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- Tuesday sick-blogging: Rock 'n Roll Reading
Tuesday, December 30, 2008
Tuesday, December 16, 2008
Here is their summary of their article:
Since the time of Darwin, biologists have worked to identify instances of evolutionary adaptation. At the molecular scale, it is understood that adaptation should induce more genetic changes at amino acid altering sites in the genome, compared to amino acid–preserving sites. The ratio of substitution rates at such sites, denoted dN/dS, is therefore commonly used to detect proteins undergoing adaptation. This test was originally developed for application to distantly diverged genetic sequences, the differences among which represent substitutions along independent evolutionary lineages. Nonetheless, the dN/dS statistics are also frequently applied to genetic sequences sampled from a single population, the differences among which represent transient polymorphisms, not substitutions. Here, we show that the behavior of the dN/dS statistic is very different in these two cases. In particular, when applied to sequences from a single population, the dN/dS ratio is relatively insensitive to the strength of natural selection, and the anticipated signature of adaptive evolution, dN/dS>1, is violated. These results have implications for the interpretation of genetic variation sampled from a population. In particular, these results suggest that microbes may experience substantially stronger selective forces than previously thought.The key to me is that it seems that many may have been using dN/dS ratios inappropriately when comparing samples within a species. For more, well, see the paper.
Monday, December 15, 2008
It is a good sign for science because it shows explicitly Obama's respect and support for science. Most recent Secretaries of Energy have been non scientists (the #s depends on whether you count an engineer as a scientist - I do - but some don't) and Bush (who I want to say is out previous president but we still have him for another month) does not believe in evidence in any way, let alone science.
It is a good sign for society because it is important for the president to understand and respect science. So - some may criticize Chu for some issues - but none of the criticisms I have seen really hit home with me. Sure, I would like a Biologist in their in the Cabinet, but Chu seems to actually understand that the biological diversity of the planet is under threat from global change and he wants to do something about it. I cannot really ask for much more from a Physicist/Administrator. For full disclosure - I have an Adjunct position at LAwrence Berkeley Lab where Chu just happens to be the Director. So maybe I am not completely objective, but anyway, I think this is a good day all around.
Saturday, December 13, 2008
Everyone interested in Open Access and the open spread of information should check out the new video from the Creative Commons folks. This is being released as part of a fundraising campaign for Creative Commons and I recommend that people consider donating to this great organization. As a side note, the video was directed by Jesse Dylan, the director of the Emmy- award winning "Yes We Can" Barack Obama campaign video and features musical artist will.i.am from the Black Eyed Peas.
Friday, December 12, 2008
|Robbins Hall Outdoor Art|
The only issue I have is that they did not highlight the bacteria that should be present on the bean roots (legumes fix nitrogen via nitrogen fixing bacteria that hang out in nodules in the roots). But if we take an artistic interpretation of the bean roots, some of the little black triangles there can be considered root nodules.
Anyway, just thought I would share the pics. The art is worth checking out if you are in the area.
Tuesday, December 09, 2008
From their conclusion:
Like all new technologies, cognitive enhancement can be used well or poorly. We should welcome new methods of improving our brain function. In a world in which human workspans and lifespans are increasing, cognitive enhancement tools — including the pharmacological — will be increasingly useful for improved quality of life and extended work productivity, as well as to stave off normal and pathological age-related cognitive declines. Safe and effective cognitive enhancers will benefit both the individual and society.
But it would also be foolish to ignore problems that such use of drugs could create or exacerbate. With this, as with other technologies, we need to think and work hard to maximize its benefits and minimize its harms
On the one hand I agree that more work in this area is good. On the other hand, people compete all the time based upon cognitive performance. The article discusses thesae and other issues and is worth looking at. As I am on Campus right now I am not sure if the letter is Open Access or not, but I hope it is.
- Smooth Pebbles: Some heavyweights vote Yes on cognitive-enhancing ...
