Worldbuilding. With SCIENCE!

Today, I felt like meandering around a random piece of my mind that is a bit outside my usual blogging territory. Most of my academic reading (and consequently, most of my stuff here) is in the general areas of evolutionary biology, developmental biology, palaeontology and intersections thereof. Occasionally I’ll see something about abiogenesis or exoplanets or animal cognition and read it for the coolness. However, besides being a scientist, I also happen to be an avid reader and occasional writer of fantasy fiction, and one of the most appealing aspects of that genre for me is worldbuilding.

I am fascinated by the diversity of human cultures; the myriad different ways of seeing the world and constructing identities for ourselves. I love reading novels with interesting, well thought-out cultures, and tinkering with my own world is one of my favourite pastimes. If I had unlimited money and weren’t the lazy sod I am, I’d probably be thinking about getting a cultural anthropology degree on top of my first one in evolutionary biology*. Since I have very limited money and motivation, I content myself with watching out for interesting titles in the generalist journals I read. Even as a worldbuilder, I can’t stop being a scientist, so I love seeing scientific takes on what makes cultures the way they are.

Music, the many ways thereof

The other day, for example, I bumped into an analysis of music from around the world in PNAS (PNAS is a pretty good general journal for the occasional worldbuilding fodder.) Savage et al. (2015) searched for universal features of human music in about 300 recordings from around the world. It was particularly interesting to me because I have a culture with what I always suspected was a really weird religious prohibition relating to music. From what I can gather from this paper, my suspicion was correct: my little religious gimmick would be very unusual in the real world.

One of the main points of the study, however, is that there aren’t really any truly universal properties of music. There are exceptions even to “self-evident” rules that stem from the way our brains work, like having a regular beat or (if the music isn’t purely percussion) a scale made of discrete pitches. (So: I can do what I want with the music of my imaginary cultures, as long as I don’t make them all weird in the same way. Science says so. *smug face*)

There’s also the fact that most of the music recorded in the database is performed by men despite the fact that women are just as capable of making music. This is a valuable piece of information for a worldbuilder, one I wasn’t (consciously) aware of before I read this paper, and also one that highlights the importance of context. Me being a girl and rather acutely aware of the curses of patriarchy from a young age, I have thought up several societies that are either gender-equal or matriarchal (most of these societies are not human). How would that change the balance? If the hypothesis that male-dominated music has something to do with sexual selection is correct, should we see pretty much equal participation in cultures where both men and women are promiscuous and participate in literal mating displays? (Playing with sexuality in a fantasy world is even more fun than playing with religion! Also, an evolutionary biology degree can give you some really funky worldbuilding ideas…)

(Incidentally, Savage et al. draw a parallel between male-dominated music in humans and male-dominated vocalisations in, among other groups, songbirds. I find it curious that they didn’t mention a recent study that suggested that actually, females probably also sang in the ancestral songbird, and pointed out that this state of affairs is still the norm rather than the exception when you look at the whole group [Odom et al., 2014].)

Religions evolving

Today, I found a paper introducing a really shiny new database in PLoS ONE (which is why I decided to ramble about worldbuilding). “Pulotu” (Watts et al., 2015a) is a free database of supernatural beliefs and practices from 100+ Austronesian cultures, designed to study the cultural evolution of religion. Austronesian peoples originated from Taiwan many thousands of years ago. Today, they inhabit a huge area including Indonesia, Papua New Guinea, New Zealand, zillions of Pacific islands (Polynesians!) and Madagascar. They are a very diverse bunch in every respect, and their family tree is pretty well understood from linguistics and genetics. A decent database of those diverse cultural traits combined with the understanding of history is truly an amazing resource for those interested in how said cultural traits evolve. (Seriously, this thing looks like a goddamned gold mine.)

The authors have clearly done thorough work, using multiple sources, ethnographies written by scholars who actually met the people in question where possible, to characterise each culture. The database has three separate time focuses to distinguish the “pristine” state of a culture from what happened after contact with major religions like Hinduism or Christianity. They recorded both characteristics of religion like the types of supernatural beings worshipped and the types of rituals practiced, and characteristics of the societies themselves such as how they get most of their food, and how many layers of political hierarchy they have. You can visualise these features on a map with a couple of clicks, so you can immediately see if they are randomly distributed or found in particular places.

