Lake arrowhead notes - UPDATED

Well I gave my talk

Seemed to go ok except getting cutoff early because the chair ignored
that the session started late but that is ok

George Weinstock is now speaking using my laptop so I am trying to
post from my phone

He said one key thing I left out ... Big scale microbial sequencing
projects are now possible thanks to next gen sequencing in particular
454-Roche tools

More later
Sent from my iPhone

-------------------------------------------------

More now

George Weinstock gave a good overview of the "Human Microbiome Project" which is a NIH Roadmap initiative to catalogue the genomic content of the microbes associated with humans. He described some of the big picture of why do the project, of the different fundingin initiatives being done through NIH and he gave some detail on the "jumpstart" project going on at the big genome centers right now. He outlined how the current plan is to select a few hundred people and to survey their mcirobiomes from multiple sites using rRNA PCR and possibly metagenomics. In addition, he described how there is also an effort to sequence 100s if not a 1000 genomes of cultured organisms that have been isolated from human environments. He did say one thing I disagreed with which is that he thinks it is somewhat reasonable to treat the environment that microbes live in in essence as a big bag of genes. In other words, if you sequence from a community, he implied that one can focus just on the genes and their functions and not the organisms that they come from. On this I disagree (and pointed this out after the next talk). But overall George gave anice overview of the project and its goals.

Eric Wommack gave a good talk about viral metagenomics work he has been doing. He pointed out that a lot of the viral world is "unknown" but that does not mean it is unimportant. And this is consistent with what I and George Weinstock said which is that we need more genome data from viral isolates. Eric presented some very useful results on the challenges of using short read sequence data in metagenomics and he referenced a few papers on this. He also referred to a cool viral genome survey project that I was not aware of by Hatfull which involved undergraduates in sequencing and analyzing the genomes of phage that infect Mycobacterium smegmatis.

Jim Bristow on Biofuels. He is now giving a summary of some of the JGI work on the genomics of cellulolytic organisms and processes. He is focusing on the termite gut community and had some good one liners about this (e.g., he said many people want to kill termites but not JGI. They are our friends; he also said "it takes a village to sequence a termite gut").

Not sure exactly how to say this, but here goes. There was one talk in the AM I was not overly fond of. This was a talk by Bernard Palsson. Now I confess, I am not overly familiar with much of his work but what I know of it suggests he does some really solid, interesting and important work on metabolic network modeling and analysis. But his talk at this meeting was disappointing. His talk was about his use of genome sequencing to characterize "adaptive evolution" in E. coli. And the results he presented seemed solid enough. The problem I had was that it was a prime example of "overselling genomics". Why? Here is what they did. They took E. coli mutants. And the then took them through cycles of growth and then dilution. And then they looked at the populations after a certain number of generations and did a variety of analyses. Included in this was some whole genome sequencing that helped identify mutations arising in the cultures. And then they did some characterization of these mutations/mutants including some competition experiments and some pretty interesting gene expression studies of some RNA polymerase mutants. And he made some conclusions based on their results like that E. coli in the lab can find new adaptive peaks and that mutations differ in different replicates, and that different mutations confer different fitness, that they can monitor the appearance of mutations over time, and so on.

So what is the problem -- the problem is that he (1) presented this as though the serial cycling of E. coli was novel when in fact it is not and that (2) he presented the conclusions as though they were novel when they also are not. People have been doing this type of experiment for many decades (in fact, one person, Rich Lenski, has been doing an experiment like this for decades). And they get these exact results. But they have not sequenced genomes as part of their experiment. And thus, at least for this talk, they were not mentioned, and the rediscovery of many truisms in population genetics was presented as novel because it involved genome sequencing.

Trent Northen created a serious buzz during and after his talk with his presentation of some of the things one can do with Nanostructure Initiated Mass Spectrometry (NIMS). I confess - I want his toys.

Lynn Silver is now talking about the challenges in the development of new antibiotics. She argues that the focus by some on trying to find new targets for antibiotics has been a bit misguided.

Julian Parkhill gave a good talk about population genomics of Salmonella. He pointed out a few things people still ignore. For example, if you want to identify polymorphisms in a species to use for population genetics/genomics studies, you really need to do a survey to identify polymoprhisms from diverse members of the population. If you do not, and then you use a biased set of polymorphisms, your population inferences will be wrong. He also said, in response to a quesiton of mine, that at least for this species, they see very little variation in copy number in genes which is different than what people seem to see in humans.

Tiffany Williams from Baylor gave a talk about using high throughput sequencing in collaborations with developing countries. She outlined some of the challenges as well as the benefits from such collaborations.

Kim Lewis gave a very interesting talk on microbial biofilms and persister cells, of which I know vanishingly little. He showed some very cool experiments trying to "complement" unculturable organisms and get them to grow.

Jeffrey F. Miller gave a talk focusing on diversity generating retroelements in bacteria which appear to be a means by which bacteria can target particular regions of the genome for mutagenesis in a comparable way to VDJ mutagenesis in humans. This was perhaps my favorite talk so far at the meeting as it combined microbial genomics, evolvability, mutation processes and other things I tend to focus on.

Steven Benner gave a talk which I had to skip out on early because I was doing a radio interview. Benner said one thing that annoyed me at the beginning - he made a comment that was complaining about prior talks that referred to "Rosetta Stone" methods of predicting function (I was one of the people who mentioned this) because he thought that we were referring to blast searches. He clearly was not paying any attention as the Rosetta Stone method is a method to predict function for genes by finding connections between non homologous proteins based upon having other proteins that have domains found in both of the original proteins of interest. Oh well, glad I had to leave early because I was itching to jump up and correct him.

Heather Allen, from Jo Handelsman's gave a very good talk about doing functional metagenomic screens for antibiotic resistance encoding genes. She has been using DNA from multiple soil sites, including a pristine site in Alaska, and screening the DNA for antibiotic resistance genes in E. coli. These screens identify a wide diversity of genes, including some novel forms. This work helps highlight the need to not just sequence the snot out of the world but to also do some functional assays at the same time. In addition she mentioned that she was able to come to the meeting because Jo Handelsman set up a fund for mothers to pay for babysitters to come to a meeting with them. All I can say is Jo Handelsman was already one of my favorite people in science and this is just another brilliant and wonderful thing that she does.

David Relman gave a talk about two studies of the human microbiome that his lab has been doing: (1) studies of marine mammals to compare the microbial diversity in their surfaces with the diversity in the water and the diversity on their insides and (2) study the response of the human gut microbial community to antibiotic treatment. I am particularly fond of the antibitotic treatment study because they are treating it as an "ecological disturbance" study and analyzing it much like ecologists would analyze recovery of a forest after fires. I think we definitely need more ecologists to bring their techniques and skills to human microbiome studies and so this was exciting to see.

Ashlee Earl gave a talk about biofilm formation in Bacillus subtilis. Much like Kim Lamb's talk earlier, this talk was in an area I know little about and I guess you could say it kind of blew my mind. It seems that in B. subtilis and I guess in many other microbes biofilms are in essence analogous to multicellular organisms. Within a biofilm there are different types of cells that have different roles and the patterns are highly reproducible and organized. It seems to me that the boundary between multicellular and single-celled organisms is getting blurrier and blurrier. Ashlee reported on some cool experiments where she collected strains from around the world and then dod comparative genetics and genomics of their biofilm formation patterns.

