Survival Machine

Request for site logo.

Hey, I know some of my readers are not too shabby when it comes to graphic design.  Is anyone out there is willing to design me a banner logo to display at the top of Survival Machine?  I’d like it to suit the violet colors of my WordPress theme, and possibly incorporate some science elements (like a DNA double-helix, a galaxy, an organic molecule, an atom, an erlenmeyer flask, et cetera).  Let me know if you’d like to take a crack at it.

I’m just getting tired of the plain text title.

The Great Catholic Cracker Crack-Up

Please read PZ Myers’ entry on what I like to call The Great Catholic Cracker Crack-Up at Pharyngula.  It’s comedy gold.

Atheist Soldier Sues The DoD, and The Evolution of Compassion

This April, The New York Times reported the case of U.S. Army Specialist Jeremy Hall, a soldier who started a chapter of the Military Association of Atheists and Freethinkers and subsequently had to be removed from Iraq due to numerous threats from his fellow soldiers.  Now, I’m not exactly surprised by this.  I’d expect the military to be drooling with evangelicals, of course.  And I could probably cynically overlook verbal harassment of an atheist in the armed forces, just because I expect that sort of bullshit from indoctrinated meat-heads.  But physical threats?  That really is beyond the pale.  Now, Spc. Hall is suing the Department of Defense and former defense secretary Donald Rumsfeld for failing to protect his freedom from religious persecution as protected by the 1st Amendment to the United States Constitution.  You go boy.

Seriously, this is not the sort of reputation the military should want, given that non-religious Americans are the largest (non) religious group after Christians.  They have enough trouble recruiting as it is!  This is just another example, sadly, of Christians thinking the world revolves around them.  It’s bad enough that brave men and women who are devoted to the service of their country were blithely thrown into harm’s way in Iraq by a callous and evangelically-motivated administration… but non-religious soldiers’ lives are threatened by their loving, Christian comrades-in-arms as well?  What a disgusting blemish on our armed forces.  I hope Spc. Hall wins his lawsuit and the DoD cracks down on prosyletizing by officers.

I haven’t posted anything in a while, have I?  Still, life marches on.  I got some paperwork done that’s been taking forever (to put it mildly).  I also was inspired by the news I wrote about in my previous post, and decided to read Robert Axelrod’s The Evolution of Compassion.  This book tells the story of his experiment: a computer tournament in the early 1980s that pitted programs submitted by game theorists from various academic disciplines (as well as an 11 year old computer prodigy) in the iterated Prisoner’s Dilemma game (a classic thought experiment).  It’s quite interesting, and you can expect me to write a more in-depth review when I’ve finished it.

P.S. - I would love to get some comments on my posts.  If you’re reading this, any feedback will be appreciated.  It’s hard to talk myself into posting when it feels like no one is reading! I’d really like to get this blog fired up.

Conclusive evidence for ‘Selfish Gene’ theory found.

I have to admit, I never really got evolution in any sophisticated way before I read Richard Dawkins‘ seminal 1976 book, The Selfish Gene.  Dawkins illustrated the foundation of a paradigm shift in evolutionary biology away from group selection or kin selection and toward the gene as the unit of selection driving evolution.  That shift shaped the whole of modern biology, and selfish gene theory is the predominant model used by scientists today, with notable exceptions such as E. O. Wilson.  Before I read The Selfish Gene, I knew that evolution by natural selection made accurate predictions about the observable biological world, but the nuances of its mechanism—gene selection—were over my head.  It wasn’t elegantly taught in my high school biology classes, if it was even taught at all.  I recall it being discussed in more depth in my undergrad life sciences courses at the University of Maryland, but that was, unfortunately, around the time I was tuning out (temporarily) academic ambition.  It was after reading Dawkins’ The God Delusion that I was so impressed with his writing tone and style I purchased The Selfish Gene.  And science, am I ever glad I did.  Each chapter seemed to evoke another Eureka! moment, where the dense veil of complexity was lifted from life and I felt a renewed calling toward the study of biology (my first declared major in college).

That said, you can understand why I am so excited about this: next month, the journal Genetics will publish research findings by University of Western Ontario biologist Graham Thompson, and Peter Oxley and Benjamin Oldroyd of the University of Sydney in Australia, who managed to isolate part of the honeybee genome that is responsible for reproductive altruism.¹  (Full text of the article is available now).²  As you may know, female worker honeybees [order Hymenoptera] are sterile.  In a honeybee colony, the queen is the only reproductively active female.  Sex determination for honeybees is haplodiploid, meaning that the queen may lay fertilized female eggs (with two sets of chromosomes, or diploid), or unfertilized male eggs (with one set of chromosomes, or haploid).  The queen, having stored sperm in a spermatheca during her numerous mating flights (what a slut!), can choose how many male and female offspring to produce.  Although all her female offspring possess the genetic potential to be queens, the overwhelming majority of them will remain sterile workers, toiling away to feed and groom the queen as she becomes a huge sibling factory.  Their ovaries will remain inactive, and they will devote their lives to the queen.  Occasionally, ‘anarchist’ colonies of honeybees are found, in which a small proportion of females besides the queen activate their ovaries and begin to reproduce.  Thompson, Oxley, and Oldroyd have at last discovered what appears to be conclusive, material evidence that the selfish gene is real!  Specifically, what they have done is identified four quantitative trait loci (QTLs) that account for 25% of the phenotypic variance in ovary activation.  These are regions of the honeybee genome that are almost certain to contain genes responsible for the selfish ‘cheating’ behavior found in the ‘anarchist’ colonies.  Although this does not mean that the actual genes have been defined, it does mean that they are now very close to doing so.  So the theoretical assumption underpinning modern biology, although quite strong on its own, finally has physical, molecular evidence to support it.  This sort of thing makes me a bit weak in the knees, so please forgive my ebullience.

