Tag Archives: Foldit

Your grandma got STEM?

Jeff Bittel thank you for a story (Mar. 26, 2013 on Slate) about Rachel Levy and the website where she gently blows up the notion/stereotype that older women don’t understand science and technology and that they are too old to learn (Note: A link has been removed),

 Is your grandmother a particle physicist? Did she help the Navy build submarines or make concoctions of chlorine gas on the family’s front porch? Or is she a mathematician, inventor, or engineer? If so, then baby, your grandma’s got STEM.

Grandma Got STEM is a celebration of women working in and contributing to the fields of science, technology, engineering, and mathematics. It is also designed to combat the doting, fumbling, pie-making stereotype of grandmatrons.

That’s why Rachel Levy, an associate professor of mathematics at Harvey Mudd College, is collecting the stories of grandmas across the various fields of STEM. She first got the idea after hearing someone utter the phrase, “Just explain it like you would to your grandma.”

At first blush, such a thing seems harmless. But think about what it means—basically, all older women are stupid.

“For two or three years I thought about how I could address this issue without just making people angry and more inclined to use the phrase,” Levy told me. “If I could come up with a million examples of grandmothers who were tech-savvy, people wouldn’t say it anymore because it wouldn’t be apt.”

While attending the conference ScienceOnline this year, Levy realized she could harness the power of the Internet to collect stories and showcase them. So far, she’s been able to upload at least one grandma a day for about a month and a half—and the stories keep pouring in. Levy’s aim so far is to be as inclusive as possible. She’s accepting any grandma currently or previously involved in STEM. They can submit themselves or you can submit for them. Heck, they don’t even have to have children with children, per se. Age’ll do just fine.

Bittel might want to reconsider that bit about children and children with children. That can be a touchy topic.

Levy’s solution was to create the Grandma Got STEM website. From the Mar. 27, 2013 posting about Mary Vellos Klonowski,

GrandmaGotSTEM

Thank you to undergraduate Math/Computer Science Major Joey Klonowski, who submitted this post about his grandmother:

This photo is from the October 3, 1951 edition of The Southtown Economist, a daily newspaper on the South Side of Chicago, when my grandmother, Mary Klonowski, was 18. She attended DePaul University against the wishes of her father, who didn’t want his daughters to be college educated. She received a BS from DePaul in 1954 and was the only woman chemistry major in her class. She later earned a master’s in mathematics education and became a high school math teacher. She is now 80 years old and still working as a substitute teacher.

There are a lot of stories (covering quite the range of grannies) on the site. Levy is asking for international submissions as well,

Seeking international submissions!

You can help promote this project by sharing the posts on your blog, Facebook wall, or by retweeting them.

The project has readers from more than 100 countries, but submissions from only a few.  Please help make this blog an international effort by submitting posts or encouraging others to post.

Call for submissions – short

Know any geeky grannies?  Seeking submissions for Grandma got STEM.  Email name+pic+story to [email protected]

Call for submissions – long

Call for submissions – Grandma got STEM.  Are you a grandmother working in a STEM (Science, Technology, Engineering, Mathematics) – related field?  Know any geeky grannies?  Email name+pic+story/remembrance to Rachel Levy:  ggstem (at) hmc (dot) edu.  Follow on Twitter: @mathcirque #ggstem  Project site:http://ggstem.wordpress.com

Presumably, the submissions need to be in English.

Getting back to Bittel’s Slate article, he mentions Foldit (here’s my first piece in an Aug. 6, 2010 posting [scroll down about 1/2 way]), a protein-folding game which has generated some very exciting science. He also notes some of that science was generated by older, ‘uneducated’ women. Bittel linked to Jeff Howe’s Feb. 27, 2012 article about Foldit and other crowdsourced science projects for Slate where I found this very intriguing bit,

“You’d think a Ph.D. in biochemistry would be very good at designing protein molecules,” says Zoran Popović, the University of Washington game designer behind Foldit. Not so. “Biochemists are good at other things. But Foldit requires a narrow, deeper expertise.”

