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.

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.

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.

Space

So Long Space Shuttle
Credit: Trey Ratcliff

NASA finalized the retirement of the Space Shuttle program with the announcement of their final resting places, with Washington DC, Los Angeles and Orlando getting real shuttles for their museums and New York getting the wooden training vessel (Nyah! Nyah! Nyah!). NASA also unveiled the Space Launch System (SLS) next generation of manned space explorations vehicles that will (hopefully) be taking us to Mars. Along the same goal, the Mars500 completed its 17 month simulated mission, complete with isolation and delayed communications as a partial proof of concept that humans can survive the trip to the red planet.

Gravity Probe B (GP-B) confirmed the geodetic effect and frame-dragging aspects of Einstein’s theory of gravity, that the Earth and other large masses swirl spacetime as they spin like a ball rotating in honey.

The Hubble successor, the James Webb Telescope barely kept its funding after it was projected to run billions over budget. We still might see further into the Universe.

China’s space race continued on its modest schedule, allowing geeks like me to vicariously enjoy the pride of its citizens as they make greater and greater strides into space.

Physics

Still No Higgs Boson Event
Credit: CERN

The world didn’t end and there’s no Higgs Boson yet, but replication of the neutrinos moving faster than light finding provided opportunity for geeky jokes like, “A neutrino and a photon walk into a bar. For 60 nanoseconds, the neutrino complains about how dark it is.” and made physicists sweat.

The LHC also found a difference in the decay rate of D-mesons that could explain why there’s so much matter in the Universe left over from the Big Bang.

By replacing one of the electrons in a helium atom with a much heavier muon elementary particle, scientists were able to get the atom to act like a hydrogen atom; within minutes the geeks at Slashdot had figured out how much less the modified atom would raise your voice.

Computer Science

IBM Watson

IBM’s Watson Computer trounced its human competitors at Jeopardy. It must be one of the greatest joys for anyone to build something greater than yourself.

MIT replicated a single synapse on a chip using 400 transistors to digitally simulate the analogue communication between neurons in the brain, with the next step to be stringing these chips together to replicate parts of the brain.

Berkeley scientists used a neat trick of having people watch videos, recording their brain waves, and then using the video to approximate what others were seeing in their mind’s eye from reading their brain waves.

Earth Science

Berkeley Earth Surface Temperature

The year marking the 150th Birthday of Climate Change Theory brought ever more support to the theory that the world is getting warmer due to human-made carbon emissions. Shortly after the sixth independent review of the “Climategate” non-story found no misconduct in August, a reanalysis of the same data (now all publicly available) partially funded by the oil industry and conducted by an outspoken climate skeptic, Dr. Richard Muller, confirmed Global Warming was happening and turned Muller into a believer.

Archaeology

The sharp-eyed, metre-long Anomalocaris.
Credit: Katrina Kenny & University of Adelade

The greatest known predator from 500 million years ago, anomalocaris, was discovered to have fantastic compound eyes.

The discovery of other raptor-like dinosaurs with feathers cast Archaeopteryx’s status as the missing link between birds and dinosaurs into doubt because there are too many candidates for the missing link.

Australopithecus sediba joined the human family tree.

A high schooler found an improved arrangement for solar cells based on the Fibonacci arrangement found in plant leaves.

Biology

African Gray Parrot
Credit: Retrolusionary

Pet parrots escaped to the wild were found to be teaching other birds to talk.

Two studies confirmed having more friend increased gray matter in parts of the brain responsible for social networking.

Roger Ebert put the smack down on 3-D movies, explaining why the muscles in our eyes and the perception of our brains cannot grok with a flat screen making 3-D demands on our perceptions.

Politics

Fool Me Twice: Fighting the Assault on Science in America
Credit: Shawn Lawrence Otto

The organization Science Debate stayed strong this year and Shawn Lawrence Otto stirred up some buzz with his new book Fool Me Twice: Fighting the Assault on Science in America. Looking forward to what the organization accomplishes this upcoming election cycle.

In a year of austerity measures, science fought to maintain funding… okay, not really, more like lay down and let politicians cut whatever they wanted, but nothing was accomplished in the gridlocked house and senate.

The American Government did manage to pass the America Invents Act, intended to stop patent-trolling, but may turn out to be a gift to large corporations as it move the country to a “first-to-file” rather than first to invent standard.

Alternative medicine killed Steve Jobs.

Republican presidential candidates fell over themselves attacking Climate Change and Evolution (and one even attacking Immunizations), and a Fox News host wondered if volcanoes on the Moon disproved Global Warming, leading to an awkward moment with Bill Nye.

On the Left, Belgian protesters destroyed a field of GM potato plants being researched for blight resistance.

Wonder

It was a great year for time-lapse videos as first someone took the photographs from the Cassini mission and merged them together into a beautiful fly-by of Saturn and its moons, a whole night at the ALMA Array Operations Site (AOS) made for Earth-bound wonder, the view from the ISS orbiting the Earth was enchanting, and, best of all, 14 years of Hubble photos showing gases jetting and expanding light years away, demonstrating just how dynamic are our night skies (see also the supernova in the Pinwheel Galaxy 21 million light years away in August).

The Sagan Series took the words of the most amazing exponent of science and provided music and imagery to do them poetic justice.

The awesomely geeky and science-riddle video game Portal 2 provided much puzzling amusement.

The Royal Society put its entire history of journals online open access.

Personal Life

Stephen Hawking and Sagan
Credit: Hawking Source Image by Rob Bodman, Sagan Photo by Vicky Somma

The biggest news in our lives is the welcoming of Sagan Charles Somma to our family fold. It’s been a big change in our lifestyles, but an ever-rewarding experience as we get to enjoy a feeling of love unlike anything we‘ve experienced before.

Vicky’s photo of a Rhododendron looming menacingly over an American Chestnut sprout won the American Chestnut Foundation’s photo contest.

I made Slashdot in November, pushing this blog to a record 7,000 hits in one day and stressing me out for a week as POGO and other organizations scrutinized my data and found some glaring and embarrassing errors. Thank the Cosmos for peer-reviews.

Borders going out of business provided me an opportunity to stock up on coffee table books, the one thing for which the digital world has failed to provide an adequate replacement.

Memexplex broke 1,000 memes (all me). The tool is fantastic for what I need it for, so I’m not worried that I haven’t found anyone else for whom it’s useful.

Although I haven’t updated my resume, I quit my job with the Coast Guard and have started working in the development of applications for Food Safety labs across the nation, making my life as a Computer Scientist now a Computer Scientist in the service of science. Woo Hoo!

Life is great, so my New Year’s resolutions are pretty light. With science as my candle in the dark, 2012 can only bring more illumination.

In 1968, Dr. Paul Ehrlich predicted a population explosion on planet Earth would result in mass starvation in his book The Population Bomb. While millions die each year of starvation, Dr. Ehrlich’s dire predictions did not come true. Many critics of environmentalism often cite Ehrlich’s failed predictions to attack anyone who raises concerns about environmental sustainability, but most of them gloss over the reason why Ehrlich was wrong which was his failure to account for human innovation. Ehrlich completely failed to factor in the work of Norman Borlaug and the Green Revolution, which saved over a billion people from starvation with irrigation infrastructure, hybridized seeds, fertilizers, and pesticides.

