Tuesday, September 28, 2010

So crappy it is awesome: Paper from Poo

Well, here is one for you microbiome fans out there.  Went to the UC Davis Vet School store on the way to work and found a display selling Paper from Poo. Not human poo of course but from animals that have a lot of fiber in their diet, like pandas, cows, horses and elephants. Some of the slogans are great such as:

"We take the 'OO' out of Poo!"

"We're number one at number two"

Here are some pics of the display:

For more on this see the PooPooPaper website.

Monday, September 27, 2010

BIS002C "Biodiversity & the tree of life" Lecture2&3 more on phylogeny & trees

Well, tomorrow is going to be a bit crazy for me.  I teach four lectures tomorrow for "BIS002C - Biodiversity and the Tree of Life" and UC Davis.  Well, actually, I do each of two lectures twice.  This happens for two reasons.  First, there are two sections for the class and the way we do it, each faculty gives each lecture for which they are responsible twice.  Second, on Mondays, we do two lectures for each section.  In total there are four lectures per week and our schedule is as follows

Section A:  MWF 11-12 M 6-7
Section B: MWF 3-4 M 7-8

So tomorrow at 11 AM I give Lecture 2 for the class to Section A.  Then at 3 PM I give Lecture 2 to Section B.  Then at 6 PM I give Lecture 3 to Section A.  Then at 7 PM I give Lecture 3 to Section B.  Well, enough trying to make it seem like I am working hard.  Especially after PZ Myers gave me a little grief about this on twitter since, well, my teaching load is not actually that big compared to many.

Anyway - back to the class.  I am going to be posting about the class here as much as I can.  To give people an idea of the whole course this is the general highly simplified schema:

Lectures 1-5 Phylogeny (me)
Lectures 6-13 Microbes (Bacteria, Archaea, microbial euks) (me)
Lectures 14-21 Plants and relatives (Jim Doyle)
Lectures 22-24 Fungi  (Jim Doyle)
Lectures 25-36 Metazoa (Susan Keen)
Lectures 37-38 Wrap up, symbioses, etc (Susan Keen)

I do Lectures 1-13 and possibly 37-38.

For the first week or so I am introducing the students to various aspects of phylogeny and phylogenetic trees.  We do this in part because the rest of the class is oriented around using phylogenies and phylogenetic trees so it is important that the students really understand them.

To that end, tomorrow here is the plan:

Lecture 2 will focus on (a) the components of a phylogenetic tree and what they mean plus (b) taxa and groups in trees.  Among the topics we will cover are rooted trees, rotating trees (e.g., vertical vs. horizontal), rotating branches in trees, monophyletic groups/clades, non monophyletic groupings, outgroups vs. ingroups and more.  Oh in addition we will show the awesome Tree of Life movie that we did not get to on Friday. See below

Lecture 3 will then focus on characters and on tracing character evolution on trees.  Among the topics we will cover include traits vs states, homology, ancestral vs. derived, synapomorphies, and the many faces of homoplasy.  Am planning to start posting slides from the class after lecture hopefully starting soon.  But I keep refining them so not going to post before I am close to done ....

Any comments or suggestions welcome ...

Thursday, September 23, 2010

BIS002C "Biodiversity & the tree of life" Lecture 1 tomorrow: Intro to phylogeny; #UCDavis

Well, tomorrow begins some serious craziness here at UC Davis for me.  School started today for the Fall Quarter here and tomorrow a class I am co-teaching (with Jim Doyle and Susan Keen) has its first lecture.  The course is labelled BIS002 C "Introduction to Biology".  It is the third class in a three course/three quarter series.  BIS 002A covers molecular and cellular biology, genetics and related topics (just lecture).  BIS 002B covers the principles of ecology and evolution (with a lab).  And BIS 002C covers "Biodiversity and the Tree of Life" (also with a lab).

A few things to note.  First, each of these courses has to get taught each quarter here, since so many students major in or do something related to life sciences here at Davis.  And on top of this, each course has some 6-700 students (or more).  Alas, since we do not have a lecture hall big enough for this number of students, we have to give each lecture twice.  This means that, for BIS 002C which I only teach a little over a third of, I end up giving 24 lectures over three weeks (2 sections x 4 lectures per week per section = 8 lectures / week).  It is a bit crazy shall we say.  But fun too.  In total, some 2500+ students go through the series per year.

