Don't Shake the Flask

Because you don't know if it'll explode

Tag: science

A Mini Thought on Megafauna

In a recent article on Tor.com, James Davis Nicoll muses on the existence of megafauna in the Star Wars universe. I’m not a Star Wars fan, but it did get me thinking about the implications of megafauna in a science fiction story that was built on a better scientific basis than that franchise. Because if megafauna exists in the universe, what does that say about the environment that they were formed in? And what does it say about the civilization(s) that either allow them to exist or have to put up with their continued existence?

If there is an expansionist society in the fictional universe, I would suspect that any megafauna present had evolved to take advantage of the new niches that the civilization had created in their bid to take over galaxies. Sort of like how invasive species have become dangerous nuisances on our world due to humanity’s behavior. And similar to our world, maybe this fictional universe would also have scientists and hunters going around trying to eradicate these pesky megafauna.

Or perhaps someone deliberately set out to create the megafauna and then things went horribly, horribly wrong. Things going horribly wrong often make for interesting stories.

Wasting Time on the Internet

One would think that with all these months trapped at home due to the COVID-19 pandemic, I would have had plenty of time to catch up on my reading, but strangely (or perhaps not strangely) enough, that wasn’t the case. I’m as busy as ever, but maybe that’s not surprising considering my field of work.

Recently I managed to finish one of those books in my gigantic to-be-read pile: Wasting Time on the Internet by Kenneth Goldsmith. This particular blog post isn’t going to be critiquing this particular book–although I will say that Goldsmith’s thesis, that the internet has changed how we live and think and spend our time, is an interesting one. Certainly, many things happening in the world now (for better or worse) wouldn’t have been possible without the internet.

This has mostly made me think of what I usually do to “waste time” on the internet. There are so many things. But perhaps I can narrow this down to just stuff I watch on YouTube and maybe I can provide kind of a hodge-podge list of what I do watch.

Cats: These are probably the most time wasting sort of videos I watch. Although–they can also be informative. I also have a cat, after all.

 

Kpop reactions: It’s not so much the kpop videos themselves that I find interesting, but the whole ecosystem of react channels that have sprung up around it. The more watchable ones, obviously, are the ones with actual commentary instead of incoherent fangirling/fanboying.

 

Book and writing commentary: Food for thought, basically. You might disagree with their picks, but it’ll get you thinking about your own literary tastes.

 

People eating weird stuff: Totally mindless but at the same time, completely entertaining.

 

Music: This is just a small selection of the type of stuff I listen to.

 

Horror/RPG: I find the storytelling and the intersection of that with this particular genre very interesting. This scratches a different itch than the book/writing commentary channels above.

 

Science: I’m a scientist. Of course I like watching science videos on YouTube. This is just a small selection. I’m sure there are some other very interesting channels I’ve missed.

 

Linguistics: These are the channels I find more engaging. I’ve tried some other linguistics/language channels which also are very popular, but I find myself wanting to fall asleep in the middle of them.

 

Culture: Just some really cool and random stuff all around.

 

License Plates Observed

Last year, I was pretty bored being stuck in rush hour traffic so I decided to make my commute a little more productive (or useless, depending on your point of view), by making a note of the location of different license plates. The following figure is a compilation of a year’s worth of data:

Slide1

There are several caveats about this geographic heat map. Since the observations were done primarily in California, of course the top number of license plates will be California. I also recorded plates from Canada (a couple) and Mexico (mostly from Baja California and about as many as Arizona plates). I actually saw zero North Dakota plates during the observation period, but about one week after the observation period ended, I saw two separate vehicles with North Dakota plates.

I suspect the map would look vastly different if I lived in a different Californian city (particularly one where there is almost no tourism), let alone in a different state.

The most frustrating aspect about the data collection was that sometimes it was impossible to tell where the plate was from because of the way it was mounted on a vehicle. Sometimes the license plate holders would cover all of the license plate except for the alphanumeric code. Occasionally, I could guess fairly confidently what the plate was if the font/color/design matched the default plate of that state, but if someone had a vanity plate, I had no clue. In the cases where I was unsure, I did not record them.

Ultimate Dinosaurs!

Ultimate Dinosaurs – one of the current exhibits at the Museum of Natural History in San Diego. One thing I found particularly clever: some interactive/virtual reality displays. Short kids, though, may need a parent’s help with those. Accessibility: in English, French, and Braille. Unfortunately, this won’t help the significant Spanish speaking population here. (The rest of the exhibits in the museum are in English and Spanish.) This exhibit was created in Canada, though, so it’s kind of understandable that nothing is in Spanish.

