The 00s Called, They Want Their Website Design Back

So hundreds googlings and SOings and two sugar-driven all-nighter’s later, I’ve got the new “placeholder” tags in my inputs, nifty-gradient backgrounds in my divs, my inputs are modern-ish looking, and my checkboxes, buttons, and selects are all replaced with images. Yay!

Shiny New Website

It’s nothing special. I’m not a web designer. I tried to become one in the 90s, but years of working UI only drilled into my head that I have awful awful awful aesthetic taste. I’m much happier immersed in code, but UIs are something we still have to deal with regularly and this little design sprint reminded me of why it’s such a bother.

Web design requires lots of hacking. CSS has come a very long way and isn’t anywhere near the agony to use that it once was, but the biggest difference between UI development and backend development is still the lack of control. On the backend, we have total control over everything. We know our database, our chosen language, and local environment. When developing a front end for the general public, you have no idea what the user is using to look at your site.

That doesn’t just mean old browsers, but new ones as well. I once lost a fantastic job opportunity because the interviewer looked at a site in my portfolio with the then-brand-new IE6 and it was completely broken. So UI designers aren’t just trying to build sites that degrade gracefully into old browsers, but having to keep up with the latest additions as well.

My weekend hackathon got inspired by this glowing form border, which I ultimately didn’t use, but did apply some gradient backgrounds and animated highlighting from the demo. Because the gradient backgrounds in the demo don’t work in IE, I found a css gradient background generator to produce gradient backgrounds (ironically hosted by Microsoft).

Totally awesome right? But check out the CSS output:


/* IE10 Consumer Preview */
background-image: -ms-radial-gradient(center, circle farthest-corner, #FFFFFF 0%, #96067E 100%);

/* W3C Markup, IE10 Release Preview */
background-image: radial-gradient(circle farthest-corner at center, #FFFFFF 0%, #96067E 100%);


Six definitions for six different browsers, sharply illustrating why web design is still such an incredibly time-consuming headache. This isn’t a hack, this is just freakin’ fugly, but state of things in the wild wild web make it a necessary evil.

Which raises the question in my mind: are design work tricks hacks or kludges? “Hack” implies an elegant solution, while “Kludge” suggests a patch or workaround. Into which category do all the little CSS, JavaScript, and HTML tricks used in design work fall?

Take this example for the Internet Explorer z-index bug, where select input show through absolutely-positioned elements placed above them. So, if I have a pop-up div, and there’s a dropdown box beneath it, the box will come through like so:

Selectors Coming Through a Div

This bug wasn’t fixed until IE8, so it’s still out there in the wild. There are two solutions, one is to use JavaScript to hide all selectors in the page before showing the div. The other, JavaScript-less solution is to put an iframe beneath the div and make it visible at the same time to hide the content below. I can’t describe either of these solutions as “elegant;” however, they get the job done and are a response to an inelegant variable in the environment: an IE bug.

Here’s one specific to this weekend’s work. So I’ve got these list evenly-spaced (fixed min-height) items with various groups of information in each div, and I want them displaying uniformly. So I positioned the folksonomies (fancy word for “tags”) absolutely at the bottom of the div (rather than float, because fixed min-height), and the grouping of related object counts absolutely to the right.


.folksonomies
{
position:absolute;
bottom:4px;
width:70%;
}

.objectcounts
{
position:absolute;
bottom:4px;
right:4px;
}


To produce the following effect (divs highlighted in red):

If only it were so easy. Because I’ve positioned these two elements absolutely, they are now free to overlap with other elements in the div. So when my application outputs an object with too many folksonomies/tags to fit on one line, it pushes the folksonomies div up into the description text like so:

I found lots of recommended solutions to this, like adding clearfixes to the div, which wouldn’t work because I don’t know how many line breaks I need to add to account for the variable number of tags and characters in them. What I ended up doing was outputting the folksonomies content to the browser a second time, positioned normally, and then hiding it. This preserves an empty space with the same height as the visible element:


.folksonomiesHeight
{
width:70%;
visibility:hidden;
}


On the “hack” end of the spectrum, I’ve now got evenly-heighted list items with sub-elements that are positioned identically in each row. Pushing this to the “kludge” side of the spectrum, I’m hiding (duplicated) semantic content on the page. I know Google and other search engines frown upon this. I’m leaning toward this being a kludge, but one that I’m a little proud of.

What do you think? How do you define “elegance” under-the-hood in web design? Is it inelegant to resort to JavaScript tricks? What about duplicating efforts for cross-browser support?

Discussion at Hackernews.

If you’re curious, here’s the site in action. It’s only really been tested in Chrome, with better cross-browser support pushed onto my future todo list. I’ve reopened the site for anyone to open an account, but it is really only intended for my personal use, so suggestions are welcomed, but please set up your own instance if a total lack of user-support is going to be a problem.

My article Never a Magic Bullet: The Personal and Public Dimensions of Gun Ownership and Gun Violence is appearing in the March/April edition of the Humanist. Much of the article is an appeal for rational, civil discourse on the subject, but I did have one dimension where I have a strong opinion. Not surprisingly, it has to do with scientific integrity:

In 1996, Congress stripped the CDC’s National Center for Injury Prevention and Control of funding for research that “may be used to advocate or promote gun control.” In 2010 the NRA successfully lobbied to have restrictions placed on the ability of doctors to gather data about patient gun use into the Affordable Health Care for America Act. In 2012 the National Institutes of Health (NIH) was prohibited from spending money “to advocate or promote gun control.” Most egregiously, a 2011 bill signed into law by Florida Gov. Rick Scott made it illegal for doctors in the state to ask patients if they own guns, preventing even pediatricians from asking parents if their guns are stored safely away from children.

The Humanist website doesn’t link to sources, so I thought I would post my references here in the interest of transparency and for anyone seeking deeper information on anything:

Never a Magic Bullet

References

• Details of the Sany Hook shooting: Wikipedia.org (2013), Sandy Hook Elementary School Shooting.
• List of recent mass shootings: Adams, Becket (2012), The List of the Deadliest U.S. Shootings – and Where This Latest One Now Ranks, TheBlaze.com.
• 40 and 47 percent of households have a gun: Saad, Lydia (2011), Self-Reported Gun Ownership in U.S. Is Highest Since 1993, Gallup Politics.
• FBI: 2011 728 murders due to beats VS 8,583 due to firearms: Block, Melissa (2013), NRA Head: Registry Of Gun Owners Would Be Very Dangerous, NPR.org.
• Mexico firearms murder rate: “2011 Global Study on Homicide”. United Nations Office on Drugs and Crime (UNODC). Retrieved 2012-12-18.
• NRA pushed to prevent doctors from gathering data about patient gun use in Affordable Health Care Act: Wallsten, Peter and Hamburger, Tom (2012), NRA fingerprints in landmark health-care law, Washington Post.
• Harvard Injury Control Research Center: Firearms Research.
• CDC on effectiveness of the Assault Weapons Ban: First Reports Evaluating the Effectiveness of Strategies for Preventing Violence: Firearms Laws, CDC, 3 Oct 2003.
• Congress stripped CDC of funding for research on gun-related injuries: Don Kates, Henry E. Schaffer & William B. Waters IV (1997), Public Health Pot Shots: How the CDC succumbed to the Gun “Epidemic”, Reason, April 1997.
• NIH Spending restrictions: National Institutes of Health (2012), Notice of Legislative Mandates in Effect for FY2012.
• Rick Scott Florida doctore/gun bill: Allen, Gret (2011), Florida Bill Could Muzzle Doctors On Gun Safety, NPR.org.
• PubMed “gun violence” (in quotes) search results.
• Violent Crime Trends: Bureau of Justic Statistics (2012), Key Facts At A Glance: Violent crime trends.

I love love love The Big Bang Theory (BBT). I love the intelligent science references, the highly-debatable geek-culture references, and the cameos only a nerd would enjoy. Most of all, the portrayal of idiosyncratic individuals who bare an incredible resemblance to people I’ve had to deal with for decades working in IT and hanging out at Cons and Comic shops.

So it comes as a shock to me that there is a lot of hate for BBT in geek culture. Many geeks seem to loathe the way the show portrays geek mannerisms, habits, and argue that the show invites normal people to laugh at geeks and encourages belittling them. The show is simply a televised extension of the bullying we had to endure in high school. Geeks see it as validating that abuse through the reactions of the “hot girl” Penny, who lives across the hall from the geeks and whose reactions to the geeks are a source of amusement for the audience.

I don’t see it, and I’m honestly offended at some of the opinions and parochialism being exhibited by some of my fellow geeks. Defending an opinion isn’t like defending a scientific position, I can’t cite journal papers and research to back it up, but I can use logic and anecdotal evidence. So here it goes…

My Nerd and Geek Cred

Before we get into the criticisms of the show, I need to take a moment to address my qualifications and my definitions of the terms “nerd” and “geek,” of which I consider myself both. But these tendencies, for myself and others, fall along a spectrum. It’s like we need a Kinsey homosexuality scale, but for individuals along the nerd-geek spectrum.

What’s the difference? To me, the term nerd refers to the intellectual, academic bent. Straight-A students, Ph.D candidates, engineers, scientists, computer programmers and other professionally-focused individuals rank high on their nerdiness. Geek refers to the gamers, comic-book readers, the Whovians, cosplayers, furries, LARPers, and other individuals obsessively interested in knowing all the trivia of a fictional mythos. The difference between nerd and geek is the difference between left and right brain, type A and B personalities, empirical and artsy, conservative and liberal. It’s the difference between CP Snow’s Two Cultures. Yeah, it’s a false dichotomy, but it’s a useful one.

I tend to straddle both worlds. On my nerd side, I’ve worked in Information Technology for 15 years, serving as Senior Software Developer at two organizations, into science and technology news, was fourth-chair on the high school chess club, and a member of Mensa through hard work and practice rather than natural talent. On my geek side, I grew up with Advanced Dungeons & Dragons (AD&D), Star Frontiers, Gamma World, and Vampire. I devoured books by Douglas Adams, Alan Dean Foster, Terry Brooks, and Arthur C. Clarke, turning to Isaac Asimov, William Gibson, David Brin, Greg Bear, and Vernor Vinge as an adult.

Credit: xkcd

For years I volunteered at a comic and gaming shop. There I setup a computer lab for LAN tournaments, and, when that failed, I continued to volunteer at watching the shop because I enjoyed being there so much. I ran and judged Friday Night Magic (FNM) tournaments for years because the energy and enthusiasm of the players was so addictive. My geek side is pure fun and entertainment, but my nerd side is what I’m trying to do productively professionally with my life.

So these are my qualifications. Let’s move on to the problems many have with BBT.

Criticisms of BBT

These are the most common complaints I hear about BBT, and I’m going to work from the most valid to the most invalid to one complaint that is outright offensive and should be condemned every time it is brought up.

Unrealistic Characters

Okay. I’ll give you half credit for this one. Yes. The characters on the show are too nerdy to be that geeky. You can’t hold a job as published academic and have the time to play MMORPGs, obsess over movies, comics, cosplay, and hang out at comic shops all the time. As I mentioned above, when I’m geeking out, my nerdy starts to slip. I can’t maintain my ability to write elegant code and burn through video games, comics, and science fiction books at the same time. There’s gotta be a balance.

But the same criticism applies to Sex and the City, where the main character spends all her time on sex or drama or shoes or whatever the show is about, because I’m pretty damn sure it’s not about her writing, despite the fact that writing is what a writer does, because that would be boring. Or how the characters on the show Friends never seem to be at the fulltime jobs they would need to maintain their large New York apartments. At least BBT spends time showing the characters in their labs and offices. Sure they are supergeeks and supernerds for being able to hold down such demanding jobs and play D&D, MMORPGs, or enjoy Star Trek marathons, but we watch television to escape the mundane reality that we can’t do everything in life, but we can vicariously enjoy the BBT gang doing it all.

The Laugh Track

The show is filmed in front of a live audience. It’s not surprising that southern Californians, who I don’t stereotype as being very geeky, might laugh at inappropriate times or at the stereotype of geeks, but I could be wrong. They could be laughing for the same reason my wife and I like to see comedies in the theater on opening weekends, even stupid ones, because you pick up the energy of the crowd and even not-so-funny things quickly escalate to hilarity because you are in a room full of laughter. Yes, there’s something Pavlovian about it, and if it makes you feel superior to point that out, then that response demonstrates an addiction to feeling superior and that is Pavolovian as well. Bazinga. As UCLA physicist Dr. David Saltzberg explains from watching the process of taping the show, it’s very scientific:

First of all, they tape in front of a live audience and they make changes based on whether the comedy works or not—whether people laugh. So I like to see which cut they went with. That’s kind of an interesting thing. Comedy is an empirical science. You can have a lot of theories about whether something’s funny or not, but in the end either the audience laughs or they don’t. So you can test your theory very quickly—quicker than the theorists get to do.

So let’s acknowledge the live audience as a useful tool to get viewers at home energized and put it aside.

The Actors Aren’t Nerds

So I’ve seen the amusing but uninspiring BBT Panels at Comic-Con, and smiled when the audience booed Jim Parsons (Sheldon) for not knowing what a TARDIS is. In the special features interviews, Parsons admits he really has to work to memorize his lines because he has no idea what any of it means.

The only actor bringing academic credentials to the table is Mayim Bialik (Amy), who has a Ph.D. in Neuroscience, but who is also anti-vaccine, and that’s disturbing. I’m troubled with some of her anti-science positions, but then her offenses are fairly mild compared with Dr. Oz, who could be the Carl Sagan of medicine if we would stop promoting dangerous unproven alternative medicines. I truly wish people would learn to go to the journals for their science and learn to take a critical eye to the research methodologies used in the peer-reviewed papers, but inadequate educational standards and a lack of open-access makes this just a wishful thinking. That beings said, I haven’t seen any unscientific opinions make it into the show.

So let’s accept that actors are meatpuppets who get far far too much admiration for their jobs than they deserve and move on.

The Sexism

io9 got really offended and snarky over the fact that BBT was previewing an episode where the female characters venture into the Comic Shop:

…in this Thursday’s episode, the show may have gone too far as it presents the utterly ludicrous premise that a girl — several of them, in fact! — would willingly go into a comic book store! Silly girls! There are no clothes or make-up in there! Just boys, who are unable to function socially with members of the opposite sex, to the point that merely seeing females puts them into a catatonic stupor! Because they’re nerds! Ha ha!

Funny thing is, I’ve personally seen firsthand what happens in the comic shop when hot girls walk in. You should have seen the hush fall over the Saturday Yu-Gi-Oh! players, watched their jaws drop, and heard one exclamation of “Whoa!” when my future wife paid a visit to me in the shop one day. You should have seen the uncomfortable silence and shoe-staring that went on one FNM when a group of six hot girls on their way to the nightclub down the block came into our shop to interrogate me about what we were up to every Friday night. The shop owner used to joke that people thought the store was a sex shop, since he’d named it Duf’s Playhouse and there were “nothing but ugly guys hanging out there all day.”

So when Amy, Bernadette, and Penny walk into the comic shop on BBT and an uncomfortable hush falls over the geeks and they stop and stare, I laughed my ass off. But I totally understand why most geeks wouldn’t laugh. It’s not funny if you’re one of those stunned, lonely fellows and you have no humor about yourself (ie. 25% of the geeks at the shop). I didn’t date much in high school or college, but I’ve (almost) always been able to keep up a sense of humor about it.

This being said. Chuck Lorre, the show’s producer, is a misogynistic fratboy and I really have a hard time with the overt sexism in first few seasons of BBT–especially the Howard Wolowitz character. But the show evolved and grew more mature over the years. Howard became a sweetheart and, in one very touching episode, renounced his lecherous past and has abstained from crass jokes since. The show brought two very strong and intelligent female characters on permanently, and even started giving them their own storylines and side plots.

The show is actually much less sexist now in a lot of ways than actual nerd and geek culture, I’m sorry to say. When I was young, there were no, none, zero, zip, nada girls into comics and RPGs, but while I’m happy to say that’s changed with women getting into video games, anime, and even MtG, there is a lot of backlash from male geeks. Nowhere is this geek territorialism more appalling than in the idiot nerd girl meme:

Idiot Nerd Girl

Not only is this meme offensive for the way it stereotypes and ostracizes, but the geeks making this stuff up are really putting their own ignorance on display with their tunnel-vision understanding of geek culture that reduces the vast world of geekdom down to their personal pet obsession (Dragonball-Z, WoW, X-Box Live). I don’t mind ignorance, and I love to share the history of science fiction memes and old-school anime with younger geeks, but the guys making up these offensively stupid images are the ones I have an uncontrollable need to publicly humiliate for their lack of depth.

Somma’s Rule of Knowledge: Public exclamations of shock at the ignorance of an individual concerning a piece of knowledge is actually a public display of personal ignorance of the vastness of human knowledge. So if you think less of someone for not getting your Whovian, Trekkie, WoW, Star Wars, LotR, Mass Effect, Starcraft, Dragonball, Walking Dead, Game of Thrones, Foundation, X-men, Batman, Hulk, Hellboy, D&D, Wheel of Time, Pathfinder, Hitchhiker’s, Portal, Zelda, Warhammer, Vampire, Red vs Blue, Akira, Star Frontiers, MST3K, Stargate, Macross, Farscape, or other reference, then you have no comprehension of the vast scope of geek culture.

Q.E. to the mother-#$%&in’ D.!

HANG YOUR HEAD IN SHAME!!!

Idiot Nerd Girl Response

So kudos to BBT for letting girls into the clubhouse

Ridiculing Nerds/Geeks

Sam Lowry of Discover Magazine blog Science Not Fiction has a post lamenting the sad portrayal of scientists on BBT:

Three of the four main characters are scientists with limited romantic prospects. Howard lives with his mother and inhabits an imaginary world where his Beatles haircut makes him irresistible to women. Raj finds himself unable to speak when the nerds’ sexy neighbor is in the apartment. Sheldon apparently has a sitcom version of Asperger’s Syndrome.

He goes on to say these negative portrayals reinforce stereotypes of nerds that dissuade kids from going into the sciences. I’m sure this is true to a degree, and that’s unfortunate, but then I read the comments in response to the criticisms and I find lots and lots of scientists and engineers like myself who find the show hilarious and really appreciate the technobabble that the writers took the time to make comprehensible to the nerds watching the show.

I’ve also seen comments on several threads comparing BBT to Amos and Andy, in the way it stereotypes and demeans nerds and geeks. This is incredibly offensive to African Americans. Think about it. These people are equating the act of making fun of someone who’s quirky and occasionally bullied to making fun of someone who doesn’t have the right to vote or could be lynched for disrespecting the wrong person. Don’t ever compare the (very real) bullying of nerds and geeks to the total systematic oppression of a group of people based on their skin color.

BBT is to geeks what Good Times or Jeffersons was to African Americans, or Queer Eye for the Straight Guy for homosexuals, or Seinfeld for Jews. BBT makes geeks and nerds a little more accessible to the mainstream public. It’s a gateway show.

And geeks need that. We are fraking weird. I’m keenly familiar with the uncomfortable feeling of being cornered in a comic shop by a male 28-year-old Sailor Moon fanatic who insists on doing his impression of every single one of the Sailor shouts for me. I’ve spent entire days continually trying to politely excuse myself from a conversation where a MtG geek or Dragonball fan won’t stop talking about their interest despite the fact that I have no idea what they’re talking about and will even tell them so. I think it’s preferable for people to feel comfortable laughing at that than to react with fear, which some people do.

An example of such fear is a bookstore owner I was talking to about science fiction. She told me her son loved to collect Yu-Gi-Oh! cards. When I told her she should bring her son out to the weekly Saturday Yu-Gi-Oh! tournament, where he could meet other fans of the game and make some friends, she lamented that she would love to, “But there are some older men at that shop too. There’s something really creepy about a man in his sixties playing children’s games.”

I didn’t know how to respond at the time, but if I had it to do over, I would have told her that man is named Pat, and Pat hangs out in the shop all day because he is independently wealthy from working on the year-2000 bug and wants to spend his retirement playing all sorts of games. That’s because Pat is a gamer, and he’s one of the most brilliant people I’ve ever met in my life. Your son could learn a lot from hanging out with Pat, who does come across as a Monty Python flavor of insane, but that’s just his sense of humor and you learn to love it when you get used to it. The kids at the shop freakin’ love Pat, and Pat would fit in perfectly with the BBT gang.

