standards

"Science education should be based on our economy" Wut?

gregladen — Wed, 28 May 2014 08:38:34 +0000

"Science education should be based on our economy" Wut?

Republican lawmakers and their kin are opposing the acceptance of National Science Standards. Why? Because those standards are based on science. What they prefer is that the standards we use to guide curriculum in America's public schools be the hobgoblin of the Koch Brothers and the rest of the petroleum industry. Way to ruin the country, man. Civilization too. Nice move.

As Chris Hays points out (see below) the anti-science industry in America is leaving Creationism behind and shifting towards the denigration of Climate Science, much to our detriment.

The following interview from All In covers this, and includes Mary Mazzio, documentary film maker, and Michael Mann, climate scientist. Watch it. Then get mad and do something about it.

While you are at it, have a look at this All In segment on the GOP ordering the Pentagon to ignore climate change. Including the Navy, which will be losing ALL OF ITS BASES if they ignore sea level rise.

gregladen Wed, 05/28/2014 - 04:38

Tags

Climate Change

Science Education

standards

Science Education

I more or less agree, but, based on the huge amount of PBS documentarie they fund, I actually think letting the Koch brothers have a lot more say in science education in our public schools would, in all fairness, be a considerable step forward.

First of all, Sanjay, I believe it's only David Koch who funds PBS documentaries. I also believe there's reason to question how rigorous the science presented in those documentaries is.

But the larger point is that our economy is largely based on science, and always has been. Consider: agriculture, based on genetics, organic chemistry, meteorology; steelmaking, based on the Bessamer process; electronics & communications, based on the work of Maxwell, Faraday, Marconi and others. That's the short list.

Yes, fossil fuels are an important part of our economy today. But they won't always be, and that change will happen whether or not we purposely cut back on CO2 emissions. The prudent policy is not to get left behind by others who do embrace the changing conditions.

Well, sure -- I've been a scientist for three decades. Those Koch-funded documentaries are pretty good, actually, and do occasionally cut into right-wing orthodoxy (e.g. on evolution). You're not giving me a reason why they're teaching bad science; in fact I don't think they are. They do seem to be propagating bad _policy_ and sometimes letting others who teach bad science slide. I don't particularly favor thje Koch's policy or societal recommendations, but the writing seems a bit of a thoughtless smear.

The Navy won't be closing all its bases if the seas rise. Instead, they will be spending bazillions to move whatever they can to higher land, and abandoning the rest. Obviously they'd rather not do that, so they want to study climate change now. Because they want to save money.

"Conservatism" hasn't been conservative for a very long time now, I'm afraid. And the right wing is now so crazy that even the military is too liberal for it, which is pretty shocking. That should be a wake-up call to the Republican Party, but so far it hasn't been.

Giving Students and Teachers the Tools for Greatness

esiegel — Tue, 25 Sep 2012 16:08:57 +0000

Giving Students and Teachers the Tools for Greatness

"It is the supreme art of the teacher to awaken joy in creative expression and knowledge." -Albert Einstein

"The mediocre teacher tells. The good teacher explains. The superior teacher demonstrates. The great teacher inspires." -William Arthur Ward

On one side of the room, the interviewer's palms begins to sweat. Although the young man has done his research, his guest is unpredictable. His guest has an agenda, his guest has a polarizing position on a very divisive issue, and his guest may lie or make up facts right there on the spot. The moderator will step aside once the debate commences, and the interviewer won't be allowed any notes. He's got an audience that he's desperate to get the truth out to, and these next ten minutes -- the interview of a lifetime -- could be the last time he's ever in this position if he fails to make his case.

Image credit: Stuart Franklin / Getty Images News.

His only saving grace? He's got a team of researchers that have his back, and a tiny microphone in his ear where the researchers can communicate to him in real-time with fact-checks, figures, sources and more. After all, while he's in the hot seat, his research team has prepared for this, too, and has a collection of information to supply him with if he gets in trouble, or if his guest tells a lie.

Image credit: smannion on Flickr / CC BY-NC-SA 2.0.

Only, this isn't the most important 10 minutes of television you'll see this year.

This is your high school classroom, or at least it can be, if you're willing to make it this way.

This type of lesson -- where you put the students into a real-life scenario that makes the lesson particularly relevant to them -- is known as an active engagement lesson, and is demonstrably the most effective way to get students to learn and retain knowledge, even years later. This type of lesson isn't static, either, but allows teachers and students to engage events and news stories in real-time, as they unfold. Thanks to the power of the internet and the near-instant availability of information, as well as the fact that public high schools now boast a student-to-computer ratio of 4-to-1, if a student can separate the signal-from-the-noise in the internet, they can perform real-time research on practically any topic.