So, tomorrow it begins for me for 3+ weeks of intensity.  But I look forward to it I guess each year since the topics I cover I hold near and dear to my heart.  For the first week of the class, I will introduce the students to phylogeny (what is it, what are phylogenetic trees, how do we infer them, how do we use them).  Then I spend two whole weeks discussing microbial diversity - phylogenetic and functional.  I view this as a privilege in many ways as it is somewhat unusual for 8 lectures to be used in an introductory course on microbial diversity.

Anyway, I will be posting here some comments and details about the class and I thought I would give this tiny introduction.  Tomorrow we will spend some time introducing the course and discussing practical details and then I will get 20-30 minutes to introduce students to phylogenetic trees.  The whole series currently uses as a textbook "Life: The Science of Biology, 8th Edition" by Sadava et al (we are switching over to the 9th edition but not for this quarter) and for class I try to use as many figures from the text as possible.  But I also mix in my own here and there.

Here is an outline for tomorrow after the course intro

1. Introduction to biodiversity of life
2. Discussion of phylogeny
   * Definition
   * Show a few trees
3. Discuss how trees are oversimplifications of true evolutionary history but are useful
   * Populations not shown
   * Not all lineages shown
   * Complication of reticulation/gene transfer
4. Describe different components to a tree
5. Walk through the course outline using a tree of life as a guide
6. 3-4 examples of uses of phylogenetic trees
7. If time permits show a little movie (see below)

Wednesday, September 22, 2010

Quick Tip: if you want someone to share job ads, announcements, etc, send links to web sites not attachments

OK I have had it. I have had it with people who send me job ads and meeting announcements and other things they want me to "share" with colleagues or students. I got six such requests today - two for job ads, two for course announcements and two for meeting announcements.

But this rant may not be what you think. I am not annoyed that they want me to share something. I actually like doing this. What I am annoyed with is how people do this. 95% of the time people send these email requests with an attachment and expect me to forward this on to all who might be interested. And much of the time these attachments are big files, sometimes written in programs that only some people can open.

Does this work some of the time? Sure. Do I sometimes forward these on? Sure. But that approach is so 2005. Here in 2010 there are better ways than email blasts to people who mostly just click delete. In my opinion, the best way to get someone to share something like this is to post your announcement on the web somewhere and then send people a link to the web site. Include a brief summary in the email you send around and if people want more information they can go to the web site. Not only does this save some bandwidth and not clutter up peoples email servers, but it also allows those of us who share via Twitter and Friendfeed and Facebook and so on to more easily send the announcement around. I am sure many people prefer the attachments, but I for one get 50+ attachments a day, almost all of which do not get looked at.

UPDATE 9/23/2012
So - the post above was written two years ago, almost to the day.  And not much has changed.  Excepted perhaps the way people share links (I mention Friendfeed above --- I guess I that could be replaced by Google+).

What is an easy way to post a document and then send people a link?  There are many ways to do this including

  • Post as a Google Doc/Presentation in Google Drive and send the link
  • Upload to Dropbox or another such site and, well, share the link
  • Post as a blog post (if you have a blog) or friggin start a blog and post it there
And of course many many other ways.  But please please please stop sending all these files around.  For a while I was posting them to my blog (I can autopost by forwarding email messages to the right address).  But I am sick of doing this for other people and am going to stop.

Sunday, September 19, 2010

Probiotic use spreading, lots of money being made, known benefits still murky

A little news report from last week prompted me to write this mini post.  The report (Global probiotics market approaching $30bn by 2015: Report) indicates that the use (and purchase) of probiotics is spreading globally.

I find the whole thing pretty interesting actually. I personally think that at some point we will be able to figure out how to use "good" microbes to manipulate and manage human health and performance in all sorts of ways.  And there is more and more evidence that in some cases probiotics can have positive effects.  So in a way it is not surprising that more and more people are buying and using probiotics.

On the other hand, the evidence showing that probiotics are actually beneficial is still limited.  I note, this is why I have started giving out an "Overselling the microbiome and probiotics award" here.  So far, the best simple site I have found discussing probiotics is from NCCAM - the National Center for Complementary and Alternative Medicine.  This may come as a surprise to some (as it did to me), since NCCAM has been severely criticized by many for its support of pseudoscience (e.g., see here).  I note I am not even remotely trying to defend much of what NCCAM does here.  I am simply pointing out that they have a decent resource on probiotics.

