evolution

Happy Darwin Day!

And an early happy Valentine’s Day:

But during both holidays, remember to only participate in evolution if you’re ready: use contraception.

Come see me for Darwin Day!

I’ll be a part of Darwin on the Palouse, a Darwin Day celebration in Pullman, WA and Moscow, ID:

  • Daniel Dennett and PZ Myers will speak in the Cub Senior Ballroom at Washington State University in Pullman on February 9, starting at 7:00 PM.
  • Fred Edwords and Jennifer McCreight will speak in the Clearwater Room at the University of Idaho in Moscow on February 10, starting at 6:00 PM. I’ll be giving my talk about Ken Ham’s Creation Museum, which is always a blast.

I find it kind of odd that I’m in fact returning to Moscow, ID. I was there when they hosted the Evolution conference a couple of years ago.

Not gonna lie, I’m kind of giddy to be part of the same event as Daniel Dennett. Thanks to the organizers for including me. Sadly I’ll miss his and PZ‘s talk, since I fly in Friday afternoon. PZ has already guilted me into buying him a beer as penance.

And I hate to look a gift horse in the mouth, but I have to point out a pet peeve. Whoever wrote the speaker bios writes that Dennett is an author and philosopher, that PZ is a biologist and has won many secular awards, that Edwords is an editor and director of secular organizations…and that I’m the blogger that did boobquake. I know that’s what I’m most famous for, but that’s all you come up with? You don’t think it’s relevant to mention that I’m the Vice Chair of the Board of Directors of the Secular Student Alliance, that I’ve published in the Atheist Guide to Christmas, that…you know, I’m an evolutionary biologist working on my PhD? For Darwin Day?

Nope, boob joke. I will never escape it, will I?

Creationism bill passes Indiana Senate

Newflash! 28 out of 50 Indiana state Senators are still complete morons (emphasis mine):

On January 31, 2012, the Indiana Senate voted 28-22 in favor of Senate Bill 89. As originally submitted, SB 89 provided, “The governing body of a school corporation may require the teaching of various theories concerning the origin of life, including creation science, within the school corporation.” On January 30, 2012, however, it was amended in the Senate to provide instead, “The governing body of a school corporation may offer instruction on various theories of the origin of life. The curriculum for the course must include theories from multiple religions, which may include, but is not limited to, Christianity, Judaism, Islam, Hinduism, Buddhism, and Scientology.”

The Senate spent less than twenty minutes considering the bill, with its sponsor Dennis Kruse (R-District 14) defending it. Kruse acknowledged that the bill would be constitutionally problematic but, he told the education blogger at the Indianapolis Star (January 31, 2012), “This is a different Supreme Court,” adding, “This Supreme Court could rule differently.” The American Civil Liberties Union of Indiana’s legal director Ken Falk was previously quoted in a story from the Associated Press (January 26, 2012) as saying that the bill is clearly unconstitutional and invites lawsuits: moreover, he added, “when lawmakers propose legislation they clearly know will end up in the courts, it wastes time and resources.”

[…] The bill now proceeds to the Indiana House of Representatives, where its sponsors are Jeff Thompson (R-District 28) and Eric Turner (R-District 32), who is also the house speaker pro tem. Thompson, interestingly, is also a cosponsor, along with Cindy Noe (R-District 87), of House Bill 1140, which would require teachers to discuss “commonly held competing views” on topics “that cannot be verified by scientific empirical evidence.” While evolution is not mentioned in the bill, Noe cohosted a controversial dinner at the Creation Evidence Expo in Indianapolis in 2009according to the Fort Wayne Reader (August 23, 2010). In any case, HB 1140 seems to have died in committee.

…You know, I got nothing. I dealt with this idiotic crap for the 22 years I lived in Indiana, and I’m running out of new material. Now it’s just time to get the popcorn and watch the stupidity play out.

The only reason I wish I still lived in Indiana is so I could be the one to petition for Pastafarianism.

Indiana Senate committee approves creationist legislation

My dad emailed me this news report with the quote “Another reason to be glad you’re not living in Indiana.” From NWI Times (our local newspaper!):

An Indiana Senate committee on Wednesday endorsed teaching creationism in public schools, despite pleas from scientists and religious leaders to keep religion out of science classrooms.

Senate Bill 89 allows school corporations to authorize “the teaching of various theories concerning the origin of life” and specifically mentions “creation science” as one such theory.

State Sen. Scott Schneider, R-Indianapolis, who voted for the measure, said if there are many theories about life’s origins, students should be taught all of them.

