Paleofantasy: When people act like cavemen because they misunderstand evolution

I’ve been waiting so long for someone to write this book.

Salon has a great interview with Marlene Zuk, evolutionary biologist who just wrote “Paleofantasy: What evolution really tells us about sex, diet, and how we live.” The Paleo diet? How evolution surprisingly supports 1950s gender roles? Yeah, those ideas aren’t actually supported by evolution after all – something that should come as no surprise to my readers.

It is striking how fixated on the alleged behavior of our hunting-and-foraging forbearers some educated inhabitants of the developed world have become. Among the most obsessed are those who insist, as Zuk summarizes, that “our bodies and minds evolved under a particular set of circumstances, and in changing those circumstances without allowing our bodies time to evolve in response, we have wreaked the havoc that is modern life.” Not only would we be happier and healthier if we lived like “cavemen,” this philosophy dictates, but “we are good at things we had to do back in the Pleistocene … and bad at things we didn’t.”

The most persuasive argument Zuk marshals against such views has to do with the potential for relatively rapid evolution, major changes that can appear over a time as short as, or even shorter than, the 10,000 years Cordain scoffed at. [...]

There are human examples, as well, such as “lactase persistence” (the ability in adults to digest the sugar in cow’s milk), a trait possessed by about 35 percent of the world’s population — and growing, since the gene determining it is dominant. Geneticists estimate that this ability emerged anywhere from 2200 to 20,000 years ago, but since the habit of drinking cow’s milk presumably arose after cattle were domesticated around 7000 years ago, the more recent dates are the most likely. In a similar, if nondietary, example, “Blue eyes were virtually unknown as little as 6000 to 10,000 years ago,” while now they are quite common. A lot can change in 10,000 years.

Read the whole piece, as it’s a great summary of why these sort of standard evolutionary psychology arguments are so flawed.

Now, I do think evolutionary psychology has a lot of potential. Obviously the brain evolves like any other organ, which has fascinating effects on behavior. But the field is in its infancy, and is currently propped up on arm chair speculation and frequently unfalsifiable claims (claims that are impossible to prove wrong).

My favorite example of this comes from the Evolutionary Psychology class I took in undergrad. Now, I was originally super excited about this class. As someone who was interested in human evolution, behavior, and sex, I thought that evolutionary psychology was my calling. That was until we got to a specific lecture on human sexuality. We were discussing a study that was investigating patterns of human promiscuity, and the professor asked us to come up evolutionary explanations to describe the data we could potentially see. Most people came up with something along the lines of “Female humans will not be promiscuous because pregnancy has more cost to them and they need a monogamous mate to help rear the child, where men will be very promiscuous  because they want to spread their seed as much as possible.”

I’m sure you’ve all heard that argument somewhere before. But I presented an alternative hypothesis: “Female humans have cryptic fertility – it’s hard to tell when they’re ovulating – so they will be equally promiscuous, because then no man will know if the child is theirs so they will all pitch in to help rear the child.” I presented this idea because evolutionary psychology often looks to primitive tribes for its hypotheses, and we see my scenario happening in many tribes of South America.

My professor nodded and said that was a good alternative explanation. I asked how we would be able to distinguish between the two hypotheses, but he didn’t seem to understand why that mattered. He saw evolutionary psychology as being able to explain either situation, so in his mind it only supported the field of evolutionary psychology because it was able to explain anything!

But the ability to come up with an explanation for anything is not what makes something scientific. Creationism can come up with an explanation for anything – “God did it” – and that is not scientific. To be scientific you need your predictions to be falsifiable, and unfortunately right now evolutionary psychology is closer to creationism than it is evolutionary biology.

Like I said, evolutionary psychology has a lot of potential because the brain evolves. But I think we need to establish a much larger base of information before we can even remotely accurately interpret data. We need to understand the staggering complexity of the brain and the genomic contribution to that complexity before we can really start investigating what’s going on, and even then it will not be as simple as thinking “What would cavemen do?”

Pokébiology 101: “Evolution” and the enigma of Eevee

PokebiologySmall

(Click here for the introductory post to Pokébiology 101)

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.

