What we can learn from ancient human DNA

What can we learn about a person just from looking at their DNA? As our knowledge of genetics continues to grow, we may even be able to figure out what they look like. Research published in Nature looked at the genome of an ancient human using 4,000 year old hair that had been preserved in Greenland’s permafrost. From looking at genes that cause known traits, we can learn a lot about his appearance.

  • Male
  • Type A+ blood
  • Brown eyes
  • Darker skin
  • Stocky body
  • Dry earwax
  • Shovel shaped teeth
  • Thick, dark hair
  • Tendency toward baldness

Okay, as an aside: Who is the lucky artist who gets to draw a reconstruction of an ancient human, or the feather patterns on dinosaurs? Is this someone’s profession, or does a grad student do it? Maybe I can finally find a way to combine my art skills with my biology skills!

Anyway, it’s pretty cool that we’re able to learn about the actual physical appearance of someone just from their genes. Think about the implications in forensics cases when all that’s left is tissue that’s beyond identification. But that’s not the thing that made this paper Nature-worthy. All of these genotypes are very similar to modern Siberians, which tweaks our current understanding of human migration. Jerry Coyne summarizes it well over at his wonderful blog, Why Evolution is True:

Oh, and the really interesting result is this: the DNA suggests that the individual had components of genes still present in East Asian and Siberian populations, but not found in modern-day Inuits or people from South and Central America. This suggests that there were two separate invasions of North America from Asia: the one that gave rise to native Americans, South Americans, and modern Inuit on the one hand, and that leading to the presence of Saqqaq in Greenland. Those latter individuals probably came across the Bering Strait, and then, hugging the Arctic, made their way eastward across North America and then to Greenland.

That conclusion is of course tentative because it’s based on only this single genome. Still, based on the sequence, and the tentative phylogeny showing that this individual’s ancestors split off from the ancestors of their closest living relatives (the Chukchis of eastern Siberia) about 5,000 years ago, anthropologists may have to revise their conclusion that there was one invasion of North America from eastern Asia around 18,000 years ago.

Very neat stuff! Though I would like to see a study using modern humans to see how accurate these sorts of predictions are. Take maybe ten individuals with various phenotypes, sequence their genomes, have the researchers try to reconstruct their appearance without previous knowledge of what they look like, send it off to an artist, and see how close we can get! I’m not sure what profound result this would show other than if this method is useful or not – just seems like a really cool thing to try out. Can’t we do science for fun every once in a while?

When art meets biology: Caddisfly jewelry

No, this isn’t jewelry in the shape of a Caddisfly – sorry, entomologists. It’s actually quite stranger than that: the Caddisfly larva are the artists!You need to know a little bit about Caddisfly life history to completely understand what’s going on:

Caddisflies have aquatic larvae and are found in a wide variety of habitats such as streams, rivers, lakes, ponds, spring seeps, and temporary waters (vernal pools). The larvae of many species make protective cases of silk decorated with gravel, sand, twigs or other debris.

They usually look something like this:Then artist Hubert Duprat got an idea:

Having been in the past a naturalist he knew that the larvae are remarkably adaptable: if other suitable materials are introduced into their environment, they will often incorporate those as well. So in the early eighties he started to collect the larvae from their normal environments and took them to his studio. There he gently removed their own natural cases and put them in tanks filled with his own materials, from which they began to build their new protective sheaths. When he began the project, he only provided the caddis larvae with gold flakes. Since then, the larvae have enjoyed various semi-precious and precious stones, including turquoise, coral and lapis lazuli, as well as sapphires, pearls, rubies, and diamonds.

Isn’t that neat? I know some people would be a little grossed out owning jewelry that was once an insect’s armor, but I think it’s pretty cool. Sometimes art created by nature is just as beautiful as art created by a human.(Via sex, art, and politics)

If you could have the answer to any question in science, what would you ask?