Last month, the Earth’s population hit seven billion, raising questions once more about sustainability as millions are threatened with starvation in Africa, conflicts arise over water, and major fish stocks collapse. We are pushing the limits of what the Green Revolution’s science has granted us as far as a sustainable global population. We need a second scientific revolution to increase the global food supply, and our best hope for that revolution is in Genetically Modified (GM) Foods.

The Promise of GM Foods

The benefits of Genetically Modified Foods are already being born out all over the world. Farmers in China and India are experiencing better health through massively reduced use of pesticides thanks to GM Crops and are experiencing higher crop yields (see here, here, and here). Flood tolerant rice being developed at the Ronald Laboratory of UC Davice will benefit poor farmers who are increasingly threatened by climate change. While Blood Rice will save lives by producing a key component of human blood. This year “Golden Rice,” engineered to be packed with vitamins, will be a huge weapon in the fight against malnutrition worldwide. Genetically modified Papaya single-handedly saved Hawaii’s Papaya farms from extinction, by inoculating them against the ring spot virus.

Papaya Yields

“Organic” food is a nice ideal, but organic farming requires more water and farmland to produce the same amount of food as modern farming. Without GM crops we will need to consume even more forests for farming, driving millions of birds and insects into extinction, and increase pesticide use. With crops that are more nutritious, resistant to pests, and can survive with less water, GM crops make organic farming a realistic possibility.

The company Aquabounty has produced a salmon that includes a genetic modification for faster growth. This innovation has a huge potential to increase the output of farm-raised salmon, which would dramatically reduce the strain on natural fish stocks. Despite the incredible benefit, Aquabounty has spent 15 years working to get their salmon approved for commercial production because of public concerns over Genetically Modified Organisms (GMOs).

The Safety of GM Foods

Google “GMO Foods” and you’ll find the majority of links are about how to avoid GM Foods and health concerns about them. There was even a TED Talk by Robyn O’Brien, where she blames increased cancer rates and other health problems on the rise of GM Foods in our diets without citing any research to build a causal link. Other anti-GM Food organizations use the term “Frankenfood” to evoke mental images of monsters and mad scientists that also elicit strong emotional reactions in readers rather than provide them with facts that support their arguments about the supposed ill health effects of GMOs.

The European Union has released a preliminary draft of a report reviewing hundreds of journal articles and decades of research on GM crops and have concluded they are safe (with some important conditionals). Additionally, humans have been consuming Genetically Engineered foods for thousands of years. Corn, cabbage, wheat, cows, chickens, bananas and numerous other foods modern agriculture brings to our plates cannot survive in the natural world. They have been created by humans through selective breeding. The genes being put into GM Foods are genes that exist in nature. Scientists are not putting anything new into our food supply .

Ultimately the potential health detriments of GMO foods are insignificant to the deleterious health effects of modern diets. I know people who will go to great lengths to avoid GMO Foods, buying anything at the grocery store that has the “Organic” label on it, but a bag of organic potato chips is demonstrably going to do far more damage to your health than has been demonstrated with any GMO food on the market today.

Into the Future

Chet Raymo succinctly summarizes the history and promise of GM Foods:

Ten thousand years ago, humans learned how to farm. It was an epochal invention that made possible settled life, cities, craft specialization, writing, organized religion, architecture, mathematics. science. Now humanity stands on the brink of a second agricultural revolution potentially as great as the one that occurred when our ancestors gave up hunter-gatherer way of life and settled down as farmers. Scientists and engineers are poised to genetically modify organisms to increase the yield, nutrition, freshness, and pest resistance of food plants and animals, and perhaps even to diminish the use of artificial fertilizers (and fossil fuels) by supplementing biotic nitrogen-fixation systems. Other possible benefits of genetically modified (GM) organisms include improved use of marginalized land—saving wild areas from the plow—and abundant production of vaccines and pharmaceuticals. possibly eliminating diseases such as cholera, hepatitis B, and malaria. The promise is great. But as always with the products of human artifice, not without attendant dangers.

In writing this post, I was unable to find any articles or posts through search engines that were about the potential and proven benefits of GM Foods. The more than a dozen peer-reviewed examples I’ve cited above I had to find by querying the online science community. That’s not right. It’s not right for unscientific viewpoints to dominate this debate and destroy the potential for this science to create a healthier environment and produce more food and more nutritious food with fewer natural resources.

It’s not right for anti-GM protestors to commit acts of violence against the scientists performing this research by destroying public property in Belgium and Australia. It’s not right for hundreds of thousands of people to starve to death in Somalia because the government rejected free grain from America that was genetically modified, citing the same “Frankenfoods” rhetoric propagated by these anti-science organizations.

Drought tolerant maize lines at Kiboko, Kenya
Credit: CIMMYT

As Chet Raymo said, there are dangers in GM food, just as there are dangers in pesticides and corporate farming, but protestors should be pushing for vigilance in studies on GMOs, not seeking a complete ban on them altogether. Anti GMer’s are directly responsible for the deaths by starvation in Somalia and other countries that refuse food aid over GM crop concerns. As we saw earlier in this article, GM Foods not only hold incredible potential to extend the limits of what we can support on this spaceship Earth, but have already proven their potential to save crop lines and improve yields. The only way we’re going to save our environment and feed the projected nine-billion Earthlings that will live here by 2050 is the same way we came to a planet capable of feeding seven billion people, through scientific innovation, not a regression to more primitive times when famine controlled our population growth.

Notes

One of the great joys of being human is our incredible powers of pattern recognition. Our brain’s ability to manifest meaningful associations out of the complex morass of sensory stimuli perpetually assaulting us is a cognitive expertise into which computers are only just starting to venture successfully. It’s what allows us to recognize faces, raed wrdos wtih smrelcabd ltretes, identify with our fellow humans, and compartmentalize the sounds, tastes, and sights around us.

The number 11 has always been my favorite whole number. Ever since I was a kid, I appreciated the way the first nine multiples of 11 are numbers that mirror the tens and ones places (in a base-10 numbers system): {11, 22, 33, 44 … 77, 88, 99}.

You can figure out the result of eleven times any two-digit number by adding the tens and ones place of the two-digit number and placing it between the two digits. For example, eleven times my second favorite whole number:

You can also do something similar when multiplying eleven against a three-digit number.

Eleven is fun.

This year, the Gregorian Calendar has been filled with 11′s in its dates: 1/1/11, 1/11/11, 11/1/11, 11/11/11. Additionally, If you take the last two digits of the year you were born and add the age you will/have turned on your birthday this year, the result will be 111. For me, this is 73 + 38 = 111.