For more on the science of probiotics see "Probiotic Microbes: The Scientific Basis" from ASM.  The report references above clearly seems to overstate the potential of probiotics by suggesting that they are being targeted for use in all sorts of health situations without presenting the caveats that these health benefits are not that well established.

Anyway, given that the evidence for benefits of probiotics is still pretty sparse, the fact that their use is spreading very rapidly is I guess a little bit disconcerting.  I would be willing to wager that a lot of the spread has to do with deceptive marketing practices by probiotic suppliers.  But there is a silver lining to this.  I think over the next few years we will see many new discoveries relating to where and when probiotics can help people and animals and such.  And the fact that the notion of "good microbes" is spreading is a good thing since we certainly need to reduce the "kill all microbes" mentality that has pervaded in some circles (consider the use of antibiotics in all sorts of materials).

Anyway, just a little post here about the spread of probiotic purchasing.  One thing I will end with - the report referenced above mentions that probiotics are being put into all sorts of new foods including "chocolates, cheese, muffins, and sausages".

Sunday, September 12, 2010

Lake Arrowhead Microbial Genomes notes, live streaming, I hope here, #LAMG10

Will be posting to Twitter notes on the Lake Arrowhead Microbial Genomes Meeting and am experimenting with FriendFeed and other embedding here. Hope this works for those not using Twitter.

Probiotics are the new viagra & the risks of overselling of probiotics

For crap's sake.  Really.  This is for crap's sake.  I have been sniffing around the web looking into stories about probiotics and, well, it is scary.  So much of the stuff out there is so incredibly awful.  There are so many sites out there offering probiotics for sale it reminds me of viagra.  But in a way this is way worse, because at least viagra sales only really offer to cure one kind of ailment.  Probiotics offer to cure everything under the sun.  And more.  And along with these offer's to cure everything come some seriously worrying practices.

Take for example this press release: New Website Offers Analysis On Top Probiotic Supplements.  This new website is "BestProbioticReviews.Com" and it portrays itself as some sort of neutral party.
BestProbioticReviews.com is a comprehensive yet easy-to-read guide offering product reviews on the top 3 probiotic supplements on the market today. Learn more about the best probiotic supplements and their review today.
They go on to report that
Based on the tests performed, the best probiotic supplement that has achieved the highest possible rating is Nutraelle DigestiveCare. The probiotic supplement received high marks because it was said to help consumers improve their overall digestive health, immune defense, and little to no side effects.
And follow this with
Of course, BestProbioticReviews.com wasn’t set out to provide just product information. We’ve included a special section outside of digestive health and showed our readers’ probiotics help in many ways other than just inside the gut. We discuss how probiotics in general can help (http://www.bestprobioticreviews.com/probiotics-IBS.html) probiotics IBS relief, bacterial vaginosis, yeast infections, and respiratory health problems like asthma.
So - they first imply they are neutral.  Then they tell you about the small benefits of probiotics and then go on to discuss how probiotics can help with lots of other ailments.  And then they link out to sites for buying the three different kinds of probiotics they recommend.  The #1 recommended priobiotic is something called Nutraelle which apparently has all sorts of benefits, though the * tells us none are supported by the FDA.

Anyone want to bet that this web site is actually somehow affiliated with one or all of the places it recommends?  Interestingly, if you look at who is running this site it says it is:

Kelly Moore
Best Probiotic Reviews.com
815 1st Avenue
Seattle, Washington 98104
(206) 624-3313

A little snooping around finds a press release from the same phone number for Alpranax - a claimed anti anxiety med.  The web site for this med has some striking similarities to the one for the probiotic promoted by Kelly Moore.

And alas, looking around the web for people selling probiotics, it really is starting to resemble those selling erectile disfunction treatments or various other therapies. Now mind you, I am not saying here that probiotics do not have potential.  They have been shown, here and there, to have positive benefits for a variety of ailments.  But I am going to repeat something here I have been posting every once in a while:
For the statement "X manipulations of microbes help treat X ailments in X people X of the time": X="some" NOT "all"
Or, in other words, the few studies that have been done on probiotics have shown that they can be effective in some people some of the time to treat some ailments.  But extending this concept to all probiotics help treat all people all of the time for (all or many) ailments is ridiculous. And alas, that is what some supporters of probiotics are doing.