Image credit: OAK Technology & Learning / OAK Tasmania.

The difficulties in doing this are threefold:

Lessons like this take a long time to design and implement for a particular subject,
Getting students to distinguish quality information and sources from misleading ones, despite its importance, is a difficult and time-consuming task to take on, and
There is a huge push -- at least in the USA -- to design lessons that are compliant with the new Common Core State Standards Initiative (CCSSI), the standards that are replacing No Child Left Behind starting this current academic year.

Image credit: Education week.

And I'm not going to lie: having taught for many years, the resources haven't been there to help teachers implement this.

So, what can you do? Well, here's what I did: I convinced the company I work for to give me the time and resources to make these resources myself, and to give them away to the entire world, for free.

This is what *I* did during my "summer vacation."

You don't want to sift through the gigantic, 66-page documents (plus supplements) that are the CCSSI? No problem; I've boiled the reading/writing/speaking/listening/language standards down across all high school subjects into a 2-page Broad Content Outline.

Don't want to have to design your own active-engagement lesson plans and assignments with researching-on-the-internet scaffolding? No problem; I've made three of them -- a Researcher Lesson Plan and Assignment, a Confirmation Bias Lesson Plan and Assignment/Handout, and the Newsbreakers Lesson Plan and Handout (which was the lesson alluded to at the top of this article) -- plus a General Lesson Plan and Handout one for those of you who do want to design your own.

And don't know how to get your students to create a stream of quality, real-time news information on the topic of their choice? That's what the company I work for specializes in, and what I specialize in -- in science and health -- for them.

Image credit: Screenshot from https://trap.it/.

So download the entire educational package I've created -- in either PDF or MS Office 2010/2011 formats (the linked files are zipped; you'll have to right-click, use the "save as" option, and rename the extensions from .jpg to .zip due to NatGeo's web security) -- complete with a Presentation for Educators, a Package Introduction, and an opportunity to give your feedback and suggestions for improvement directly to me.

If you can teach the generation on the precipice of adulthood today the value and utility of evaluating the quality of their information, the sources it comes from, and to recognize misleading rhetoric and logical fallacies, you may just help create the world we all wish we lived in. Making these materials was a labor of love on my part to help get us there; now, teaching the lessons and sharing them with the next generation is up to all of us.

Let's give students and teachers complete and open access to the tools to achieve greatness, and encourage everyone to make the next school year amazing. Empower them to make the world the way it ought to be, and I can't wait to see what comes next.

esiegel Tue, 09/25/2012 - 12:08

Tags

education

CCSSI

common core state standards initiative

Congrats Ethan on doing something specific in service to us all. This looks really good. I hope it takes off. I took your advice on using Trapit and realize that they trap odd sources as well as strong sources. But that is the nature of the internet. It allows people with the time and energy and a pet to do something about it. That's what I do too in my blog life as a poet, so I can't really complain about the guy who has a complete reinterpretation of quantum mechanics.

Christopher,

First off, thanks for going for it! Positive and/or constructive feedback is always welcome.

Second off, if you've found an "odd" source -- or more explicitly, a source so bad it deserves to be completely banned -- let me know and I'll take a look at it. I don't have complete, unilateral control over the system but I do hold some sway in terms of what sources can be eliminated.

If you find something truly offensive in one of your traps, click the "share" link and send me that URL (either here or via email to ethan AT trapit DOT com), and I'll see what I can do. :-)

Wow. Just, um, wow. That seems stunningly awesome. Do you (or does TrapIt) have any mechanism to track (or to request tracking) how many teachers make use of these resources? It would be really cool to come back in a year or so and see how they've been deployed in the real world.

Hi Ethan,

What a wonderful resource. What permissions do I need to make this available to my teachers on my website?

Marjan,

You have my permission. Go for it. (But please, if you can, put the proper .zip extensions on the complete package files!)

Michael,

I've got a small number of teachers who've signed up to do pilot studies; the rest are not being tracked in any way. It was very important to me that we ensure and respect the privacy of both students and teachers; as such, we only gather information that does not allow us to identify individual users.

But I am hopeful that many will voluntarily contact me, and then I'll have an "at least" number.

Ethan,

on many browsers, clicking your links may trigger an "this image cannot be opened" error message -- users are required to right-click your links and choose "save as..." (or "save target as...", depending on their browser).

