Friday, August 31, 2007
Too eager for ethanol?
What would make more sense is to first make better use of all the wasted biomass from various agricultural systems and from solid waste. Lots of material is still being burned on farms for example (see pictures below of a fire near Davis --- these are going all the time, even on "spare the air" days). Sure - one can make lots of money from corn to fuel right now. But that does not make it the right thing to do when there are plenty of sources of biomass being wasted all around us. Lets hope that more of the biofuels projects work on converting leftovers not new crops.
Thursday, August 30, 2007
Adaptationomics Award #1 - Wolbachia DNA sneaking into host genomes
Gould and Lewontin railed against this type of thing many years ago and others have since. Just because something is there does not mean it is adaptive (e.g., it could be neutral or detrimental). And even if something is adaptive, just because you can think of an adaptive explanation does not mean your explanation is correct.
And this is so common in genomics I have decided to invent a new word - Adaptationomics. And I am giving out my first award in this to Jack
Basically, in their study (led by a past colleague of mine from TIGR, the brilliant up and coming Julie Dunning Hotopp) they showed that there have been multiple lateral transfers of DNA from Wolbachia (which are intracellular parasites that can infect germ cells) into invertebrates. Furthermore they showed that that the DNA transfered to the host genome is not completely transient and that in many cases it is passed on to future generations. This is interesting because it is the first report of strong evidence for such "stable" transfers from bacteria into multicellular species. Of course, one could say that this finding is not that surprising given that Wolbachia infect germ cells and given that DNA transfer from organellar genomes to nuclear genomes is quite common. But Wolbachia are not organelles and since it appears that their DNA can readily move into genomes of multicellular species, this opens up a new window into our understanding of gene transfer.
This of course does not mean that the DNA is anything but "junk" in terms of functions in the host genome. And this is where the adaptationomics comes in. One of the press releases associated with the paper has a bit of an outrageous adaptationomics claim that I would like to counter. In response to their finding of a nearly complete Wolbachia genome in the nuclear genome of a fly
The chance that a chunk of DNA of this magnitude is totally neutral, I think, is pretty small, so the implication is that it has imparted of some selective advantage to the host.And Dunning Hotopp in a Nature article says:
The discovery also hints that the bacterial genome must have provided some sort of evolutionary advantage to its host. "You're talking about a significant portion of its DNA that is now from Wolbachia," says Julie Dunning Hotopp, a geneticist at the J. Craig Venter Institute in Rockville, Maryland, who led the study. "There has to be some sort of selection to carry around that much extra DNA."This notion that the DNA MUST have an beneficial function is pure adaptationomics. Consider the movement of DNA from organellar genomes into the nucleus. Such movement occurs at an incredibly high rate and the DNA seems to be maintained in the host genomes for millions of years. For example, when we were sequencing the Arabidospsis genome, we found at least one if not more whole copies of the mitochondrial genome embedded in the nuclear genome and we concluded this was likely a non adaptive event. That is, the mt DNA was not conferring some advantage on Arabidopsis plants. There is extensive work on what are called "numts" (nuclear mitochondrial DNA) in humans and other species that makes similar conclusions - the mtDNA in the nucleus is basically junk but it is maintained for long periods of time. Sure, occasionally, the DNA confers some selective advantage. But this is a very rare event and one cannot infer that some DNA is advantageous simply because it is present. This is especially the case for eukaryotes which are generally more able than bacteria to maintain DNA that confers little selective benefit.
So I would argue that
Anyway - as is the case more and more. Read the paper. Ignore the interviews and the press releases.
Tuesday, August 28, 2007
Calling for a Boycott of of AAP - Association of American Publishers
- Leah Arhibald's mumbo jumbo cartoon
- Steve Mount's bit on PRISM
- Boing Boings Discovery that PRISM was illicitly using copyrighted material on their website
- Peter Suber's got much more detail here
- Bora's great compilation of blogs about PRISM here
- Wired Science on PRISM
- The PISD spoof of PRISM (THIS is F*$&NG BRILLIANT)
- Steven Harnad on PRISM
Full list of AAP from the AAP web site:
Academic Learning Company, LLC
Aequus Technologies Corporation
Al-Basheer Publications and Translations
American Academy of Pediatrics
American Association of Cancer Research
American Association of Pharmaceutical Scientists
American Foundation for the Blind
American Institute of Aeronautics and Astronautics
American Psychiatric Publishing, Inc.
American Psychological Association
American School of Classical Studies at Athens (The)
American Scientific Publishers
American Society of Clinical Oncology
Association for Computing Machinery (ACM, Inc.)
Association of Research Libraries
Athena Media, Inc.
Barnhardt & Ashe Publishing, Inc.
Berkshire Publishing Group, LLC
Cadmus Professional Communications
Cold Spring Harbor Laboratory Press
Colorado Independent Publishers Association
Cornell Maritime Press
Council on Foreign Relations Press
Council on Library and Information Resources
Cover Publishing Co.