Oh, and in case you couldn’t tell, I <3 honeybees.

¹ Western News - The University of Western Ontario

² Genetics Volume 179, No. 3, July 2008.  Four quantitative trait loci that influence worker sterility in the honeybee (Apis mellifera), by Peter R. Oxley, Graham J. Thompson, and Benjamin P. Oldroyd.

Ninja bears?

I know I haven’t posted recently, and thus have really not kept up with my new years resolution to post at least once a week. But, I probably cursed this blog with that resolution. So, in an attempt to humble my high-and-mighty scientific ambitions and set the bar lower to allow more frequent updates, I present you with:

NINJA BEARS!

Photographer unknown.

What would a Barack Obama administration do for science?

So I was (again) reading over Barack Obama’s campaign press release about his plans to promote scientific research and education, and there’s a lot to like in there. Obama is aggressively in support of expanding federally funded embryonic stem cell research. So much has been said about that topic that I am not going to go into it right now, but to be clear: that’s a 180 degree reversal from the Bush administration policy on stem cell research. I also had not been aware already that Obama helped write and was an original cosponsor of the Minority Health Improvement and Health Disparity Elimination Act, which hopefully will become law after the current criminal administration is sent packing. The whole text of the bill is in the last link, but the Obama press release describes it thus:

The bill puts new emphasis on disparity research by reporting health care data by race and ethnicity, as well as socioeconomic status and health literacy. The legislation outlines mechanisms to conduct educational outreach to minorities, increase diversity among health care professionals, and improve the delivery of health care to minorities.

If we’re going to have national health care, this sort of thing is critical and taxpayers should actually be demanding it! Preventative medicine is always cheaper than treating ailments and disease, and the potential benefits of a healthy population go far beyond the lower cost of health care (increased economic productivity, decreased poverty, decreased crime, decreased drug abuse, the list is endless).

What really turns me on the most about Obama’s priorities, though, was this part of the document:

Improve and Prioritize Science Assessments: Assessments should reflect the range of knowledge and skills students should acquire. Science assessments need to do more than test facts and concepts. They need to use a range of measures to test inquiry and higher order thinking skills including inference, logic, data analysis and interpretation, forming questions, and communication. High-performing states like Connecticut, Maine, New Hampshire, and Vermont, use an assessment that calls for students to design and conduct investigations, analyze and present data, write up and defend results. Barack Obama will work with governors and educators to ensure that state assessments measure these skills.

I cannot overemphasize how crucial that is! American science education is fast becoming a joke on the international level. With rare exceptions, I was not taught how to use inference, logic, or data analysis in the public high school system, and I went to a half-decent public high school—ten years ago! Most inner-city and some rural schools are far worse. Prioritizing how to think over what to think is the key to producing bright, engaged, and enthusiastic students who actually get what science is all about and are well prepared to hit the ground running when they find the field of science that really inspires them. After I finish graduate school, to the extent possible, I’d like to be involved in changing American science education. One dream I have is to work for Eugenie Scott and the National Center For Science Education, which does great work defending public school curricula against religious zealots who try to force intelligent design into the science classroom. I donated $10 to them to offset the damage done when I bought a ticket to Ben Stein’s disgusting crock-umentary Expelled: No Intelligence Allowed. If you ever doubt the sniveling academic dishonesty of I.D. proponents, watch that film (download a pirated copy off the internet, please) and read how well the good people who made ExpelledExposed.com eviscerate just about every claim the film makes.

So, having veered just a bit off topic for a moment there, I’ll try to bring this back to the Obama science plan and wrap it up. From what I’ve read, I am cautiously optimistic that a Barack Obama administration would be a very science-friendly one. I think he doesn’t go quite far enough in emphasizing the need for interdisciplinary physical, chemical, and biological systems research. He also needs to use that generic science document better to tie into other large issues that are addressed elsewhere on the campaign website, and which I haven’t yet had time to peruse. I hope to post in the near future my thoughts on Obama’s proposed energy and environmental policies, and his position on NASA (as well as contrasting these with those of John McCain). For the rest of tonight, though, I would be glad just to get enough sleep so as not to be a total zombie at work tomorrow. I haven’t quit my day job yet; the blogging doesn’t have me rolling in benjamins yet like I hoped it would

For now, I’ll leave you with this video from a few weeks ago when my favorite artist and role model Dr. Greg Graffin was presented with the Lifetime Achievement Award in Cultural Humanism by the Harvard Humanist Chaplaincy. It’s got him playing a few acoustic Bad Religion songs as well as talking about the award and why he prefers the label “naturalist” versus “atheist.” Wish I could have been there for this!