BulbasaurEvolution

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.

shinyven1

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:

shinyven2

If we’re still around to observe this population many generations later, it may look like this:

shinyven3

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-evolutions

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.

eeveebee2

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.

EvolveMankey

 

So confused.

Welcome to Pokébiology 101

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Hello there! Welcome to the world of Pokémon! My name is Jen! People call me the Pokémon Grad Student!

…Okay, I don’t think anyone has actually called me the Pokémon Grad Student. But I’m a PhD candidate studying evolution and genomics who has been playing Pokémon since its release in 1998. My friend showed me his Red version, and soon after I owned my first video game – Pokémon Blue. I’ve been hooked since then.

As I progressed through my training as a biologist, I started to look at the Pokémon world in a new light. At first, it was irritation. Everything seemed wrong. They confused metamorphosis for evolution. Breeding didn’t make any sense – different Pokémon species could interbreed, but the offspring were always the same species as mom. Gender ratios didn’t reflect biological mechanisms, but rather a game designer’s attempt to keep certain Pokémon rare. Why, it was if they were trying to design a fun game with no regard to biological accuracy

Darwin_fefc90_728208

darwin heart piplup by claudetc

But as I learned more biology, I started to realize nature isn’t as simple as it seems. There are all sorts of strange biological phenomena that result in counter-intuitive mechanisms, traits, and organisms. Nature is really, really weird. So I started viewing the Pokémon world as a puzzle. If I were Professor Oak, what experiments would I be doing? Are there any natural processes in the real world that could explain Pokémon biology?

Bulbasaur Anatomical Study by JoshuaDunlop

Some of you must be thinking, “Jen, it’s just a game. It’s not supposed to make sense. Chill.” I know, I know. I don’t expect all games to be 100% scientifically accurate at the expense of fun. But I like daydreaming about how the biology of Pokémon could “work.” It’s as if I’ve discovered a whole planet of alien life to study, and what biologist wouldn’t want that?

But more importantly, I see the Pokémon world as a great way to teach people about actual biology. And I’m hardly the first person to think this – the creator of Pokémon originally conceived of the game as a way to share his childhood hobby of collecting insects with the children of a modern, urbanized Japan. But I’ll be discussing what I know best: evolution and genomics. How do Pokémon species differ from species here on Earth? What does genomic imprinting have to do with breeding? Can an organism like Eevee actually exist? I’ll be exploring these topics in future PokéBiology 101 posts.

Now, there are some things in the Pokémon Universe that are above my pay grade. I’m not even going to attempt to explain how a tiny mouse generates thunderstorms or how some Pokémon have psychic abilities. I have no clue how a Pokéball can transform Pokémon into pure energy and back again (maybe a bored Physics grad student can hazard a guess). And there’s certainly no explanation for how Onix, a ground/rock type, suddenly becomes vulnerable to electric attacks because a sprinkler system came on (yes, I am still bitter about that episode).

pokeball

 I have no idea how this works.

For all of those things, I’m willing to suspend disbelief. But when it comes to the biology of the Pokémon world, I’ve found it’s not necessary to invoke “magic!” as an explanation. Because oddly enough, that bizarre biology is already happening here on earth.

Welcome to PokéBiology 101!

Next in series: “Evolution” and the enigma of Eevee

Republican lawmaker wants to criminalize aborting your rape baby because it’s “tampering with evidence”

I’d say it’s a new low for Republicans, but really, it’s their usual low:

A Republican lawmaker in New Mexico introduced a bill on Wednesday that would legally require victims of rape to carry their pregnancies to term in order to use the fetus as evidence for a sexual assault trial.

House Bill 206, introduced by state Rep. Cathrynn Brown (R), would charge a rape victim who ended her pregnancy with a third-degree felony for “tampering with evidence.”

“Tampering with evidence shall include procuring or facilitating an abortion, or compelling or coercing another to obtain an abortion, of a fetus that is the result of criminal sexual penetration or incest with the intent to destroy evidence of the crime,” the bill says.

Third-degree felonies in New Mexico carry a sentence of up to three years in prison.

