artwork of Anna Dumitriu.  I found out about it from a Tweet from Dumutriu:

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And it is right up my alley (being interested in the interface between art and science, especially in relation to microbes).  Lots of interesting sections here including:

Sequence
Super-organism
Don’t Try This At Home
[micro]biologies: the bacterial sublime

Modernising Medical Microbiology

And many more.  I do not know much about the artist but really glad she pointed me to 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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The best writing in science papers: Part II

Guest post by Stephen Heard (scientistseessquirrel.wordpress.com)
Over 2 years ago now, Jonathan posted “The best writing in science papers: Part I”.  I stumbled across that post and searched excitedly for Part II – only to discover there wasn’t one.  Well, now there is, as Jonathan has kindly allowed me to guest-post this.
Jonathan’s Part I identified the butterfly-taxonomy papers of Vladimir Nabokov as containing flashes of beautiful writing, and I agree (although my favourite bits differ from his).  But Jonathan wondered if picking Nabokov (an acclaimed novelist) was “a bit unfair” and he later told me he’d never done a Part II because other examples were too hard to find! 
Actually, other examples can be found, and not only in the papers of scientists who are also accomplished novelists.  I collected a few in my recent paper “On whimsy, jokes, and beauty: can scientific writing be enjoyed”.  For example, here is Nathaniel Mermin on a surprising result in quantum mechanics:

      “There are no physical grounds for insisting that [Alice] assign the same value to an observable for each mutually commuting trio it belongs to – a requirement that would indeed trivially make her job impossible. The manner in which the nine-observable BKS theorem brings Alice to grief is more subtle than that. It is buried deep inside the mathematics that underlies the construction that makes it possible, when it is possible, to do the VAA trick.”

Here is Bill Hamilton setting up a simulation model of antipredator defence via herding:

      “Imagine a circular lily pond.  Imagine that the pond shelters a colony of frogs and a water-snake…Shortly before the snake is due to wake up all the frogs climb out onto the rim of the pond… [The snake] rears its head out of the water and surveys the disconsolate line sitting on the rim… and snatches the nearest one.  Now suppose the frogs are given opportunity to move about on the rim before the snake appears, and suppose that initially they are dispersed in some rather random way.  Knowing that the snake is about to appear, will all the frogs be content with their initial positions? No…and one can imagine a confused toing-and-froing in which [desirable positions] are as elusive as the croquet hoops in Alice’s game in Wonderland.”

And here is Harry Kroto describing the structure of C60 buckyballs:

     “An unusually beautiful (and probably unique) choice is the truncated icosohedron…All valences are satisfied with this structure, and the molecule appears to be aromatic.  The structure has the symmetry of the icosahedral group.  The inner and outer surfaces are covered with a sea of πelectrons.”

Finally, read this by Matthew Rockman – too much, too good, to even excerpt here.

So, “regular” scientific writers can achieve beauty, too (and please share your own favourite examples in the comments). But I’d have to agree with Jonathan that we don’t do so very often. Why not? I can think of three possibilities:

It could be that writing beautifully in scientific papers is a bad idea, and we know it. Perhaps readers don’t respect scientists who resist the conventional turgidity of our writing form. I don’t think this is true, although I’m aware of no formal analysis.

Or it could be that beauty is a good idea, but well-meaning reviewers and editors squash it. In my paper I argue that beauty (like humour) can recruit readers to a paper and retain them as they read; but that reviewers and editors tend to resist its use. But again, there’s no formal analysis, so I was forced to make both halves of that argument via anecdote.

Or it could be we just don’t have a culture of appreciating, and working to produce, beauty in our writing. I think this is most of the explanation: it’s not that we are opposed to beauty as much as it doesn’t occur to us that scientific writing could aspire to it.

All of which makes me wonder: if we wanted to make beauty more common in scientific writing, how could we do that?  Well, that could make for a really long post.  I’ll mention a few thoughts, and encourage you to leave more in the comments.  
First, we could write with small touches of beauty in our own papers.  Of course, that’s not as easy as it sounds, because most of aren’t trained or oriented that way.  To oversimplify, it’s a chicken-and-egg problem: most of us come from science backgrounds that lack a culture of beauty in writing.  Perhaps we even came to science as refugees from the arts and humanities where beauty is more valued.  That’s true for me, at least; and I know a fair bit about how to write functionally, but almost nothing about how to write beautifully.  But if there’s a path to writing beauty, it probably starts in reading beauty, wherever it can be found.  Nabokov? Sure… but also science blogs, lay essays and books aboutscience and nature (for a start, sample the science writing of Rachel Carson, Lewis Thomas, Karen Olsson, Barbara Kingsolver, or John McPhee), and really, anything we can get our hands on.  And when we read, we can be alert for language that sparkles, so as to cultivate an ear for beauty and to build a toolbox of techniques we can deploy in our own writing.  (For some other thoughts on this, see Helen Sword’s book “Stylish Academic Writing”).
Second, and much easier, we could encourage beauty in the writing of others.  As reviewers and editors, we could decide that style and beauty are not incompatible with scientific writing.  We could resolve not to question touches of style, or unusual but beautiful ways of writing, in the work we are judging.
Finally, we could publicly recognize beauty when we see it.  We could announce our admiration of beautiful writing to the authors who produce it or to colleagues who might read it.  What Jonathan and I have done with these posts is a small start on this, and I’ve promised myself I’ll praise wonderful writing whenever I can.  Thinking bigger, though, wouldn’t it be great if there was an award for the best scientific writing of the year?  I don’t mean the best science – we have plenty of awards for that – but the best writingto appear in our primary literature.  Such awards exist for lay science writing; if one existed for technical writing I’d be thrilled to make nominations and I’d volunteer to judge. 
As Jonathan and I both found, examples of beautiful scientific writing do seem to be unusual; and those that exist aren’t well known.  I don’t think it has to be this way.  W could choose to change our culture, a little at a time, to deliver (and to value) pleasure along with function in our scientific writing.
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By the way: I became interested in beauty in scientific writing while working on a guidebook for scientific writers.  It’s not available yet, but to learn more about it, see my web site.  For more of my (somewhat scattered) thoughts on writing and on doing science, visit my blog.