In all fairness, if we are to take a critical eye to BBT’s portrayal of nerds and geeks, then we also need to look at how the show portrays “norms” like Leonard’s love-interest Penny. The show had a great time with one of her boyfriends, Zack, an attractive, well-meaning man, who is also a total airhead. The quartet of nerds made fun of him endlessly right to his face with jokes that went over his head (There’s also a great opening bit where the gang reflects lasers off mirrors placed on the Moon and Zack gets freaked out that science might destroy it (The Moon.)).

Then there’s Penny herself. A lot of people argue the show is making fun of nerds because we are supposed to identify with her character and share her reaction to their weirdness. This ignores the fact that Penny, while attractive, isn’t a role model. She’s ditzy, underemployed, promiscuous, drinks too much, and is superficial. If audience members who identify with her are laughing at me, then, when I watch Penny, I am laughing at them. Take this exchange as an example:

Penny: I’m a Sagittarius, which probably tells you way more than you need to know.

Sheldon: Yes, it tells us that you participate in the mass cultural delusion that the sun’s apparent position relative to arbitrarily defined constellations at the time of your birth somehow affects your personality.

Penny: Participate in the what?

Or consider Amy’s jab at Penny in comparing her to Leonard’s new girlfriend, “Granted, Penny, your secondary sexual characteristics are reasonably bodacious, but Priya is highly educated, she’s an accomplished professional, and she comes from the culture that literally wrote the book on neat ways to have sex. Whereas you on the other hand are a community college dropout who comes from the culture that wrote the book on tipping cows.”

Yeah. This is a show that helps stupid people laugh at nerds and geeks. <sarcasm>RIGHT.</sarcasm>

Making fun of “Special Needs” People

One of the most offensive criticisms of BBT is the disturbing number of people who claim that Sheldon is autistic and the show invites us to laugh at his illness:

The way that even the three guys laugh at Sheldon seems especially cruel. Yes, he’s painted as annoying, as an inconvenience and as just plain rude, however he is also read by many as autistic. So much so that my friend who works at a school for autistic children believed he had Asperger’s Syndrome and once asked me how they got away with ridiculing a character with special needs. I explained to her that no, Sheldon is not canonically autistic and she was shocked. She told me that he was a totally accurate portrayal of someone on the autistic spectrum and had many characteristics of someone with Asperger’s – specifically the inability to recognise sarcasm or understand human emotion as well as the obsession with “his spot” and his distress when routine is changed. Sheldon is consistently positioned as someone to be laughed at. It’s made to seem ok by the fact that his friends are laughing at him too and, of course, he isn’t technically autistic he’s just almost indistinguishable from someone who is.

If you think Sheldon is autistic, then you have never met an autistic person. We had an autistic kid who hung out at our shop on Saturdays. It was tough. He would bring boxes of toys in with him to pile up on one of the tables. The slightest thing could set him off into a screaming rage fit. His mom appreciated us because we didn’t think anything of it. What’s the difference between an autistic teenager throwing a temper tantrum over forgetting one of his toys and a geek teenager throwing a temper tantrum over his 8th level dwarven barbarian getting killed in a fictional barfight? (Yes, that actually happened one night.)

That last comparison bit is a joke, but autism is not a laughing matter. When you argue that Sheldon is a “totally accurate portrayal of someone on the autistic spectrum,” then you have broadened the definition of autism to the point where you have rendered the word meaningless. That seriously offends me. It offends me on behalf of the mothers and fathers who are living with autistic children who are now adults and still require constant supervision, are still in diapers, or still have violent humiliating outbursts in public. Go listen to this account of the daily trials of two parents living with an autistic child, and you’ll understand how ignorant and disrespectful it is to compare the quirky physicist on a sitcom to someone with a seriously debilitating mental illness that consumes the lives of those caring for them.

While he does not have autism, Sheldon certainly does seem to have a mild/more-than-mild case of Obsessive Compulsive Disorder (OCD), urging him to seek out the seat in the movie theater with optimal acoustics, secure a favorite seat in the apartment, perform actions in threes, agonize over keeping his comic book collection pristine, submit Leonard to an extensive legalistic roommate contract, or maintain a “five napkin system” at lunch. I don’t know if making fun of people with OCD is okay, but the TV show Monk, Howard Stern, and films like As Good as It Gets have been doing so for years.

But people claiming Sheldon qualifies for any Diagnostic and Statistical Manual illness are missing the most important criteria for diagnosing a mental disorder: Is the individual suffering? Sheldon is not suffering. He is proud. He is genuinely superior to those around him and has no problems pointing it out. I’ve got 15 years working in Information Technology; I’ve met plenty of fully-functional, perfectly happy and incredibly irritating OCD people over the years. So I’m not laughing at Sheldon, I’m laughing with the characters who have to deal with him because I’ve been there.

Why I Love BBT

The Intro

My 18-month-old son loves this intro, and so do I. There’s just so much going on, it takes many viewings to appreciate it. I’m not a Bare Naked Ladies fan, but this song is awesome (TMBG would be better though, sorry):

The Science References and Cameos

A search for scientific inaccuracies in BBT turned up this single example:

I was re-watching Big Bang and noticed that on Season 3, Episode 3, The Gothowitz Deviation, they completely screwed up their reference to and use of operant conditioning. The core tools of operant conditioning, are either positive (delivered following a response), or negative (withdrawn following a response). In Big Bang theory they use the popular forms of “positive” and “negative,” as in, it’s a “positive” experience to get yummy chocolate and a “negative” experience to be electrocuted, however by the rules of operant conditioning both of these things would be positive because they add stimulus following a behavior.

True. BBT got that wrong, but thanks to Dr. Saltzberg, the show gets much much more right. Schrodinger’s Cat, Isaac Newton, Richard Feynman, Occam’s Razor, Sheldon getting caught in an infinite loop of his own algorithm, the list of accurate science references that provide an additional level of humor for those in the know or those willing to hit Wikipedia to get in the know goes on and on.

Sheldon’s “Doppler Effect” costume.

Then there’s the cameos. Niel DeGrasse Tyson, Stephen Hawking, Ira Flatow, and many other big names in science popularization appear on the show, humanizing science in the process. This scene making fun of popular science author Brian Greene is hilarious, puts a human face on quantum physics, and provides in-jokes for those of use immersed in science culture:

Another example is Sheldon’s comment to Nobel laureate George Smoot when arguing over whose name should take precedence on a research work, “You won the Nobel prize, what, three years ago? So you must deal with a whole lot of “what has Smoot done lately?” My thought is we continue my research as team, you know, Cooper-Smoot, alphabetical. When we win the Nobel Prize, you’ll be back on top.”

The Jokes

Here are more concrete examples of what I keep talking about. These are funny jokes, but they are only funny if you understand enough of the technobabble to get the joke:

Accurate Technobabble: “Yes! Well, I’m polarized tree sap and you’re inorganic adhesive, so whatever verbal projectile you launch in my direction it’s reflected off of me, returns on its original trajectory and adheres to you.”

Leonard remarks that a Tequila Sunrise is a “wonderful example of how liquids with different specific gravities interact in a cylindrical container.”

On Star Trek transporters: “Assuming a device could be invented, which would identify the quantum state of matter of an individual in one location and transmit that pattern to a distant location for reassembly. You would not have actually transported the individual, you would have destroyed him in one location and recreated him in another.”

Wolowitz: Have you tried rebooting him?

Leonard: No, I think it’s a firmware problem.

Evolutionary adaptation: “If influenza was only contagious after symptoms appear, it would have died out thousands of years ago. Somewhere between tool using and cave painting, Homo habilis would have figured out to kill the guy with the runny nose.”

“We have to take in nourishment, expel waste, and inhale enough oxygen to keep our cells from dying. Everything else is optional.”

In response to the question, “why is this letter in the trash?”: “Well, there’s always the possibility that a trash can spontaneously formed around the letter, but Occam’s Razor would suggest that someone threw it out.”

“I trusted you with my e-mail address, and you betrayed that trust by sending me Internet banality.”

Sheldon: It’s a bust of Sir Isaac Newton.

Penny: Oh sure, sure. Very Christmasy.

Sheldon: Well, excuse me, it’s much more Christmasy than anything you put on the tree.

Leonard: Here we go…

Sheldon: December 25th, 1642. Julian calendar. Sir Issac Newton is born. Jesus, however, was actually born in the summer. His birthday was moved to coincide with the traditional pagan holiday that celebrates the winter solstice with lit fires and slaughtered guts, which frankly sounds like more fun than twelve hours of Church with my mother, followed by fruit cake.

That reminds me, BBT is the only show on television that I’m aware of having an unabashed atheist as its most popular character. That’s awesome too.

The Pain of Being a Geek

If there is one complaint I have about BBT, is that it does make light of the fact that oftentimes it’s really painfully lonely to be a geek. Being a Geek means being ostracized, demeaned, and bullied, and it’s very difficult to let that go. “Geeks have scars.” as one commenter succinctly noted.

It seems to me that a lot of the resentment toward BBT and the new wave of nerd-girls stems from this pain. It’s not fair, many geeks reason, that people are being let into the club without paying their dues. Like Hipsters with their “I was into X before X was cool.” There’s a division between the geeks who grew up playing pencil and paper RPGs, programming C64s, BBSing, and put together model space ships, versus the new wave of geeks into the highly-commercialized anime, superhero movies, and video games with a very low entry bar to indulgence. I can understand the anger at our former bullies suddenly wanting to be geeks. People who are into “Watching movies based on comics instead of reading the comics,” as one commenter put it.

Today there are so many subcultures of geek, we are all geeks in relation to other geeks. I respect Dr. Who, but I don’t have the time to watch it. I’ve recently become obsessed with the science fiction worlds of Mass Effect, but that’s geekery I must keep to myself. Fantasy-dorks are geeks to me because science fiction is sooooo much more rewarding. I’m fairly over superhero comics, so there are some more geeks to me, but I love a select few independent, limited-run stories. In the end, however, I respect all of my fellow geeks, even if I don’t share their particular sub-genre interests.

I admit, I hold a bit of envy for the kids who get to watch the mainstream anime on “Toonami,” and even share their enjoyment of those cartoons in conversations with girls at school, while the only way I could get anime growing up was through an underground network of grainy, untranslated VHS bootlegs. I remember observing in my 30s that my sister’s high school friends were into anime and comic books, thinking, How times have changed, and wishing I could have grown up at time when I could share my geeky interests with attractive girls–but then, maybe my personality would have driven me away from anime as too mainstream, and pushed me into the new Maker culture, tinkering with arduinos, or something equally esoteric.

My wife Vicky as Rogue after letting her gray grow out.

I’m very familiar with the uncomfortable furrowed-brow a woman would give me when I accidentally slipped from cool, mature Ryan who works out at the gym into excited, animated Star Trek fanboy Ryan. I lucked out and found a nerdy woman who loves me and is very enthusiastic about watching Star Trek, checking out the latest special-effects scifi movie in the theaters, or reading the occasional gem of a science fiction novel I get excited about. Introverts get their energy from ideas and not people, where the dating scene is all about people getting energy from people. Geeks are about ideas, so it’s very hard for them to find love.

BBT acknowledges that loneliness and pain, but maybe its offense is that it doesn’t take it seriously enough–and I don’t know how it could approach the subject seriously. The nerds get bullied, but I’m not laughing with the bully, I’m laughing sympathetically with the nerds because I’ve been there. The nerds are awkward with women, but I’m not laughing at their loneliness, again I’m laughing with the sympathy of someone who’s been there–and as someone who knows that it gets better.

It really does, and maybe that’s how BBT appropriately handles the very real downsides of being a nerd or geek, by showing how nerds and geeks are ultimately superior to the norms. Laugh at Sheldon all you want, his character is rolling in cash he doesn’t even need. Go ahead and laugh at Howard, but his character got to look down on you from the ISS. Laugh at all of them, but they are traveling the world and living life to the fullest. BBT portrays the fact that the nerds seriously begin to outpace the norms at the game of life the older we get. Beauty fades, popularity becomes trivial, the life of a “norm” is often one of stasis, but intellectual pursuits only become more rewarding as we grow older. BBT celebrates that, and I think that’s a good thing.

SMBC comic

Update: This post kicked off a lively debate over at HackerNews.

Mount Ranier Panorama
Credit: Tyler Foote

I hope everyone enjoyed their holiday dinosaur this Thanksgiving, and thank you joining me in this delightful excursion out into the wide wonderful world of ideas and expressions in evolution.

Chronicle Canyon

History in the layers and controversies in the stories they tell.

MicroCosmos Pond

The smooth surface hides a tiny world packed with ideas.

Slime Molds Against a Pink Background
Credit: Alex Wild
This image is copyrighted, posted here as fair use. You can order prints of these photographs at: Alex Wild Photography

Alex Wild of Compound Eye brings us Starving to be Social: The Odd Life of Dictyostelium Slime Molds that features a photo essay of slime molds he took from a visit to Joan Strassmann and David Queller’s lab at Washington University in St. Louis. You can also see more his spine-tingling photos and order prints at Alex Wild Photography. (Via Bjørn Østman’s of Pleiotropy)

Adaptation Ascent

A tough climb challenges your fitness.

Walking striped hyena
Credit: Tambako the Jaguar

Guest blogger at Scientific American Kate Shaw’s How Aggressive Hyena Moms Give Their Kids a Boost takes the reader through the social hierarchy of hyena clans, which she has spent countless hours studying in person, to help us understand why the females of the species are so masculinized, even having “pseudopenises that mimic male genitalia.” (Via Bjørn Østman’s of Pleiotropy)

IAD Model

Bjørn Østman’s post Pleiotropy saves the day for evolving new genes explores the origin of new genes via Näsvall et al’s innovation-amplification-divergene model (IAD), where a gene “becomes pleiotropic, is copied, followed by divergence, and then loss of pleiotropy.”

Disputation Pass

Don’t lose your way at this rocky intersection.

The Trail to Forester Pass
Credit: Alan Grinberg

Unique Overlook

Take a breather here and stretch your mind.

Tree of Animal Life

David Morrison of The Genealogical World of Phylogenetic Networks has an article up on Family trees, pedigrees and hybridization networks, illuminating the fact that a “family tree” is actually a pedigree, a hybridization network, where branches fuse at points as a result of inbreeding. He then starkly illustrates this using the family tree of the Spanish Habsburgs royal family.

While family trees are really networks, Morrison also provides many examples of Relationship trees drawn like real trees throughout history.

Editor’s Parking Lot

For the ride home.

Be sure to check out CoE #55 at Genome Engineering on January 2, 2012! Be sure to get your submissions in!

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The Science Fiction of Meditation

Star Wars: The Phantom Menace was a deeply flawed movie on many levels, but there was one moment in the film that I thought was brilliant. The Jedi master Qui-Gon Jinn is in the heat of a duel with the Sith lord Darth Maul, when a force field comes in between them, momentarily pausing their battle. Darth Maul impatiently paces back and forth along the shield, staring at his opponent with murderous rage. Qui-Gon, in contrast, drops to his knees and begins meditating.

Qui-Gon Jinn Meditating
Credit: 20th Century Fox / Lucasfilm

I recently spent a Saturday morning at a meditation workshop hosted by Amma Sri Karunamayi, where I followed a warm-up yoga session taught by my brother (yes, the same one from this epic debate of religion vs science), who was also her devote, with three straight hours of mindfulness meditation interrupted every half hour with my need to change sitting positions in order to restore feeling to my legs. As a skeptic, I had to resist the urge to roll my eyes when they spoke of magical energies stirred by the yogic practice, feeding jade idols butter, and sitting in the presence of a woman who is supposedly the latest incarnation of some Hindu goddess, but also as a skeptic I am open to new experiences and practicing mindfulness meditation for three hours in a group setting where social pressures would help keep me focused was something I strongly desired to try, and I confess I came out of the experience fairly high. I felt like I was floating, calmly detached from the world around me. The feeling carried me through an hour of beltway traffic and I remained non-stressed for the rest of the day.

It was a high very similar to one I would get as a youth from immersing myself in a good book or going deep on a programming task for several hours. Not surprisingly, I was also discovering Star Trek at that time in my life, and was idolizing Mr. Spock for his emotional detachment the cool logic I hoped would help me survive middle school and admired later in life for the idealization of mental discipline. Vulcans are often portrayed in a state of meditation, and Trekkers describe three types of Vulcan meditation:

Mental meditations have the purpose of developing the intellect. One might consider doing a logic puzzle or studying a foreign language a mental meditation, albeit a simple one. Emotional meditations explore the breadth and flavor of our emotions: for one cannot hope to control a thing without first understanding it. Physical meditations consist of various strenuous exercises done in a particularly mindful manner.

I do like the idea of mental and physical meditations, and do practice such disciplines in real life, but the definition here of “emotional meditations” is highly lacking. It doesn’t make sense that one would “explore the breadth and flavor” of something one wants mastery over, but is it possible to cognitively master one’s emotional states and calm the mind of all its chatter?

Mindfulness Meditation

Be Here Now
Credit: debs

The scientific mind can “entertain a thought without accepting it,” to quote Aristotle. So I can consider meditation, a practice that “has been employed as spiritual and healing practice for more than 5,000 years” objectively based on what scientific scrutiny is out there (Chiesa, 2011). Just because something has been around five millennia, doesn’t mean it’s not nonsense, and just because something finds its origins in religion doesn’t mean it is nonsense.

The word “meditation” invokes mental images of Buddhist monks, drums, gongs, and mountaintops. In fact, the Dalai Lama has done much to promote this stereotype by submitting monks to scientific scrutiny as they meditate. However, as a skeptic, if there are cognitive benefits to meditation, then I want just the secular essence of the practice, trimming away as much ritual and philosophy as possible. For this reason, science is primarily interested in mindfulness meditation as defined by psychologists, which is properly defined, not by the spiritual dimensions of its religious origins, but the observable measurable cognitive and behavioral changes it produces in the practitioner:

Across religions and practices, it is generally believed that meditation leads to a minimization of or reduction of thinking and conceptual activity that allows the practitioner to experience the world without cognitive bias, filters, or models built up from past experience. For example, after meditation, the practitioner should be able to approach a typically stressful situation, such as getting stuck in traffic, with a new perspective or response, such as realizing that being stuck gives him or her extra time to talk with his or her child in the backseat. The idea is that the automatic and typical reaction, such as swearing and brooding about disdain for the driver coming up the breakdown lane, now becomes a choice as opposed to an inevitability (Wenk-Sormaz, 2005).

So mindfulness meditation (MM) should help us overcome our “cognitive bias, filters, or models built up from past experience.” In Zen Buddhism, this is known as the concept of Shoshin or “Beginners Mind”:

Rather than observing experience through the filter of our beliefs, assumptions, expectations, and desires, mindfulness involves a direct observation of various objects as if for the first time …mindfulness practice should facilitate the identification of objects in unexpected contexts because one would not bring preconceived beliefs about what should or should not be present (Bishop, 2004).

By eliminating preconceptions, MM should open the mind to see things to which our experiential biases would normally blind us. In much of the literature studying MM the concept of “automation,” our kneejerk reactions to stimuli and tasks we perform without thinking, is studied:

Both Deikman and proponents of early models of automaticity described automatization as the process that occurs with the repetition of an action or behavior wherein the intermediate steps of the behavior disappear from consciousness awareness.

This is also known as the Enstellung effect or the “creation of a mechanized state of mind,” demonstrated with Luchins’and Luchins’ Water Jar Experiment where subjects got into the habit of using the same algorithm to solve all problems, when some problems could be solved with simpler more efficient steps. I personally fall into this trap all the time working on the computer, copying-and-pasting things manually for an hour when I could write a simple script or use a spreadsheet formula to streamline a task or neglecting keyboard shortcuts for the habit of using the much more inefficient mouse to navigate the user interface.