I previously blogged about eleven focusing on the trivia associated with the number, but I’ve come to understand that eleven is a wonderful number for all the patterns we can find in it, and nowhere do these patters become more clear than in Pascal’s Triangle:

Creating a Pascal’s Triangle
Credit: Hersfold

Each row of Pascal’s Triangle sums to the set of exponents of two {1, 2, 4, 8, 16, 32, 64, 128, 256, 512, 1024…}, and that’s interesting.

What’s more interesting? The digits of each row represent an exponent of eleven {11, 121, 1331, 14641, 161051, 1771561…}. It takes just a little bit of addition to see how this works for the rows with multiple-digit numbers. You have to think of each number as occupying a place value, like ones, tens, hundreds, thousands, etc. Then you carry the additional digits up to their appropriate place. For example, row six in Pascal’s Triangle is:

So Pascal’s Triangle is a tower of powers of eleven, and the patterns within it continue. We can see the first set of diagonals going down the outsides of the triangle are all ones, and the second set of diagonals just inside this are all the natural numbers {1, 2, 3, 4, 5, 6, 7, 8, 9, 10…}. The third set of diagonals is Triangular Numbers, the number of building blocks needed to make triangles of increasing size:

Triangles One Through Six

The fourth set of diagonals are Tetrahedral Numbers, the number of building blocks needed to make tetrahedrons of increasing size.

Number Sets: Ones, Natural, Trangular, Tetrahedral, Pentatope

The fifth set of diagonals are Pentatope Numbers, which I don’t understand, but they sound like the number of building blocks needed to make 4-dimensional tetrahedron.

5-Cell (4D Tetrahedron)
Credit: Jason Hise

And the patterns continue! If we align all the numbers in Pascal’s Triangle up on one side, the diagonals add up to the Fibbonacci Set {1, 1, 2, 3, 5, 8 … 55, 89, etc, etc}, which relates back to my favorite irrational number Phi:

Fibbonacci Set in Pascal’s Triangle
(Diagonals colored, Sums Shaded Gray)

There is something fractaline about the conceptual patterns we are seeing in this numeric construction. There are triangles within triangles in the number sets. In fact, highlighting all the odd numbers within Pascal’s Triangle and zooming out far enough, we find an actual geometric fractal, a Sierpinski Triangle:

Animated Construction of a Sierpinski Triangle
Credit: Dean Moore

Powers of 10 Day celebrates the concept of exponential growth, a meditation on the size of our universe as we zoom in or out from our position within it. Powers of 11 Day seems like a good day to look at the patterns that emerge when we zoom out to look down on the big picture. There are patterns within patterns when we line up the powers of eleven in this way, beautiful symmetry, dimensions beyond our three, and geometry that echoes across the function. Our brains evolved to find patterns everywhere in the world, and this mathematical object is perfect for enjoying the immense potential of this natural cognitive proclivity within us.

Further Reading

The images of Pascals Triangle that I composed myself for this post were put together in Microsoft Excel, and you can download the spreadsheet if you’d like to play with the numbers yourself.

Special thanks to Math Forum for the best, most simplest page on the web exploring Pascal’s Triangle and the powers of 11.

In hacker slang, “Elite” is transformed into “leet” which is transformed into “1337″ which is transformed to “1331″ which is transformed into “leel” which is the highest form of elite. 1331 is 11 to the third power.

I admit it. I knew better when I posted the story about the kraken lair to my Facebook for my less scientifically literate friends to awe and wonder at. I could tell from the scant evidence provided in the press release that there really wasn’t anything there but a collection of bones from 45-foot-long ichthyosaurs mysteriously piled together at a site in Nevada. To infer the bones were gathered together by a gigantic ancient cephalopod whose soft tissues left no trace in the fossil record was an admirably imaginative idea, but I knew this extraordinary claim didn’t pass the Sagan Standard’s “extraordinary evidence” requirement. As Samuel Clemens best expressed it, “There is something fascinating about science. One gets such wholesale returns of conjecture out of such trifling investment of fact.”

And still I posted it to Facebook, where it got eight Likes, three comments, and one share. That’s eight more Likes than my link to Discovery’s Faces of Our Ancestors gallery, featuring facial reconstructions for 11 ancestors of Homo sapiens and for which there is plenty of direct fossilized evidence to support their stories.

Stories. We only have a few millennias’ worth of stories from the written and oral history of the human race, but the archeological record is brimming with billions of years’ worth of them. Like detectives at the scene of a crime, archeologists have reconstructed events out of the shared story of our origins to tell engaging tales of our ancestors trials and tribulations.

There are tragedies, like the 3-year-old Taung child, whose skull bares the scars of an eagle attack. The Australopithecus africanus child was carried away by a bird of prey 2.8 million years ago. We sense the tragic nature of the story when we consider the horror his parents must have experienced, and at the same time there is the fantastic element of our ancient ancestors having to guard their infants against birds of prey.

Easter Island, Moai Rano raraku
Credit: Aurbina

I’ve listened to New Age believers explain the giant statues of Easter Island as being erected with the help of aliens, who took the island’s inhabitants away with them into the Milky Way, but there is an important lesson in what we know really happened to this treeless island in the Southeastern Pacific ocean. Jared Diamond reconstructs the history Easter Island with the help of painstaking research by paleontologists and archaeologists, telling the tale of a materialist war, where competing inhabitants chopped down all the island’s trees for transportation and scaffolding so they could erect monolithic statues of increasing size to demonstrate their wealth and prestige. After the trees vanished, so did the large game, and the trash sites on the island show the inhabitants resorted to eating rats and eventually human corpses to survive. The Easter Islanders didn’t have magical powers for levitating boulders, they were an ancient mirror of our modern materialism. The archaeology of Easter Island tells the story of a civilization that fell prey to conspicuous consumption and provides a cautionary tale for a modern society that would sacrifice environmental sustainability for short-term greed.

Then there’s the 3.6 million-year-old Laetoli footprints of Austrolopithecus preserved in volcanic ash, large and small, male and female, close together as if they were huddling–perhaps the male had his arm around his mate, and the female’s footprints lopsided as if she were carrying an infant. Imagine what it was like for them, walking fearfully across an ash-covered landscape, a distant bellowing volcano preparing to rain even more ash on them. This story of fear and wonder is reconstructed in this famous diorama:

Australopithecus
Credit: Me

There are also the mysteries. Homo erectus, who spread halfway across the world before mysteriously vanishing. Imagining her environment, we know there were a greater number of large fauna back then, as humans would come along much later to drive the big animals and predators into extinction wherever they migrated across the Earth. She had stone tools, hand axes she used to chop up game, but was primitive enough and intelligent enough that I read one naturalist refer to her as the “velociraptor of our human ancestors,” which is why I love this statue of her at the Smithsonian Hall of Human Origins lugging a rotting ibex carcass across the Serengeti on her back:

Homo erectus
Credit: Me

She was a total badass… and then she was extinct.

Where did she go?

As many stories as humans have written in our few millennia of civilization, imagine the number of stories still waiting to be discovered in 3.5 billion years’ worth of geological strata. Stories of tragedy, wonder, mystery, and profundity are all around us, written into the natural world, just waiting for us to read them.

This post has been submitted for the NESCent Blog Contest for Evolution-Themed posts.

