Hi! I’m alive! After not posting for so long, I figured I probably should start with that.
As you all probably (hopefully) are aware, there’s a little thing called coronavirus going around. I live in the Bay Area now*, which means I currently can’t leave my house except for essential stuff like groceries and medical care. So how do I choose to cope?
Tune in at 6pm PST tonight to come hang out and watch me play…probably Overwatch? Does it even matter? The world seems like it’s ending and I just need some people to shoot the shit with. But in the future you can expect games like Stardew Valley, Civ6, XCOM2, and Crusader Kings 2 (maybe with the Game of Thrones mod?).
I have also been pretty active on Twitter still, if you want to follow me there.
Even if you don’t join me on Twitch or Twitter, take care, wash your hands, and STAY THE FUCK HOME.
*Since my last post I received my PhD, moved to Silicon Valley, have been managing 23andMe’s science communication program for 2.5 years, and got engaged. You know, just some minor things!
There’s this old Greek woman and her stocky son who live on our corner who remind me of my Yia Yia and Uncle, especially since she has this beautiful garden that he’s always tending to for her. Her house is on the way to the coffee shop I’ve been writing my thesis at a lot, so frequently I pass by and see the old woman sitting on her porch, especially now that the weather is getting nicer.
I can’t help but smile at her when I go by since they remind me of my family. She always smiled back, and our smiles have upgraded to smiles and waves. When I walked by this morning, she said to her son “That’s the smile lady!”
I’m glad I could brighten her mornings enough that she’d tell her son just from a smile. But at the same time, I think of the hundreds of other people who must walk by her and not even notice she’s there, and that it’s kind of sad that I’m notable because I just smile her way.
Called my grandparents after that.
My talk on how we can learn what makes us human from genetics and evolution is now online! I hope you enjoy it.
Thanks for not only remembering my website, but actually visiting it! I guess that must mean you were at least vaguely intrigued or entertained by my talk, so hooray! If you’d like to check out some of my favorite science communication pieces from the past, I’ve compiled a little list of favorites for your viewing pleasure:
- Skeptical Genetics – debunking common misconceptions people have about genetics
- When Dinosaurs Walk With God: A Godless Biologist’s Trip to the Creation Museum
- PokeBiology 101 – What can the fictional world of Pokemon teach us about real biology?
And if you’d like to know more specifics about what I actually study instead of just the vague research field, I have 4 short posts that explain the wonderful world of microRNA [1, 2, 3, 4]. I hope you’ll stick around for more science ramblings in the future!
I know I’ve been in a blog/speaking hibernation for a while – grad school can do that to you. But I’m happy to announce that I’ll be coming out of my cave to give a talk about my research at Town Hall Seattle this Monday, May 11. This talk is specifically tailored for non-biologists and will not be overly technical or jargony – at least, that’s my goal! Here are the details for all of you locals:
What Makes Us Human: Decoding Our DNA
“What makes us human? Scientists and philosophers have been asking the question for years. This age-old query is also the subject of UW genome sciences student Jennifer McCreight’s research. She’ll compare the DNA of humans to chimpanzees, monkeys, and lemurs, sharing how genetic differences help paint a picture of how Homo sapiens walk, talk, and have larger brains.”
6:00PM, Monday, May 11, 2015
Downstairs at Town Hall
$5, UW students (with Husky card) get in for free.
Double feature with Leonard Mlodinow’s talk “The Evolution of Scientific Discovery” at 7:30pm.This event is part of the University of Washington’s Engage program, which teaches effective communication skills to scientists who may not otherwise receive that training. I absolutely loved the class and recommend it to all UW grad students, and I’m excited that it gave me the opportunity to speak at Town Hall.
Please spread the word, and I hope to see you there!
A federal judge has struck down Indiana’s same-sex marriage ban, and couples can marry right now. I know I should probably have something more eloquent to say as an escapee Hoosier who’s a huge LGBT rights activist, but all I can come up with is:
I think that’ll do.
