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Fold.it – the Protein Folding Game

Foldit is a revolutionary new computer game enabling you to contribute to important scientific research. This is another awesome combination of technology, distributed problem solving, science education…

Essentially the game works by allowing the person to make some decisions then the computer runs through some processes to determine the result of those decisions. It seems the human insight of what might work provides an advantage to computers trying to calculate solutions on their own. Then the results are compared to the other individuals working on the same protein folding problem and the efforts are ranked.

This level of interaction is very cool. SETI@home, Rosetta@home and the like are useful tools to tap the computing resources of millions on the internet. But the use of human expertise really makes fold.it special. And you can’t help but learn by playing. In addition, if you are successful you can gain some scientific credit for your participation in new discoveries.

Related: Expert Foldit Protein Folder, JSnyderResearchers Launch Online Protein Folding GameNew Approach Builds Better Proteins Inside a ComputerPhun PhysicsProtein Knots

The site includes some excellent educational material on proteins and related material. What is a protein:

Proteins are the workhorses in every cell of every living thing. Your body is made up of trillions of cells, of all different kinds: muscle cells, brain cells, blood cells, and more. Inside those cells, proteins are allowing your body to do what it does: break down food to power your muscles, send signals through your brain that control the body, and transport nutrients through your blood. Proteins come in thousands of different varieties, but they all have a lot in common. For instance, they’re made of the same stuff: every protein consists of a long chain of joined-together amino acids.

structure specifies the function of the protein. For example, a protein that breaks down glucose so the cell can use the energy stored in the sugar will have a shape that recognizes the glucose and binds to it (like a lock and key) and chemically reactive amino acids that will react with the glucose and break it down to release the energy.

Proteins are involved in almost all of the processes going on inside your body: they break down food to power your muscles, send signals through your brain that control the body, and transport nutrients through your blood. Many proteins act as enzymes, meaning they catalyze (speed up) chemical reactions that wouldn’t take place otherwise. But other proteins power muscle contractions, or act as chemical messages inside the body, or hundreds of other things.

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Bacteriophages: The Most Common Life-Like Form on Earth

photo of bacteriophage

There are more bacteriophages on Earth than any other life-like form. These small viruses are not clearly a form of life, since when not attached to bacteria they are completely dormant. Bacteriophages attack and eat bacteria and have likely been doing so for over 3 billion years. Although initially discovered early last century, the tremendous abundance of phages was realized more recently when it was found that a single drop of common seawater typically contains millions of them. Extrapolating, phages are likely to be at least a billion billion times more numerous than humans. Pictured above is an electron micrograph of over a dozen bacteriophages attached to a single bacterium. Phages are very small — it would take about a million of them laid end-to-end to span even one millimeter. The ability to kill bacteria makes phages a potential ally against bacteria that cause human disease, although bacteriophages are not yet well enough understood to be in wide spread medical use.

Photo credit: Wikipedia Electron micrograph of bacteriophages attached to a bacterial cell. These viruses have the size and shape of coliphage T1.; Insert: Mike Jones

Related: webcast of Bacteriophage T4types of microbesWhat are Viruses?Amazing Science: RetrovirusesUsing Bacteria to Carry Nanoparticles Into Cells

Robot Finds Lost Shoppers and Provides Directions

robot

Robovie droid helps lost shoppers:

The Osaka-based Advanced Telecommunications Research Institute (ATR) has developed a crowd-monitoring humanoid robot that recognizes when people are lost and helps them find their way.

Relying on data from 16 cameras, 6 laser range finders and 9 RFID tag readers installed in and around the area, the robot was able to watch up to 20 people at a time, pinpoint their locations to within a few centimeters, and classify each individual’s behavior into one of 10 categories (waiting, wandering, walking fast, running, etc.).

Whenever Robovie spotted people who looked disoriented, the child-sized droid wheeled up to them and asked, “Are you lost?” If so, the robot provided simple directions to the destination and pointed the way. If not, the robot proceeded to recommend nearby shops and restaurants.

Using the cameras to identify those that might be lost and then navigating to them is pretty cool if it actually is successful.