Although it was not listed in the peer-reviewed articles I read, another reason for pursuing Mindfulness Meditation could be to practice seeing the world in a clearer light, without the perceptual illusion of existence distinctive from the world around us. Susan Blackmore, in her book The Meme Machine, describes something very akin to Mindfulness Meditation as a means of overcoming the selfplex, the illusion that there is a conscious self inside our heads distinct from the physical world:

If my understanding of human nature is that there is no conscious self inside then I must live that way–otherwise this is a vain and lifeless theory of human nature. But how can ‘I’ live as though I do not exist, and who would be choosing to do so?

One trick is to concentrate on the present moment–all the time–letting go of any thoughts that come up. This kind of ‘meme-weeding’ requires a great concentration but is most interesting in its effect. If you can concentrate for a few minutes at a time, you will begin to see that in any moment there is no observing self. Suppose you sit and look out of the window. Ideas will come up but these are all past- and future-oriented; so let them go, come back to the present. Just notice what is happening. The mind leaps to label objects with words, but these words take time and are not really in the present. So let them go too. With a lot of practice the world looks different; the idea of a series of events gives way to nothing but change, and the idea of a self who is viewing the scene seems to fall away.

Another way is to pay attention to everything equally. This is an odd practice because things begin to lose their ‘thingness’ and become just changes. Also, it throws up the question of who is paying attention (Blackmore 1995). What becomes obvious, in doing this task, is that attention is always being manipulated by things outside yourself rather than controlled by you. The longer you can sit still and attend to everything, the more obvious it becomes that attention is dragged away by sounds, movements, and most of all thoughts that seem to come from nowhere. These are the memes fighting ti out to grab the information-processing resources of the brain they might use for their propagation. Things that worry you, opinions that you hold, things you want to say to someone, or wish you hadn’t–these all come and grab the attention to everything disarms them and makes it obvious that you never did control the attention; it controlled–and created–you.

These kinds of practices begin to wear away at the false self. In the present moment, attending equally to everything, there is no distinction between myself and the things happening. It is only when ‘I’ want something, respond to something, believe something decide to do something, that ‘I’ suddenly appear. This can be seen directly through experience with enough practice at just being.

This insight is perfectly compatible with memetics. In most people the selfplex is constantly being reinforced. Everything that happens is referred to the self, sensations are referred to the observing self, shifts of attention are attributed to the self, decisions are described as being made by the self, and so on. All this reconfirms and sustains the selfplex, and the result is a quality of consciousness dominated by the sense of ‘I’ in the middle–me in charge, me responsible, me suffering. The effect of one-pointed concentration is to stop the processes that feed the selfplex. Learning to pay attention to everything equally stops self-related memes from grabbing the attention; learning to be fully in the present moment stops speculation about the past and future of the mythical ‘I’. These are tricks that help a human person (body, brain and memes) to drop the false ideas of the selfplex. The quality of consciousness then changes to become open, and spacious, and free of self. The effect is like waking up from a state of confusion–or waking from the meme dream.

Similar to Blackmore’s above concept of losing the “I” illusion is the concept of “decentering” in psychological circles:

A shift in one’s cognitive perspective known as decentering or disidentification is thought to lead to a change in one’s relationship to negative thoughts and feelings such that one can see negative thoughts and feelings simply as passing events in the mind rather than reflections of reality (Lau, 2006).

Professor J. H. Flavell observed that children do not think about thinking, and coined the term metacognition to describe the phenomena of adults being able to pause and evaluate why we feel certain ways. This “cognition about cognition” is an important piece of an adult’s emotional maturity. “Cognitive strategies are invoked to make cognitive progress,” Flavell writes, “metacognitive strategies to monitor it (Flavell, 1979).”

So mindfulness meditation is a kind of metacognition, but also the practice of eliminating cognition. It is the practice of not thinking, but when a thought arises, as our brains have evolved to do, we observe it and let it go. This practice of becoming a blank slate is hypothesized to alleviate our biases, restore our plasticity of mind, allow us to perceive the world more clearly, and improve our emotional well-being.

Science of Mindfulness Meditation

When we look at the iconic photo of Thich Quang Duc’s self-immolation, we cannot help but feel his decades of meditative practice gave him the strength to so stoically endure such a gruesome death.

Journalist Malcolm Browne’s photograph of Thich Quang Duc during his self-immolation.
Credit: wikipedia

How do scientists quantify the emotional and cognitive benefits of meditative practices that are taking place entirely inside the practitioner’s head? When people work out, scientists can observe the growth in their muscles and performance at physical tasks after observing their nutritional intake and workout practices. When people study, scientists can subject them to intelligence and subject matter tests throughout the process to see how effectively they are learning based on source materials and study habits.

Studies on meditation tend fall into two categories: the effects of short-term Mindfulness-Based Stress Reduction (MBSR) courses on the abilities of individuals to perform various tests and the effects of long-term disciplined meditative practice on the physiological structure of the brain.

A justifiable skepticism in the scientific community concerning MM studies because meditation has its origins in religion and is therefore subject to selection bias. Studies must eliminate the religion bias by using secular meditation and random subjects (Wenk-Sormaz, 2005). An additional problem with studies involving long-term meditators is that results are only corollary, as we don’t know if meditative practice results in improved cognition or if individuals with better cognitive skills are drawn to meditative practice. The problem with short-term subjects taking part in a weekend retreat is that we don’t get to measure the long-term effects of MM; additionally, since most studies are performed by psychology college professors, they are also subject to the selection bias of using college students, the “white rat” of human experimentation (Smart, 1966). None of the studies I read on this subject seemed to really get away from these biases, so their findings need to be considered in that light.

Another issue in studying the effects of mindfulness meditation is establishing a consensus definition of what it means to practice it. MM is Incorporated into Mindfulness Based Stress Reduction (MBSR), Mindfulness Based Cognitive Therapy (MBCT), Dialectical Behavior Therapy (DBT), Acceptance and Commitment Therapy (ACT), each with their own slightly different take on it. So what is the essence of MM? Here’s one summary of the literature:

The first component of mindfulness is usually referred to as a mental state characterized by full attention to internal and external experiences as they occur in the present moment. The second component is usually described as a particular attitude characterized by non-judgment of, and openness to, current experience, which is supposed to lead to higher levels of exposure to negative stimuli and emotions as well as to higher acceptance and concurrent reduction of experiential avoidance (Cheisa, 2010).

There is also the issue of quantification. What are we to measure in the MM practitioner? Meditation must result in a distinctive and reproducible state with reportable phenomena, the state must develop specific traits, there must be measurable progress in the practices (Lutz, 2007). Here is a survey of different results various studies have attempted to measure in subjects:

A number of processes have been proposed to underlie training in mindfulness. The most commonly cited of these is relaxation (Dunn, Hartigan, & Mikulas, 1999), although it has been suggested that this is at most a beneficial side effect of mindfulness practice, rather than an inherent process (Baer, 2003). Another hypothesized process is a reduction in over-general autobiographical memory (Williams, Teasdale, Segal, & Soulsby, 2000). There may also be an erosion of the use of literal, evaluative language (Hayes, 2003; Hayes & Shenk, 2004). Acknowledging rather than evaluating thought processes circumvents the usual cognitive defenses which attempt to prolong or avoid such processes. This results in an increased range and flexibility of actions (Hayes, 2003) and has been termed cognitive flexibility (Roemer & Orsillo, 2003). Mindfulness training may also facilitate metacognitive insight (Bishop et al., 2004; Mason & Hargreaves, 2001; Teasdale, 1999; Teasdale, Segal, & Williams, 1995). This represents a transition toward viewing thoughts as ephemeral mental events, rather than as direct representations of reality. Such “decentering” somewhat distances us from our problematic thoughts and emotions, allowing us to address them consciously rather than merely reacting to them (Chambers,2008).

How are these measured? With a wide variety of psychological assessment tools such as the Tellegen Absorption Scale (TAS), Situational Self-Awareness Scale (SSAS), Cognitive Failures Questionnaire (CFQ), Dissociative Experiences Scale (DES), NEO-Five Factor Inventory (NEO_FFI), Psychological Mindedness Scale (PMS), Rumination-Reflection Questionnaire (RRQ), Marlow-Crowne Social Desirability Scale, Kentucky Inventory of Mindfulness Scale (KIMS), Mindful Attention Awareness Scale (MAAS), Mindfulness Questionare (MQ), Revised Cognitive and Affective Mindfulness Scale (CAMS-R), and many others (Where possible, I have attempted to link to actual versions of tests, then wikipedia articles, and finally abstracts on them).

One very common test is the stroop task for measuring deautomization, where participants identify the color of a word that identifies a different color.

Stroop Task

The stroop task is a favorite for measuring deautomation because:

The automatic semantic activation of the word meaning must be overridden in order for participants to respond correctly when faced with incongruent words. As reading is automatic for proficient readers less attentional resources are required for reading irrelevant (neutral) words than for ink colour naming. Consequently, the reading of the word appears obligatory and results in an increase in reaction times and errors when attempting to process incongruent colour words. Increasing the performance in this task would therefore require the reinvestment of attention (deautomatisation) and a non-habitual response (Moore, 2009).

Other tests are intended to measure autobiographical memory, which “works by first recalling a generalized memory, then specific events are recalled from that generalization. If the process is interrupted, then we are left with only the overgeneralized memory (OGM).” Subjects are tested on their ability to recall details of past events, requiring focus, reflection, and emotional stability.

Still others test subjects’ attention. For instance the Change Blindness Flickering Task flashes the same photo twice with one difference between the two instances (ie. the height of a railing behind a couple), or the Gorrilla Video, where the subject is tasked with counting dribbles and passes of basketball players in a video and a person in a gorilla suit walks behind the scene, but 22% of participates don’t notice (Hodgins, 2010).

Experimentally-Observed Benefits of Mindfulness Meditation

Cognitive Flexibility

A picture–or in this case a scatter plot graph–paints a thousand words, so check out how meditators do against non-meditators on the stroop and concentration tasks:

Meditators VS Non-Meditators
(Moore, 2009)

These near-linear results explained:

Positive correlations were found with the d2-scores TN (r = .510, p < .001), TN _ E (r = .620, p < .01), CP (r = .667, p < .01) and the Stroop-score TNP (r = .331, p < .05). This indicates that high levels of mindfulness are correlated with high processing speed, good attentional and inhibitory control, and a good coordination of speed with concurrent accurate performance. Negative correlations were found with the d2-errors E (r = +/-.527, p < .001), E1 (r = +/-.493, p < .001), E2 (r = +/-.398, p < .01) and the Stroop error SE (r = +/-.780, p < .001), signifying that higher levels of mindfulness are linked to reduced errors across measures, suggesting greater attentional control, accuracy of visual scanning, inhibitory control, carefulness, cognitive ?exibility and quality of performance. These results support the hypothesis that mindfulness would correlate positively with task performance. (Moore, 2009)

The sample-size for the above study was small however, consisting of 25 Buddhist meditators and 25 non-meditators recruited from a local credit management company. So the study doesn’t isolate the meditative practice from the religious practice, but it is interesting that the Buddhists outperformed “telephone operatives, team leaders, IT technicians, finance workers, account managers, upper management and marketing executives,” as these are professionals whose jobs demand high-levels of concentration.

Another small sample size of 20 “Western meditation practitioners” found “meditation is associated with increased thickness in a subset of cortical regions related to somatosensory, auditory, visual and interoceptive processing” in participates who practiced meditation for an average of nine years for six hours a week (Lazar, 2005):

Cortical Thickening in Meditators
(Lazar, 2005)

In addition to the small sample size, the authors remind us that “correlation is not causation.” It might be possible that individuals with a pre-existing thickening of these cortical regions are drawn to meditation; however, looking at the scatter plot, it is interesting to see the way the blue-circles (meditators) and red-squares (non-meditators) diverge with age. As we grow older we lose our plasticity of mind, and if this cortical thickening is not pre-existing, then meditative practice would appear to provide another tool in the kit of strategies for staving off this cognitive decline as we grow older.

Another more recent experiment that included a mixture of experienced meditators and individuals interested in learning meditation, some given actual mindfulness training and a control group, found meditators experienced reduced cognitive rigidity in tests:

following repetitive experience with a complex problem solving method, experienced mindfulness meditators were less blinded by experience and were better able than pre-meditators to identify the simple novel solution… similar results were obtained following mindfulness training in which participants were randomly assigned to mindfulness training vs. waiting list groups. These findings lend support to the notion that mindfulness involves cultivation of a “beginner’s mind,” and demonstrate that mindfulness practice reduces cognitive rigidity via the tendency to overlook simple novel solutions to a situation due to rigid and repetitive thought patterns formed through experience (Greenberg, 2012).

Brain Regions Activated by Seeing Words and Non-Words
(Pagnoni, 2008)

Brain scans of meditators and controls performing tests for automated thinking, distinguishing words from non-words, in another study found experienced meditators had faster reaction times in distinguishing words from non-words in tests where texts were flashed at them at random, suggesting meditative practice improves the brain’s ability to switch tasks by suppressing its tendency to wander into spontaneous thought:

While behavioral performance did not differ between groups, Zen practitioners displayed a reduced duration of the neural response linked to conceptual processing in regions of the default network, suggesting that meditative training may foster the ability to control the automatic cascade of semantic associations triggered by a stimulus and, by extension, to voluntarily regulate the flow of spontaneous mentation. (Pagnoni, 2008)

Memory

Studies have also found meditation to improve memory specificity:

Compared to matched controls, MBCT participants showed increased autobiographical memory specificity, decreased overgenerality, and improved cognitive flexibility capacity and capacity to inhibit cognitive prepotent responses. Mediational analyses indicated that changes in cognitive flexibility partially mediate the impact of MBCT on overgeneral memories. (Heeren, 2009)

My understanding of this science is shallow, but it appears that when we try to remember events from our lives, we are able to locate the general memory quite easily, but if other thoughts get in the way, we aren’t able to go deeper to summon specific details about the event. This might be because feelings get in the way or spontaneous cognition interrupts the process. MBCT may improve autobiographical memory by encouraging:

…patients to practice noticing elements of their experience and to do so in a nonjudgmental way. In this way, it encourages not only more specific encoding of events but also more specific retrieval of past events by reducing the tendency for individuals to abort the search process. Further research will be needed to establish how much of the change in memory comes about as a result of the MBCT’s effect on encoding versus retrieval. (Williams, 2000)

Cognitive Well-Being

Finally, mindfulness meditation is found to promote an overall improved sense of well-being and emotional maturity. One of the most challenging finds came from a study that found meditators were capable of overcoming their sense of personal offense in a situation and accept what was best for themselves. In a study of the Ultimatum Game, where an acquaintance is given $20 and told to share it with you, if you decline what they offer, neither of you get any money. When offered $1, most people will reject the offer to punish the person’s selfishness, even though this isn’t a rational decision. Meditators were much more likely to make the rational decision to accept the offer of $1 (Jones, 2012).

I did not read the research into MBCT being used for treating mental disorders such as depression, but summaries of the research did find positive results in specific cases (Chiesa, 2010). Additionally, more experienced Meditators had more curiosity and a higher level of decentering (Lau, 2006). Mindfulness training reduces maladaptive ruminative thinking and increases adaptive ruminative thinking (Heeren, 2011). Subjects given mindfulness training “demonstrated significant improvements in self-reported mindfulness, depressive symptoms, rumination, and performance measures of working memory and sustained attention, relative to a comparison group who did not undergo any meditation training (Chambers,2008).”

How to Meditate

Meditation is focus, a balance between not letting the mind become bored or falling asleep and not letting the mind become too excited and run away into daydreams. You are cultivating two faculties: “a meta-awareness that recognizes when one’s attention is no longer on the breath, and an ability to redirect the attention without allowing the meta-awareness to become a new source of distraction (Lutz, 2007).” Err on the side of focus starting out, focusing on the present moment and on your breath until you are able to focus on nothing and pursue the goal of thinking nothing at all.

But it is also practicing the meta-awareness of your thoughts:

Although mindfulness, or insight meditation, also includes some concentrative practices, the focus of attention is unrestricted such that the meditator develops an awareness of one’s present experience, including thoughts, feelings, or physical sensations as they consciously occur on a moment-by-moment basis (Lau, 2006).

This is cognitive diffusion “the ability of recognizing thoughts as thoughts and not necessarily as an accurate readout of reality.” It is looking at our thoughts in the third-person, so instead of thinking “I am a bad person,” you observe yourself having the thought “I am having the thought that I’m a bad person (Chiesa, 2011).”

Vulcan Meditation Lamp
Credit: Paramount

Although it sounds easy, meditation is an exercise in self-regulation. It’s very similar to physical exercises in that the longer your session goes, the harder it is to maintain. Just as you reach a point of exhaustion at the gym, where even the lightest weights become too heavy to lift or the slowest pace on the treadmill becomes too difficult to run, there is a point of mental exhaustion during a meditation session. It seems to me that this cognitive weariness is probably related to the fact that we appear to have a limited reservoir of willpower in our brains, but we can strengthen that area of the brain with practice just like anything else.

The goal of meditation is to carry over the state of mind from the act of meditation into the non-meditative daily life (Lutz, 2007). That’s why, like exercise, you have to work it into your daily life and not just when you escape to retreats removed from the world. It’s easy to be mindful and at peace when you don’t have the stress of the everyday world on your shoulders. What’s tough is remaining mindful and relaxed despite work deadlines, traffic jams, slow fast food lines with a grumbling stomach, irritating peers, political attack ads, and the thousand little cuts that push us into ruminative thinking and automated behaviors.

Science Koans

Zen meditation has the practice of “focusing on a koan, a specific riddle that is unsolvable by logic, which is said to lead the practitioner to an insight into the true nature of reality (Chiesa, 2011).” Scientists don’t need riddles like the “sound of one hand clapping” or falling trees making sounds in forests, we have the riddles of reality to meditate on. Here are some “science koans” to deeply consider at the opening of a meditation session to ease you into deeper meta-awareness:

• Erwin Schrodinger: Life Feeds on Negative Entropy, “sucking orderliness from its environment.”
• Carl Sagan: The Cosmos is just right intellectually, where things are knowable, making existence bearable for thinking beings, but complex enough to offer us seemingly endless challenges.
• Lord Kelvin: Atoms are so small that if you poured a glass of water into the ocean and gave them time to distribute evenly, when you later took a glass from the ocean you would find a hundred of the original molecules within it.
• Lewis Fry Richardson: “Big whorls have little whorls / Which feed on their velocity / And little whorls have lesser whorls, / And so on to viscosity.
• Willem de Sitter: We live in a Universe where gravity pulls galaxies towards one another, but universal expansion pulls them apart.
• Jacques Monod: All life is made of lifeless sub-components below the level of the cell.
• Sir John Randall: An egg is a chemical process with the power to become a lifeless omelet or a living chicken.
• Sir James Hopwood Jeans: Everything is vibrations, light and other forms of radiation are roaming vibrations and matter is bottled up vibrations.
• Stephen Hawking: The total energy of the Universe is Zero.
• Arthur Koestler: The Cartesian Duality, the idea that our mind is separate from our matter, is an illusion.
• Banesh Hoffman: Light is both spread out and localized.
• Granville Stanley Hall: Everything society builds and every social interaction we have with others is a plexus of motor habits.
• A. S. Eddington: All matter is mostly empty space.
• A. S. Eddington: The second law of thermodynamics as a profound distinction between past and future.
• George Gaylord Simpson: The origin of the universe is ultimately unknowable.

Meditation for the Scientist/Skeptic

Scientists and intellectuals have a jump on the average person when it comes to meditation. We have spent countless hours deeply immersed in texts, focusing on the single object of the book and preventing the mind from wandering. Similarly, when we work for long hours on a problem, we are highly focused in the moment. The high I get from reading a good book or programming for an extended period of time is similar to the one I get from an hour of meditation. Intellectuals have the attention part down, we simply need to move our attention from a specific thing to no-thing. Chet Raymo describes prayer as silent observation, which is essentially mindfulness meditation. Simply pay attention without judgment, and when we do judge, note it and let it go.

Easier said than done, but that’s why we practice it.