Or as it turns out, more than one. Some gamers have a preternatural ability to recognize patterns, an innate form of spatial reasoning most of us lack. Others—often “grandmothers without a high school education,” says Popovic—exercise a particular social skill. “They’re good at getting people unstuck. They get them to approach the problem differently.” What big pharmaceutical company would have anticipated the need to hire uneducated grandmothers? (I know a few, if Eli Lilly HR is thinking of rejiggering its recruitment strategy.) [emphases mine]

There’s an interesting question and I didn’t see it answered in Howe’s article. What kind of grandmother who doesn’t have high school graduation joins a protein-folding game? I ask because neither of my parents had or have a high school education. Neither of them would have joined the game as neither would have had the confidence.

What I’ve tried to present here is a range of possibilities regarding age and education. Being older (female especially but also male, on occasion) doesn’t equal stupidity. As for education, I’ve never found that having high school graduation or a university degree(s) to be a guarantor of an exciting intellect. I mention these two points because it seems to me that people are being ranked as to age and education in ways that are unnecessarily exclusionary. Thank goodness for games like Foldit and websites like Grandma’s Got STEM which suggest alternatives to this relentless and ruthless form of ranking which disallows participation from the great bulk of us.

Citizen science = crowdsourced science?

Deirdre Lockwood’s Nov. 12, 2012 article (Crowdsourcing Chemistry) for Chemical & Engineering News (C&EN) offers a good overview of the various citizen science projects and organizations while using the terms citizen science and crowdsourcing science interchangeably. For me, it’s  a ‘poodles and dogs’ situation; all poodles are dogs but not all dogs are poodles.

Here are two examples from the article,

Although the public has participated in scientific research since at least the first Audubon Christmas Bird Count of 1900, so-called citizen science has gained momentum in the past decade through funding, enthusiasm, and technology. This trend is dominated by projects in biology, but chemists are getting on board, too. NSF’s funding of citizen-science projects has grown from a handful each year in the early 2000s to at least 25 per year today.

Online gaming project Foldit has attracted many participants to find the lowest-energy configuration of proteins. Foldit players recently solved the structure of a retroviral protease that had long stumped structural biologists (Nat. Struct. Mol. Biol., DOI: 10.1038/nsmb.2119).

There’s a difference between going out and counting birds (citizen science) and 50,000 or more people solving a problem in biology (citizen science and crowdsourcing science). In the first instance, you’re gathering data for the scientist and in the second instance, you’re gathering, analyzing, and solving a science problem alongside the scientists. There is, of course, a great big grey zone but if you’re looking to participate in projects, the distinction may be useful to you. Do take a look at Lockwood’s article as she mentions some very exciting projects.

H/T to the Nov. 14, 2012 news item about Lockwood’s article on phys.org.

RNA (ribonucleic acid) video game

I am a great fan of  Foldit, a protein-folding game I have mentioned several times here (my first posting about Foldit was Aug. 6, 2010) and now via the Foresight Insitute’s July 16, 2012 blog posting, I have discovered an RNA video game (Note: I have removed links),

As we pointed out a few months ago, the greater complexity of folding rules for RNA compared to its chemical cousin DNA gives RNA a greater variety of compact, three-dimensional shapes and a different set of potential functions than is the case with DNA, and this gives RNA nanotechnology a different set of advantages compared to DNA nanotechnology … Proteins have even more complex folding rules and an even greater variety of structures and functions. We also noted here that online gamers playing Foldit topped scientists in redesigning a protein to achieve a novel enzymatic activity that might be especially useful in developing molecular building blocks for molecular manufacturing. Now KurzweilAI.net brings news of an online game that allows players to design RNA molecules …

Here’s more from the KurzwelAI.net June 26, 3012 posting about the new RNA game EteRNA,

EteRNA, an online game with more than 38,000 registered users, allows players to design molecules of ribonucleic acid — RNA — that have the power to build proteins or regulate genes.