Credit: watchingfrogsboil

For 10 years of my life, I was one of those $300 toilet seats or $600 hammers you hear about in the Pentagon’s spending. I was the waste, fraud, and abuse that everyone complains about in government, but up until a year ago, I had no idea just how much my job was costing American taxpayers.

A study by the Project on Government Oversight (POGO) found the Government pays IT Contractors nearly twice as much as its own IT Workers.

This begs the question: What service is the Federal Contractor providing to justify charging double what it would cost the Federal Government to employ these same personnel directly?

They don’t provide us the facilities to do our jobs. No. The Federal government provides our computers, office space, and pays for all the utilities to keep it running. The government buys all the software, hardware, and pays for any training we need to bring our skills up to date to effectively do our jobs. This appears to be a fairly standard practice in Federal Contracting as a GAO review found “that significant numbers of defense contractor employees work alongside DOD employees in the 21 DOD offices GAO reviewed. At 15 offices, contractor employees outnumbered DOD employees and comprised up to 88 percent of the workforce.” In my department contractors outnumbered government employees by about four to one.

The contractor also doesn’t have to manage us, because the government employees serve as supervisors. In fact, it’s policy in our department that government employees supervise the contractors directly. Our Project Manager was the most expensive billet on the contract but I only met with him once a year for my annual evaluation, where I had to explain what I had been working on for the past year and why I deserved a raise. He never had the foggiest idea what anyone in the department was working on and relied on complaints from Government employees to know when he needed to chew someone out.

The only thing the Contractor is responsible for is ensuring that our timesheets are filled in correctly and on time; otherwise, they might experience a delay in invoicing Uncle Sam. They handle my 401k, medical benefits, and direct deposit my paycheck twice a month. Guess what America? You are paying twice what it costs the government to employ personel directly for the added value of having a contractor manage the human resource functions for 73 employees. The cost for the Federal government to handle this itself would be a fraction of the yearly salary of a single GIS employee, someone who is already serving as the HR rep for all the other government employees for between $50k and $80k a year.

We also have to consider the quality of the service provided by the Federal Contractor in light of its fixed-priced profit motives:

What the POGO report doesn’t mention is that the IT Workers employed by federal contractors are making as much or less than Federal IT workers. When you’re only overhead is your employees’ salaries, you have a very strong incentive to keep those salaries artificially low. Whenever a government position would open up in our department, contractor employees would jump at the opportunity for stability and better benefits.

Why does the Federal Government operate this way, outsourcing millions of jobs to contractors who could be more cheaply employed through directly? The answer, unsurprisingly, is politics. Politicians hand out billions of dollars to Federal Contractors who, in turn, use the revenues to lobby the politicians. “The top 20 service contractors have spent nearly $300 million since 2000 on lobbying and have donated $23 million to political campaigns,” according to the New York Times. It’s a self-perpetuating system.

But there’s a less visible political reason for the outsourcing. Every time a worker leaves the Federal Payroll to become a private-sector Federal Contractor, the President and Congress can claim to be reducing the size of government. They publicize the fact that “1990 total government employment… was 5.23 million,” which fell to “2.84 million in 2009.”

But the number of people whose job depends on funding from the Federal Government: University Grants, Defense Contractors, Construction Workers, Public Schoolteachers, Regulators, etc. etc. has skyrocketed. Redefining “Federal Worker” to include all of these jobs increases the number of people employed with tax dollars to between 14.6 million and 17 million, translating to between 10% and 12% of America’s total employed population. The true number is incredibly hard to pin down because there are no hard data publicly available on how many American jobs depend on funding from the Federal Government. This obfuscation of employment data is why many critics refer to federal contractors as the Government’s “Shadow Workforce.”

I loved my job developing applications for the Coast Guard, but it angered me that the contractor was raking in taxpayer money by delivering sub-quality service to the government while overworking and underpaying employees. When I confronted management about what I considered fraud and demanded solutions, the answer was we will not pay for training, we will not pay for qualified personnel, and we will not bring your salary up to the national average. They even welcomed my resignation despite the fact that it meant the project I had been working on for two years would completely collapse shortly after my absence. Any project failures are the fault of government employees managing them, not the contractor who merely fills the billets.

Between socialism and capitalism, Government Contracting takes the worst of both worlds. It’s capitalism’s greed mashed up with socialism’s inefficiency. With America struggling to define austerity measures that will reduce the federal deficit, eliminating Federal Contractors and employing personnel directly seems like an obvious place to start.

Additional Food for Thought:

The top 100 Defense Contractors cost taxpayers $306,521,269,483.

There was $442 billion in contractor funds available to small businesses in 2009. What gets hidden in this number is the fact that many small business team up with a large corporation to bid on these contracts.

For a particularly egregious example of Federal Contractor fraud, waste, and abuse, I refer you to the Coast Guard’s $24 billion effort to modernize its fleet, which sounds like it actually ruined more ships and equipment than it produced, but the contract was written so that the Federal Contractors could not be held accountable.

This American Life (TAL) is one of the most successful shows on NPR, it started in 1995, has won numerous awards, and one of my conservative friends even described the show as “single-handedly justifying the existence of NPR.” I’ve heard shows from time to time over the years, but a few months ago I downloaded a torrent of every show in the cannon and have been completely hooked ever since. So when I heard Ira Glass’ was coming to Chrysler Hall in Norfolk I jumped at the chance to see him talk about the show, behind the scenes, and how the show is so effective at communicating and connecting with the audience.

Ira Glass started the show with the lights off, simulating the experience of radio as he spoke to the audience. When the lights came up, he joked, “You don’t look like what I expected either.” Carrying a touchpad filled with audio samples, Ira deftly played music, narrated, and mixed interview clips into his talk, oftentimes improvised.

He played a clip from the opening of a CNN special covering an aircraft carrier taking part in the war on terror. With deadly serious narration and a soundtrack Ira accurately described as “straight out of the opening credits of Battlestar Gallactica,” CNN was working overtime to make the story dramatic, working so hard as to be downright silly when you thought about it. News makes the world “scary, simple and small” Ira noted, and TAL wanted to take a different angle of life on the carrier, which he described as a “giant floating nuclear-powered dormitory.” So they started the story covering the kind of mundane work the majority of soldier on the carrier perform, specifically with a woman tasked with keeping the vending machines stocked and the day-to-day operations of that job.

Ira Glass emphasized the importance of storytelling in keeping the audience’s attention. Something happens, and then something, and then something, and then a universal principle is revealed. I recently heard the same advice from Jane Goodall that the best way to get people to see your side of things was to tell stories.

With this technique of storytelling TAL has made me see from the perspective of and sympathize with idealistic Tea Party members, stressed-out gang members, alleged terrorists, and wide wide world of diverse backgrounds and cultures. One show convinced me of the ideological diversity in the Republican Party by taking a varied perspective on the party at that time. At one point in the talk, Ira Glass described Iraq as Ireland with the Shias being the Catholics and the Sunnis the Protestants, a perfect analogy that explained the cultural conflict there better than any mainstream news story I’ve ever heard on the situation.