References

Anderson ND, Lau MA, Segal ZV, Bishop SR (2007) Mindfulness-based stress reduction and attentional control. Clinical Psychology & Psychotherapy 14(6): 449–463. 10.1002/cpp.544. (link)

Bishop SR, Lau M, Shapiro S, Carlson L, Anderson ND, et al. (2004) Mindfulness: A proposed operational definition. Clinical Psychology: Science and Practice 11(3): 230–241. (link)

Camerer, Colin; George Loewenstein & Mark Weber (1989). “The curse of knowledge in economic settings: An experimental analysis”. Journal of Political Economy 97: 1232–1254.

Chambers R, Lo BCY, Allen NB (2008) The impact of intensive mindfulness training on attentional control, cognitive style, and affect. Cognitive Therapy and Research 32(3): 303–322. 10.1007/s10608-007-9119-0.

Chiesa A, Calati R, Serretti A (2010) Does mindfulness training improve cognitive abilities? A systematic review of neuropsychological findings. Clin Psychol Rev 31: 449–464.

Chiesa A, Malinowski P (2011) Mindfulness-based approaches: Are they all the same? J Clin Psychol 67(4): 404–424. 10.1002/jclp.20776.

Colin, Loewenstein, Mark, The curse of knowledge in economic settings: An experimental analysis, Journal of Political Economy , 97: 1232–1254
(link)

Flavell, J. H. (1979). Metacognition and metacognitive monitoring: A new area of cognitive-developmental inquiry. American Psychologist, 34, 906–911.

Greenberg J, Reiner K, Meiran N (2012) “Mind the Trap”: Mindfulness Practice Reduces Cognitive Rigidity. PLoS ONE 7(5): e36206. doi:10.1371/journal.pone.0036206 (link)

Heeren A, Philippot P (2011) Changes in ruminative thinking mediate the clinical benefits of mindfulness: Preliminary findings. Mindfulness 2(1): 8–13. (link)

Heeren A, Van Broeck N, Philippot P (2009) The effects of mindfulness on executive processes and autobiographical memory specificity. Behav Res Ther 47(5): 403–409. (link)

Hinds, Pamela J. (1999).The Curse of Expertise: The Effects of Expertise and Debiasing Methods on Predictions of Novice Performance. Journal of Experimental Psychology: Applied 1999, Vol. 5, No. 2,205-221 (link)

Hodgins HS, Adair KC (2010) Attentional processes and meditation. Conscious Cogn 19: 878. (link)

Jha, A.P., Krompinger, J., & Baime, M.J. (2007). Mindfulness training modifies subsystems of attention. Cognitive, Affective, & Behavioral Neuroscience, 7(2), 109–119. (link)

Jones, Sarah Bruyn (2012), An endless exploration, The Roanoke Times. (link)

Lau, M., Bishop, S.R., Segal, Z.V., Buis, T., Anderson, N.D., Carlson, L., Shapiro, S., Carmody, J., Abbey, S., & Devins, G. (2006). The Toronto Mindfulness Scale: Development and validation. Journal of Clinical Psychology, 62(12), 1445–1467.

Lazar, S.W., Kerr, C.E., Wasserman, R.H., Gray, J.R., Greve, D.N., Treadway, M.T., McGarvey, M., Quinn, B.T., Dusek, J.A., Benson, H., Rauch, S.L., Moore, C.I., & Fischl, B. (2005). Meditation experience is associated with increased cortical thickness. NeuroReport, 16, 1893–1897. (link)

Lutz A, Dunne JD, Davidson RJ (2007) Meditation and the neuroscience of consciousness: An introduction. Anonymous The Cambridge handbook of consciousness. New York, NY, US: Cambridge University Press. pp. 499–551.

Moore A, Malinowski P (2009) Meditation, mindfulness and cognitive flexibility. Conscious Cogn 18(1): 176–186. (link)

Pagnoni G, Cekic M, Guo Y (2008) “Thinking about Not-Thinking”: Neural Correlates of Conceptual Processing during Zen Meditation. PLoS ONE 3(9): e3083. doi:10.1371/journal.pone.0003083 (link)

Smart, Reginald G. (Apr 1966) Subject selection bias in psychological research. Canadian Psychologist/Psychologie canadienne, Vol 7a(2), Apr 1966, 115-121. doi: 10.1037/h0083096

Wenk-Sormaz H (2005) Meditation can reduce habitual responding. Adv Mind Body 11: 48–58. (link)

Williams, J.M.G., Teasdale, J.D., Segal, Z.V., & Soulsby, J. (2000). Mindfulness-based cognitive therapy reduces overgeneral autobiographical memory in formerly depressed patients. Journal of Abnormal Psychology, 109(1), 150–155. (link)

Zeidan F, Johnson SK, Diamond BJ, David Z, Goolkasian P (2010) Mindfulness meditation improves cognition: Evidence of brief mental training. Conscious Cogn 19(2): 597–605. (link)

Download a PDF Version Here (9MB)

Download a PPTX Version Here (14MB)

I was walking through the local forest trail a few months ago, and it was getting dark. As the sky shifted from blue to black, the full moon rose up through the trees creating a stunning scene. I realized my ancient ancestors were just as awe-inspired by that glowing orb in the sky, but my present-day awe was much deeper for knowing the moon as an object in space several hundred thousand kilometers away, circling the Earth for the same reason things fall to the ground, much of its mass once belonging to the Earth, lit up by the Sun, and causing the oceans to rise and fall as they follow its orbit.

At once I realized how crucial it was that this cherished knowledge of my place in the Cosmos was something I needed to give my son, Sagan.

Where You Are

For the following months, I’ve been editing and re-editing a power-point slide presentation that I hoped would serve as a children’s book guide to why we are here and what is our purpose in life according to our present scientific understanding of reality. I wanted to communicate, in the simplest terms the following four points:

1. Where You Are: on a planet some of us call Earth, orbiting a star that is the source of all energy on our planet, orbiting a galaxy full of stars, in a Cosmos full of galaxies.

2. How You Got Here: an unbroken chain of mommies who slowly changed over billions of years from a single cell to multi-cells, to worms, to fish, to lizards, to crawling mammals, to cultural mammals.

3. What You Are: a member of a communal species that lives all over the Earth and even in space, working together to increase knowledge and improve our quality of life.

4. Where You Are Going: as your parent, I’m going to try and raise you to be as smart and successful at life as myself, as my child, you’re going to try to be even smarter and more successful at life than me.

Of course, no children’s book alone can communicate such complex and sophisticated points, but I wanted to be prepared to start the dialogue. Superstitious people usually have one strong singular narrative about our origins and purpose to guide their children, as a scientist I need the same. This book is the outline of that strong singular narrative, which will grow larger and more complex as I expand on these core ideas and as Sagan’s neurons branch and branch away into the details of our shared reality.

It’s Mommies All the Way Down

I’ve included the Power Point working file, so you can download it, replace my photo of Sagan with your own child/children. Even cooler though, you can edit the book in other ways. Try replacing the animal photos with your own favorites from flickr (just make sure they’re CC-licensed if you plan to post your own version of the book). Maybe you can add more pages to the book with your children, using the PPT as the starting point of a creative learning adventure.

Happy Secular Parenting!

Sagan is a Homo Sapiens

Photo Credits

This book would not be possible for a design-challenged fool like myself without the generous efforts of these creative commons photographers, taxpayer-funded science programs, and a copyright that had the ability to expire once upon a time.

Cover

• Andes Hike by Trey Ratcliff

Page 4

• Sun by Pranav Yaddanapudi

Page 5

• Moon by Anita Ritenour

Page 3, 6 , 7, 8, 20

• Photos by NASA

Page 9

• Marie Curie, Ada Lovelace, Hypatia, Minerva, Nefertiti, and Woman from Brassempou in Public Domain

Page 10 – 11

• A Mother’s Touch by Eric Heupel
• Ring Tail Lemur in Berenty by David Dennis
• African Giant Shrew – A Fascinating One by Joey M.
• Eryops by ellenm1
• Tiktaalik by Linden Tea
• Coelacanth by Sini Merikallio
• Aquatic Caecilian by Brian Gratwicke
• Jellyfish by Giorgos Vintzileos
• Slime Mold by Richard Droker
• Single Cell by Wikipedia User Perezoso

Page 12

• Cells by Patrick Hoesly
• Multicellular by Daniel Kulinski

Page 13

• Kelp by NOAA
• Sea Urchin by cassimano

Page 15

• Tarantula by calwest
• Milipede by e_monk
• Damselfly by Thomas Shaha

Page 18

• Images by NHS Human Services

Page 21

• A Face in the Crowd (detail) by Michelle Tricca
• On Flickr

Page 22

• New York by Nathan Siemers
• Rio de Janero by Ashley Ringrose
• Dubai by Kamel Lebtahi
• Hong Kong Skyline by Spreng Ben

Page 23

• Eastern Virginia Medical School by Wugging Gavagai
• Large Hadron Collider by CERN
• Oxford by Fr Lawrence Lew, O.P.
• ISS – NASA

Page 24

• Yosemite by Justin Kern

Welcome to Life

A Creative Commons Children’s Book for New Members of Species Homo Sapiens

I hate doing top 10 lists because I am going to make some huge embarrassing oversite and I really don’t have any objective way to order what makes the list. That being said, this list consist of my own personal favorites from the world of literature as someone who grew up in a western society with all the cultural baggage that comes with it. These are books where the aliens are alien, and their otherness gives us a new perspective on our own identity and culture.

10. War of the Worlds

HG Welles’ story about martians landing on planet Earth is still a hauntingly gripping tale and inspired nearly a century of alien-invasion stories and film adaptations. Welles sets the standard for otherness storytelling by wisely never explaining the meaning behind much of the Martians’ actions, leaving the reader to wonder in horror along with the protagonist navigating the war-torn landscape. I’ve written more on this novel here.

9. Mote in God’s Eye

Larry Niven and Jerry Pournelle’s 1974 story of first contact with an alien race the humans refer to as the “Moties,” is filled with twists and turns. The alien race is ancient to the point of having evolved into many different species that coexist through different specializations, but its technological progress is strangely stunted and the human delegation discovers museums around the planet meant to help rebuild civilization after a collapse, which appears to happen on a regular basis throughout Motie history. The reason for these collapses has to do with a dark secret about Motie biology, which serves as a warning to human civilizations as well.

8. Blood Music

Greg Bear’s 1985 novel about a scientist engineering living cells to store information and who injects those cells into himself when prosecuted for unethical research, is also an apocalyptic story about the pandemic this act causes. The cells find their way into the population, transforming the bodies of those they infect to better serve their own needs, quickly transforming North America into a mass of alien organs networked with veins. The story is told from a variety of viewpoints, from those who are uninfected but stuck in the alien landscape to those of people in foreign countries watching in horror at what has become of America’s population.

7. Nor Crystal Tears

The extremely prolific science fiction author Alan Dean Foster has taken readers to a myriad of planets and alien concepts, but this first contact novel that supplies the origin story of his Humanx Commonwealth was special for telling the story of first contact with humans from the perspective of the aliens, who, among other things, are disturbed by the way we wear our skeletons “on the inside.”

6. More Than Human

I first encountered Theodore Sturgeon’s 1953 novel in a college course on science fiction and it has kind of stuck with me ever since. The story chronicles the formation of a gestalt organism out of misfit, outcast human beings who all possess different powers, from telepathy, teleportation, to computation. Together they are a mouth, limbs, and brain.

5. Expedition

Wayne Douglas Barlowe’s illustrated account of the 2358 A.D. Voyage to Darwin IV has become a collector’s item and was made into a fictional documentary by the Discovery Channel titled Alien Planet. It resembles the books written by 18th century naturalists, brimming with illustrations of fascinatingly alien life, some of which runs on two legs one in front of other like horses, some are lumbering behemoths taking nutrients in through their feet, some float in the air using balloon-like organs, but none have eyes that receive photons like ours do. You can check out a nice sampling of these aliens here.

4. Flatland

Edwin Abbott Abbott’s 1884 Romance of Many Dimensions explores what life is like in two dimensions, but the story was also a scathing criticism of Victorian culture with its class hierarchies and chauvinism. I’ve written more on this book here and a comparison of its two film adaptations here.

3. Fiasco

Stanislaw Lem wrote some of the most thought-provoking science fiction out there, and it’s difficult to choose one of his many novels dealing with the concept of Fermi’s Paradox and his explanation that if extraterrestrial life exists out there, it is too alien to contact. Fiasco involves a ship sent to make contact with an alien civilization with tragic consequences. From their first encounter, the aliens are impossible to comprehend; from their legion of communications satellites apparently at war with one another to the ring of ice put into orbit for the purpose of producing a perpetual rain of moisture down on the planet, the human visitors are first puzzled and later angered by their inability to establish contact with the inhabitants through demonstrations of awesome military power and laser projections into the clouds blanketing the planet. When the aliens are finally revealed, the mystery only deepens.

2. Kabloona

I’ve previously written about Gontran De Poncins’ nonfiction tale of the anthropologist’s experience visiting Eskimo tribes, heading further and further north in hopes of finding one that had never encountered a westerner before. It’s remarkable for the way is objectively relates the customs and thought-patterns of these native peoples, from their practice of euthanizing old people, sharing their wives with visitors, and thinking little of murder. They never come across as malicious, but innocent in simple in their thinking, as when westerners begin to prosecute them for murder and tales of warm jail cells with free food spark a crime wave of Eskimos seeking to be imprisoned.

1. Fire Upon Deep

Vernor Vinge’s 1993 novel is one of the deepest, most brilliant world-building exercises I’ve ever read. What makes the otherness of his aliens so intriguing is the way he lets the reader into their heads when possible. There are the skroderiders, tree-like aliens that a more advanced unknown race equipped with wheels to make them mobile and computers to give them short-term memory. There are the “Powers,” consciousnesses that have transcended our reality, with motivations and behaviors beyond our comprehensions, and there is the “Blight,” a sort of sentient computer virus that uses the galactic internet to destroy worlds and spread confusion throughout the galaxy.

Credit: Unknown

But the most intriguing aliens in the novel are the Tines, doglike creatures that form multi-bodied organisms. A pack of these creatures will form a single individual, their brains networked through sound vibrations to form a single consciousness. Because these networks rely on sound, individual tines cannot get very close to each other, lest their brains begin to interfere with one another and mating is an act of pure bestial confusion. When too many members of an individual Tine die, the remaining members are crippled. When one of the tines obtains the technology of radio broadcasting, it is able to spread its different bodies out far and wide, making it quasi-omniscient compared to other members of the species. All of these different forms of consciousness and culture take place in a story that is both exciting and satisfying intellectually.

Honorable Mentions

Solaris: Another of Lem’s great books about a planet covered in an ocean of living cells that begins to experiment with the human visitors exploring it.

Forge of God: Greg Bear’s novel about a variety of alien visitors who appear on Earth following the disappearance of one of Jupiter’s moons is about the concept of Von Neumann Machines that replicate across the Universe, but their intentions are hostile.

Sentenced to Prism: Alan Dean Foster’s book exploring the concept of silicon-based life has a fantastic and creepy first half, but kind of falls apart halfway through in terms of otherness, but is a fun pulpy fiction nonetheless.

Before becoming a parent, I was well-acquainted with the word “colic.” According to my mother, I suffered from severe colic as a baby, keeping her up all night for weeks with my crying. I’ve also heard parents toss the term about when talking about their baby-raising trials and tribulations. After having our son Sagan, I got to hear the term from one of our pediatricians concerning him having a crying episode one night as a possible explanation for the outburst.

Curious about this seemingly common medical condition, I decided to look up the definition myself:

The strict medical definition of colic is a condition of a healthy baby in which it shows periods of intense, unexplained fussing/crying lasting more than 3 hours a day, more than 3 days a week for more than 3 weeks. [Bold Mine]

There’s that word there, unexplained. For years I thought this word “colic” described a phenomenon that was understood and therefore natural. The etymology of the word, pertaining to “disease characterized by severe abdominal pain” in the early 15th century suggests the infant’s crying is explainable, but in reality the term colic is just a fancy way for your pediatrician to say, “I don’t know why your baby is chronically crying.”

And the more I thought about the word, the more it disturbed me. The phrase “just colic” returns 47,100 google results and is a sentiment I’ve heard more than one parent use. “Just colic” implies that there is nothing to worry about, but not knowing the cause of your baby’s crying is something to worry about. “Just colic” implies that there is little to be done about it, but if you can figure out the cause of the infant’s discomfort then you can do something about it. The word colic is dangerous, because it is ignorance masquerading as knowledge, where the knowledge that your child has acid reflux, the stomach flu, or a food allergy empowers you to do something to treat it and improve your quality of life and your child’s.

The erroneous assumption that because something has a name it also has an explanation is known as the nominal fallacy, and it’s a trap the scientifically-minded fall into all the time that damages our understanding of the world. In his 2011 Edge Question response, Stuart Firestein suggests that recognizing instances of the nominal fallacy in our everyday life would greatly improve our perspective on what we know and don’t know:

Too often in science we operate under the principle that “to name it is to tame it”, or so we think. One of the easiest mistakes, even among working scientists, is to believe that labeling something has somehow or another added to an explanation or understanding of it. Worse than that we use it all the time when we are teaching, leading students to believe that a phenomenon that is named is a phenomenon that is known, and that to know the name is to know the phenomenon.

[...]

In science the one critical issue is to be able to distinguish between what we know and what we don’t know. This is often difficult enough as things that seem known, sometimes become unknown or at least more ambiguous. When is it time to quit doing an experiment because we now know something, when is it time to stop spending money and resources on a particular line of investigation because the facts are known? This line between the known and the unknown is already difficult enough to define, but the nominal fallacy often obscures it needlessly.

“An instance of the nominal fallacy is most easily seen when the meaning or importance of a term or concept shrinks with knowledge,” Firestein explains, using the word “instinct” as an example. The word instinct applies to a living organism’s inclination to a specific behavior in response to a stimulus; in other words, instinct is a label we apply to any animal behavior which we cannot explain as the product of environmental conditioning. Instinct is the nature side of the nature/nurture false dichotomy, and it explains absolutely nothing.

Another example is death by natural causes as it is used in everyday conversation is synonymous with “death by old age,” but there is no such thing in the scientific world. Some failure within the deceased’s body caused the death. If you can explain what happened, it is no longer “natural causes” in the common use of the term; the deceased expired from a specific, nameable cause.

In the medical world death by natural causes is any death by any illness or malfunction of the body; as opposed to, unnatural death which includes accidents and homicides. But this can be extremely misleading as well. When an alcoholic dies of cirrhosis’s of the liver, a lifetime smoker dies of lung cancer, or a family living downwind of a coal power plant dies from pollution exposure, “natural causes” seems inadequate, vague, and outright lazy.

George Gaylord Simpson applied this same logic to a word many people still invoke today as a faux explanation for things we don’t yet understand and who often use it as an excuse to shutdown further inquiry:

Call that great Unknowable by any name you wish, call it X, or Yahweh, or God, or say that God created it. Applying the letters “g”, “o”, and “d” to it or what created it is no explanation and no consolation. It is a common failing, even more among scientists than among laymen, to think that naming a thing explains it, or that we know a thing because we can put a name to it. But to say that God created the universe means nothing whatever.

At the same time, we cannot deny that naming, if used properly, is an important step towards understanding. As Chet Raymo explains:

To name a perceptible thing has some advantage; it makes it possible to talk about it. There can be no theory of the electron, for example, until we have a word for the electron. But naming is not understanding. Before we say we understand a thing, we must weave it into the web of concepts that constitutes a theory. Only when the concept “electron” is enmeshed in a matrix of other ideas — atoms, fields, valency, molecular bonds, etc. — by taut, quantitative connections, do we have confidence that we know what an electron is.