TBR Pile #3 – Dreamland by David K. Randall

Note: The TBR Pile series of posts aren’t strictly book reviews. It’s my excuse for writing a rambling blog post. While it will contain some of my thoughts about the book, I’ll may digress into other topics.

I really enjoy reading popular science books, mostly because if anything I get to learn something from them. Especially if the book’s subject is outside of my expertise. And if I get entertained by the author’s anecdotes and storytelling ability, that’s a bonus. In David K. Randall’s Dreamland, I got to learn all about the science of sleep.

What I found the most fascinating was that much of sleep is cultural. It’s not just about sleeping in separate beds because of middle-class morality or the lack of study in dreams because it’s considered woo. It’s also habit, too. Babies in different countries sleep in different ways. Type of mattress actually doesn’t make a lick of difference in sleep quality. What matters most is consistency, not the type of sleep habit one engages in.

But despite all the sleep labs and pharmaceutical companies touting their solutions for insomnia, there’s still a lot that we don’t know about sleep. I think this is just part of the bigger problem: that we still don’t know much about the brain.

One caveat, though. Randall is a reporter and not a doctor or scientist. He initially got into the topic because he had a problem with sleepwalking and much of the book, I feel, delved into the historical and societal implications of sleep. I would have liked a lot more science (especially since the book was billed as a discussion on the science of sleep)–particularly the neuroscience behind the phenomenon of sleep and the biochemistry used for the drugs that manipulate sleep. But then again, that may just be me. I’m not afraid of reading the technical details about this stuff. The general public, however, would probably be bored to sleep.

Writing, Reviewing, and Rambling about Women in Science

Yep, it’s the beginning of July and you all know what that means: Camp NaNoWriMo. I will be working on a novel project which I had already outlined in May. At the moment, I’m not particularly happy with the beginning. I want to keep the scene–it just needs to be rewritten. In any case, onwards. I’m still excited about the story, particularly with the puzzle-like nature of fitting the different time lines together. It’s been a while since a story idea has also engaged my more analytical side.

I’ve also been invited back to lead writing sprints over at NaNoWordSprints. I kicked it off with a handwritten tweet session which was partially inspired by the fact that I am currently conducting a week-long project on my personal Twitter account where I’m handwriting tweets for a week. Anyways, I don’t think I’ll be doing another handwritten tweet session for the sprints any time soon, especially since that kind of thing takes a while to set up. I will also be archiving all the prompts this month on this blog in case anyone has missed one of my sprint sessions.

And speaking of writing projects, I (possibly foolishly) made a bet to get a short story ready for submission in a month. Specifically for Fantasy & Science Fiction because they’re opening it up for electronic submissions. At the moment, though, I’m feeling pretty pessimistic. I’m still in that funk where I think all my ideas for short stories are crap. I don’t think my writing skills and craft and style are up to “professional” standards yet (where “professional” means “whatever the editors find awesome which could be anything”). It doesn’t mean that I won’t try, but I’ve had enough “close but no cigar” moments which have made me think that it’s pretty much a waste of time to hope for anything.

* * *

I have a book review out over at Smart Bitches Trashy Books on the paranormal romance novel Diamond Dust by Vivian Arend. I’ve been a long time follower/lurker of SBTB. I really like the blog’s snarky style and its serious commentary on a much maligned genre (the podcasts are highly recommended), so I thought it would be very cool to volunteer to do a book review for them.

* * *

Today, I found out the real reason why I had a really unpleasant episode many years ago which had royally screwed my career path for a while. At the time, I had thought the failure was my fault, but now I know it was probably something I couldn’t have done anything about.

It doesn’t make me feel any better about it, though. It just makes me feel sad. All I’m going to say is that even though there are constant cries for more women scientists, there are women scientists out there who do not like other women scientists because they think they are the only exception.

I personally think it’s better to nurture relationships with other female scientists (all scientists, actually) and to mentor students (of any gender) who have an interest in science. To do otherwise and burn bridges, well, it doesn’t take a genius to figure that it’s a bad idea.