This morning I received an email from a professor at Harvard (who’s currently one of my top grad school choices) that she would like to talk to me over the phone sometime this week. After much flailing of happiness, I also had to answer one preliminary question that I enjoyed so much that I had to share it with all of you:

If you could have the answer to any question in biology, what would you ask?

I would have to ask “How did life originate?” It’s probably not particularly original, but it’s simply too fascinating to ignore. We have plenty of hypotheses about the origin of life, but I would love to know exactly which one is correct. What was the biochemical process that slowly took inorganic molecules to the first cell? Are our hypotheses about an RNA world correct? Were there other “life-like” systems totally different than the cells we know today that didn’t withstand the test of time? Could this same process conceivably take place on other planets?

I guess I’m cheating a bit by asking a question that ultimately leads to many more questions, but such is the nature of science, right?

This question isn’t exactly something I would want to personally research – I’m good at chemistry, but not passionate enough about it to devote my whole life to organic and biochem. I still find it very interesting, probably because it’s human nature to wonder “why are we here?” And as an atheist, I’m always looking for the scientific explanation for things. Is there a naturalistic way that life came about on its own? Or are more “creative” ideas involving aliens or gods really true? I doubt the latter, but heck, if that really did happen, I’d want to know!

I suppose in a way it’s tangentially related to my interests in evolution. I often hear people (falsely) claiming that since scientists can’t explain the origin of life, evolution must be false. It would be nice to be able to go, “Um, actually, here’s the natural way life did come to be” and whip out a flowchart from hammerspace. Though I doubt that would convince everyone – we all know how much scientific facts affect most creationists – but at least I’d feel a bit more intellectually fulfilled.

I know everyone here isn’t a biologist, so I’ll propose the question to you a little more vaguely: If you could have the answer to any question in science, what would you ask?

The creationist persecution complex continues

My friend Mike, who blogs over at Politics and Pucks, recently posted a little rant on the conservative and religious environment around Cincinnati, OH. Such a rant cannot be complete without mentioning the Creation Museum, which he did several times. Apparently the Creation Museum is a lot like Beetlejuice – say its name too many times, and one of their representatives will pop up crying “Persecution!” Mike, feel honored that you hurt their feelings enough to get a comment from Mark Looy, co-founder of the Creation Museum:

So the implication is that Bill Cunningham is also a bigot because he supported the Creation Museum after the Cincinnat Zoo — during the Christmas season — stopped its promotional package that offered families a discount to visit both attractions. The zoo yielded to the pressure of dozens of intolerant (often hateful) people who demanded that the zoo stop its ticket partnership with us. And somehow Mr. Cunningham is a bigot for exposing this intolerance and hate? Mark Looy, CCO, Creation Museum, Petersburg, Kentucky

Dear Mark Looy and other Creationists who Just Don’t Get It,

I am tolerant of your outright lies and delusions in the sense that I will never threaten you or your families and I support your right to freedom of speech. Shame on anyone who has done so, atheist or not. However, tolerance does not equal respect or support, which you have to earn.

Your museum (which I had the misfortune of visiting) is a complete sham and an insult to human intelligence, reason, and curiosity. Having a place that supports learning and scientific inquiry even associate itself with you is totally inappropriate. The Cincinnati Zoo should not support the Creation Museum, a World War II museum should not support Holocaust deniers, and an Astronomical Observatory should not support flat Earthers. You are absolutely no different from these wacky fringe groups. Freedom of religion does not mean we have to think you’re awesome and suck up to you.

Until you realize this, I have every right to point and laugh at you, just as you have every right to put dinosaurs munching alongside Adam and Eve. Crying about how you’re a victim and those godless scientists are the real meanies is only going to continue making you the laughing stock of America.

Sincerely,

Godless Scientist Meanie

The Endangered Species Print Project

I just found out about a really neat project used to raise awareness and funding for endangered species: The Endangered Species Print Project.