“Electron,” “photon,” “quark,” or other name we give an elementary particle is really just a label for a collection of repeatedly observed characteristics. When we talk about atomic orbitals, we intuitively think of electrons orbiting a nucleus in a manner similar to planets orbiting the sun, like this:

Model of a Helium Atom
Credit: me

In reality, the “orbit” metaphor only works insofar as to describe the fact that the electron stays in proximity to the atomic nucleus, but beyond that it completely fails. The “orbit” of an electron only defines the area around the atom in which it is most likely to be found, meaning it could be found well outside its orbit at times. I remember how mind-bending it was the first time I saw Wikipedia’s table of orbitals, trying to rationally understand what I was seeing, which the article explains should be thought of as “waves on a circular drum” for some examples and planetary orbits for others:

Electron Orbits
Credit: Wikipedia

When we think about the atom and other quantum relics, it’s okay to imagine it in metaphors drawn from our macro-world, so long as we always remember that these are only metaphors, shadows representing a reality completely alien to us. As Niels Bohr best explains it, “We must be clear that when it comes to atoms, language can be used only as in poetry. The poet, too, is not nearly so concerned with describing facts as with creating images and establishing mental connections.”

The wave-particle duality, gravity, dark matter, and dark energy are other examples of phenomena we have named, but for which we do not have truly satisfying explanations. Naming them, acknowledging their existence, was the first step toward understanding through observation and experimentation.

A name for a thing should never mark the end of an inquiry into its nature, but rather a beginning.

Single Nucleotide Polymorphism (SNP)

Introduction

It’s been over a year since I signed up with 23andMe and several months now since I downloaded my raw genomic data from them and started seeing what I could learn from it on my own. Although very few services out there will fully sequence your personal genome, by focusing on sequencing an individual’s Single Nucleotide Polymorphisms (SNPs), pronounced “Snips” for short, which are the variables between human genomes, we can focus on what’s of interest in our personal genomic data and get this data relatively cheaply. By comparing the differences in our genes, our genotypes, my wife and I could learn about how they differently express themselves in our lives, our phenotypes, to gain insights about our health risks as well as interesting traits about ourselves that may explain our behaviors and experiences throughout life.

Closed-Source Genetics

For $1,100 deCODEme will “Calculate your genetic risk for 47 conditions and traits,” but not include any ancestry analysis. Alternatively, Navigenics offers genome scans for $2,750 according to a 2009 Wired article (they don’t post prices online themselves), and Knome offers total genome sequencing for $3,750.

So at $207 test + year-subscription deal 23andMe has far and away the best deal for getting your personal genome sequenced. Although 23andMe doesn’t fully sequence your genome, it does sequence 960,520 SNPs and you get to download the whole thing to keep and take with you–which is crucially important (as I will get to in the open-source part further down).

The Good Stuff

My Traits

The best thing about 23andMe is the interface. They take your results and break them down into your disease risks, drug responses, and various traits. Right off the bat it impresses me for correctly identifying my phenotype as expressing brown eyes (rs12913832(A;G)), curly hair (what hasn’t fallen out (rs17646946(G;G))), lactose tolerance (rs4988235(A;G)), and a tendency to smoke like a chimney if I smoked (which I did at a pack or more a day for 10 years (rs1051730(A;G))).

But it’s the stuff you don’t know about yourself that makes it worth it. I learned that I cannot perceive bitter tastes (rs713598(C,C)), which was interesting, while my wife’s apparent ability to taste bitter could explain some of our differing culinary preferences (although we couldn’t think of anything). Then there was the norovirus resistance (rs601338(A;A)), which could explain why I usually get off easy when a stomach flu goes around.

ACTN3

But most enlightening was finding I lack any copies of alpha-actinin-2 (ACTN3) in my fast-twitch muscle fiber (rs1815739(T;T)), meaning I am a terrible sprinter and throughout my public school years I was indeed consistently a poor-performer at short-distance sprints. As my father, a runner of marathons now approaching his 70s, liked to say, “In the running world there are gazelles and there are plough horses. I am a plough horse.” Now I know that my inability to make a half-marathon in less than two hours is likely hereditary. At the same time, the TT genotype may confer some ability to make greater gains at strength training, which would explain my enjoyment of weight lifting.

Neanderthal DNA

23andMe also offers some fun stuff, like calculating how much Neanderthal DNA you have. I was proud to learn that I share 3.0% of my genes with our distant cousins, putting me in the 96th percentile, which I hope means that my ancestors made a bigger contribution to breeding them out of existence.

The Neutral Stuff

Disease Risk

According to the “Disease Risk” section of 23andMe, I’m 1.22 times more likely than the average person to develop Type II Diabetes. If this was Type I Diabetes, which is purely genetic, this result would mean something to me, but Type II is largely a matter of lifestyle. So what does it mean for me to have an elevated risk? The site says that the disease is only 26% heritable, meaning if I eat right and exercise, I should be fine… right? According to this survey my risk is extremely low and my BMI is borderline–but then BMI is useless for people who lift weights. Then there’s also the fact that, drilling down into the data, I find this “risk” is computed using 11 genetic markers, the red ones show increased risk, the green ones decreased risk:

Diabetes Markers

I’m ambivalent about the usefulness of this data. It’s really difficult to determine how concerned or unconcerned I should be or even how seriously I should take this information. Apparently I’m also at risk for a greater tendency to overeat on average if I were an “Old Order Amish woman.”

But these are less criticisms of 23andMe and more problems with the whole of personal genomics in general. The research is still coming in and will continue coming in for decades, maybe even centuries. So it’s important to not just accept the initial third-party extrapolations from your genetic data, but to check in on it from time to time and learn what new developments have come up.

The Bad Stuff

23andMe Parkinsons Disease Campaign

The one complaint I have about 23andMe’s services is the monthly subscription fee. Paying even $5.00 a month is unacceptable, even for a great service, when it is accompanied with constant pressure to take research surveys to help the company determine the purpose of even more genetic markers. 23andMe appears to have the research to extrapolate the phenotypic expression of some genotypes, like my having curly hair, from just these surveys that no other genotyping service can offer. The site even features an advertisement with Muhammed Ali that they are using the surveys to hone in on the markers for Parkinson’s disease.

To be clear: I don’t mind the surveys and I don’t mind the subscription fee. I mind the combination of the two. I mind paying a company for access to their research while simultaneously contributing to their research to give them a proprietary edge over the competition. If 23andMe were a free service where you had to take one survey a month to maintain your access, I would think it the greatest thing in the world. The company has tremendous potential to harness information from its user community in the name of Citizen Science and reap fantastic profits from that data, but I’m not going to pay them to collect my data and then let them go off to make even more money from it.

Make access to the site conditional on buying a gene test from them and taking monthly surveys and I think 23andMe could be a wonderful thing for society.

Open-Source Genetics

Because 23andMe lets you download your results, you are free to take them with you to other online services or even conduct your own research. That’s awesome and a bit daunting at the same time. Looking at a spreadsheet with nearly one-million SNPs on it doesn’t seem like the best place to start, and plugging SNPs Reference Cluster IDs (rs#) into google at random will only confuse you (despite the fact that you will get results from lots of databases). Probably the best source for randomly plugging in rs#’s is the National Center for Biotechnology Information’s (NCBI) Single-Nucleotide Polymorphism (SNP) database, where plugging in a random SNP will get you a wonderfully comprehensive block of information that looks something like this:

Partial View of NCBI Results

Incomprehensible to me, and I bet if someone were to explain it I would find that data fairly boring and irrelevant too.

So we’ll leave it to the many many many experts out there to figure out what’s interesting and what’s important. Luckily, a great, fairly down-to-earth resource I found online is SNPedia, a human genetics wiki. I’ll read about a trait or risk factor in the wiki and then run a “find” in my spreadsheet, locate the marker, and make a note beside it about what it means–but there’s an even better way.

Promethease

Promethease

SNPedia has a free software tool called Promethease that will take results from 23andMe or another service and run through your results to generate a custom report based on the information in the wiki. It takes about four hours to generate the report, but for a $2 Amazon payment, you can get the report in a few minutes (it took 412 seconds versus six hours for me running the report paid versus unpaid).

Ryan and Vicky Chromosome 1 Comparison

One of the cooler enhancements you get with the paid version of the report is the ability to compare your results to someone else. I ran my report with a comparison to Vicky’s results and got some experimental results back comparing our genomes. In the above image you can see our comparison for the first chromosome with light blue being a match (57%), dark blue being a halfmatch (37%), and the red being conflicts (6%).

A video tutorial of the features in the paid Promethease 0.1.99 version report shows some really neat additional comparison reports that did not show up in my report, such as seeing the probabilities of genotypes showing up in Vicky and my offspring and a Venn diagram of our genetic relatedness. I was unable to find out why, but I did find other ways of looking at my results in the report, such as the following screenshot (not that I’ve figured out what this means yet):

Promethease Visualization

The Promethease report gave me some additional tidbits about myself that 23andMe either didn’t provide or didn’t present as important such as my SNP for being “optimistic and empathetic” (rs53576(G;G), increased memory performance (rs17070145(C;T)), and better odds of living to 100 (rs2542052(C;C)). The information suffers the same issues of probability and environment as the 23andMe presentation, but the exercise demonstrates that it’s interesting and important to look at your genomic information in different ways.

DIY Genealogy with Personal Genomics

Ryan’s Maternal Haplogroup (h1)

Ryan’s Paternal Haplogroup (J2)

Five years ago, I paid $100 to get my genealogical results from the Genographic Project, which took a DNA sample from my cheek and then showed me where in the course of human migrations my ancestors got off the caravan.

Using 23andMe’s Maternal and Paternal Line reading of our haplogroups, we can now save $100 and take our haplogroup information to National Geographic to find out for ourselves. Navigating to the Atlas of Human Journey, we can look up these haplogroups for more detailed information from their Genetic Markers list.

Genographic Project Maternal (H1)

Genographic Project Paternal (J2)

International Society of Genetic Genealogy provides an index to Y-DNA SNPs that I, unfortunately, could not figure out how to use to divine my haplogroups from my raw data. Maybe in the future I’ll figure out how to get this information without going through 23andMe.

Going Public with My Genome

SNPedia has a long list of users who have shared their genomes with the online world that includes entrepreneur Esther Dyson, author Steven Pinker, biologist and entrepreneur Craig Venter, and Nobel-prize winner James D. Watson. PersonalGenomes.org also gathers genomic data from users who freely donate their results for citizen science.

When 23andMe had their genome test sale last year and I promoted it, I got a lot of feedback from friends who said they would never submit to such a test because they were afraid of the Government or Corporations getting ahold of that data. The Genetic Information Nondiscrimination Act of 2008 bars health insurance companies from denying you coverage for a genetic predisposition and employers from discriminating against you for what’s in your genotype. There are legitimate debates over whether the law goes too far or not far enough, but the intention is clear and based on the uncertainty of what’s revealed in a personal genomics test, the threat appears small.

But that does not mean I approach posting my genetic results lightly. SNPedia has a cautionary rs#, rs666, a fictional SNP that represents the worst possible genetic trait you could possibly imagine. What would it mean if future research revealed to the world that you had this genotype? Such a revelation would not only impact you, but your children as well.

I am posting my genetic data, raw and in reports, online for others to view (see below), but it is not something I do lightly. I believe information should be free, and I believe in the ideal of a world where I shouldn’t need to fear sharing this data.

My 23andMe Ancestry Painting (100% European)

The Future of Healthcare with Personal Genomics

Erza Klein predicts personal genome sequencing spells the death of Health Insurance Companies:

As we sequence more genomes, mine more data, and conduct more studies, we’ll find a lot more of these connections. Eventually, genomic testing will be a powerful predictor of future illness. And it raises the potential that young people will get themselves tested and then purchase insurance based off the result. So those with a clean genomic result might go for a cheap catastrophic plan, while those with a high risk of developing pricey illnesses will opt for more comprehensive insurance.

The result would be, in insurance terms, an “adverse-selection death spiral,” as the healthy opt out of expensive insurance, the sick opt into it, and premiums spin out of control.

“For all of human history, humans have not had the readout of the software that makes them alive,” Larry Smarr, a member of the Complete Genomics scientific advisory board, told The New York Times. “Once you make the transition from a data poor to data rich environment, everything changes.”

The problem with this is, as I mentioned before, my results don’t predict my likelihood of getting a disease, they give me a better understanding of the odds to bet on, but if I have a 1.22-times chance of Type II Diabetes, there’s no way to customize my insurance plan to these odds. It’s all or nothing. Not only that, but would this even be legal? Congress has made it illegal for my insurance company to drop me for having an increased chance of manifesting one disease, so giving me a discount for having a lower propensity for another disease discriminates against those who have a higher propensity for it.

Better Living Through Personal Genomics

With states like New York and California having strict laws prohibiting or severely restricting genome tests or requiring the test results be explained by a doctor and the American Medical Association (AMA) lobbying the FDA to restrict access to our genomes, we have to wonder: What’s the harm?

My gut reaction is that doctors don’t like giving up their power. As I’ve discussed above, the data being provided only speaks to increased and decreased chances, and then we are talking about such tiny differences that it’s impossible to make an informed decision about what learned, especially in regards to cancelling a health insurance policy or forgoing doctor visits. Despite the best and worst-case prediction from both sides of the personal genomics debate, it would be foolish to do anything but work to improve your health after learning about your disease risks and genotypic traits.

Nature VS Nurture

My SNP Rs9834312 expresses as (G,G), which should make me an inch taller than other expressions, but I was a scrawny, malnourished nerd-boy in grade school, which stunted my growth to 5’9″ by the time I turned 20, about an inch shorter than the average American male. My lifestyle as a youth stunted my growth, but I don’t think knowing I had the genes for growing tall would have further encouraged that lifestyle. In fact, I think just the opposite would be true.

Knowledge of my genetic predispositions and education about how lifestyle choices impact phenotypic expression encourage people to take better care of themselves. The Navigenics website’s purpose statement hits the nail on the head that this information has the capacity “…to empower you with personal, confidential genetic insights to help motivate you to improve your health.” Knowing about our disease risks and other genetic shortcomings should inspire us to work harder for better health to improve our quality of life and odds of going further through it.

Appendix: DIY Genomic Sequencing for Programmers

This part of my article is technical, so feel free to skip it unless you are a computer programmer who wants to fill in the gaps in your genomic data.

SNPedia

SNPedia runs on MediaWiki, the same software running Wikipedia. Additionally, it runs Semantic mediawiki, meaning you can run semantic queries against it using the Ask Page:

Which will produce results like so:

Semantic Results

Each of the nodes in this table has a “class” attribute with the property name, making it fairly easy to pluck the data from the table. You can then iterate through your results and query SNPedia with a query string like so, adjusting the RS# to match:

http://www.snpedia.com/index.php/Special:Ask?title=Special%3AAsk&q=%5B%5BRsnum%3A%3ARs1234%5D%5D
&po=%3FRsnum%0D%0A%3FAllele1%0D%0A%3FAllele2%0D%0A%3F
Genotype%0D%0A%3FCategory%0D%0A%3FIn+gene%0D%0A%3F
On+chromosome%0D%0A%3FChromosome+position%0D%0A%3F
Magnitude%0D%0A%3FSummary&sort_num=&order_num=ASC
&eq=yes&p%5Bformat%5D=broadtable&p%5Blimit%5D=&p%5B
sort%5D=&p%5Boffset%5D=&p%5Bheaders%5D=show&p%5B
mainlabel%5D=&p%5Blink%5D=all&p%5Bsearchlabel%5D=&p%5B
intro%5D=&p%5Boutro%5D=&p%5Bdefault%5D=&p%5B
class%5D=sortable+wikitable+smwtable&eq=yes

SNPedia also offer tips for getting bulk data, RDF Export (which I could not get to provide useful data), and MediaWiki API.

dbSNP

The NCBI also makes its data available for querying, but it’s more technical and complex to find useful information to align with your personal results. Using the list of SNP Database Fields and the Entrez ESearch Interface for query strings, you can get document summaries or SNP Properties in XML format.

dbSNP ER Diagram (Partial View)

Most intriguing is the fact that you can Dowload Entire dbSNP Database (179.81 GB) (MySQL), or query the database directly (see also database diagrams (PDF)).

My Personal Genomic Results

You can browse my Promethease report online here and I’ve got an XLSX spreadsheet with both my 23andMe and Promethease data here to download. Alternatively, you can download a tab-delimited copy of my 23andMe Results or my Annotated Promethease results.

Further Reading/Viewing

BBC The Ghost in your Genes documentary on epigenetics.

Esther Dyson Interview about her decision to Share her Genome.

Nature article on the Rise of Genome Bloggers.

I remember unexpectedly having that conversation with my mother in law while riding in the car recently:

“What do you mean Sagan isn’t going to be raised Christian?” she asked when we accidentally let slip that he wouldn’t be going to a Christian church.

“There’s lots of possible belief systems out there,” Vicky answered, “and we’re going to let him decide for himself.”

“When he’s old enough, he can read the Bible if he wants,” I said.

“Old enough?” Grandma asked.

“Ummm,” I hesitated and decided to just let it out, “Yeah. When he’s old enough to read stories about daughters getting their father drunk to have sex with him, a husband giving his wife to be raped by a mob and then chopping her up into pieces to mail to his allies, a prophet summoning bears to devour children for teasing him about his male-pattern baldness, fathers sacrificing their virgin daughters to god as thanks for victory in war, mothers entering contracts to eat one another’s’ sons, … You know, when he’s old enough to be exposed to those kinds of stories.”

“Ha. Ha,” Grandma chuckled. “Yeah. I see what you mean.”

It’s so strange that in a world where humans can see to the edge of the Universe, live to a century through modern medicine, access unimaginable volumes of information online, and fly all over the world that I am still put in the awkward position from time to time of having to explain to someone that I don’t believe in any of the mythical invisible entities known as “gods.” It’s also awkward because I don’t walk around all day thinking about the fact that I don’t think about such deities. I don’t identify as a non-theist any more than I identify as a non-Mr. Snuffleupagusist. I identify as a Scientist a person who focuses on our shared empirical understanding of the natural world revealed through experimentation and inductive reasoning.

Mr. Snuffleupagus

Technically I’m a non-believer, but technically everyone is atheistic to a degree. There are thousands of gods and everyone on planet Earth doesn’t believe in most of them, and even when two people believe in the same god they often have major discrepancies in their personal understandings of it. Carl Sagan puts it best:

The word god is used to cover so many different points of view… First of all, you can be religious without believing in god. Buddhists, certainly religious without having any notion of god. Secondly, the word god, it’s amazing how diverse the definitions are. Let me give two extremes. One is the sort of god that I gathered by osmosis during my childhood, which is an outsized white male with a long white beard who sits on a throne in the sky and tallies the fall of every sparrow. Now that kind of anthropocentric god there is, as far as I can tell, no compelling evidence for at all. None.

At the other extreme, there’s the kind of god that Einstein and Spinoza talked about, not too different from the sum total of the laws of nature. Now there are laws of nature, and not only that they apply everywhere, to a quasar ten billion light years away as to the Eastern seaboard of the United States. And it’s a very remarkable fact that the same laws do apply so generally. It could have been a different set laws applies in every county. So that kind of god of course exists. Who would deny that there are laws of nature.

So I claim you learn absolutely nothing about someone’s belief if you ask them “Do you believe in God?” and they say yes or no. You have to specify which of the countless kinds of god you have in mind. I don’t myself like to use the word in that context, because it doesn’t illuminate at all. If I say I believe in god or if I say I don’t believe in god, and I say no more, you’ve learned nothing about what my belief system is.

For the sake of argument, we’ll put this fact aside and pretend that the term “atheist” only applies to people who don’t believe in the supernatural world whatsoever.

The Reason Rally 2012

This last weekend Vicky, our son Sagan, and I made our way out to the Reason Rally to see some of our favorite public intellectuals, like Adam Savage and Richard Dawkins, speak on secularism and rationality. We arrived just in time to witness Adam Savage of the Mythbusters show on Discovery deliver an enlightening and lighthearted speech in support of science and human potential:

Adam Savage

Testable, provable phenomena, and the predictions they allow, big and small, brought me here to in front of you today and they will take me back to my family when I am done. They allowed me to drive to DC on a bus, type my speech on a screen, ride to this rally in a car, walk on shoes that support my feet, and wear clothes and a hat that protects my pale skin from the sun. To fly on a plane home. That plane I will get on exists and stays in the air because of a million million large and tiny tested predictions lift, drag, material performance, physics, electricity, radio waves, wear, tear sheer, checklists, human error, machine error and redundancy. It is a miracle of engineering. It is the result of an ancient and very human drive. A drive that makes us what we are in all of our unique specialization. A drive to solve problems.

