biology

You’re invited: Genomics of Non-model Organisms

I’m on the student/postdoc-lead organizing committee for the following symposium. If the topic sounds appealing and you’re near Seattle, come check it out! As a warning, the talks won’t be tailored for a totally layman audience, but if you have some biology background or just passionate interest, it should be really great!

2012 Genome Training Grant Symposium:
“The Genomics of Non-Model Organisms”
Monday, June 11, 2012

1:00PM to 5:15PM
South Foege Auditorium (S060) on the University of Washington’s Seattle Campus
No registration or fee

Schedule and speakers:

  • 1:00-2:00PM: panel discussion with our speakers
  • 2:00-3:00PM: Cheryl Hayashi (University of California, Riverside)
    Molecular characterization and evolution of spider silk proteins
  • 3:00-3:15PM: break w/ coffee and snacks
  • 3:15-4:15PM: Katie Peichel (Fred Hutchinson Cancer Research Center)
    Genetics of adaptation, reproductive isolation, and speciation in stickleback fishes
  • 4:15-5:15PM: Jay Storz (University of Nebraska-Lincoln)
    Natural variation and genomic architecture of high altitude physiological adaptation in birds and mammals

If you know anyone who may be interested, please invite them! We want a great crowd for our speakers.

Apples – you can’t explain that!

More tweets I get from Christians:

I replied with this link.

Next someone’s going to try to make the argument that bananas were designed by God to perfectly fit in our hands! Ha! …Oh wait.

Want to learn more about the future of genomics?

My department is hosting a panel on “The Future of Genome Sciences” that is free and open to the public. Here are the details:

Panel Discussion: The Future of Genome Sciences
Monday, May 7th
7:00 pm, Kane Hall EDIT: 120
University of Washington
Seattle, WA
free, no registration required

The speakers will be:

Dr. Bruce Alberts who President Obama has appointed as one of his first Science Envoys.  Dr. Alberts is editor of Sciencemagazine, author of The Cell, and former President of the National Academy of Sciences.

Dr. Natalie Angier who is a science writer for The New York Times and the Andrew D. White Professor-at-Large at Cornell University.  In 1991 she received the Pulitzer Prize for Beat Reporting.

Dr. James Evans who is the Bryson Distinguished Professor of Genetics and Medicine at University of North Carolina and directs the Clinical Cancer Genetics Services at UNC.

Dr. Keith Yamamoto who is Vice Chancellor for Research, Executive Vice Dean of the School of Medicine, and Professor of Cellular and Molecular Pharmacology at the University of California, San Francisco.

The moderator is Dr. Maynard Olson, who is a Professor in the Departments of Genome Sciences and Medicine at the University of Washington and is one of the founders of the Human Genome Project.

If you’re near Seattle, I hope I’ll see you there!

Dear E. O. Wilson: Please retire or stick to ants

Tonight I went to a talk at Seattle Town Hall by E. O. Wilson, one of the most famous evolutionary biologists still alive today. I admit I went for two different reasons. One, Wilson is super famous and also very old, and I wanted a chance to see him speak because another chance might not come. But two, I saw that the topic was how group selection shaped human evolution, and I wanted to see what controversial arguments he would make.

Controversial because Wilson has recently been stirring the pot by trumpeting group selection and saying kin selection has been debunked. I don’t want to rehash the whole event, but Carl Zimmer has a good summary in the New York Times. The basic thing you need to know is that most biologists consider group selection to only occur in very rare and specific circumstances, and that selection usually takes place at the level of the individual or the gene.

But you wouldn’t know that from the talk. Wilson asserted that his controversial Nature paper definitively overturned kin selection theory and that “no one” responded to his critique of kin selection. This set off a red flag in my head, because I definitely remembered reading criticism of the paper at least in the blogosphere. I grabbed my phone and instantly dug up this critique by Jerry Coyne and this one by Richard Dawkins.