The Endangered Species Print Project offers limited-edition art prints of critically endangered species. The number of prints available corresponds with the remaining animal or plant populations. For example, only 45 Amur Leopards remain in the wild, so for this edition, only 45 prints will ever be made. A different organization, whose mission is to the ensure the survival of the species depicted, is chosen for each print. 100% of the sales of ESPP prints are donated to these conservation organizations.

As both an artist and a biologist, I think this is an excellent idea. If your walls are looking a bit bland and you have a little extra money, consider contributing to this great cause. The also have a corresponding blog where you can keep up with information about endangered species.

(Via bioephemera)

No G-Spots?! …Wait, what?

If you have the same taste in blogs that I do (aka you’re obsessed with sex), you’ve probably been inundated with posts about how a new study has proven that G-spots don’t exist!

The scientists at King’s College London who carried out the study claim there is no evidence for the existence of the G-spot — supposedly a cluster of internal nerve endings — outside the imagination of women influenced by magazines and sex therapists. They reached their conclusions after a survey of more than 1,800 British women.

Well, I’ll be damned. I was fairly certain from personal experience that G-spots do exist, but I can’t argue with scientists, can I? They must have carefully inspected all 1,800 of those British women (what a lucky grad student!), right?

In the research, 1,804 British women aged 23-83 answered questionnaires. All were pairs of identical or non-identical twins. Identical twins share all their genes, while non-identical pairs share 50% of theirs. If one identical twin reported having a G-spot, this would make it far more likely that her sister would give the same answer. But no such pattern emerged, suggesting the G-spot is a matter of the woman’s subjective opinion.

And what was that questionnaire? Just a single question:

“Do you believe you have a so called G spot, a small areas the size of a 20p coin on the front wall of your vagina that is sensitive to deep pressure?”

…Alright boys and girls, it’s time for a lesson on why this is “Bad Science.”

Questionnaires are always a bit subjective and iffy – especially when asking someone about their anatomy. If you ask people how many chambers their heart has, and some say 3, that doesn’t mean they’re actually missing a chamber. Simply asking people if they have a G-spot doesn’t confirm it’s existence or lack thereof. I can’t believe that this study would rely on opinion rather than medically examining females to see if it is there or not.

The fact that they didn’t see any correlation in identical twins just illustrates that personal opinion about the existence of a G-spot is not genetically determined. Their initial logic that genetically identical twins should have identical sexual responses is flawed. Sexual response has a huge environmental component, which the study finds but apparently ignores:

While 56% of women overall claimed to have a G-spot, they tended to be younger and more sexually active.

That makes perfect sense. Finding the G-spot isn’t easy. It usually takes a patient partner, sex positions other than missionary, or specialized sex toys – all of which are more likely to be found in younger, sexually active people. What’s more likely: that these women are partaking in activities that make them more likely to find their G-spot, or that the majority of women are all delusional about a specific area that causes intense pleasure? I don’t know about you, but if I’m going to hallucinate a pleasure button, I’m going to put it somewhere I little easier to reach.

A quote from the researcher also sends up a red flag for me:

Andrea Burri, who led the research, said she was anxious to remove feelings of “inadequacy or underachievement” that might affect women who feared they lacked a G-spot.

Yep, it’s always great to go into research with an agenda and preconceived result in mind!

This all may be the result of bad science reporting, which is always a likely cause, since the actual paper is coming out next week. I’ll look forward to reading it and seeing if it’s also so strident in its claims.

The joys of parents learning science

We’re always hearing stories about kids making skeptical insights or getting interested in science. They’re exciting because these kids are our future, and maybe we see a bit of our nerdy selves in them. I don’t have kids, but I still get excited about something similar – parents learning science.

My parents have always been very pro-science. They always encouraged me in my science classes and Science Olympiad, and were elated when I decided to major in genetics. However, they’re not particularly science oriented. My dad was a history and special ed teacher, and my mom was an art teacher. My dad is into politics and sports, and my mom is obsessed with decorating and traveling. They treat science how rational people should – scientists are experts in a certain area, and even though my parents don’t personally understand the topics, they put their faith in scientists. It’s no different than putting faith in a mechanic or a pilot – everyone has their specialty, and we can’t know everything. They don’t believe that evolution and global warming are just giant conspiracies precisely orchestrated by hundreds and hundreds of evil scientists. Just because they personally don’t have the background to interpret the data doesn’t render it false (if only creationists could understand this simple concept).