If you wish, I can upload the files to my dropbox and post the links here -- but obviously any time you change something, you'd need to inform me... So -- do you think uploading the files would be more helpful or more harmful? :)

Philipp

Philipp,

Thank you for the offer; it's very kind. I should edit my instructions to include "right-click to save as..." in order to avoid confusion.

If you would rename them with the appropriate extensions, dropbox them, and link to them in the comments, I would be more than happy to moderate and publish that comment even though it will have more than the (standard) allowable number of links in it.

Again, thanks for the generous offer!

Bravo! While it may be many years before my own small ones can use this specific lesson, I can hope that others take inspiration and follow suit. I've been doing research recently on preschool and kindergarten level education. The results gap between traditional education and the more active engagement methods are astounding.

This looks incredible. Do you have instructions for someone like me who has no clue about the tech language you use to access it. I know PDF. Beyond that. ..... Lost.

Please help.

Emily,

I have sent you an email; contact me if you need any further assistance.

Ethan,

here are the links:

https://dl.dropbox.com/u/82295446/Trapit-Education-MS-Office.zip
https://dl.dropbox.com/u/82295446/Trapit-Education-PDF.zip

Please let me know if you change something in your files; I can then re-upload them.

Philipp

Make the next school year amazing for your students!

esiegel — Wed, 20 Jun 2012 14:53:26 +0000

Make the next school year amazing for your students!

“If you end up with a boring miserable life because you listened to your mom, your dad, your teacher, your priest, or some guy on television telling you how to do your shit, then you deserve it.” -Frank Zappa

Inside of every student I've ever taught lives a passionate, curious mind that can either flourish or stagnate, both inside and outside the classroom. The teachers that get it -- that get you -- are the ones that help bring you there, but that is not all teachers, not by any means. I think everyone, by this point in their life, has had experience with at least one teacher that stands out in their minds as inspirational: a teacher that's helped you become a greater person in this world.

Image credit: University of Nebraska-Lincoln, via http://www.unl.edu/ucomm/aboutunl/.

Ideally, every one of the teachers a student encounters in their life would be great: would take pride in being the best teacher they can, would love what they teach, would be empowered to teach their own style and their own lessons and curriculum, and would genuinely care about the students as individual people. But not every teacher can do this, and not every teacher knows how to be this.

What makes matters even worse is that this isn't what the system values. I think one of the most misguided attempts to make teachers more effective has been the focus on standardized testing and rewards based on test performance, as best exemplified in the U.S. by the disastrous No Child Left Behind program.

Image credit: Endeavor Tutoring and Test Preparation.

Having students score higher on a standardized test doesn't necessarily give you any information about what a student can do other than succeed at taking that test. But success on those tests is what's been financially rewarding for teachers and schools, and so that's what has been prized by administrators, school districts, and entire states. This is disappointing, to put it mildly, because as I've noted before:

1.) There is no amount of control you can take away from a bad teacher that will turn them into a good teacher.

2.) There is nothing worse you can do to a good teacher than take away their autonomy as to how and what they teach to their students in their classrooms.

The teaching system isn't set up to reward whether teachers are inspiring and empowering students to go out and learn, think critically and competently, evaluate information and sources, see through ruses and faulty logic, and to care. To care about whether they've found the more relevant, accurate information, whether they've synthesized it logically and consistently, and whether their conclusions and arguments are robust and high-quality. Appallingly, it's set up to care about a test score.

Image credit: The Art of Teaching Science / Jack Hassard.

And I'm telling you, right now, that I intend to change that, and I want to get every teacher I can on board to help. Because we have got to let students know that they are not defined by what anyone else has to say about them. They aren't defined by awards and accolades, nor by defeats and reprimands, and they certainly aren't defined by how they score on a standardized test, or by how much funding their school gets based on those tests.

But they should take pride in what they achieve, and they should definitely take pride in what they can accomplish, create, and do.

Image credit: Jimmy Walker-Pearson.

So, what can we do about it, to help everyone get there; to help every student achieve, and care, and develop these critical skills?

First off, I'd focus not on standardized testing, but on the standards of "what can you do?"

And, perhaps unbelievably, there's a huge push away from the mess that was No Child Left Behind and towards teaching students with the goal that they'll be able to be mathematically, verbally and analytically literate at a high level throughout their education.

Image credit: http://www.corestandards.org/.

