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Designing the Future of Synthetic Biology

I'm a little late in posting about the recent work of Tuur Van Balen, a Belgian designer who uses art and design to explore the boundaries between people and technology. His work has explored synthetic biology and biotechnology for years, and I first was introduced to his work through news of his Urban Biogeography project. A recent focus in synthetic biology has been the design of simple biosensors, strains of bacteria or yeast that can sense an environmental pollutant and produce a measurable output such as color change. Thanks to the work of several very creative iGEM teams, the Registry…

The Game of Life, On Life

Light interacts with and controls biological systems in diverse and fascinating ways. Our eyes are made up of thousands of cells that respond to light, sending signals to our brain as light in different colors and shapes moves across them. Photosynthetic cells are full of receptors that can sense and respond to many wavelengths of light, allowing cells to absorb light for photosynthesis, but also to move towards areas of more sunlight and know when the seasons are changing. Synthetic biology takes these light-responsive systems as parts that can be recombined, shuffled and integrated into…

Part of this nutritious nano-breakfast

The Woodrow Wilson Center released a report on engineered nanomaterials used for food applications. The aren't common (we think), but there are a few technologies that are making their way to the market. One for instance would have a nanofilm that has anti-microbial properties. Of course, it may also leach into your food. Yum! (Okay, it probably wouldn't taste any different but untested films don't sit that well with me.) One of the things I love about these type of reports on emerging threats/risks is how they put a bunch of options on the table for industry and regulators as if they are all…

More on race and IQ

I was surprised by the response to my brief post on the question of whether group (race or gender) differences in intelligence are a valid topic for scientific investigation: not only because of the volume of comments, but also because the ensuing debate was largely civil and on-topic. The post was sparked off by two conflicting essays in the most recent issue of Nature, one by Steven Rose opposing research into such differences, and another by Ceci and Williams arguing that sealing off certain lines of enquiry - however contentious - is dangerous and unscientific. There's now more on this…

A More Reality-Based Poll

Remember that strikingly inept poll analysis about the Tea Party movement from The New York Times last month? Well, the new Washington Post-ABC News poll addresses the same topic, and the Post's analysis seems to actually be rooted in reality: The conservative "tea party" movement appeals almost exclusively to supporters of the Republican Party, bolstering the view that the tea party divides the GOP even as it has energized its base. That conclusion, backed by numbers from a new Washington Post-ABC News poll, also suggests that the tea party may have little room for growth. Most Americans --…

This Is a Very Dumb Poll

Actually, I should say that this is a very dumb analysis of a poll. The New York Times is really promoting its new NYT/CBS poll right now; as I write this, the top headline on the Times' homepage reads "Poll Finds Tea Party Backers Wealthier and More Educated." When I first saw that headline and read the email news alert that the Times sent out, I did agree that these appeared to be interesting and surprising findings. And, as I read the article, my interest--and then skepticism--continued to grow. According to the article, these "Tea Party supporters" are "wealthier and more well-educated…

Chad Orzel on Science Blogging

Chad Orzel, of Uncertain Principles, has a nice article today in Inside Higher Ed about the value of science blogging, both in his own career and in the scientific process in general. This is a view that I of course agree with and think is important, and Chad brings a unique perspective on the issue. Go check out his article, but here's a taste: As essential as this [communication] step is, it is in many ways the weakest link in the scientific process today. While there are more scientific papers published today than ever before, a combination of technical sophistication and scientific…

Bush Administration Muzzled Surgeon General

Add one more to the list. Yesterday, former Surgeon General Richard H. Carmona testified before congress that he was subjected to extensive and systematic political interference in his work by the Bush Administration. From Gardiner Harris of The New York Times: Former Surgeon General Richard H. Carmona told a Congressional panel Tuesday that top Bush administration officials repeatedly tried to weaken or suppress important public health reports because of political considerations. The administration, Dr. Carmona said, would not allow him to speak or issue reports about stem cells, emergency…

The Scientific Activist Ranked #5 in Science Blogging

This Thursday's issue of Nature ranks the top 50 science blogs on the internet and, somewhat surprisingly, The Scientific Activist lands in the #5 spot. The top 5, with their Technorati ranks in parentheses, are as follows: Pharyngula (179) The Panda's Thumb (1,647) RealClimate (1,884) Cosmic Variance (2,174) The Scientific Activist (3,429) You can guess which blog is the odd one out.... Still it's quite an honor to be placed among such prestigious company. Blogs considered in the rankings "as far as can be established, are written by working scientists and are about science (not their…