Earthquake Engineering Research Institute
Emida International Publishers
Ernst & Young, LLP
Federation of American Societies for Experimental Biology
Focus Publishing/R. Pullins Company, Inc.
Gallaudet University Press
Hampton-Brown Company, Inc. (The)
Health Affairs/Project Hope
Hearst Book Group
Human Factors and Ergonomics Society
Institute for Electrical and Electronics Engineers, Inc. (IEEE)
Institute for International Economics
Institute for Scientific Information
Institute of Physics Publishing
Instrumentation, Systems, and Automation Society (The)
The Institute, Inc.
J. Paul Getty Trust Publications
James A. Rock & Company Publishers
Johns Hopkins University Press (The)
Key Education Publishing Company LLC
Library of Congress Publishing Office (The)
Lidenmeyr Book Publishing Papers
Lippincott Williams $ Wilkins Journals
Lousiana State University Press
Massachusetts Medical Society/New England Journal of Medicine
Medical Group Management Association
Minnesota Historical Society Press
Modern Language Association of America
Mooring Field Books, Inc.
Morgan & Claypool Publishers
National Computer Systems/Pearson
National Education Standards
National Publishing Co.
National Science Teachers Association (NSTA)
New England Journal of Medicine
New York Botanical Garden (The)
Pan American Health Organization
Pennsylvania State University Press (The)
Pillsbury Winthrop Shaw Pittman, LLP
Pub Smarts, LLC
Publisher's Group Incorporated
Rainbow Books, Inc.
Ray of Light Publishing Company, Inc.
Recording for the Blind and Dyslexic
Resources for the Future/RFF Press
Saferock USA, LLC
Scholatic Testing Services, Inc.
Scientific American/St. Martin's College Publishing Group
Springer-Verlag New York, Inc.
Teachers College Press
Tighe Publishing Services, Inc.
The University of Hawaii Press
University of California Press
University of Illinois Press
Veronis, Suhler & Associated, Inc.
Whitston Publishing Company, Inc.
William Morrow & Co., Inc./HarperCollins Publishers
Saturday, August 25, 2007
PRISM - Partnership for Research Integrity in Science and Medicine - Seems like a spoof but it is real, and sad
- "undermines the peer review process." Yes that's right. If an article is freely available for all to read, that must mean that peer review has been compromised. Nevermind that openness in other areas (e.g., politics, law, etc) is well established to promote critical review (anyone heard of freedom of the press). But apparently in science, openness is bad.
- "opens the door to scientific censorship". Yup. Making publications freely available apparently means that you will stifle communication. Again, the logic here is completely silly - how on earth is openness connected to censorship?
- "undermining the reasonable protections of copyright holders." Yup, the publishers of scientific articles, who do not deserve the copyright to articles in the first place, are now saying that because they have stolen the copyright from many scientists, now we should defend them because they have the copyright. Kind of like saying that someone who steals some money should not give it back because of finders keepers rules.
For more on Prism see
Thursday, August 16, 2007
Anyone else having gmail spam filtering issues?
The incoming messages included diverse messages - some with the word "FWD" in the subject line but some appearing as normal as can be.
Anyone else out there experiencing a sudden increase in missing email?
Wednesday, August 15, 2007
Save the Bay Delta
Overselling Genomics Award #2
Using molecular markers to study the formation of skeletal cartilage in embryos of the spotted catshark, UF scientists isolated and tracked the activity of Hox genes, a group of genes that control how and where body parts develop in all animals, including people.Now admittedly, this is not genomics here - but the press release just had to use genomics in the title so my automated google search for "genome" and "evolution" picked it up. So - why do they get the overselling award? Read more in the press release:
The finding shows what was thought to be a relatively recent evolutionary innovation existed eons earlier than previously believed, shedding light on how life on Earth developed and potentially providing insight for scientists seeking ways to cure human birth defects, which affect about 150,000 infants annually in the United States.Yes that is right, this genome-ish gene expression study in sharks is going to help cure human birth defects (note the paper in PLoS One seems entirely reasonable ... this is another case of press releases being disconnected from the science - and is another reason to support OA publications because here you can actually all go and read the paper and ignore the press release).
In addition, the press release says
“We’ve uncovered a surprising degree of genetic complexity in place at an early point in the evolution of appendages,” said developmental biologist Martin Cohn, Ph.D., an associate professor with the UF departments of zoology and anatomy and cell biology and a member of the UF Genetics Institute. “Genetic processes were not simple in early aquatic vertebrates only to become more complex as the animals adapted to terrestrial living. They were complex from the outset. Some major evolutionary innovations, like digits at the end of limbs, may have been achieved by prolonging the activity of a genetic program that existed in a common ancestor of sharks and bony fishes.”Now I accept that the specific details of Hox gene expression here might have been surprising but what friggin evolution textbook are these people reading if they are surprised that there is not a chain of life going from less complex to the pinnacle of complexity in humans? Hopefully not mine.