The Common Core State Standards Initiative (CCSSI) is a collaboration among a number of different groups, including the National Education Association (NEA), American Federation of Teachers (AFT), National Council of Teachers of Mathematics (NCTM), and National Council of Teachers of English (NCTE), to create a set of K-12 standards in language arts, literacy and mathematics that will be suitable for all students, nationwide, in every state.

They're very transparent as to how they made these standards, what the key english language arts and mathematics points are, what some common misconceptions are, and where you can download the full standards for yourself. So far, across the U.S., they've been adopted by 45 states plus the District of Columbia.

Image credit: Education Week.

They are poised to take effect in these states at the start of this upcoming academic year, and understandably, there's a lot of anxiety over them. For one, the standards are long, detailed, and difficult to digest. For another, it's unclear how funding will be tied to these standards; they are still very likely to incorporate some type of high-stakes standards-based testing, which will surely be controversial. And finally, because it's new, there are no pre-existing, comprehensive educational resources that are compliant with these standards. It's very likely that many of the early ones will be lazy and uninspiring, and with this push towards standardization, it seems like it's going to be more and more difficult to create individualized education plans and projects, tailored to students' individual needs.

And you know that every student has different needs.

Image credit: origin unknown, retrieved from Vincent Chong.

But I think I can help, at least for high school-level (9-12) classrooms where any reading, writing, or analysis is required. If you can forget about the tests and focus on education, on your students learning, staying interested and engaged, on finding and pursuing their passions, then this is for you. For the past seven months, I've been working for a company called trap!t, growing and developing their science and health sections for quality, breadth, depth, and -- perhaps most importantly -- the truth. (I'll keep on doing that, and writing here, so don't worry about either of those suffering.) But you don't have to restrict yourself to the topics I've chosen, nor to science and health; each user can create their own collection of high-quality content on any topic they choose. For example...

Image credit: screenshot from http://trap.it/.

Maybe you teach history, but even the most up-to-date textbooks don't cover current events. So you tell each student to pick a current event that interests them, and to write a paper on it, citing and evaluating sources. Or you teach biology, or physics, and want your students to write about a recent discovery / breakthrough / controversy. Or maybe you want to teach them how to make a written argument, and so you allow them to choose a politically polarizing topic. All of these (and more) make excellent assignments, and trap!t can be an invaluable resource to a classroom; just put your topic in to the discovery engine and let it go.

What they get out is a collection of relevant articles from websites across the world, chosen from over 100,000 quality sources, on that topic. This works for any news, science, environment, politics, education or health issue, as well as for recent books, theatre productions/performing arts, and media topics. And it gives them this information with a strong visual interface, with quick and easily scannable summaries, a variety of perspectives, and in an extremely organized layout.

Image credit: screenshot from http://trap.it/.

But best of all, it's trainable and personalizable so that each student's experience will be unique. By liking and disliking (with justified reasons!) different articles, students can be at the controls of their news-gathering experience. The ability to perform quick, simple research on any topic, to follow breaking and timely stories, and to train and personalize their own experience is a unique new tool in this age of digital learning, and it couldn't come at a better time. How do I know?

Because I, personally, have gone through the new Common Core State Standards Initiative for literacy, language arts, and for subject-specific reading and writing goals, and have synthesized for you a short version. Below, you can see what the general reading, writing, speaking/listening and language standards are for high school students, as well as (in yellow) what standards trap!t excels at helping students meet, and (in green) for what standards trap!t is a truly exceptional tool.

Image credit: created by me, synthesized from the CCSSI.

This has also been vetted in actual classrooms, so I know it can be a tremendously positive experience! In fact, here's what a public school teacher who used trap!t in her classroom had to say:

I love the way their faces light up when they realize that this isn’t a typical search engine, and that research doesn’t need to be tedious. [...] It’s also fun watching them become meaningfully engaged in something that’s digital. When they’re on the computer, they’re switching back and forth between many different websites, and it’s hard to get them to stay focused. But Trapit “traps” them; it caught their attention, and held it. When a site is sticky, then I know it has great potential.

By providing current, breaking news in a way that no textbooks can, with a variety of hand-checked, quality sources that no single periodical or newspaper can match, and combining it with the students' abilities to personalize it and tailor it to their own particular interests and point-of-view, I am convinced that this is not only a great tool from a student's perspective, but from a teacher's, as well.

Image credit: Mother of Many, taken at Crenshaw High School from the LAUSD, my old teaching grounds.