Old Documentary Recommendations

Even as a kid, I really enjoyed watching documentaries. Especially science and culture documentaries. I’m not sure if my preference for documentaries grew out of my preferences for the topics or simple necessity. There was no cable and going to the movie theater was a rare thing. Most of the time, if I wanted to watch a film, I’d have to wait until the library got the VHS. (Even now, childhood habits die hard. I have no TV and I go to the theater maybe three or four times a year, tops.) I was always pretty excited when Nova, Nature, or National Geographic came on. While I loved reading stories, too, documentaries showed that the real world could be even more weird and wonderful.

Lately I’ve been watching Cosmos: A Personal Voyage and Cosmos: A Spacetime Odyssey (one episode of the former each Sunday, the newest episode of the latter on Mondays). My view of them, admittedly, is influenced by the fact that this is also my first time watching the Carl Sagan series as well as the one hosted by Neil deGrasse Tyson. I enjoy both series and I would be hard pressed to say which one is better. I think both are the product of their times.

Anyways, this has reminded me of some older documentaries that I think still hold up well:

Civilisation. (YT playlist) This series is a pretty thorough interpretation of Western Civilization by Kenneth Clark. It was a huge thing during its day and I think the modern viewer can still see why. (Apparently it also inspired the documentary series America, presented by Alistair Cooke. I haven’t watched it yet, but it’s on my to do list.)

The Tribal Eye. (YT playlist) It’s presented by David Attenborough, need I say more? Besides, has there really been such a keen series on African, Native American, and Polynesian culture since?

The Silk Road. (YT playlist) I first stumbled onto this by accident at the local library. And I just thought this was pure awesomeness packaged as a documentary series. I keep thinking that the film crew must have had some unforgettable adventures as they trekked across the sandy Asian interior.

Antonio Gaudi. (YT link) Simply feast your eyes on great weird art.

The Queen of Trees (YT link) and Deep Jungle: Monsters of the Forest. All right, so these are more recent ones, but I really like these two because they depict how interconnected nature is by using the tree as a central character.

The Fine Line Between Mundane SF and Lab Lit

(Note: The following is more of an analysis of genre classification rather than a book review. However, there is discussion about story elements that some may consider spoilers even though there is no examination of the plot.)

After seeing The Galaxy Express post on Red Shoes for Lab Blues by D.B. Sieders, I figured I had to read this because the main characters are scientists and the hero is Asian. Mostly because there are so few Asians and/or scientists as main characters in general. However, I had certain trepidations about reading this, too. Because I am both Asian and a scientist and if there was anything off about the technical or cultural details, I would be disinclined to like it.

Overall, I did like Red Shoes for Lab Blues, mostly because it was spot on about the research academic life and the technical details. Anyone who has ever worked in a lab (or read PhD Comics, I suppose) has encountered the personalities and mindsets populating this story. And I got the characterization of Henry (the hero). For instance, there is a scene where he and the heroine Stacey are arguing and he says something that she considers coming totally out from left field. But as a reader, I thought this was really well done because it does not gloss over the inherent social conflicts that many Asian Americans have between living in a Western culture and still being seen as Other.

It is primarily a romance, but I found Henry and Stacey’s relationship sweet rather than steamy. Well, the two characters certainly do more than just kiss, but I found the publisher blurb’s implication that it was erotic misleading. (Aside: If you want to read about scientists doing really steamy sexy stuff, Delphine Dryden’s The Theory of Attraction would fit the description better. However, unlike Red Shoes for Lab Blues which I found did characterization very well, the characters in The Theory of Attraction behaved more like caricatures from The Big Bang Theory.)

So back to the blog post that started all of this. Heather Massey from The Galaxy Express posits that this is mundane science fiction. (Personally I hate the term “mundane sci-fi” because it implies that it’s boring. “Contemporary sci-fi” might be a better term.) One of the commenters on that blog post even said that the word “lab” in the title made her think that this was sci-fi. I’m going to disagree and say that this is not science fiction at all but romance crossed with lab lit. Maybe even part of the subgenre of geek/nerd romance.

However, I must qualify this and say that genre definitions are fluid depending who defines them. Someone could say that Frankenstein was chicklit and never be convinced otherwise because their definition of chicklit was anything written by a woman. So I’m going to explain why this does not fit my definition of science fiction. And what’s my definition of science fiction? It is this: fiction containing speculative science elements integral to the world building, characters and/or plot. Just because a story contains laboratories and scientists and science that you (as an individual and not as the whole scientific field) doesn’t understand does not mean that it is sci-fi.