Alas I missed Mary Lidstrom's talk which based upon prior experiences I am sure was fascinating. She has been working in studying processes inside single bacterial cells and has been developing a suite of techniques and tools to carry out such studies. Maybe someone else from the meeting can post details about her talk.

Unfortunately, I had a conference call during some of the next talks that I had to do so I do not have details for the blog. Then I returned and served as chair for a session. I did take some notes so here goes.

Byung-Kwan Cho gave a tour de force talk about reconstructing the transcriptional regulatory network in E. coli. He presented results from a dazzling and dizzying array of genome-scale methods (e.g., ChipChip, tiled arrays, sequencing, etc etc) to characterize transcription regulation. In addition he did some complex and big scale computational work to combine all of the data together to characterize networks. It was quite impressive stuff.

Ginger Armbrust talked about her favorite critters - diatoms and focused on how they used the genome data to characterize silicon deposition processes. She was convincing as to the importance of diatoms and to the value of having the genome sequences from some species. She did discuss some of the challenges of using the genome data including the challenges in gene prediction for microbial eukaryotes. She also discussed her dream of utilizing some of the new genomic information as part of real time sensors in the oceans.

Anthanasios Typas discussed work to build tools for carrying out genome-scale analyses of genetic and chemical-genetic interactions. For example they are working on taking two comprehensive gene KO libraries from E. coli and using them to create all possible double mutants and to then screen those mutants for whether they have the same or different phenotypes than the single mutants. This allows them to look for gene-gene interactions. They also are doing this type of analysis with chemical-gene interactions.

Devaki Bhaya gave a brief talk on what I think is the single most interesting thing in all of microbiology right now - CRISPRs. These are clustered regularly interspaced short palindromic repeats. She is studying them in cyanobacteria from Yellowstone hot springs

Good quotes from the meeting:

• So we simply sequenced the genome of the different variants
• Antibitoics do not kill things, they corrupt them
• Dormancy is the default mode of most bacterial life
• Who knows what a yoctomole is?
  
• I am going to defend genomics
  
• There comes a point in life when you have to bring chemists into the picture
• Gosh, was that today or yesterday
• The rectal swabs are here in tan color
• I'll try to let the pictures do the talking and I will get out of the way
• Our model system de jour
• And there's Jeffrey Dahmer
• And this is my cheesy analogy here
• He could not be here so I am here. His loss. My gain. Hopefully not your loss.
• We are the environment. We live the phenotype.
• If I have time I will tell you about a dream
• Every fifth breath - thank a diatom
• While we still have poles
• A paper came out next year

Oh brother there art though (Uh oh, my brother has a blog)

Well, just in case people out there did not have enough trouble distinguishing my brother, Michael Eisen,  from me (me - UCD - him UCB, me microbial genome evolution, him drosophila and yeast genome evolution, me - OA fanatic PLoS Biology AEIC, him PLoS founder and board member, and so on), here comes a new thing to deal with.

My brother has launched a blog (http://michaeleisen.org/blog). 

Seems worth checking out.  First posts are 

• Science Debate 2008 questions are really lame
  
• Congressional testimony on NIH Public Access repeal effort
  
• Identifying individuals in "anonymous" genetic studies
  
• Legislative threat to NIH public access policy
  
• Scientists cynical use of "Junk DNA"

It's Miller Time - Lake Arrowhead Microbial Genomes Conference -- about to begin

Well, I am back.  Every two years I come back to this small meeting about small genomes.  The meeting is officially the "16th Annual International Meeting on Microbial Genomics at Lake Arrowhead, CA" but in reality, every two years it is at Lake Arrowhead and every other two years it is elsewhere.  And I rarely go to the other one -- but I keep coming back to Lake Arrowhead.

Why?  Well, you might guess it is because it is at UCLA's conference center up in the mountains.  But you would be wrong.  You might guess it is because I generally hate big meetings and this one is nice and small/medium.  But you would be wrong again.  For there are lots of meetings in pretty places.  And there are lots of medium sized meetings an omnivore like me could go to.  I go back every two years because of Jeffrey H. Miller, the organizer.  He invites me.  I can never say no.  

Why? Well, many reasons.  Sure one is that I like him.  Another is that he does meetings in the right way (not too many talks in one day --- some time to relax and talk with other people and to interact, etc).  But the truth is, I say yes because he is one of the few people I know who is interested in both DNA repair processes and microbial genomes.  And his meetings reflect this interest.  So I guess even though I do not spend enough time working on DNA repair any more, I did do my PhD on it, and I did basically try and copy some classic Jeffrey Miller mutator experiments.  So I just have to go to this meeting.  And here I am (see my 2006 meeting notes here) - despite having been very sick this summer and getting ready to teach a new class in the fall with 400+ students.

Anyway - More on the meeting coming.Here are the talks for those interested

James C. Liao
University of California, Los Angeles, CA
“Non-fermentative Pathways for Synthesis of Branched-Chain Higher Alcohols as Biofuels”

Jonathan Eisen
University of California, Davis, CA
“A Genomic Encyclopedia of Bacteria and Archaea”

Bernhard Palsson
University of California, San Diego, CA
“The Genetic Basis for Adaptive Evolution in E. coli”

George Weinstock
Baylor College of Medicine, Cambridge, MA
“The Human Microbiome: Progress and Challenges”

Gary Siuzdak
The Scripps Research Institute, La Jolla, CA
“Metabolomics Reveals Large Effect of Gut Microflora on Biochemistry and Activation of a Host Response”

Jim Bristow
DOE Joint Genomme Institute, Walnut Creek, CA
"Microbial Sequencing for Biofuels Applications"

 Eric Wommack
University of Delaware, Newark, DE
“Making sense of the chaff: What will metagenomic approaches tell us about viral ecology?

Valérie de Crécy-Lagard
University of Florida, Gainesville, FL
“Making Sense of Genomes: Linking Gene and Function by Comparative Genomics”

Trent Northen
The Scripps Research Institute, La Jolla, CA
“High Throughput Mass Spectrometry Based Metabolomic and Enzymatic Assays for Functional Genomics”

Matteo Pellegrini
University of California, Los Angeles, CA
“New Methods for Processing High-throughput Sequencing Data: Improving the Solexa/Illumina Data Analysis Pipeline”

Sabeeha S. Merchant
University of California, Los Angeles, CA
“Transcriptomics of Nutritional Copper Homeostasis in Chlamydomonas”

Lynn L. Silver
LL Silver Consulting, LLC, Springfield, NJ
“The State of Antibacterial Discovery in 15 minutes”

Julian Parkhill
Welcome Trust Sanger Institute, Cambridge, UK
“Discovering Variation in Genetically Monomorphic Bacteria: SNPs and the Evolution of Salmonella Typhi”

Tiffany Williams
Baylor College of Medicine, Houston, TX
“Global Health and Next Generation Sequencing Technologies: Streptococcus pneumoniae sertoype 1 in Africa”

Kim Lewis
Northeastern University, Boston, MA
“Persister Cells and Biofilm Resistance”

Jeffery F. Miller
University of California, Los Angeles, CA
“Diversity-Generating Retroelements”

Steven A. Benner
Foundation for Applied Molecular Evolution, Gainesville, FL
“Molecular Paleoscience”

