Some answers to "Wanted-good simple guide to the statistics of sampling design for field ecology studies"
I asked a question on twitter "Wanted - good simple guide to the statistics of sampling design for field ecology studies" and got some useful answers, which I have "storified" below. Any additional suggestions welcome.
Full list of 2012 American Academy of Microbiology Fellows Announced
Just got this email and well, I thought I would share. I would share even if I was not on the list since, well, I love microbes and microbiology. Note the list is also available on the AAM Web site here.
The American Academy of Microbiology is honored to welcome these new Fellows, elected in recognition of their records of scientific achievement and original contributions that have advanced microbiology:
- James B. Anderson, Ph.D., University of Toronto, Mississauga, ON, Canada
- Dan I. Andersson, Ph.D., Uppsala University, Sweden
My obsession with a Field Guide for Microbes
Recently I gave a talk at the AAAS Meeting in Vancouver on my dream of having "A Field Guide to the Microbes". The talk was part of a session on the "Earth Microbiome Project" organized by Jack Gilbert and others.
You can see a slideshow with audio of my talk below:
It seems that my talk has sparked a lot of interest as I have been interviewed by various people and publications about this concept.
For example, Holly Menninger recently interviewed me for a blog post for the "Your Wild Life" blog:
Is a Field Guide for Microbes in Our Future? Q & A with Microbiologist Jonathan Eisen.
And today a wonderfully illustrated piece came out at Wired.Com by Daniela Hernandez titled "Book of Germs: A Quest for a Field Guide to Microbes."
If you are interested in some more background on what I have been thinking about a Field Guide to the Microbes here are some previous things I have written or said or commented on relating to this topic:
You can see a slideshow with audio of my talk below:
It seems that my talk has sparked a lot of interest as I have been interviewed by various people and publications about this concept.
For example, Holly Menninger recently interviewed me for a blog post for the "Your Wild Life" blog:
Is a Field Guide for Microbes in Our Future? Q & A with Microbiologist Jonathan Eisen.
And today a wonderfully illustrated piece came out at Wired.Com by Daniela Hernandez titled "Book of Germs: A Quest for a Field Guide to Microbes."
If you are interested in some more background on what I have been thinking about a Field Guide to the Microbes here are some previous things I have written or said or commented on relating to this topic:
- Editorial I wrote in 2009 w/ Catrionna MacCallum for a collection of articles in PLoS Journals on the Genomics of Emerging Infectious Diseases: PLoS Biology: Genomics of Emerging Infectious Disease: A PLoS . It has a box on a Field Guide to the Microbes.
- Microbe Magazine Article interviewing me: Genomic Analyses Could Lead to “Field Guide to Microbes”
- Press release from project in 2005: Poison + water = hydrogen. New microbial genome shows how
- Talk I gave in November 2011 at the Compass Summit on 'The Dark Matter of Biology."
And if you want to check out some "Field Guide" like books on the topic of microbes I am posting some recommendations on an Amazon Page. My favorite is "A Field Guide to Bacteria" by Betsey Dyer.
Task force investigating #UCDavis Pepper Spray Incident report to be released 3/6
Just got an email from UC Communications
"Former California Supreme Court Associate Justice Cruz Reynoso, chair of the task force investigating the pepper-spray incident on November 18, 2011, said today the task force is working toward public release of findings and recommendations on Tuesday, March 6, at a time and location on the UC Davis campus to be determined.
Additional information will be provided as soon as it is available."
Guest post from Russell Neches @ryneches, PhD student in my lab "Blogging his qualifying exam"
Below is a guest post from Russell Neches a PhD student in my lab.
Blogging my Qualifying Exam
Because this seems to be my default mode of organizing my thoughts when it comes to research, I've decided to write my dissertation proposal as a blog post. This way, when I'm standing in front of my committee on Thursday, I can simply fall back on one my more more annoying habits; talking at length about something I wrote on my blog. Or, since he has graciously lent me his megaphone for the occasion, I can talk at length about something I wrote on Jonathan's blog.
About a million years ago (the mid-Pleistocene), one of Kamchatka's many volcanoes erupted and collapsed into its magma chamber to form Uzon Caldera. The caldera floor is now a spectacular thermal field, and one of the most beautiful spots on the planet. I regularly read through Igor Shpilenok's Livejournal, where he posts incredible photographs of Uzon and the nature reserve that encompasses it. It's well worth bookmarking, even if you can't read Russian.
The thermal fields are covered in hot springs of many different sizes. Here's one of my favorites :
The experienced microbiologists on the expedition set about the business of pursuing questions like Who is there? and What are they doing? I was there to collect a few samples for metagenomic sequencing, and so my own work was completed on the first day. I spent the rest of my time there thinking about the microbes that live in these beautiful hotsprings, and wondering How did they get there?
Extremophiles are practically made-to-order for this question. The study of extremophile biology has been a bonanza for both applied and basic science. Extremophiles live differently, and their adaptations have taught us a lot about how evolution works, about the history of life on earth, about biochemistry, and all sorts of interesting things. However, their very peculiarity poses an interesting problem. Imagine you would freeze to death at 80° Celsius. How does the world look to you? Pretty inhospitable; a few little ponds of warmth dotted across vast deserts of freezing death.