EteRNA players manipulate nucleotides, the fundamental building blocks of RNA, to coax molecules into shapes specified by the game.

Those shapes represent how RNA appears in nature while it goes about its work as one of life’s most essential ingredients.

EteRNA was developed by scientists at Stanford and Carnegie Mellon universities, who use the designs created by players to decipher how real RNA works. The game is a direct descendant of Foldit — another science crowdsourcing tool disguised as entertainment — which gets players to help figure out the folding structures of proteins.

Here’s how the EteRNA folks describe this game (from the About EteRNA page),

By playing EteRNA, you will participate in creating the first large-scale library of synthetic RNA designs. Your efforts will help reveal new principles for designing RNA-based switches and nanomachines — new systems for seeking and eventually controlling living cells and disease-causing viruses. By interacting with thousands of players and learning from real experimental feedback, you will be pioneering a completely new way to do science. Join the global laboratory!

The About EteRNA webpage also offers a discussion about RNA,

RNA is often called the “Dark Matter of Biology.” While originally thought to be an unstable cousin of DNA, recent discoveries have shown that RNA can do amazing things. They play key roles in the fundamental processes of life and disease, from protein synthesis and HIV replication, to cellular control. However, the full biological and medical implications of these discoveries is still being worked out.

RNA is made of four nucleotides (A, C,G,and U, which stand for adenine, cytosine, guanine, and uracil). Chemically, each of these building blocks is made of atoms of carbon, oxygen, nitrogen, phosphorus, and hydrogen. When you design RNAs with EteRNA, you’re really creating a chain of these nucleotides.

RNA Nucleotides (from the About EteRNA webpage)

Scientists do not yet understand all of RNA’s roles, but we already know about a large collection of RNAs that are critical for life: (see the Thermus Thermophilus image representing following points)

  1. mRNAs are short copies of a cell’s DNA genome that gets cut up, pasted, spliced, and otherwise remixed before getting translated into proteins.
  1. rRNA forms the core machinery of an ancient machine, the ribosome. This machine synthesizes the proteins of your cells and all living cells, and is the target of most antibiotics.
  2. miRNAs (microRNAs) are short molecules (about 22-letters) that are used by all complex cells as commands for silencing genes and appear to have roles in cancer, heart disease, and other medical problems.
  3. Riboswitches are ubiquitous in bacteria. They sense all sorts of small molecules that could be food or signals from other bacteria, and turn on or off genes by changing their shapes. These are interesting targets for new antibiotics.
  4. Ribozymes are RNAs that can act as enzymes. They catalyze chemical reactions like protein synthesis and RNA splicing, and provide evidence of RNA’s dominance in a primordial stage of Life’s evolution.
  5. Retroviruses, like Hepatitis C, poliovirus, and HIV, are very large RNAs coated with proteins.
  6. And much much more… shRNA, piRNA, snRNA, and other new classes of important RNAs are being discovered every year.

Thermus Thermophilus – Large Subunit Ribosomal RNA
Source: Center for Molecular Biology (downloaded from the About EteRNA webpage)

I do wonder about the wordplay EteRNA/eternal. Are these scientists trying to tell us something?

Picture still not worth 1000 words but here are the 2011 International Science and Engineering Visualization Challenge winners

About this time last year I wrote an impassioned piece on the importance of words (Feb. 22, 2012 posting) while making note of the 2010 International Science and Engineering Visualization Challenge winners. For the record, I haven’t changed my mind about the importance of either words or visuals; I still don’t believe that there’s a one size fits all approach to communicating about anything let alone science. (I have had more than one convo with graphic designers who bring up that ‘picture worth …’ as they explain why my words on the page are in a four-point font [I exaggerate but only mildly], so this protest was based on previous bad experiences rather than any hostility towards the Challenge.)