Joe Zhou
University of Oklahoma, Norman, OK
“Metagenomics Insights of the Feedback Responses of a Grassland Ecosystem to Elevated Atmospheric CO2”
Heather Allen
University of Wisconsin-Madison, WI
“Using Functional Metagenomics to Discover Antibiotic Resistance Genes in Natural Environments”

David A. Relman
Stanford University School of Medicine, Stanford, CA
“Response of the Human Distal Gut Mircobiota to Disturbance: The Effect of Antibiotics”

Ashlee Earl
Harvard Medical School, Boston, MA
“Bacillus subtilis Biofilm Diversity”

Mary E. Lidstrom
University of Washington, Seattle, WA
“Coupling Function to Phylogeny via Single-Cell Phenotyping”

John Dueber
University of California, Berkeley, CA
“Use of Synthetic Protein Scaffolds to Balance Pathway Flux of Engineered Metabolic Pathways”

Maria L. Ghirardi
National Renewable Energy Laboratory, Golden, CO
“Hydrogen Fuel Production by Microalgae: Issues and Future Directions“

Caroline S. Harwood
University of Washington, Seattle, WA
“Redirection of Metabolism of Hydrogen Production”

Byung-Kwan Cho
University of California, San Diego, CA
“The Reconstruction of the Transcriptional Regulatory Network in E. coli ”

E. Virginia Armbrust
University of Washington, Seattle, WA
“Molecular Insights into Silicon Bioprocesses in Marine Diatoms”

Athanasios Typas
University of California, San Francisco
“High-throughput Quantitative Analysis of Genetic and Chemical-Genetic Interactions in E. coli”

Devaki Bhaya
Carnegie Institution for Science, Stanford, CA
“Germ warfare in a microbial mat community: CRISPRs provide insights into the co-evolution of host and viral genomes.”

Erin Sanders-Lorenz
University of California, Los Angeles, CA
“Integrating Discovery-based Undergraduate Research Experiences into UCLA Courses Using a Collaborative Curriculum Model”

Cheryl Kerfeld
DOE Joint Genome Institute, Walnut Creek, CA
“The JGI Microbial Genome Annotation Program”

Fredrick Blattner
University of Wisconsin, Madison, Wisconsin
“Insights from the Genomes of Commonly Used Lab Strains”

Colin J. Ingham
Wageningen University, Wageningen, The Netherlands
“Reinventing the Petri Dish: Miniaturized Tools for High Throughput Microbial Culture”

Maureen Hillenmeyer
Stanford University, Stanford, CA
“The Chemical Genomic Portrait of Yeast: Uncovering a Phenotype for All Genes”

Simon Prochnik
DOE – Joint Genome Institute, Walnut Creek, CA
“The Genome Sequence of the Deep-Branching Amoeboflagellate Naegleria gruberi Reveals Ancestral Eukarotic Functions”

Elizabeth Fozo
National Institute of Allergy and Infectious Diseases, Bethesda,MD
“Regulating Bacterial Expression of Short Hydrophobic Toxic Proteins with Small RNAs”

Mariusz Nowacki
Princeton University, Princeton, NJ
“RNA-mediated Epigenetic Programming of a Genome-Rearrangement Pathway”

Barry L. Wanner
Purdue University, West Lafayette, IN
“Development of the www.EcoliHub.org Information Resource”

Hirotada Mori
Nara Institute of Science and Technology, Nara, Japan
“Systematic Analysis of Genetic Interaction of Esccherichia coli”

Open Science Required Reading: MSNBC on "Era of scientific secrecy nears its end"

There is a must read out there about Open Science. Robin Lloyd has a excellent article on Open Science (Era of scientific secrecy nears its end) posted at MSNBC. I am not sure whether this was originally written for MSNBC or not nor the whole history of the piece. But the article discusses some of the issues associated with Open Science.

It has some good sections like:

The openness at the technological and cultural heart of the Internet is fast becoming an irreplaceable tool for many scientists, especially biologists, chemists and physicists — allowing them to forgo the long wait to publish in a print journal and instead to blog about early findings and even post their data and lab notes online. The result: Science is moving way faster and more people are part of the dialogue

It also lists some of the aspects of Open Science including

• Blogs where "scientists can correspond casually about their work long before it is published in a journal";
• Social networks "that are scientist friendly such as Laboratree and Ologeez"
• Sharable sites like "GoogleDocs and wikis which make it easy for people to collaborate via the Web on single documents"
• Citation sharing sites like "Connotea that allows scientists to share bookmarks for research papers"
• Preprint servers "such as Arxiv, where physicists post their "pre-print" research papers before they are published in a print journal"
• OpenWetWare "which allows scientists to post and share new innovations in lab techniques"
• Video sharing sites like "The Journal of Visualized Experiments, an open-access site where you can see videos of how research teams do their work"
• Sequence databases like "GenBank, an online searchable database for DNA sequences"
• "Science Commons, a non-profit project at MIT to make research more efficient via the Web, such as enabling easy online ordering of lab materials referenced in journal articles";
• "Online open-access (and free) journals like Public Library of Science"
• "Open-source software that can often be downloaded free off Web sites"

Sure the article gets a few things a little mixed up. For example, software can be free even if it is not open source. And not all open access journals are the same. But the article is overall very good and has some of my favorite Open Science advocates in it like Cameron Neylon and Jean-Claude Bradley.

Follow up to Amy Harmon's NY Times Story on Evolution

The NY Times published a few letters that are follow ups on Amy Harmon's excellent story on evolution teaching in Florida.  

Check out the letters here: Letters - Teaching Evolution in Hostile Territory

Also check out my blog posting about her story which has links to the story and some other information.

Open Access Pioneer Award #3: Joe Derisi

So I was reading the web page of WTOP radio, which I used to listen to all the time in DC and somehow still have their page near the top of my bookmarks. And there was a headline I could not resist. It said: "Malaria Researcher Wins Heinz Award." As I know a few people studying malaria here and there I had to check it out. And indeed, one of the winners of the award is Joe Derisi, from UCSF, who I know reasonably well and like very much. I am very pleased to see him win one of these Heinz Awards

The Heinz Site says "Joseph DeRisi receives the Heinz Award in Technology, the Economy and Employment for his extraordinary breakthroughs in detecting both new and existing viruses."

In addition to his science they say

"Joseph DeRisi has made breakthrough discoveries in the laboratory that have provided clarity and insight into the detection of some of the world's most threatening viruses as well as distinguished himself as a generous and tireless advocate for the free and open sharing of scientific research. With a brilliant mind and expansive heart, he has ennobled the field of science."

Here here. Derisi is one of the true pioneers of Open Science, not only promoting Open Access publishing but also promoting open sharing of methods, equipment, data, and everything. And, not that he needs another award (to go with his Heinz, his HHMI position, and his Macarthur among many things), but I am giving him my Open Access Pioneer Award #3 for his firm commitment to open science.