Texting As Killer, As Savior

Source. Second place winning design, from Kayla Rivera at Valencia CC, Wiley Student Advertising Design Challenge: Texting & Driving Don't Mix Any driver knows the dangers of texting. Yet this practice has become commonplace. Dr. Robin Landa recently challenged students to design an ad campaign about the dangers of texting and driving; the design above is one of my favorites. But texting can also save lives, even for the illiterate. Let me explain. There are emerging open source technologies, based on network science and crowd sourcing that promise to transform how we respond to…

Science conspires to make me feel really old now

Virginia Hughes tells us about techniques to look inside the zebrafish brain. The gang at HHMI are using two photon imaging and clever image analysis to get very clear, sharp images of fluorescent neurons. Oy, that's pretty. This old codger did some of that stuff, many years ago, but you know what we had to do? Point injections of tracer dyes, followed by serial sectioning and reconstruction. Early on we use injections of horseradish peroxidase into, for instance, the muscle, so that neurons in transit through the lesion site would pick up the enzyme…and then we'd have to fix and process…

Implanted bionic eye allows the blind to see again

Researchers  at the Institute for Ophthalmic Research at the University of Tübingen have restored vision in blind patients using tiny retinal implants embedded in the eye. Nine patients were chosen because they had all suffered hereditary diseases where the retina had degenerated to the point of blindness, but left the remainder of the visual pathway intact. Eight of the nine could still detect some light, although could not locate its source. One was completely blind. Each was implanted with a tiny 3x3mm film square containing 1,500 photodiodes which send out electrical signals when they…

Neutral Markers and Conservation Genetics

I have mentioned before that at one point in my life I wanted to study conservation genetics. This field can be thought of a subdiscipline of molecular ecology -- wherein researchers use molecular markers to test hypotheses regarding demography in their population of interest. Jacob at Salamander Candy has a post on the usefulness of neutral markers in conservation. Here's a taste: The problem is, a growing body of evidence suggests that patterns of variation and divergence in adaptive traits are not well reflected by neutral markers (refs 1-8). In the hypothetical species mentioned above, a…

Go away, cold fusion

A guy named Andrea Rossi has been promoting this device call the E-Cat that produces huge amounts of energy by nuclear fusion: specifically, that it fuses hydrogen and nickel to produce copper and energy. And now there is a claim that this amazing result has been verified, in a remarkably gushing and credulous review. I am not a physicist, not even close. I am at best a moderately well-read layman. I also understand the general principles of fusion -- it's how stars work, it's how heavier elements have been built up over the history of the universe from lighter ones. I might be willing to…

More Bill Foster

If you follow the creationist news stories from around the country, you get a lot of the same exact thing over and over again, and it is hard to identify the novel or persistent elements in the flow of information. But increasingly it is clear that Bill Foster of St. Petersburg Florida is somewhat novel and starting to look persistent. Foster was a relatively typical family values fiscal conservative kind of city council member. Term limits have forced him out of his job, which is too bad because maybe he would have just continued along that course minding his own business and not doing…

How not to teach biology

Almost two weeks ago, I wrote about that creationist teacher who was fired in Sisters, Oregon — Kris Helphinstine had been showing his freshman biology class some PowerPoint presentations designed to cast doubt on biology, rather than to inform the students about the facts and evidence. Now a Bend newspaper has given a few more details of the grounds for firing, and most entertaining of all, has put up copies of the PowerPoint presentations! Aficionados of both bad creationism and bad PowerPoint will savor these. Both are afflicted with ugly and inconsistent layout, and it's always reassuring…

Leslie Nielsen is Dead

And I don't refer here to his humor, his lifestyle, or even his hair. Leslie Nielsen never produced an original piece of humor in his life. All of his jokes were stolen from my friend Karl and me, from stuff we did back in middle school. But, I do have to give Nielsen credit for getting that garbage produced so others could enjoy it. Nielsen, of course, is famous for his Naked Gun series, starring OJ. Simpson. Which just goes to show you that his casting director was not named Claire Voyant. But I have to say one of my favorite productions of his was Wrongfully Accused, written and/or…

