Vicky was googling local trails Saturday morning, when she started getting the following screen for each link she clicked:

Google’s Malware Warning

This is the screen Google provides when it detects a website as having maleware, which is a great service, but why was every link coming up malicious? I ran some searches myself. The White House and Wikipedia were showing up bad:

WhiteHouse.gov has Malware

Microsoft was showing up bad, which kinda makes sense if you consider Vista:

Microsoft.com has Malware

Even this blog was suspect!

ideonexus.com has Malware

But kittens??? Why kittens??? What did kittens every do to anyone???

Kitten Sites have Malware

It was obviously just a bug in Google’s application, and cleared up in fifteen minutes, but it was a fun moment of chaos, as Google blocked access to every link it provided. When something like this happens to a major godlike web-presence like Google, it’s worth documenting.

You think you’re doing some damage? Two plus Two is *shzzzt* ten… IN BASE FOUR, I’M FINE!!! Ha! Ha! Ha! – GLaDOS

Infinite Portals

I had seen previews for this game online, and thought it looked pretty spiffy, but it wasn’t until I dabbled with the flash version that I was really intrigued (plus I found it was priced at $10, a bargain). I haven’t played a puzzle game since the original Tomb Raider, back in 1996, and this one totally sucked me in.

The Computer is Watching

You wake up in a glass cell. A computer, GLaDOS, begins taking you through a series of potentially fatal obstacle courses. “Cake and grief counseling will be available at the conclusion of the test,” she promises.

You Play Chell, an Orphan of “Bring Your Daughter to Work Day” and Equipped with Heel Springs to Survive Falls This Screenshot was captured by Opening two portals next to each other and looking through

To help you navigate each level, you are given an Aperture Gun, which you may shoot into walls, ceilings, and floors to produce portals. You can open portals to cross chasms or drop weights on military drones. Open a portal in the ceiling above you, open one underneath your feet, and you can fall forever, gaining velocity as you do. With this strategy, you can fling yourself across great distances.

Portal Physics Velocity is Maintained, but Direction Changes Credit: Pbroks13 at Wikimedia

The levels are difficult enough to make the game challenging, but easy enough to make you feel smart. The basic game isn’t very long, I beat it in about six hours, but a collection of bonus advanced stages have driven me batty since then.

The Cake is a Lie!!!

Any game is only as good as the story it tells, and in Portal’s case, a delightfully twisted computer provides a witty and insane narration for the action, which itself has you thinking in strange ways. I found myself chuckling throughout the many levels at GLaDOS’ silliness, and even went and downloaded the song Still Alive from the soundtrack, sung by the GLaDOS (voiced by Ellen McLain).

I highly recommend this relaxing, mentally challenging game. It’s a rare treat in a world of first-person-shooters to find something so original and well written. Plus, at $10, you have less than the cost of a DVD at Wal-Mart to risk on what might provide 6-10 hours of fun.

This video of an extremely advanced bonus level of some sort demonstrates Portal’s craziness (The player has disabled the drones somehow in this demo):

Note: Portal is the “spiritual successor” of a freeware game, Narbacular Drop, which is also a puzzle game with portals, however it is a much simpler one.

Another Note: After beating Portal, it’s fun to read the Wikipedia entry for it, as the history behind the game’s story just gets more and more twisted.

Photosynthetic Electron Transport Chain (Powered by the Sun) Credit: Tameeria at the wikipedia

So the recent news of researchers synthesizing RNA that can replicate indefinitely kind of stuck with me, particularly the word indefinitely. This isn’t perpetual motion, because the molecule only works so long as it has a supply of molecules to manipulate.

But what if you had a molecule, probably a protein, that interacted with molecules of the same type, bending to modify the structure of the other molecule, and then springing back into its original shape. The next molecule in the chain manipulates the next, and so on, until the chain loops back to the original molecule and the process starts all over again. Wouldn’t that be perpetual motion, this molecular machine running off an infinite transfer of a single electron?