Blogs getting a bit more respect at UC Davis

Well, to go along with the FreindFeed discussions I have been having recently here is a tidbit of interest. Blogs keep getting a bit more respect at UC Davis. First, there was Egghead, a blog about research at Davis sponsored by University Communications the College of Biological Sciences and edited by Andy Fell of the UC Davis News Service. And now there is "UC Davis Blogs" a web site with details about blogs by UC Davis people also maintained by University Communications. And here is their current list:

Behind the Lens by Karin Higgins

Arts and humanities

• The Huffington Post — Bob Ostertag:
• Ecology Without Nature: by Timothy Morton,
  
• The Pull of Gravity: by Julie Wyman

Business and law

• Anupam Chander:
  
• Harga-Blog: by Andrew Hargadon,
  
• ImmigrationProf Blog: A blog edited by Kevin Johnson,
  

Science and agriculture

• Tomorrow's Table: by Pam Ronald,
  
• The Tree of Life: by Jonathan Eisen
• ANR News Blog:A agricultural news commentary from the UC Division of Agriculture and Natural Resources
• Bug Squad: by Kathy Keatley Garvey,
  

Social science

• Beyond Homophobia: by Gregory Herek,
• The Edge of the American West: A team blog including UC Davis history professors Ari Kelman and Eric Rauchway
• Eric Rauchway’s blog: by Eric Rauchway

They have left out a few including one of my favorites: "Mario's Entangled Bank" by Mario Pineda-Krch but the listing by UC Davis is a good thing.

Darwin on the Wall

Lots of other bloggers posting about this but I got to put it out there too.  Check out the remarkable story of the Darwin Shaped Wall Stain and how it is galvanizing the evolution community - See Evolutionists Flock To Darwin-Shaped Wall Stain.  It is from the Onion.  One of my favorite "news" sources.  Hat tip to many many people for pointing this out.

Predicting the future (for molluscs)

As many of you know, I spend a decent amount of my blogging time trying to come up with funny evolution or genomics related posts. Well, if you like that type of thing, you really have to check out this new site:

The Molluskan Zodiac

The site states

"While most people are familiar with western astrology and with the Chinese zodiac, much less is known about the ‘molluskan zodiac’ (sometimes known as the mariners zodiac). But ask any fisherman, and they will tell you instantly which of the ten signs of the molluskan zodiac they were born under."

It is very very funny. And real of course. Kudos to Keith Bradnam, who happens to be from the UC Davis Genome Center (where I work) for revealing the inner secrets of these wonderful invertebrates. And while you are checking out the Zodiac, check out Bradnam's new PLoS One paper on intron length which he authored with Ian Korf. Science humor, invertebrates, and Open Access publishing. Now what could be better than that?

Tracing the evolutionary history of Sarah Palin: links to a parasitic nematode and the pathogenic fungus Botryotinia fuckeliana

You see, as a total sequence analysis dork, when I see names, I frequently ask whether the letters in the name include only letters which are used as amino acid abbreviations. I started this game when the brilliant notes/letters came out in Science in the early 90s about whether ELVIS was overrepresented in protein sequences. Of course, despite being 20 years old, Science still keeps these under wraps requiring registration to see them (see for example the Stevens letter).

Anyway, alas, three of the major candidates for the US election have names that do not use traditional amino acid abbreviations so I am stuck with analyzing Sarah Palin. But that is OK because of her professed aversion to evolution and support to Creationism (and since sequence analysis is inherently an evolutionary study).

So - I took here name and went to the NCBI Blast page and did some searches. And what came up? Well, here are some of the top hits from the blastp searches (which I used to compare the pretend peptide "SARAHPALIN" with all the peptides in the non redundant collection at Genbank).

>ref|XP_001545292.1|  hypothetical protein BC1G_16161 [Botryotinia fuckeliana B05.10]
gb|EDN25226.1|  predicted protein [Botryotinia fuckeliana B05.10]
Length=383

GENE ID: 5425746 BC1G_16161 | hypothetical protein
[Botryotinia fuckeliana B05.10]

Score = 26.9 bits (56),  Expect =   189
Identities = 8/9 (88%), Positives = 8/9 (88%), Gaps = 0/9 (0%)

Query  1    SARAHPALI  9
            SARA PALI 
Sbjct  209  SARAQPALI  217

>ref|YP_061725.1|  homoserine dehydrogenase [Leifsonia xyli subsp. xyli str. CTCB07]
gb|AAT88620.1|  homoserine dehydrogenase [Leifsonia xyli subsp. xyli str. CTCB07]
Length=451

GENE ID: 2939000 thrA | homoserine dehydrogenase
[Leifsonia xyli subsp. xyli str. CTCB07] (10 or fewer PubMed links)

Score = 26.9 bits (56),  Expect =   189
Identities = 8/9 (88%), Positives = 8/9 (88%), Gaps = 0/9 (0%)

Query  1    SARAHPALI  9
            SAR HPALI
Sbjct  267  SARVHPALI  275

>ref|ZP_02031476.1|  hypothetical protein PARMER_01474 [Parabacteroides merdae ATCC
43184]
gb|EDN87136.1|  hypothetical protein PARMER_01474 [Parabacteroides merdae ATCC
43184]
Length=299

Score = 26.1 bits (54),  Expect =   340
Identities = 7/8 (87%), Positives = 8/8 (100%), Gaps = 0/8 (0%)

Query  3    RAHPALIN  10
            RAHPAL+N 
Sbjct  170  RAHPALVN  177
>ref|XP_567332.1|  hypothetical protein CNJ01520 [Cryptococcus neoformans var. neoformans
JEC21]
ref|XP_773201.1|  hypothetical protein CNBJ1950 [Cryptococcus neoformans var. neoformans
B-3501A]
gb|EAL18554.1|  hypothetical protein CNBJ1950 [Cryptococcus neoformans var. neoformans
B-3501A]
gb|AAW45815.1|  hypothetical protein CNJ01520 [Cryptococcus neoformans var. neoformans
JEC21]
Length=437

GENE ID: 3254188 CNJ01520 | hypothetical protein
[Cryptococcus neoformans var. neoformans JEC21] (10 or fewer PubMed links)

Score = 26.1 bits (54),  Expect =   340
Identities = 8/9 (88%), Positives = 8/9 (88%), Gaps = 0/9 (0%)

Query  1    SARAHPALI  9
            SAR HPALI 
Sbjct  415  SARQHPALI  423

>ref|YP_001626035.1|  citrate synthase [Renibacterium salmoninarum ATCC 33209]
gb|ABY24621.1|  citrate synthase [Renibacterium salmoninarum ATCC 33209]
Length=386

GENE ID: 5822379 RSal33209_2898 | citrate synthase 
[Renibacterium salmoninarum ATCC 33209]

Score = 25.7 bits (53),  Expect =   456
Identities = 9/11 (81%), Positives = 9/11 (81%), Gaps = 2/11 (18%)

Query  1    SARAHP--ALI  9
            SARAHP  ALI 
Sbjct  218  SARAHPYAALI  228

>ref|YP_001817256.1|  integral membrane sensor hybrid histidine kinase [Opitutus terrae
PB90-1]
gb|ACB73656.1|  integral membrane sensor hybrid histidine kinase [Opitutus terrae
PB90-1]
Length=936

GENE ID: 6208547 Oter_0366 | integral membrane sensor hybrid histidine kinase
[Opitutus terrae PB90-1]

Score = 25.2 bits (52),  Expect =   611
Identities = 7/7 (100%), Positives = 7/7 (100%), Gaps = 0/7 (0%)