But maybe he meant a published critique. So I googled “response to Nowak 2010” and instantly found a list of papers also published in Nature criticizing his paper:

Abbot, P., Abe, J., Alcock, J., Alizon, S., Alpedrinha, J., Andersson, M., Andre, J., van Baalen, M., Balloux, F., Balshine, S., Barton, N., Beukeboom, L., Biernaskie, J., Bilde, T., Borgia, G., Breed, M., Brown, S., Bshary, R., Buckling, A., Burley, N., Burton-Chellew, M., Cant, M., Chapuisat, M., Charnov, E., Clutton-Brock, T., Cockburn, A., Cole, B., Colegrave, N., Cosmides, L., Couzin, I., Coyne, J., Creel, S., Crespi, B., Curry, R., Dall, S., Day, T., Dickinson, J., Dugatkin, L., Mouden, C., Emlen, S., Evans, J., Ferriere, R., Field, J., Foitzik, S., Foster, K., Foster, W., Fox, C., Gadau, J., Gandon, S., Gardner, A., Gardner, M., Getty, T., Goodisman, M., Grafen, A., Grosberg, R., Grozinger, C., Gouyon, P., Gwynne, D., Harvey, P., Hatchwell, B., Heinze, J., Helantera, H., Helms, K., Hill, K., Jiricny, N., Johnstone, R., Kacelnik, A., Kiers, E., Kokko, H., Komdeur, J., Korb, J., Kronauer, D., Kümmerli, R., Lehmann, L., Linksvayer, T., Lion, S., Lyon, B., Marshall, J., McElreath, R., Michalakis, Y., Michod, R., Mock, D., Monnin, T., Montgomerie, R., Moore, A., Mueller, U., Noë, R., Okasha, S., Pamilo, P., Parker, G., Pedersen, J., Pen, I., Pfennig, D., Queller, D., Rankin, D., Reece, S., Reeve, H., Reuter, M., Roberts, G., Robson, S., Roze, D., Rousset, F., Rueppell, O., Sachs, J., Santorelli, L., Schmid-Hempel, P., Schwarz, M., Scott-Phillips, T., Shellmann-Sherman, J., Sherman, P., Shuker, D., Smith, J., Spagna, J., Strassmann, B., Suarez, A., Sundström, L., Taborsky, M., Taylor, P., Thompson, G., Tooby, J., Tsutsui, N., Tsuji, K., Turillazzi, S., Úbeda, F., Vargo, E., Voelkl, B., Wenseleers, T., West, S., West-Eberhard, M., Westneat, D., Wiernasz, D., Wild, G., Wrangham, R., Young, A., Zeh, D., Zeh, J., & Zink, A. (2011). Inclusive fitness theory and eusocialityNature, 471 (7339) DOI: 10.1038/nature09831

Boomsma, J., Beekman, M., Cornwallis, C., Griffin, A., Holman, L., Hughes, W., Keller, L., Oldroyd, B., & Ratnieks, F. (2011). Only full-sibling families evolved eusociality Nature, 471 (7339) DOI: 10.1038/nature09832

Strassmann, J., Page, R., Robinson, G., & Seeley, T. (2011). Kin selection and eusociality Nature, 471 (7339) DOI:10.1038/nature09833

Ferriere, R., & Michod, R. (2011). Inclusive fitness in evolution Nature, 471 (7339) DOI: 10.1038/nature09834

Herre, E., & Wcislo, W. (2011). In defence of inclusive fitness theory Nature, 471 (7339) DOI:10.1038/nature09835

Yeah, and he said “no one” responded. And it’s not just that Wilson is out of the loop – he came off as being purposefully disingenuous. Not only did he publish a response to the responses (Nowak, M., Tarnita, C., & Wilson, E. (2011). Nowak et al. reply Nature, 471 (7339) DOI: 10.1038/nature09836), but during the Q&A he changed his story and said that people did respond but they were 1. Wrong and 2. In the minority. Even though 1. He never explained why their critiques were incorrect and 2. The vast majority of biologists disagree with his views of group selection and the authors of the critiques weren’t random nobodies; they were very important and accomplished researchers.