- Mind Hacks: Mainstreaming cognitive enhancement
- Key Words: Nature Magazine Supports Cognitive Enhancing Drugs
- Brain doping: academics say yes
Monday, December 08, 2008
I should note, in one of the symbioses like this that I have studied with Nancy Moran we found that there were two symbionts contributing to the nutrition of the host. We found that one of the symbionts was likely making amino acids for the host (an insect called the glassy winged sharpshooter which eats only xylem sap) and the other symbiont was likley making vitamins. Nancy showed later with John McCutcheon that the symbiont that was making vitamins also was predicted to be making methionine for the host. So it seems possible there might be a missing symbiont in the aphid study? Although it would be cool if the aphid has figured out how to make an amino acid most animals are not able to make.
Hat tip to Max Lambert for pointing this out.
Kits are convenient collections of tools and tips that will help your family and friends reduce your environmental impact. By grouping what you need in one handy package, a kit makes it easy and fun to take energy-saving steps. Each kit is ultimately a gift to our environment, but will also save you money in reduced energy costs.* And every kit comes with our innovative "rebate." Check them out!
- UC Davis Scientists Develop Flood-Resistant Rice
- USDA Discovery Award Recognizes Rice Research
- UCD researcher honored for rice breakthrough
- Waterproof rice coming soon
Thursday, December 04, 2008
Go to this web site to learn more ....JGI - CSP Overview.
Monday, December 01, 2008
Hey - thanks UC Davis. Thanks for promoting blogs on your front page (under the Blogs, iTunes and Facebook section) and thanks for promoting my "Things Scientists should be thankful for"posting.
Thursday, November 27, 2008
10 things scientists should be thankful for
- Teachers. Scientists had to learn science at some point. And most of us have had some stellar science teachers, or teachers of science-related things like math, along the way. We should give thanks to these people.
- Inspirers. Similar to #1 except in many cases we have been inspired to become scientists by someone who may not have been a teacher of ours. Perhaps it was a famous scientist, or even a fictional one. Or even someone we knew. It is that inspiration that frequently gets one through the tough times.
- Benefactors In general, scientists have a pretty nice life. We get paid (sometimes well, sometimes poorly) and are given research funds, to unlock the secrets of the universe. How cool is that? We should therefore be very thankful for the immediate source of our funds - such as the institutes where we work and the agencies that provide us funds.
- Taxpayers. Unless one is funded by private foundations, taxpayers are the ultimate source of those funds mentioned in #3. This source of funds is frequently overlooked but should never be forgotten. Don't forget - we take money people from people that in theory they could have gotten to keep if their taxes were lower. We should thank these taxpayers..
- Research personnel (including student researchers, post docs, technicians, etc). Most of the time, scientists get credit for some work that was in a large part actually done by people in our labs. They deserve our eternal gratitude.
- Students we teach. Overall, for those scientists who teach, though it may be a required part of our jobs, it is also a great way to learn and to become a better scientist.
- Staff at publishers. An important part of communicating science is of course publishing. And though I am a big fan of new ways to disseminate information, let us not forget that there are many many people who aid and abet this dissemination by working for publishers. These folks deserve our thanks.
- Study subjects or objects. Whether one studies organisms, rocks, molecules, planets, forces, or whatever, we should all be thankful that there is interesting stuff out there to study. And for those who study living things, if one disturbs them along the way, we should
- Librarians and library staff. Access to information is critical for both learning to become a scientist and being a scientist. And libraries play a key role in providing this access.
- Family and friends. Late nights at the lab? Working on a grant over the weekend? Writing papers all the time? In school for years and years? All of this takes a toll on friends and family. And we owe them some props.
Wednesday, November 26, 2008
The new paper describes further work on the MAC genome including finishing many of the chromosomes (which was done spectacularly by Luke Tallon and Kristie Jones), sequencing and analyzing a larger number of ESTs, refining the annotation (coordinated by Mathangi Thiagarajan), and some other analyses. The new paper was led by Bob Coyne, who, with Barb Methé took over coordinating the work at TIGR/JCVI after I moved to UC Davis a few years back. I think they did a stellar job (ni biases here).
Note - I took the title of the posting 'Tackling a Hairy Best" from an NIH press release that was put out when we got the grants for this project.