With the way the news makes the world so simplistic, caricatured, and tiny, is it any wonder the public getting its information from these sources seems to grow increasingly cynical about the state of things? News sources like NPR and the Economist try to convey the complexity, but their droll, elitist tone really turns people off to them. Ira Glass has spent years trying to convince someone in the media to do a news show in the format of TAL, and the show itself has even tried an episode focused on the events of the previous week.

The episode This Week, covering current events, also happened to be the week Osama Bin Laden was assassinated. So they sent a reporter to Cairo to interview people’s reactions there, but the lives of Egyptians were much too busied with the task of rebuilding their country after the recent revolutions. So the story from Cairo was about the Muslim fundamentalists and the liberals getting together to try and find some way to coexist in a functional Democracy. It’s easy to see how such a weekly portrayal of current events could not just be popular, but could calm people down by giving them a peek into the complex worlds everyone else out there is dealing with as well.

Additional Notes

During the question and answer session an audience member asked Ira if there were any other programs that had adopted TAL’s storytelling style, and, to my great pleasure, he mentioned one of my favorite recent discoveries RadioLab, a show about science that uses storytelling to make the factually-fascinating subject matter engaging on a personal level (Ira has a very nice essay about the show).

A funny moment in the talk was when Ira declared “Radio is your most visual media…” which made sense in respect to the way the show must paint a picture in your mind, but then, after a long pause, he said, “That’s not actually true… Turns out having pictures is very very visual.”

Ira invoked Arabian Nights in expressing the importance of storytelling. He described Scheherazade as “very Buffy the Vampire Slayer Season 3″ and how she used storytelling to keep the king from killing her for years, after which he could not kill her because the many stories had made him sensitive to the perspective of others, especially Sheherazade’s father, who had spent night after night wondering if this would be the morning he would find his daughter dead.

Stages of Fetal Development
Credit: NHS Pregnancy Desktop

One of the first things Vicky and I established when we first became romantically involved is that we both wanted to have children. We share a deep love of science and the natural world and wanted to share our sense of wonder with children of our own. At the same time, in our sharing we were hoping to experience the world vicariously through fresh eyes, reliving the thrill of learning and discovery.

When the pregnancy test finally came up positive, we were launched into a whole new realm of learning: reading up on diet, lifestyle, and fetal development. We were also put into an unanticipated tour of various types and standards of prenatal care. This post covers what we learned and what we are continuing to learn about pregnancy and childcare.

Researching Pregnancy

Medical Science has doubled of our lifespans over the last 200 years, but it has also made some horrible mistakes when it comes to childbirth. When we asked Vicky’s grandmother about her birthing experiences, she described the days when doctors would administer women in labor the Twilight Sleep drug, which prevented the woman from remembering the act of giving birth, but would also make her lose all self-control, so that she had to be strapped to the hospital bed and wear a helmet so she could wail and thrash. When we asked Vicky’s mother about breast feeding, she told us about how the doctors discouraged the practice, saying it was unsanitary and had less nutritional value than formula. Pre-1950s psychology took the position that showing affection for children was unhealthy and discouraged kissing or otherwise cuddling babies lest they have serious issues later in life. These were unfortunate ideas that manifested lifetimes worth of problems for children born during the times they were popular, but science is a self-correcting algorithm, so I made a point of doing some heavy reading in hopes of learning the latest, most refined understanding of what’s best for pregnancy, labor, and child-rearing.

Pregnancy and Baby Care Books

Anne Marie Paul’s Origins: How the Nine Months Before Birth Shape the Rest of Our Lives made for a good overview of how life in the womb is affected by the pregnant mother’s environment. It explains, in down to Earth terms, what the mother should eat, what she should avoid, and what lifestyle choices, such as exercise and stress, she should engage and avoid for the health of her developing baby. Humans are a highly-adaptable species, and Paul argues that the fetus is taking in information about the environment into which it will be born so that its brain and body will be customized to best survive in that world.

Meredith Small’s Our Babies, Ourselves: How Biology and Culture Shape the Way We Parent is an important part of the attachment parenting philosophy, which stresses being keenly sensitive to the child’s needs to form a strong emotional bond with them. I appreciated the book’s evolutionary perspective on the subject, advocating co-sleeping and breastfeeding because our ancestors adhered to these practices. The book looks at various cultures and their differing parenting styles to help come to its conclusions. This foundation in anthropology and evolutionary psychology really appealed to me.

Gopnik, Meltzoff, and Kuhl’s The Scientist in the Crib: What Early Learning Tells Us About the Mind was a fascinating peek into an infant’s cognitive development. I loved the premise that babies are like scientists, testing hypotheses and adjusting their worldview according to the results. The book has an explanation of the “Terrible Twos” that impressed me: infants at that time are learning that your perspective is different from their perspective and they are having a hard time adjusting their understanding of the world accordingly. The book lays out its ideas exquisitely, bringing all the ideas together into a summary at the end that highly intellectually satisfying.

Lise Eliot’s What’s Going on in There? : How the Brain and Mind Develop in the First Five Years of Life is an exhaustive overview of every single aspect of the fetus and infant’s development and is also my favorite of all the books I read. The book covers the physiological development all five senses and several other senses that I didn’t even know about. It provides exercises for stimulating these senses so that the child’s brain wires up properly to best take advantage of them. The book can also be a bit scary as it goes over all the things that can go wrong in a child’s development, which set me on edge, but they are important things to be aware of so you can recognize them and get your child the help they need should they manifest.

John Medina’s Brain Rules for Baby: How to Raise a Smart and Happy Child from Zero to Five felt like the Cliff Notes version of Lise Eliot’s book, and that’s a good thing. It’s down to Earth and gets right to what you want to know about turning your child into a supersmart superhuman. I really appreciated some of the worldview adjustments Medina gives, such as to avoid praising your child for being smart, instead, praise them for working hard. Smart is out of our control, but failing a test because you didn’t work hard is something you can overcome.

Depending on your personality, there were a series of “easy reading” books that were less scientific and more about commiseration and practically dealing with parenting and childbirth. For nerds I recommend the Baby Owner’s Manual, found on Think Geek, for its clinically humorous way of covering baby care. For regular guys I suggest the The Expectant Father: Facts, Tips, and Advice for Dads-to-Be, which was pretty in-depth and covered a whole lot of territory focused on the male’s role in things. While men’s men should go with Be Prepared: A Practical Handbook for New Dads, which actually works on a whole lot of levels, is the funniest of the books I picked up, and has great “circuit training” advice for exercising your baby.

Dr. Benjamin Spock’s Dr. Spock’s Baby and Child Care: 8th Edition was the “Manual” that everyone took when they kidnapped the baby in the film “Raising Arizona.” It’s criticized for using inductive reasoning rather than evidence-based medicine, and I found some glaring errors in an early edition of the book, like advising parents to put their baby to sleep face down, which we now know puts them at a higher risk of Sudden Infant Death Syndrom (SIDS); however, later editions of the book correct these errors and overall the book works as a great big encyclopedia of baby care advice. At the same time, while the book is on my shelf, I’m still more likely to hit a search engine to find out why there’s a white fungus growing on my baby’s tongue (It’s called thrush and it’s perfectly normal).