Not good, and worse because I’m a woman.
Now, I’ve known that for a long time. But it’s not until today that I could see a number representing just how lousy my odds are. In a paper published in Current Biology, three scientists were able to take citation data from PubMed to calculate your odds of becoming a PI (Principal Investigator, or in layman’s terms, a professor who is the head of a research lab). They built a statistical model that took into account how various factors – number of publications, highest number of citations on a paper, gender – affected your chances, which you can figure out using their app.
My current odds of becoming a PI are 14%, but they’d be 26% if I were male. If I publish at least two first author papers before I graduate (a reasonable assumption), my odds go up to 23% (still not as much as a male scientist with my current status), while a man would have 34% chance.
Just to give these numbers some perspective, they’d be depressing even without the glaring gender differences. Most grad students nearing their defense are going to have odds around mine; some better, some worse. I have three papers (one first author), they’re in average journals and have almost no citations (hey, kangaroo rat copulatory plug genetics is a pretty niche field, ok?). I’m pretty average when it comes to the variables that affect your chances. And our odds are still crummy. Or at the Onion put it in “New STEM Education Initiative Inspires Girls To Earn Less Than Men In Scientific Career,”
“”Today’s girls have the potential to become the physicists and chemists of tomorrow, powerlessly watching as their male counterparts are promoted over them, their intellects are ignored, and their research is underrepresented in scientific journals. Our mission is to let every young woman know that such a future isn’t a fantasy; it’s a reality they can most certainly achieve.” Grant admitted, however, that such opportunities depended upon the slim chance that these girls even managed to be hired from a predominantly male applicant pool in the first place.”
It’s not often that my day job as a geneticist overlaps with my love for video games, but that’s exactly what’s happening in the new Sid Meier’s Civilization: Beyond Earth. In early interviews about this sci-fi edition of the Civ series, it seemed like genetic engineering would play a large part in shaping your space colony’s future. As a genetics grad student and a Civ superfan (I’m not sure if I should feel guilty or proud when Steam tells me the number of hours I’ve played), I was itching for more information. I was lucky enough to interview Co-Lead Designers Will Miller and David McDonough about what role genetics will be playing in Beyond Earth.
Q: Civilization: Beyond Earth has been called the “spiritual successor” to Sid Meier’s Alpha Centauri. In Alpha Centauri, one of the first techs you can research is Biogenetics, which enables you to make the Human Genome Project. Co-lead designer David McDonough mentioned, “When you start the game, you’re not really that far from where we are today.” What real life biological research inspired some of the genetic techs we will see early in the game?
A: There’s more than one piece of biological research that’s been an inspiration to us, going all the way back to the cloning of Dolly the sheep. But growing human organs in pigs and other transgenetic medicine and biocompatibility developments have been particularly interesting to us. The recent developments in custom-designed viruses as weapons for medical sciences – is incredibly fascinating to us. For example, the genetically engineered measles that selectively kill cancer cells as is the idea of taking something that is bad for us and turning it into something that has a positive result. Selectively infecting mosquitos with a disease that prevents them from developing the saliva necessary to transmit dengue fever is another example of research we find fascinating. We think the most interesting research has been channeling forces that are at best neutral (and mostly harmful) and turning them into things that are helpful to us.
Q: Alpha Centauri was released in 1999, and the Human Genome Project was completed in 2003. While still incredibly useful to scientists, we consider the HGP old news. Are there any technologies in Beyond Earth that are currently science fiction, but you believe may become reality in the next decade?
A: The tech that we most hope gets adopted in the next decade is the thorium reactor, which is a building that you unlock through the Engineering technology. Dave McDonough in particular will talk your ear off about its many upsides and how it has potential to revolutionize our power. So please don’t ask him about thorium reactors in the next decade or we won’t have time to finish this interview.
Q: Were there any particular books, movies, or TV shows that shaped how you treat genetics in the game?