I want to give Wilson the benefit of the doubt. Maybe when he said “no one responded” he meant “no one responded in a way that we think invalidates our hypothesis.” But even then, the rest of his talk was incredibly sloppy. He asserted that human eusociality evolved via group selection, but didn’t offer a shred of evidence the whole time. No proposed mechanism, no genetic evidence, nothing. He just waved the Wand of Group Selection and asserted it happened. He asserted that humans first ate cooked meat by scavenging carcasses from wildfires. That’s one hypothesis among many, but he presented it as a known truth and gave no evidence or citation for it. He asserted that eusociality only evolved recently but again gave absolutely no evidence as to why he thought so. I mean, maybe he’s right, but eusociality isn’t exactly something that fossilizes well, so it could have possibly existed in past species. At least put some sort of qualifier or explanation of your reasoning out there.

When someone in the Q&A asked him to explain why people disagree with group selection so much, he didn’t explain the objections or why he thinks kin selection was wrong. He instead stated that his paper was reviewed by a mathematician from Harvard and that it got into the prestigious journal Nature. Therefore it is right, or something. Here’s an alternative hypothesis: Your paper got published in Nature because you’re insanely famous and it was incredibly controversial, which Nature eats up. Nature is more about prestige and sexy topics than good science nowadays. Its retraction rate has increased ten fold in the last ten years when the number of papers published in all journals has only increased by 44%.

Look, I’m not a priori against group selection. Maybe Wilson is right and group selection is applicable in more situations that we currently think. But I’m not going to accept it until he presents compelling evidence, which he utterly failed to do. You can’t just say “Harvard” and “Nature” and leave it at that.

The most irritating thing about the night was that this was a talk given to an educated general public. These people are smart enough to appreciate science and know Wilson is a famous scientist, so they’re going to believe whatever he says. On the way out people were raving about how interesting the talk was. But he presented none of the controversy, no evidence, no reasoning, no citations, no qualifiers…nothing. I understand that a talk to the general public isn’t going to get into extreme detail, but asserting your incredibly controversial ideas as scientific fact is incredibly dangerous. This talk reminded me more of stuff I’ve seen from creationists and climate denialists than scientists.

Honestly, I left feeling bad for him. E. O. Wilson made huge advances to evolutionary biology, sociobiology, and conservation. “Huge advances” is an understatement. But tonight he went outside his expertise and left science behind, and it was kind of embarrassing. I would have loved for him to give an hour long talk about ants instead.

Another academic accomplishment!

A new paper that I’m an author on has just been published in DNA and Cell Biology!

It’s a slightly atypical paper, though. When I was a senior undergraduate at Purdue, the Department of Biology staff nominated me to help develop the curriculum of a new NSF-funded, research-based, freshman honors biology laboratory course called CASPiE (Center for Authentic Science Practice in Education). That description is a mouth-full, but it basically means these freshman Biology majors were doing real research for a semester, instead of your typical cookbook lab experiments where the outcome is already known. The class was taught by a professor, a graduate student, and me. I like to say that my main duty was making sure the students plated their bacteria on the correct media and didn’t set themselves on fire*, but I also got to give a lecture on evolution and help out with general concepts throughout the semester.

And now that research has been published in a special undergraduate research edition of the journal DNA and Cell Biology. And it’s atypical because the subject matter is vastly outside of my normal field and interests: Isolation and Preliminary Characterization of Amino Acid Substitution Mutations That Increase the Activity of the Osmoregulated ProP Protein of Salmonella Enterica Serovar Typhimurium. That is going to look bizarrely random on my CV.

But the main congratulations go to the undergrads. They’d be juniors now, and having a paper published by then in a major accomplishment. So kudos to them!

*Though one somehow managed to set the rubber tubing connecting to the gas source on fire. I had a moment of “WTF” and then calmly turned the gas off, and the fire went out. Yay lab classes!

Guest Post: Skeptical dog training

The following is a guest post by Julie Lada, a veterinary student and skeptic who blogs at My DVM Vacation.