Related: Toyota Partner RobotA Robot to Clean Your Room

See our full tag cloud of science and engineering posts.

Understanding the Evolution of Human Beings by Country

graphic showing countries understanding of evolution I recently wrote about evolution and scientific literacy. The graph on the left shows the percentage of the population that understands evolution is a core scientific principle. The graph based on data from 2005 for 34 countries.

Blue indicates those that know that “human beings, as we know them, developed from earlier species of animals.”
Yellow are those that are unsure
Red are those that don’t know that it is true

Evolution Less Accepted in U.S. Than Other Western Countries, Study Finds, from National Geographic News:

A study of several such surveys taken since 1985 has found that the United States ranks next to last in acceptance of evolution theory among nations polled. Researchers point out that the number of Americans who are uncertain about the theory’s validity has increased over the past 20 years.

The United States is is second to last place in this question of scientific literacy with only 40% of the population knowing the truth. The USA was between Cyprus and Turkey in this measure of understanding of scientific knowledge. The most knowledgeable countries have about twice the rate of knowledgeable respondents (with nearly 80% knowing).

Related: Scientific Illiteracy by Country (the USA managed to stay in the top 10 for overall scientific literacy rate of 8th graders in 2003) – Understanding Evolution (University of California at Berkeley)Scientifically IlliteracyRetrovirusesDNA Repair ArmyMassive Project Will Reveal How Humans Continue to EvolveGene Study Finds Cannibal PatternNigersaurusRare Chinese Mountain Cat

Amazing Science: Retroviruses

One of the great things about writing this blog is I find myself more focused on reading about interesting science. Retroviruses are very interesting and frankly amazing. Darwin’s Surprise by Michael Specter, The New Yorker:

A retrovirus stores its genetic information in a single-stranded molecule of RNA, instead of the more common double-stranded DNA. When it infects a cell, the virus deploys a special enzyme, called reverse transcriptase, that enables it to copy itself and then paste its own genes into the new cell’s DNA. It then becomes part of that cell forever; when the cell divides, the virus goes with it. Scientists have long suspected that if a retrovirus happens to infect a human sperm cell or egg, which is rare, and if that embryo survives – which is rarer still – the retrovirus could take its place in the blueprint of our species, passed from mother to child, and from one generation to the next, much like a gene for eye color or asthma.

When the sequence of the human genome was fully mapped, in 2003, researchers also discovered something they had not anticipated: our bodies are littered with the shards of such retroviruses, fragments of the chemical code from which all genetic material is made. It takes less than two per cent of our genome to create all the proteins necessary for us to live. Eight per cent, however, is composed of broken and disabled retroviruses, which, millions of years ago, managed to embed themselves in the DNA of our ancestors. They are called endogenous retroviruses, because once they infect the DNA of a species they become part of that species. One by one, though, after molecular battles that raged for thousands of generations, they have been defeated by evolution. Like dinosaur bones, these viral fragments are fossils. Instead of having been buried in sand, they reside within each of us, carrying a record that goes back millions of years. Because they no longer seem to serve a purpose or cause harm, these remnants have often been referred to as “junk DNA.” Many still manage to generate proteins, but scientists have never found one that functions properly in humans or that could make us sick.

How amazing is that? I mean really think about it: it is incredible. The whole article is great. Related: Old Viruses Resurrected Through DNADNA for once species found in another species’ GenesNew Understanding of Human DNARetrovirus overview (Tulane)Cancer-Killing Virus
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Cool Crow Research

photo of crow vending machine

Very cool project – A Vending Machine for Crows

The goal of this project is to create a device that will autonomously train crows. Initially we’re training them to deposit dropped coins they find on the ground in exchange for peanuts, but eventually we hope to be able to train them to search and rescue, or to collect garbage, or who knows!

This is the highest-risk segment of the machine’s operation. At this point coins alone are made available whenever the bird lands on the perch. However, should a bird peck or sweep coins off the tray and cause a coin to fall down the funnel, the device then produces some peanuts. This stage is designed to cement in the crows’ mind the relationship between coins going down the funnel and peanuts being made available.