But John Staver, professor of chemistry and science education at Purdue University, said evolution is the only theory of life that relies on empirical evidence from scientific investigations.

“Creation science is not science,” Staver said. “It is unquestionably a statement of a specific religion.”

The Rev. Charles Allen, head of Grace Unlimited, an Indianapolis campus ministry, said students would be served better by teaching religion comparatively, rather than trying to “smuggle it in” to a science course.

The Republican-controlled Senate Education Committee nevertheless voted 8-2 to send the legislation to the full Senate.

What? Indiana is being backwards and ignorant? I am shocked – shocked, I say!

Dear Indiana legislators,

What you are doing is unconstitutional. That is not an opinion of mine – the Supreme court decided this in Edwards v. Aguillard (1987). Your attempt to weasel Christianity into public science classrooms is going to fail. You can either choose to vote it down now, or you can waste years of time and money in a pointless legal battle. Not to mention your continued efforts to destroy science make intelligent young people like me dying to evacuate the state and never come back. You wonder why you have a brain drain? This is it.

Indiana voters – figure out your Senate district here and send your state Senator a reminder about why creationism has no place in a science classroom.

Kentucky’s priorities

Governor Steve Beshear (D) of Kentucky has just approved the state’s new budget for 2012-2013: millions of dollars cut from education, while the Creation Museum’s $43 million dollar Ark Park still stands. The $11 million going toward highway development for the amusement park was also untouched.

I can see Beshear’s airtight logic now. If we keep Kentuckians uneducated, they’re more likely to visit that intellectual black hole, thus increasing money spent on tourism! Budget problem solved!

And to think states like Kentucky wonder why they experience a “brain drain.”

Indiana DEFINITELY isn’t perfect

At least Seattle limits its scientific ignorance to a piece of bad journalism. Indiana has anti-evolution legislation bubbling up:

Senate Bill 89, prefiled in the Indiana Senate and referred to the Committee on Education and Career Development, would, if enacted, amend the Indiana Code to provide that “[t]he governing body of a school corporation may require the teaching of various theories concerning the origin of life, including creation science, within the school corporation.” The sponsor of the bill is Dennis Kruse (R-District 14), who chairs the Senate Committee on Education and Career Development. In 1999, while serving in the Indiana House of Representatives, Kruse pledged to introduce a law to remove evolution from the state’s science standards, according to the South Bend Tribune (August 27, 1999). Instead, however, he introduced bills with the same wording as Senate Bill 89, House Bill 1356 in 2000 and House Bill 1323 in 2001. Both died in committee.

It’s irritating enough that people want to legislate their religion into science classrooms. But this is obviously unconstitutional and has no chance of surviving a legal battle. Stop wasting the time and money of Hoosiers and focus on issues that actually matter.

…One day, one day I will receive positive news from my home state.

Seattle isn’t perfect

As much as I agree with the hilarious post about how “Seattle is objectively superior to the place you grew up,” I have to admit it’s not perfect. Like our main news station running a terrible piece on how Arizona sandstones prove Noah’s flood. Thanks for the uncritical support of young earth creationists, KOMO! I understand you’re busy and couldn’t get around to interviewing any legitimate researcher at the University of Washington. It’s hard picking up the phone or riding a bus for ten minutes.

Of course, Seattle is home to the Discovery Institute, so maybe it shouldn’t be so shocking when biased journalism like this springs up.

INJUSTICE

I was playing Cranium with my family, and as luck would have it, my team got an evolutionary question. My dad and grandma turned to me, since, you know, I’m an evolutionary biologist and stuff. This was the question:

“True or False: Dogs are more closely related to cats than they are to bears.”

I knew it was false. I don’t have an evolutionary tree of every species in my head, but I had heard of this comparison before. People intuitively think dogs and cats are more closely related because they’ve both been domesticated – but that has nothing to do with evolution. I also knew this was an example of an evolutionary tree that had been tweaked as we gained more knowledge. Very preliminary, simple genetic studies shows dogs more closely related to cats. But as we expanded the comparison to the whole genome, we found that dogs were more related to bears.

I was very annoyed when I flipped the card to find this answer:

“True – The three species are all distantly related, but genetic evidence has established that bears split off from a common ancestor well before cats and dogs had their big split.”

My family immediately started giggling. “Good job, Miss PhD.” This would not stand. I flipped out the iPhone and searched for a modern phylogenetic tree of carnivores. I immediately found one in Nature Reviews Genetics based on karyotype data, indeed showing that dogs were more closely related to bears than cats.