Science magazine (published by the American Association for the Advancement of Science [AAAS]) announced the winners for the 2011 International Science and Engineering Visualization Challenge today. Tomorrow, Science will feature the winning entries in its Feb. 3,  2012 issue. From the Feb. 2, 2012 news release on EurekAlert,

The international competition, currently in its ninth year, honors recipients who use visual media to promote understanding of scientific research. The criteria for judging the 212 entries, from 33 countries, included visual impact, effective communication, freshness and originality.

Here’s a brief description of the some of the winning entries,

Solve the Protein Puzzle: A multiplayer online computer game puzzle, called “Foldit,” that allows users to bend and fold amino acids into realistic proteins and solve the problem of protein folding was developed by Seth Cooper of the University of Washington, Seattle and his team.

“We strove to make the visualizations in folding both fun to look at and informative about where there are problems with the protein that players might be able to fix,” said Cooper, a first-place winner in the Interactive Games category. “We tried to make the visualizations clear and approachable, so the game can be played by people who don’t have a scientific background.”

View a Cell in 3D: The movie “Rapid Visual Inventory & Comparison of Complex 3D Structures” depicts a novel three-dimensional model view of a whole cell in minute detail and helps biologists better understand complex visual data for a general audience. The video was selected as the first-place Video category winner by the judges as well as the People’s Choice.

“Morphing the cell from the complicated native model to the simplified version and back gets general audiences excited about the subject matter and reminds even expert audiences of the complex interplay of randomness and specific interaction that enables life to exist,” said winning animator Graham T. Johnson of the Scripps Research Institute in San Diego, California, and now at the University of California San Francisco.

See the Beauty of a Mouse’s Eye: The first-place photograph, “Metabolomic Eye,” is a metabolic snapshot of the diversity of cells in a mouse eye retina, derived from a technique called computational molecular phenotyping (CMP), explained neuroscientist Bryan William Jones of the University of Utah’s Moran Eye Center in Salt Lake City. The image shows a unique view of normal tissue functioning and reveals complex metabolic signals while preserving the anatomical context of a tissue, added Jones.

Build a Human Body: “Build-a-Body is a great way to virtually learn about human anatomy,” said game designer Jeremy Friedberg of Spongelab Interactive about his educational science game, which won an Honorable Mention, that allows users to use drag and drop tools to learn about organs of the human body. “Our free, open platform fosters a global science community by stitching together educational content, teaching tools and powerful data surrounding class and student performance.”

Since I try to focus on nanotechnology for this blog, here’s a carbon nanotube image that won an honourable mention in this year’s competition in the illustration category,

Variable-diameter carbon nanotubes This 3-D illustration shows the production of variable-diameter carbon nanotubes. University of Nebraska-Lincoln electrical engineering professor, Dr. Yongfeng Lu, discovered laser-based production techniques that can precisely control the length, diameter and properties of carbon nanotubes. Using these highly electrically and thermally conductive nanotubes, Lu’s team developed methods to improve transistors and sensors that may one day speed up computers and other electrical devices, while minimizing energy consumption and heat generation. They also discovered how to control a carbon nanotube’s diameter from one end to the other, which alters its characteristics. Lu envisions variable-diameter nanotubes customized for specific uses. This 3-D illustration was developed to help Dr. Lu’s team to visualize these nano-scale discoveries for diverse audiences. [Image courtesy of Joel Brehm, University of Nebraska-Lincoln Office of Research and Economic Development

To me, they look like bowling pins made of pine cones.

 

Math, YouTube, and opening science

There’s a charming post (May 17, 2011) by James Grime, mathematician, at the Guardian Science Blogs about his and other science communicators’ YouTube videos. From the posting,

I’m a mathematician – and have the chalk marks to prove it – but I do not come from a family of academics. Growing up, my only access to that world was through the television. I remember Johnny Ball jumping up and down talking excitedly about the parabolic path of projectiles; Horizon’s documentary on the Andrew Wiles’ proof of Fermat’s Last Theorem; and at Christmas the theme music of the Royal Institution’s Christmas Lectures filled me with even more excitement than the bike that came with six sound effects.