I just got this note from my close personal friend Joe Biden

This is quite serious. Better have a look. Greg -- Our opponents think they have this election in the bank. While you all are reaching out and talking to 7 million voters one on one, they're getting $7 million checks from billionaires and special interests to fund attack ads. That is all you need to know about the choice in this election. We're in a battle for the future of this county -- a battle between corporate special interests and hard-working Americans. And if we want that future to be written by us -- not by a handful of anonymous billionaires -- I need you to do all you can over…

Software Needed: Enhanced web search

Google is great, and yes, I know all those tricks that make it greater. But I still want to use REGEX in some cases. So, I figured out a way to do that, in theory, all I need now is the code... Briefly, the software I need, which I shall call googlereg for now, feeds the harvest from a google search through a regex filter and produces a list of hits. There are three streams of data that could be fed through the regex filter: The basic output of the Google search (what you see as results on a Google search page), the actual pages found by the Google search, and the entire site at the domain…

Americans Who Don't Identify with a Religion No Longer a Fringe Group

You've certainly heard of the ARIS 2008 survey from Trinity College. One of the more interesting aspects of the survey is the demonstration that there is a sex difference in patterns of religions identification. Below I give some links where this has been discussed, but I want to note that in many discussions one of the first things people say ... quite reasonably ... is that the differences seem small and potentially well within the normal sampling error of a survey. The reason people think that is because they are accustom to survey data in relation to political polling where sample error…

Should we be happy about this?

So today we learn that Rep. Pete Stark admits to being godless. There is only one member of Congress who is on record as not holding a god-belief. Rep. Pete Stark (D-Calif.), a senior member of the powerful House Ways and Means Committee, Chair of the Health Subcommittee, and member of Congress since 1973, acknowledged his nontheism in response to an inquiry by the Secular Coalition for America. Although the Constitution prohibits religious tests for public office, the Coalition's research reveals that Rep. Stark is the first open nontheist in the history of the Congress. Recent polls show…

From Fit to Fat to Fit: Lenora

When working with a personal trainer, the first thing you have to do is to calibrate. Then, if the trainer does not crank it up to a higher level, she's probably not worth her fee. Continued .. By this time it had become clear that I was joining this gym with a life membership. I'd lay out a few hundred bucks and be a member for about $50 a year forever after. That may seem like a lot and these sorts of things are not always good deals. But part of my motivation for choosing the super-membership was to put the money down up front so I would be motivated to stick with the program for a…

Reaching Agreement On The Public Domain For Science

Photo outside the Panton Arms pub in Cambridge, UK, licensed to the public under Creative Commons Attribution-ShareAlike by jwyg (Jonathan Gray). Today marked the public announcement of a set of principles on how to treat data, from a legal context, in the sciences. Called the Panton Principles, they were negotiated over the summer between myself, Rufus Pollock, Cameron Neylon, and Peter Murray-Rust. If you're too busy to read them directly, here's the gist: publicly funded science data should be in the public domain, full stop. If you know me and my work, this is nothing new. We have been…

Don't eat the, um, weeds

So one summer evening in 2008, a Maryland family sits down to a dinner of home-made beef stew flavored with mint from the backyard and, oh yeah, some other plant growing in the leafy borders by the fence. It looks like this:An hour after dinner, another relative shows up to find the members of the dinner party dazed and incoherent, some giggling uncontrollably, some staggering with hallucinations. Then they start to throw up. The dismayed relative calls 911; by the time all six of the stew-eaters arrive at the emergency room, two are unconscious. All are struggling for breath, their heart-…

Assessing libraries and open access

Much is murky in open access, but this at least is clear: academic libraries have committed different amounts of money and staff toward an open-access future, from a flat zero up to hundreds of thousands of dollars' worth. It's the zeroes and near-zeroes that concern me (why, hello there, Yale, and hello again, Yale), though I also believe quite strongly that libraries that have made significant investments of money, staff, and/or political capital should be recognized and praised for it. The difficulty here is that it isn't just the scale of open-access investment that varies. The nature of…

Revenge of the Cats!

