Category Archives: Engineering

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.

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.
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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.
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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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No AP Stories

Michael Arrington, at Techcrunch, has announced a new policy Here’s Our New Policy On A.P. stories: They’re Banned. Good for him. I have long not linked to Associated Press stories due to their pointy haired boss understanding of the internet. The New York Times took awhile to understand how to respond to the new world but seems to be doing well now (so now I link to them). Other good sources: BBC (though they need to do better with webcasting), NPR, National Geographic, Science Blogs, PLoS.

Getting links is a good thing. When you have lawyers threatening people that are helping you, that is just plain dumb (and not the behavior I want to support by directing traffic to your site). Yes some bloggers do go to far and appropriate content they should not. So fine, do something about that. But you need to act sensibly, not like they have been (and that is not just limited to the problems that have landed them in trouble recently but their lack of making effective use of the internet for years).

The A.P. doesn’t get to make it’s own rules around how its content is used, if those rules are stricter than the law allows. So even thought they say they are making these new guidelines in the spirit of cooperation, it’s clear that, like the RIAA and MPAA, they are trying to claw their way to a set of property rights that don’t exist today and that they are not legally entitled to. And like the RIAA and MPAA, this is done to protect a dying business model – paid content.

So here’s our new policy on A.P. stories: they don’t exist. We don’t see them, we don’t quote them, we don’t link to them. They’re banned until they abandon this new strategy, and I encourage others to do the same until they back down from these ridiculous attempts to stop the spread of information around the Internet.

Buckminster Fuller: Dymaxion Man

Dymaxion Man

Fuller’s schemes often had the hallucinatory quality associated with science fiction (or mental hospitals). It concerned him not in the least that things had always been done a certain way in the past. In addition to flying cars, he imagined mass-produced bathrooms that could be installed like refrigerators; underwater settlements that would be restocked by submarine; and floating communities that, along with all their inhabitants, would hover among the clouds. Most famously, he dreamed up the geodesic dome. “If you are in a shipwreck and all the boats are gone, a piano top . . . that comes along makes a fortuitous life preserver,” Fuller once wrote. “But this is not to say that the best way to design a life preserver is in the form of a piano top. I think that we are clinging to a great many piano tops in accepting yesterday’s fortuitous contrivings.” Fuller may have spent his life inventing things, but he claimed that he was not particularly interested in inventions. He called himself a “comprehensive, anticipatory design scientist—”a “comprehensivist,” for short—and believed that his task was to innovate in such a way as to benefit the greatest number of people using the least amount of resources. “My objective was humanity’s comprehensive success in the universe” is how he once put it. “I could have ended up with a pair of flying slippers.”

Related: Buckminster Fuller $100,000 Challenge – Golden Buckyballs – Everything I Know, the historic 42-hour session with Buckminster Fuller

How Computers Boot Up

Things start rolling when you press the power button on the computer (no! do tell!). Once the motherboard is powered up it initializes its own firmware – the chipset and other tidbits – and tries to get the CPU running. If things fail at this point (e.g., the CPU is busted or missing) then you will likely have a system that looks completely dead except for rotating fans. A few motherboards manage to emit beeps for an absent or faulty CPU, but the zombie-with-fans state is the most common scenario based on my experience. Sometimes USB or other devices can cause this to happen: unplugging all non-essential devices is a possible cure for a system that was working and suddenly appears dead like this. You can then single out the culprit device by elimination.

If all is well the CPU starts running. In a multi-processor or multi-core system one CPU is dynamically chosen to be the bootstrap processor (BSP) that runs all of the BIOS and kernel initialization code. The remaining processors, called application processors (AP) at this point, remain halted until later on when they are explicitly activated by the kernel. Intel CPUs have been evolving over the years but they’re fully backwards compatible, so modern CPUs can behave like the original 1978 Intel 8086, which is exactly what they do after power up. In this primitive power up state the processor is in real mode with memory paging disabled. This is like ancient MS-DOS where only 1 MB of memory can be addressed and any code can write to any place in memory – there’s no notion of protection or privilege.

Pax Scientific

Nature Gave Him a Blueprint, but Not Overnight Success

Mr. Harman is a practitioner of biomimicry, a growing movement of the industrial-design field. Eleven years ago, he established Pax Scientific to commercialize his ideas, thinking that it would take only a couple of years to convince companies that they could increase efficiency, lower noise or create entirely new categories of products by following his approach.
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His radical ideas have so far found a cautious reception in the aircraft, air- conditioning, boating, pump and wind turbine industries. Mr. Harman’s experience is not unusual. Rather than beating a path to the door of mousetrap designers, the world seems to actively avoid them.
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Even in fields such as the computer industry, which celebrates innovation, systemic change can be glacial.
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In another hopeful sign, a world that long ignored energy efficiency is suddenly thinking of nothing else. “We tried for years to promote energy conservation, and we couldn’t find one who was interested,” he said. “Now the world has done a U-turn.”

Yet another example that new knowledge is not enough. It takes much longer for good ideas to be put into practice than seems reasonable (until you get your head around the idea it takes a fair amount of time for new ideas to be adopted).

One positive aspect of this reality is that if you can take advantage of new ideas before others you can gain an advantage. It isn’t necessarily true that just because now everyone knows about some new idea that you have no opportunity to use the knowledge before others.

The Science Barge

The Science Barge is a prototype, sustainable urban farm and environmental education center. It is the only fully functioning demonstration of renewable energy supporting sustainable food production in New York City. The Science Barge grows tomatoes, cucumbers, and lettuce with zero net carbon emissions, zero chemical pesticides, and zero runoff.