Today the profile of science communication on TV may be at an all time high. My mum may not know what the Large Hadron Collider does, but she knows who Brian Cox is. But television remains a very 20th century method of communication. A channel will gear their science programming towards their perceived audience, be that BBC1 , BBC4 or a Channel 4 audience.

However, with the rise of new media, like YouTube, you no longer need to chase the audience. They find you.

He goes on to share one of his videos and a selection from other science communicators. It’s a great read and has attracted comments that include links to even more science videos.

Clearly, Grime’s main focus in this post is educational/popularizing/awareness raising for the general public.

Some scientists are trying to use social media such as YouTube to better communicate with each other. There are science videos (not many) wherein scientific papers are given video abstracts. For example materials scientists are doing this on their Materials’s Views Channel on YouTube. This is all part of a movement to make science more open through social media.

Science has been been opened up before according to the Open Science Manifesto,

In 1665, the first two scientific journals were published, and science was dragged out of its dark age of cryptic anagrams, secret discoveries, and bitter turf wars. Today we are living in another dark age of science: pay-per-access journals, unreleased code and data, prestige-based metrics, and irreproducible experiments.

As I kept on digging (clicking on the link to the dark ages reference), I found Michael Nielsen, previously an academic working in quantum computation (he has a PhD in physics according to Wikipedia) and now the writer of a forthcoming book, Reinventing Discovery, from the Princeton University Press in November 2011. He advocates strongly for the use of social media amongst scientists as you can see in this approximately 16 mins. March 2011 TED talk at Waterloo (Ontario, Canada),

I notice that his focus is on scientists using social media as a means of communication amongst themselves (and anyone else who may choose to join in) but control remains firmly with the scientists. In other words, science is practiced by scientists and there’s no discussion of citizen scientists where people reach beyond their general science awareness for some form of science activity. I believe it’s an unconscious assumption that the experts (scientists) are the only ones expected to participate while the rest of us gaze on. This is true too of James Grime’s piece where the rest of us are more or less passive viewers of his science videos and not expected to practice science.

There’s nothing wrong with these approaches and, most of the time, I’m perfectly to have scientists do their work and I’m hugely happy when they choose to share it with me.

However, when scientists talk about opening up science they usually mean that the public should learn more about their work (i.e. we are the tabula rasa and not expected to be able to reciprocate; our role is to listen and to be educated by the expert) or that research should be more easily available (mostly amongst themselves). There are some crowdsourced science projects (e.g. Foldit, which boasted some 50,000 authors and there’s also the recently launched Phylo at McGill University [my most recent posting on these projects] amongst others) where members of the public are invited to participate in science activities directly related to answering research questions.

My point is that ‘open science’ means more than one thing.

Democracy, participation, and science culture

Should citizens have any input into how science research is funded? Dan Hind in his Dec. 14, 2010 article, Time to democratise science, for New Scientist argues yes persuasively (from the article),

THE natural and social sciences exert a huge influence on the ways our societies develop. At present most of the funding for scientific research is controlled by the state and the private economy. Perhaps it is time to look at their track record and consider an alternative.

Science is not, and can never be, disinterested insofar as its objectives are concerned. Decisions to fund this research instead of that research can never be purely technical. Assessments of what is likely to produce interesting or useful knowledge are inevitably alloyed with the desires of those who control the money to develop particular forms of knowledge and with them new resources of power.

Given the mixed track record of the patrons of science it is surely time to consider an alternative. If we are serious about science as a public good, we should give the public control over the ways in which some – and I stress “some” – of its money is spent.