Finally we shift the device into its intended, and long-term state of only providing peanuts when coins go down the funnel. Nothing is otherwise provided aside from coins scattered around the device at the beginning of the project.

Joshua Klein Thesis presentation definitely watch this! (the webcast takes like 30 seconds before the talk starts – it is worth the wait). Watch a video from the University of Ithaca site (with Dr. Kevin McGowan).

Other sites that also are mentioned as possible sites: Dr. Anne Clark, University of Binghamton (with a captive population of crows); Dr. Natalie Jeremijenko (seed podcast), Dr. Carolee Caffrey, Harvard and Dr. James Ha, University of Washington. Read the Paper by Joshua Klein about the plans for the experiment.

Related: The Engineer That Made Your Cat a PhotographerBackyard Wildlife: FoxAnts on Stilts for Science

The Engineer That Made Your Cat a Photographer

photo by Binky the cat or another catThis article is the result of the first Curious Cat engineer interview. My favorite post detailed the great engineering project Jürgen Perthold undertook to engineer a camera that his cat could wear and take photos. So I decided to interview him.

The Engineer That Made Your Cat a Photographer by John Hunter:

This time I thought about our cat who is the whole day out, returning sometimes hungry sometimes not, sometimes with traces of fights, sometimes he stay also the night out. When he finally returns, I wonder where he was and what he did during his day. This brought me to the idea to equip the cat with a camera. The plan was to put a little camera around his neck which takes every few minutes a picture. After he is returning, the camera would show his day.

The Amazing CatCam is not only a great product but a wonderful engineering story. See our past post for some background on how an engineer allowed you to help your cat become a photographer. On the development of the CatCam Jürgen Perthold says, “More or less it was just a joke, born with a crazy idea.” Such a great sentiment and with wonderful results.

What path led him to the desire and ability to pursue the crazy idea and become the Curious Cat engineer of the year? He was born in Aalen, Germany. He started playing with electronics as he was 13. At 15 he added computer programming and with a friend they programmed games, applications and hardware control over the years. He studied Optoelectronics at the University of Aalen, Germany extending his knowledge further.

For the last few years he has worked for Bosch, an international manufacturing company, in the automotive hardware section. Last summer, he transfered from Germany to Anderson, South Carolina as a resident engineer for transmission control unit in a production plant for automobile parts. On a side note, the United States is still by far the largest manufacturer in the world.
photo by Binkey the cat, from under a car
The demand for the cameras is still higher than his capability to produce the cameras. He has raised the price, to limit the demand. When I first saw the prices I couldn’t believe how inexpensive it was. And, in my opinion, they are still a incredible deal. Order your CatCam now: it is a great gadget for yourself or it makes a great unique, gift. Most orders have been from the UK, Germany and the USA.

Most people don’t have technical background so they buy the full unit. But he reports that some brave souls order a kit because of price or availability although they have not done anything similar before. What a great way to challenge yourself and, if you succeed, end up with a wonderful creation when you finish.

He is in discussion with several different groups to ramp up production. The main problem is that producing the device requires electronics, optics, software, mechanics and logistics expertise. So, for the time being, he continues to modify the cameras by hand because no investments are necessary and the production can be scaled according to the demand. The required soldering, electronics and system knowledge makes it a challenge to outsource. So, for now, CatCam production is adding to the USA manufacturing output total. He is also planning to produce more products.
photo of Jacquie the cat wearing a CatCam
Jürgen believes that getting the cat camera working was not that challenging. You can take a look at his explanation of how he did so to decide for yourself. He does admit that challenges do arise if you want to produce cameras for others. To do that you must create a product that is foolproof, reliable, and easy to use and manufacture.