We’re all intelligent, but in different areas – and sometimes that causes problems. The more I study biology, the less in common we have to talk about when I come home. Usually conversations consist of my dad rambling about some history book he’s reading and me trying to keep my eyes from glazing over. But this time I had a plan. I brought home Why Evolution is True by Jerry Coyne (who also has an excellent blog). My dad will read science books if given them (he loved Guns, Germs, and Steel and Hot, Flat, and Crowded), and I figured this time I can kill two birds with one stone: Get my dad to learn more about my interests, and get him to ramble about something I’m actually interested in.

Success!

It’s only been a day and he’s halfway done. He says he loves it and that it does a great job of explaining concepts to a non-scientist. He’s keeping a little notepad nearby so he can write down especially awesome facts to share with me, or questions to ask me so I can clarify. There’s just something really cool about my dad running up and ranting, suddenly realizing the frustrating creationist logic I have to constantly deal with.

Dad: How do people deal with the fact that 99% of all species that have existed are extinct? Why would God design things to all die? That doesn’t seem very intelligent to me.
Me: God works in mysterious ways *wink*

Dad: We have fossils! What more proof do they need?
Me: Satan buried them there to test your faith. That or the scientists made it all up.

Dad: Now he’s talking about examples of unintelligent design. Did you know women have painful childbirth because we evolved from four legged ancestors?
Me: I thought it was because God was punishing Eve.

Playing the devil’s advocate is fun. My dad knows I’m an atheist, and he’s not religious at all either, so it’s all for laughs. But it’s great seeing him react to all the religious “arguments” that I have heard people seriously make. Not only that, but it mirrors how my dad instilled good skeptical thinking in me. I’d often ask questions (How did they get the squirrels to talk in that commercial? It has to be a computer) and he would reply with a ridiculous answer (Squirrels just talk when you’re not looking). I would then go about explaining why that was silly, and logical thinking was developed!

I look forward to his future comments and questions as he finishes the book. Then my mom is going to take a crack at it! Soon the whole family will be well-read evolutionists, mwahaha!

An eerie resemblance

Brought to you by the same relatives who produced the best blasphemous birthday gifts, I now show you my new awesome Christmas gift:Look familiar? I’ll help you out:Yep. Chris and Erin got me the same awesome, soft, cuddly, adorable octopus plushie from the PZ photo. And it wasn’t a coincidence – they got it because they know I love PZ’s blog and would know the photo.

The funny part is when I walked in and saw an octopus plushie under the tree I exclaimed, “Man, I want that!” thinking it was for my nephews (since 99% of the presents were for them, naturally). At the time I didn’t recognize exactly which exact plushie it was, since it was upside down and half buried by the twins’ toys. Later on I was telling Erin how awesome it was, and she went “Well good, because it’s for you!” Yaaaay!

Nothing makes a better pillow than a cephalopod. Well, maybe a kangaroo rat…

Flip a switch; become a dude!

Okay, so it’s not exactly that simple; but researchers have found a gene that keeps females being…well, female. FOXL2, which was known to be involved with ovary growth, apparently keeps a woman’s body from turning into a man. Switch off FOXL2, and ovaries will start turning into testes and testosterone-producing cells will develop. Just think what this says about the human gender binary, or future less invasive methods for people undergoing gender reassignment.

*obligatory SCIENCE IS COOL flailing*

Sorry, that’s all the commentary you get, since my tonsils currently feel like they’re turning into…uh…inflamed…spikey…polka-dotted sadness*. Which I guess is better than testicles? Check out the article for a more detailed explanation, or for the genetically-inclined, read the original paper here.

*My wit fails me when I don’t feel well. I apologize.