So what can you learn about cultural evolution from this treasure trove? One example the paper gives concerns something I came across years ago when I was researching theories about the evolution of religion for an undergrad assignment. The idea is that fear of supernatural punishment, particularly the belief in “high gods” who punish immoral acts, fosters cooperation and promotes the formation of large and politically complex societies. The supernatural punishment hypothesis has been around for a while, but I think I first encountered it in Johnson (2005).

Johnson tried to test the idea by looking at correlations between belief in moralising high gods and various proxies of cooperation (e.g. size of the society, presence of money lending, centralised authorities) in a cross-cultural sample. However, correlation does not equal causation, so that kind of study leaves it unclear whether moralising gods lead to complex societies or the other way round. However, with a solid family tree of cultures, you can add a historical dimension to a cross-cultural comparison, which allows you to infer causality.

When the Pulotu authors did this (Watts et al., 2015b), they found that Johnson probably got his causal arrow pointing the wrong way. If moralising gods do indeed lead to complex societies, then societies with moralising gods should increase in complexity more often than societies without. What actually seems to be happening in Austronesia is that complex societies came first, and they were more likely to develop beliefs in moralising gods. Nonetheless, a more general version of the supernatural punishment hypothesis, in which agents that aren’t high gods (e.g. karma, ancestors) may do the punishing, is supported by the analysis.

That’s mostly irrelevant for worldbuilding, where the correlation alone is enough to work out what’s “realistic”, but I also find the science fascinating in its own right. And while I’ve not tried downloading the Pulotu dataset (as I said, I only found out about it today, and I’ve been writing this post since), from a brief look it’s a handy text file that appears to be useable by anyone who knows the first thing about spreadsheets. I might have to go and play with it. Just have to think of some interesting questions…

So, now you know. I’m a hopeless geek even when I’m not officially being a scientist. (Does this surprise anyone?)

Notes:

*If I had unlimited money, I’d probably spend my entire life at university…

References:

Johnson DDP (2005) God’s punishment and public goods. A test of the supernatural punishment hypothesis in 186 world cultures. Human Nature 16:410-446

Odom KJ et al. (2014) Female song is widespread and ancestral in songbirds. Nature Communications 5:3379

Savage PE et al. (2015) Statistical universals reveal the structures and functions of human music. PNAS 112:8987-8992

Watts J et al. (2015a) Pulotu: database of Austronesian supernatural beliefs and practices. PLoS ONE 10:e0136783

Watts J et al. (2015b) Broad supernatural punishment but not moralizing high gods precede the evolution of political complexity in Austronesia. Proceedings of the Royal Society B 282:20142556

More genes from scratch

Following on from the yeast “proto-gene” study, I’ve started paying more attention to news about gene birth from non-coding DNA. (Or “junk” DNA, if you will, though “junk” is… something of a misnomer :-P) The yeast paper explored protein-coding genes in the process of birth. This new one I found in PLoS Genetics looks at genes that have already been born, and argues that the sequences they came from were functional long before they began to serve as templates for proteins.

Paternity testing for genes

So how do you know that a protein-coding gene came from non-coding DNA? Xie et al. (2012) looked specifically for genes born along the ape lineage, that is, the group that includes gibbons, orangs, chimps, gorillas and ourselves. They searched for human genes that had no protein-coding homologue in non-apes including rhesus macaques, mice, dogs and a handful of other mammals, but did match some of the other animals’ DNA sequence. It was also important that there were no other similar sequences in the human genome itself, which might have indicated that the “new” gene actually originated by duplication.

To ascertain that the selected genes represented gene birth in the ape lineage as opposed to a dying gene in other mammals, they also looked at the sequence changes that garbled the would-be protein product of the non-ape sequences. If these are the same in all non-ape versions of a gene, that probably means that they were inherited from the common ancestor of apes and all these species, that is, the non-coding version of the gene came first. Only genes that really seemed to have been born in our lineage were kept.