Monday, August 13, 2007
SciFoo Camp - The End and New Beginnings
For Day 3, I got up early, packed up my bag, and then polished up my presentation for a session on "The Human Microbiome." This was particularly difficult for me since I do not really at this time work on the human microbiome much (although I want to). But I figured, of all the things microbial I know about, this would be the one that would be most fun to talk about to scifooers and would catalyze the most interest. So I searched around for slides and figures and ideas on the web for a while and then said "WTF - I can do a chalk talk if I need to" and I headed downstairs to the lobby in the hopes of getting over to Googleplex and enjoying the last bits of scifoo.
There was quite a crowd in the lobby and I ended up talking to a few other evolutionary biologists which was good and then finally got a bus ride over to camp. At Google, I had a bit of breakfast and then went inside to sit at a table to do the last bits of preparation for my talk. If I had been at a normal conference I would have simply skipped the first two sessions to prepare for my talk at 11:30 (the last session of the meeting). But I said this would be silly and decided to go to a session at 9:30. My choices were:
|Golem: Data Mining for Materials (and Non-Programmers): sketching information systems (Andrew Walkingshaw) --AND-- Searching the Edges of the Web||Novel Biofuels, smart materials in energy production, the energy mix in the short term.||Genome Voyeurism -- Let's poke through Jim Watson's genome||International polar year, an opportunity to... (Dave Carlson)||Simplifying citation linking (Dan Chudnov)||Would You Upload? (Melanie Swan)|
|Future health care delivery and transport models: When "science" is not enough, benefit of new research vehicles (Berman and Neelagaru)||Reforming Patent Systems, patent informatics and innovation||5 mins on your favorite science website / tell us your dream science web tool (Richard Akerman)||How to Celebrate Darwin in 2009 (Phil Campeck)||Innovation is Not Pointless...But It's So 20th Century (Bingham)|
And again, the choosing was brutal. Though I really wanted to go to Lincoln Steins Genome Voyeurism session, I followed my rule of going to things I did not know a lot about and went to the session on the International Polar Year. This was one of those sessions in a giant room and I expected a huge crowd. Instead, there were about seven people. But boy did the others miss something brilliant. Dave Carlson not only told us about the whole IPY project but proceeded to tell us about how their project was completely Open Science. That is, everyone involved was required to post their data on the web for anyone to use. OK - well apparently they are allowed to publish in non Open Access journals, which seems counter to their whole philosophy, but their openness about data is brilliant (Note - I just found out from a Google search that a childhood friend of mine, Thomas Nylen, is participating in the IPY project -- see this blog here for some of what Tom has been up to).
Unfortunately, I missed the next session due to my computer having issues and me freaking out about whether it would work for my presentation at 11:30. The choices for the session I skipped were:
|Science Blogging||Towards an open source science learning collaboratory (Ted Kahn Design Worlds)||Opening the scientific literature: OpenLibrary, Google Scholar (Aaron Swartz)||21st century medicine: electronic medical records, privacy, and data mining (Erez L. and Kevin F.)|
Then it was time for the final session. And I was up -- the Human Microbiome. Here is what I was up against
|Social limits of scientific knowledge - can too much information impede science? (Dalton Convoy)||Culture of Fear: Scientific Communication and Young Scientists|
(Alex Palazzo, Andrew Walkingshaw)
|Towards DataWiki (Hugh Rienhoff, Alan Littleford)||Do systems organize themselves to produce entropy at the maximum rate? (Ralph Lorenz)|
|Science on the Stage, "science-in-theatre" (Djerassi)||Human Microbiome, microbes in and on us (Jonathan Eisen)||Science fiction: what is it for? (Henry Gee)|
It would have been funny if I had gone to someone elses session and skipped mine, but I am glad I did not as actually quite a few people showed up to mine. I started by saying I had a presentation but would prefer if people just asked questions along the way. And the great part was - did they ever. This included some by Freeman Dyson - kind of cool to have the guru asking me questions about microbial colonization of babies. Finally, after I had spent too much time on background - Drew Endy said something to the effect of "Lets get to the technically hard stuff" and I briefly discussed using genome sequencing to study microbes that live in and on humans. And then - we just had to stop.
I decided to linger for the wrap up session after lunch so I had lunch, made some phone calls, and then we had a wrap up which was mostly an open mike for comments and this ended up being a bit too much of "It was great" and not enough of "How could we make it better." But hey - it was great so I guess I understand. I went around saying thanks to the Google team and the Nature and O'Reilly folks and then moseyed on to the train back to Davis.
Some brief notes about the end and the new beginnings:
- I got lots of ideas for new projects and new things to do from this meeting as with the last one.