For fun, here are some links discussing some issues with claims about probiotics

Here is some interesting reading relating to the potential for government regulation of claims about probiotics:

I hate to see more regulation by the government without justification.  But I am starting to wonder here if some more stringent regulation may be needed here.

Personally, I think probiotics have a lot of potential.  And more and more scientific studies are telling us where that potential is, and where it is not. But this risks getting lost in the midst of overselling, scams, and deceptive practices.  Here's hoping evidence becomes more a part of the culture (pun intended) here.  

Friday, September 10, 2010

Searching twitter for science related topics; best strategies? favorite searches?

I have been experimenting with different twitter searches relating to genomics, microbiology, evolution, and other work things and find it actually somewhat fascinating.  The key thing has been to try and find searches that pull out useful / interesting stuff but not crap.  For some topics, this is easy, like microbiome and metagenomics.  These work well for a few reasons I think including that they are technical but used somewhat commonly within the fields in which I am interested.

You can try to get a bit more specific with them if you look for the hashtag version of these words: #microbiome and #metagenomics.  This works OK for #microbiome but #metagenomics yields nothing right now.

Unfortunately, some potentially useful terms have been coopted by all sorts of non-interesting stuff. Consider evolution and bacteria, for example.  In these cases, the words are too commonly used either for non sciency stuff (e.g., evolution of skateboards just came up) or for non interesting stuff (e.g., kitchen cleaners come up a lot with the bacteria search).  In these cases, the hashtag versions are better though imperfect: #evolution and #bacteria.

The key seems to be to find terms that are used somewhat narrowly to be only about the topic you care about but are also used widely enough so that a lot of people in the field of interest use them.

Here are some of my current favorite/most useful search terms:

If you want, you can always go beyond these and do more advanced searches.  But I tend to stick to the simple ones much of the time.  I know many people do all their searching within twitter clients, and each has their own flavors of options, but for a few reasons I prefer to do searching directly at the twitter site.   

I continue to experiment with different approaches to this and would welcome any ideas for best ways to pull out useful material. 

Also, I am curious.  Do others out there who use twitter have some favorite terms they search for?

Wednesday, September 08, 2010

Blog sponsorship spam - no thanks; wonder if this is how Pepsigate started?

Got this one today (see below).  Been nice knowing everyone.  Will be getting rich soon and will drop this blog like a stone.
Hi my name is Taj Jones and I'm a blog spotter. I basically scour popular blogs in an effort to find great writers. I loved your post on A complete summary, nice job!

I'd like to get straight to the point.

Our client wants people like you to sponsor their products and will pay you to do so.

They're launching an educational product on September 7th that teaches others how to make money on the internet by using Facebook and Social Media.

We want to pay you for recommending that product to your loyal blog readers and we will pay you up to $200 for each person that you refer. If you make just one sale a day you're looking at making around $6000 per month.

All you need to do is create a few blog posts that recommend this product. You may also use one of our nice banners and place it on your blog.

It's pretty simple, takes very little time (10 minutes or so) and will be very rewarding.

All sales that you refer are tracked through your own special link and you will get paid every week. Payments are always on time and will be sent to you via Check.

This deal is totally legitimate and we will NEVER ask you for any fee, or to sign any contracts.

What do you need to do if you are interested?

I have more details, a video and instructions for you here:

(Sorry all, I am not posting the link)


Taj Jones

Tuesday, September 07, 2010

More of the worst conference descriptions ever

Well, I got invited to another conference that is brought to you by the same people who brought us what I thought was possibly the worst conference ever: Science Conference SPAM: ICEME2011 on all of engineering & metaengineering.  But amazingly this one is just as bad.  Well, actually, these ones - it is two conferences. See http://www.iiis2011.org/imcic/website/default.asp?vc=28 and http://www.iiis2011.org/imcic/website/default.asp?vc=3. I guess I could show you the title of the conference but the web address is informative.  I would bet that some other numbers at the end end up being used for other conferences.