At the end of the article there is this note about the author,

Dan Hind is author of The Return of the Public (Verso), which argues for a new kind of participatory politics

There does seem to be seem sort of trend towards more participatory science as per citizen science or crowdsourced science projects such as Foldit (my Aug. 6, 2010 posting) and Phylo (my Dec. 3, 2010 posting).I’m not sure how much traction participatory science research funding is going to find. That said, there was a UK project run by EPSRC (Engineering and Physical Sciences Research) where members of the public were allowed to ‘vote’ on particular projects. You can read more about the project in the May 25, 2009 news item on Nanowerk describing the grants that were chosen. From the news item,

Ten research grants to help solve some of the biggest health problems facing the UK have been awarded by the Engineering and Physical Sciences Research Council (EPSRC)

The projects focus on developing new techniques for screening and treating major public health issues such as cancer, stroke, AIDS, influenza, MRSA and dementia.

The grants, worth £16.5m, have been given by the EPSRC, acting as the lead Research Council in a cross Research Council Programme called “Nanoscience through Engineering to Application.”

Segue: As for participatory politics (as per Dan Hind), I’ve noticed a local (Vancouver, Canada) backlash response to the notion of public consultations (city government officials want to increase population densities). Oddly enough, when people take the time to participate in a ‘consultation’ they expect that at least some of their comments will have an impact on the decisions that are being made. I gather some experts find this irksome and a challenge to their professional authority.

Back to the main topic: My impression is that the UK enjoys a science culture that is not to be found in Canada—not yet, anyway. There is discussion about public dialogue and engagement in science not just in the UK but elsewhere too that simply doesn’t exist in Canada. Yes, there are a few fragile attempts at creating a science culture here. I’m thinking of the Café Scientifique groups, Canada’s National Science and Technology Week, and the open houses put on by the universities but there really isn’t much.

The Year of Science (a science culture project) was declared in the province of British Columbia (BC) in the fall of 2010. From my Oct. 14, 2010 posting,

To inspire young minds across the province and foster a culture of research and innovation Premier Gordon Campbell today proclaimed the 2010-2011 school year as the Year of Science in B.C.

It’s good to see these kinds of initiatives, unfortunately this particular one is undercut by news such as this (from the Dec. 2, 2010 article, Teacher blasts cuts to Vancouver school science budgets; School science budgets slashed by 56 per cent compared to last year, by Naiobh O’Connor for the Vancouver Courier),

School science budgets were slashed by 56 per cent compared to last year and the district now allots only $4.61 per student each year to cover expenses—far below what Mike Hengeveld, Templeton secondary’s science department head and teacher, argues is adequate.

Limited budgets mean it’s difficult to replace equipment like broken beakers or to buy new equipment. Hengeveld even worries about buying a dozen eggs for a relatively cheap egg drop experiment or what’s needed to grow crystals for chemistry class.

“If I went and bought iodized salt or de-iodized salt and [students] make a solution by heating stuff in a beaker—which I hope doesn’t break—if I spend 15 bucks on salt at the store, I’ve blown three or four students’ worth of budget for them to learn how to grow crystals. It’s neat, but I can’t do that in a science class every day. I would just completely and totally run out of money and that’s just on cheap stuff,” he said.

I’m not trying to fault the Year of Science initiative just pointing out that the initiative is problematic when the science education budget for schools cannot support even simple research projects.

This is a larger issue that I can adequately cover in this posting but I did want to draw attention to some of the fragilities of the Canadian situation (and our own situation in BC) vis à vis creating a science culture and/or democratizing science.

Meanwhile, I read with some envy a report titled, International Comparison of Public Dialogue on Science and Technology,  from a UK organization, Sciencewise-ERC – the UK’s national centre for public dialogue in policy making involving science and technology issues. Canada is not mentioned and I imagine that’s due to the fact that we don’t have any public dialogue to speak of.

ETA Mar.3.11: I made some minor changes for clarity (added Segue: and Back to the main topic: and removed an extra space.