Tuesday, November 25, 2008
Another fun metagenomics related paper in PLoS Biology. In it Pascal Hingamp et al discuss an Open Source, Open Science system for metagenome annotation (see PLoS Biology - Metagenome Annotation Using a Distributed Grid of Undergraduate Students).
They do this as part of a course on metagenome annotation. And the software for running this is all Open Source and available. They say
"Teachers wishing to use the Annotathon for their courses are invited to create new teams on the public server at http:IN a way this is a metagenomics version of the Undergraduate Genomics Research Initiative (UGRI) which was described in a PLoS Biology paper previously.
/(course logistics and team management are detailed in the instructor manual:http: /annotathon.univ-mrs.fr / /). The underlying open-source software (PHP and MySQL scripts, under a General Public License) is also available for local installation (https://launchpad.net/annotathon/). In addition, a special “Open Access” team is available for freelance students (volunteer instructors are most welcome to help oversee the Open Access team)." /annotathon.univ-mrs.fr /Metagenes /index.php /Instructor_Manual
Well, this is really the end all be all for me combining so many things I like - genomics, metagenomics, annotation, OA publishing, open source software, etc. Nice job Pascal et al ...
Monday, November 24, 2008
Two new papers that just came out in PLoS Journals are definitely worth checking out. They are
- PLoS Genetics: Exploring Microbial Diversity and Taxonomy Using SSU rRNA Hypervariable Tag Sequencing
- PLoS Biology - The Pervasive Effects of an Antibiotic on the Human Gut Microbiota, as Revealed by Deep 16S rRNA Sequencing
And in the second paper, the same two labs present an in depth study using the 454-Roche rRNA sequencing to characterize the response of microbes in the human gut to antibiotic treatment. Though there have been a few other such studies this is the one that has the deepest characterization of the microbes present.
Note - one thing I find kind of humorous is that one of the authors is listed as Susan M. Huse in one of the papers (she is the first author on the PLoS Genetics paper) and Sue Huse in the other.
Huse, S., Dethlefsen, L., Huber, J., Welch, D., Relman, D., & Sogin, M. (2008). Exploring Microbial Diversity and Taxonomy Using SSU rRNA Hypervariable Tag Sequencing PLoS Genetics, 4 (11) DOI: 10.1371/journal.pgen.1000255
Dethlefsen, L., Huse, S., Sogin, M., & Relman, D. (2008). The Pervasive Effects of an Antibiotic on the Human Gut Microbiota, as Revealed by Deep 16S rRNA Sequencing PLoS Biology, 6 (11) DOI: 10.1371/journal.pbio.0060280
Friday, November 21, 2008
Controlled simulations of genome evolution are useful for benchmarking tools. However, many simulators lack extensibility and cannot measure parameters directly from data. These issues are addressed by three new open-source programs: GSIMULATOR (for neutrally evolving DNA), SIMGRAM (for generic structured features) and SIMGENOME (for syntenic genome blocks). Each offers algorithms for parameter measurement and reconstruction of ancestral sequence. All three tools out-perform the leading neutral DNA simulator (DAWG) in benchmarks. The programs are available at http://biowiki.org/SimulationTools.
Tuesday, November 18, 2008
Sunday, November 16, 2008
"Hypochlorous acid is an important part of host defense," Jakob said. "It's not just something we use on our countertops."Whether this is true or not, I do not know. But what I do know is that microbes are in the news. And that is good.
Friday, November 14, 2008
one of eight Bioinformatics Resource Centers (BRC) for Biodefense and Emerging/Re-Emerging Infectious Diseases. Funded by the National Institute of Allergy and Infectious Diseases (NIAID), ERIC serves as an information resource for five members of the bacterial family Enterobacteriaceae.So if you want to learn more about E. coli and its relatives and their genomes, this is a good place to start
Thursday, November 13, 2008
The scientists will focus on marine viruses and other tiny life called protists and their roles in the food chain. These organisms prey on bacteria, a primary food that sustains the vent ecosystem.Some friends/colleagues of mine are involved in this adventure and it sounds like some cool stuff could come out of it. Also you might want to check out the blog of Lisa Z (ExtremeVirus), who is posting about the cruise.