Many tens of thousands of people combine their collective genius to make an impossibly fast and efficient, thin, inflated bubble of aluminum so stable and secure that you’d have to fly for several thousand years before the odds gave you an even chance of being in an accident. Everything that we have that makes our lives possible exists because human beings have tested the things they found in their surroundings, made predictions based on those tests, and then improved upon them. This is reason, the human capacity to make sense of the world.

I was also extremely impressed with Nate Phelps the atheist son of Westboro Baptist Church Pastor Fred Phelps, who spoke so eloquently at the rally while his family picketed him at the sidelines. His story and others like it are why I wasn’t comfortable with people at the rally pointing to my son Sagan with a smile and referring to him as “future atheist.” Like most atheist parents, I will expose Sagan to a wide variety of belief systems, most likely through a community such as a Unitarian Church, let him decide for himself what to belief, and respect that choice. Leave the predestination nonsense to the Calvinists.

Secular Coalition

By definition, independent thinkers are an individualistic bunch. Over 20 secular and atheist organizations were present at the rally, each with their own flavor of skepticism, atheism, or Enlightenment values. There was the James Randi Educational Foundation, with its focus on debunking supernatural claims made by new agers and faith healers. There was the Richard Dawkins Foundation which actively promotes atheism, but also promotes the beauty and wonder of scientific ideas. My favorite organization was also making a strong showing, the American Humanist Association whose slogan is “Good Without God” and presents one of the most positive and uplifting secular messages of any organization present that day. One of my heroes, Isaac Asimov took more joy in being president of the AHA than he did in his leadership of Mensa International.

Richard Dawkins gave an overall good speech, where he lamented the absurdity of needing to hold such a rally, “How could anyone rally against reason? How is it necessary to have a rally for reason? Reason means basing your life on evidence and the logic which is how you deduce the consequences of evidence. In a hundred years’ time it seems to me inconceivable that anyone would want to have a rally for reason. By that time we’ll either have blown ourselves up or we’ll have become so civilized that we no longer need it.” I enjoyed the parts where he praised the natural world and our scientific understanding of it, but grew uncomfortable when he called for everyone to “ridicule and show contempt” for religion.

Richard Dawkins straddles, but never crosses, the line between what I love about science and why I get worried when scientists focus too much on religion-bashing. Christopher Hitchens, PZ Meyers, and the other outspoken atheists who argue atheism for the sake of atheism, on the other hand, come across as hostile and belligerent. They ridicule rather than seek to persuade, seeking to stir up feelings of outrage and contempt in their audiences, framing everything in terms of “Us VS Them,” and portraying theists as not just wrong, but oftentimes as evil. You know who else does that? Religious extremists and political pundits. We walked out of PZ Meyer’s speech at the Reason Rally for the same reason I turn the dial when Rush Dimbulb is on the radio, and I fear these “New Atheists” as they call themselves and “Militant Atheists” as they are called by their opponents are doing more damage than good.

The Origins of New Atheism

The New Atheism, the outspoken, in-your-face controversial atheism is a reactionary movement resulting from the perpetual attempts of theists to impose their supernaturally-inspired belief systems on the public. Theists changed the motto of the United States to “In God We Trust” in 1956, replacing E Pluribus Unum which was the nation’s motto since 1782. Over and over and over again they try to force their supernatural explanations into public school science text books, failing to realize in their short-sightedness that allowing alternatives to factual knowledge would open a Pandora’s box of creation stories from religions around the world. They push legislation defining life as beginning before pregnancy and making it a felony for doctors not to tell abortion patients they will have an increased risk of breast cancer for which there is no scientific evidence. On top of all this churches get to keep $100 Billion a year in donations tax-free, enjoying all the taxpayer-funded benefits of our society without having to contribute anything in return.

Westboro Baptist Church Sign

And yet somehow theists have managed to construct an elaborate scary fantasy of religious persecution in America. They falsely claim they are not allowed to pray in public schools, but the law only prevents them from using official school policy to impose prayer on students. They claim that religious groups are being banned from college campuses, but it is groups that practice discrimination that are being banned. Courts have ruled that private religious groups can discriminate against whomever they like, and organizations, like the Boy Scouts of America and religious organizations can and do discriminate on religious grounds.

America was founded on secularism, when you look inside the Library of Congress you see America portrayed as the science nation. The ceiling of the dome of Congress has a painting of Greek Gods giving the Founding Fathers Enlightenment through the sciences. We have led the world in publishing scientific research and have led the world innovatively and economically because of that, but now China is projected to surpass us in the near future. It’s remarkable that in the same country inspired by the heretic Thomas Paine to revolt against Kings appointed by god in favor of popular rule, so many people care less about our power to innovate through science and more about whether the leader of 300 million Americans shows proper reverence to a supernatural deity for which there is absolutely no evidence.

China Projected to Surpass America

When confronted with such an assault American values, it is easy to fall into a rut of outrage. The antidote to outrage is perspective, doing what scientists do best: looking realistically at the big picture.

The percentage of people who identify as “none” on religious surveys grows every year. Among scientists only 1/3 believe in god and that includes the deistic definition of god.

But most telling is the 3/4 of Americans who believe in god. They disparage scientific knowledge while driving in cars designed by our engineers, proselytizing on our televisions, and commenting on our World Wide Web. When they get sick, it is to our doctors they run. They are immersed in the gifts of science every moment of every day, and we don’t begrudge them this wonderful quality of life science provides, but we can allow ourselves a small degree of knowing condescension at their oblivious hypocrisy.

Atheists Have to Keep it Real

The problem I have with New Atheism is that I’m also a secularist. I might not believe in god, but so long as a person doesn’t use their understanding of a personal deity as an excuse to attack anyone’s freedoms then it’s harmless. People can entertain any supernatural fantasy they like if it gives them comfort, but when they participate in the arena of public discourse, they must confine themselves to the reality we all share. Barack Obama once eloquently explained this point:

Democracy demands that the religiously motivated translate their concerns into universal, rather than religion-specific, values. It requires that their proposals be subject to argument, and amenable to reason. I may be opposed to abortion for religious reasons, but if I seek to pass a law banning the practice, I cannot simply point to the teachings of my church or evoke God’s will. I have to explain why abortion violates some principle that is accessible to people of all faiths, including those with no faith at all. Now this is going to be difficult for some who believe in the inerrancy of the Bible, as many evangelicals do. But in a pluralistic democracy, we have no choice. Politics depends on our ability to persuade each other of common aims based on a common reality. It involves the compromise, the art of what’s possible.

You can argue whatever position you like in America, but when the only argument you have is because an invisible man in the sky said so, then you don’t have a legitimate argument. Supernaturally revealed knowledge is not universal in a pluralistic, democratic country. As Obama points out in the above speech, if we saw Abraham preparing to murder his son today, we would lock him up and put Isaac in child protective services.

Secular/Atheist Protest Signs

But we atheists have to look in the mirror and see how we are guilty of this very same fallacy when we argue there isn’t a god. Technically we must accept that atheism is not a position that has any bearing on reality any more than saying there is or isn’t extraterrestrial life in the Universe. These are not scientific positions. The distinguished planetary scientist Carolyn Porco best explains why:

If you were to ask me, if I believed in god. Since I am a professional scientist, I would want to give you two answers. In my capacity as a professional scientist I would have to–I would be required to–be agnostic on the subject since I couldn’t cite with scientific certainty say that there is a god and I couldn’t with scientific certainty say that there isn’t.

But if I were allowed to respond as just a regular non-scientist and if you allowed me to take the very same indulgences that all other non-scientists are allowed to take and that is I’m allowed to reject the training I’ve received as a scientist that taught me–that drilled into my head–not to accept anything as fact that can’t be scientifically proven, but instead I’m now allowed to do what many many others do and profess–I’m allowed now to profess to know something and to profess to strongly believe it in the complete absence of facts…then I’m gonna have to say that my very strong faith, my very very strong belief is that there is no god. But on this level, on this level now, my belief is perfectly equivalent to religious belief. We’re both doing the same thing.

Ryan, Technically an Atheist

This is why I don’t define myself as an atheist any more than I would define myself as an a-dittohead, a-flat-earther, or a-astrologer. As American environmental activist Van Jones put it, “Martin Luther King didn’t get famous for giving a speech called ‘I have a complaint.’” There’s a point where you have to say what you stand for. I am an Enlightenment Scholar, like the American Founding Fathers before me, and I’m pretty damn proud of it.

Spiritual and Atheist

Science has expanded our vision, revealing what we could not see before and in such a way that anyone who wants to follow the procedure can see it. Science convinced me to my present worldview because it presents a world that so much more majestic and moral than any theistic philosophy. Science wins mindshare because it successfully improves our quality of life every single day. Is it any wonder so many great minds have mused on the wonders of nature revealed to us through science?

The Magic of Reality

Richard Dawkins expresses it:

After sleeping through a hundred million centuries we have finally opened our eyes on a sumptuous planet, sparkling with color, bountiful with life. Within decades we must close our eyes again. Isn’t it a noble, an enlightened way of spending our brief time in the sun, to work at understanding the universe and how we have come to wake up in it? This is how I answer when I am asked—as I am surprisingly often—why I bother to get up in the mornings.

Carl Sagan articulates it:

In its encounter with Nature, science invariably elicits a sense of reverence and awe. The very act of understanding is a celebration of joining, merging, even if on a very modest scale, with the magnificence of the Cosmos. And the cumulative worldwide build-up of knowledge over time converts science into something only a little short of a trans-national, trans-generational meta-mind.

Science is not only compatible with spirituality; it is a profound source of spirituality. When we recognize our place in an immensity of light years and in the passage of ages, when we grasp the intricacy, beauty and subtlety of life, then that soaring feeling, that sense of elation and humility combined, is surely spiritual.

Albert Einstein conveys it:

The fairest thing we can experience is the mysterious. It is the fundamental emotion which stands at the cradle of true art and true science. He who knows it not and can no longer wonder, no longer feel amazement, is as good as dead, a snuffed-out candle. It was the experience of mystery — even if mixed with fear — that engendered religion. A knowledge of the existence of something we cannot penetrate, of the manifestations of the profoundest reason and the most radiant beauty, which are only accessible to our reason in their most elementary forms-it is this knowledge and this emotion that constitute the truly religious attitude; in this sense, and in this alone, I am a deeply religious man. I cannot conceive of a God who rewards and punishes his creatures, or has a will of the type of which we are conscious in ourselves. An individual who should survive his physical death is also beyond my comprehension, nor do I wish it otherwise; such notions are for the fears or absurd egoism of feeble souls. Enough for me the mystery of the eternity of life, and the inkling of the marvelous structure of reality, together with the single-hearted endeavor to comprehend a portion, be it never so tiny, of the reason that manifests itself in nature.

Richard Feynman elucidates it. Chet Raymo enunciates it. Walt Whitman poeticizes it. Ralph Waldo Emerson glorifies it. Teddy Roosevelt appreciates it.

Everyone should sing praise to science!

Spiritual Naturalist

Chet Raymo succinctly explains the dimensions and complexity of my own belief system (minus the last bit):

So this is my Credo. I am an atheist, if by God one means a transcendent Person who acts willfully within the creation. I am an agnostic in that I believe our knowledge of “what is” is partial and tentative-a tiny flickering flame in the overwhelming shadows of our ignorance. I am a pantheist in that I believe empirical knowledge of the sensate world is the surest revelation of whatever is worth being called divine. I am a Catholic by accident of birth.

The Apotheosis of Washington
(Minerva giving Science to the Founding Fathers)

I am an Enlightenment Scholar, like the American Founding Fathers. Experiments are my sacred rights. Quiet attention to the natural world around me is my prayer. Every school, laboratory, and library is my place of worship. My spiritual leaders are physicists, chemists, biologists, engineers, doctors, and professors. My scripture is in the ATGC of each link in the chain of a DNA molecule, the 1420.40575177 MHz frequency of a Hydrogen atom, The He, C, Ne, O, Si, and Fe atoms forged in stars, and the galaxy of elements produced from supernovas. My sense of mystery is the dark fog from the beginning of time at visible limits of our Universe, the inadequate metaphors of waves and particles we use to try and conceptualize the behavior of a sunbeam, and the infinite complexity of Pi, Phi, and e.

This is all so very precious. As the Dawkins Foundation magnets handed out at the Reason Rally said, “It took 13.7 billion years to make something this perfect. So don’t mess it up.”

From time to time I find myself deeply fascinated with the Golden Ratio and its relation to the Fibbonacci set. I even bought a cross-section of a nautilus shell to proudly display in my cabinet of curiosities because they grow along the golden ratio. Then this article clearly illustrated that nautilus shells grow in a logarithmic spiral. Now I’m even prouder of my nautilus cross-section because it tells a story of just how wrong I was about a beautiful hypothesis.

I feel as though a similar thing happened with the band They Might Be Giants, who released a song in 1993 titled Why Does the Sun Shine?, a cover of a song by Tom Glazer & Dottie Evans, that included the following lyric:

The sun is mass of incandescent gas,
a gigantic nuclear furnace,
where hydrogen is built into helium
at a temperature of millions of degrees.

Not bad, but 16 years later on their album Here Comes Science, they rereleased this cover and followed it with a new song titled Why Does the Sun Really Shine? that presents a more accurate description:

The sun is a miasma
Of incandescent plasma
The sun’s not simply made out of gas
No, no, no
[...]
(Plasma!)
Forget that song
(Plasma!)
They got it wrong
That thesis has been rendered invalid

They didn’t try to erase the fact that they (and the original songwriters) were wrong; they republished the inaccurate song and accompanied it with a correction, turning it into a teachable moment. The original song doesn’t lose any value, the tune is just as catch as it ever was, only now the listener has additional, more accurate insights into its meaning.

xkcd: Airfoil

Here’s the thing: It’s OK to be wrong, but it doesn’t always feel that way. We live in a world where less emotionally mature minds equate being wrong on even a few points with being fully discredited. Under such silly zero-sum-game social pressures, people are backed into ideological corners, unable to concede any error or alter their position on a subject in light of new evidence. We see this in politics all the time, where any politician who changes their mind is labeled “flip-flopper.”

But in the world of science and academia admitting to being wrong demonstrates integrity and exhibiting the plasticity of mind to adjust one’s position to fit the evidence is a virtue. Richard Dawkins tells the story of a Professor at Oxford being presented with incontrovertible evidence falsifying one of his strongly-held beliefs (emphasis mine):

I have previously told the story of a respected elder statesman of the Zoology Department at Oxford when I was an undergraduate. For years he had passionately believed, and taught, that the Golgi Apparatus (a microscopic feature of the interior of cells) was not real: an artefact, an illusion. Every Monday afternoon it was the custom for the whole department to listen to a research talk by a visiting lecturer. One Monday, the visitor was an American cell biologist who presented completely convincing evidence that the Golgi Apparatus was real. At the end of the lecture, the old man strode to the front of the hall, shook the American by the hand and said – with passion – ‘My dear fellow, I wish to thank you. I have been wrong these fifteen years.’ We clapped our hands red. No fundamentalist would ever say that. In practice, not all scientists would. But all scientists pay lip service to it as an ideal – unlike, say, politicians who would probably condemn it as flip-flopping. The memory of the incident I have described still brings a lump to my throat.

Every time a fundamentalist rejects empirical evidence, they put the vice of obdurateness on display. Every time an ideologue exclaims “Ah-Ha!” in response to someone conceding a point in expressing a nuanced position, they parade their nescience before the public. We feel embarrassed for these diminutive minds because they lack the awareness necessary to feel embarrassed for themselves, and rightly so, but it is never appropriate to feel embarrassed for someone who believes in even a large number of inaccurate ideas because that’s simply being human.

xkcd: Certainty

One thing that becomes apparent when talking to members of the Baby Boomer generation for longer than a few minutes is that they have a lot of misinformation in their heads, but that’s not surprising. They grew up in a world without an Internet and instantaneous fact-checking. Memory is incredibly fallible, and without perpetual reinforcement from easily-accessible references, the data in our heads corrupts and degrades. In fact, it seems that the more we recall a memory the more our brains alter the details.

As part of Generation X, I grew up in a world without an Internet. Then for the first decade of the mainstream World Wide Web, it was considered a cesspool of disinformation. It wasn’t until I was in my 30′s that the Internet became a resource for reference material, and I remember discovering the habit of checking every bit of knowledge I took for granted online at that time and being shocked at all the disinformation in my head.

Ideologues and fundamentalists simply don’t understand the world well enough to know they are as fallible as the rest of us. “Ignorance more frequently begets confidence than does knowledge,” as Charles Darwin said.

Consider one of the most famous examples of brilliance in the modern world. “Einstein” is synonymous with “genius,” but history forgets Albert Einstein was wrong about key tenants quantum physics that he rejected because he could not understand them. The world of physics, in turn, largely ignored his later efforts to develop a Unified Field Theory. Einstein doesn’t stop being a genius for being wrong many times in his life, but he does start being human.

The moment you realize it’s okay to be wrong, you are free. The moment you can recognize when you are wrong about something and shrug off the faulty factoids without a moment’s hesitation, the more adaptable and youthful your brain will remain. As William Cowper mused:

Knowledge and wisdom, far from being one,
Have ofttimes no connection. Knowledge dwells
In heads replete with thoughts of other men,
Wisdom in minds attentive to their own.
Knowledge is proud that he has learned so much,
Wisdom is humble that he knows no more.

“Time is the fire in which we burn.” ~ Tolian Soran, Star Trek Generations

The Dilemma

We have a finite amount of time in this life, and we should be mindful of how we spend it. I’ve recently become highly cognizant of the fact that the majority of games are simply Skinner Boxes, tricking players into pushing buttons in return for meaningless rewards. Truly challenging games like Portal and SpaceChem keep you playing because the gameplay is its own reward, while Skinner Box games keep you performing repetitive tasks with virtual rewards. Other games, like Skyrim or Final Fantasy VII, keep you playing because the story and graphics are simply that engaging.

The Original Earth Starbase Was Just Okay

The Redesigned Earth Starbase Looks More Familiar

For the past two years I have played Star Trek Online (STO) casually, probably investing maybe a hundred hours in the game, two weeks of my life out of 104. So the question arises: Is STO time wasted? The game was never challenging, but was it at least entertaining? I think this is a question we should be mindful of with any game in which we choose to invest our time to make sure we aren’t burning it.

The Star Trek Online Grind

I love Star Trek. I mean I really love love love it. When STO came out, it was going to be my MMORPG, I wanted to fully immerse myself in it. I purchased a lifetime membership precisely so I wouldn’t feel pressured to play all the time, and I measured my engagement with the STO universe into the storyline missions, avoiding defend sector space and exploration missions which are vapid and repetitive.

Memory Alpha is the Science Hub of the Federation, but “Science” really means “Crafting”

I previously complained about the game’s focus on combat while I prefer exploration and discovery, and learned from reading World of Warcraft forums that this problem is known as the grind.

Starship battles can be a grind at times. They are slow and ponderous, which is exactly what I was looking for in this game. I want every battle to feel like The Wrath of Khan, and STO does a great job with it. The problem is that there are too many starship battles and too little variation between them. I dreaded missions where the goal was to eliminate all enemies from around a planet, where you fly from battle to battle, phasers and torpedoes auto-firing at the same kinds of ships over and over again. I’d have preferred fewer, longer space battles where I would need to concentrate on exploiting an opponent’s failing shields or strategically deal with an enemy ship’s special abilities. STO space battles can be quite tactical at times, but they can also be repetitive at others.

My Character Using a Hologram Display to Set an Opponent on Fire. “Any sufficiently advanced technology is indistinguishable from magic.” ~ Clarke’s Third Law

During my two years of playing, ground combat was a total chore. It was also slow and ponderous, with every phaser blast taking off just a tiny bit of an opponent’s shields or life. It got to the point where I would set my away team to fight for me while I read a book or surfed the web. Recently, however, STO has dramatically improved ground combat, making it much more face-paced and interesting. Ground combat is also much more tactical than space combat, which is nice. I enjoy having my engineers set up some mines and turrets and then leading enemies into an ambush; unfortunately, there are still missions where there is just too much combat.