- Over the next few weeks I will be posting about some of the other things I saw there and discussing why/how they are interesting.
- I think this "un-conference" style would be really good to emulate for other gatherings. Not sure how to pull it off though.
- I know I will get in trouble from some of my Open Access colleagues, but I definitely came away from the meeting being really impressed with some of the things Nature Publishing group is doing. They really seem to be trying to move into the Web 2.0 area for science communication with Nature Preceedings, and the Nature Network and Scintilla and Connotea and Podcasts and of course Scifoo. Sure there were probably too many people from Nature at Scifoo, but hey, they were sponsoring it so why shouldn't they send them? Here's hoping that they continue to experiment with Open forums and Open material and that they change to OA for all their publications as a way to bring in more people to their Web services. And lets hope other publishers, especially truly open ones build similar resources for the community.
- Thanks to Timo Hannay, Tim O'Reilly, and all the folks at Google, Nature, and O'Reilly for organizing this and inviting me.
- Nature network discussion of Open Science
- Alex Palazzo's discussion of Open Science
- Nature.Com's SciFoo compilation
- Lexical SciFoo Campfire
- Timo Hannay's overview
Saturday, August 11, 2007
New Textbook on Evolution
JonJonathan Eisen FoE (Friend of Egghead) is coauthor of a new college-level textbook on evolution that incorporates recent developments in genomics and molecular biology alongside traditional evolutionary principles. Evolution (Cold Spring Harbor Laboratory Press, 2007) is intended for undergraduate courses in evolution and for biologists looking for a guide to the current state of evolutionary science.
The authors are Nicholas H. Barton, University of Edinburgh, U.K.; Derek E.G. Briggs, Yale University; UC Davis’s Eisen; David B. Goldstein, Duke University Medical Center; Nipam H. Patel, UC Berkeley. Eisen holds appointments at the Section of Evolution and Ecology and the Department of Medical Microbiology and Immunology at UC Davis.
An accompanying website, http://evolution-textbook.org/, contains supplemental illustrations, additional online chapters, class problems and other material, all freely available
From Cold Spring Harbor
Public release date: 10-Aug-2007
[ Print Article | E-mail Article | Close Window ]
Contact: Ingrid Benirschke
Cold Spring Harbor Laboratory
New textbook illuminates the close links between evolutionary and molecular biology
COLD SPRING HARBOR, N.Y. � In an innovative approach to the subject of evolutionary biology, a new book, Evolution, combines the contemporary fields of genetics and molecular biology with traditional evolutionary theories to provide an elegant, cohesive view of biology. The book, which was recently released by Cold Spring Harbor Laboratory Press (www.cshlpress.com), is geared toward all biologists seeking a clear, current, and comprehensive account of evolutionary principles and processes. It is a new and innovative choice of textbook for undergraduate courses in evolution.
�It is the most comprehensive book out there, with an admirable and clear presentation of the facts,� wrote Trevor Price, Ph.D., in a pre-publication review of the text. �I personally learnt a great deal...the book as a whole would be useful for workers in the field as a source of reference and to give them breadth.�
The branches of biology concerned with molecular events and evolutionary principles have developed independently of one another. But with recent breakthroughs in fields such as genomics, developmental biology, human genetics, and biochemistry, it has become yet more evident that evolutionary principles guide biological phenomena at all levels, and are essential to a practical understanding of these phenomena.
The authors, who are world-renowned experts from diverse biological backgrounds, illustrate how basic processes such as natural selection, optimization, and conflict occur at the molecular level as well as the organismal and ecological levels. They illuminate evolutionary principles and mechanisms with examples from across the spectrum of life�from �jumping genes� and RNA molecules, to populations of yeast and E. coli reared in the laboratory, to dung flies, lizards, and deer in their natural habitats.
�Evolutionary biology underpins all our knowledge of the living world,� write the authors. �[It] is a synthesis of Darwinian natural selection and Mendelian genetics. It allows us to ask not just how life evolved, but why it is as it is: Why do organisms develop from a single cell? Why is the genetic code as it is? Why is there sexual reproduction?�
The book is divided into four sections. The first three sections detail the history of evolutionary and molecular biology, describe the origin and diversification of life over the past 3.5 billion years, and explain the fundamental mechanisms underlying evolutionary change. The final section is devoted to human evolution and diversity, merging recent insights from molecular techniques with paleontological evidence. For a complete table of contents, see http://www.cshlpress.com/link/evolutn.htm.