I pointed at the image on my screen.

“Too bad” my family said, as they continued on with the next question.

It may no longer matter for the game (though my team did win – neener neener), but in case you’re interested… yes, dogs are more closely related to bears than cats. They’re all carnivores. Dogs and bears both belong to the suborder Caniformia, while cats are in suborder Feliformia.

So why was Cranium wrong, if it’s claiming its answer is based on genetic information? The answer lies in the date. I checked the box, and this edition of Cranium was made in 1998. In the rapidly expanding field of evolutionary genetics, that’s ancient. We can now compare whole genomes, while before we were limited to a single gene (at best). Different parts of the genome can evolve at different rates if they’re under selection (or not), so it’s important to look at the big picture instead of a tiny snippet. Our methods and technologies are improving, so our results get more and more accurate.

Hooray for science!

Still looking for Christmas cards?

Don’t forget I have some evolution themed Christmas cards for sale!

Christmas Tree of Life:

Evolution of Christmas:

Have no idea what to actually write in your godless Christmas cards? Digital Cuttlefish has oodles of atheist Christmas poems.

And if you still need to buy a gift for PZ, you can bid on this awesomely blasphemous piece of art by Joshua Bennett:

He’s auctioning off the piece, and all proceeds go to the American Humanist Association.

Accepting evidence is not dogmatic

Update: I have decided to restore this post with some minor edits. I will write more about my decision to do so in another post, since I think the topic of self censorship in terms of the social structure of academia is an interesting topic.

Hrmph.

I’m frustrated. As I talked about before, I’m working on my NSF Graduate Fellowship proposal. Part of this process is getting a ton of students and professors to critique your paper. I honestly shouldn’t be too annoyed, because overall the reviews of my proposal have been very good. But a critique that I got from many – but not the majority of – my reviewers happens to be a major pet peeve of mine.

I was too “dogmatic.”

The offending part was the opening paragraphs of my personal statement. I’ll post it here for full disclosure:

            “College was a bit of a culture shock for me. I grew up in a nurturing environment that embraced science – Bill Nye the Science Guy was the program of choice, and competing in Science Olympiad was cool. But when I moved a tad farther south into the heartland of Indiana for my undergraduate education at Purdue University, I quickly realized this was not a universal truth. The attitude toward evolution was terrible amongst non-scientists on campus. One of the local churches was a major donor to the infamous Creation Museum in Kentucky, activists handed out anti-evolution tracts on the main quad, and anti-evolution letters in the campus newspaper were commonplace. I was shocked to learn that even many of my fellow biology majors did not accept evolution.

The fact that so many people didn’t share my fascination with evolutionary theory troubled me on a personal level. This wasn’t simply someone disagreeing with how I earned a paycheck: Learning about evolution was the key event that led me to adopt a skeptical, naturalistic worldview. I felt like people were rejecting the ideals that shape my humanist ethics. I wanted others to understand my feelings of awe as I contemplate the universe, or how lucky I feel to have evolved the necessary traits to contemplate the universe in the first place. I quickly learned that many of these people still valued science, but never had the opportunity to become educated about evolution.

That realization motivated my passion for science communication and mentoring. […]”

Now, I’m not claiming that’s perfect. It’s a draft that can obviously still do with some tweaking. And I realize I have to walk on egg shells and be politically correct if I actually want to get funded. It doesn’t matter if I’m being honest or if I’m technically right if I happen to get three Christian biologists who read this as a belligerent attack against their belief. Which is apparently how it came off to my reviewers.

Fine. Whatever. I don’t read it that way, but I guess I can see how you can read it to be negative. I thought I was being as diplomatic as I could possibly be, but apparently it’s still not diplomatic enough – I’ll have to change some of the wording.

If we would have stopped at “This could potentially be interpreted negatively,” I would not have been writing this post. But it didn’t. Some of my reviewers, including a professor, insisted that I was “dogmatic,” and “wanted people to believe in evolution just because that’s what you happen to believe in.” That rejecting evolution isn’t a “terrible” attitude. That I shouldn’t be “shocked” that some biology majors don’t believe in evolution, because not everyone has to be like me. That wanting to help people learn about evolution means I thought they were stupid.

That I came off as, I quote, “Dawkins-esque.”

I think that was supposed to be negative remark, but I took it as a compliment.