But don’t worry, Cathrynn Brown! I know you’re not a geneticist so this wouldn’t have occurred to you, but I have the solution to your problem. You can do paternity analysis using the DNA from an aborted fetus, the placenta, or (thanks to new technology produced from my very own department) fetal cells that are circulating in the mother’s blood. Why, you don’t need a live baby at all! It’s a win win situation. Women aren’t forced to give birth to and raise their rapist’s child as some sort of bizarre punishment for being raped, and evidence is still obtained to identify rapists.

I’m sure Rep. Brown will rescind the bill now that science has come to the rescue. It’s not as if this is actually some underhanded attempt to outlaw abortions, right?

Come see me at Nerd Nite Seattle!

I am living the dream: I’ve been invited to give a talk of extreme geekiness this Monday:

Pokébiology 101
There may not be a Pikachu Genome Project, but the unusual biology of the Pokémon Universe can teach us about biology in the real world. How do Pokémon species differ from species here on Earth? What does genomic imprinting have to do with breeding? Can an organism like Eevee actually exist? You won’t need to be a Pokémon Master or geneticist to catch the concepts, so come, have fun, and grab a beer – it’s super effective.

Nerd Nite Seattle
Monday, January 21st
7:30 Talks (Doors open at 6:30)
$5 Cover
LUCID Jazz Lounge

If you drop by, make sure to say hello!

Flickr helps scientists discover a new species

This story on NPR is great. An entomologist was browsing insect photos on Flickr when he saw one he didn’t recognize. After talking to his colleagues, they confirmed that this was probably a new species:

A full year later, Winterton received an email from the photographer; Guek had returned to the region of the original sighting and found another lacewing with the same wing pattern.

“He told me, ‘I’ve got one in a container on my kitchen table — what should I do with it?’ ” Winterton says.

The specimen was sent to Steve Brooks, an entomologist at the Natural History Museum in London. Brooks confirmed that the lacewing was new to science. He also found a matching specimen that had been sitting in the museum’s collection, unclassified, for decades.

The new species was dubbed Semachrysa jade — not after its pale green color, but after Winterton’s daughter.

It’s pretty awesome that we live in a time where information is spread so rapidly that a random photographer and a bored scientist browsing Flickr can make a new discovery. What other scientific discoveries do you think social media can contribute to?

Microbiology haikus

Commenter VeritasKnight requested a post full of haikus; Joe McKen asked for them to be microbiology themed.

Peptidoglycan
damn you, I am positive
You blue my cover

It was chilling there
Before genomes went mainstream
The retrovirus

S. cerevisiae
The brewer, not the screwer
Fuck C. albicans

Ten percent human
The rest, essential strangers
Am I really me?

And for those who are curious, the themes (in order) are gram staining, endogenous retroviruses, baker’s yeast versus the species that causes vaginal yeast infections, and the human microbiome.

This is post 34 of 49 of Blogathon. Donate to the Secular Student Alliance here.

Today in traumatizing wildlife videos…

Nature is often weird. But sometimes, it’s REALLY fucking weird. I give you the pearlfish:

For those of you who can’t watch the video (though if you can, you really should)… Adult pearlfish are long skinny fish that live in open habitats. In order to not get eaten, they need to find a suitable place to hide. The problem is, they tend to live in places that are missing the typical hiding places like rocks and corals. They are, however, surrounded by lots of large sea cucumbers…so they hide by swimming up a sea cucumber’s butt and living inside of it. Most don’t harm their hosts, but some are parasitic, nibbling away at the sea cucumber’s gonads for nourishment.

This is post 14 of 49 of Blogathon. Donate to the Secular Student Alliance here.

My research part 4: How did microRNA convergently evolve?

How could microRNA have evolved to have such similar structure and function in plants and animals after evolving independently? You must be thinking, “What are the odds?!”

If evolution boiled down to nothing but random chance, the odds seem staggering indeed. No, I’m not about to say God guided evolution. What happens is there are certain traits about the system that constrain it to act in a certain way, making similar outcomes more likely.

To understand more fully, I have to teach you a little bit about microRNA biogenesis. Awww yeeeaaah!