Query  3    RAHPALI  9
            RAHPALI 
Sbjct  256  RAHPALI  262

>ref|YP_001757871.1|  putative anti-sigma regulatory factor, serine/threonine protein
kinase [Methylobacterium radiotolerans JCM 2831]
gb|ACB27188.1|  putative anti-sigma regulatory factor, serine/threonine protein
kinase [Methylobacterium radiotolerans JCM 2831]
Length=331

GENE ID: 6141303 Mrad2831_5232 | putative anti-sigma regulatory factor,
serine/threonine protein kinase [Methylobacterium radiotolerans JCM 2831]

Score = 25.2 bits (52),  Expect =   611
Identities = 7/8 (87%), Positives = 8/8 (100%), Gaps = 0/8 (0%)

Query  2    ARAHPALI  9
            ARAHPAL+
Sbjct  299  ARAHPALV  306

>ref|ZP_01466013.1|  hydrolase, TatD family [Stigmatella aurantiaca DW4/3-1]
gb|EAU63211.1|  hydrolase, TatD family [Stigmatella aurantiaca DW4/3-1]
Length=209

Score = 25.2 bits (52),  Expect =   611
Identities = 7/7 (100%), Positives = 7/7 (100%), Gaps = 0/7 (0%)

Query  3   RAHPALI  9
           RAHPALI 
Sbjct  79  RAHPALI  85

>ref|YP_001558323.1|  glycosyl transferase group 1 [Clostridium phytofermentans ISDg]
gb|ABX41584.1|  glycosyl transferase group 1 [Clostridium phytofermentans ISDg]
Length=357

GENE ID: 5743305 Cphy_1206 | glycosyl transferase group 1
[Clostridium phytofermentans ISDg]

Score = 25.2 bits (52),  Expect =   611
Identities = 8/10 (80%), Positives = 8/10 (80%), Gaps = 0/10 (0%)

Query  1    SARAHPALIN  10
            S RAHP LIN 
Sbjct  113  SERAHPLLIN  122

There does not appear to be a perfect match in the NCBI NR protein database. But take a close look at the #1 scoring hit. That is right, it is from and organism called Botryotinia fuckeliana. No comment on the appropriateness of this name, but it does contain a term I will probably use a lot if she gets elected.

Of course, anybody who has heard me blather on and on about evolution knows that I am always talking about how blast top hits are not a good measure of relatedness per se (see my NAR paper where I first talked about this in 1995). So - I decided to build a tree of Sarah Palin. I used the NCBI Distance Tree option which you can do from blast searches.










Since most likely you cannot see that in enough detail - here is a zoom in.








That one did not come through on the Blog so well either so I decided to output the tree in Newick format and then I searched for a program that could draw a better figure on the web (we have tools in my lab to do this but I am trying to do this all on the web as an exercise). And I found a web site that makes drawtree available. And I plugged in the Newick format and it made a nicer one.




Though making trees from really short sequences is not ideal, in this tree, Sarah Palin is shown to be at the root of a branch including a protein from the parasitic nematode Brugia malayi. So if we take an evolutionary interpretation it seems that this causative agent of filariasis (well, a protein from this agent) is descended from SarahPalin. In other words, she seems to be ancestral to this parasite.

So in conclusion - by similarity - SarahPalin is closest to a plant pathogen with an unusual name. And by phylogeny SarahPalin is ancestral to a parasitic nematode. Sounds about right.

Science Faux Pas Example #2: V = MA

OK.  This is far and away my favorite Science Faux Pas I have seen.  I cut this out of some magazine many years ago and posted it on my door in college, grad. school and in my previous job, so it is a little beat up.  But you got to hand it to Mathey-Tissot - promoting a precision watch with "Velocity equals mass x acceleration (V = MA)." Must be one heck of an interesting mechanism inside that watch. 

Science Faux Pas Example #1: 97% of internet users have internet access

I am starting a new series here on Science Faux Pas.  Here is one of my favorites from Nature a while back.  They report in this promotion that 97% of Nature's readers have internet access.  How did they determine this? By an online readers survey.  The real question is - who are the 3% that completed the survey but said they did not have internet access?

I am going to try and make a collection of these over time so if you have any or can point to some out there please let me know.  It may not be as fun as Carl Zimmer's tattoo series, but there are some doozies out there.

Help save the world and get $100,000 seed grant to do it

Just got this email and thought I would share since it does relate to some of the themes of my blog. I note that the Gates Foundation is VERY supportive of Open Access publishing as one of their previous grants helped support the journal "PLoS Neglected Tropical Diseases." I am hoping that at some point the Gatges Foundation will require OA publishing for all of the projects they fund.

The Bill & Melinda Gates Foundation is now accepting grant proposals for Round 2 of Grand Challenges Explorations, a US$100 million initiative to encourage unconventional global health solutions.

Based on your feedback, we have made changes for Round 2 of Grand Challenges Explorations. We modified the topics from Round 1 and added two additional topics. We will no longer require applicants to register for a topic in advance of submitting their proposals. We also updated the application form in response to feedback from the initial round.

Grant proposals are being accepted online at http://www.gcgh.org/explorations until November 2, 2008, on the following topics:

New! -- Create new vaccines for diarrhea, HIV, malaria, pneumonia, and tuberculosis
New! -- Create new tools to accelerate the eradication of malaria
-- Create new ways to protect against infectious diseases
-- Create drugs or delivery systems that limit the emergence of resistance
-- Create new ways to prevent or cure HIV infection
-- Explore the basis for latency in tuberculosis

Initial grants will be $100,000 each, and projects showing promise will have the opportunity to receive additional funding of $1 million or more. Full descriptions of the new topics and application instructions are available at http://www.gcgh.org/explorations.

We are looking forward to receiving innovative ideas from scientists around the world and from all scientific disciplines. Anyone can apply, regardless of education or experience level. If you don't submit a proposal yourself, we hope you will forward this message to someone else who might be interested.

Thank you for your commitment to solving the world's greatest health challenges.

Quick Post - Spore Sounds Cool

Nothing conclusive here. I have not tried it yet. But Spore sure sounds like a cool evolution game to play. See Carl Zimmer's NY Times article and his blog for more.

I see PLoS in everything III: PLoS Hats

Thanks to my mom for this one.  PLoS Hats rule.

Cool Plant Comparative Genomics Resource: Phytozome

I spent the last few days at a "retreat" for the Joint Genome Institute and heard about a few things there worth sharing with everyone. I will try and post about some of them in the next few days. Here is one. The JGI and the Center for Integrative Genomics have made a pretty cool tool for comparative analyses of plant genomes. It is called Phytozome and has a variety of simple and nice features. JGI is doing more and more work on plant genomes as part of their energy research and I think Phytozome could turn into a good place to go to get the latest plant genome information. Go to http://www.phytozome.net to see the real thing.

Sarah Palin on EvolutionCreationism

Well, it seems McCain has further embraced an anti-science agenda with his pick as Sarah Palin as his running mate.

The Science Bloggers are a bit up in arms over this. I think there is some hope that she/McCain will drift back to the middle on this at some point but they both now seem to fall in the camp of the Intelligent Design supporters. It is the "independent" streak both do seem to show occasionally that gives me hope that if they do get elected, they will not be as tied to the ID supporters as they will be during the election.

Anyway, here are some things I found on the web about Palin's evolution views:

NewMiner.Com: in response to written questions in a 2002 election ...

