flickr-free-ic3d pan white
View allAll Photos Tagged scifoo

flies under water like a falcon, instead of using ballast like a zeppelin

I sent my saliva to China,

 

to the largest sequencing lab in the world,

 

and they did a whole genome sequence of me,

 

and most of me is not human.

 

Here are the bacteria living in my mouth, a pre-launch test from the first commercial service to offer a whole genome sequence of the whole lot:

 

Genus — Mapped reads

Prevotella — 2,573,674

Neisseria — 2,327,172

Haemophilus — 2,222,674

Streptococcus — 1,556,743

Rothia — 1,232,209

Veillonella — 945,180

Fusobacterium — 560,693

Campylobacter — 234,182

Atopobium — 231,213

Aggregatibacter — 202,541

Capnocytophaga — 116,289

Leptotrichia — 85,449

Bacteroides — 67,333

Clostridium — 41,490

Porphyromonas — 36,489

Paracoccus — 36,061

Actinobacillus — 26,650

Malassezia — 26,553

Selenomonas — 23,646

Pseudomonas — 14,293

N.gonorrhoeae — 10,950

Burkholderia — 10,630

Ruminococcus — 10,403

Staphylococcus — 9,584

Mannheimia — 8,730

Pasteurella — 8,134

Riemerella — 6,762

Megasphaera — 6,576

Streptomyces — 5,041

Laribacter — 4,230

Acinetobacter — 2,752

Other bacterium — 174,580

 

I saw a few things in there that struck me as quite peculiar... things that one might expect, ummm, elsewhere on the body... and so I shared the results with some microbiome experts who have a keen interest in this. Here’s what U.C. Davis Professor Jonathan Eisen had to say:

 

“The first thing I usually do for samples is look at % by phylum. See pie chart for yours below.

 

The #s for each microbial group (i.e., Staphylococcus, Neisseria, etc.) do not seem out of the ordinary too much. Though I note - some studies have found high levels of Haemophilus in oral samples, and others seem to have not found them. Not sure why at this point but looking into it. The high levels of Neisseria (the genus that N. Gonorrhoaeae is in) is a common one, so nothing to worry about there. Prior studies have sometimes found high #s of Corynebacteia. These are not there on your list.

 

Also - the Malassezia is interesting. It is a fungus genus. Commonly found on the skin of various mammals including humans. Some types are found to be infectious, but I think most are just hanging out doing nothing. I have never seen it in mouth-microbe data, but if it was there, it would probably be missed by most studies since they focused on bacteria.”

 

Eisen also pointed me to the studies below. The microbiome was one of the major topics of interest at scifoo this year, where they claimed “20% of what’s in your blood is from the bacteria in your gut.” (I found earlier studies supporting 10%).

 

Looking at the bigger picture, New Scientist summarized some of the recent findings:

 

“One aspect of your uniqueness isn’t, strictly speaking, part of you at all. It comes from the 100 trillion bacteria that live both on and in you. They outnumber the body’s cells 10 to 1 and in genetic terms they are even more dominant… You’re 0.7% human

 

A recent study found that a unique bacterial fingerprint is transferred from our fingers to the things we touch, such as a computer keyboard or mouse, and will hang around for up to two weeks [think of the forensic applications! ]

 

Bacteria also contribute to uniqueness by modifying our metabolism. All humans share a basic biochemistry, but layered on top of this is a microbial biochemistry that is much more diverse. The metabolites that microbes produce affect a range of things, including cholesterol and steroid metabolism.

 

What this ultimately means is that without our non-human component, we wouldn’t be ourselves at all.”

 

And in rat studies, you can turn obesity on and off with a flush and refresh of new gut bacteria. (summary, more).

 

You are what they eat.

Some people have turned their back on the semantic web stack, its a rubik's cube now, you can mix and match components to your hearts content.

 

Architecture? Pah! You can even cheat by peeling the coloured stickers off too. Will it keep everyone happy? Does anyone care anymore?

 

Via Eric Neumanns presentation at SESL09, looks like it is based on the newer semweb logos at www.w3.org/2007/10/sw-logos.html.