Adapted from Berezikov 2011

In animals, a microRNA gene is transcribed to make what’s called “primary microRNA.” This pri-microRNA forms a hairpin structure – that is, it folds over and complementarily base-pairs to itself, forming a step and loop. This pri-microRNA is trimmed by the protein Drosha and is then shipped out of the nucleus as an ~80 nucleotide precursor microRNA. In the cytoplasm, the protein Dicer cleaves the pre-microRNA to form the mature ~22 nucleotide microRNA, which will go on to be involved in gene regulation.

In plants, pri-microRNA still forms hairpins, but their size can be far more variable. Plants also lack Drosha – all of the processing is done by a Dicer homologue.

You’re probably thinking, “So they’re processed differently. This doesn’t really convince me of the odds.” But what’s important to notice is that both of these systems share a couple of key things, which make convergent evolution more likely:

  1. Both use the protein Dicer to process mature microRNA. This is thought to be an exaptation – where a trait initially evolved to have one function, but has subsequently come to have another. Dicer is thought to initially be used to cleave foreign RNA particles, for example from viruses. There’s also evidence that suggests Dicer plays a role in repairing double stranded breaks in DNA. Since Dicer was already present in plants and animals because of these more ancestral functions, it was available in both lineages to be used for something else. Plants and animals didn’t have to evolve a totally new protein to process microRNA – they used the machinery they already had sitting around.
  2. Both process microRNA from hairpins. RNA hairpins spontaneously occur all the time, and some of these spontaneous hairpins give rise to new microRNA. That’s because if a hairpin happens to process into a mature microRNA that conveys a fitness advantage to an organism, natural selection will act to perpetuate it. If a hairpin results in an unfavorable outcome like disease, purifying selection will purge it from the population. Because RNA hairpins spontaneously occur and Dicer was already around, natural selection would act favorably on a system where processing hairpins leads to a fitness benefit.
I have only one thing left to say:

This is post 9 of 49 of Blogathon. Donate to the Secular Student Alliance here.

My research part 3: MicroRNA in plants

Since my research focuses on primates, I don’t exactly work with plant microRNAs. But they’re still fascinating enough that I wanted to touch on them. Plant and animal microRNAs are very similar – they’re approximately 22 nucleotides in length, they’re processed from larger hairpin structures, and they function by downregulating messenger RNA. But they have a number of differences because microRNA in plants and animals evolved independently.

Yes, this similar system arose separately in the plant and animal kingdoms. No, this is not proof for God. This is an example of convergent evolution, where the same trait is acquired independently in different lineages. Think of the ability to fly in insects, birds, and bats. The evolution of microRNA is the same, it’s just more molecular instead of having an obvious effect like flight, which is visible to the naked eye.

Why do we think plant and animal microRNA evolved independently? One major piece of evidence is that there are no homologous microRNAs between plants and animals (homologous meaning shared through a common ancestor). This is especially striking when you compare it to microRNAs within animals, a number of which are homologous. There are some animal microRNAs present throughout the whole animal kingdom, from sponge to fruit fly to orangutan, that just don’t exist in plants. Plants have their own set.

Another thing supporting independent evolution is that plants and animals have different processes for generating mature microRNA. In plants, microRNA is fully matured in the nucleus before being shipped out to the cytoplasm for use. In animals, much of the processing takes place out in the cytoplasm. Animals have additional proteins that are involved in processing – I’ll touch on it a little more in my next post. Also, plant and animal microRNA differs in how it targets messenger RNA. In plants, the whole ~22 nucleotide microRNA is involved in complementary base-pairing with the messenger RNA. In animals, only a 7 nucleotide “seed region” of the ~22 nucleotide mature sequence determines which messenger RNA it’s supposed to match up with.

A final piece of evidence is that microRNAs are missing in other forms of life. They’re absent in fungi, placozoans (the most basal animal lineage), and choanoflagellates (the closest living relative to animals). It’s more likely, especially considering the other evidence, that microRNA arose twice independently, rather than microRNA being lost multiple times in the specific lineages that happen to make it look like it arose twice independently. The latter would be getting into “Satan buried the dinosaur bones to make it look like a natural process” territory!

This is post 8 of 49 of Blogathon. Donate to the Secular Student Alliance here.