Phylo and crowdsourcing science by Canadian researchers

Alex Kawrykow and Gary Roumanis from McGill University (Montréal, Québec) have launched Phylo, a genetics game that anyone can play but is actually genetic research. From the article by Neal Ungerleider at the Fast Company website,

The new project, Phylo, was launched by a team at Montreal’s McGill University on November 29. Players are allowed to recognize and sort human genetic code that’s displayed in a Tetris-like format. Phylo, which runs in Flash, allows users to parse random genetic codes or to tackle DNA patterns related to real diseases. In a random game, a user found himself assigned to DNA portions linked to exudative vitreoretinopathy 4 and vesicoureteral reflux 2.

Players choose from a variety of categories such as digestive system diseases, heart diseases, brain diseases and cancer. All the DNA portions in the game are linked to different diseases. Once completed, they are analyzed and stored in a database; McGill intends to use players’ results in the game to optimize future genetic research.

This reminds me of Foldit (mentioned in my Aug. 6, 2010 posting) another multiplayer online biology-type game; that time the focus was protein folding. As Ungerleider notes in his article, gaming is being used in education, advertising, and media. I’ll add this,  it’s also being used for military training.

I was interested to note that the McGill game was made possible by these agencies,

* Natural Sciences and Engineering Research Council of Canada
* McGill School of Computer Science
* McGill Centre for Bioinformatics
* McGill Computational Structural Biology Group

On a side note, there’s another biology-type game called Phylo, it’s a trading card game designed by David Ng, a professor at the University of British Columbia. From the Phylo, trade card game About page,

What is this phylo thing? (Some interesting but relatively specific FAQs here)

Well, it’s an online initiative aimed at creating a Pokemon card type resource but with real creatures on display in full “artistic” wonder. Not only that – but we plan to have the scientific community weigh in to determine the content on such cards, as well as folks who love gaming to try and design interesting ways to use the cards. Then to top it all off, members of the teacher community will participate to see whether these cards have educational merit. Best of all, the hope is that this will all occur in a non-commercial-open-access-open-source-because-basically-this-is-good-for-you-your-children-and-your-planet sort of way.

The Phylo, trading card game is in Beta (for those not familiar with the term beta, it means the game is still being tested, so there may be ‘bugs’).

It’s nice to be able to report on some innovative Canadian crowdsourcing science.

Folding, origami, and shapeshifting and an article with over 50,000 authors

I’m on a metaphor kick these days so here goes, origami (Japanese paper folding), and shapeshifting are metaphors used to describe a certain biological process that nanoscientists from fields not necessarily associated with biology find fascinating, protein folding.

Origami

Take for example a research team at the California Institute of Technology (Caltech) working to exploit the electronic properties of carbon nanotubes (mentioned in a Nov. 9, 2010 news item on Nanowerk). One of the big issues is that since all of the tubes in a sample are made of carbon getting one tube to react on its own without activating the others is quite challenging when you’re trying to create nanoelectronic circuits. The research team decided to use a technique developed in a bioengineering lab (from the news item),

DNA origami is a type of self-assembled structure made from DNA that can be programmed to form nearly limitless shapes and patterns (such as smiley faces or maps of the Western Hemisphere or even electrical diagrams). Exploiting the sequence-recognition properties of DNA base paring, DNA origami are created from a long single strand of viral DNA and a mixture of different short synthetic DNA strands that bind to and “staple” the viral DNA into the desired shape, typically about 100 nanometers (nm) on a side.

Single-wall carbon nanotubes are molecular tubes composed of rolled-up hexagonal mesh of carbon atoms. With diameters measuring less than 2 nm and yet with lengths of many microns, they have a reputation as some of the strongest, most heat-conductive, and most electronically interesting materials that are known. For years, researchers have been trying to harness their unique properties in nanoscale devices, but precisely arranging them into desirable geometric patterns has been a major stumbling block.