A team of Princeton University scientists has discovered that chains of proteins found in most living organisms act like adaptive machines, possessing the ability to control their own evolution.It sounds like complete nonsense to me. But I am not sure. Anyone else out there know more?
"Our new theory extends Darwin's model, demonstrating how organisms can subtly direct aspects of their own evolution to create order out of randomness."
"What we have found is that certain kinds of biological structures exist that are able to steer the process of evolution toward improved fitness,"
Unlike Darwin, Wallace conjectured that species themselves may develop the capacity to respond optimally to evolutionary stresses. Until this work, evidence for the conjecture was lacking.
"In this paper, we present what is ostensibly the first quantitative experimental evidence, since Wallace's original proposal, that nature employs evolutionary control strategies to maximize the fitness of biological networks,"
Wednesday, November 12, 2008
Underselling Genomics Award #1: David Whitworth for "Genomes and Knowledge: A questionable relationship"
In the end, when faced with the astonishing diversity of microorganisms, if all we manage to do is to describe a few random organisms in painstaking detail, then we will have failed to understand microbiology. To suggest we curtail the remit of microbial genomics is bad enough; to suggest it now, when we are on the brink of finally being able to truly study genomic diversity, is absurd.So sure, sometimes we in genomics oversell the benefits of genome sequence data (and in fact, I give out a little award here for those people). But Whitworth is at the other end of the spectrum, wearing, as Parkhill states "blinkers" to the benefits of genome sequence data. As a reflection of how much I disagree with most of Whitworth's implications, I am giving him my first "Underselling Genomics Award".
Saturday, November 08, 2008
Wednesday, November 05, 2008
Tuesday, November 04, 2008
((Note added later --- in retrospect, I (and others I talked to) felt Steve G's talk had way way too much detail for an after dinner talk so I spent the next day taking out much of the detail from my talk to lighten it up. What did this get me? After my talk and later after drinks Steve G. made it clear he thought it stunk because it was too light on details of something he thought should have been in it. Oh well, I guess this goes to show you cannot make everyone happy.)).
Monday, November 03, 2008
"This one is such a complete no brainer. Obama is so far and away the fitter candidate. Plus if Palin and McCain do not believe in my greatest work, well they can ..." (we cannot print the rest)So there it is. Of course, most living well known scientists who have made public statements also endorse Obama, but getting Darwin's support is an extra feather in his cap.
Friday, October 31, 2008
Wednesday, October 29, 2008
"This journal does not have a vote, and does not claim any particular standing from which to instruct those who do. But if it did, it would cast its vote for Barack Obama."For more detail, I think the key point is here:
On a range of topics, science included, Obama has surrounded himself with a wider and more able cadre of advisers than McCain. This is not a panacea. Some of the policies Obama supports — continued subsidies for corn ethanol, for example — seem misguided. The advice of experts is all the more valuable when it is diverse: 'groupthink' is a problem in any job. Obama seems to understands this. He tends to seek a range of opinions and analyses to ensure that his own opinion, when reached, has been well considered and exposed to alternatives. He also exhibits pragmatism — for example in his proposals for health-care reform — that suggests a keen sense for the tests reality can bring to bear on policy.They basically reiterate my concern for the McCain-Palin platform regarding science but they do not really go far enough. McCain and Palin have expressed decidedly anti-science positions recently (well, Palin has expressed them previously too). And thus it is not simply what advisors they surround themselves with but whether they would listen to any of them. Sadly the hints are that McCain and Palin will not listen to scientific advisors on many issues. Obama has made it clear that he will. Not that he puts science above all else (nor should he) But at least he will listen and make rational decisions that include science as a component. McCain and Palin seem dead set against "evidence" of any kind much of the time (note - McCain still exhibits occasional glimpses of the reasonable person he used to be on some issues like Global Warming - but these are few and far between).
Hat tip to Oliver M. for sending this around ...