I fumed the whole bus ride home, wishing I could have responded then and there – but a meeting for a review of your work is not the place for a philosophical debate. But these are things I hear over and over – not just from professors and classmates I like and respect who accept evolution but think I’m too “dogmatic” about promoting it. Because they’re so common, I feel that it’s important that I address those types of ideas here.

1. Wanting people to adopt an evidence-based view of the universe is not dogmatic. In fact, it’s the very opposite of dogma. I want people to be able to change their minds when confronted with new evidence. Admitting you were wrong is one of the most intellectually honest things you can do. The only “dogmatic” thing about living in reality is that some things are true, and some things are not. You don’t get to flap your arms and start flying through the air just because you wish that was the way the universe works.

2. I don’t want people to “believe in evolution because that’s what I believe in.” I want people to accept evolution because there’s an insurmountable mountain of evidence supporting it. This isn’t a subjective opinion that’s up for debate. I’m not forcing people to think that chocolate ice cream with peanut butter swirls is the best flavor (though it totally is). To deny evolution is either based on ignorance or willful delusion. I know, what mean words. That doesn’t make them less true. People have either not learned about evolution or not had it explained to them well, or they’re people who go and build Creation Museums and think people walked with dinosaurs because of their religious convictions. There may be less hope at getting the latter to accept evolution, but being a science educator is important to me, and I want to tackle the “ignorance” side of that equation.

In my future draft, I plan to explicitly say that I accept evolution because of that mountain of evidence. I thought that would be self-evident to biologist NSF reviewers, but might as well be safe…

3. Rejecting evolution is certainly a “terrible” attitude. Again, why should we pat people on the back for ignoring scientific facts?

4. We don’t give chemistry degrees to people who believe in alchemy. We don’t give aerospace engineering degrees to people who think planes are held up by fairies. We don’t give geology degrees to people who think the Earth is made of chocolate pudding.  But we have no problem giving biology degrees to people who think an invisible supernatural being created life, despite it having as much evidence as Puddingology. I should feel shocked that people who reject the fundamental concepts of their field can still successfully earn a degree.

5. I don’t think that everyone who rejects evolution is stupid. I do, however, think they are wrong. Those things are not equivalent. And when ignorance – the lack of information – is the cause of their rejection, that can be fixed. And should be fixed – but apparently it’s dogmatic to think people should be educated.

Why do I even need to have this discussion? Why, if I had proposed educating people about gravity or plate tectonics, would there have been no debate? Why would any other drive to educate be seen as positive, rather than dogmatic? Why are we expected to roll over and simply accept that some people are going to ignore the fact of evolution?

Because religion is protected in our culture. Telling someone they’re wrong is “dogmatic” if it’s contradicting their religious beliefs even if, you know, they’re wrong. Mincing words and avoiding hurt feelings is more important than education and reality.

Religion does not deserve this special status. We don’t have to tiptoe around, pretending the universe bends to their wishes when all of the evidence says otherwise.

Of course, I have to wonder if this whole “dogmatic” thing came up because later in my personal statement I mention my involvement with some secular organizations. They were relevent – I talk about various pro-science events we’ve done, and the organizational and leadership skills I’ve gained from them. Or if it came up because these people aren’t reading my proposal in a vacuum – they all know I’m a strident, outspoken atheist in my free time. Even if I don’t say that in my proposal and I mince words as much as possible, that knowledge still colors their interpretation. Without the atheism side, would my drive to educate about evolution have been a problem? Did my classmates who mentioned teaching students about evolution in their applications get called dogmatic?

I hate that I even have to wonder about it.

An intro to the neutral theory of evolution

From a top donor:

“I’d like you to write a blog entry (primer) about neutral theory aimed at the layperson.”

Okay, I’m not going to lie. I’ve been secretly hoping someone would bump this question out of the top ten, mainly because neutral theory is kind of boring and vaguely confusing and hard enough to explain while using biology buzzwords. It’s even harder to explain when you only have 30 minutes to write about it and it’s supposed to be targeting non-biologists. When I shared this question with some fellow genetics grad students, the general response was “Ewwwww.”

But I will try my best!

When most people think about evolution, they think of adaptations. Something in the environment puts selective pressure on a certain trait, and organisms with that trait are more “fit” (reproduce more). For example, rabbits that live in snowy climates are more likely to survive (and reproduce) if they have white fur that helps them blend into the snow. If a mutation randomly arises that make their fur white, or just lighter, that rabbit has an advantage over the other rabbits – the dark brown ones are going to be the first ones that are eaten.