Q: The education section of the Republican Party of Alaska’s platform states “We support giving Creation Science equal representation with other theories of the origin of life. If evolution is taught, it should be presented as only a theory.” Do you support this position? Why?

A: I support this plank in the Republican Party’s platform. I believe society can have healthy debates on scientific theories, so equal representation of creation and evolution shouldn’t be an offense.

Anchorage Daily News in 2006 reported

The volatile issue of teaching creation science in public schools popped up in the Alaska governor's race this week when Republican Sarah Palin said she thinks creationism should be taught alongside evolution in the state's public classrooms.

Palin was answering a question from the moderator near the conclusion of Wednesday night's televised debate on KAKM Channel 7 when she said, "Teach both. You know, don't be afraid of information. Healthy debate is so important, and it's so valuable in our schools. I am a proponent of teaching both."

Most other thigns I have seen are rehashing these two stories in some way. If anyone has any other detail I would love to see it.

Examples of blog posts on this issue include:

• Sarah Polin, another victim of "Teach the Controversy" nonsense ...
• Palin’s dangerous views on science education
• VP Candidate Palin Supports Teaching Creationism
• Sarah Palin as McCain’s VP pick: time to buy some Obama election ...
• McCain's VP Wants Creationism Taught in School
• McCain’s VP pick is Not Good for Science

I see PLoS in everything #2

OK - I cannot help it. Whenever I see this little train letters in stores everywhere I spell something related to PLoS. If you support OA, please continue the conspiracy and spell something OA-related wherever you find letters like this. PS - Vaughn this is for your kid.

Redefining Tomorrow's Table

Tony Trewavas has an interesting review (Redefining “Natural” in Agriculture) in PLoS Biology of my friend and colleague Pam Ronald's new book "Tomorrow's Table: Organic Farming, Genetics and the Future of Food."

I was planning on eventually writing my own review of her book but not sure when I will get to it. I personally like the book a great deal, and enjoy how it switches back and forth between the authors (Pam and her husband Raoul Adamchak) and how it interweaves personal stories with discussion of the science and practice of organic farming and plant genetic engineering.

Trewaras has some things in the review I agree with a great deal like

"The text deals with many of the questions raised by the public about GE crops in a sensible and balanced manner, quoting various sources of reliable information on the concerns about risks to health and environment that often recur. It also mentions Richard Jefferson, who is Chairman of CAMBIA, a non-profit organisation that attempts to make the tools of biotechnology widely and freely available (http://www.cambia.org/). As a scientist, I cannot help but applaud!"

I personally love what CAMBIA is doing and found the discussion of CAMBIA in the book to be interesting. I have gotten to know Richard Jefferson over the last few years and think he is a true pioneer in revolutionizing biotechnology and freeing it from the shackles of over protectionism.

Trewavas also has a very interesting thread about the value of different opinions. Since this was printed in PLoS Biology and is under a CC license I can reprint it here (with acknowledgment of the source - Citation: Trewavas T (2008) Redefining “Natural” in Agriculture. PLoS Biol 6(8): e199 doi:10.1371/journal.pbio.0060199) and it is worth doing so:

The continuing conversation did not resolve the issues between them. It convinced me, however (if I needed convincing), that while everyone is entitled to their opinions, when dealing with detailed technical matters of science or medicine or any subject that requires enormous qualifications and experience, the notion that all opinions have equal validity is simply downright wrong. If you want real information on the safety of heart surgery procedures, do you follow the advice of a qualified heart surgeon or the local butcher? If you want advice on flying a jumbo jet, do you ask the local bus driver or a pilot with 10,000 hours of experience flying jumbo jets? And if you want advice on how to captain a supertanker, do you ask a person whose experience is limited to rowing a dinghy? Mistakes by surgeons are not uncommon, 70% of air crashes result from pilot error, and occasionally supertankers hit the rocks. But relying on rank amateurs instead of professionals would guarantee instant catastrophe. Many branches of science are very complex. However, being a scientist isn't enough, of course, as being a scientist doesn't qualify you to advise on any subject except your specialty. To provide advice that can lead to sensible policy requires not only a thorough understanding of the workings and literature of the particular scientific area but many decades of experience in that field.

It is unfortunate that for the past 40 years, agriculture in particular has been damaged by opinionated groups of the public that have forcefully used fear and anxiety and carefully selected information to try and coerce policy makers to adopt their own mistaken and unqualified views. Fear and emotion do not make for good policy. I applaud Ronald's conclusion that “if citizens vote, it should be for a specific matter on which they are well informed, not because of general concerns about a new technology.”

The corollary is that on most technical matters, the public can never be well enough informed. If scientific knowledge does not form the basis of policy on technology, basing such policy on ignorance can be guaranteed to generate disaster. It was Slovik in his classic Perception of Risk [3] who demonstrated that non-experts overestimate the frequency of death from rare causes while underestimating the frequency of common causes of death, and who established clearly how additional knowledge changed expert understanding. The use of the local ordinance by activist groups to stop GE farming is only too reminiscent of the damage done by Lysenkoism to Soviet farming in the 40s, which took decades to recover from, once it was abandoned.

Basically, he is indirectly agreeing with Ronald/Adamchak that some negative opinions of GE are simply not valid. Here I think I disagree with all of them. I think much of the objection to GE modification of plants is an esthetic objection and thus presenting scientific arguments for why it is OK to do is a bit off tangent. It is kind of like when someone says "that house is ugly." Do you respond by saying "Well, actually, the shape and color patterns have been shown to appeal to human sensory systems" Not too helpful. I feel that the same is happening with GE plants --- if people's instinctively do not like them, telling them about the science is not necessarily going to help. Nothing wrong with educating about the science, but I think it is a red herring to say that some of the anti-GE folks do not understand the science and therefore their objections must be wrong. I feel similar vibes in the evolution education discussion going on around the world. I think many people latch on to ID and Creationism because it appeals to them in a esthetic sense. And one needs to be really gentle/careful about bringing science into the discussion (except of course, when one is teaching a science class --- then you teach the science).

So sure - I have some quibbles about parts of the book. As does Trewavas (he has to raise some objections - any book review that does not have them seems like fan mail and not a review).

Despite my quibbles here and there, the book really is a must read for those interested in GMOs and/or the organic farming movement as well those thinking about "slow food" and other related topics. In addition it is a wonderful personlized story, with a mixture of recipes, stories of research, discussions of teaching about organic agriculture, and some minor family drama. For the same reason that I like Amy Harmon's New York Times stories (such as the recent one on evolution) I like this book - it personalizes what is frequently a boring impersonal discussion.

And of course it does not hurt that the heart of the story / discussion is good. Ronald/Adamchak present an overall idea I have a hard time arguing against - GE and organic growth practices both have a lot to offer the world and if we took the good parts of both, a "GE-Organic" system might be highly beneficial to all. For example, in principle, GE plants can lead to a reduction in the use of pesticides and fertilizer. Similarly, they could lead to a reduction in water use and higher crop yields. Since it seems unlikely that the current organic movement will embrace the benefits of GE crops, it will probably require a whole new movement to merge the two. It will also require the companies and organizations that push GE to do it with the environment and health of people and the planet in mind. To me, the biggest problem with GE food and farming is that it seems to be used more to help the farmers and the companies selling stuff than the consumers and the public. If that changed, I can see people embracing GE plants in much the same way they embrace GE medicines.