The supplementary Web site (www.evolution-textbook.org) will be useful to biologists who incorporate Evolution into their undergraduate- or graduate-level courses. The site includes two Web-only chapters, downloadable figures and tables from all chapters, a glossary, author notes with complete reference lists, discussion questions, chapter problems, links to useful Web sites, and other material, all of which are freely available.###
About the book: Evolution ISBN 978-087969684-9, � 2007 Cold Spring Harbor Laboratory Press Hardcover, 833 pp., 8.5� � 11� trim size, 1200 color illus., glossary, index http://www.cshlpress.com/link/evolutn.htm, www.evolution-textbook.org
About the authors: Nicholas H. Barton�s early research was on narrow zones of hybridization that subdivide many populations, with work on a variety of species, including grasshoppers, butterflies, and toads. More recently, his research, which has been mainly theoretical, is attempting to understand the influence of selection on complex traits, models of speciation, the evolution of sex and recombination, and the coalescent process. He is professor of Evolutionary Genetics at the Institute of Evolutionary Biology, University of Edinburgh.
Derek E.G. Briggs works on preservation and the evolutionary significance of exceptionally preserved fossils, including those of the Cambrian Burgess Shale of British Columbia. His current research focuses on the chemical changes that occur during the transformation from living organism to fossil. He is Frederick William Beinecke Professor of Geology and Geophysics at Yale University and Director of the Yale Institute for Biospheric Studies.
Jonathan A. Eisen uses a combination of genomic sequencing and evolutionary reconstruction methods to study the origin of novelty in microorganisms. Previously, he applied this phylogenomic approach to cultured organisms, such as those from extreme environments. Currently he is using phylogenomic methods to study microbes in their natural habitats, including symbionts living inside host cells and planktonic species in the open ocean. He is Professor in the Department of Medical Microbiology and Immunology and the Department of Evolution and Ecology at the University of California, Davis.
David B. Goldstein�s principal interests include human genetic diversity, the genetics of neurological disease, population genomics, and pharmacogenetics. His laboratory currently investigates how human genetic variation influences the response to drug treatments for common neurological and cardiovascular disorders. He is Director of the Center for Population Genomics and Pharmacogenetics at the Duke University Medical Center.
Nipam H. Patel initially studied the development of several model and nonmodel species, including cows, chickens, grasshoppers, and Drosophila melanogaster. His research group studies the evolution of development, with a focus on the evolution of segmentation, neurogenesis, appendage patterning, and gene regulation. He is Professor in the Department of Molecular and Cell Biology and the Department of Integrative Biology at the University of California, Berkeley and an Investigator of the Howard Hughes Medical Institute.
About Cold Spring Harbor Laboratory Press: Cold Spring Harbor Laboratory Press is an internationally renowned publisher of books, journals, and electronic media, located on Long Island, New York. Since 1933, it has furthered the advance and spread of scientific knowledge in all areas of genetics and molecular biology, including cancer biology, plant science, bioinformatics, and neurobiology. It is a division of Cold Spring Harbor Laboratory, an innovator in life science research and the education of scientists, students, and the public. For more information, visit www.cshlpress.com.
Wednesday, August 08, 2007
SciFoo Camp Day 2 - Afternoon
Session 4: Here were the choices:
- Collecting More Data Faster Can Make an Organization Dumber (Jeff Jonas)
- Skepticism and Critical Thinking in an Age of Marvels (Guido Nurez)
- Computable Data/Mathematics (Theodore Gray) --AND-- $100 laptop demo (Ted Kaehler)
- Evolutionary robotics (Lipson Olliver)
- Ocean Exploration
- why a mouse? Multi-touch, physical and social interfaces for manipulating data (Philip Tiongson)
- Scientific Communication in 2030 (Kurte-Bilder) --AND-- The selfish scientist (Carole Goble)
- Universe or Multiverse? (Martin Rees, Frank Wiligat, Lee Smolin)
- Reuse of Sewage to Grow Food and Provide Sanitation (Frank Rijsbertian)
- Is Collaborative Policy Making Possible? (think wikipedia, economic/government simulation games) (TimHubbard, Beth Noveck)
- Viral Chatter (Nathan Wolfe)
- Freebase Demo
- Biodiversity on the Web: Science Publishing
- Prioritizing the World's Problems
- Display of Greater than 2D Data or Lots of 2D Data All at Once Tamara Munzner.
- E-Science Beyond Infrastructure /RichardAkerman/
- Implantable Devices and Microchips for Healthcare --AND-- Diver Assistance Devices
- Using Evolution for Design and Discovery
- Stem Cells (a.k.a. How to Get Scientists to Care about Web 2.0
- Machine Reading & Understanding Science
- Science & Fundamentalism (Durant)
- Biological Data & Research --AND-- Open Source Biomedical Research for Neglected Diseases
- My Daughter's DNA: Hacking Your Genome / Towards a Data Wiki
- Network-Centric Biomedicine (Ken Buxton)
- Squishy Magnets, Talking Paper and Disapearing Ink: How can inventables.com open its doors to kids for free?
