Genetics is a weak spot for me. I took the requisite courses in college, but still get woozy headed when wading too deep into the topic. If anyone has recommendations for a basic refresher text, I’d be obliged. And feel free to correct me if I get any of the following wrong.
Part of my problem is the whole new level of jargon required to comprehend the subject. Take the word gene itself. It is a term many people use but don’t always understand. We say, “it’s in our genes,” or, “he’s wading in the shallow end of the gene pool.” But a gene is not something we can easily point to or see. Instead, the common usage is more of an abstraction. It is the notion that there are characteristics that we inherit from our parents, like being tall or short, blonde or brunette, or predisposed to cancer.
More precisely, a gene is a portion of a DNA molecule that actually means something. Like the number of pages that make up a chapter in a book, the amount of a DNA molecule that makes up a gene can vary. It can be a small portion or a large portion. How do we map out a gene and know where a sequence begins and where it ends? That’s part of what I need to go back and review.
Genial Expressions
When geneticist do identify sequences of DNA that correspond to a gene, they usually give them names. There are formal guidelines for doing so, but as Jack Shedd notes, there are still some strange results:
tribbles: related to cells that divide uncontrollably
Cleopatra: The Cleopatra mutation is lethal only if Asp gene is also present.
Grunge: a regulator of the teashirt gene
Further reading
Genetic is a messy business, and scientist still struggle with a precise, technical definition for a gene.
Welcome to the first installment of what I hope to make a weekly feature: Scidays. Inspired by Ira Flato (amongothers), I’ve decided to devote a post at the end of the week to science and technology news.
Underwater Blogging
I told my wife that someday I will be able to blog while underwater. She replied that I was already all wet. But the day of my dream might ever be so nearer with the xTablet T8700 from Mobile Demand.
The T8700 is actually billed as water-proof and not really for use at depth. But it is a nice counter-example of something I’ll be writing a bit more about tomorrow, which is the fragility of electronic devices as a barrier to their wider use in environmental education.
Also, if you know of devices that are rated for scuba and that could really be used for underwater blogging, let me know.
I have an avatar in Second Life called Calamari Ricardo. He wandered into the lair of Grendel’s Children the other day and came across a new undersea option for avatars (see below).
Randy Olson cheekily suggested that the next Science Blogging Conference be conducted in Second Life. If so, maybe we could hold it on the newly expanded NOAA sim and all the ocean bloggers could go dressed up as Vent Nymphs.
Vent Nymphs
MiniHUD controls the black smoker effect & sound, and includes a unique skin and sculpted tubeworm growths! Both genders included. Created by Flea Bussy.
SciVee is about the free and widespread dissemination and comprehension of science. Created for scientists, by scientists, SciVee moves science beyond the printed word and lecture theater taking advantage of the internet as a communication medium where scientists young and old have a place and a voice. SciVee is operated in partnership with the Public Library of Science (PLoS), the National Science Foundation (NSF) and the San Diego Supercomputer Center (SDSC).
SciVeealpha is a video sharing site for science. The concept is that a researcher links the PubMed ID or DOI of their paper to SciVee, then records ten minutes of video or audio discussing the highlights and concepts in the article. The site allows the video or audio to be synchronized with figures from the article. The next step involves the SciVee community then commenting on and discussing the new pubcast.
Currently the site is in its alpha release. There does not appear to be any way to embedded SciVee videos on your own blog, a la YouTube. It would also be nice if their was a recommendation scheme, where the site suggested related materials or similar research. But it might be too early to effectively do that with a small database.
In addition to discussions of original research, there are several educational science shorts you can view. In particular, BioMEDIA has snippets from several of their videos on animal diversity (see below). BioMEDIA allows some limited educational use of their content. They are also offering a couple of free posters if folks register with their site.
So what do you think? Can scientist master the art of communicating to an Internet audience? Should they be expected to? Know anyone who has uploaded content to SciVee?
The Prelinger Archives are a great source for royalty free videos. They have many vintage instructional films and ephemra.
Its goal remains to collect, preserve, and facilitate access to films of historic significance that haven’t been collected elsewhere. Included are films produced by and for many hundreds of important US corporations, nonprofit organizations, trade associations, community and interest groups, and educational institutions.