For all of the cat lovers out there, this entry is for you! You may recall the recent post on how dogs are smarter than cats. Admittedly, I love our little feline friends as well although my cat is certainly no Einstein...more like Garfield... Based on the ratio of brain to body size size alone, cats have larger brains than dogs, but now we may also know how so many mice and birds outsmart our furry little friends: Many cat owners will tell you stories of their pets being able to open windows and doors, especially if that door leads to their food or to cozy blankets and towels in a cabinet…

Speaking of dogs...Social mammals have bigger brains than solitary mammals

You know that age-old argument dog people and cat people can't ever seem to agree on? The one about whether dogs or cats are smarter? Well, we may finally have an answer! (Spoiler alert: I'm pretty stoked, as a dog person.) According to a new study by Oxford University, researchers have discovered extreme differences in how the brains of different mammals have evolved over time. The study notes there is a link between the level of social interaction of mammals and the size of their brain relative to their body size. Lead author Dr. Susanne Shultz said, "Cooperation and coordination for…

Administration Testimony: One + One Still = Three

Bill Brennan, acting director of the Climate Change Science Program, was spinning the White House's treatment of scientists at this morning's Senate Commerce Committee Hearing on Climate Change Research and Scientific Integrity. "The administration takes the concerns of its scientists very seriously, and each department and agency is reviewing -- and modifying, if necessary -- its policies to ensure government scientists do not face censorship on any scientific matter," Brennan said. Source (subscription required) Brennan's written testimony is available here (PDF). It does not address any…

HuffPo---the Great Attractor of idiocy

The shamans of stupidity over at Huffington Post recently wrote a completely insane article whining about how unfair it is that science keeps winning. Orac did his usual best to illustrate how bizarre these folks are (and how wrong). But I also love the comments to the piece. They were an interesting mix of jaws hitting the floor in shock at the inanity, and "crank magnetism", as other idiots piled on science, which despite its successes must somehow bow to an alternative magical belief system. This comment was the best (broken down for your convenience): Having been trained in the…

Primary Care Challenge, Part II

Some time ago I issued a naturopath challenge in which I invited naturopaths to analyse a typical primary care problem. Today, I'd like to issue a broader challenge. With health care reform in the works, it would be wise to look north (or in my case, south) to our Canadian neighbo(u)rs, but not for the reason you think. Assuming we are able to extend health insurance coverage to millions of more Americans, we will need primary care practitioners (PCPs) who can care for these new medical consumers. In Canada, legislation to deal with a shortage of PCPs by giving modest new powers to other…

Thank you for desecrating my grave

I try not to get involved over at PZ's place, but his post today just sucked me right in. To catch you up, in a case before the Supreme Court, Justice Scalia argued that a cross can actually be a secular symbol used to honor the dead. "I assume it [the cross] is erected in honor of all of the war dead. The cross is the most common symbol of ... of ... of the resting place of the dead." Um, Tony? My cemetery doesn't have a single cross. In fact, none of my relatives is buried at a cemetery with crosses in it. What's up with that? I must be some sort of freak. If these cross things are…

King at SCSU Scholars botched criticism of the Lancet Study

King at SCSU Scholars has updated his post attacking the Lancet study with a response to my post. He admits error on one point, but on the rest he has the nerve to accuse me of bringing biases rather than facts to the debate. To see who is bringing facts and who is bringing biases let's look at one of the points he contests: King originally claimed (my emphasis): They also chose both to change their list of randomly sampled areas so they didn't have to drive as much; this meant they stayed close to Baghdad and the Sunni triangle, probably oversampling high-…

Brignell, again

John Brignell has an odd response (scroll down to "Hit Parade") to some of my criticism. He doesn't link, or dare to even mention my name, so it's probably rather mystifying to his readers what he is responding to. Brignell goes on the Michael Fumento road, boasting about how the 2,488 hits he got on Monday vastly exceeds the 10 hits he got from me. Trouble is, he got those hits from a link in a comment in a two-day old post, so it's hardly a meaningful comparison. For what it's worth, his web counter shows 230k visits in five years, which is less than what I have…

Lott and Bellesiles, together again

John Lott and Michael Bellesiles are both mentioned in a new book, Historians in Trouble by Jon Wiener. Wiener argues that the reason why Lott still has his job but Bellesiles doesn't is power: The answer briefly is power---especially power wielded by groups outside the history profession. Historians targeted by powerful outside groups can face intense media scrutiny and severe sanctions for transgressions, while historians connected to powerful outside groups can be shielded from the media spotlight as well as from the consequences of malfeasance;…