Blogging my Qualifying Exam
Because this seems to be my default mode of organizing my thoughts when it comes to research, I've decided to write my dissertation proposal as a blog post. This way, when I'm standing in front of my committee on Thursday, I can simply fall back on one my more more annoying habits; talking at length about something I wrote on my blog. Or, since he has graciously lent me his megaphone for the occasion, I can talk at length about something I wrote on Jonathan's blog.
Introduction : Seeking a microbial travelogue
Last summer, I had a lucky chance to travel to Kamchatka with Frank Robb and Albert Colman. It was a learning experience of epic proportions. Nevertheless, I came home with a puzzling question. As I continued to ponder it, the question went from puzzling to vexing to maddening, and eventually became an unhealthy obsession. In other words, a dissertation project. In the following paragraphs, I'm going to try to explain why this question is so interesting, and what I'm going to do to try answer it.
Last summer, I had a lucky chance to travel to Kamchatka with Frank Robb and Albert Colman. It was a learning experience of epic proportions. Nevertheless, I came home with a puzzling question. As I continued to ponder it, the question went from puzzling to vexing to maddening, and eventually became an unhealthy obsession. In other words, a dissertation project. In the following paragraphs, I'm going to try to explain why this question is so interesting, and what I'm going to do to try answer it.
About a million years ago (the mid-Pleistocene), one of Kamchatka's many volcanoes erupted and collapsed into its magma chamber to form Uzon Caldera. The caldera floor is now a spectacular thermal field, and one of the most beautiful spots on the planet. I regularly read through Igor Shpilenok's Livejournal, where he posts incredible photographs of Uzon and the nature reserve that encompasses it. It's well worth bookmarking, even if you can't read Russian.
The thermal fields are covered in hot springs of many different sizes. Here's one of my favorites :
Each one of these is about the size of a bowl of soup. In some places the springs are so numerous that it is difficult to avoid stepping in them. You can tell just by looking at these three springs that the chemistry varies considerably; I'm given to understand that the different colors are due to the dominant oxidation species of sulfur, and the one on the far left was about thirty degrees hotter than the other two. All three of them are almost certainly colonized by fascinating microbes.
The experienced microbiologists on the expedition set about the business of pursuing questions like Who is there? and What are they doing? I was there to collect a few samples for metagenomic sequencing, and so my own work was completed on the first day. I spent the rest of my time there thinking about the microbes that live in these beautiful hotsprings, and wondering How did they get there?
Extremophiles are practically made-to-order for this question. The study of extremophile biology has been a bonanza for both applied and basic science. Extremophiles live differently, and their adaptations have taught us a lot about how evolution works, about the history of life on earth, about biochemistry, and all sorts of interesting things. However, their very peculiarity poses an interesting problem. Imagine you would freeze to death at 80° Celsius. How does the world look to you? Pretty inhospitable; a few little ponds of warmth dotted across vast deserts of freezing death.
Nice #openaccess review on the ecology of chemosynthetic symbioses from @chicaScientific & Guus Roeselers
 |
Figure 1 from 10.1007/s00253-011-3819-9. Sediment cross section
exposing the characteristic Y-shaped burrow dug by S. velum.
Positioning itself at the triple junction of the Y, the bivalve alternates
between actively pumping oxygenated water from the upper arms of
the burrow through the mantle cavity and across the gills and
accessing reduced sulfur compounds diffusing up from the anoxic
zones below and pumped through a ventral incurrent opening in the
mantle. Scale bar equals 2.5 cm
|
For those who do not know, I got my first taste of microbiology research when I was an undergrad at Harvard and I did my senior/honors research project in the lab of Colleen Cavanaugh. Colleen studied (and in fact still studies) symbioses between invertebrates and chemosynthetic bacteria. The bacteria basically allow these invertebrates to function like plants in many ways. Some of these invertebrates (like the giant tube worms in hydrothermal vents) have lost their mouths and digestive systems and basically live by bringing in high energy chemicals for their symbionts which then make sugars, vitamins, amino acids and other goodies for the host.
My favorite new thing/site on the web: Download The Universe
I am completely fascinated by this new site: Download The Universe. It is a group effort from (so far) some 16 science writers. The main goal of the site is summarized in a post from Carl Zimmer who appears to be the instigator in chief of this effort:
"... It is still tough for readers to discover new science ebooks. Traditional book reviews limit themselves to works on paper. Some ebooks may appear in computer magazines, but buried in reviews of laptops and printers. In between, we need a community.
Download the Universe is a step towards that community. It is the work of a group of writers and scientists who are deeply intrigued by the future of science books. (You can find our names and links to our web sites on the right.) Here we review science ebooks--broadly defined, except for ebooks that are just spin-offs of print books. We hope to build up a library of titles that curious readers can browse. Some reviews will be positive, others negative. We welcome your own judgments, and we look forward to vibrant (but civilized) discussions in the comment threads. We will also write essays from time to time about the changes that publishing is undergoing.