NHS Pregnancy Desktop

Beyond books, I highly recommend parents check out the UK National Health Services’ (NHS) – Pregnancy Desktop application, especially for expectant dads. One problem I had early on during Vicky’s pregnancy was that she was completely on top of what needed to be done at what week in the process, so that I felt like I was just following along under her guidance. The Pregnancy Desktop application sits on your desktop, opening on startup, and serves as a constant reminder of how many weeks and days you have left until your due date, what’s going on with the baby, and what you should be doing to prepare. Some of the information it provides is UK-specific, but there is also a bounty of good information for mothers in any country. Again, highly recommended.

By far, the most beneficial preparation we made was in attending Bradley Method Classes to learn about Husband-Coached Natural Childbirth based on Richard Bradley’s Husband-Coached Childbirth: The Bradley Method of Natural Childbirth, where the husband takes a strong supporting role in the wife’s labor, monitoring contractions, tending to her needs and making sure she’s comfortable, and providing emotional support to help her achieve an unmedicated delivery. In addition to practice exercises to prepare for labor, the classes are also fantastic for the way they educate students on the mechanics and physiological aspects of labor. We learned about various medical interventions the doctor’s might use, pregnancy complications we may experience, and lots of information about what’s going on with the baby and mother’s bodies during labor. One factoid I found very interesting had to do with the health effects of cutting the umbilical cord after delivery, which doctors rush to do, but is probably best to hold off on in order to allow the placenta to pump all of its blood into the baby. The classes are important because the books and software are all just theory (in the non-scientific sense of the word) and you need to get active and increase your kinesthetic intelligence to see yourselves through this.

Pregnancy Lifestyle

Vicky had an extremely easy pregnancy, which we attribute to a healthy diet and active lifestyle. Vicky was great at practicing squatting to strengthen her pelvic floor and hit the gym every day, where she found the fetus became very active while she was on the elliptical, but became less active later in the pregnancy to conserve oxygen while Vicky’s consumption went up. She also gave up caffeine, alcohol, and other environmentals that could harm the developing fetus. As a show of support, I gave up caffeine and alcohol too; unfortunately, I couldn’t convince Vicky that this same logic would apply to scooping cat poop.

Here’s the factoids we incorporated into our pregnancy lifestyle:

Diet: As I covered recently, good nutrition is crucial to cognitive development in the developing brain, which is why in our enlightened civilization we have social services like welfare. But what food choices should the pregnant mother make?

Eats lots and lots of fish, which increases infant cognition. Unfortunately, with so much pollution in the environment, this principle has also become a balancing act between good protein and omega 3s and elevated mercury content that gets concentrated in certain species of fish. Vicky and I referred to tilapia and salmon dinners as “IQ points for baby” meals.

Another thing is to make your plate colorful. Our Bradley Method instructor had Vicky turn in a list of all the foods she ate each week, which was first checked to sufficient protein intake, but then turned to variety. One of Vicky’s homework assignment was to eat a yellow or orange vegetable, similar to Michael Pollan’s advice in his excellent book In Defense of Food.

Lifestyle: Avoid the three characteristics of stress: too frequent, too severe, and too much for you. A great way to counter effect stress during pregnancy is exercise, as it reduces stress hormones that can hurt the baby’s development. Exercise also reduces the amount of time spent in the pushing phase of labor compared to women who do not exercise. There is some concern that exercise robs the baby of oxygen and therefore harms cognitive development; however, there is also evidence that exercise improves intelligence and the fetuses show the same benefits of cardiovascular exercise as the mother experiences.

Things to Avoid: Limit caffeine, which appears to have no effect on the child’s IQ but does cause developmental problems in rats when taken in extreme doses. Definitely avoid smoking, which lowers birth weight, increases the child’s chances of neurological impairment, increases the risk of miscarriage, and increases the risk of SIDS after birth. Also avoid alcohol, which is “thought to be responsible for at least 4,000 cases of mental retardation in the United States each year and perhaps ten times that number of children with mild learning or behavioral problems.” Also avoid the chemical Bisphenol A, which is in certain plastics and causes developmental issues in animal embryos. For knowing which plastics are safe a good mnemonic about recycling numbers to use is “Four, five, one, and two/All the rest are bad for you.”

Vicky has a more detailed post about her Nutrition Worksheets and diet during pregnancy as well as her exercise regimen.

Where to Deliver?

My mother has her Doctorate in Obstetrics Nursing with a lifetime of experience working in the field and is a huge advocate for natural childbirth, that is, vaginal childbirth without pain medications. There are numerous health advantages for babies born vaginally as compared to C-section, including their oxygen level rising more rapidly after birth, increased ability to regulate their body temperature, and higher scores on reflex tests. Additionally, pain medications given to the pregnant mother during labor also drug the baby, hindering its ability to adapt to the dramatic environmental changes it experiences going from the womb to the outside world. There is no such thing as a “local” anesthetic.

Northeastern OB-GYN Logo

Vicky started out attending Northeastern OB-GYN in Elizabeth City North Carolina, which was very good at the prenatal care they provided her. In addition to having a very nifty logo (the above is the largest I could find it online), they also gave us our first look at Sagan through ultrasound. The eggsack in the below photo is actually a vestigial trait from when our ancestors developed in an egg with a yolk.

Sagan Ultrasound 14 Weeks into Pregnancy

After moving to Norther Virginia, we first tried attending About Women OBGYN at Potomack Hospital website makes it sound like they have midwives on staff, which they don’t. We learned that it’s a standard practice in prenatal care to rotate the doctors so that every patient gets to meet every doctor so that when it’s time to deliver the patient isn’t stuck with a complete stranger. The only problem with this clinic was that there was no transfer of knowledge. We had to start from scratch with every doctor we met and there was much confusion about where Vicky was in her pregnancy. As a result, appointments for tests were miss-scheduled and prescriptions were mismanaged.

This experience of being on some sort of poorly-managed pregnancy assembly line prompted us to seriously look into midwife-assisted delivery. Usually this means home birthing; however, four dogs, three cats, and four other residents in the house made this option impractical. So we looked into birth centers staffed with midwives.

An question that comes up with delivering outside of a hospital setting is how safe is it? Studies demonstrate home birthing is as safe as hospital birthing, and studies suggesting otherwise tend to be deeply flawed (see also here). I surmise that these equivalent safety numbers have a lot to do with the fact that midwives and birth centers won’t accept high-risk pregnancies and rely on hospitals as a backup option for when labor does not progress.

In our search for certified midwives, we tried out Birth by Design, who was opening a new birth center in Fairfax Virginia. While the midwives there were very nice, there were some things that didn’t grok with me. They were very focused on herbal remedies and said that Vicky would have to agree to drinking an herbal tea every day for a healthy pregnancy. This seemed a little too New Age-y for me and I was further troubled when they said they had herbal solutions to breach pregnancies and other complications.