Blowing up your brain with ubiquitin

I just came back from a Wade Harper talk where we were subjected to an obscene amount of ubiquitin biology and even more ubiquitin nomenclature. This blasting of your brain with technical terms is becoming more and more common with big Biology talks. But to be honest Prof Harper gave a good talk about an RNAi screen to identify new cell cycle regulators. He's a pretty smart guy (although he needs to take a little more caffeine). A major focus of the talk was on the modulation of Ubiquitination by E3s. Ubiquitin as you know, is that small peptide that gets conjugated to proteins that are…

ARCHIVE: 25 Things You Should Know About the Deep Sea: #11 A Variety of Organisms Inhabit the Deep

I personally love doing this series because it allows me to explore and solidify a variety of ideas I mull over on daily basis. Previously in this series I have discussed the difficulty of sampling, the variety of habitats, linkages to the oceans surface, body size, conservation, undiscovered species, biodiversity, unexplored regions, the large spatial extent, and the very definition of the deep sea. For #11 in the series I will discuss who the movers and shakers are in deep-sea environments going all the way from fish to bacteria. We typically think of the deep-sea benthos (seafloor habitats…

ARCHIVE: 25 Things You Should Know About the Deep Sea: #6 The Deep Sea Needs is Under Threat and Needs Protection

Unlike other marine environments, the threats to the deep sea and it species are relatively new. Only recently has it been both economically and technologically feasible to exploit this environment. This means we have the unique opportunity to instigate conservation policy at the beginning, before drastic damage has been done, instead of trying to restore damaged habitats. Although action needs to be quick. Reuters reports this... Deep-sea fishing trawlers are bulldozing 4,500 year-old cold water coral reefs off western Ireland, a British marine biologist said on Monday. Dr Jason Hall-…

Ask & You Shall Receive

When I sent the original email to Rick enquiring about obtaining one of these, I thought I would have to send him multiple emails. Apparently, Rick is bit of push over because I received one in less than week of the email. As an exrucker myself (second and scrumhalf), I was obsessed with these jerseys from Rick's initial post. What better than a rugby jersey with sea turtle on it that represents the commitment of locals, rugby players, WWF, and the Coral Reef Alliance to conserve/protect a marine corridor in Fiji. I have been wearing mine with pride and maybe someday I will take it off to…

Wild Turkey Nest

What could've been the national symbol of the USA if Ben Franklin had his way, the wild turkey (meleagris gallopavo) is having a bit of a resurgence as of late. In our neck of the woods (central New York state) they have become a common sight and small bands of them are often seen crossing the country roads during the day. But we had a lovely surprise these past few weeks. Recently, I had begun clearing some trails through the woods behind our house. This project included building three bridges across a couple of small creeks (the construction of which may be the topic of a future blog post…

Name That Orb Weaver!

Since Labor Day weekend has passed, it's time to put away those white shoes and to take note of the late summer orb weaver spiders. Orb Weaver spiders are members of the Araneidae family. These include the ubiquitous yellow and black garden spider and familiar genera such as Mangora spp. and Araneus spp. When my kids were little, they referred to the more common Araneidae as "Charlottes" after E.B. White's Charlotte's Web. Chimp Refuge field observers, Dawn & Bobby, recently shared a photo of an Araneidae arachnid that has set up her shop behind their house: This is a pretty spider to…

Dragons. And Unicorns. And God.

People don't realize how insane the literal interpretation of the Bible can get. There is no room for ambiguity or error in the book of Genesis, so when God tells Noah to put at least a pair of every living thing on the big boat, he didn't offer any exceptions — therefore, every living thing had a representative aboard. And of every living thing of all flesh, two of every sort shalt thou bring into the ark, to keep them alive with thee; they shall be male and female. Of fowls after their kind, and of cattle after their kind, of every creeping thing of the earth after his kind, two of every…

Not even wrong, again

Creationists say the weirdest things. Every once in a while, someone sends me a creationist quote that reveals exactly how clueless and ignorant these guys are, because they start lecturing people on biology, a subject they clearly know nothing about. We've got a local boy named Brock Lee in Owatonna who is fond of writing amazing letters to the newspapers — I've mentioned him before — and here's a remarkable example of creationist inanity. Look at the conclusions he draws from the biological species concept: What is a species? The evolutionary answer seems simple enough: a species is an…