Dog training is a hot button issue right now. Dozens of TV, magazine and book personalities are dying to tell you the best way to get your dog to stop jumping up on your guests or going through your trash. In some ways, that is a great thing. Traditionally, dog training consisted of a rolled up newspaper. Getting the issue of dog behavior and training into the public awareness is a huge step for behaviorists and people who are passionate about pet welfare. However, as usual, anytime a topic becomes popular and a profit can be made off of claiming to be an expert, you get bad ideas and bad information being promoted just as heavily as the good. Television shows in particular focus on which host is the most charismatic rather than the most knowledgeable or accurate.

Part of the challenge for me personally, being a vet student and passionate animal behavior geek as well as a skeptic, is the pervasiveness of bad ideas in my field of study. From acupuncture and homeopathy being commonly accepted practices within veterinary medicine to witnessing a colleague perform an “alpha roll” right in front of me, it’s a daily struggle to balance my desire to address these issues with the need to still maintain good relationships and not become known as the token naysayer.

Dog training is one of those topics that must be handled with a delicate touch. A method isn’t purely a method anymore when you’re talking about its application toward an animal that a person feels a strong emotional connection with. The method becomes the person employing it, and its effectiveness becomes intrinsically tied to their value as a pet owner. Like it or not, as any trainer or behaviorist will tell you, the moment you say something like, “Dominance-based training is not as effective as we previously thought and can actually have detrimental effects on an animal” it becomes translated by the person you’re talking to as, “You’re a bad owner and you abuse your dog.”

The problem with any topic in medicine is that bad arguments can be made to sound very persuasive and convincing by using the lingo. The argument behind dominance-based training methods is an excellent example of this (BARF diets are another good example). Advocates such as Cesar Millan point to wolf pack hierarchy models as an example of “natural” applications of dominance-based behavioral conditioning. They tell dog owners to be their dog’s “alpha” by using techniques employed by wolves such as throat holds and alpha rolls. They also attempt to shame owners by telling them that disobedience is a form of dominance which proves that their dog doesn’t respect their status as “pack leader.” The appeal to nature fallacy is something we skeptics are well aware of but it is unfortunately remarkably persuasive with the general public.

A huge, glaring problem with the dominance hierarchy argument is that it makes the assumption that behavior models which we have obtained based on the study of captive wolf packs are reflective of natural behavior in the wild. This is patently false. Firstly, the dominance-based hierarchy suggested by Millan only occurs in captive wolf packs. Wolf packs in the wild consist of genetically related members with the breeding pair being the “alphas.” The frequent displays of aggression and dominance seen in captivity do not occur in a natural setting. Secondly, feral dog “packs” – the aggregates formed by stray dogs – do not display this hierarchy model, so even if it were true of wolves in the wild this model does not appear applicable for domestic canines. (Mech, 1999; Taylor & Francis, 2004)

And then there’s the problem with the word “dominance” itself. Common usage would lead most people to believe that dominance is a personality trait; something a dog just is. A common thing we hear from our clients is, “She’s just so dominant!” Or claim that their dog is trying to be dominant over them. Dominance has a very specific meaning within the context of animal behavior and it isn’t something an animal just is. This is a common misunderstanding and something I’ve even seen my colleagues use. Dr. Sophia Yin, a DVM with a Master’s in animal behavior and a widely renowned expert in dog behavior does a pretty good job of summing it up here. She has written extensively on the topics of dominance, aggression and training and I highly encourage anyone with a dog to spend several hours reading her articles. The American Veterinary Society of Animal Behavior reinforces Dr. Yin’s position with their official statement on dominance theory:

“Dominance is defined as a relationship between individual animals that is established by force/aggression and submission, to determine who has priority access to multiple resources such as food, preferred resting spots, and mates (Bernstein 1981; Drews 1993)… In our relationship with our pets, priority access to resources is not the major concern. When it comes to food, you will want to check with a specialist if you want to put your dog on a special diet, you could also have a look at sites online to check whether your dog can eat certain foods, can dogs eat oranges for instance. The majority of behaviors owners want to modify, such as excessive vocalization, unruly greetings, and failure to come when called, are not related to valued resources and may not even involve aggression. Rather, these behaviors occur because they have been inadvertently rewarded and because alternate appropriate behaviors have not been trained instead.”