At Google this weekend. On display here is one of the early production servers, with four motherboards jammed on each shelf and cork sheets inserted in between. It overheated quite easily, so they built a wall of fans on the backside.

 

Here is today’s agenda. I have removed all of the names of the cool people leading these talks since there are Chatham House rules in effect.

 

So many sessions I want to see... I am in this session now: "What if extinction is not forever?"

It is quickly becoming feasible to reconstitute the genomes of vanished species using genetic material from preserved specimens and archaeological artifacts. Three different techniques are being deployed. Revivals already under way include mammoths, aurochs, and passenger pigeons. Candidate species include the dodo, the Carolina parakeet, the thylacine (Tasmanian tiger), and the Xerces blue butterfly. If we can actually revive an extinct species, should we? If so, why bother? Are some species more desirable, valuable, or ethical to bring back than others? Is it ethical to “improve” a revived species—for example to make a formerly extinct bird resistant to avian malaria? Do revived species have a “right” to be returned to the wild? Should revived species be treated as genetically modified organisms? In this session we can discuss the rapidly evolving science making all this possible and the downstream implications and opportunities.

 

Here is the lineup… So many great ones overlap. Sadly, right now, I’m missing the trillion-fps camera imaging the movement of light. Decisions, decisions…

 

10:00am

•What happens if we don't do anything about climate change? and what do we do about it if things go horribly awry?

•Robots (nanotechnological, synthetical biological, intelligent, for control) To Solve The Brain (understanding, fixing)

•Experiments in (informal) education: what can one magazine do?

•The coming war on general purpose computing and the civil war that comes after.

•Impostor Syndrome (and the culture of science)

•Spidersilk using silk worms.

•Smartphones to save lives, prevent disaster

•Open access commoditizing science - what next?

•What is Time

 

11:00am

•Neuroprediction: Does your brain predict if you will do bad things? p.s. all about psychopaths

•Optogenetics & Neural Imaging & Dynamics of the single cell

•Reversing climate change, land, air, ocean.

•What can new imaging hardware and software solve next? Trillion frames per second. Look around corners

•A fundamental problem in digital systems.

•De-Extinction: Practices and Prospects

•What I learned by doing capitalism and what you need to know

•Future of music

•Funding Science

 

12:00am

•Will the human race cause its own extinction

•Discovering new materials by computation.

•Data driven societies.

•Grand challenges in neuroscience.

•Long tails and big heads: Big data in science.

•Neurolaw

•Consumer biotechnology ie tissue engineering meat, leather, and other daily needs.

•What can we invent to raise the level of public discourse even slightly? A face to face debate platform on the internet

•Information that lives - digital lives and intelligent agents

•Detecting asteroids before they hit us.

 

13:00Lunch

 

14:00

•Starshade show & Tell. Hunting Exo-Earths and aliens

•Can "big data" solve healthcare?

•Art/Science Collaborations. Visualizing biology, conservation, innovative data exploration, and more.

•Internet education for teachers.

•City science.

•Open Science FTW - Oopen access, open data.

•Visual Music Brain Synesthesia;

•Stealth diagnostics Hidden biosignals & communicity health.

•The brain's flaws as a computational device. How they shape our lives.

•Fighting against anti-science and winning - new strategies.

 

15:00

•Your genome, your health. How long will we just kick the tyres of your car?

•Ocean acidification.

•Do we have free will and why does it matter?

•Big data sets and using them intelligently e.g. climate data,

•Storytelling vs the whole truth and nothing but the truth. Also, comics

•DIY and makers as international policy. Jose Gomez-Marquesz TH Culhane (fuel from garbage electricity , aluminum demo)

•What Microbes are on you your phone.

•a new artificial intelligence Brains Minds Machines

•Revolutionizing Education.

•The reproducibility crisis in biology.

 

16:30

•Tenure from Tweets? evaluation beyond citations

•African floating communities.

•Large-scale learning on the internet & Talking to the brain in its own language. Making prosthetic devices that work.

•Role of the ocean in carbon and climate.

•Biohacking and citizen synthetic biology How far can we go?

•Visual Tools for Science and Engineering.

•Do or should humans have an off world future?