A: Slant by Greg Bear is a great source, taking the theme of genetic manipulation as form of fashion, and science as a plaything as our vanity. Older and darker but also important is the graphic novel series Transmetropolitan, which has some absolutely fascinating ideas in it, not only about biology but about the future more generally.
Q: One of the most memorable characters from Alpha Centauri is the leader of University of Planet. Can we expect to see another scientist leading a Faction in Beyond Earth?
A: Yes! Daoming Sochua is the leader of the Pan-Asian Cooperative. She’s a certifiable genius with a quad Ph.D. in nanoelectronics, nuclear physics, bubble physics, and electrical engineering. That last degree was a lagniappe from working on the other three. In addition to her formidable research skills, she’s also a talented administrator. While defending her theses, her committee became acutely aware of their impending obsolescence.
Q: Could you tell me more about the new “Gene Vault” wonder? Are there other genetics-themed buildings or wonders available to players?
A: There are quite a few Wonders based around genetics, and Gene Vault is the earliest of these, as well as the Stonehenge of the new planets. The Gene Vault is a Svalbard for the new world – a massive, secure repository of the genetic library the settlers bring with them to their new planet. Think about how incredibly important this library would be for space colonists! The Gene Vault is also important because it represents a strong link back to the aspirations and hopes of Old Earth.
Q: One major feature of Beyond Earth is the three affinities: Harmony, Purity, and Supremacy. Harmony specializes in embracing the alien planet, and will “allow the planet to change them right down to their very own DNA.” Will other affinities utilize genetic manipulation, or will this be specific to Harmony?
A: All three affinities would have their own take on genetic manipulation. A Purity civ, for example, would probably find genetic manipulation perfect for eliminating genetic disorders like Huntington’s or other disorders with a strong hereditable component. A Supremacy civ would see it as another tool in the proverbial toolbox of adaptive technologies, although they’d be more likely to point out that it’s a lot easier to update firmware than nucleotides. But in the end they see everything as code that can be reprogrammed.
Q: Harmony also allows you to get “alien creatures on your team and breed new units based on their genes.” Can you tell me more about how this breeding system will work?
A: Right now these are units that are unlocked by researching Harmony-affiliated techs. The notion of breeding is reflected in the fact that these units are not identical to those you find wandering out in the world.
Q: What is Harmony’s relationship with the alien life like? Is it a mindless swarm doing the bidding of their leaders like the Zerg, a symbiotic beneficial relationship like Avatar, or something completely different?
A: Harmony can have any relationship towards the planet’s native life, and in fact, part of the Harmony approach usually means clearing out nearby alien nests as part of your own city development. Preserving humanity is usually an overriding priority over preserving the planet! A Harmony civ will be trying to change humanity to be a better biological match to the world, but that doesn’t mean rejecting technology or ignoring existential threats – the world will certainly need to be changed a bit to accommodate the Harmony civ. They’re just less interested in radically changing the world than Purity, or rejecting the environment entirely like Supremacy.
It’s also not true that a Harmony civ is inherently more peaceful than any other civ. An aggressive Harmony civ is a tidal wave of mandibles and chitin directed consciously at its enemies.
Q: In Firaxis’s other incredibly popular game X-COM: Enemy Within, you have the ability to give your soldiers various abilities through genetic engineering. Will this be an option in Beyond Earth’s new Unit Upgrade system?
A: Yes! In fact, certain upgrades are tied specifically to your Affinity, and require a certain devotion to your affinity in order to unlock. This helps differentiate the Affinities and their approach to combat.
Q: McDonough has mentioned that most of the game’s technology will be realistic/plausible, but by the end you’ll see “pretty fun wild crazy things, very fictitious stuff.” Can you hint at any crazy genetic technologies you may unlock? Should I be looking forward to an “X-Gene” that enables my soldiers to shoot laser beams from their eyes or read minds?
A: Artificial Evolution is probably the most out-there genetics tech, and it’s got some impressive leaf techs underneath it (aggressive Harmony players, this is one tech to aim for). It won’t do anything for your soldiers per se, but keep in mind that your soldiers are only one part of your arsenal.