I recommend checking out two selections from the extensive archive. The first is the Hanford Science Forum, featuring “science student of the week” Doyle Burke, circa 1950s:
Television program (one of a series) sponsored by General Electric Company for telecasting to residents of the Richland, Washington area. This interview with Dr. Richard F. Foster, manager of the Aquatic Biology Division at the Hanford plutonium plant, presents his research that the plant’s radioactive effluents have no effect on aquatic life in the Columbia River.
You might also want to check out one of my personal favorites, Fish from Hell Part I and Part II. Some might argue that our attitudes towards the oceans have not changed much since then.
Essentially, this “film” is just murky stock footage of men on a fishing trawler. What transforms it into an epic tale of Man vs. The Sea is an amazing narration by somebody named Wilfred Lucas. Mr. Lucas pulls no punches; in this violent world, decent men kill every fish they meet. But that’s okay, because — as Mr. Lucas explains — fish are evil and deserve to die. A manta ray gets a harpoon in its skull because it’s a “devil fish,” and a “terror of the deep.” An octopus barely escapes with its life, even though it’s a “slimy, death-dealing monster” and a “black-hearted scoundrel.” Even porpoises are slandered, being derisively referred to as “clowns” and “good for lubricating oil.” As if this weren’t enough, a whole section of this film is devoted to a battle between a whale and a swordfish, which is the whale’s “greatest enemy” (something many ichthyologists would be interested to learn). As the camera cuts rapidly between stock shots of a leaping swordfish and completely different footage of a sleeping whale, Mr. Lucas tells us that “no one has ever been lucky enough to photograph a scene like this before.” Truly a triumph of style over content; great fun to watch. Look for the cameo by Wumpy the parrot.
Attention marine biologists of the world! Gather up your plankton nets and Nansen bottles! You are urgently needed to star in the “most rockin” music video ever.
Toren Atkinson, lead singer for the Lovecraftian rock band, The Darkest of the Hillside Thickets will soon release a new track from their forthcoming album “The Shadow Out of Tim.” The track is called “A Marine Biologist” and is all about “bathyscaphes, benthic trawlers, architeuthis, etc.” They want to create a video for this song that features marine biologists from around the world. All they need is any video, even previously produced footage, of you doing anything marine biological.
If you want to help out, contact Toren Atkinson at thickets [at] uniserve [dot] com. I believe cephalopod costumes are optional. Or if you are not a marine biologist (or only play one on TV), please spread the word to any marine biologists you know.
More details from Toren’s initial request over of the TONMO forums
Back in May 2006 I came across Hackshaven Harford and the early efforts to bring NOAA/ESRL into Second Life. Since then, NOAA has purchased its own Second Life island and it’s almost ready for the public. Exhibits on the sim were developed by Aimee Weber Studios and include a demonstration of tsunamis, glaciers and undersea life.
If you are wondering why NOAA is in Second Life, you can find the FAQ here:
Second Life (SL) provides a unique ability to create an immersive simulated learning experience. It is a cost effective way of reaching large numbers of people that otherwise would not have access to the wealth of knowledge that NOAA and ESRL possess. Currently, NOAA/ESRL are exploring SL as a way of visualizing the vast amouts of educational material and data at their disposal.
The Science Center in Second Life will get a sneak peek at NOAA/ESRL’s Meteroa Sim. The beta-test tour will be on Wednesday, Decemeber 6, at 8:00 AM PST. You must be part of the Science Center to take part.
There are a lot of good reasons to start a blog. Mine is not necessarily one of them. I started on the ‘Net back in the old Prodigy era (circa 1993). I was initially loath to communicate authentically online, taking pains to preserve my anonymity. But nowadays I realize that Google and other spiderbots are inexorably gathering information about us anyway. It’s an illusion to think there aren’t already little pieces of us scattered across sundry servers. So rather than let chance or my minor participation in conferences or listservs determine how I was indexed, I decided to start staking a claim to my own unreal estate and start blogging.
The nice thing about coming out of this shell is that I get to participate in the participatory Web and produce the Cephalopodcast podcast. It also has allowed me to (virtually) meet some very fine folks. In particular, I’ve been hanging around the educators and webcasters at Worldbridges.net. Some of them have also been venturing into the MMO1 world of Second Life. Naturally enough, they have been webcasting and podcasting these explorations. And you can now see the latest adventures at Virtualbridges.net.
The International Spaceflight Museum is a museum in the virtual world of Second Life. It hosts exhibits and events about spacecraft, rockets, and space travel. The museum is located on the island sim Spaceport Alpha.