Anyway see the letter at the end of this post - it is very similar to the one for the ICEME meeting.  The best part is when one goes to the "About the conference" sections.  For example see here
CCCT 2011 is an International Conference that will bring together researchers, developers, practitioners, consultants and users of Computer, Communications and Control Technologies, with the aim to serve as a forum to present current and future work, solutions and problems in these fields, as well as in the relationships among them. Consequently, efforts will be done in order to promote and to foster the analogical thinking required by the Systems Approach for interdisciplinary cross-fertilization, "epistemic things" generation and "technical objects" production.

Can't wait for this meeting on Microbial Communities as Drivers of Ecosystem Complexity

I truly can't wait for this meeting: Keystone Symposia Conference | Microbial Communities as Drivers of Ecosystem Complexity - Program

Organizers: Jacques Ravel, Vincent B. Young, Mitchell Sogin and Trina McMahon. March 25 - 30, 2011 • Beaver Run Resort  •  Breckenridge, Colorado

The current program is listed below.  Still time to register.  Oh, and it is in Breckenridge, CO, which is kind of nice.  If you are interested in microbial communities, especially molecular studies of said communities, this could be the place to be ...
  • Norman R. Pace, University of Colorado at Boulder, USA 
    Molecular Analysis of Microbial Communities - Historical Perspective
  • Mitchell Sogin, Marine Biological Laboratory, USA Long-Tailed Microbial Communities
  • Susan Lynch, University of California, San Francisco, USA Microbial Community Analysis Using the PhyloChip
  • Jonathan A. Eisen, University of California, Davis, USA Phylogenetic and Phylogenomic Approaches to Metagenomic Analysis
  • Joseph Petrosino, Baylor College of Medicine, USA Sequencing Technologies Applied to Studying Microbial Ecology
  • Patrick D. Schloss, University of Michigan, USA Developing and Validating Tools for Computational Microbial Ecology
  • Rob Knight, University of Colorado, USA Quantitative Insights into Microbial Ecology
  • Jed Alan Fuhrman, University of Southern California, USA Integrating Molecular and Environmental Data to Evaluate Community Patterns
  • John Heidelberg, University of Southern California, USA Metagenomic Analysis of Marine Microbial Communities
  • Peter J. Turnbaugh, Harvard University, USA Metagenomic Analysis of the Human Gut
  • Susannah Tringe, DOE Joint Genome Institute, USA Bioenergy Metagenomics
  • Stanislav Dusko Ehrlich, Institut National de la Recherche Agronomique (INRA), France A Human Gut Microbial Gene Catalogue Established by Metagenomic Sequencing
  • Trina McMahon, University of Wisconsin-Madison, USA Functional Genomics of Polyphosphate Accumulating Bacteria: 'Eco-Systems' Biology for Wastewater Treatment
  • Gregory J. Dick, University of Michigan, USA Talk Title to be Determined
  • Robert L. Hettich, Oak Ridge National Laboratory, USA A Proteogenomic Approach for Characterizing the Molecular Activities of Gut Microbiomes
  • Brendan Bohannon†, University of Oregon, USA Environmental Microbial Ecology
  • Claire Horner-Devine, University of Washington, USA Biogeography of Microbial Communities
  • Thomas Schmidt, Michigan State University, USA Ecologic Strategies of Environmental Microbes
  • Margaret Riley, University of Massachusetts Amherst, USA Antibiotic-Induced Changes in the GI
  • Jacques Ravel, University of Maryland School of Medicine, USA The Temporal Dynamics of the Vaginal Microbiota
  • Forest Rohwer, San Diego State University, USA RNA Virus Communities Associated with Human
  • Zoe G. Cardon, Marine Biological Laboratory, USA Soil Microbial Ecology
  • David A. Stahl, University of Washington, USA Metabolic Modeling of a Mutualistic Microbial Community
  • Jay P. Tiesman, Procter & Gamble, USA Microbial Community Analysis from a Systems Biology Perspective
  • Edward F. Delong, Massachusetts Institute of Technology, USA Systems Biology of Planktonic Marine Microbial Communities
  • David A. Relman, Stanford University, USA Perturbation of the Human Microbiome: Unrest at Home
  • Julie Segre, NHGRI, National Institutes of Health, USA The Skin Microbiome
  • Vincent B. Young, University of Michigan, USA Integrating Human Microbial Ecology in a Clinical Setting

Sunday, September 05, 2010

A complete summary (probably TMI) about my time at the human #microbiome meeting #HMP2010

Well, I am writing this on my flight heading back from St. Louis after going to the "Human Microbiome Research Conference"

I have already posted some summaries of the meetings Day 1 and Day 2  and will soon do one about Day 3.  And you can find out more about the meeting from multiple other sources such as here, here, here and here.  But what I thought I would do here is give some of the story behind the meeting - why I went and what it was like behind the scenes, at least for me.  Note - I know this is very long - but hopefully it will give people a feel both for some of the science, some of the behind the scenes, and some of (my) history relating to this meeting.