The Guardian Introduces One of My Favorite Episodes

Your typical STO mission goes like this: (1) Warp to system X to [investigate, protect, deliver] something. (2) Fly around the [planet, asteroid field] either blasting [badguy ships, badguy stations] or [scanning, repairing, sabotaging] [anomalies, bases, satellites] at four to six different locations. (3) Beam down to the [space station, planet, enemy base]. (4) Run around [blasting badguys, sabotaging stuff, scanning stuff] at four to six different locations. Repeat (2) through (4) as needed until the mission is completed and collect the reward. Deconstructing the action down to this makes it sound extremely tedious, but it depends on the path you take through the game.

A Borg Cube Haunts the Skies of the Deferi Homeworld

The average STO player takes 50 – 90 hours to peak out at the rank of Vice Admiral. As a casual player, I spread that out over two years. I’ve seen people on the forums get ridiculed for taking more than 100 hours to top-out in the game; after all, if you just focus on exploration missions, you can max out in just 40 hours!

The problem is that the exploration missions are also the most generic and boring. You don’t even have to pay much attention as your ship will fire its weapons automatically while you cruise lazy circles in space and your away team can take care of most bad guys while you watch Big Bang Theory episodes. Playing through the game like this is a complete waste of your life. So why bother?

The Star Trek Online Odyssey

STO takes place in the universe Spock left when he failed in his mission to save Romulus from its star going supernova and got wormholed into the Star Trek reboot universe of the 2009 movie. The Romulan Empire is in chaos, the Klingons have declared war, the Gorn are back, and the Borg are invading. The Universe feels dark, intense, and dramatic, and there are some great storylines to play out filled with characters and references that Star Trek fans will appreciate and the technology is more advanced than anything seen in the shows.

Contitution and Excelsior Class Starships in Drydock

Also working in STO’s favor is that the game is beautiful, and keeps getting more dazzling. I knock the exploration missions, but they make nice filler for discovering fascinating-looking planets. The game is also very large; however, it doesn’t feel as big as it should because of the way the game designers compartmentalized environments (deep space doesn’t flow into planet space, planet space doesn’t flow into ground locations), and you can tour the entire universe in under an hour. With each promotion through the ranks, you get to explore deeper in space with each new area introduced through narration by Leonard Nimoy.

Ferengi, Gorn, Romulans, Undine, Klingons, and Orions, Oh My!

Undine, Remans, Romulans, Vulcans, Klingons, Orions, Gorn, Cardasians, Mirror Universe Federation, Hyugen, Devidians, Ferengi, Jem’Hadar, and other aliens infuse STO with variety as well. Just as each of these aliens has their own cultures and strategies in the show, they present different challenges in the game as well. What makes the storyline missions great is meeting recurring villains who get you more invested in the action.

The STO developers have also demonstrated what’s really possible in game with their feature episodes. There are large cities heavily populated with aliens and skies filled with ships , space stations the size of V’ger to fly through, giant monsters, and engaging plots in these extended storylines. With new content always on the way, I really do look forward to each new episode.

Human-Players Push the Boundaries of Interesting Avatars

Most importantly however, is the importance of remembering that STO is an MMORPG. The twin M’s in that acronym are the deciding factor in whether the game is a hit or miss, and the Star Trek franchise has the greatest fans on Earth. I loved participating in chats during the game’s first few months, reminiscing about favorite episodes, trading treklore and tips on good in-game episodes and events. There are also Player VS Player (PvP) sessions, which are like team deathmatches with starships and phasers, and the Player VS Environment’s (PvE), which are missions requiring teamwork to complete.

Assimilated Gorn is a Concept so Cool only a fan could come up with it

But STO has taken the “MM” part of the equation even further with player-authored missions, which is pure genius. The fans are designing missions that are more epic, faster paced, and more creative than anything else in the STO universe and that’s because their doing it out of love. The rewards for these missions are minor, but they are by far more fun than anything else in the game and are keeping me playing.

Is STO Worth It?

Since STO has gone Free To Play (F2P), with all missions and content available to anyone who downloads it, that doesn’t mean it’s really FREE. There is still a sizable time investment required to play the game and we have to weigh that against other activities on which we could be spending this precious hourglass sand. My conclusion is that it is worth it if you’re a fan and play casually.

Vice Admirals Get Access to Borg Technologies to Trick Out their Ships

The gamers who reached Vice Admiral in 40 hours fell prey to the Skinner Box. They behaved no better than rats pushing a button to get a reward, and you need to be aware of the animal propensity to fall into this trap if you play STO. I wasn’t fully cognizant of how in-game rewards were tainting my perceptions until I reached Vice Admiral, where experience points are capped and you can no longer increase your skill levels.

The ships I earned in STO Waygate, Asimov, Beagle, Sagan, Odyssey, Feynman, and the Enlightenment.

As a reward to myself for maxing-out my character, I splurged on the $25 to purchase a Galaxy Dreadnought Starship. My thought was that I would go sightseeing and just appreciate the game play. I visited the planet Vulcan and picked up a detective-style mission to find out who threatened the life of a visiting Romulan dignitary. I ran around the planet, picking up clues for awhile, and realized, Wow, this is really lame.

Without the rewards, the mission seemed quite silly. Sure, I was learning interesting stuff about Vulcan and Romulan history, but I was having to run back and forth and all around to pick up each tidbit of trivia. I realized that, without the Skinner Box rewards, I simply didn’t have the patience for most missions and would abandon them once they got tedious.

Player Ships Hanging Out at DS9 Look Like a Formidable Fleet

I could jump back in the Skinner Box, I’ve got six character slots left on my account, but that holds no appeal. I could also try playing through the game as a member of the Klingon Empire, but the idea of playing one of those backwards-evolving meatheads is antithesis to what appeals to me about Star Trek.

To maintain my enjoyment of the game, I’ve decided to focus on playing it in moderation, which is how I mostly played it through the last two years. It’s like getting a Next Generation box set and only watching a few episodes a week. It’s F2P, so there’s no urgency, just play an episode a week, do a little exploring, adventure with some other players, or try out a fan-fiction episode for some real novelty. It’s a wide, expansive virtual world, and it’s best to savor and appreciate what it gets right.

Further Reading

List of all STO Mission. Stick to “storyline” and “episode” content. These missions take longer and give you less rewards for your time, but they are also the most engaging and interesting. Also a filterable list of missions here.

My flickr collection of my adventures in STO.

Here’s my original post on STO, complaining about the lack of science in the game. There still isn’t much science in the game.

These reasons will work from the general to the specific. I’ve used links to articles in Wikipedia as much as possible because Wiki articles are refined over time with our understanding of the subjectmatter and are less subject to link-rot. This post is licensed Creative Commons and all photos listed here are available under some form of free-to-use licensing. Please feel free to refine this list and repost it, just please preserve the photo credits and links to photographers. Also, suggestions for improvement on any items is welcome as this is a lot of material over a wide range of scientific fields, so I have certainly bungled some things here.

Over time, new evidence will certainly find some of these examples in error, and that’s a good thing because science is about refining our understanding of the truth. The Theory of Evolution is strong enough that nearly half these examples could be disproved and the evidence would still be fairly overwhelming. There is so much in this world that only makes sense in the light of Evolutionary Theory.




Age of the Earth and Its Fossils

We live on a very old Earth.

1. Lithologic Stratigraphy

Looking at Millions and Millions of Years
Credit: cobalt123

The Earth’s crust has layers. Some of these layers are from the decomposition of sediment, others come from chemical precipitation, others from decaying organic matter, and others from volcanic lava. The reason we can see the layers is because they were formed in different ways.

2. Law of Superposition

Geologic strata at bright angel trail

Layers are laid down on top of each other, with the bottom layers laid down first and the top layers laid down last; therefore, the layers on the bottom are the oldest and the ones on the top are the youngest.

3. Fossilized Footprints

Dinosaur trackways
Credit: jacashgone

Dinosaur footprints, slug footprints, Australopithecus footprints and other footprints on top of any layer in the strata means that layer was at the top of the stack long enough for something to walk on top of it before it got covered by subsequent layers and hardened into solid rock.

4. Fossils

Petrified Wood

The process of permineralization, where mineral deposits form internal casts of organisms, provides us with a vast quantity of fossils that give us an idea of the different forms life has taken in the past.

5. Fossils of Extinct Species

A collection of skeletons mounted in museums of various dinosaurs

We have lots and lots and lots of fossils of species that don’t exist anymore. Lots and lots and lots of them in just the superorder Dinsosauria alone.

6. The Law of Faunal Succession

Agate Springs Block
Credit: IslesPunkFan

You will never find a Neanderthal bone in the same stratum as a Tyrannosaurus rex bone. Tyronnosaurus rexes weren’t alive at the same time; therefore, their stratum didn’t get laid down at the same time.

7. Seashell Fossils on Mountaintops

Strata – Lulworth Cove
Credit: mgjefferies

Benjamin Franklin saw that there were fossilized sea shells on top of the mountains of Appalachia, some of them imprinted into solid rock, and concluded, “Tis certainly the Wreck of a World we live on!” The shells were deposited in layers on the Ocean floor over millions of years, layers that would be violently broken up and rippled into a mountain range 480,000,000 years ago by a catastrophic earthquake.

8. Plate Tectonics and Continental Drift

First known illustration of the Opening of the Atlantic Ocean, by Antonio Snider-Pellegrini, 1858.

South America fits into Africa, rocks get younger the closer you get to where the crust is spreading under the ocean, and satellites have observed the drift. The continents drift at a rate of a few centimeters a year and the distance between the Americas and Africa is 455,000,00 centimeters.

9. Same Fossils on Both Sides of the Atlantic

Snider-Pellegrini Wegener fossil map

There are matching fossils on both sides of where the continents appear to have split apart. Cynognathus, a Triassic land reptile, fossils are found in South America and Africa. The Triassic era was between 250,000,000 and 200,000,000 years ago.

10. Radiometric Dating

Uranium Decays to Lead Inside Zircon

Take a quantity of uranium-238 and in 4.5 billion years half of it will have turned into lead-206. When molten rock hardens into a solid, the uranium-238 within it begins to decay. By comparing the ratio of uranium-238 to lead-206, we can estimate how old the rock is. The same thing can be done with Samarium-neodymium, Potassium-argon, Rubidium-strontium, and Uranium-thorium transitions.

11. Radiocarbon Dating

1. Formation of Carbon-14
2. Decay of Carbon-14
3. The “equal” equation is for living organisms, and the unequal one is for non-living ones, in which the C-14 then decays (hence the 2).

Carbon-14 has a half-life of 5,730 years. There is a semi-constant ratio of carbon-14 in the air and ocean as it is constantly being created by cosmic rays. Plants take in carbon from the atmosphere and ocean and fix it into themselves. Animals eat plants and fix the carbon into themselves. By measuring the ratio of carbon-14 in a younger fossil, scientists can estimate its age.

12. Dendrochronology

1341 year-old Redwood
Credit: Me

Many trees grow a new ring in their trunk every year, meaning the tree is as many years old as it has rings, meaning trees can be used to calibrate Radiocarbon dating to confirm its accuracy.

13. Stromatolites

Stromatolite
Credit: Me

These fossilized bacterial colonies date back 2.7 billion years and may extend 3.4 billion years. Stromatolites grow at a maximum rate of 5cm every 100 years and a stromatolite 1.5 meters in diameter was found in Virginia and a 500cm high stromatolite was found at the foot of Wutai Mountain in China.




Genetics

How genes and mutations work give us insights and tools into how evolution works.

14. Heredity

Table showing how genes exchange according to segregation or independent assortment during meiosis and how this translates into the Mendel’s Laws.

Offspring inherit the characteristics of their parents, which are controlled by genes.

15. Universal Genetic Material

Chemical structure of DNA

All life on Earth uses a three-letter code to produce 20 standard amino acids. Researchers have artificially expanded the genetic code to produce additional amino acids as tools, but all natural life use the same 20 amino acids from our common descent.

16. Miller–Urey Experiment

Miller-Urey experiment (1953).

In 1952 Stanley Miller and Harold Urey synthesized organic compounds from inorganic precursors found in the Earth’s original atmosphere, producing more than 20 different amino acids using electrical sparks to simulate lightning.

17. Mutations

DNA Covalently Bonded to the Cancer-Causing Mutagen in Tobacco Smoke, benzo[a]pyrene.

The genomic sequence in cells is under constant mutation pressure from radiation, viruses, chemicals, and copying errors.

18. Speciation


Spatial Aspects of Speciation

Speciation is the process by which new species are formed. When a species gets split into two groups by a river, mountain range, island, lake, or ocean via earthquakes, floods, droughts, climate change, or continental drift, the two populations will begin to drift genetically.

19. Natural Selection


Selection Pressures on a Sexually Reproducing Organism

Mutations that reduce an organism’s ability to survive and reproduce will be less likely to end up in offspring. Mutations that give an organism a survival and reproductive advantage will be more likely to show up in offspring.

20. RNA/DNA Codon Table

RNA/DNA Codon Table

Genes that code for proteins are composed of three-nucleotides (U/T, A, G, or C). All the different ways these nucleotides can combine to produce the various amino acids is listed in the above table. Note that the third nucleotide usually makes no difference on the amino acid produced, meaning it can change (mutate) without having any effect on the gene’s expression.

21. Noncoding DNA

Screenshot of tiny portion of the human genom in hdv (n’s are non-coding)
Credit: Markus Kison

A large portion of eukaryotic organisms’ total DNA does not produce amino acids. In humans, more than 98% of the genome is noncoding. Much of this DNA is vestigial–it expressed in our ancestors but not longer serves a purpose. DNA that does not serve a purpose can mutate without having any affect on the organism.

22. Molecular Clock of Mutations

Cytochrome C Protein Sequences Compared to Humans

The number of genetic differences between two species will increase with the time since they originally diverged. Mammals and birds will be equally divergent from fish, and vertebrates will be equally divergent from yeast.

23. Hox Genes

Legs Replacing Antennae on a Fly

These genes provide for the basic blueprint of all segmented life, such as arthropods, insects, and organisms with backbones. They define what, if anything, should grow out of each segment of the body plan. Mutations in hox genes can replace antennae with legs, as in the above photo of a fly, or give humans a sixth finger, but they also make it much easier for species to mutate in useful ways to produce body plans adapted to a wide variety of environments.

24. Sexual Reproduction

The sexual cycle

While asexual reproduction is more efficient in nature because it prevents an organism from having to find a mate to reproduce, it also condemns a species to only produce clones of itself. Sexual reproduction improves a species ability to survive by constantly varying the traits of offspring, making it more likely that some will be able to survive a dramatic environmental change such as drought or famine.

25. Mitochondrial DNA

Human Migrations Across the Earth
Credit: Me

While sexual reproduction mixes up the genes from generation to generation, the mitochondria, energy-factories of the cell, have their own DNA and get passed down directly from the mother to her offspring.

26. Genographic Project

Genographic Map

This DNA survey of human beings has traced our migration out of Africa into Europe and Asia and then over to North America and finally South America.

27. Mitochondrial Eve and Y-chromosomal Adam

Early diversification

Because mitochondrial DNA are transferred from the mother to her offspring unchanged, scientists can use the variation in mitochondrial DNA across modern humans to estimate a rate of mutations (one every 3,500 years) and estimate a time back to a common ancestor who lived around 200,000 years ago.

Because Y-chromosomes are transferred from father to son unchanged, we can trace our ancestry using this DNA sequence. Using a survey of Y-chromosomes from all over the world and a reconstruction of ancestral Y-chromosome DNA from reversing mutated DNA segments, we can estimate a common ancestor to us all between 60,000 and 142,000 years ago.

28. Neanderthal DNA in Humans

A map depicting the range of the extinct Homo neanderthalensis

Non-African humans have between 1% and 4% Neanderthal DNA from when our ancestors interbred with the extinct species.




Comparative Anatomy

Comparing species traits, their DNA, and their geography are tools for outlining their evolutionary progression and relatedness.

29. Nested Hierarchies

Phylogenetic groups

We don’t just have a list of species, we have a tree logically laid out according to the similarities and dissimilarities among all the different species on Earth now and fossilized in the past.

30. Cladistics

Cladogram

Cladistics is a methodology for classifying species into groups based on their characteristics. While some characteristics like eyes and sexual reproduction have emerged more than once in the history of life on Earth, for the most part we may assume that a organisms sharing a trait such as a jaw, central nervous system, lungs, or mammary glands share a common ancestor.

31. Comparative DNA

16S rRNA secondary structure

Phylogenic trees are built from comparing genomes in addition to comparing anatomical structures.

32. Statistical Probability of Congruent Phylogenetic Trees

Phylogenic and Molecular Cladograms

When comparing the phylogenetic tree to the molecular tree, they match so well that the significance is P <= 0.00077.

33. Thompsonian Transformation Grids

Illustration from On Growth and Form

D’Arcy Thompson in his book On Growth and Form saw that one species could be turned into another through the application of mathematical transformations to alter their proportions.

34. Homology

Homology in vertebrates

The bat’s wing, seal’s flipper, cat’s paw, and human hand all have the same bones and muscles because they all share a common ancestor. For example, giraffes have the same number of neck vertebrae as humans, seven.

35. Embryonic Recapitulation

Human Embryo (7th week of pregnancy)
Credit: euthman

While the specific hypothesis of Recapitulation, that embryos retrace the evolutionary steps of their ancestors in their growth, has been discredited. Embryos do temporarily take on the characteristics of their ancestral species, such as human embryos having gill arches, a tail, eyes on the sides of the head, a tube-shaped heart, and ear-bones in the jaw during development, all of which vanish in later development. Just as Hox Genes make is possible for species to easily change forms and configurations, the stages of fetal development can change to produce very different characteristics in an organism.

36. Neoteny in Humans

Infant Chimpanzees More Closely Resemble Humans

Chimpanzee infants more closely resemble humans, suggesting an easy route from our ancestors to us would be to simply stop the development of many features earlier, leaving our heads larger in proportion to our bodies and our faces flatter.

37. Atavisms

Atavistic Tail in Human Infant

While a species may no longer express the traits of its ancestors, the DNA for those traits may still exist in the organism’s genome and occasionally come out in individuals. As a result, we see hind legs on whales and snakes, hind fins on dolphins, extra toes on horses, teeth in chickens, humans with extra nipples or a tail, and many other traits.

38. Blood Salinity

Haemoglobin

Terrestrial vertebrates “have body fluids roughly the same osmotic concentration as fresh-water fish, roughly 1/3 the concentration of sea water.”

39. Endosymbiotic Theory

Endosymbiosis

There is strong evidence that Mitochondria and plastids were once bacteria that evolved on their own before being ingested by our cells into a symbiotic relationship. These organelles resemble bacteria that exist in nature and carry similar DNA.

40. Endemic Island Species

Varanus komodoensis

Islands comprise 30% of the world’s biodiversity hotspots and some of the most unusual species, as we would expect from habitats where species are left to evolve in unique ways.

41. Species Not Found on Oceanic Islands

Hawaii

Islands that have never been a part of a continent, but formed from volcanoes do not have terrestrial mammals, amphibians, or fresh water fish, as we would expect if the island could only be populated by seeds and birds over the air or small animals carried on rafts of vegetation.




Transitional Fossils

The fossil record shows endless “in between” forms. The word “to” used in these examples does not mean a direct ancestry between two fossils, but rather refers to the evolving characteristics found in them over millions of years of time.

42. Dinosaurs to Birds

Iberomesornis

Pedopenna to Anchiornis to Scansoriopteryx to Archaeopteryx to Confuciusornis to Sinosauropteryx to Eoalulavis to Ichthyornis

43. Fish to Tetrapods (Life from Sea to Land)

Tiktaalik

Osteolepis to Eusthenopteron to Panderichthys to Tiktaalik to Elginerpeton to Ventastega to Acanthostega to Ichthyostega to Hynerpeton to Tulerpeton to Pederpes to Eryops.

44. Synapsid (“mammal-like reptiles”) to Mammals

Thrinaxodon Lionhinus

Protoclepsydrops to Archaeothyris to Clepsydrops to Dimetrodon to Procynosuchus to Thrinaxodon to Morganucodon to Yanoconodon.