But beyond the implausibility of the theory behind the use of dominance and physically aversive stimuli in dog training, as well as the misuse of the term “dominance”, there is the added factor that it just doesn’t have a wide range of practical use. Meaning in the majority of cases, it doesn’t work. Several recent studies have confirmed that dominance/positive punishment training methods have a number of negative effects on dogs (including physical injury and death in cases of choke chains and prong collars being used incorrectly) and can actually impair learning ability. These methods also cause fear and escalate aggression in terms of frequency, magnitude and situational aggression – meaning a dog that wasn’t previously aggressive becomes aggressive, or a conditionally aggressive dog begins to display aggression in situations where it previously did not (Husson et al, 2009; Hiby et al, 2004; AVSAB, 2008). This is particularly worrisome for vets and shelter workers. An owner employing dominance-based techniques toward their dog who is aggressive toward other dogs can actually cause that dog to not only be more aggressive toward other dogs, due to the added negative association with pain and fear, but also cause the dog to redirect its aggression toward its owner. In which case the problem goes from being something that could possibly be solved via proper training to what is a probable euthanasia case.

Positive reinforcement techniques such as clicker training are gaining in momentum, and it’s got behaviorists cheering in the streets (or rather, their offices). These techniques avoid the negative associations with pain and fear seen with dominance-based techniques and thus the ramping-up effect on aggression.

Finally, I know that this is a contentious topic and no doubt the comments will be full of anecdotes from those who have used Cesar Millan’s or other dominance-based techniques successfully. A few words on that.

First of all, there are always outliers. I saw something recently that I quite liked and determined to borrow that said that between 80-90% of smokers will develop lung cancer, which means that 10-20 out of every 100 smokers will not develop lung cancer. So you will often hear claims such as, “My father smoked two packs a day for forty years and died in his sleep at 85 years old!” And while true, it does not disprove the fact that overall smoking is highly associated with lung cancer.

Also consider that the effect of fear on the cessation of all forms of behavior is fairly well documented. Simply put, a fearful animal will stop doing anything, including what you wanted them to stop doing. A dog that is fearful of inviting a painful stimulus can appear to an owner to be “cured” of the unwanted behavior. In fact, the underlying issue of why this dog was exhibiting the unwanted behavior is still unaddressed. A dog that is fear aggressive toward strangers, for example, is still terrified of strangers but simply stops reacting. Don’t confuse this with being a happy, healthy, well-adjusted dog. An animal that has stopping displaying observable fear signals is still fearful, and the use of punishment can contribute to a more unpredictable animal that will give no warning before attacking (AVSAB, 2007)

Just to sum things up on a personal note… A couple of years ago while in undergrad, I was finishing up a meeting with my animal behavior professor and Millan’s name came up. He told me, “You know, every conference I go to, at some point we behavior types get together for drinks and he always comes up. We take turns bashing him over martinis.” So the next time you’re tempted to watch his show or buy one of his books, do so knowing that Millan is the Ray Comfort of the canine behavior world. And dominance theory is the Crocoduck.

Another thing fruit flies and humans have in common

I’m kind of loving this research published in the latest issue of Science, titled “Sexual Deprivation Increases Ethanol Intake in Drosophila.” Science NOW has a good general summary of the paper:

Offer a male fruit fly a choice between food soaked in alcohol and its nonalcoholic equivalent, and his decision will depend on whether he’s mated recently or been rejected by a female. Flies that have been given the cold shoulder are more likely to go for the booze, researchers have found. It’s the first discovery, in fruit flies, of a social interaction that influences future behavior.

Read the rest here.

The genetic “proof” for ancient aliens

I have a new, horrible obsession – the History Channel’s show Ancient Aliens.