Senator Barack Obama Wins The Democratic Party Nomination For President!

Well, after about 5 months of primary elections, the Democratic Party of the United States of America has nominated Senator Barack Obama of Illinois to be their candidate for President.

Congratulations, B! You’re going to the White House. Now please, please, please don’t pick Hillary Clinton for V.P.  What about Bill Richardson? He’d be great.

Space Shuttle Discovery launches.

I just watched the space shuttle Discovery launch from Kennedy Space Center on tv a few minutes ago. It was pretty. Sorry I didn’t let you know about it in advance, I wasn’t keeping track of the launch schedule very well.

It’s a nice, cool day in Baltimore after some thunderstorms passed through the area. Here comes June! My birthday’s in two weeks… holy shit, I’m getting old faster and faster.

Phoenix lands undamaged on Mars!

I’m a bit disappointed in myself for not posting anything on this earlier. Most of you already know by now that on Sunday, NASA’s Phoenix probe successfully performed a rocket-assisted landing on Mars’ northern arctic plains.  It was the sixth successful attempted (of twelve total, worldwide) Mars landing.  Phoenix is a joint project of a number of international universities and space agencies, and its primary goal is to analyze the water ice covering much of the ground near Mars’ north pole.  In doing so, it will help researchers look for evidence of past or present Martian life.  I think we are on the right track with robotic exploration, as the ethical complexities involved in manned missions to Mars (at least in this technological era) are very limiting.

Anyway, the landing occurred at 23:53:44 UTC; that’s the Earth-received time.  That means the time that mission control received the first radio signals.  The landing really took place 15 minutes and 20 seconds before that, which is the amount of time it takes radio signals from Mars to reach Earth.  Forget what you know about relativity; Earth and Mars are too close together in space, and the relative speed between them is too tiny a fraction of the speed of light for relativity to matter in this case.  As far as we need be concerned, the Earth-received time minus 15m 20s is simultaneous to Mars time.  That’s one of the dilemmas that any future human Mars explorers would face: it would take over a half hour, at least, to receive any reply to a message radioed to Earth.  Keep in mind too that Mars’ and Earth’s orbits around the sun are not synchronous; the half hour delay is the best of scenarios!

A bit more info: Phoenix was launched on August 4, 2007 atop a Delta II rocket from Cape Canaveral, Florida.  It took nearly ten months to complete the 680 million kilometer journey to Mars.  How about a picture of the launch, you ask?  Why, I’ve got one for you right here:

And so, dear readers, space exploration marches on!  I know it’s perhaps just a little unlikely, but I’m still crossing my fingers that I’ll be able to land on the moon before I die.  I know that may seem to contradict what I said a moment ago about robotic exploration being the right track, but things may change for the better.  We may discover safer, less expensive ways to escape Earth’s gravity, and better portable protection from solar radiation.  I don’t even care if it’s not really all that safe.  If I’m 45 or older, and I’m offered a seat on a moon shuttle, you better believe I’m going.  Hell, I’d go to Mars, too.  Apart from the obvious atmospheric differences, the terrain doesn’t look too different from the Black Rock Desert where I’ve camped at Burning Man several times now

The first image of Mars’ horizon sent by Phoenix:

The Black Rock Desert, Black Rock City, NV:

Until next time, kiddies.  Keep watching the skis… I mean, keep watching the skies!

Dense brittlestar colony discovered on Macquarie Ridge seamount.

Deep sea exploration is one of the last and most exciting scientific frontiers on our planet. The 10-year long Census of Marine Life project has already made some pretty cool discoveries. Last month, scientists aboard the Research Vessel Tangaroa of New Zealand’s National Institute of Water & Atmospheric Research (NIWA) discovered an seemingly unlikely colony of starfish-like echinoderms called brittlestars living at the summit of a huge seamount in the Macquarie Ridge, a large underwater mountain range between New Zealand and Antarctica (see map at the end of this post). These critters take advantage of the dramatic 4km/hr ocean current at the summit, capturing prey as it is blown over the seamount. 4km/hr may not sound like much, but you have to consider the immense breadth of the current. According to Dr. Mike Willams of NIWA, “This current is estimated to be 110 to 150 times larger than all the water flowing in all the rivers of the world.” Wow. The ridge where the colony was discovered was about 750 m above the ocean floor, and 90 m below the ocean surface.

While fishermen often catch rare organisms from these places (and toss them overboard), relatively little scientific exploration of the world’s approximately 100,000 seamounts that are taller than 1km above the sea floor has been done (less than 200 of them have been sampled in detail, by CoML’s count). Most have been dominated by corals and sponges, which is why the brittlestars were an unexpected discovery. It’ll certainly be exciting to see what else CoML finds. Check out the press release and the image gallery from the Tangaroa expedition to the Macquarie Ridge.