- Since I was planning to go to a session half way through I was not sure which to do for the beginning and so I went to "Prioritizing the Worlds Problems" - a discussion led by Bjorn Lomborg about a new book he is working on. Basically the deal is - he and a bunch of economists thought a bunch and picked 10 world problems that might be solvable: climate change, communicable diseases, conflicts, education, financial stability, corruption in government (or something like that), malnutrition and hunger, sanitation and water access, and subsidies and trade barriers. And then they did an exercise basically asking - if you could spend some money in the next five years, could you solve any of these problems.
- He had some skeptics in the audience (which is not surprising given the semi-controversy over his book the Skeptical Environmentalist). For example Richard Jefferson of CAMBIA said that these were symptoms not problems and someone else said that it was bad to encourage governments to think on short time scales like a few years.
- I had to leave early for my Terraforming session and wished I had stayed. Not sure what I thought about the exact details of what he was presenting, but he was certainly not the demon some people implied he would be.
- A bunch of us met up outside the room where we were to have our Terraforming session only to find out that the occupants of the room were apparently circling the wagons and would not let us in. So we did the scifoo thing and took over the lobby area - doing an excellent job of sofaforming and chairforming.
- Then we had a discussion of Terraforming with SciFi writers and scientists and technology folks and reps from NASA. It was a pretty good discussion.
- In the end we concluded that if there is to be a Terraforming effort it should be on a near Earth asteroid encosed in some type of shell to retain gases. Sort of Biosphere 4 or something like that. Now we just need an asteroid.
- Give us your Data! Google's effort to archive and distribute the world's scientifcic datasets. (Noel Gorelick)
- Personal Impact Factor: Measuring Scientific Contributions Outside the Literature --AND-- Sensible organizations of sociometric badges
- Kids, Science, Math & Rational Thought
- Where are the aliens? (David Grinspoon, Steve Benner)
- Visual communications, graphics gesture (Barbara Teresky)
- Godel and the draft board (George Dyson)
- Dinosaurs, ancient humans, expedition science (Paul Sereno, Gabrielle Lyon)
- Machine Learning in the Natural Sciences
- why does science suck on TV, and what can we do about it? (Adam Rutherford)
- Hunch Engines /Eric Bonabeau/
- For this one I was completely torn. I really wanted to go to Noel Gorelicks discussion of Google's efforts to collate scientific data. But then I remembered my vow to stay away from things I might know something about.
- So I went to a session on MicroUAV. That is, small unmanned aerial vehicles. Holy *$%$. This was the best session I went to. Simply put - it was incredible. The leader (who I found out later was Chris Anderson the editor in chief of Wired) showed the evolution of his attempts to make cheap small UAVs.
- Here is the deal. He started off with trying to figure out all the things he would need to make robust small UAVs - and originally pieced together multiple various gizmos to control the planes and do things like communicate with ground and get GPS signals and take pictures. And then he realized he could use a GPS enabled cell phone with a CAMERA for all the functions and this helped reduce the costs of the planes such that one can now make one for < $700. Really. See DIYDrones.com.
- And then he showed us pics he had taken that AM of a fly over of Google HQ. Friggin' incredible. It was amazing from the fun point of view but also - I hope to use such UAVs to do sampling of microbes in air ...
- And one of the last things I heard in the session "And the sky will darken with Robots"
Session 7. Here the choices were:
- Data Mining the Sky, knoledge extraction and real-time discovery (Tony Tyson)
- All-Fluidic Computing, large-scale biological
- Science vs. Capitalism: Utopian Effots in the Overshoot Century. (KIm Stanley Robinson)
- Buildings engergy use and behavior change - can the built environment be an interface?
- The Paperless Home (Martha Stewart)
- Provenance Analytics: Illuminating Science Trails and the Future of Scientific Publications
- And here I chose to see what Martha Stewart had to say about the Paperless Home.
- Just before the session, Bora asked her about whether that meant no toilet paper and she responded by saying everyone should use bidets (really).
- She started off really well I thought - saying that homemakers are underserved by technology.
- She also complained about organizers made by other companies including Microsoft and said her plan was to make a better organizer for the homemaker.
- She also said that people need this because they need time for their families and she mentioned that many men spend less than 15 minutes a day with their kids. She also said she wanted this to help support the family unit, whatever that family was (referring back to her introduction when she said that the family has changed a lot but not saying that she thought new family structures were bad).
- She made a bunch of digressions that were basically the equivalent of "My magazine is brilliant and perfect" but I guess this did not surprise me since I think it is good that she is a perfectionist
- She did say she considers herself a typical customer for such an organizer - which made many people literally groan. Yes, Martha, with her 100s of millions of dollars, her boyfriend who pays 30 million to go into space and her many homes and giant houses and teams of assistants, she is the perfect customer.
- She did make some insightful comments about home technology like "I don't mind my talking to my computer but I do not want my refrigerator talking to me" when she was complaining about all the noise some gadgets make.