In fact, couldn’t we harness the power of atoms themselves, their random movements, perpetually? Dr. Richard Feynman conceived a device precisely to harness and put this energy to work with his Brownian ratchet:

Feynman’s Brownian Ratchet Credit: Bdkoivis at the wikipedia

It’s important to remember that this device is built on a nano-scale. A proper drawing would render it as a molecular construct. The red dots represent hydrogen atoms, actual-size. These are bouncing all over the place through Brownian Motion. All atoms vibrate, even those sequestered in crystals.

T1 represents an itsy-bitsy turbine. As the hydrogen gas atoms bounce into it, they transfer their kinetic energy into it, turning it and the axle leading to T2. The molecular prawl on the molecular gear in T2 makes it so the gear can only turn one way.

With this set up, the turbine will slowly turn around in one direction as the hydrogen atoms bump into its blades, producing work that can be used to wind the string around the axel and lift “m”.

Perpetual Motion, right?

We know it can’t be, despite the fact that someone has tried to patent the idea, so the question becomes, Why not?

Because the ratchet is small enough to be subject to brownian motion itself. In order for it to be small enough to work, it also has to be small enough to shake in such a way that the prawl will slip, allowing the turbine to spin both ways.

One way to overcome the brownian motion is to cool the mechanism to the point where the atoms are no longer vibrating as strongly. In this case, the hydrogen atoms would be warmer, in order to keep them bouncing around, and, as a result, each time a hydrogen atom hit the turbine, it would also transfer some of its heat energy, until the whole system was in equilibrium and work would stop being produced.

Once again, the Second Law of Thermodynamics wins the game.

There’s a lot of transitioning going on in American culture right now. Barack Obama’s Presidency is bringing dramatic changes in American Policy in just its first few days. A recent news story that caught my eye was how the brilliantly satirical Daily Show was wrestling with how its narrative will adapt to the new administration.

I’m wondering what’s going to happen to punk rock. Green Day experienced a revival with their number-one album American Idiot. Bad Religion released what was, in my opinion, their most intellectual albums The Process of Belief and The Empire Strikes First:

Bad Religion “Materialist” (2002)

The process of belief is an elixir when you’re weak
I must confess, at times I indulge it on the sneak
but generally my outlook’s not so bleak

I’m materialist
Call me a humanist
and I guess I’m full of doubt,
but I’ll gladly have it out with you

Also NOFX popped onto my radar as a new favorite punk band for all the intellectual political references and wit on their albums The War on Errorism and Wolves in Wolves’ Clothing (ht Vicky).

NOFX “Idiots Are Taking Over” (2003)

Mensa membership conceding
tell me why and how are all the stupid people breeding
Watson, it’s really elementary
the industrial revolution
has flipped the bitch on evolution
the benevolent and wise
are being thwarted, ostracized,
what a bummer
the world keeps getting dumber
insensitivity is standard
and faith is being fancied over reason

For all his faults and missteps, I can at least be thankful to the 43rd President for eight fantastic years of punk rock music.

There’s a Cabinet of Curiosities at Amsterdam’s NEMO Science Center, the Vrolik Collection. This display is one of many examples of the differences between Science Centers in Europe and America. There are some “gross-out” displays in American Children science centers, but lion penises and elephant clitorii are definitely not something we find in our centers here in the states.

Conjoined twin monkey

From the NEMO description of this display:

During their lives, Gerard Vrolik (1175-1859) and his son Willem Vrolik (1801-1863) began a collection for the ‘Museum Vrolikanium’. Housed in the residence of Gerard Vrolik, the museum was very well known in Europe at that time. Together, father and son collected for 70 years, resulting in an enormous collection of 5103 specimens.

Many of these specimens were used for scientific research. At that time, one often had to rely on such specimens because many techniques that we now use did not yet exist.

See the complete flickr set here. <warning>These images might disturb some readers</warning>

Cameron Neylon of the Science in the open, Deepak Singh of business | bytes | genes | molecules (bbgm), and several panelists from Science Blogs and members of Nature Network discussed the merits of community blogging versus indy (“Garage”) blogging.