Sokaling integrative medicine

Funny business, this. Professor John McLachlan corresponded with the organizers of an international conference on integrative medicine, proposing some very peculiar ideas that he wanted to present. They were…intrigued. They asked him to flesh out his concepts in a formal abstract so that they could evaluate whether they were worthy of inclusion in their prestigious meeting, so he did, and here it is. Abstract Intensive study of the development of early human embryos indicates that there is a reflexology style homunculus represented in the human body, over the area of the buttocks. This…

Smithsonian announces that art can't be controversial

Bill Donohue is on a roll. First he bravely put up a billboard that reassures everyone that Jesus was real, which is no problem, as far as I'm concerned; it's not true, but he isn't interfering with other people's right to express themselves. But now he has really done it: he has successfully pressured the National Portrait Gallery to remove an art work that Donohue did not like. That is obstructing the right of free expression, and is deplorable. The work in question was a video about the pain of AIDS victims in Mexico, and references the Catholicism of that country by showing a crucifix…

Defining Science

Misogynistic authoritarian Vox Day requests a definition of science. His commenter suggests: Science - sci·ence (sī'əns) n. - The organized attempt to disprove the existence of God so we can do whatever we want without feeling bad about it. Anyone involved in the arguments over creationism will recognize this sentiment that science is about morality and theology, but it really and truly isn't. Dr. Myers offers a much better tripartite definition. He puts science-as-encyclopedia first, which I think is unfortunate. People tend to think of science as a collection of facts, which ignores the…

Churning up bad arguments about job churn

Deputy Secretary of the Treasury Robert M. Kimmitt tries to explain Why Job Churn Is Good: More than 55 million Americans, or four out of every 10 workers, left their jobs in 2005. And this is good news, because there were over 57 million new hires that same year. Those workers spent an average of 15 weeks seeking their new job. That means that they spent 15 weeks without insurance, not to mention a salary. One hopes that their new employer offers insurance, and that the insurer doesn't have bizarre rules about preexisting conditions. It's also worth remembering that the United States is…

Armistice Day

Woodrow Wilson's last speech to the nation, delivered on November 10, 1923. The anniversary of Armistice Day should stir us to great exaltation of spirit because of the proud recollection that it was our day, a day above those early days of that never-to-be-forgotten November which lifted the world to the high levels of vision and achievement upon which the great war for democracy and right was fought and won; although the stimulating memories of that happy time of triumph are forever marred and embittered for us by the shameful fact that when the victory was won-won, be it remembered-chiefly…

Sebelius still strong in latest poll

Election Poll 2006: Kansas Governor: Now that Republican State Senator Jim Barnett has won the August 1 primary, Governor Kathleen Sebelius leads her challenger 48% to 37%, a drop from seventeen percentage points to eleven. …the incumbent continues to enjoy high favorables and job ratings, with 35% viewing her "very favorably," only 11% "very unfavorably." Thirty-two percent (32%) "strongly approve" of her performance as Governor. Barnett is viewed very favorably by only 19%, and although fewer (9%) see him very unfavorably than see the Governor that way, he's still an unknown to 18%. By…

Who needs history? [I do!]

If I believed what my high school teachers taught me, from them I received the distilled wisdom of the ages. The knowledge was compartmentalized and packaged; there was no need for history in science class, at least outside of snarky little asides like how foolish Lamarck must have been to think evolution involved the inheritance of acquired characteristics. Everything involved the bare minimum, disparate notions offered up for consumption and near-immediate regurgitation, but very little understanding. There was no context, no narrative, and no sense. There is very little I remember from my…

PZ's Mutating Genre Meme, pt. 2

Yesterday I put up v. 1 of PZ's patented Mutating Genre Meme that had been passed on from The Primate Diaries, but today I'll be passing on The Anterior Commissure version. In case anyone hasn't seen them, here are the rules again; There are a set of questions below that are all of the form, "The best [subgenre] [medium] in [genre] is...". Copy the questions, and before answering them, you may modify them in a limited way, carrying out no more than two of these operations: * You can leave them exactly as is. * You can delete any one question. * You can mutate either the genre, medium, or…