PS - For more on the book see Pam's blog here.

Twisted Tree of Life Award #1: Salk Institute Press Release on Kinases

I am starting a new award here --- for people or sites that do something silly in regard to the "Tree of Life" but should know better. That is, this is for scientists or sciency sites that do something unseemly with the Tree of Life. And the first award goes to the Salk Institute for their press release relating to a paper on kinases in single celled choanoflagellates (OK - the pres release is a month and a half old but I was out sick - and I drafted this 7/8/08). In the press release, which discusses a PNAS paper by Gerard Manning and colleagues (Manning does some really great comparative work on kinases and helped me look at kinases in a few genomes such as that of Tetrahymena thermophila). I note - it seems Manning or someone has paid the OA fee for this paper so anyone can read it.

The paper seems both sound and interesting. And it has a really really cool tree figure.




But the press release has a few doozies. The worst (or best, I guess, depending on your point of view) is the following:

It commands a signaling network more elaborate and diverse than found in any multicellular organism higher up on the evolutionary tree, researchers at the Salk Institute for Biological Studies have discovered.

Yup that is right. A modern organism, living today is somehow "lower" on the tree of life than we are. Too bad the person who wrote the press release did not read Amy Harmon's recent Times story on evolution education. Or they could have gotten help from the high school science teacher Harmon featured, who taught his students about how modern organisms did not evolve from other modern organisms.

And for using one of my most hated metaphors in all of evolution (higher and lower organisms), Salk gets my first "Twisted Tree of Life Award"

Building a new Alvin

Quick post here. For those interested in Deep Sea research, you should check out the story by William Broad in the NY Times on building a replacement for Alvin (New Submersible to Expand Deep-Sea Exploration). Alvin is a wonderful little submarine that I and many others have relied upon for much of our research. But it definitely has some issues. And it looks like Woods Hole Oceanographic Institute is in the processof building a replacement.

Tree of Life Imagery at Starbucks

Not the best resolution (damn that iPhone camera) but just thought I would post the picture I saw at a Starbucks in San Francisco where I was for a DARPA meeting discussion the "laws of biology". You see - even Starbucks is a fan of the Tree of Life.

------------------------------------------

Follow up.  After Laura wrote in asking about the origins of this picture I have searched around and found many others interested in it.  I note - the caption says "The Deeper the Roots - the Higher the Reach".  I have not found the origins of the print but here are some other discussions

• Scott Hodge
  
• Paul Dazet
• Serving Strong
• Asheyan
• Nate
• Vicky Beeching

Open Access Pioneer Award #2: R. Preston McAfee

Great article in the LA Times on August 18 by Gale Holland about "Free digital textbooks." (see Free digital texts begin to challenge costly college textbooks in California)

The article discussed some issues in open source textbook publishing including in particular R. Preston McAfee's work on creating a free online economics textbook. McAfee is a professor at Caltech and is a self described right winger.

"I'm a right-wing economist, so they can't call me a communist," McAfee said.

And he goes on to say

"What makes us rich as a society is what we know and what we can do," he said. "Anything that stands in the way of the dissemination of knowledge is a real problem."

The article discussed other open source educational materials including:

• Merlot, from Cal. St. Universities which is a "a searchable collection of peer-reviewed, online multimedia materials."
• Connexions, from Rice University , which "stores free, open-licensed educational materials in fields such as music, electrical engineering and psychology.
• OpenCourseWare from MIT which includes "virtually its entire curricula online -- video lectures, problems sets and exams for more than 1,800 courses in 33 disciplines."
• Wikibooks, a collection of editable textbooks
• The Digital Marketplace, from Cal. St. U. which is a "website for selecting, comparing, sharing, approving and distributing both open-source and commercial online educational materials."

Now, I am not saying here there is not a place for textbooks in the normal model (I have one).  Unlike basic science papers, for which the cost of making a presentable paper is relatively low, the cost of producing a textbook can be very very high.  Thus I think publishers are welcome to work with authors to come up with their own models for how to publish the texts.  But nevertheless, the more we can get good open source textbooks out there, the better off we will be.  And thus, for his role in promoting the release of what seems to be a high quality open source textbook, I am giving R. Preston McAfee my second "Open Access Pioneer Award.

Hat tip to Jeremy Peterson and Eilleen Hamilton for pointing this out.

Update - required evolution reading/ Harmon story/ Mickey Mouse

Yesterday I posted about Amy Harmon's excellent story in the NY Times about evolution education.  For more on it see my post - Required evolution education reading - Amy Harmon on Florida Evolution teaching

I just wanted to give an update here as I have seen a few postings out there discussing the Mickey Mouse example in the story.  In the story, Harmon described how David Campbell, the Florida high school science teacher uses the evolution of Mickey Mouse as an  example of natural selection.  

From the Times article:

He started with Mickey Mouse.

On the projector, Mr. Campbell placed slides of the cartoon icon: one at his skinny genesis in 1928; one from his 1940 turn as the impish Sorcerer’s Apprentice; and another of the rounded, ingratiating charmer of Mouse Club fame.

“How,” he asked his students, “has Mickey changed?”

Natives of Disney World’s home state, they waved their hands and called out answers.

“His tail gets shorter,” Bryce volunteered.

“Bigger eyes!” someone else shouted.

“He looks happier,” one girl observed. “And cuter.”

Mr. Campbell smiled. “Mickey evolved,” he said. “And Mickey gets cuter because Walt Disney makes more money that way. That is ‘selection.’ ”

Some bloggers have questioned using this example (see john hawks weblog for example as well as Bora's excellent post about this story here) because it seems more like Intelligent Design than natural selection.  I disagree and wanted to point out that this is a classic Stephen Jay Gould teaching case study which he detailed (see A BIOLOGICAL HOMAGE TO MICKEY MOUSE Stephen Jay Gould).  

In fact, when I was an undergrad at Harvard and was taking Gould's class, we played around with a cool new computer program called MacClade to track the evolution of Mickey Mouse. Little did I know I would still be using Macclade and its descendants today.

Required evolution education reading - Amy Harmon on Florida Evolution teaching

Amy Harmon has done it again. First it was the series on the "DNA age" which had a suite of interesting pieces on the more personal side of DNA and genomics and won her one of those little pulitzer thingamajiggers. And now she has published a piece on the personal side of evolution education. This piece "A Teacher on the Front Line as Faith and Science Clash", which I think will be in tomorrow's Sunday New York Times, is really a must read for all interested in evolution education and evolution in general.

In the article, Harmon details the story of a Florida high school science teacher, David Campbell, and his efforts to teach evolution in a Biology class. I find the whole story fascinating in many ways. First, despite thinking I was paying attention, I was not really aware that Florida now required evolution to be taught in high school biology classes. Harmon details some of the history of how this came to be including how Campbell founded Florida Citizens for Science and helped push for new standards in biology teaching. Campbell's efforts to put science at the front of science teaching and to keep religious beliefs out is inspiring.

Harmon also details the trials and tribulations of Campbell actually trying to teach about evolution to high school students, many of whom come armed with anti-evolution ideas and literature. And Campbell does a great job with some subtle details --- in fact he seems to have a better grasp of evolutionary biology than many active biologists. For example, he does a good job with emphasizing that humans did not evolve from chimps but instead both evolved from a common ancestor. This is something many many biologists do not always get accurately.