•Ignorance - can we admit it and keep credibility?

•Demo SharkFinder Citizen Science Kits

 

17:30

•Emotions in motion. Get acquainted in nonverbal communication

•Post Natural History and the Future of Evolution.

•The technology and politics of spectrum ( the invisible resource you need) Why you need to understand more.

•Science Diplomacy

•Cheap energy, growth, global change.

•Build a puzzle/sculpture. I brought the parts, can you assemble them?

•Nature Porn - pollination, mushrooms etc. How beauty and seduction is nature's tool for survival. Film shorts & brief talks.

•Haploid stem cells and the future of disease genetics

•Smartphone science. Primary v suppport v citizen .

•Grand challenges in biology.

•"Scientific analysis on all the world's satellite images. Earth engine demo.

 

20:00

•Organizational Manipulation: how to social engineer your company, university, grantor, or colleagues

•fMRI Brain Reaction so what?

•IP & patents in biotech/education/community labs etc. What are the issues? What needs fixing? What's the future?

•Economics Comedy with stand-up economist + open-mic if desired

•Imagining post capitalism: a call for help.

•Of course Mars has life, but does Europa?

•Automating science to Accelerate Discovery with Demo

•The coming age of brain decoding.

•Images & Anecdotes from 17 years of astronomy picture of the day.

•Scaling research up - moving outside the lab with demo of smartphone brain scanner.

•Will the microbiome and inflammation explain all diseases?

 

Moments after the prior photo, with an attempt at coordinated action. I got a promo video with the footage from our Zero-G flight. It does a better job than my photos in showing what the weightless astronaut trainer is like.

 

We also get a great view of Danny Hillis’ cranium, a muse for my blogging about the power of evolutionary algorithms in computer science.

 

This photostream comes with an iTunes mix. =)

 

Resurrection (Space Club remix), PPK, Oakenfold Ibiza (found on a Russian website). This song samples radio communications from Yuri Gagarin's first human space flight. My friend, Eric, was the first person I know to do a weightless parabolic flight. Just a few years ago, the only option he had was to go to Russia and fly with the Russian space program.

This shiny new LOC Expediter rocket is ready for induction into the Telstar Logistics fleet. It has been heavily reinforced to take the stress of big motors and a strap-on video camera to catch the launch action.

 

For example, I Kevlar-wrapped the body tubes (the reduction coupler shows it unpainted) and fiberglassed the fins, tip-to-tip. The battery connections are soldered. I used a custom motor tube than runs up through the yellow coupler

 

To streamline the videocam cylinder, I glued half of a plastic Easter egg on top and fiberglassed the seam.

 

And the laser-cut vinyl flames come from GraphixnStuff. I met Dave at BALLS and was delighted to see a site dedicated to rocket decoration!

 

This will be my third camera to try to survive the g-loads of launch and the mishaps of reentry. The first one shredded on a V2 + K700 motor. Here is a “successful” Norad flight photo and video from camera #2 on an H210 motor (the next launch became a ballistic lawn-dart into the Black Rock Desert). This Expediter kit is a scaled up version of that earlier Norad rocket, and I will try successively larger motors to test its limits (J350, K550, L730… see ya! That last motor would certainly remove the camera as RockSim shows it screaming through Mach1... need a plan for that =)

There is no predefined agenda; instead attendees collaboratively create one during the first evening of the event.

 

Right now, I am listening to a discussion of entropy and the mathematics of time by Lee Smolin, Jaron Lanier and Neal Stephenson…

 

So many cool but concurrent sessions… I’m open to your votes on which ones to attend…

 

Saturday, August 4th

 

09:30

1.The Next Big Programming Language

2.Open Science 2.0

3.Digital Data Libraries

4.Citizen Science - Where Next?