I got a chuckle as a few participants refered to Science Blogs as “the Borg,” even by the people who blog there. On the plus side of not being part of a blogging community, is the fact that we indies have total freedom in how we design our blogs (even if some changes irritated my readers). One of the reasons I jumped the wordpress.com ship to roll my own blog again was the freedom to install whatever widgets I wanted in the sidebar.

At the same time, being a member of Science Blogs certainly has its appeal. Some participants talked about the increase in traffic they got from Sb, and others talked about how being part of Sb “legitimized” their blogs in some ways, that they could feel comfortable putting their blog on their CVs.

Comments from a few former Sb bloggers brought up the potential negatives of being part of the community, how they all get overshadowed by PZ Myers and that people assume all Sbers are militant Atheists.

Per Bora’s comments, the organization of Sb appears to give the bloggers a union of sorts. They have the power to get advertising they don’t like removed from the site, and have raised protest about their employer in the past.

My favorite line from the session pointed out that we are all online, and we are all part of a Science Blogging Community, “Google is the community.”

Wiki for this Session

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ideonexus Blocked at the Coast Guard Base

In the interest of enabling attendees to speak candidly about personal conflicts they have experience between their professional or personal lives and their online persona, speakers were kept anonymous for this session (not sure how posting their names on the conference program affects this). It was suggested that all panelists should be referred to as {PZ1, PZ2, PZ3…} in honor of Science Blogs’ most controversial author, PZ Myers of Pharyngula fame, who couldn’t make it.

This session was also the most packed of all, and had some of the most interesting stories. PZ2 talked about how his employer wanted to put an editor on his blog, and how he expects to be fired any moment now for refusing to allow it. PZ3 talked about her employer took no interest in her personal blog until they thought they could benefit from its publicity. Another blogger talked about how he had to stop criticizing a company on his blog when he started receiving grant money from them.

One attendee talked about how someone dredged up an inflammatory post he had written years ago and submitted it to his present employer, demanding action. The employer, luckily, was sophisticated enough to realize the post was a personal one and did not represent the publication, but it does raise the idea of our online histories coming back to haunt us, not all of it under our control. Someone suggested that people should blog respectfully under their real name as a means of pushing the unfavorable websites down the search results.

I thought PZ3 had one of the most insightful observations, when she talked about the naivety of scientists, and their belief in intellectual honesty. It doesn’t occur to them that they can’t speak their mind.

“We need a bloggers union,” someone said, and someone else mentioned the Online News Association.

At the very end of the session, a moderator asked if there were any bloggers who worked for the Federal Government who had some stories to share. I didn’t think there was enough time left to squeeze in my experiences, but because I work for the Federal Government, on a Coast Guard base, I have to be extremely careful about my online actions while on my work computer.

Five years ago, I quite foolishly downloaded my ideonexus beta blog to my server at work to make some tweaks on my lunch break. It just happened that we were undergoing a security audit that week, and guess what they found when they looked at my computer?

I got pulled into the Project Manager’s office, where my blog, specifically a political rant, was pulled up in a browser window, being broadcast from my workstation to the intranet. After being properly chewed out, I was made to sign a statement that I would be fired if I ever screwed up like this again.

The real issue, I would learn later, wasn’t that I was using my workstation for non-work activities during my break, it was that I was using my computer to post political content that others could read. It is seriously illegal to use Federal property to promote a political ideology, and it would have been proper to fire me on the spot.

Recently, CGblog has me identified as an unofficial Coast Guard blogger; although, my blog really has very little to do with the Coast Guard, except for my post on Phytoremediation projects on base. This isn’t a big deal, as everyone at work knows I blog science and geekery for the local paper, but I do have two posts out there that could catch me some heat. One post brags about my ridiculously expensive tax-payer-funded chair and another jokes about getting away with having the Flying Spaghetti Monster on my desk.