Q: Genetics is already a divisive topic in our world, with many differing opinions on the ethics of GMOs, personalized genomics and medicine, and “designer babies.” Will this division play out in Beyond Earth? For example, am I going to get a diplomatic penalty with Purity aligned Factions if I decide to make an army of mutant super soldiers?
A: Yes, but it will be predominately because you as a Harmony civ (which I’m assuming here) will have a wildly different vision for the planet than the Purity civ. You will want people to live more comfortably on the planet by changing people, and the other civ will feel the planet needs to be turned into a new Earth. However, you can still go heavily into genetic techs and focus on Purity as your affinity, and so you may have more in common with that other Purity civ than you might expect.
Q: Religion in Alpha Centauri was limited to a few Factions. But in Beyond Earth it seems that everyone will have access to religion, suggesting it will be more customizable like in Civ 5. Will we have the ability to make a religion centered around genetic engineering or opposed to it?
A: We’re not looking at implementing specific religious themes or proscriptions. Certainly you can think of the Affinities as being sort of larger meta-philosophies in terms of how they perceive the best path for humanity going forward, and as you increase in your devotion to an Affinity you’re making a conscious rejection of the other two. Whether or not that rises to the level of “thou shalt not” for your people is up to the player.
Q: In Alpha Centauri, the player was able to engage in genetic warfare that would reduce the population of a city by half and greatly damage military units in the city. Will genetics or biological warfare play a role in combat or as part of the new espionage system?
A: Biological warfare is something that’s hard to feel good about, as a player. We were trying for a more optimistic tone with Beyond Earth, and not browbeat players for the choices they make in the course of the game. Designer plagues don’t really fit the tone we’re trying to achieve.
Q: Sci-fi books and video games frequently have a dystopian view of genetics that can disappoint researchers who see a lot of good coming out of their field. What sort of philosophy did you take when addressing the role of genetics in Beyond Earth? Are you going to leave the morality up to the player? For example, will a Harmony aligned Faction be able to make choices that allow them to play as a utopian society that’s free of disease, a dystopian society with genetic classes like Gattaca, or some ethical gray area in between?
A: The approach to the technologies in the game was driven by a larger approach we take in design which is: players should feel like the decisions they’ve made were positive ones. We don’t want players to make a choice and then immediately regret it because of something the game says. Now, consequences as a result of those decisions – that’s perfectly appropriate! So to that end, we’ll let players decide what the moral valence of their choices should be.
Q: How do you think your job as game developers affects public perception of science? For example, Carl Sagan’s Contact greatly inspired me to fall in love with science and become a scientist, and clearly had an impact on Beyond Earth since it is effectively one of the victory conditions. Do you see Beyond Earth as playing a similar role in inspiring others to appreciate science?
A: We’re not setting out to give a science lesson in Beyond Earth, although we do like to think we’ve paid attention to actual science and our speculative courses are at least plausible. If someone experiences something in the game and then says: “Gee, I wish I knew more about these ‘thorium reactors,’” and they go out and educate themselves, then we’re incredibly happy and proud. Sid always says that people like to learn, and there are plenty of opportunities to dig into the science behind the game here. We also do a lot of research after the game gets made, so we’ll keep reading up on science long after the game ships.
I’m currently watching Star Trek: The Next Generation for the first time (just started season 6). I know, I know – how did a nerd like me miss the boat? Part of it was the fact that I was born the same year the series started, so you’ll have to excuse my past baby self for not tuning in. I’m also the only person in my family who likes sci-fi, so I wasn’t exposed to it there. But frankly, I avoided Star Trek for a long time because I thought it was the world of asocial uber-nerds who liked to blow up stuff with phasers and fabricate technobabble to pretend to be scientific. However, when a friend of mine told me that it was one of the best SciFi series ever, I had to watch it.
First of all, the science on the show is fantastic overall. There are so many moments where I find myself thinking as a biologist, “Hey, yeah, that’s completely plausible!” You can imagine my glee when it was revealed that a Klingon spy was managing to sneak messages past the transporter’s filters by encoding them as amino acid sequences.