Some prelude to the meeting

I headed out to the meeting from Davis on the afternoon on the Monday the 30th.  I was originally planning on only going to the meeting for the last day, Thursday. that was because, well, the 31st was my birthday, and I wanted to spend it with my family.  normally, I reserve important family events and do not travel or schedule things that conflict with them.  So, when George Weinstock invited me to give a talk at the meeting, I told him that I could probably only come for the last day.  So that is when he scheduled my talk.

But then as the meeting approached I changed my mind.  You see, in the last few months I have gotten more and more interested in the human microbiome as a research area.  I had done some work on the human microbiome.  For example, my lab was involved in a collaboration with Michael Zasloff at Georgetown University in which they were conducting human ileal transplants and we looked at the microbial recolonization of the ileum after transplantation.   This project was headed by a stellar student, Amber Hartman, who just finished her PhD in my lab.  Her paper was published recently in PNAS (which I note, we paid for the Open Access option there and really wish more people would do similarly).

Anyway, that project had been my main foray into human microbiome studies.  However, I have led or been involved in dozens of studies looking at the genomics of symbioses (good and bad) between animals and microbes (e.g., see these Open Access papers on Wolbachiasharpshooter nutritional symbiontsdeep sea worm epibiontsa cellulolytic symbiont of shipworms).  In fact, I have been moving more and more towards studies of communities of microbes that live in or on animals and plants.  And I have been writing on and off about the microbiome in my blog including the following posts:
And I guess as the meeting approached I realized I really do want to do more human associated studies.

Wednesday, September 01, 2010

Human microbiome project meeting (#HMP2010) Day 2 wrap up

Well, Day 2 is over now for the Human Microbiome Meeting.  See my previous post for information about the meeting and about Day 1.

I enjoyed Day 2, though some things are starting to wear me down a little bit.  In particular, the fact that the meeting starts at 8 AM, or 6 AM California time, has been really rough.  I missed the first 1.5 talks today because of that.  Not to organizers of meetings everywhere - don't start meetings so early.  And don't have too many talks in one day.  It is better, far better, to just have fewer talks, than it is to wear people out.  Also not to meeting organizers - do not change the order of talks in concurrent sessions at the last minute.  Very bad idea.  Anyway - onwards.

As with Day 1, I think the best way to get a feel for the meeting would be to look at Twitter posts with the hashtag #HMP2010.  Unlike what I did with my post for Day 1 I am going to put only my tweets below, not everyones.

Today was split up into one series of talks in the AM and then concurrent sessions in the PM.  What lessons did I learn today?  Well here are a few, with some overlap to those on Day 1 but that is OK by me.
  1. Again - correlations ≠ causation.  Those of you out there who do not get this should GTF out of science.
  2. For statement "X manipulations of microbes help treat X ailments in X people X of the time": X="some" NOT "all" 
  3. Seems like we are really on the cusp of publications of 100s of clinical studies of microbes and their association with health status
  4. Some of these studies are even starting to get at causation
  5. It should be remembered that all of the methods used in microbiome studies are just methods; none are per se better than others; it is the science that should be judged not the tools themselves
  6. With some effort it seems one can culture many more organisms from a system than might be expected
  7. Cultures have many many uses
  8. But culture based studies do not really get at population genetic frequencies and relative abundance information very well
  9. Be wary of those who stick relentlessly with one idea or method
  10. Very strange how few pharma reps there were here (more on this in my next post)
  11. Please please please do not confuse data with knowledge.  Data can be very very useful and I completely support some projects that just are focused on generating data sets.  But knowledge comes from thinking about the data, and carefully analyzing it.
  12. Microbes, I think, run our lives much more than we would like to believe
Anyway - that is a brief update.  Back to preparing my talk for later this AM ...

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