From May to October 2007, the Science Barge hosted over 3,000 schoolchildren from all five New York boroughs as well as surrounding counties as part of our environmental education program. In addition, over 6,000 adult visitors visited the facility along with press from around the world.

NY Sun Works: The Science Barge

Limited growing space means growing upwards, with stacked pots for strawberries, and vines that grow up to the ceiling and are then folded over to grow back down. Instead of using pesticides, pests are kept in check using ladybugs, parasitic wasps, and other predators as needed. Environmentally friendly substrates such as rice husks, coconut shells, and Earth Stone (recycled glass), are used to aerate the root systems for the plants.

Most fascinating of all was the Aquaponic system for providing nutrients to the plants using catfish. Nutrients from the plants and worms feed the catfish, who produce nitrogen-rich waste, which feeds the plants. Tilapia were originally used, but eventually replaced with catfish, which were better suited to the climate. The result of all this effort is a bounty of fresh fruits and vegetables given out to all the children who visit the barge.

Printing Buildings

Projections indicate costs will be around one fifth as much as conventional construction. Using this process, a single house or a colony of houses, each with possibly a different design, may be automatically constructed in a single run, embedded in each house all the conduits for electrical, plumbing and air-conditioning.
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The machine will cost between $500K to $700K for average size (2000 sq ft — 200 m2) detached houses. This is not much given that a concrete pump truck is now $300k-$400K. Note that with one machine numerous homes can be built. The first commercial machines to be available this year, 2008. The machine will be collapsible to form into an easy truck load. The unloading and setup will take between 1-2 hours.

Behrokh Khoshnevis is the visionary who has been driving this concept. He is the Director of the Center for Rapid Automated Fabrication Technologies (CRAFT) and Director of Manufacturing Engineering Graduate Program at USC.

Very cool stuff. Related: Open Source 3-D Printing – A plane You Can Print – $35 million to the USC School of Engineering – Contractor Warned NYC About Crane – Sandwich Brick, Reusing Waste Material

Antimicrobial Wipes Often Spread Bacteria

Can we ‘wipe out’ hospital MRSA?

Led by microbiologist Dr Jean-Yves Maillard, the study into the ability of antimicrobial-surface wipes to remove, kill and prevent the spread of such infections as MRSA, has revealed that current protocols utilised by hospital staff have the potential to spread pathogens after only the first use of a wipe, particularly due to the ineffectiveness of wipes to actually kill bacteria.

The team is now calling for a ‘one wipe – one application – per surface’ approach to infection control in healthcare environments.
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The research, supported by a grant from the Wales Office of Research and Development for Health and Social Care, involved a surveillance programme observing hospital staff using surface wipes to decontaminate surfaces near patients, such as bed rails, and other surfaces commonly touched by staff and patients, such as monitors, tables and key pads, which were later replicated in the lab.

A three-step system was also developed to test the ability of several commercially available wipes to disinfect surfaces contaminated with strains Staphylococcus aureus, including MRSA and MSSA. The system tested the removal of pathogens, the transmission of them, and the anti-microbial properties of wipes.

It was found that the wipes were being applied to the same surface several times and used on consecutive surfaces before being discarded. It also revealed that although some wipes can remove higher numbers of bacteria from surfaces than others, the wipes tested were unable to kill the bacteria removed. As a result, high numbers of bacteria were transferred to other surfaces when reused.
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“On the whole, wipes can be effective in removing, killing and preventing the transfer of pathogens such as MRSA but only if used in the right way. We found that the most effective way is to prevent the risk of MRSA spread in hospital wards is to ensure the wipe is used only once on one surface.”

Engineering Education in India

Report recommends steps to improve engineering education in India

The number of engineering doctorates awarded in India each year is about 1,000 which is less than one per cent of the total engineering graduate degrees awarded every year. The international comparison showed that, in most countries, the number of PhD degrees awarded annually range between 5-9 per cent of the engineering graduate degrees awarded. Involvement of industry to sponsor special doctoral fellowships was one of the ways to attract good students to the PhD programme, the report noted.

Majority of engineering graduates not employable: Experts

On the other hand, tier-I and tier-II colleges, namely the IITs, IISc and the NITs produce , less than 1% of engineering graduates, 20% M.Techs and 40% PhD in India

The issue is not the best universities which are excellent. But the huge numbers of graduates are not receiving that type of education.

Robotic Prosthetic Arms for People

Dean Kamen latest invention was funded by DARPA. Once again he is doing amazing stuff. It is great what engineers can do (many worked together to get the progress so far) when given the opportunity. We need many more such efforts.

Dean Kamen Lends a Hand, or Two (August 2007):

DARPA has spent almost $25 million funding two independent teams, Mr. Kamen’s DEKA Research & Development Corp. and a group at Johns Hopkins’ University in an effort they hope will ultimately lead to commercial prosthesis that can be controlled from the human brain.

The innovation in the DEKA arm lies in its ultra light weight carbon shell, giving the user an exoskeleton with which to gain the leverage necessary to do some of the extraordinary things the system makes possible, such as lifting a 40 lb. weight.

To make the system function, the DEKA engineers coated the inside of the shell with a mosaic of thin air bladders that can be individually filled with air to offer padding and rigidity necessary to make possible normally ordinary tasks such as operating a portable power drill. When the arm is not in use the system deflates, or can even alternately fill and empty to offer a massage effect, so that it is not painful to wear for long periods.

The DEKA system is controlled by a joystick that is moved by the remaining portion of the user’s arm and by a second control mechanism in the user’s shoe. Mr. Kamen said that despite the complexity of controlling an ensemble of motors and mechanical servo devices, a user can gain basic functional control in just one day.