I also can’t stop thinking how damn progressive the show is, especially when I remember it was made over two decades ago. I had no idea that an integral part of every episode is discussing ethics, humanism, and social justice. Or that half the scenes would be in meetings, trials, or diplomacy. To me, one of the most striking example of the show’s progressive values is the relationship between Will Riker and Deanna Troi. I swear they have the most supportive, healthy fuckbuddy relationship that I’ve ever seen on television.
But of course, there are some things in the show that bug me. I think this is inevitable when dealing with speculative sci-fi, since there are always some consequences of technology that writers don’t immediately thing about. Thankfully nitpicking these conundrums seems to be an essential part of being a Star Trek fan, so I have to get these off my chest:
- Why doesn’t anyone on the Enterprise wear gloves? If this has a simple explanation like “the ship generates an invisible glove force field when required,” please tell me. Because right now, every time Dr. Crusher touches a patient with some horrible alien disease, or Geordi handles some hazardous substance in the cargo bay, or someone touches a piece of evidence with bare hands, the scientist in me dies a little.
- Why does everyone conveniently ignore the curative power of the transporter? When Dr. Pulaski is rapidly aged by an antibody that alters her DNA, the crew uses her old genome sequence as a filter in the transporter to transport her back in her previous state. No one mentions that they’ve come up with a cure to all cancer, but perhaps that’s because by the 24th century, cancer has already been cured in a different way. But they’ve also cured aging – just use an old transporter scan and you’ll keep being loaded as your 25 year old self.
- How is Lt. Broccoli – sorry, Barclay – able to see and grab creatures in the energy stream during transport? If every molecule in your body is being turned into energy…how is sight or movement possible?
- Why doesn’t anyone on the Enterprise seem to have any sense of urgency? I swear it took a couple of seasons to see anyone break into a light jog, let alone a run. I don’t know how many scenes I’ve watched where Worf and his security team casually walk to part of a ship to apprehend a dangerous alien/crew member/what have you. You think they’d be liberally using the transporter. You think you’re going to get away? BAM, Worf just teleported right in front of you! Or better yet, we teleported you to a holding cell.
- When Geordi and Ensign Ro are believed to be dead but they’re actually on the Enterprise out of phase, at the end of the episode Geordi is ravenous because they haven’t eaten in two days. So we know even though they’re out of phase, they’re still having normal bodily functions. …So where did they poop during these two days? I know it’s not the most important question in the Star Trek universe, but knowing there’s phased poop hidden on the Enterprise fills me with endless mirth.
- But the most baffling thing of all…why the hell does Synthehol exist? Why would you keep the awful taste of alcohol and get rid of the main point of drinking it, the intoxicating effects? If there’s anything in Star Trek that makes it hard for me to suspend disbelief, it’s this.
You know I had to start my Pokébiology 101 series with the most famously scientifically inaccurate part of Pokémon: evolution.
In the Pokémon world, “evolution” means something different from what you might have learned in your biology classes. …Well, what you should have learned in your biology classes, assuming the religious right failed to push their agenda into your science classroom. Pokémon evolution is when a Pokémon transforms into a different looking creature once some criterion is met. Most often this means reaching a certain level (levels increase as you gain experience, experience comes from participating in battles). Some Pokémon evolve under weirder circumstances like being exposed to a particular item, being traded to another player, reaching a certain level of happiness, and so on.
For example, a Bulbasaur evolves into an Ivysaur at level 16, and an Ivysaur evolves into a Venusaur at level 32.
This is not evolution. This is metamorphosis.
What’s the difference? Why are Pokémon actually metamorphosing, and not evolving? They both imply some sort of change is taking place, which is why the terms are so easily confused. But there’s a major difference in when and where that change happens:
- Metamorphosis is the change in body structure of an individual that happens conspicuously and abruptly during their lifetime. The most common real world example is a caterpillar turning into a butterfly. This is exactly what happens in the Pokémon world. Well, instead of forming a cocoon, Pokémon flash a bright light and make cheery beeping noises…but I’m going to chalk that up to the games being from the point of view of a ten year old with an overactive imagination. Wee, shiny!