Is there a Sword of Damocles hanging over my head?

Wiki for this Session

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Kevin Zelnio of Deep-Sea News and Grrrlscientist of Living the Scientific Life

Grrrlscientist of Living the Scientific Life and Kevin Zelnio of Deep-Sea News co-hosted this session, which I attended and Vicky snuck into. While I don’t consider myself a nature blogger, I do like to cover Take a Child Outside Week, and my flickr sets are much more about using museum specimens to catalogue what you find outside than taking inspiring photos.

A good deal of the session kept returning to the question of “What is Nature Blogging?” as opposed to science blogging. One participant made the insightful observation that Henry David Thoreau was a nature blogger, but not a science blogger. Someone else noted that The Origin of the Species was both scientifically rigorous and filled with natural philosophy.

Richard Carter, answered via Twitter, “Nature Blogs are unlikely to cover the large hadron collider.” To which a commenter replied, “I take that as a challenge.”

Another, related question, was “How much Science should be in Nature Blogs?” Several commenters agreed that including science definitely enhanced their reading experiences, and that nature blogs, because they tend toward a softer scientific emphasis, provide a “Lower barrier to entry” for their readers to understand the science they do bring into the mix. In other words, have fun, but sneak some science into the enchanting photography and emotional experiences.

Nature blogging isn’t a subset of science blogging because it includes people who post photos from their back yard, wondering about what they’ve photographed. Nature blogs, it was raised, are interwoven with advocacy. They bring attention to the myriad conservation efforts going on all around the world, and encourage people to participate in Citizen Science projects like the Audubon Christmas Bird Count.

It was at this point Vicky and I learned about the amazing website iNaturalist.org, where members upload photos of species they photography along with coordinates. The site has fantastic potential for citizen science, and Vicky has all ready signed up and started contributing to it. She sees the site as way to track decimated American Chestnut populations. Vicky has been uploading photos all night to keep up with the California submissions.

I would probably blog more outdoor excursions if I wasn’t so uptight about properly identifying the species I photograph outside. Museums have these convenient labels on everything, while outside is just so incredibly overwhelmingly biodiverse. The world outside is filled with the promise of adventure, overwhelmingly complex and inspiring in a way I find difficult to accurately articulate. I’m thankful for the bloggers out there who are able convey that sense of wonder.

Wiki for this Session

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“No compulsory learning can remain in the soul… In teaching children, train them by a kind of game, and you will be able to see more clearly the natural bent of each.” – Plato, the republic, Book VII

Janet Stemwedel of Adventures in Ethics and Science

Janet Stemwedel of the Adventures in Ethics and Science blog ran a session that made a personal project in my life so much easier. I’ve wanted to compile a give-away CD at the science center of links to the best science sites for kids on the web. Dr. Freeride has done all the work on that, for which I am very grateful.

One of Stemwedel’s criteria for including a link, is that it be of interest to parent’s as well as kids. She cited Sesame Street’s habit of including lots of jokes and satire for adults to enjoy while watching the show with their kids. I think NASA’s Spaceship Spitzer cartoon does a great job of appealing to kids while sneaking in jokes and references for adults. Also the show is served in small doses, which is nice for not getting stuck in front of the monitor for long stretches of time.

Beyond the World Wide Web, I realized afterwards the resources available in Virtual Worlds. The International Space Museum, NASA’s COLAB, and the NOAA in Second Life are also fantastic playgrounds for parents to let their children do the exploring, while riding along over their shoulder to help them get the most out of the experience.

Crayon Physics was mentioned as a great science game. To that I would add the Federation of American Scientists’ free video game Immune Attack and Hopelab’s game ReMission, both of which involve flying around inside the human body, battling viruses and cancer cells. For physics, I’m currently playing Portal, which is witty and involves thinking about velocity and momentum in interesting ways, but the game is for older kids due to its complexity. Spore is a game that scores low and high marks in various areas from scientists, so, while the game is kid-friendly, parents need to be able to explain to kids why the depiction of biological and cultural evolution is somewhat misleading… or they might come away believing in Creationism.