In the end, they came up with 24 genes that passed all muster. Some of these coded for proteins in both chimps and humans, others only in humans. Based on RNA-sequencing data from rhesus macaques, 20 non-coding versions of these genes were active in monkeys – and this is where things get interesting.

Function in the junkyard

The big question the team asked was this: are these non-coding RNAs just random noise in transcription, or are they already functional even without a protein product? They decided to answer this question by looking at the structure and expression patterns of the RNAs in macaques, chimps and humans.

By “structure”, they mean how the RNA is edited after it’s transcribed from the gene sitting in the DNA. The RNA from most genes in animals and other eukaryotes isn’t taken straight through protein synthesis. First, pieces called introns are chopped out and the rest (called exons) are spliced together to yield the final template for the protein.* When the researchers looked at RNA sequencing results from the three primates, they found that the non-coding sequences in macaques were cut and joined at the same points that the protein-coding human sequences were: a bunch of RNA sequences from macaques spanned both sides of a human splice site, and contained none of the intron in between. Such conservation, the authors argue, is indicative of functionality.

Expression patterns also suggested that the macaque sequences weren’t just noise: when they compared the abundance of the different RNAs between different tissues in the three primates, Xie et al. found that the non-coding RNAs weren’t just expressed all over the place – they were significantly more abundant in some parts of the body than others. This pattern was consistent across species: a sequence that was most abundant in the macaque’s brain was also likely to be brain-specific in humans, even though the macaque version didn’t code for a protein and the human gene did. (By the way, a lot of the 24 were most active in the brain, which is apparently something of a trend among new human genes regardless of their mode of origin. Guess our brains evolved rather a lot in the last few million years ;))

This is very cool, but I’m kind of worried about the arguments used for functionality. Maybe this is just me being a newbie in this area, but I’m not sure that useless non-coding RNAs should be expressed all over the place. One of the salient features of the 24 genes in this study is that they are nearby other genes, sometimes even overlapping them. In any case, they are close enough to use the switches that normally regulate the activity of the other gene(s). That would mean that they’d be most highly expressed wherever their neighbours are, which doesn’t depend on them having a function. If some of them happened to acquire proteing coding potential by mutation, presumably it’d only be kept by natural selection if the resulting proteins did something useful in those places, hence the conservation of expression patterns.

Likewise, splice sites may well arise by accident (they aren’t all that complex), and they don’t have to disappear just because a mutation somewhere else makes the sequence suitable for protein synthesis. Though in fact, splice site conservation sounds more convincing than expression conservation to me as far as arguments for function go. Because splice sites can come and go quite easily, there’s no reason they should be particularly conserved between any two sequences unless they’re important. And the splice sites can only be important if the sequence they’re in does something. Who cares where you cut a strand of random RNA that’ll only end up eaten by housekeeping enzymes anyway?

So, while I get all excited about the whole new genes side of things, and I love this sort of genomic detective work, I think I still have to sleep on that point about function coming before protein. It’s a pity they didn’t check if any of the “non-coding” RNAs in macaques (and chimps) were occasionally translated into a protein, albeit a smaller one than the human counterpart. The yeast people did that and it was awesome, and it would have been such an informative thing to do in this case.

(Also, it would have been darn cool if they’d tried knocking out some of them and seeing if they got screwed up monkeys, but let’s be realistic. Macaques don’t breed like mice, they take a hell of a long time to grow up, and we’re kinda reluctant to mistreat our close relatives like that. You’d have to be comic book supervillain insane to embark on that experiment.)

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*This may sound like a weird way to run a genome, but it’s actually quite good for making more than one product from the same gene. It’s pretty important in real life – nearly all human genes with multiple exons are spliced in at least two different ways, and many genetic diseases originate from messed up splicing.

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Reference:

Xie C et al. (2012) Hominoid-specific de novo protein-coding genes originating from long non-coding RNAs. PLoS Genetics 8:e1002942