Sagan Ultrasound 20 Weeks into Pregnancy

Luckily, that same week we got taken off the waiting list for Birth Care in Alexandria Virginia. The midwives at this birthing center were very professional and clinical in their approach to labor and delivery. Their prenatal care was conditional on the patient taking responsibility for their health with prenatal vitamins, filling out their own chart for blood pressure and weight, setting up pediatric visits, proper diet, and, most importantly, taking birth classes to prepare for the experience.

Dr. Bradley believed there were instinctual behaviors animals were engaging to manage the pain and stress of childbirth. Looking to the animal kingdom for how other mammals handle labor we find the mother needs darkness, solitude, quiet, physical comfort and relaxation, controlled breathing, closed eyes, and the appearance of sleep. Our tour of Birth Care revealed an environment catered to providing such an environment, with a homey feel to the place, real beds, baths, and other comforts to allow the laboring mother to relax her body let her uterus do what it needs to do.

The Big Day: Labor and Delivery

(Note: Vicky has posted here birth story here, which is much more detailed than my abbreviated description. I highly recommend it for the detailed version of our birth story and how she prepared for labor.)

The Bradley Method classes were the most important thing we did to prepare for the big day, and that’s taking into consideration the fact that we only got halfway through them since Vicky’s water broke a month early and on July 12, 2011 Sagan Charles Somma was born at 4 pounds 13 ounces. The timing put him two days too early for us to go to the Birth Care Center, and we transferred to Alexandria Inova Hospital, a hospital we had never attended with doctors and nurses we had never met and had never discussed our desires for a natural, unmedicated birth.

We lucked out, however, as the staff was fantastic. Dr. Kenneth Adhoot observed that my wife was progressing through labor well and was admirably willing to step back and allow nature to take its course under the guidance of your nursing staff and midwife. Midwife Donna Greenfield was very professional and attended the actual delivery of our son, taking measures to avoid an episiotomy. Our nurse Heidi was a huge help, offering suggestions and coaching Vicky through her pushing.

We lucked out in another way in that just the night before we had gone shopping for all the supplies we would need for labor; unfortunately, I failed at the “Don’t let the gas tank go below 1/2 mark the last two months” bullet point and had to stop for gas on the way to the Birth Center, which Vicky was much less than thrilled about. Once at the hospital, our Birth Classes were invaluable in understanding all the procedures and anticipating the sequence of events, like when Vicky went into the Transistion Phase of labor and began doubting herself and her ability to go through a natural birth, but this passed within minutes and she focused to get through Active Labor like a champ.

Sagan Newborn

Despite being premature, Sagan was very healthy. He had a perfectly normal problem with his blood sugar dropping, and we got that rising within 24 hours by feeding him colostrum with a teaspoon. He had problems with jaundice for the first few days because Vicky is an A-Negative blood type and I am O Positive, which prompted Vicky’s immune system to attack Sagan’s red blood cells, but this cleared up quickly by putting him in sunlight and Vicky diligently forcing him to eat and flush out the bilirubin from his system. The only minor problem we had at the hospital during our two day stay there was in keeping Sagan’s body temperature up, which the nurses blamed on our inability to keep him properly swaddled; however, I quickly solved the problem by having the hospital turn off the air conditioning to our room, after which the nurses switched to complaining about how hot it was every time they came in. I owe it to the Birth Care midwives and their policy of keeping their center air conditioned during labor, but unairconditioned afterwards to keep the baby warm and healthy for knowing to ask for this.

Our Parenting Choices

Here’s a grab-bag of notes on some of our early parenting choices:

Breast Feeding: There are myriad health advantages to breast feeding over the health problems caused by formula feeding. We intend to breastfeed exclusively for the first six months and continue the practice for a full year. This sparked some controversy as a family member argued that breast feeding will prevent our conceiving another child until Sagan is weaned and we are nearing our 40s, where we start to move into high-risk pregnancy territory. Our ancestors breastfed exclusively for two years and continued to breastfeed for up to four years. This not only had the benefit of providing excellent nutrition to the child, but also prevented the mother from conceiving until the current child was sufficiently developed. There is also the monetary savings to consider, and Vicky demonstrates on her blog, the Medela breast pump has given us an exceptional return on our investment over the cost of formula feeding.

Immunizations: We have been and continue to get Sagan any and all immunizations suggested to us. Children who aren’t immunized result in hotspot breakouts of measles, pertussis (whooping cough), polio, and diphtheria. If you are considering postponing or foregoing vaccinations, please think about Benjamin Franklin’s personal lament about not vaccinating his son against smallpox:

In 1736 I lost one of my sons, a fine boy of four years old, by the small-pox, taken in the common way. I long regretted bitterly, and still regret that I had not given it to him by inoculation. This I mention for the sake of parents who omit that operation, on the supposition that they should never forgive themselves if a child died under it; my example showing that the regret may be the same either way, and that, therefore, the safer should be chosen. [emphasis mine]

At the time of my writing this in 2011, 738 people have died since 2007 that were vaccine preventable.

Circumcision: Decided against it despite being circumcised myself. The idea that a civilization of people who thought the all the animals in the world lived within walking distance of Noah’s home had better medical science than millions of years of penis evolution through natural selection seems pretty silly. The foreskin has a bundle of sensitive nerves, it keeps the head of the penis lubricated for easier vaginal penetration (this is why we substitute spit so much in modern sex) and allows the penis to move within the shaft during intercourse as nature intended, and a very promiscuous friend once told me uncircumcised men make better lovers. Don’t mutilate your child, let them make their own decision when they get older (You can read a good factsheet on this subject here).

Co-Sleeping: We have been cosleeping with Sagan rather than having him sleep in a separate crib. It makes sense to us from an evolutionary perspective. As Mark Vonnegut puts it, “The truth is, almost all mammals (including humans) sleep with their babies. Indeed, most human babies in most cultures sleep with their parents, and always have.” The breathing reflex is stimulated not directly by the absence of oxygen but rather indirectly by the presence of carbon dioxide, so sleeping next to the baby and sharing their breathing space increases the carbon dioxide levels in the air and should reduce apnea (I don’t have research to support this however, so take it as my opinion, not science). There is also a convenience element. Baby cries, one of us rolls over to feed him, baby goes back to sleep. With breastfeeding, the mother can roll over to offer a breast and go back to sleep while the infant feeds.

This is a controversial ideal in Western cultures, and each parent needs to read up on it and make their own choice about it. The American Academy of Pediatrics will eventually release an advisory on the subject, but until then, definitely do not cosleep if you are a smoker, on medication, or have been drinking, and if you do, research how to make your bed as safe as possible.

Baby Sign Language: This will surely be the subject of a future post, but thanks to a friend of ours with a Ph.D. in Anthropology, we will be trying out Baby Sign Language as a means of communicating with Sagan before he is able to express himself verbally. I’m hoping to experience some of the same insights into how the infant understands concepts as this blogger writes about with her daughter.