The ability to incorporate digital learning into a classroom is crucial, but not as crucial as the ability to get a student internally motivated in furthering their own education. The combination of being able to make individualized assignments while simultaneously meeting the new core standards is going to be one of the toughest challenges for all teachers, and trap!t gives everyone a great tool -- maybe even the best tool -- for making it happen. But I can't make this happen on my own; I need your help if we want to improve education under these new standards and keep classrooms from being invaded by micromanagerial administrators and curriculum experts, and particularly from test-preparation companies.

What I need are teachers and educators -- preferably public high school teachers, but any educator, including home-schoolers, is still extremely helpful -- who are brave enough to be willing to give this tool a chance. Would you be willing, during the first couple of months (September or October) of the school year, to give it a try?

Image credit: Suite 101.

I want to help you help your students across all disciplines, improving their reading, writing, and critical thinking skills. How do they evaluate the quality of information in a source? Can they identify bias and perspective? Can they determine what's a fallacious argument, and apply their own reasoning to discriminate between two opposing points of view? Can they justify why articles are good or no good, and what makes a source reliable vs. unreliable? And will you join me on the cutting edge of this education frontier? Leave a comment below and/or email me at -- ethan AT trapit.com -- if you are willing to do any of the following:

Incorporate using trap!t with students in a classroom during the upcoming school year,
Provide any feedback or ideas as to how trap!t could be integrated in a specific classroom,
Be willing to help answer questions that ensure students will have a high-quality educational experience,
Design a lesson plan that can be used in any digital classroom that both incorporates trap!t and the CCSSI,
or, most usefully, be willing to use trap!t in your class and participate in a Proof-of-Concept study, which means filling out a Q&A sheet and possibly having a conversation with me about your experience.

You know how passionate I am about giving everyone the highest-quality educational experience we can, and I'm working to marshal all the resources I have access to in order to help make that happen. If you know of a school, classroom, or teacher where this might help, spread the word and pass it on. Trap!t is free for all users, and if you have any issues, technical, political or otherwise, I'll do everything in my power to help you overcome them.

Education with trap!t isn't the answer to everything, of course; students need more than any one tool, no matter how good it is, by itself. They need great teachers who care about them. They need to make and accomplish things. But they also need to learn how to find, sift through, analyze, think critically about, synthesize and evaluate information, and communicate what they've found effectively. Don't just help them get there; help them blaze their own paths towards that goal!

esiegel Wed, 06/20/2012 - 10:53

Standardization Walks a Fine Line

milhayser — Thu, 24 May 2012 12:45:31 +0000

Standardization Walks a Fine Line

On Denialism Blog, Mark Hoofnagle argues that unless homeschooling is better regulated, it should be banned altogether. He writes "universal primary and secondary education is part of why our country has been so successful." While Rick Santorum can teach his kids that global warming is a hoax and the earth was created in a day, other parents can withhold sexual education, or, in one example, forbid their daughters from getting a GED. Hoofnagle concludes, "for parents to say it's a matter of religious freedom to deny their children education, or a future outside their home, can not be justified." Meanwhile, in an actual classroom or lecture hall, too much regulation can drag the learning experience down. Ethan Siegel writes "the most difficult course to teach is the one where you, the teacher, cannot control what or how you are teaching." He calls such courses unreasonably standardized, and says they result in a shallow understanding of the curriculum, or the omission of important topics. The most important thing, says Siegel, is to have a great teacher. His post was inspired when Chad Orzel originally asked what course is most difficult for students on Uncertain Principles. The answer—well, pick your poison. Classical electromagnetism or literary theory?

milhayser Thu, 05/24/2012 - 08:45

Tags

education

standards

Scientific Color

cagapakis — Wed, 20 Oct 2010 09:49:37 +0000

Scientific Color

We can babble philosophically about whether or not what we call "red" looks the same from another person's eyes, we can compare the adjectives we use to specify colors--is it maraschino red or cayenne?--but when we're talking to our computers, categorizing flowers, designing objects for mass production, branding a company, or establishing a flag's official colors we have to be able to be specific about which exact shade of red we want.

These days we have standard color systems that define colors as specified mixes of red, green, and blue pixels on screen, specific mixtures of pigments in paint, or different levels of cyan, magenta, yellow, and black in print but before we could refer to these numerical standards there had to be a central repository that held the definitions of every color and distributed them as reference color dictionaries.

This Horticultural Colour Chart was just such a color dictionary, prepared by the Royal Horticultural Society in 1938 for use in identifying and matching flower colors. This standard was used for decades in horticulture and in other scientific disciplines that needed to be precise about color, in particular analytical chemistry, where identifying chemicals based on how their colors changed in response to different processes was a common technique. How did this old timey chart find its way into my lab, more than 70 years later?