- Then she said nobody wants a drier that buzzes when it is done (I agree with her that this is annoying). She then asked the crowd if anyone wanted the buzzer and Paul Ginsparg said yes. So she skeptically dissed him and asked him why when he could just wait a little bit and put in the load a bit later. So he said "He wants to get another load in as fast as possible so he can spend more time with his kids", referring back to her comment about fathers not spending time with their kids. She knew she had lost this argument and she moved on to another topic.
- She made a funny reference to "Nature" magazine as though it was about you know, plants and bugs and well, "nature."
- She also said she wants scents out of the houses, which I agree with too. And she told a bizarre story about some worker who came over to her house with smelly pants because he had used a smelly dewrinkler. And she made him go and change into a new set of clothes because he smelled so bad.
- In the end, I guess I agree with Anna Kushnir in her brilliant "Letter to Martha" that she missed a chance to get technogeeks interested in helping the homemaker. I felt this was happening and asked her a leading question trying to get her to say something about what technogeeks could do to help but she misunderstood and answered some other question.
- In the end, I am glad I went to her talk --- it was off the beaten path and memorable even if it was not technogeeky enough for me.
And finally we had the last session. The choices here were:
- Reinventing scientific publication (Web 2.0, 3.0, and their impact on science)
- Piracy, Murder and a Media Revolution
- Engineering Living Instruments, android sensors
- Nanohype: The volumnious vacuous vapid world where only size matters.
- Biohacking science security society (Greg bear)
- The user-generated content I like (anyone can show the content they like on the internet)
- Science communication with comics... come turn your science into comic books
- And here I went to Greg Baer's session on Biohacking. It was quite interesting with a wi
- de ranging discussion of biohacking, biodefense, biosafety, etc.
- I am not sure everyone came out with the same conclusion though. I came out thinking -- we should not worry about biohecking compared to normal pathogens. But many other people said later they came out of it scared about hackers making nasty viruses and killing us all. I mean - I think the community should worry a bit about genetic engineering and put into place safeguards against terrorists and accidental released. But I still worry more about MRSA and XTR TB and so on.
Tuesday, August 07, 2007
SciFoo Day 2 - Morning
I got up pretty early and headed down to the lobby in the hopes of getting a bus over to Google and getting the good Google food and coffee. But alas the bus was a little behind schedule and so I was forced to hang out with other campers in the lobby area. Eventually a bus came and we went back to Googleplex. We had a lazy breakfast and I got to talk to many interesting folks.
- For the first session, the choices were:
The Next Big Programming Language /Josh Block & Bob Lee/ Open Science 2.0 /BoraZivkovic/ Digital Data Libraries /Mike Halle/ Citizen Science - Where Next? /John Durant/
Future of Healthcare /Richard Satava/
Visual Garage - We'll Fix Your Graphs and Visuals /Felice Frankel/ Quantum Computing - What, Why, How /Frank Wilczek/ Synthesizing Life /Steve Benner/
- Well, actually, I could not chose as I told Bora I would help with his session on Open Science. This one turned into a passionate conversation about many topics relating to Open Science. There was also quite a collection of people there including young and old. Much of the initial discussion was around the problems and difficulties in doing Open Science (see here and here and here for more detail on this and the session overall - in particular the young scientists, who I felt did not get enough time to talk in this session, had many concerns). I felt Pam Silver expressed the most important and interesting concern which was that she said that students in the Systems Biology program at Harvard seemed most dismayed by the slow pace of publishing). Some other comments by the village elders that were present (e.g., Eric Lander and Carl Djerassi) were not overly encouraging in terms of how people get jobs in the field (I am not sure Eric understood what the young scientist's concerns were completely and I think he may have made them feel worse about things when he was trying to make them feel better).
- I think I sent the session down the wrong path at the way beginning by talking about the need to identify roadblocks to Open Science and to figure out ways to circumvent them. This is a true need but it made the beginning of the session seem more about problems than visions for the ideal future, which is what most people seemed to have expected.
- But then Paul Ginsparg and Dave Carlson got us back to talking about the good, positive things about Open Science. Most importantly for me, we got a brief look at Jean Claude Bradley's Open Notebook system which I would like to use in my lab.