45. Artiodactylans to Whales (Land to Sea)

Ambulocetus

Pakicetus to Ambulocetus to Kutchicetus to Artiocetus to Dorudon to Aetiocetus to Basilosaurus to Eurhinodelphis to Mammalodon.

46. Horse Evolution

Equine evolution

Hyracotherium to Mesohippus to Parahippus to Merychippus to Pliohippus to Equus.

47. Human Evolution

Skulls from Human Evolution
Credit: Me

Apidium to Aegyptopithecus to Proconsul to Pierolapithecus to Ardipithecus to Australopithecus to Homo habilis to Homo erectus to ‘Archaic’ sapiens… and there’s alot more fossils than these.




Convergent Evolution

Different species will evolve similar adaptations to the similar challenges.

48. Placental Mammals and Australian Marsupials

Mammals and Marsupials

Despite evolving in geographic isolation, the marsupials of Australia have evolved many analogous features of placental mammals in the rest of the world.

49. Ichthyosaurs and Dolphins

Ichthyosaurus

The ichthyosaurs, a marine reptile from 250 million years ago, and dolphins are both air-breathing and both descended from land animals. They adapted to life in the ocean with a hydrological design that includes fins and a body shape like that of a fish.

50. Birds and Bats

Bat and Bird Wings

Birds and bats both have wings made out of bones that were arms in their ancestors.

51. The Eye

Eye Evolution

Complex image-forming eyes have evolved some 50 to 100 times, with the first eyes appearing in the fossil record 540 million years ago.

52. Succulents in the Americas and Africa

Succulents from Different Continents

Although they evolved on different contents, the succulents of Africa and the Americas adopted very similar traits to survive in arid climates and soil conditions.

53. Homo floresiensis and Dwarf Elephants

Homo floresiensis – reconstruction

The “hobbit” human of Indonesia and Dwarf elephant both adapted to limited food sources on the island of Indonesia by shrinking in size 840,000 years ago.




Adaptations

Many of the same organs in species are adapted to specific tasks both within a species and across them.

54. Coevolution

Sexually-deceived
Credit: ~Squil~

Flowers bribe insects and hummingbirds with nectar in exchange for acting as their instruments of sexual reproduction by carrying pollen from plant to plant. Orchids use deception by mimicking the pheromones and appearance of insects to trick them into attempting to mate with the flower. The existence of unknown insect species has been predicted by the discovery of orchid flowers.

55. Beaks


Bird Beaks

Birds exhibit a wide variety of beak shapes that are adapted to their feeding habits.

56. Insect Mouthparts

Insect Mouthparts

The primitive mouthparts of grasshoppers have evolved to a wide variety of specialized feeding strategies in other insects.

57. Tall Trees

Coastal Redwood

Trees grow tall in order to get above the competition for access to sunlight. Shorter trees get left in shadow while the tallest trees get to photosynthesize.

58. Human Skin Color

Skin color map

Humans rely on sunlight to generate vitamin D. As humans migrated north, they recieved less sunlight; therefore, natural selection favored lighter skin that produced more vitamin D in response to sunlight.

59. Sickle-Cell Disease

Sickle cells

The gene for this disease is prevalent in Sub-Saharan Africa, where malaria is common. Individuals who carry only a single sickle-cell gene are more tolerate of malarial infection.

60. Lactase Persistence

Modern-day lactose intolerance in humans

Most mammals develop an intolerance to lactose, the sugar found in milk, as they grow older, but humans in some regions are able to continue digesting milk, the result of humans consuming the milk of livestock such as cows, goats, and camels (this is also an example of convergent evolution).

61. The shape of the penis.

Mushroom
Credit: Fluffymuppet

The human male penis has a bulbous end that maximizes its ability to displace the semen of rival males from the vagina.




Vestigial Traits

Various species, including humans, have numerous physical traits that are leftovers from our ancestors.

62. Hip bones in Whales


Baleen whale Pelvis

Baleen whales still have hip bones inside them, serving as anchors for muscles, from when their ancestors had legs.

63. Laryngeal Nerve in Giraffes


Scheme of path of the recurrent laryngeal nerve in Giraffa camelopardis

Although the most direct route for this nerve is just a few inches, it may be up to 13 feet long in giraffes as it goes all the way down the neck, loops back, and comes all the way back up again. This nerve takes a similarly crazy route in humans too. The nerve is long because our fish ancestors had no neck, and the nerve looped around a gill arch that would become the dorsal aorta in mammals.

64. Veriform Appendix

Veriform Apendix Connected to Large Intestine

In our ancestors, the appendix is used to digest plant fibers. As humans began cooking our food, we did not need to digest plant cellulose, so this organ shrunk to its current pinky-size. A recent hypothesis suggest the veriform appendix now serves as a reservoir for bacteria to repopulate the large intestine after illness wipes them out.

65. Coccyx

Pelvic girdle, posterior view
Credit: Rob Swatski

The tailbone is the final segment of the vertebral column in tailless primates, all that remains from our ancestors’ tails. Today it serves as an attachment point for muscles and something to sit on.

66. Goose Bumps

Goose Bumps

These bumps on our bare skin occur in cold weather or when experiencing fear. In our ancestors they would cause the fur to rise up, increasing insulation against the cold and increasing the appearance of size against threats.

67. Maxillary Sinuses

maxillary sinuses

These sinus cavities have their drainage hole in the top. This is because, when our ancestors walked on all fours, the drainage hole was positioned in the front.

68. Blind Spot in Vertebrate Eyes

Vertebrate VS Octopus Eye

The optic nerve that carries information from our eyes to our brain actually comes through the eye, creating a spot where there are no photoreceptor cells on the optic disc to recieve light. As a result, our brains fill in the blank spot using surrounding details and information from the other eye. The optic nerve of octopus eyes stays behind the photoreceptor cells, so they experience no blind spot.

69. Blind Cave Fish

cavefish and zebrafish embryos
Credit: wellcome images

Animals that move to a dark environment will quickly lose evolutionary adaptations that are no longer useful. Cave fish embryos begin to develop eyes, but then stop and skin grows over them.

70. Flightless Birds

Ostrich
Credit: Doug Wheller

Similarly to cave fish, the wings of birds that no longer need to fly will grow smaller and the birds will become flightless.

71. Tyrannosaurus rex’s Arms

Tyrannosaurus resting pose

Contrary to popular belief, Tyrannosaurus rex’s arms are not vestigial, but show large areas of muscle attachment. They may have been used in mating or in helping the animal rise from a prone position.

72. Wisdom Teeth

Impacted wisdom teeth

Similar to the appendix, these teeth helped us grind up plant cellulose. As we began cooking our foods, our jaws atrophied, leaving less room for these teeth to come in. As a result, many people have them pulled today.

73. Plica Semilunaris of Conjunctiva

Plica Semilunaris

This fleshy part found in the inner corner of our eyes is what remains of our ancestors’ third eyelid. Today it produces eye-boogers.

74. Palmar Grasp Reflex – Infant grasping reflex

palmar grasp reflex
Credit: Geoffrey Wiseman

From birth until five or six months of age, human infants will instinctually grasp things that brush their palms. This is a vestigial reflex from our primate ancestors who had fur to which infants could cling.

75. Ear Muscles

Ear Muscles

Humans have fairly useless ear muscles from when our ancestors were able to manipulate their ears independent of their head, like in cats.

76. Antarctic icefish

Icefish

This fish has clear blood because it contains only 1% hemoglobin, the metalloprotein that carries oxygen in our blood, because it lives in oxygen-rich cold water but still has the genes to make hemoglobin that it got from its ancestors.

77. The Panda’s Thumb

Panda Hand
Credit: Travis S.

Panda’s, which are related to carnivorous bears, have five clawed fingers and a modified wrist bone that sticks out to function like a primitive thumb, which they used to grab bamboo–which they can barely digest because they are descendent of carnivores.

78. Route of the vas derens

Route of vas deferens from testis to the penis

This tube routes sperm from the testicles to the base of the penis in anticipation of ejaculation in humans. Although the direct route is only a few inches, the vas deferens loops up and over the tubes connecting the kidneys to the bladder and back down again because our ancestors testes were on the inside. Human male embryos start out with their testes on the inside, but they descend to the scrotum during development.




Artificial Selection

For thousands of years humans have bred various species to maximize desirable traits.

79. Wild Silver Foxes into Puppies

young silver fox
Credit: matt knoth

Dimitri Belyaer, by selecting for non-aggressive behavior and non-fearful behavior, was able to turn wild silver foxes into tail-wagging, friendly animals very similar to domesticated dogs in just 10 generations.

80. Dog Breeding

Great Dane and Chihuahua mixed-breed

Humans have produced a wide variety of dogs in many shapes and sizes by selecting for traits in just 10,000 years.

81. Corn

Teosinte, Maize-teosinte hybrid, Maize.

Maize is a domesticated descendent of teosinte, a wild grass. Although they appear very different, two genes control the differences between them.

82. Chickens

Different breeds of domestic chicken in comparison with the wild ancestor, the Red Jungle Fowl
Credit: Staffan Ullström

Farm chickens are descendants of Red Jungle Fowl.

83. Domesticated Turkey

Wild and Domesticated Turkeys

When you look at the domesticated turkey, it’s hard to believe Benjamin Franklin lamented to his daughter that the turkey should be the American mascot rather than the bald eagle, but the wild turkey is a very athletic and rather majestic animal.

84. Brussel Sprouts, Kale, Cauliflower, Turnips, Rutabega, Kohlrabi

Brassica oleracea

Brussel Sprouts, Kale, Cauliflower, Turnips, Rutabega, Kohlrabi are all descendants of Brassica oleracea, a wild cabbage plant.




Evolution in Action

Natural selection has been observed to happen in the real world, with species evolving right before our eyes.

85. Prions

bovine spongiform encephalopathy
Credit: Public Health Image Library, APHIS

Prions, an infectious protein, are protein molecules that fold other proteins into their state, causing diseases like Mad Cow disease. These molecules have been found to evolve under selective pressures, such as medical treatments, despite not having DNA.

86. Peppered Moth

Biston betularia

The most famous example of natural selection, during the Industrial Revolution in England, the lichens on trees died and the bark was stained black with soot. Peppered moths that were light grey and speckled lost their camouflage and black peppered moths were able to hide better, so dark moths became more prevalent whereas grey moths were formerly more prevalent.

87. Antibiotic Resistance


Antibiotic resistance
Credit: Wykis

The widespread use of antibiotics has put selective pressure on bacteria to evolve resistances to drugs, which they rapidly achieve.

88. Pesticide Resistance

Pest resistance
Credit: Delldot

Fruit flies, houseflies, rats, mosquitoes, and Colorado potato beetles are among some of the species observed to evolve a resistance to a variety of pesticides.

89. Nylon-Eating Bacteria

variants nylon 6 and nylon 6,6
Credit: Michael Ströck

In 1975, Japanese scientists discovered bacteria eating the byproducts of nylon 6 manufacture in the wild despite the fact that those substances are thought to not have existed before nylon production in 1935.

90. E. coli Long-Term Evolution Experiment

Lenski’s long-term lines of E. coli
Credit: Brian Baer and Neerja Hajela

For over two decades Richard Lenski has tracked the changes in generations of 12 initially identical populations of asexual Escherichia coli, freezing every 500th generation to track evolutionary changes. The project reached 50,000 generation in 2010 and observed numerous adaptations, most strikingly one strain evolving to consume citric acid–something the species was previously thought incapable of (Experiment website here).

91. Speciation of Fruit Flies

allopatric speciation in the fruit fly
Credit: Diane Dodd

William Rice and G.W. Salt were able to breed a population of fruit flies into two species by selecting them for their food preferences in just 35 generations.

92. Ring Species

Ring species seagull

Seagulls around the North Pole, salamanders around California’s Central Valley, and Warblers around the Himalayas are species that can breed with their neighbors all the way around the circle, but cannot breed with species opposite them in the circle, meaning neighbors are the same species, but those at opposite ends of the circle are different species.

93. Cancer

Brest cancer

One of the reasons cancer is so difficult to treat is because the disease evolves through natural selection to grow more resistant to treatments.




Sexual Selection

Natural selection doesn’t just apply to climate, food, and predators. Members of a species that sexually reproduce must compete with one another for mates.

94. John Endler’s Guppies

Poecilia reticulata
Credit: Silvana Gericke

Endler documented the colors of guppies and the competing forces of predator and sexual selections. Where there were fewer predators, the guppies got more colorful to attract mates.

95. The Peacocks Tail

Indian Peacock Plumage
Credit: Vidhya Narayanan

Peafowls have huge ungainly tail feathers that, while beautiful, seem like more of an encumbrance when dealing with predators; however, peacocks display this plumage to peahens as part of courtship, suggesting the peahen discerns something about the health of the male’s genes in the display.

96. Babirusa Tusks

Babyrousa babyrussa Crane
Credit: Didier Descouens

These canines drive through the skin and curl back towards the forehead, providing a defense for intra-species fighting while the bottom canine-tusks provide an offense.

97. Bowerbird

Bowerbird Sorting His Treasures
Credit: dracophylla

Male bowerbirds construct elaborate bowers, decorating them with colorful objects, berries, piling twigs, stones, and other displays of which female bowerbirds will evaluate several before choosing a mate. After mating, the female then builds a nest elsewhere to raise the young alone.

98. Irish Elk Antlers

Irish Elk
Credit: Franco Atirador

Stephen J. Gould argued that these enormous antlers, which required great mineral resources from plants to support and prevented the elk from navigating through forests, were largely responsible for their extinction. The positioning of the antlers were poor for combat between males, but were great for intimidating rivals and impressing females.

99. Bird-of-Paradise

Bird of Paradise

These birds have evolved a wide variety of plumage displays for the sole purpose of attracting a mate.

100. Duck Penis

Duck genitalia and mechanical barriers
Credit: Patricia L. R. Brennan1,2,*, Christopher J. Clark1,2 and Richard O. Prum

Ducks copulate through rape. As a result, females have evolved mazelike vaginas, complete with dead-ends to prevent insemination. Male ducks have evolved one of the longest penises in relation to body-size of any vertebrate as well has having a penis that takes on a corkscrew shape to better navigate the female’s vagina.

101. Waist-to-Hip Ratio in Human Females

Waist-to-Hip Ratio
Credit: Mikael Häggström

Waist-hip ratio is a significant measure of female attractiveness in humans, which makes sense as the waist is an indicator of fertility while the hips are an indicator of being able to give birth to human infants with their extremely large heads.




And the List Goes On and On…

Aphids go from asexual to sexual in times of stress. Eating Cicadas can trigger a shellfish allergic reaction. Antifreeze proteins and lots and lots of other examples of convergent evolution. The Phylliidae Convention in Japan. Dr. J. Craig Venter engineering the first self-replicating semi-synthetic bacterial cell. Artificial cell membranes. Yeast evolving into multicelluar yeast in two months in a lab. The Triune brain. Radiotrophic fungi. Urban wildlife. Chromosome 2 in humans. Cytochrome c. Examples of mutations that occur in humans when you change just one amino acid. The extensive list of fossil sites from around the Earth. Boa constrictors have hip bones. Domestic Pigs. Domesticated Cows. Alligators and frogs taste like fishy chicken. Male nipples. Tibetan high-altitude genes and the Milano mutation. The science of memetics. Chalk mountains are made from piles of forminifera shells. The convoluted contortions of flat-fish growth. Cannibals in Papua New Guinea developed resistance to prion protein disease. Tibetans evolved genes for higher red blood oxygen carrying capacity after diverging from the Han Chinese 3,000 years ago. Smallpox and HIV resitance. The Black Death and the CCR5-Delta32 mutation. Beta-thalassemia. Asian alcohol flush syndrome. The Palmaris longus muscle. Blue Eyed people. The Vomeronasal organ. The Plantaris muscle. Darwin’s tubercle. Scientists regressed a bacteria and got it to retrace it’s evolution to its current state.

And there’s more and more being discovered all the time. Without the theory of evolution, this is just a list of trivia. Through evolution, all of these facts fit together into one incredibly beautiful painting of how we came to be here today.

Further Reading

• Talk Origins has a much more erudite list 29+ Evidences for Macroevolution.
• Dr. George Johnson’s Backgrounders has a step by step walkthrough of the evidence in plain English.
• Wikipedia has an extensive page outlining the evidence for common descent.

An important rule of evolution is that species lose adaptations they aren’t using. Cave fish have eyes that do not work because they live in an environment without light. Crocodile icefish blood has lost its hemogloblin because they live in oxygen-rich water where they don’t need the protein to transport oxygen throughout their bodies. Kiwis, chickens, and ostriches have wings but can’t fly. Humans lack the gene to make Vitamin C, forcing us to get our ascorbic acid from dietary sources.

This happens because when a trait isn’t in use, natural selection does not discriminate against mutations that break the trait. For example, when an individual impala is born with a mutation that gives it bad eyes, it gets eaten by a lion, but when a fish in the total darkness of a cave gets bad eyes, they are just as likely to survive as the fish with working vision; in fact, they have a slight advantage for not having to put resources into building and maintaining eyes that provide no advantage.

Crocodile icefish larvae (note the clear blood)
Credit: Unknown Wikipedia User

A question that comes up regularly in popular science media is, Are humans evolving? And the answer depends on what we mean by evolving. If we are talking about the popular public use of the term, which is synonymous with a species getting better (taller, smarter, faster, etc), then the answer is: only in those parts of the world where natural selection is still at work. In Africa, for instance, where famine, disease, and, in some cases, lions are at work there is also natural selection in effect. The inhabitants of famine-stricken areas are being selected for resistance to starvation. Sickle-cell Anemia came out of Africa as an adaptative resistance to Malarial infection by mosquitos; people with the sickle-cell gene survived longer than those without it despite the trait also having a deleterious effect on the carrier.

If we are talking about the scientific definition of evolving, meaning gradual genetic change in a species population over time, then that is occurring in all humans, selected or not; but in First World societies, the change that is occurring is not of the improvement kind, but more of the cavefish kind. Eyeglasses and eye surgery allow people like me to survive. Insulin shots allow type-I diabetes patients and obese people to survive. Immunizations eliminate natural selection for natural immune system resistance to bugs. C-sections have eliminated the need to give birth vaginally. Fertility clinics allow people to reproduce who could not in the past. AIDS drugs allow anyone who is infected to survive rather than select for a natural resistance. Wheelchairs, hearing aids, orthopedic shoes, braces, and a wealth of other medical innovations and modern conveniences have drastically reduced any need for athletic prowess or even most physical abilities in order to survive in modern society.

These are wonderful things. Without them, Vicky and I would not be able to have additional children and our son Sagan might likely have died due to our incompatible blood types (I’m O+, she’s A-), but thanks to a shot of Rh immune-globulin and our pediatrician coaching us, our newborn son overcame his jaundice in his first week of life. Science makes it possible to support 7 billion people on our planet, and keeps most of them in good health and comfort. I am perpetually grateful to scientific progress.

New Zealand Kiwi, Flightless Bird
Credit: The.Rohit

The complication this creates for us is that every lost survival trait in every human being is a survival trait their children will likely not have. When a couple undergoes fertility treatment, then their children will inherit the need to have fertility treatment. As the medical and engineering sciences discover ever new means for us to survive comfortably despite our flaws, they also perpetuate the inventions that keep so many of us alive.

In other words, as our genes fail us, our memes take over.

H. G. Wells wrote that “Civilization is in a race between education and catastrophe.” He was right in deeper dimensions than he realized. Consider what would happen if we were somehow magically stripped of all our technology so that tomorrow morning the human race were to wake up to a world without modern medicine, agricultural science, textiles, plastics, electricity, and all the other scientific conveniences we take for granted each day. How many of our planet’s 7 billion people would still be alive after a week? We would quickly be reduced to the tribal population levels of just a few brief centuries ago as only the fittest and healthiest survived.

Our ideas are keeping us alive. That means we must work for a society that keeps our ideas alive. Libraries, public schools, laboratories, and institutions of higher learning aren’t just conveniences, they are crucial to our survival, and the more we depend on them the more we will need to depend on them and that’s a good thing.