“I was surprised how famous one can get with ‘boring’ technical engineering stuff. I like this not only for me but for all other engineers out there who daily work hard on challenges which others don’t even understand. We as engineers make the world moving but usually we are not recognized.” Everyone enjoys the products of the labors of engineers (such as cell phones, MP3 players, cars, planes, bridges, internet connections) but few see the required knowledge, work and the people that bring those products into being.
photo by Jacquie the cat of a vine
Jürgen “hopes that I made ‘engineering’ a bit more visible to people who did not think about it before, for example, female cat owners who never had a solder iron in the hand and bought plain SOIC chips because they wanted the cat camera…”

I think he has done a great job illustrating the engineering behind the CatCam and making engineering fun. And in so doing hopefully is making more people aware of the engineers that make so many wonderful modern gadgets. Go buy a CatCam now (and if you are adventurous buy the parts and create your own – you will learn a lot about what makes all your modern gadgets work). And then send in the pictures your cat takes so everyone can see the wonderful things engineers make possible.

The photos here show the results of several new cat photographers (Binky the cat [first 2 photos] and Jacquie the cat [last 2]). Only a small percentage of CatCam owners have shared there pictures so far.

Over the next few years he would like to learn to sail, visit Yellowstone national park, walk the Camino de Santiago again, move on to other international assignment (maybe far east) and continuing raising his two children.

The Curious Cat Science and Engineering Blog is written by John Hunter and tracks a wide variety of developments, happenings, interesting under-publicized facts, and cool aspects of science and engineering.

One Species’ Genome Discovered Inside Another’s

Video describing genome inside genome Watch video of Professor Werren describing the genome-in-a-genome at the University of Rochester.

More incredible gene research. Scientists at the University of Rochester and the J. Craig Venter Institute have discovered a copy of the genome of a bacterial parasite residing inside the genome of its host species. The research, reported in today’s Science, also shows that lateral gene transfer—the movement of genes between unrelated species—may happen much more frequently between bacteria and multicellular organisms than scientists previously believed, posing dramatic implications for evolution.

Such large-scale heritable gene transfers may allow species to acquire new genes and functions extremely quickly, says Jack Werren, a principle investigator of the study. If such genes provide new abilities in species that cause or transmit disease, they could provide new targets for fighting these diseases.

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The results also have serious repercussions for genome-sequencing projects. Bacterial DNA is routinely discarded when scientists are assembling invertebrate genomes, yet these genes may very well be part of the organism’s genome, and might even be responsible for functioning traits.

“This study establishes the widespread occurrence and high frequency of a process that we would have dismissed as science fiction until just a few years ago,” says W. Ford Doolittle, Canada Research Chair in Comparative Microbial Genomics at Dalhousie University, who is not connected to the study. “This is stunning evidence for increased frequency of gene transfer.”

Related: Opossum Genome Shows ‘Junk’ DNA is Not JunkBdelloid Rotifers Abandoned Sex 100 Million Years AgoScientists discover new class of RNAWhere Bacteria Get Their GenesNew Understanding of Human DNAOld Viruses Resurrected Through DNA

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Best Research University Rankings – 2007

There are several rankings of universities. They can be interesting but also have obvious limitations. I find Shanghai’s Jiao Tong University’s the most interesting (especially the international nature of it). Their real focus seems to be in providing a way for China to get a feel for how they are progressing toward developing world class universities (interesting slide presentation on their efforts). The methodology values publications and faculty awards and is provides a better ranking of research (rather than teaching). Results from the 2007 rankings of Top 500 Universities worldwide showing country representation of the top schools:

location Top 101 % of World
Population
% of World GDP % of top 500
USA 54     4.6%   27.4%  32.7%
United Kingdom 11  0.9  4.9 8.3
Germany   6  1.3  6.0 8.1
Japan   6  2.0  9.0 6.3
Canada   4  0.5  2.6 4.3
France   4  0.9  4.6 4.3
Sweden   4  0.1  0.8 2.2
Switzerland   3  0.1  0.8 1.6
Australia   2  0.3  1.6 3.3
Netherlands   2  0.3  1.4 2.4
Israel  1  0.1  0.3 1.4
Finland   1  0.1  0.4 1.0
Norway   1  0.1  0.6 0.8
Denmark   1  0.1  0.6 0.8
Russia   1  2.2  2.0 0.4
China  20.1  5.5 2.8
India  17.0  1.9 0.4

China has 1 ranked in the 151-202 range as do Taiwan, Korea and Brazil. Singapore has one in the 102-151 range. The other country without any in the top 101 with representation in the next 101 is Italy with 3 schools in the 102-151 range and 2 in the 152-202 range. India has 2 in the 305-401 range.