There are lots of examples of adaptive evolution through natural selection, and people know them more because they make good stories. The most famous example of evolution, Darwin’s finches, is a case of adaptive evolution.

But not all evolution takes place because of natural selection. Evolution is at its simplest defined as the change in allele frequencies over time. That’s where neutral theory comes in. Neutral theory states that most evolutionary changes are the result of random drift of neutral mutants.

Buzzwords buzzwords, I know. So let’s take it one step at a time and pretend that we’re looking at a population of unicorns (if we’re pretending, might as well pretend all the way).

Alleles are just two different forms of a gene. Genes are usually hundreds or thousands of basepairs long, but let’s pretend we’re zooming in on three bases in a gene for fur color. If you have the sequence AAA, your fur is white. But if you have AAG, your fur is pink. AAA and AAG are different alleles.

Now let’s say all of the unicorns start as AAA, and then from mutation you get a unicorn who’s AAG. Being pink has no effect on the unicorn. He’s not more likely to get eaten, he doesn’t live longer, he doesn’t have more luck with lady unicorns. It’s a “neutral” mutation because it doesn’t change the unicorn’s fitness.

That’s where random drift comes in. Drift simply refers to the frequency of one allele changing due to random chance. That is, nothing is selecting for pinkness. Maybe that unicorn just happened to have more offspring. Maybe the population underwent a bottleneck and was reduced to just a few unicorns, the pink one happened to survive, and now his pinkness will make up a larger percentage of the population. Maybe a couple of unicorns, including the pink one, happened to get isolated on one side of a river, so that side eventually had a lot of pink unicorns, while the other has a lot of white ones. Through random chance alone, a neutral mutation can grow to high frequency or even reach 100% (what biologists call “becoming fixed in a population.”)

When you get into the mathematics, you assume that random neutral mutations occur at the same rates across individuals. This is how biologists get things like “molecular clocks” where they can tell when two species diverged from each other.

…And I have no idea if that made any sense, but I’m out of time. You have all now been exposed to (a shoddy summary of) evolutionary theory, congratulations. If anyone would like to explain further or correct me in the comments, please do so!
This is post 20 of 49 of Blogathon. Pledge a donation to the Secular Student Alliance here.

Why did we evolve to die?

Second donor question (might as well get them out of the way when I’m still awake!):

“I would like you to tackle the question of why there is death in terms of evolution.”


What a good question! I should preface this by saying this isn’t my particular field of research, so I don’t know any relevant studies to cite off the top of my head – but I’ll try to explain death in general evolutionary terms.

So, why do things die? At first glance, it seems counter intuitive. The whole driving force behind evolution is “survival of the fittest” – fittest being those who produce the most viable offspring. Wouldn’t it benefit an organism to live as long as possible, continuously producing more and more offspring?

The roadblock is that organisms are constrained by the laws of physics. When you boil it down to the basics, living things are just really complex molecular structures and chemical reactions. And it takes a lot of energy to keep the entropy or “disorder” of a system from increasing (which is a vast oversimplification of the Second Law of Thermodynamics, I know – forgive me). That energy comes from things like the sun (woooo photosynthesis!) or metabolizing food (woooo citric acid cycle!).

Aging is basically the general decay of processes. As you build up more and more errors, things just don’t work as well. And there becomes a point where you make a trade off. Do you expend lots of energy to keep the old structure alive so you can inefficiently reproduce, or do you scrap it and focus on the newly made organisms?

Now, that’s a painfully anthropomorphic view of evolution, but it’s basically how it works. Keeping a decaying organism alive doesn’t significantly increase its fitness. In fact, it can even decrease its fitness! If you’re in an environment where resources are scarce (aka, pretty much every environment), you’re competing with your children for those resources. So resources you use to keep yourself alive could alternatively be going into making grandchildren for you. Sometimes it’s in your best evolutionary interest to die!

I think this can sometimes be an odd concept for humans to grasp, since we’ve recently been able to avoid nature’s typical limitations. Back in our savanna days, we’d usually get eaten or die of disease before aging took place. There was no evolutionary benefit to have mechanisms in place to stave off aging even longer when we’d usually die before getting to that point. Evolution doesn’t care if your joints start hurting or you don’t reproduce as well, because you wouldn’t have been around anyway!

And that’s what differentiates scientists from the rest of people. I find this absolutely fascinating, while I probably just depressed a lot of you by calling you decaying bags of molecules that nature doesn’t care about. Ah well.

This is post 7 of 49 of Blogathon. Pledge a donation to the Secular Student Alliance here.