I think the whole piece should be required reading for all evolutionary biologists, all biologists, and all science teachers. I confess, Harmon did ask me to glance the piece over a few days to give some feedback on a few sections, so I am perhaps a bit biased. But I am really hoping Harmon stays on this topic and does for evolution what she did for the DNA age, with a whole series on the personal side of things. This is so desperately needed with too much of the debate focusing on an argument about facts and faith and too little about the people in the trenches.

Addendum: Clearly lots of other bloggers liked this.  Here are some:

• A Teacher on the Front Line (NYT)
  
• Creationism - Pseudo-science that lingers
  
• The Evolution Debate Continues
  
• Evolution in the classroom - great NY Times article
  
• Now THERE's a Teacher
  
• Evolving to the Anywhere Human
  
• A Teacher on the Front Line (NYT)
• How to Teach Evolution
  
• The Evolution Debate Continues

Good Open Access News from Max Planck

Mark Patterson reports in the PLoS Blog some really good OA news (see Max Planck Society covers publication fees for PLoS journals). The Max Planck Society which has always be a strong OA supporter, will now pay the PLoS Publication fee for all papers articles where an author is affiliated with the Max Planck Institute. So now any author from there will not have to think about fees if they choose to publish in PLoS. I hope lots of other institutes follow this (not just for PLOS papers but for all OA journals).

Some outdated webpages of mine need external links

Here are some links to some very outdated webpages of mine.  I want them to come up in Google Searches and this seemed the best way.  I am back posting this a year to hide it from the front of my blog.

• RecA Family Page
• SNF2 family
• S. velum
• UvrA
• MutS
• Mutator
• GNRH
• GDE
• Arabidopsis Repair

Shameless Self Promotion # 200: Are We Alone

Just a little quick link here. People might be interested to check out the "Are we alone" Radio Show from July 21, 2008 (Are We Alone). A direct MP3 link is here. Here is there summary of the show from that date:

Remember Mr. Potato Head? You changed his look by snapping in plastic mustaches, googly eyes and feet. Now imagine doing the same with a living cell: inserting the genes you want to create the organism you want. Welcome to the world of synthetic biology. It has potential to create new bio-fuels and life-saving drugs. It also ushers in a host of ethical and safety concerns. We examine both when we discuss this emerging science of mix and match genes. Plus, does doing an end run around Mother Nature challenge the essence of life itself?

Guests:

• Jay Keasling - professor of chemical engineering and biological engineering at UC Berkeley and founder of Amyris Biotechnologies
• Jonathan Eisen - biologist at UC Davis
• Jim Thomas - researcher at ETC group in Ottawa, Canada
• Ed Regis - science writer and author of What Is Life: Investigating the Nature of Life in the Age of Synthetic Biology
• Michael Dosmann - curator of Living Collections at the Arnold Arboretum of Harvard University

This show is produced by the SETI institute and has some interesting topics on different science things.

Campus Open Access Policies: The Harvard Experience and How to Get There (SPARC)

SPARC has a nice set of talks online about Harvard's move towards a University wide open access system (see Campus Open Access Policies: The Harvard Experience and How to Get There (SPARC))

From the web site
"This spring, Harvard’s Faculty of Arts and Sciences voted to enable open access to their scholarly articles in an institutional repository. This vote granted the university the rights necessary to archive and make freely available on the Internet articles written by Arts and Sciences faculty members. It is the first time the faculty of a U.S. university has voted for an open access directive and the first time a faculty has granted permission to the university to make its articles available through open access. It is because of this vote, and the efforts leading up to it, that the Harvard FAS was named as the SPARC Innovators for June 2008.

The forum offers an exploration of the motivations behind the Harvard policy, the groundwork invested in its creation, reactions and outcomes to date, and the broader implications of this historic step. Headlining the event is Stuart M. Shieber, professor of computer science at Harvard, director of the Center for Research on Computation and Society, faculty co-director of the Berkman Center for Internet and Society, and the key architect of the policy.

Shieber is joined by Catherine Candee, executive director, Strategic Publishing and Broadcast Initiatives, from the office of the president of the University of California, who relates similar activity in the UC system; and by Kevin L. Smith, JD, scholarly communications officer at Duke University, who suggests legal considerations for institutions following the open access policy path."

Hat tip to Michael Rogawski from U. C. Davis for pointing this out. In particular, he and I are very interested in the discussion by Catherine Candee about why the UC system did not do this before Harvard (we are hoping to get the UC to do something like this). Rogawski has also pointed me in the direction of some nice tools for sharing my publications through the UC system (see his BE Press site here).

Happy Birthday Anna Eisen 8-8-8 at 8:08 PM

Happy Birthday Anna Eisen (my niece)

8/8/08 at 8:08 PM

New Yorker on Superbugs

Still catching up after being out sick with an antibiotic resistant infection. But I had to post on this one. The New Yorker has new piece by Jerome Groopman on, well, antibiotic resistant bacteria. See Medical Dispatch: Superbugs: Reporting & Essays: The New Yorker

Thanks to Saul J for pointing this out.

I particularly like the ending

No one, Moellering said, has developed a way to disarm bacteria sufficiently to allow the human body to naturally and consistently defend against them. I asked him what we should do to combat these new superbugs. “Nobody has the answer right now,” he said. “The fact of the matter is that we have found all the easy targets” for drug development. He went on, “So the only other thing we can do is continue to work on antibiotic stewardship.” Meanwhile, new resistant bacteria, Moellering asserted, aren’t going to go away. “We can temper things, we might be able to slow the rate of emergence of resistance, but it’s unlikely that we will ever be able to conquer it.”

Open Metagenomics Highlight: Comparative Analysis of Human Gut Microbiota by Barcoded Pyrosequencing

OK - it is not quite metagenomics, but there is new paper in PLoS One worth looking at if you study uncultured organisms. This paper (Comparative Analysis of Human Gut Microbiota by Barcoded Pyrosequencing) reports on a slightly new twist in carrying out deep rRNA surveys of uncultured microbes using one of the "next" generation sequencing methods.

Open Metagenomics Highlight - PloS Biology paper reporting more from Banfield lab on the Acid Mine Drainage

Just a quick "Open Metagneomics" posting here. There is a very interesting paper in PLoS Biology that just came out reporting more detail from Jill Banfield's lab on their studies of an Acid Mine Drainage (AMD) site. This paper is ostly a population genomic study of the microbes living in the AMD. See the paper at PLoS Biology - Population Genomic Analysis of Strain Variation in Leptospirillum Group II Bacteria Involved in Acid Mine Drainage Formation.

Closed Access Award #2: Andrey Rzhetsky, Michael Seringhaus and Mark Gerstein

Just got pointed to a new paper by someone near and dear to me. In this paper (Seeking a New Biology through Text Mining), Andrey Rzhetsky, Michael Seringhaus and Mark Gerstein seem to argue for the importance of text mining for the future of biology research. Text mining is indeed an important new tool in biology. Of course, it works best if you have access to the text. Alas, I would tell you more about their paper, but I have been out sick and stuck at home, and I do not have access to their paper, which was published in Cell. And thus, even without seeing their paper, I am giving them my second "Closed Access Award" for apparently outlining a path for a new biology that will be only available to some, not all.