- Evolution is the change in heritable characteristics of a population over successive generations. A characteristic is heritable if it is genetic, and thus will get passed on from parent to offspring, and from that offspring to its offspring, and so on. The key here is that this change happens over many generations and affects the whole population.
What would be a hypothetical example of actual evolution in the Pokémon world? Let’s say we’ve stumbled upon a population of Venusaurs in some jungle untouched by Pokémon trainers. Most Venusaurs have pink flowers, but a rare individual has a gold flower because of a mutation. In case you’re wondering, this alternative color scheme exists in-game and is known as a “shiny,” and shiny Pokémon are incredibly rare. Like, “I’ve probably played 1000 cumulative hours of Pokémon games and I only found one shiny Sentret a decade ago” rare.
Now, let’s say that shiny Venusaur is very successful in producing a lot of baby Bulbasaurs for whatever reason. Maybe gold flowers attract more prey, so shiny Venusaur is well fed and can have more babies (directional selection). Maybe other Venusaurs find the rare gold flower extra sexy, so shiny Venusaur has more mates and thus more babies (sexual selection). Maybe it’s all due to random chance and shiny Venusaur just gets lucky (genetic drift). When that generation of Bulbasaurs grows up, the new generation of Venusaurs might look something like this:
If we’re still around to observe this population many generations later, it may look like this:
The shiny trait has now become “fixed” in the population – that is, every individual now has the gold flower. Now the population of Venusaurs looks different than it used to – and that is evolution! If this population is isolated from other Venusaurs and continues to evolve novel traits, one day this population might be so different that it can’t even mate with other Venusaurs anymore. And that, folks, is when you have a new species.
But back to metamorphosis. The common caterpillar example is linear: a caterpillar makes a cocoon and becomes a butterfly. But not all Pokémon have a set fate. I give you the most enigmatic example, Eevee.
Eevee is special in the world of Pokémon because it has the largest number of ways it can evolve depending on your actions. Want a Flareon? Give Eevee a Fire Stone. Espeon? Make Eevee very happy and level up during the morning or day. Leafeon? Level up while near a mossy rock.
It seems like this couldn’t possibly exist within the confines of our natural world, right? How does an Eevee have the ability to metamorphose into such different creatures just from what its exposed to in the environment? How can a Vaporeon, Jolteon, Flareon, Espeon, Umbreon, Glaceon, and Leafeon all have the same genome as their starting Eevee, but such different traits?
Not to erode Eevee’s specialness, but this happens right here on Earth.
This is known as polyphenism: when multiple discrete phenotypes (a set of observable characteristics) can come from the same genetic background because of differences in the environment. The most common example is different castes in bees. You may know that within a hive, one female gets to be the queen bee, and the other females are worker bees. A queen bee is made by feeding a larvae what’s known as “royal jelly,” which contains chemicals that alter the larvae’s development. If that larvae has a twin sister that didn’t get a special meal, sis will grow up to be a worker. They’re genetically identical, but very different thanks to their environment.
The only thing distinguishing bees from Eevees are the number of choices in development.
In which I speculate on what would happen if you gave a bee a Fire Stone or Macho Brace.
It will forever irritate me that the game designers chose the term “evolution” instead of a totally accurate, also cool-sounding alternative word. My best guess is that “Bulbasaur is metamorphosing” took up too many pixels, so “evolving” won out. Sadly, this kind of sloppy terminology can cause a lot of misconceptions about what evolution really means. But hopefully now that you’ve learned some Pokébiology, you’re less confused.
…I’m trying to decipher mysterious comments I left in an old piece of code. Comments that made perfect sense a couple of months ago and that were painstakingly written so they would still be clear in the future, which still despite all that end up being completely nonsensical.