On Saturday I found myself drinking with a group of my boyfriend Sean’s friends, when one of them announced that we must play an Ancient Aliens drinking game. I had no idea what the show was, but became intrigued when they started discussing the rules of when to take a drink:

  • Whenever someone being interviewed has no relevant credentials like a PhD
  • Whenever someone says the phrase “Some scientists say”
  • Whenever someone says the phrase “ancient astronaut theorists”
  • Whenever an ancient manuscript is displayed
  • Whenever there’s a terrible CGI reenactment
  • Whenever Giorgio starts talking

Me: Who’s Giorgio?
Them: Oh, you’ll know who Giorgio is soon enough.

This is Giorgio, by the way:

…That’s all I’m going to say.

They decided to reduce the list so we would wouldn’t get alcohol poisoning. But I found myself following my own rule of “drink whenever someone says something that blatantly defies logic or is a total non sequitur.” Which meant I was pretty much constantly drinking for an hour and a half. Especially when you’re jumping from pyramids, dragon drawings, Tesla coils, and the Bible all being proof of aliens (just to name a few).

For those of you who’ve never seen the show…I’m not quite sure how to summarize it. The footage looks professionally done since it’s on the History Channel, and some of the shots of the ancient artifacts are cool to see. But if I had to summarize the major theme, it would either be “Brown people never could have done <insert amazing feat here> because they were too lazy and/or stupid, therefore aliens had to help them.” I think my favorite mindblowing moment was when Giorgio explained that:

  • People worship “Gods”
  • But people only believe in things they have evidence for
  • They had written/drawn evidence for these “Gods”
  • Written/drawn evidence is always realistic and never abstract, imaginative, or metaphorical
  • But “Gods” don’t actually exist
  • Therefore they were actually aliens

Oh, Giorgio. How I wish point #2 was true.

Something about the show hooked me in its terribleness. My emotional reaction was actually very similar to the time when I visited the Creation Museum. Yes, I was mad at how they were twisting science, using terrible logic, and spreading blatant lies. But the absurdity of it all was oddly amusing. By the end you find yourself playing along, like you’re watching a fantasy novel… and not something people actually believe.

Also, being heavily inebriated helps.

So Sean and I plowed forward to episode two, since the first two seasons are conveniently available on Netflix. Our “game” was to guess what sort of bizzaro conspiracy theory the show would provide to explain a phenomena they were hyping before the show made the reveal. Sean was a little too excited when he correctly guessed the “Humans and aliens had sex and interbred” plotline. To which I replied, “But they’re an alien. Humans can’t even breed with chimps. Humans would have to actually be aliens seeded here or something for interbreeding to be possible.”

And then that’s exactly what the show said, and I nearly peed my pants laughing.

But the real kicker came when the show brought up the human genome. Sean and I both study genomics and evolution, so we exchanged a wary look. I’ll let you see it for yourself. The clip begins at 7:34 in the first video, and continues until 3:03 in the next.

http://youtu.be/aK687ZHtijY

http://youtu.be/_ncym6es7x0

In case you can’t watch the video or had trouble following that pristine argument, let me summarize:

  • Geneticists discovered the gene HAR1, which is unique to humans and plays a critical role in the development of the human brain.
  • Did it develop through evolution? Francis Crick says human genes couldn’t have evolved because there’s not enough time for DNA to evolve by accident. He said it would be as improbable as a hurricane going through a junkyard making a Boeing 747.
  • Since it couldn’t have evolved, the aliens performed a targeted mutation in HAR1 to make us “human.”
  • We only understand 5% of the genome. If you wanted to record an eternal message that could be decoded by a creature that eventually evolved enough intelligence to decode it, you shouldn’t put it in a monument or text that can be destroyed…put it in the DNA! OMFG THAT’S WHAT JUNK DNA IS! SECRET MESSAGES!