Top 10 schools (same schools as last year, Cambridge moved from 2nd to 4th):

  • Harvard University
  • Stanford University
  • University of California at Berkeley
  • Cambridge University
  • Massachusetts Institute of Technology(MIT)
  • California Institute of Technology
  • Columbia University
  • Princeton University
  • University Chicago
  • Oxford University

University of Wisconsin – Madison is 17th :-) My father taught there while I grew up.
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Great Speech by Marissa Mayer on Innovation at Google

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Marissa Mayer speech at Stanford on innovation at Google (23 minute speech, 26 minutes of question and answers). She leads the product management efforts on Google’s search products- web search, images, groups, news, Froogle, the Google Toolbar, Google Desktop, Google Labs, and more. She joined Google in 1999 as Google’s first female engineer. Excellent speech. Highly recommended. Google top 9 ideas:

(inside these are Marissa’s thoughts) [inside these are my comments]

  1. Ideas come from anywhere (engineers, customers, managers, executives, external companies – that Google acquires)
  2. Share everything you can (very open culture)
  3. Your Brilliant We’re Hiring [Google Hiring]
  4. A license to pursue dreams (Google 20% time)
  5. Innovation not instant perfection (iteration – experiment quickly and often)
  6. Data is apolitical [Data Based Decision Making - common errors in interpreting data - read the related links too]
  7. Creativity loves Constraints [process improvement and innovation]
  8. Users not money (Google focuses on providing users what they want and believe it will work out)
  9. Don’t kill projects morph them

So far every time I hear one of Google’s leaders speak I am happier that I own a bit of stock – this is another instance of that.

Related: Technology Speakers at GoogleGoogle’s Page urges scientists to market themselvesInnovation at GoogleAmazon InnovationScience and Engineering Webcast directoryEngineers – Career Options

Economic Strength Through Technology Leadership

One of the topics I keep coming back to is the future economic impact of science, engineering, technology and the supporting structures in countries for the same. I believe a significant part of the benefit we enjoy today and will enjoy in the future is tied to how well those areas are integrated with economic factors (raising capital, open financial markets, infrastructure…). Some past posts include: The Future is Engineering, U.S. Slipping on Science, Diplomacy and Science Research, Shrinking Science Gap and Engineering the Future Economy. Fortune discusses the issue in – The United States of Technology?:

As we celebrated the nation’s birthday, I asked myself a patriotic question: Does the United States still lead in tech? As an American myself, my lens is inevitably distorted. Even so, the answer is hardly an unqualified yes.

I agree. While I still think the USA leads the question is debatable in various fields and as I have said before the future looks to be moving in the other direction. This is more due to the rest of the World improving than the USA failing. The continued reduction in advanced science and engineering degrees awarded to USA citizens compared to the rest of the world is a leading indicator I believe. Along with my belief that we will attract fewer leaders to the USA than we have in the past.

No other country can duplicate the American environment of tech creativity, which arises from a unique stew of entrepreneurs, academics, engineers, imaginative marketers and savvy financiers packed together in an atmosphere of risk-taking and plentiful capital. There is nowhere outside the United States remotely like the three places where this formula is most clearly at work – Silicon Valley of course, plus Austin and Boston.

True but the precursors for doing so are being created, the question is whether countries can pull all of it together. If only one country had a shot, I would guess that they would fail, because it is a difficult thing to do. But given how many places have a chance (including: China, Japan, UK, Singapore, France, India, Germany, Korea, Canada, Finland…) it seems very possible other centers of such excellence will appear. I must admit I would not put Austin in such a class, but maybe I am uninformed…

Related: Education, Entrepreneurship and ImmigrationGlobal Technology LeadershipThe World’s Best Research UniversitiesAussies Look to Finnish Innovation ModelScience, Engineering and the Future of the American EconomyChina challenges dominance of USA, Europe and JapanChina and USA Basic Science ResearchAsia: Rising Stars of Science and EngineeringBasic Science Research Funding

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