5.Future of Healthcare

6.Visual Garage - We'll Fix Your Graphs and Visuals

7.Quantum Computing - What, Why, How

8.Synthesizing Life

 

10:30

1.Efficient Inverse Control: Through the Users Not the Resources

2.Clinical Problems in Neuroscience / Towards Practical Cognitive Augmentation / Towards Practical Cognitive Augmentataion

3.How to Build Intelligent Machines

4.Why aren't there more Scientists on the Covers of Magazines

5.Future of Human Space Flight and Ocean Exploration

6.Science and Art

7.3D Video Applications: How to Publish Science in Video

8.The Nature of Time and Mathematics

9.Alternate terms of Science Education

10.Future History of Biology

11.Human Cell and Regeneration Map or is it worth building a cellular resolution database for the whole human body?

 

11:30

1.3D Printing / Robot Printing / Food Printing / Printer Printing

2.Just When You Thought It Was Safe to Teach Evolution

3.Sequencing the Genome: Implications, Ethics, Goals

4.Are Patents Preventing Innovation?

5.Tricoder is Finally Here

6.Ethical Implications of the Information Society

7.Reversible Computation and Its Connections to Quantum Interpretations

8.Mapping Science and Other Big Networks

9.A Magician Looks at the Irrational and Pseudo-Science

10.Listening to the World: Voices from the Blue Deep

 

14:00

1.Collecting More Data Faster Can Make an Organization Dumber

2.Skepticism and Critical Thinking in an Age of Marvels

3.Computable Data/Mathematics

4.$100 Laptop Demo

5.Where Are the Aliens?

6.The Selfish Scientist

7.Evolutionary Robotics

8.Buildings, Energy Use and Behavior Change - Can the Built Environment be an Interface?

9.Why a Mouse?: Multi-touch, Physical and Social Interfaces for Manipulating Data

10.Scientific Communication in 2030

11.Universe or Multiverse?

12.Reuse of Sewage to Grow Food and Provide Sanitation

13.Is Collaborative Policy Making Possible? (think wikipedia, government simulation games)

14.Viral Chatter

 

15:00

1.Freebase Demo

2.Biodiversity on the Web: Science Publishing

3.Prioritizing the World's Problems

4.Display of Greater than 2D Data or Lots of 2D Data All at Once

5.E-Science Beyond Infrastructure

6.Implantable Devices and Microchips for Healthcare / Diver Assistance Devices

7.Using Evolution for Design and Discovery

8.Stem Cells (a.k.a. How to Get Scientists to Care about Web 2.0

9.Machine Reading & Understanding Science

10.Science & Fundamentalism

11.Biological Data & Research / Open Source Biomedical Research for Neglected Diseases

12.My Daughter's DNA: Hacking Your Genome / Towards a Data Wiki

13.Network-Centric Biomedicine

14.Squishy Magnets, Talking Paper and Disapearing Ink: How can inventables.com open its doors to kids for free.

 

16:00

1.Give us your Data! Google's effort to archive and distribute the world's scientifcic datasets.

2.Personal Impact Factor: Measuring Scientific Contributions Outside the Literature

3.Kids, Science, Math & Rational Thought

4.Micro-UAVs

5.Machine Learning in the Natural Sciences

6.Hunch Engines

 

17:00

1.Data Mining the Sky

2.All-Fluidic Computing

3.Science vs. Capitalism: Utopian Effots in the Overshoot Century

4.Dinosaurs and Ancient Sarahans

5.The Paperless Home

6.Provenance Analytics: Illuminating Science Trails and the Future of Scientific Publications

 

20:00

1.Piracy, Murder and a Media Revolution

2.Engineering Living Instruments

3.Nanohype: The volumnious vacuous vapid world where only size matters.

 

Sunday, August 5th

 

09:30

1.Golem: Data Mining for Materials (and Non-Programmers): sketching information systems Andrew Walkingshaw / Searching the Edges of the Web

2.Novel Biofuels

3.Genome Voyeurism – Let's poke through Jim Watson's genome

4.Would You Upload?

5.Reforming Patent Systems

6.How to Celebrate Darwin in 2009

7.Innovation is Not Pointless...But It's So 20th Century

 

10:30

1.Large Scale Molecular Simulation

2.Tree of Life: Fractal Data Problem

3.Planetary Defense Against Asteroids

4.The Automation of Science and the Technological Singularity

 

11:30

1.Science on the Stage

2.Human Microbiome

3.Out Future Lies in Space

4.Climate Crisis vs. Environmental Justice

A featherweight fern-mower, with Giro-helmet styling, this offbeat dino skull houses over 500 needle shaped teeth, jammed together in a row (with 50 columns of replacement teeth). No other known animal has a row of teeth quite like it, extending wider than the skull… and it lacks gnashing molars.