… To integrate the carbon nanotubes into this system, the scientists colored some of those pixels anti-red, and others anti-blue, effectively marking the positions where they wanted the color-matched nanotubes to stick. They then designed the origami so that the red-labeled nanotubes would cross perpendicular to the blue nanotubes, making what is known as a field-effect transistor (FET), one of the most basic devices for building semiconductor circuits.

Although their process is conceptually simple, the researchers had to work out many kinks, such as separating the bundles of carbon nanotubes into individual molecules and attaching the single-stranded DNA; finding the right protection for these DNA strands so they remained able to recognize their partners on the origami; and finding the right chemical conditions for self-assembly.

After about a year, the team had successfully placed crossed nanotubes on the origami; they were able to see the crossing via atomic force microscopy. These systems were removed from solution and placed on a surface, after which leads were attached to measure the device’s electrical properties. When the team’s simple device was wired up to electrodes, it indeed behaved like a field-effect transistor

Shapeshifting

For another more recent example (from an August 5, 2010 article on physorg.com by Larry Hardesty,  Shape-shifting robots),

By combining origami and electrical engineering, researchers at MIT and Harvard are working to develop the ultimate reconfigurable robot — one that can turn into absolutely anything. The researchers have developed algorithms that, given a three-dimensional shape, can determine how to reproduce it by folding a sheet of semi-rigid material with a distinctive pattern of flexible creases. To test out their theories, they built a prototype that can automatically assume the shape of either an origami boat or a paper airplane when it receives different electrical signals. The researchers reported their results in the July 13 issue of the Proceedings of the National Academy of Sciences.

As director of the Distributed Robotics Laboratory at the Computer Science and Artificial Intelligence Laboratory (CSAIL), Professor Daniela Rus researches systems of robots that can work together to tackle complicated tasks. One of the big research areas in distributed robotics is what’s called “programmable matter,” the idea that small, uniform robots could snap together like intelligent Legos to create larger, more versatile robots.

Here’s a video from this site at MIT (Massachusetts Institute of Technology) describing the process,

Folding and over 50, 000 authors

With all this I’ve been leading up to a fascinating project, a game called Foldit, that a team from the University of Washington has published results from in the journal Nature (Predicting protein structures with a multiplayer online game), Aug. 5, 2010.

With over 50,000 authors, this study is a really good example of citizen science (discussed in my May 14, 2010 posting and elsewhere here) and how to use games to solve science problems while exploiting a fascination with folding and origami. From the Aug. 5, 2010 news item on Nanowerk,

The game, Foldit, turns one of the hardest problems in molecular biology into a game a bit reminiscent of Tetris. Thousands of people have now played a game that asks them to fold a protein rather than stack colored blocks or rescue a princess.

Scientists know the pieces that make up a protein but cannot predict how those parts fit together into a 3-D structure. And since proteins act like locks and keys, the structure is crucial.

At any moment, thousands of computers are working away at calculating how physical forces would cause a protein to fold. But no computer in the world is big enough, and computers may not take the smartest approach. So the UW team tried to make it into a game that people could play and compete. Foldit turns protein-folding into a game and awards points based on the internal energy of the 3-D protein structure, dictated by the laws of physics.

Tens of thousands of players have taken the challenge. The author list for the paper includes an acknowledgment of more than 57,000 Foldit players, which may be unprecedented on a scientific publication.

“It’s a new kind of collective intelligence, as opposed to individual intelligence, that we want to study,”Popoviç [principal investigator Zoran Popoviç, a UW associate professor of computer science and engineering] said. “We’re opening eyes in terms of how people think about human intelligence and group intelligence, and what the possibilities are when you get huge numbers of people together to solve a very hard problem.”

There’s a more at Nanowerk including a video about the gamers and the scientists. I think most of us take folding for granted and yet it stimulates all kinds of research and ideas.