For that we have to thank my labmate Jake, whose passion for all the old-timey things in life has extended out to the experimental techniques he chooses. Jake is using synthetic biology to make different chemicals in yeast and needs to be able to identify which compound his yeasts are making when different metabolic enzymes are added or taken away. For this there are a lot of methods that can separate chemical compounds and identify them, most based on the principle of chromatography.

If you draw a dot in black ink near the bottom of a piece of paper and place the bottom of the paper into water just below where the dot is, the water will slowly creep up the paper pulling pieces of the ink up with it (try this at home!). Black ink is made up of many different colors mixed together, and each of the colored pigments will travel a different amount up the paper, separating the mixture into its individual colors--hence chromato- meaning color and -graphy meaning writing in Greek. Chromatography can be done even on uncolored compounds, but there has to be some way to visualize how far up the paper (or more often some kind of silica gel) they have travelled, which can be done by shining UV light (think CSI) or by adding reagents that cause a visible color change. Nowadays, chromatography is often done by machines filled with tiny capillary tubes instead of on paper, separating out mixtures based on many different properties, then sending them off to many other sophisticated machines that can determine the identity of the individual components.

Jake, of course, would never want to use such fancy modern equipment when there is an antique option available. Instead he's using the thin-layer chromatography technique where the compound is spotted on the bottom of a layer of silica gel which is then dipped in a solvent, allowing the spot to to travel up the length of the plate and separate out. To visualize the constituents of his chemical mixtures he's using the van urk-Salkowski reagent (PDF) which reacts with many of the compounds he's interested in and turns bright colors depending on what chemical is present. Each of the colors is matched against the official Horticultural Colour Chart, listed in the original paper with the exact page number where it the color can be found.

There are dozens of compounds, each with a very descriptive color matched to it, allowing you to relatively quickly (but not too quickly) identify what is present in your mixture.

I may joke around about Jake's old-timeyness but there is something valuable in being able to do these kinds of procedures with tools that don't cost half a million dollars, something really beautiful about Jake's color chart, and something so fun about thinking about old standards and how new tools can often necessitate new standards to go along with them.

cagapakis Wed, 10/20/2010 - 05:49

Tags

Blueness doth express trueness. -Ben Jonson

I used thin layer chromatography in a CSI type lab class I taught to match the color of pens used in a "crime" It was fun!

Great blog post! Although I do like big and fast machines, I have an appreciation for more "hands-on" stuff. It tends to be elegant, clever, and aesthetically appealing.

There are international standards for just about everything, but not, to my knowledge, color. I would think that primary colors could be defined by their wavelength, so when a red, for example, was specified, everyone of interest would be able to repeat it.

Brett (comment #4) - that's what the CIE was established for. In the 1930's of course, they were more worried about the new fangled technologies of colour photography and printing, but it's the same CIE who's standard "primaries" are used to describe the behaviour of your monitor to your computer via a colour profile.

As for a database of names to spectra (which I assume is what you really mean by "wavelength") that simply wouldn't work for cultural reasons: where we see one colour ("blue") other cultures may see two (Russians see "seeniy" and "golubiy").

I think when considering color for marketing to the majority, red that is red in the eyes of most people is the one you go with.

Biology is Power

cagapakis — Mon, 12 Apr 2010 08:47:24 +0000

Biology is Power

I got a lot of interesting responses to my post about DIYbio and how modeling innovation in biotech on computer hacker culture may lead to a science that is less "democratized" than what is being proposed. My friend Adam pointed me to Jaron Lanier's work criticizing the "open" and "free" culture movements online as both unfair and leading to cultural stagnation. While I don't agree with all of Lanier's arguments about the prospects of an open digital culture, he makes a lot of really important points that resonate with my feelings about the future of science based on the open online model, in particular for synthetic biology. He addresses synthetic biology specifically in his book You Are Not a Gadget, but it is his discussions of the difficulty in building large software even as hardware improves exponentially according to Moore's Law, the lock-in of stultifying software standards, and the economics of the cloud that are particularly interesting and valuable to a discussion about the future of synthetic biology.