 

The body is the size of an elephant, but the pneumatic construction of the skull and skeleton makes it quite a delicate fossil find. Some of the vertebrae are paper thin, part of a backbone that is more air than bone.

 

Paul Sereno gave an exciting docent’s tour of some of his recent finds at the O'Reilly foo camp at Google.

 

This 110 million-year-old Nigersaurus Taqueti is a distant cousin of Diplodocus, but shared African waterways with SuperCroc.

 

I thought it looked like Jar Jar Binks… maybe with googly Golem eyes.

 

This hypnogram shows the pattern of my sleep last night. I finally got the strap-on EEG from scifoo to stay on for the night.

    

Zeo classifies sleep into the broad categories of:

    

• REM – Essential for mental acuity through organizing memory to better apply what you learn

    

• Deep – Critical for restoring muscle and building immunity

    

• Wake – time you were awake after having fallen asleep, including short periods throughout the night

    

And, rolling it all up, they say I sleep better than 90% of people (ZQ 91) and that my SleepAge is that of a 28 year old.

 

“Zeo's ZQ sleep score and sleep breakdown are based on actual sleep stage data we get when people sleep with Zeo, including REM and Deep sleep. The information behind Sleep Age comes from the largest consumer sleep database in the world.”

 

Yet Another Semantic Web Stack, this one from Semantic Web Architecture: Stack or Two Towers? by Ian Horrocks, Bijan Parsia, Peter Patel-Schneider and Jim Hendler.

 

If the link above is inaccessible to you, try this one from Ian Horrocks publications page

 

You may also be interested in Dan Brickleys alternative stack for the New, improved semantic web, (now with added meaning!)

 

DOI:10.1007/11552222_4

 

[single-tower-4.png]

RepRap is a self-replicating 3D printer. It builds its own gears and components. (detail photos)

 

The coiled polymer feed looks like an IV bag bobbing over the working tip. The dual print head is affectionately called Zaphod.

 

Scattered about are sci foo camp tents… and the ubiquitous “foo bar” beckons in the background, serving variable drafts.

The secret world of mind control (posted with permission).

 

Try to relax. This will feel a little weird. — Morpheus

 

SciFoo day two, whatcha' gonna do?

  

10:00

•Micro air vehicles indoors with demo. MIT micro air vehicles group

•The post-antibiotic era.

•How to model & design whole cells (unplugged)

•Science of the "impossible" (invisibility mind reading, light-driven cancer treatment & more!)

•Painting with blood dancing with DNA - biology on screen and canvas. Biology's movement into art & entertainment. interactive music & biology with Bjork. Viruses as doilies, blood paintings. Bio form sculpture

•BEL: Biological Expression Languages. An expressive shorthand for capturing biology in a computational format. .

•Hold a piece of Mars and one of the oldest materials

•"Lightning Talks”

1.uniform coatings from asymmetric particles.

2.A communications primer.

3.Autistics in Science.

4.Network Interventions.

5.De-extraction.

6.Stem cells to fund the genome

•Thin film, comms, autism, networks, de-extinction, and more"

 

11:00

•Trip to a black hole movies!

Deepflight. Deep ocean space now open!!! Who goes first? What is best use? Sub all ready to go.

•So you built an awesome tool. How do you get people using it????

•Virtual you! Medical patient records as simulations predicting your future health. {Medical, technical, social, financial} challenges. p.s. I'll show image data and cool visualizations to start out

•The coming age of brain decoding.

•Rebooting science communication.

•Radical shifts in relations with life, art, & biology.

•Crowdsourcing science (discussion).

•Donating health data - medical, devices, consent.

 

12:00

•How the languages we speak shape the ways we think and what should we do about it?

•Beyond Turing machines.

•Public participation in scientific research aka citizen science

•Where are the null results? Science is positively biased. Can or should we fix this?