And now, for a quick debunking:

  • HAR1 is present in all mammals and birds, not just humans. But in all non-human species, the sequence is effectively the same, or conserved. The human copy in particular has a number of differences compared to other species, so we consider the human copy of HAR1 divergent. This is not at all the only human gene to be divergent. And all species have uniquely divergent genes – that’s precisely what makes things different species. But no one is arguing that marmosets or fig trees or syphilis are actually aliens with special alien genes inserted into them. Well, maybe people are arguing that. There’s four seasons of this crap, and I’m only on episode 3 of season one. Maybe the syphilis aliens are right after the episode titled Aliens and the Third Reich (I shit you not).
  • Francis Crick has always been a strong supporter of evolution and has spoken passionately about how evolution shaped his scientific investigation. He was one of the Noble laureates who advised US courts bogged down by creationists that “Creation-science’ simply has no place in the public-school science classroom.” He also was an advocate for making Darwin Day a British national holiday. While he was initially doubtful of the origin of the genetic code and wondered if panspermia could be the answer, he later published a retrospective article where he and his colleague “noted that they had been overly pessimistic about the chances of abiogenesis on Earth when they had assumed that some kind of self-replicating protein system was the molecular origin of life.” So, um, no.
  • Francis Crick did not come up with that 747 argument – Fred Hoyle did. That’s why it’s called Hoyle’s fallacy. It’s already debunked a bajillion times by biologists – Dawkins wrote two books about it – so I won’t waste time trouncing it here.
  • Whatever alien thought junk DNA would be a great place for an eternal message is a dumbass. Because junk DNA doesn’t code for a protein or have some sort of regulatory role, it’s what geneticists refer to as “neutrally evolving.” It means it’s at liberty to gather mutations because they don’t have any major effect that would weed them out via natural selection. This is especially true when the show’s premise is that the message was placed there eons ago, and had tons of time to accumulate changes. It also doesn’t explain why chimps share a lot of junk DNA with us, or why a huge proportion of junk DNA are remnants of ancient viruses. I’m sure Giorgio would say that those aliens were trying to throw us off the scent by making it seem like our genomes had evolved through natural processes.
  • They never address the fact that the hypotheses they present throughout the show aren’t even internally consistent. At one point they say all life on earth was put there by aliens, and it evolved naturally. Then they say we ARE the aliens. So what, were the aliens unicellular organisms? How can we interbreed – like they say we do – if we’re that distantly related?! But then they say the proof that we’re aliens is that we look like the aliens…so how about those billions of years of evolution?

In poking around the internet about this show, I discovered that Giorgio had a twitter account, which included this gem:

Lizard people? Total nonsense. Aliens? Of course, duhhhhh.

Oh, History Channel. How the mighty have fallen. I remember when I was little and I’d watch you with my history-buff dad, and learn all sorts of cool things about Egypt and Rome and WWII. But now I watch you to point and laugh.

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.

Scientific publication title of the day

Desperately Seeking Stable 50-Year-Old Landscapes with Patches and Long, Wide Corridors” in PLoS Biology.

I’m not sure if the authors purposefully came up with a title reminiscent of a personal ad, or if it’s just my overactive imagination. Either way, it makes me giggle. I mean, “long, wide corridors”? What a size queen.

For anyone wondering what the paper is actually about, the authors are looking for particular types of environments in order to investigate if corridors effectively conserve biodiversity. Human urbanization (roads, housing developments, Walmarts) serves as barriers that plants and animals have a hard time crossing. This fragments large populations into a lot of smaller ones that can’t interbreed as much. Small populations are more susceptible to events that reduce genetic diversity, like inbreeding and genetic drift. Decreasing genetic diversity is generally considered Bad, because…well, I’m lazy and Wikipedia does a good job at explaining:

“Genetic diversity serves as a way for populations to adapt to changing environments. With more variation, it is more likely that some individuals in a population will possess variations of alleles that are suited for the environment. Those individuals are more likely to survive to produce offspring bearing that allele. The population will continue for more generations because of the success of these individuals.”

Corridors are often used to attempt to make up for this fragmentation, and the authors want to see if the corridors are actually successful in promoting gene flow between populations. Thus their personal ad that made me giggle.