On synthetic biology he writes that "wikified" biology, science that breaks down the already loose institutional barriers between individual scientists and between individual species--as genetic sequences are passed between people who put them into different organisms--will limit both biological evolution and technological innovation. He argues that cellular boundaries around early genetic sequences are what drove evolution out of the primordial ooze, and by breaking down the importance of those cellular boundaries, that encapsulation, we lose the locality that drives evolutionary novelty. He says the same of academia:

Academic efforts are usually well encapsulated, for instance. Scientists don't publish until they are ready, but publish they must. So science as it is already practiced is open, but in a punctuated, not continuous, way. The interval of nonopenness--the time before publication--functions like the walls of a cell. It allows a complicated stream of elements to be defined well enough to be explored, tested, and then improved.

Here I agree that academic science is already quite open, although perhaps not open enough in some cases. If you publish a paper that includes genetic constructs that you built, you are required to send that genetic material to anyone from an academic lab that asks to use it for research purposes. I have never had a problem getting something I needed from labs in the synthetic biology community or from anywhere else. The ultra-secretive nature of some labs before publication, however, can certainly be detrimental. I have friends who aren't allowed to present their work at department lab meetings, for fear of being scooped by colleagues down the hall. This overprotective, fearful environment holds back the students who can't get any outside feedback on their work, and can hold back genuinely collaborative scientific progress.

At the same time I don't want to build off of work that hasn't been vetted or proven in some way (which doesn't necessarily have to be publication). A totally open repository of genetic parts, as it basically exists now in the form of the synthetic biology Parts Registry, therefore can have a lot of problems. The registry has countless parts that are essentially nonfunctional, but you can only tell after considerable time wasted searching for a part, finding and getting it, and then sequencing, testing, and verifying part functions. This work does improve the quality of the registry, "wikifying" biological data collection by outsourcing quality control to unpaid users, but we still won't necessarily approach the quality of parts made and maintained by individual scientists. By divorcing the part from its original context, the lab or scientist who built and tested it, we end up losing some of the value of the work that went into producing it, and we lose some of the ability for genuine collaboration. DNA (and even DNA plus detailed data characterizing its function in a specific lab) alone isn't necessarily enough for a creative and innovative project in synthetic biology.

Completely abstracting the functions of genetic material, environmental contexts, and species boundaries is dangerous as well, and I don't agree with Lanier that this is the future we're headed towards, if only because this is just not how biology works. Biology is powerful exactly because it doesn't work like computers. There is no standard way of doing anything. Genetic pieces are passed between bacterial cells (or even between food and the bacteria in our guts) but context and evolution within individual cells and populations matter for life. Interactions between genetic material and the cellular environment, and each cell with its ecological and "social" context creates the adaptable, evolvable, beautiful diversity we seen in the natural world.

By defining arbitrary standards early on in our understanding of how these genetic elements work in their rich biological contexts, and early in our ability to engineer novel functions, we lose sight of much of the complexity of biology and get stuck in what could become difficult and useless technological cycles. Indeed, the BioBrick standard as it was first defined a decade ago does not allow for proteins to be fused to one another in-frame, and uses restriction enzymes that are rare and expensive. BioBrick cloning is wonderfully convenient for certain applications, but enforcing a standard that doesn't take into account the realities of how biological parts are made and used in different contexts and for different projects is inefficient, which is why there are almost as many "standards" for pseudo-BioBrick cloning are there are labs in synthetic biology today.

Lanier warns against any movement to enforce a specific way of doing things, any locking in of standardized forms in technology development. By defining one industry standard, we may open up an easier way to make things at industrial scale, but we also lose diversity in how we think about and use whatever we're standardizing, making true innovation more difficult. He argues that this is particularly true in software development, where standards locked in during the early days of computing are difficult to throw off, particularly when designing and maintaining large-scale software packages and operating systems. Small programs are easy to make in new paradigms, but large programs are slow to change and extremely costly to manage and innovate, despite leaps and bounds in the speed of computer hardware.

The same can be said for synthetic biology, where small genetic networks with innovative but limited novel behaviors can be routinely and relatively easily made, but large-scale combinations of smaller networks or synthetic pathways with more than a dozen genetic components remain elusive. Many commentators on biological technologies claim that they are progressing even faster than Moore's Law, with the prices of gene sequencing and synthesis dropping precipitously every year. But this price drop does not necessarily equate to a similarly exponential ability to understand gene sequences or create complex new biological behaviors. Synthetic biology will not necessarily follow Moore's Law because human scientific creativity and evolutionary change are fundamentally different from how transistors work.