ZomBees Why do they do what they do? Are parasites controlling us all?

•Catastrophe planning & recovery (as a cool tech hobby!) Vernor Vinge

•Implanting bionic eye device - transformation technology, implications, interaction, performance. Surgery free version

•Currents in Neuro vascular Disease - Alzheimer's, Multiple Sclerosis, Parkinson's

Who knew? In zero gravity, I get giddy lock jaw!

 

We were trying to coordinate a group shot. The next photo shows what happened a moment later…

Slide credit, lower right: W Hermann, Quantifying Global Exergy Resources

[update: photo replaced with an Googlesaur hunting near the Google volley ball pit... until I can figure out the thread below; other dino head photo was embargoed for a bit]

 

A featherweight fern-mower, with Giro-helmet styling, this offbeat dino skull houses 1000 needle shaped teeth, jammed together in a row. No other known animal has a row of teeth quite like it, extending wider than the skull… and it lacks gnashing molars.

 

Paul Sereno gave an exciting introduction to some of his recent finds.

 

This 110 million-year-old Nigersaurus Taqueti is a distant cousin of Diplodocus, but shared African waterways with SuperCroc.

 

I thought it looked like Jar Jar Binks… maybe with big Golem eyes.

 

Wouldn't it be nice if there was Google Metabolic Maps?

 

[Imgp5220.Jpg]

Paul Ginspargs interests include (quote):

 

physics

information science

electronic publishing

data mining

 

and....

 

extraterrestrial astrology (!)

 

unquote

 

Imgp5772.Jpg

Google colored cafeteria trays.

iPhone pictures on my recent Bay Area (San Francisco, Silicon Valley, Googleplex) trip: 2007, August, 1- 8.

Freeman Dyson added personal remembrances to a wonderful historical tale by George Dyson about Gödel’s difficulties with government bureaucracies while trying to return to Princeton from Austria during WWII… then trying to get his “enemy alien” designation removed…. and then getting promptly drafted. The series of absurd telegrams highlighted the inconsistency and incompleteness of the formal systems of law.

 

Sir Martin Rees smiles in the foreground.

Martha Stewart talked about astronaut food and the sort of things you can prepare to send into space. In space, you can add water and you can heat it, but otherwise, it's whatever you put in a can or tube before launch. And you have to give the astronauts something they'll eat (no fish for Charles).

The main hall at Scifoo08.

Cory has since migrated to using laptops running Ubuntu Linux.

Martin Rees (left) looks on as Freeman Dyson talks about working with Kurt Godel at the Institute for Advanced Science.

View full size to see the people...from the top:

  

Steve Silverman

Tim O'Reilly

Richard Jefferson

Cat Allman

Simon Field

Chris DiBona

Nathan Torkington

Steve Benner

Jim McBride

Deepak Singh

Joshua Bloch

Joe LaPenna

Stefan van Holzbrinck

Kat Townsend

Hugh Rienhoff

Brady Forrest

Jean-Claude Bradley

Felice Frankel

Udi Manber

Oliver Morton

Ann Copestake

Nick Dragotta

Nikita Bernstein

Beth Noveck

Paul Sereno

Jacqueline Floyd

Kovas Boguta

Meg Stalcup

Steve Bryant

Philip Campbell

Martha Stewart

Laura Pence

Eva Vertes

Jeff Hawkins

Dean Kamen

Richard Akerman

Adam Rutherford

Esther Dyson

Rob Carlson

Roger Brent

Eric Lander

Ritu Dhand

Natalie DeWitt

Doug Church

 

IMGP5740

Just a few of this year's SciFoople!

We all lined up to get out pictures taken for the SciFoo rogue's gallery.

 

So many interesting amazing people in one place with so many great talks planned. People are here this year from the Galaxy Zoo (Chris Lintott and Arfon Smith) and I am especially eager to hear their session which will be called I think "Citizen Everything."

Yet another reason to basically live at the Googleplex...

Or road-capable airplane, as I think they want us to call it.

Ah, yes, the bliss of childish scientists

 

Warms my heart. =)

1 3 4 5 6 7 ••• 18 19