Tuesday, October 28, 2008
So - I was having breakfast with my daughter this morning and she was in a funky mood. She wanted some stories so to make life easy and not get up, I opened up the only thing near the table to read - a copy of Nature Biotechnology that I received for free in the mail (not sure why) - and was going to show her some pictures of things. And there was a review of my friend and colleague Pam Ronald's book "Tomorrow' Table." And so I told my daughter that this was a story about a book by my friend Pam and reminded her about how we had gone over to Pam's house and how she worked in the office next to mine. And then I asked my daughter if she wanted to see Pam's book, which I had in the office and she said yes. And so I got the book and then we told stories about Pam. So - here in living color is a picture of my daughter and Tomorrow's Table the book and the review of Tomorrow's Table on my table, today.
Monday, October 27, 2008
"We asked federal agencies to give us a summary of key words relating to research projects and we found an enormous number of them focused on homosapiens. I kid you not."
"You probably are a homosapiens no? Or have many friends that are? What we need to do is spend money on helping people change and not on studying these homosapiens"
Sunday, October 26, 2008
"No person shall photograph, videotape, or otherwise record the image of a voted official ballot for any purpose not otherwise permitted under law."So instead of a picture I am going to simply put words here. And since a picture is worth 1000 words, here are mine.
No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8. No on 8.
Saturday, October 25, 2008
- Sarah Palin: Ignorant and anti-science [Pharyngula]
- Palin Balks at Scientific Research
- Sarah Palin: Ignorant and anti-science
- Genetically Ignorant
- Think Progress » Memo To Palin: Fruit Fly Research Has Led To ...
- Palin.. fruit flies…and ignorance
Tuesday, October 21, 2008
Como muestra, algo que empezó como una broma. "Los centros del NIH (los Institutos de Salud de Estados Unidos) pedirán a todos los científicos que quieran optar a sus ayudas y subvenciones a que pasen pruebas antidopaje para comprobar que no han tomado estimulantes cognitivos para aumentar su rendimiento intelectual". Una supuesta World Anti-Brain Doping Authority (WABDA) se encargaría de los análisis. Es el mensaje de una nota de prensa falsa. Una fake lanzada en Internet el pasado 1 de abril, el día de los inocentes en Estados Unidos, por Jonathan Eisen, biólogo evolucionista de la Universidad de California. Comenzó como una travesura, pero el rumor acabó por extenderse por la red.
La broma apunta, sin embargo, a un debate abierto entre la comunidad científica. Si se controla el dopaje en deportes como el ciclismo, ¿por qué no controlarlo en la comunidad científica, donde también compite el intelecto por conseguir becas, ayudas e incluso premios en reconocimiento de su inteligencia? Esa era la reflexión original que, según explica Eisen, le llevó a colgar su broma de Internet. Sin embargo, también afirma que nunca aceptaría que se realizasen ese tipo de controles.
Monday, October 20, 2008
Friday, October 17, 2008
Thursday, October 16, 2008
Dr. Chris Somerville
Director, Energy Biosciences Institute (EBI)
UC Davis ARC Ballroom October 16, 2008, 3:00-4:00 PM
Tuesday, October 14, 2008
I should note - I really really like Genome Biology as a journal - even though they have been rejecting many of my papers lately (or maybe in part because of this). I am really glad this one got in there. I published my first fully OA paper in Genome Biology in 2000 (on symmetric genome inversions in bacteria and archaea -- a paper co-authored with Steven Salzberg, Owen White and John Heidelberg - see Evidence for symmetric chromosomal inversions around the replication origin in bacteria). It is one of my favorite papers from my entire career, as in it we report on a pattern that turns out to appear to be one of the few rules of bacterial and archaeal genome evolution. Anyway - glad to be back in Genome Biology.
Lecture #2, Responsible Authorship:
Thursday, August 7, 2008; Speaker: Jonathan Eisen, Ph.D., "Responsible Authorship and the Ownership of Scientific Knowledge: Thoughts on Open Access Publishing"
To view the lecture, click here: Flash Player version, Windows Media Player version, or QuickTime Player version (for QuickTime players you may have to open the player and paste the url: rtsp://media.depts.washington.edu/uwbri/BRI_Eisen_2008.mov)
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