Home Microbiome- Day 0

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I consider Twitter the social media tool that has been most useful for me. It is not only a real time pulsating (and often distracting) flow of news and information, but also a way to make professional and casual connections. And lately, those virtual conversations have started to show tangible results. From tweetups where you get to meet in real life those people you have been talking to (and often feel you have known for quite a while), to exchange of information, and in extreme cases, to a freezer.

image of a mini freezer

The mini freezer, sitting in the garage

This freezer is part of the Home Microbiome Project, of which you can read here. How did it happen?

Well, of course everything starts with me being an instructor of (among other things), microbiology.  The past years have been exciting in micro, and the fun thing is that the breakthroughs in research have filtered rather quickly to the general public, including students.  I am not sure if it is a general phenomenon related to the availability fo information, or is it that bugs are so interesting- probably a combination of both. The case is that I follow some of the science stuff going on in micro, and one of the threads is the whole microbiome concept. My main interest is still the human microbiota and how it affects health and disease; but still, when I read the word microbiome I usually pay attention. Add Twitter. There are several very active tweeps who are involved with microbiome studies, among them @gilbertjacka, and I became aware of his Home Microbiome project, in which they follow the microbial populations of a home and people before and after a move.  That project sounded really exciting, and when two months ago I got a new position that involves a move, I asked if the study was still going. Not long afterward, a box full with Falcon tubes containing swabs and a bunch of paperwork arrived. Some days later, the freezer made entrance, and was ceremoniously placed in an honorary place in the garage. It has been plugged in for a while, and it seems to work well. 

I am writing this just after midnight. I just activated the gizmos that will record environmental data, and sorted the tubes for early morning’s first swabbing. Two humans and a cat getting swabbed for 6 weeks, every two days. This is so cool.

I guess it is just a geek thing. In my distant past, in places where regulations were not tight, my blood cells became controls of many experiments. Even now, every iteration of a blood lab I volunteer for smears and blood group tests. I have swabbed my wallet, cell phone, and skin at countless micro labs and looked with amazement at the little Staphs growing on the plates.

Anyway, it is day 0 today. The cat has been sneezing, hope he is not getting sick. Hope the microbes filtering from the micro course I will be teaching next week will not upset our microbial ecosystem.

Swab on!

Poisson and Guinness

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picture of Guinness beer

Guinness Beer (By Sami Keinänen (www.flickr.com) [CC-BY-SA-2.0 (http://creativecommons.org/licenses/by-sa/2.0)%5D, via Wikimedia Commons)

The title of Chapter 25 of Zar is Testing for Randomness. Which sounds pretty philosophical.

Definition of random distribution can be applied to objects (each portion of space has the same probability of containing an object, and the occurrence of one does not influence the occurrence of the other), events in time (substitute space for time, and object for event), or periods of time.

The Poisson distribution is important in describing random occurrences when their probabilities are small.

A practical application of this distribution was made by Ladislaus Bortkiewicz in 1898 when he was given the task of investigating the number of soldiers in the Prussian army killed accidentally by horse kick; this experiment introduced the Poisson distribution to the field of reliability engineering.

(Copying here shamelessly from wikipedia): The Poisson distribution arises in connection with Poisson processes. It applies to various phenomena of discrete properties (that is, those that may happen 0, 1, 2, 3, … times during a given period of time or in a given area) whenever the probability of the phenomenon happening is constant in time or space. Examples of events that may be modelled as a Poisson distribution include, among others, the number of yeast cells used when brewing Guinness beer. This example was made famous by William Sealy Gosset (1876–1937).

This interesting fact made me digress from Poisson long enough to learn about Gosset, who seems to be a very interesting character. From Tales of  Statisticians:

Gosset earned a degree in chemistry at Oxford, and joined the Guinness brewery firm in 1899. His work for Guinness led him investigate the statistical validity of results obtained from small samples (previous statistical theory had concentrated instead on large samples). He took a leave of absence to spend 1906/1907 studying under Karl Pearson at University College, London. His publications in Pearson’s journal Biometrika were signed “Student,” not because of a Guinness company policy forbidding publication, as is often said, but more precisely because of a company wish to keep secret the fact that they were gaining an industrial advantage from employing statisticians. Gosset’s most important result is known as the “Student’s t” test or distribution, published in 1908.

Returning to Poisson_ still working on it, but found some pointers.

You will have a variable “x” which is what your random variable is,

then u is the average success (divide n by X)

and you have to use the constant e in your calculations

Poisson Formula. Suppose we conduct a Poisson experiment, in which the average number of successes within a given region is μ. Then, the Poisson probability is:

P(x; μ) = (e) (μx) / x!

where x is the actual number of successes that result from the experiment, and eis approximately equal to 2.71828.

Life became much simpler when I found an online calculator.


To be continued…

Apropos Cell Polarity

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We started Bio620 (Seminars in Cell Biology) yesterday with a guest speaker (more to come) and a discussion of general design principles of cells, a review by Rafelski and Marshall.

Part of the discussion was about how cells become polarized, and so this morning a blog posting caught my eye. It was Elio’s (Moselio Schaecter’s) blog Small Things Considered, which you absolutely want to follow if you are into Microbiology.

picture showing auroras around the Earth poles

NASA’s Polar spacecraft captured the first-ever movie of
auroras dancing simultaneously around both of Earth’s
polar regions.

Today’s posting  refers to polarity in bacteria and, and discusses an article with some novel approaches to identify molecules associated to poles.

The title is: Polar Enchantment.

BioTechniques – Remote-Controlled Gene Expression

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BioTechniques - Remote-Controlled Gene Expression

BioTechniques – Remote-Controlled Gene Expression.

To Keep Yourself Healthy: Brush, Floss, and Measure Your Microbes Daily?


To Keep Yourself Healthy: Brush, Floss, and Measure Your Microbes Daily?.


Very interesting!

Science blogs


a painting by Artologica, showing themes from biology

Exploration 1, by Artologica

Today I ran across a Twitter posting by Paul Knoepfler ‏ @pknoepfler: Professors who blog: academia’s love hate relationship with social media http://bit.ly/JFzB2R @phylogenomics @pzmyers

It was retweeted by Jonathan Eisen (aka @phylogenomics, one of the most engaged and social media-savvy scientists I am aware of). The blog posting by Dr. Knoepfler, a known stem cell researcher, decried the low number of professors who blog. As it happens when somebody posts about a relevant and controversial issue, the comments were as interesting to read as the original post. I hope you will visit it- it has a lot  to do with how “official” science looks with suspicion on side-activities such as blogging, writing, or even outreach- we are talking now of research-intensive universities, where teaching is a distraction and it is number of publications and grants that count in the pursuit of the Holy Grail = tenure.

I got distracted enough to follow the trail of comments and links for almost an hour. One thing that bothers me a lot about academia (and here I talk about high octane, research intensive institutions) is their disconnect from real life and real people. Science writers and bloggers do a lot to make science understandable to non-specialists (and by this I mean both non-scientists or scientists from another speciality), and this is an effort that should be applauded and encouraged. Science funding comes from many sources, and it is just fair that people should understand where their money is going to. Not to mention that we scientists need to make science interesting so young people want to go into science. We are already seeing the anti-science backlash in the climate change and vaccine deniers.

Going back to blogging, I was happy to see a new posting about reader recommended science bloggers, and already checked out some. Check this out also: the best science writing of 2012, in Amazon.

And, keep writing your blogs, please. This is not only a class assignment, it is also a reflection of your journey into deeper science, an online portfolio of your thoughts and interactions with others, and maybe a vehicle that will help your career.

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