Creativity in synthetic biology designs, in novel syntheses of biological knowledge, bio-technical expertise, and engineering concepts are done by groups of individual hard-working people. These people and their work should be valued as something special, something that can't be done by simply increasing the number of base pairs of DNA being synthesized. So too should we value the power of evolved biological systems as something different from the designed electronic systems that inhabit our world today. What do we gain by trying to fit biology into the structures that have become locked into computer engineering? What would we gain if instead we created a new kind of engineering, one that centered on learning more from and about the biological world?

cagapakis Mon, 04/12/2010 - 04:47

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May All Your Standards Be Simple and Evolvable

jwilbanks — Wed, 05 Aug 2009 10:05:36 +0000

May All Your Standards Be Simple and Evolvable

I was in a roundtable yesterday talking about Health IT with a bunch of very smart people in the bay area. It was sort of a briefing of ourselves and others about the real issues underpinning what it would take to generate real disruptive innovation in health technology and health costs. The vast majority of the conversation centered on payment reform, which is outside my ambit.

But we did spend some time talking about health data standards, and the problem of getting standards that are so geared to the existing market-dominant companies that they actually froze out new market entrants. My contribution in all this was pretty small, and to me seemed obvious. The standard that works best tends to be the least powerful solution to the problem, especially if it's an openly released solution. This can be counterintuitive - why wouldn't we want the most powerful one? - but it's been proven again and again.

In technology, standards propagate like kudzu. Most of them go nowhere, representing an enormous sunk cost of time and money. And that's because most of them are way too complex. The more powerful they are, the more brittle they are, the more expensive they are to implement, and the more they restrict the re-use of the system.

Tim Berners-Lee calls this the Rule of Least Power, and it's one of the most important lessons I learned working at the W3C. There's a simple reason for this - the more basic the markup of the content, the easier it is to write applications that process the content.

Thus TCP/IP, created simply to move bits between computers, begat a variety of new protocols like FTP, Gopher, Finger, many other protocols that layered atop the basic bits standard. Complexity from simplicity. Attempting to embed file transfer into the bits protocol would have made this whole process a lot harder.

And of course HTML/HTTP begat the entire Web, all the way to YouTube and Amazon and everything else. Writing video codes into HMTL wouldn't have worked nearly as well as writing a standard that was simple enough to be extended by smart users coming along ten years later.

To the rule of least power we can add the rule of openness - the standards process should be as open as is feasible, and the standards themselves must be open. Users have to be able to read a standard, and to have the freedom to implement the standard, to be able to innovate atop it with new systems.

There's a lesson here. Gathering the relevant powers that be to figure out a standard is an important task. The W3C, the IETF, the OMG (that's Object Management Group, not the internet acrony, for you younguns), and what feels like every different data discipline on earth does standards this way.

But there's a lot of fingers on the scale for most of this work. That's because data standards tend to get created by well-meaning, overworked, and underpaid people who are making a real sacrifice to work on the standards. And those people are going to depend on a lot of in-kind work from the interested parties, who are always going to try to bend the standards to their will.

That can go multiple ways. The paranoid conclusion is that the for-profits involved will try to use the standard to increase stock prices, which is why smart standards efforts include patent policies to prevent enclosure. But there's a bigger problem out there, which is much less visible but much more of a force in the creation of standards that don't get used, or that don't do what we want them to do.

It's what I call the problem of standards completeness. Experts in the field, interested parties, impassioned volunteers - these people by their nature tend to want to make the standard they build as complete as possible. They want to cover the most ground with the standard. They understand the space so well that they want to build standards that address vast swaths of work.

But that violates the Rule of Least Power. And as we move towards a web of data, even a web of patient data, we'll do well to make our standards by solving real problems with the simplest possible solutions, then releasing those solutions for others to build on.

The impact of the simple evolvable standard in short term is probably less than a more complete, perfect standard. Certainly TCP/IP didn't scare the systems integrators at its inception. But it's the power of the crowd that can build on the open standard that breaks open the market. Thanks to simple standards, two talented programmers can start a company in a garage that changes the world.

If we're going to bring that level of innovation potential to health IT, we need to keep the lessons of the simple standard in mind. Because right now, if you're a bright young entrepreneur, you don't get into health IT. And the lack of not just standards, but the right kinds of standards, is the first barrier we have to knock down to change that reality.

jwilbanks Wed, 08/05/2009 - 06:05

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Standards are a great thing...frankly as a programmer I'm surprised why there is such a huge lack of standards outside of a few niches.

Standards make everything so much easier, instead of having to think through what the other person is trying to do, you get an instant understand based on a few little snippets.
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