The organization that manages and develops the museum is the Spaceflight Museum Planning Group, a group of Second Life residents from around the world who share an interest in spaceflight.
So if you want to see practical examples of the educational potential of MMOs, check out the videos at Virtualbridges.net.
UPDATE: I’ve been made a manager at Virtualbridges.net, so I will be helping out with the posting there. The next jaunt into Second Life will be this Sunday, July 9, 5:30pmPDT/8:30pmEDT/12:30amGMT. Feel free to join us as we take a tour of Second Life’s Public Library and the Info Island sim.
Okay, I know it’s the second post in a row about this, but I found something interesting last night. Looks like NOAA’s Earth System Research Laboratory has some unreal estate in Second Life! Got a chance to chat with Eric Hackathorn (aka Hackshaven Harford, pictured at right), who was kind enough to demonstrate some of the features of the NOAA/ESRL area. From their in-game notecard:
The structure before you is called “Science on a Sphere.” You can see the real world version at a museum close to you or by visiting http://sos.noaa.gov/. In the meantime, please enjoy a few sample animations by clicking on the controls on the right. Here are the animations currently available:
Martian Surface A topography of the surface of Mars colored by elevation.
2004 Indian Ocean Tsunami The different colors in the ocean represent the average sea surface elevation for the 24 hour period following the 9.0 earthquake that triggered a devistating tsunami in the region.
Sea Surface Temperatures The temperature of the sea surface over time. You can see the formation of an El Nino of the coast of South Africa.
Make sure streaming video is enabled under your preferences and then hit play on the movie control at the bottom of the interface.
Everything is still pretty new, but Eric and I both agreed there are plenty of possibilities for demonstrating science concepts in synthetic environments like SL. I look forward to seeing and hearing more.
UPDATE: “Come see what NOAA/ESRL has been doing in Second Life and what our plans are for the future. A proof of concept, “Science on a Sphere” (http://sos.noaa.gov/), has been implemented and an overview of our future plans will be presented.” Monday, 05/15/2006 at 12:00pm MST.
Thanks to Meno Rich and company for the Second Life meetup and simultaneous Skypecast. The snapshot at right is what my avatar looks like when shot into orbit around Second Life. If you want to know how that happened, send me an email.
There will be a grand opening of the World Bridge’s Second Life site from May 12-14.
After a bit of resistance, I finally took the plunge into Second Life. It is my first trip into a synthetic world, or MMO1.
In Second Life, users can fashion all manner of structures and objects. Most of these seem fairly primitive and industrial. There doesn’t seem to be much capacity for organic expression. I suspect this is mainly due to limitations in bandwidth. That is, it’s easier to simulate the repeating, rectilinear pattern of a brick wall than it is to recreate a convincing tree. But as a consequence, even though most users try to emulate the real world, I have found little evidence for any kind of ecology in Second Life. This is especially noticable underwater. Most of these areas are devoid of any kind of development and look more stark than the abyssal plane. So whenever I am in the game, I make an extra effort to look for examples of aquatic life. So far I’ve found a shark, an orca and a horseshoe crab. If you know of any others, please send me a note. And if you are in SL, look for my avatar, Calamari Ricardo.
Update: Thanks to Eric Rice (aka Spin Martin) for the aerial and aquatic tour of Slackstreet.
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Cephalopodcast.com - The Ocean Podcast: Featuring science education and information about our oceans. Produced in south Florida, it includes news and ideas for marine educators and those who wish to learn more about the other 71% of our planet.
![SciVee.tv [250x120, 12K]](http://cephalopodcast.com/blog/wp-content/uploads/2007/11/scivee.jpg "SciVee.tv")
![Screen grab from the Prelinger Archive, Fish from Hell [160x110, 10K]](http://www.cephalopodcast.com/img/pic/pic_070724_Prelinger1945.jpg "Prelinger Archive: Fish From Hell")
![Virtual rockets in Second Life [200x150, 12K]](http://www.cephalopodcast.com/img/pic/pic_060703a.jpg "Virtualbridges.net tour of the Spaceflight Museum in Second Life")
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![Calamari Ricardo distorted in orbit above Second Life [200x150, 12K]](http://www.cephalopodcast.com/img/pic/pic_060508b.jpg)
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After a bit of resistance, I finally took the plunge into 
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