Which brings up another issue for parents who want to weave science into the everyday fabric of their children’s lives, as Janet Stemwedel does, the problem of science anxiety. Dr. Stemwedel notes that much of science has changed since we were kids, Pluto was a planet and brontosaurus was a dinosaur. Parents might not feel qualified to teach their kids science, but they need to understand that science isn’t static, that it’s always changing. Continuing education is an important principle in every adult’s life, and the education of our children is a wonderful opportunity to practice it.

Extending the Virtual into the physical, I realized that Geocaching often offers wonderful opportunities for outdoor science lessons. Many contributors to this hobby require people to identify trees or answer other nature questions in order to find the cache. Kids can also collaborate with their parents to set up their own geocaches, including a bit of science trivia in order to locate it. If I were a kid, I would love to return to my cache year after year and see the growing list of signatures on it.

My recent most favorite example of a parent teaching their child science is the Energy Game Dr. Richard Feynman used to play with is father growing up, where he was challenged to answer where something got its energy (ie. a spring wound up by a person), and where that energy came from (person ate food), and where that came from, etc, until the energy chain was always traced back to the Sun.

Wiki for this Session

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Glendon Mellow of Flying Trilobite

Glendon Mellow of the Flying Trilobite hosted a very enjoyable session, where he started out by covering what he considered the various types of science art:

Scientific Illustration: drawings to illustrate the content of an article. I post many of these for links having to do with dinosaurs or extinct creatures.

Fine Art: a high-culture art, often inspired by science. An interesting and somewhat disturbing example would be Mark Quin’s sculpture of himself made out of his own blood.

Art Inspired by Scientific Subjects: self explanatory, includes optical illusions and Salvador Dali. Awhile back I blogged the MoMa exhibit Design and the Elastic Mind (my photos of it here), which I would put into this category.

Science Fiction: interesting examples of this were invented ecosystems and the speculative dinosaur project.

To this list, I think I would add Found Art. This would include putting a cast of dinosaur bones together into an action pose, propping up a taxidermied animal, mounting forminifera, or any other sort of museum display. A Cabinet of Curiosities would be a great example of found art. This form of art is much more scientifically rigorous, but also very creative. One attendee mentioned that there are many artistic choices in science, such as how to color astronomy photos to best bring out their details.

After the introduction, Mellow said that he felt his relationship with science was “parasitic,” where he’s getting a lot of inspiration from science, but doesn’t feel like he’s giving back. I was glad to see the overwhelming response from the room was essentially, Keep doing what you’re doing. That art inspires science, and scientific illustrations go a long way toward communicating scientific discoveries to the general public.

As part of this art communicating science, I would stress the importance of the metaphor as a tool for illustrating concepts. In Computer Science, we would be lost without metaphors. In fact, our Windows and Macintosh operating systems are basically a collection of metaphors for all the inner mechanical and electronic workings of our computers. Metaphors are indispensable in describing atoms and quantum physics. So writers take heed, remember the importance of metaphors in your work.

A few times the specter of the two cultures debate was raised, but I was glad that one attendee decided to shoot down the whole thing as “tedious.” I agreed with the idea that there are artists who see science as oppressive and scientists who see art as frivolous. These people have personal problems, not cultural ones, and need to free their intellects.

The reality is that there are not two cultures. Someone brought up a younger scientist, who grew up playing with Transformers Beast Machines and therefore had no problem relating biological to mechanical. Another raised the phenomena of Jurassic Park encouraging scientists to fact-check its many portrayals.

So the two cultures is a myth, propagated by scientists who don’t like art, and artists who don’t like science. The reality is that science inspires art, and art, science. The two cultures should continue to work toward our common good. Sessions like this, hosted by thoughtful people like Mellow, are this principle put to practise.

You can see the various artwork referenced at the Wiki for this Session. Highly recommended.

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