UPDATE 1/25/15

Now posted on Heard’s Blog.

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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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New Marketing Campaign by Apple

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“An Apple a day keeps the doctor away” – Apple’s New Slogan

Apple has launched a new marketing campaign in an attempt to revitalize interest in their MacBook computers after a researcher found a virtually undetectable mac virus known as  Thundercat  that can effect Apple computers running OS X LabRat.  This campaign involves inoculating Apple MacBook computers with the naturally occurring GMO free bacteria, Canislupis tonitrui, found on organic Red Cumulus strains of apples. Researchers studied a variety of microbes from a variety of apple types before discovering this bacteria which releases anti-viral compounds into its environment.  Apple claims that inoculation with this apple microbe will help prevent MacBook infection by Thundercat and provide other benefits to computer health including longer battery life and decreased frequency of internet pop up ads. Apple also plans to sell this bacteria to current Apple users through a “patch” that you can stick on your computer. These patches will be available for order from the App store shortly.

What do you think of Apple’s new marketing campaign? Will you buy the new microbe “patch” to protect against the Thundercat virus?

A long (and I think good) listen: Tim Ferriss podcast on "the microbiome"

So – I have been travelling a lot lately.  On one of my trips – to Las Vegas and neighboring areas – I was interviewed by Tim Ferriss for his blog.  Jessica Richman of uBiome was also interviewed – she was in SF, Ferriss was somewhere else, and I was on the phone in Vegas.  As soon as it was over I got caught up in the work I was doing there (field work for a new NSF Funded Project on “microbial dark matter”.  Anyway – the interview was entertaining and I think interesting.  And then it came out while I was on the road again for another trip.  So I am just getting around to posting about it now.  Anway – here are some links for the podcast.

Ferriss’ blog post about it: Are We Really 10% Human and 90% Bacteria? Exploring The Microbiome…

Direct links

I note – I have never done such a long interview for a show before (it was about two hours) but Ferriss was remarkably adept at making it relaxing and fun (for me at least).  Even the part about Jim Watson …

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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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Open Faculty Position, Asst. Professor Microbiologist Plant-Soil Systems

Bayer Crop Science in West Sacramento hiring a Bioinformaticist …

Just got this email

Dear Dr. Eisen

I am a Sr Bioinformatics Scientist working within the Biologics Division at Bayer CropScience. We are looking to fill a Bioinformatics Scientist position here in our West Sacramento facility. We are interested in hiring someone with either a MSc and relevant years of experience or someone with a PhD and 1-3 years of postdoctoral experience. I would greatly appreciate it if you could circulate the attached job position or forward the attached job ad to the appropriate candidate(s).

Many thanks.

Best,
Dilara Ally
Senior Bioinformatics Scientist

Biologics

BioinformaticsScientistII_2014.pdf

UC Davis MARS Symposium Wrap Up #globalfood #UCDavisMARS

Yesterday I went to a symposium at UC Davis that was the launching of a new partnership between UC Davis and the Mars Corporation. I note – I have been collaborating with some people at Mars on multiple microbiome related projects and generally have had great interactions with the people there. I am not directly involved in the planning for this new partnership between UC Davis and Mars and thus I was interested in hearing more about it at the symposium.

The symposium was at the Mondavi Center on UC Davis campus and I zipped in on my bike through the cold (for Davis) air and got there just before they opened the doors to the main theater. I saw a few folks I knew milling around in the lobby and said hello and then went inside with some people from my lab for the “show”.

 I will try to write more about this later but just one note – I found some of the big picture discussions about the importance of the nexus between food, agriculture and health to be pretty inspiring. For now – I hope the Storify I made and embedded below will give some idea as to the goings on of the symposium.

//storify.com/phylogenomics/uc-1/embed//storify.com/phylogenomics/uc-1.js[View the story “Symposium at #UCDavis on new partnership w/ Mars: #UCDavisMARS #GlobalFood” on Storify]
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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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