- Here the choices were:
Efficient Inverse Control: Through the Users Not the Resources /Wefi Vardi aka Neuman/ Clinical Problems in Neuroscience / Towards Practical Cognitive Augmentation /Vaughn Bell/ / Towards Practical Cognitive Augmentataion /Ed Boyden/ How to Build Intelligent Machines /Jeff Hawkins/ Why aren't there more Scientists on the Covers of Magazines /Jackie Floyd/ Future of Human Space Flight and Ocean Exploration /D Mindell/ Science and Art /Brian Derbey/ 3D Video Applications: How to Publish Science in Video /Steve Silverman/ The Nature of Time and Mathematics /Jaren Lanier & Neal Stephenson & Lee Smolin/ Alternate terms of Science Education Future History of Biology /Rob Carlson/ Human Cell and Regeneration Map or is it worth building a cellular resolution database for the whole human body? / AhilaAttila Csordas /
- I was completely torn here and even ended up being late because I was staring at the bulletin board trying to decide. Finally I went to "the future of human space and ocean exploration" since I thought this was going to be split into space for the first half hour and ocean for the second. Instead they talked about space the whole time I was there and the ocean exploration representative did not get too many words in. But the space discussion was actually really interesting with Pete Worden, the head of the NASA Ames Research Center there discussing future space flights and many other space afficionados present. I thought the most insightful and interesting comments in the session came when everyone was talking about how to better publicize space travel such that it got better attention. And then Larry Page from Google said, basically, that this was simply "marketing" and that the key was to do really cool things in space and not worry about the marketing. This also relates to the safety culture of NASA and other space travel agencies - many of us pointed out that 1000s of people die every day from various causes and that if space travel cannot take risks and accept that some people will die, we have no hope of doing anything interesting in space (e.g., Page pointed out that more people probably dies in the making and moving of the space shuttle than have died in the accidents).
3D Printing / Robot Printing / Food Printing / Printer Printing /Lipson, Olliver, Bonabeau/ Just When You Thought It Was Safe to Teach Evolution /Eugeinee Scott/ Sequencing the Genome: Implications, Ethics, Goals /Linda Avery, Steve Benner/ Are Patents Preventing Innovation? /S Patton/ Tricoder is Finally Here Ethical Implications of the Information Society /Luciano Floridi/ Reversible Computation and Its Connections to Quantum Interpretations /Gary Flake/ Mapping Science and Other Big Networks /Carl Bergstrom/ A Magician Looks at the Irrational and Pseudo-Science /James Randi/ Listening to the World: Voices from the Blue Deep /Chris Clark/ dISSEMINATION AND aCCESS TO dISCOVERY - cOMMUNICATION OF sCIENCE /gABE lYON/
- And though I promised myself I would go to things I knew nothing about, I simply had to go to this one by Eugenia Scott on evolution education.
- Here I found the discussion quite varied and interesting. Some people suggested that evolutionary biologists should be careful about what they say because intelligent design supporters might use it for their own good. Henry Gee and I were adamant that one should not temper ones science for such fears.
- Other interesting things in the session: Dwayne Spradlin did a good job of making everybody justify assumptions that they made about people and Sarah Keller pointed out that it would be useful to have evolution education in chemistry classes
- Then it was time for a Googlicious lunch (OK - it was not as good as I had expected but it was better than any other conference food I have had). Paul Ginsparg and I went through the line together and decided to sit outside the tent. Good choice as inside the tent was absurdly loud. Really good talking to Ginsparg for a while about PLoS and Open Access. He is one of those people who, when you find out he won a Macarthur "genious" award you are like "well, duh - how could he not win one?"
- After we sat down Larry Page and Lucy Southworth sat down as did some others who I have already spaced out on. The best part of the conversation at lunch was Larry Page giving Ginsparg grief about some technical annoyances Google found in their early days with the Arxiv preprint archive. Apparently, Google had to shut down some connections/services to Arxiv for a while and this was the first conversation about it.
- Also interesting was briefly hearing about Lucy's work at Stanford on mouse aging and changes in gene expression. This was particularly interesting to me since I hope to study how microbial populations inside animals change with aging. I unfortunately did not get enough time to interrogate her about her project - the perils of having too many interesting things going on.
SciFoo Camp Day 1 - More notes
Some more comments on Day 1.
- Paul Serano and colleagues had a display of dinosaur fossils in the main reception area. They announced that they did not want anyone publishing pictures of the fossils since they were unpublished, following the big trend among paleontologists to not be too open about anything. Funny since Serano also gave some lip service to the idea of openness and sharing --- clearly what he meant was different from what many others meant.
- I talked to Eugenia Scott for a bit before the sign ups and gave her the lowdown on SciFoo, and encouraged her to have a session on Evolution education, which thankfully she did.
- The three words I chose for my introduction were "Microbes Rule Planet, " which of course is true.
- Tim O'Reilly was the grandmaster of introductions. He was running around introducing as many people as he could to others he thought they would find interesting. He introduced me to Jim McBride (who is currently I think working with Howtoons). We had a good conversation about how the best way to attract good mathematicians to something in biology is to make sure the math is really hard (and why in general it is fun to work on something hard).
- Martha Stewart gave a brief summary of how she made food for Charles Simonyi's space flight and trip to the International Space Station.
- The food, as always at Google, was quite good.
- I hope Felice Frankel would be happy that my notes for her talk on "Envisioning Science" are all drawings and no words. Her key point was "Representation clarifies scientific thinking." I could not agree more.
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