What We’ve Learned at 12 Weeks

What’s surprised me most about having a baby is what an ongoing learning experience we have gotten ourselves into. Specifically, it feels like we’ve gone on an anthropology expedition, observing the ethology of the human family. We are seeing how life was like for hundreds of thousands of years for our ancestors on the Serengeti.

The first thing we’ve learned is the importance of grandparents. Evolutionists suspect that menopause in human females is actually an evolutionary adaptation because it frees the woman up to contribute care for the children of her own children; in other words, grandmother’s are a human adaptation, contributing to the care of offspring as well as contributing to the transfer of cultural knowledge. Vicky’s mother has been invaluable in caring for Sagan, happy to play with him while we use the time to get some work done. Both Vicky’s mother and my own mother have been fantastic resources on the knowledge-front as well, leading to many phone calls for questions about childcare and issues that come up, and such cultural transmission from grandmothers is why humans needed increasingly larger brains. Vicky has a great blog post up about the importance of Grandmas in helping with childcare.

Something that has taken me by surprise is the complete helplessness of the human infant. Science has demonstrated that infants are not blank slates; however, they certainly appear to be blank slates. I was blown away by how incredibly discombobulated is a newborn. They cannot focus on anything except bright lights and make no social connections with those around them until they are a few month old.

This again is the result of evolution. Humans have big brains, which make us incredibly adaptable to any environment; unfortunately, those big brains can’t fit through the birth canal without the mother’s hips being too wide to allow them to walk upright. So biology found a compromise, the infant is born with its brain only partially developed with the remainder of the development taking place outside of the womb. After a few months of oftentimes patience-straining nights up with Sagan, he started making eye-contact with us and now returns our smiles, building the social bonds that endear him to us as such behaviors endeared infants to our ancestors so that they would raise them the many years it takes to become autonomous members of the clan.

Watching baby level-up appears to have the effect of leveling us up as well.

Sagan Smiling

Further Reading

You can see the Thank You letter I sent Inova Hospital here.

You can see the still-rough draft of our Birth Plan here.

I highly recommend the opening portion of This American Life’s episode Unconditional Love, which covers the history of psychology, the pre-1950s idea that affection and tenderness were bad for children, and the psychologist who proved the importance of love, who was a callous person himself.

Just this week I started reading Geek Dad’s book of suggestions for parenting with things like RPG Parenting and weekend projects with your kids. Looking forward to trying some of them out in a few years.

Update

A complete oversight, I meant to give a huge Hat Tip and Thanks to An American Expat in Deutschland for lending Vicky and I so many of the great books we read!

“I cannot live without books.” ~ Thomas Jefferson

I had the great joy of attending this year’s National Book Festival on the Washington DC Mall. With over 100 authors in attendance, CSPAN’s BookTv.org covering the event, PBS Kids, Scholastic, and the greatest library on Earth providing educational materials, this was a fun activity for kids and adults, all celebrating the most important cultural invention in human history: the written word.

As Carl Sagan explains, books changed everything:

For 99 per cent of the tenure of humans on earth, nobody could read or write. The great invention had not yet been made. Except for first-hand experience, almost everything we knew was passed on by word of mouth. As in the game of ‘Chinese Whispers’, over tens and hundreds of generations, information would slowly be distorted and lost.

Books changed all that. Books, purchasable at low cost, permit us to interrogate the past with high accuracy; to tap the wisdom of our species; to understand the point of view of others, and not just those in power; to contemplate – with the best teachers – the insights, painfully extracted from Nature, of the greatest minds that ever were, drawn from the entire planet and from all of our history. They allow people long dead to talk inside our heads. Books can accompany us everywhere. Books are patient where we are slow to understand, allow us to go over the hard parts as many times as we wish, and are never critical of our lapses. Books are key to understanding the world and participating in a democratic society.

The Library of Congres

Thomas Jefferson

I’ve written about my love of the Jefferson Room in the Library of Congress and compared it to a modern day Library of Alexandria in my book The Spiraling Web. Just as the British Empire defined itself as the time keeper for the world symbolized through the monumental clock Big Ben, the Library of Congress symbolizes the United States’ status as the world’s cultural hub. The entire world sets its watch by Greenwich Mean Time (GMT) and it sets it intellect by America’s eclectic melting pot of diversity and open discussion of ideas.

From the Library’s website:

The Library of Congress is the largest library in the world, with more than 147 million items on approximately 838 miles of bookshelves. The collections include more than 33 million books and other print materials, 3 million recordings, 12.5 million photographs, 5.4 million maps, 6 million pieces of sheet music and 64.5 million manuscripts… in some 470 languages.

Digital Preservation at the Library of Congress

The Library also supports the acquisition of its own collection through the issuance of copyrights, where anyone seeking to obtain copyright protection under the American government is required to submit two copies of their work (electronic copies are preferred now). Additionally, the Library (capital-L) has numerous other projects going on such as Digital Preservation, which includes web archiving and educational outreach efforts to encourage Americans to backup their digital media for long-term preservation. The LoC also has lots of great online educational resources like the World Digital Library, Gateway to Knowledge, Knowledge Quest, and a vast archive of photographs and other media, including photos of the Jefferson Room.

And did you know that the Library of Congress is also a Unit of Measurement in Information Science? 20 Terabytes; although, the LoC has far surpassed that.

Children’s Tents

Electric Company Coloring Poster

Three very large tents hosted a wide variety of games and activities for children. There were lots of folks in cartoon character costumes, presentation, and giveaways. My favorite activity here was the “Klutz Build a Book,” which included all sorts of decorative items to glue into the pages of a spiral bound book. Sort of like scrapbooking, but fictional.

Authors

After the festival, I found out there were tons of authors I would have enjoyed seeing, but, since I didn’t plan my trip out, I only made the effort to see two.

Neal Stephenson

Neal Stephenson, one of the most interesting cyberpunk novelists today and whose book Cryptonomicon I couldn’t finish (gave up at page 300), but did inspire me to buy an autographed copy of IT Security Guru Bruce Schneir’s book Applied Cryptography: Protocols, Algorithms, and Source Code in C, was reading from his latest tome. I happily stood in line for 50 minutes to get an autographed copy of the book Reamde for my brother-in-law who is a huge Stephenson fan and is confused as I am as to why I don’t grok this speculative hyper-geek of an author. His writing is kind of dry, but incredibly witty and his science fiction is hardcore and erudite, all wonderful qualities for his subject matter.

Garrison Keillor

A special treat was seeing Garrison Keillor of A Prairie Home Companion fame. He was reading from a collection of poems he had assembled titled Good Poems, American Places, which included a nice prayer for the existence of god (YouTube of him reading it), which was a request for god to simply be out there somewhere, and included the amusing line, “for I shall sure be pissed if I should have been an atheist.” Keillor related his experiences in writing, including rewriting scripts on the PHC as the actors were reading them. He also made one of the best observations about the craft I think I’d ever heard, “Writing is never finished; it’s just taken away from you.”

I can’t wait till next year’s festival.

Further Research

You can check out my Creative Commons Flickr Set Here, which includes lots of photos of Neil and Garrison.