As we continue to build Download the Universe, we may change our minds about the scope of its mission. We can't say what those changes will be. We can only be sure they will be here before too long."
I confess - I have never read an ebook of any kind - science or not. And I really really love "real" books - I have collected them for years and years. But I think I am going to start on the ebooks thing. And this site is giving me some ideas for what to start with ... This site is definitely worth checking out, and keeping an eye on ...
In case you didn't hear - #openness WON - Research Works Act shelved
See this story from infojustice.org: Research Works Act Shelved by Sponsors
This is just awesome news. The act was completely inane.
Hooray for Open Access and Open Science and Openness in general.
(Data driven life)^10 featuring Larry Smarr @lsmarr
I saw (briefly) Larry Smarr today at a TTI Vanguard Conference on Hacking Life. I missed his talk yesterday unfortunately but after my talk today on microbes he sent me this article: The Patient of the Future - Technology Review.
For those of you who do not know Larry, well, you should get to know him as he is a pioneer in getting to know himself. As background - I have known Smarr for about 7 years now as I have interacted with him over metagenomic analysis.
If you want to know more about Smarr's background, well, it is amazingly impressive as all heck (see his Wikipedia entry for example). He has been a pioneer in computing, supercomputing, and engineering - and is a member of the National Academy of Engineering as well as the head of CaLIT2.
Anywho, a few years ago Smarr had an epiphany of sorts - he became - well - a bit obsessed with his own personal phenotype. This came in part from medical issues that cropped up in his life but I am sure it also came in part from his nature. So rather than sit back and let the winds of general indifference from MDs knock him around, he decided to take control. And now he has gather more information about himself than virtually anyone on the planet.
Over the years Larry has told me about some of his explorations of his own personal information. But I confess I was not really getting the point. But slowly I have come around to the notion. One thing that helped move me in this direction was when I went to a party for the release of Thomas Goetz's book "The Decision Tree." (I note - I also ended up losing a dollar bill to Jason Bobe - but that is another story). I got a copy of the book and read it - and this made me realize that technological advances - which are a big part of my work on microbes - are also making it easier for people to gather data about themselves. Goetz in the book discusses in part how technology can help enable people to engage more in decisions about their health by providing them with more information.
And though I read Goetz's book it all still seemed a bit abstract to me. Certainly - more and more people were engaging in what has been called "The Data Driven Life" or the Quantified Self or the Measured Life. And on some topics I know people were recording information quite obsessively (e.g., about sleep wake cycles, or food consumed, or whatever). But what really opened my eyes to the whole notion was a meeting I had with Smarr about a year ago.
I was in San Diego to give a few talks and participate in some meetings about "Beyond the PDF." And for my talk at UCSD I told my host(s) that I really did not want too many meetings - I just wanted to meet with a couple of people. And Larry Smarr was one of them. I had lunch with Larry and then went to his office where he showed me his data about himself. Holy crap. It was completely mind blowing. In a fascinating way. And a strange way. But more fascinating than strange. He had been ordering blood tests, and microbe tests and genetic tests and reading all the literature and then ordering more tests and recording his health status regarding all sorts of things.
And this is when I think it hit me - this is real - this is about specific individual people. The data is not just a bunch of numbers that a scientist will use to do an in depth study of a person. This is a person doing an in depth study of themselves.
Going back to the new article about Smarr - it discusses his continuing efforts to learn about his own medical ailments as well as predict and monitor his health condition. He will dig and dig and dig as much as he can - even more so than the last time I saw him. For more about Smarr and his self-data question see for example: How one quantified-self patient is working to transform health care and his website which has links to talks, videos, papers, etc.
Here is a recent video of a talk of his: It is clear in this that Smarr is a pioneer. But he is not alone. Much more is coming. With electronic medical records, with cheaper and cheaper sensors, with better data storage and processing tools - many more people will do this.
Of course, data is not knowledge. I see this issue every day in "metagenomic" studies and in the general and continued overhyping of genomics. But massive amounts of data gathered smartly and used smartly could really revolutionize medicine. Imagine if we all did this. Even better - imagine if we all did this AND shared the data. This notion is in part what the "personal genome" project from George Church is about. In that project people are releasing their genome data as well as personal medical data openly. But as far as I know the Personal Genome Project (PGP) is not driving the massive continuous collection of information about the participants in the way of Smarr. I note - after I saw Smarr in San Diego I began to move more towards sharing my own personal data and now, for example, have posted data to the PGP.
Certainly there are challenges ahead. Privacy for example is a big issue. Target may be able to infer a lot about ones medical conditions from their shopping patterns, but using that information has risks. And of course, even if one is not worried about one's own privacy there are risks. Information about you can reveal information about others. This is obvious in terms of genetics - releasing information about yourself does reveal at least probabilities for your relatives. But it also is true for all sorts of other data. Your microbes for example, could say a lot about other people you interact with (consider the extreme - finding gonorrhea on ones skin ...).
Anyway - just thought it would be good to post about this issue. Sorry if it rambled a bit - been a bit of a long day. Now if only I had been recording all my personal health stats all day I could now if, while I was writing this, I was all here or not ...
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