I did not find any speculative elements in Red Shoes for Lab Blues. I can see why some would think it is sci-fi, though. There is a bit of technical jargon non-scientists would be unfamiliar with and the characters are researchers trying to find a new drug to cure breast cancer. But despite that, nothing is new or imagined. The “compound Z” that the characters are testing is very similar to what real life researchers do. Drug companies have whole libraries of chemical compounds that they send scientists to test. Even the experimental setup for testing this imaginary compound Z is regular procedure that biomedical scientists use all the time. The science behind the fictional drug is sound, but it isn’t innovative. Rather than innovation and speculation, the story is about research and academic culture–working in the lab, teaching undergrads, backstabbing postdocs, getting tenure, publish or perish–hence lab lit.

So what would edge lab lit into mundane sci-fi? Wild speculation, for one. Let’s take the example of the cancer killing drug compound Z. In real life, there are a kazillion compounds that kill cancer cells–not all of them may make it to clinical trials, but the very fact that compounds kill cells is not new. However, what if this compound Z doesn’t kill the cell but alters them in some fundamental way which completely changes our understanding of cancer cells and how cells live and die? What if the compound is one step towards achieving immortality? Now that would be speculation and sci-fi. But only if this was somehow integral to the plot line and not just some character running her mouth at some flights of fancy.

There is definitely a fine line between science fiction and a fictional story simply about science and scientists. For me, science fiction must have a speculative element that is integral to the story, regardless of settings, tropes, and character. While sci-fi and lab lit can be combined, I consider them distinct from one another. And in the particular case of the story I read last night, solidly in the latter and not the former.

Some Rambling About Sampling

Last night, a small bit of conversation about study subjects got me thinking about experimental design. A first year grad student was trying to figure out the logistics in recruiting pregnant women and women who had just given birth for her research project. Another grad student remarked that she should get some contacts in the local LDS community since there seemed to be no shortage of Mormon pregnant ladies. While the student with the study became really enthusiastic that there was this pool of subjects almost right under her nose, I wondered what it would really mean if she got only Mormon pregnant ladies as subjects. In that particular case, I’m not sure if the results could be in any way generalized. Mormon pregnant ladies as a group–especially in these parts–is a spectacularly homogeneous sliver of humanity. The most you could say about the results is that it worked for this group and that a larger, and more diverse, sample size would be needed in another trial.

There are, of course, experiments where genetic homogeneity is preferred or even necessary. These experiments tend to be the sorts that try to answer basic scientific questions like measuring one factor against another without the confounding problem of differing genetics. For example, let’s say you’re trying to figure out if microbe A or microbe B might cause mice to become obese. To do that, you’d feed microbe A, microbe B, or a control mixture with no microbes to three groups of mice that all have the same genetic background. If the mice came from different strains, then you wouldn’t know if the results were due to the microbes, the mouse genetics, or a combination of both. If one were to do such an experiment in humans, you’d need twins or at least a relatively genetically homogeneous population like the Amish or the Icelanders.

Then there are the experiments that try to answer more general scientific questions–where the results are used to generalize something fundamental about an entire species, groups of species, or even all of life. Here, things get problematic. Especially if sampling is limited. Take, for instance, psychology research. Much of the results that have come out of that research for oh so many decades had been generalized to the entirety of humanity. It’s only recently that people are beginning to question this assumption because a lot of the study subjects for this research had been done on volunteer college students. One doesn’t need a degree to immediately realize that self-selected college students in the west is only a subset of the entire world population.

But I don’t think one should completely blame the scientist for using small sample sizes. There are a lot of other things to consider. For one thing, ethics. It’s one thing using animals (which already requires approvals and justifications). It’s another using humans. A group of human subjects will always be biased because they’re volunteers. Another is convenience. It’s just easier and cheaper to recruit a bunch of cash-strapped students from the local university than attempting to round up a bunch of people (with different ages, ethnicities, socio-economic backgrounds, etc.) from all over the world. I suppose one could also argue that you could get around all of this with statistics, but you can only massage the numbers so much before somebody catches you doing something a little too creative with the math. So I wouldn’t write off any results per se, but I would be cautious how the results could be generalized, if at all.

Microbes for the Lovelorn

The host-centric view of the numerous symbiotic, commensal, and pathogenic bacteria living on and in us is that they’re merely microbial hitchhikers and roommates. They’re small organisms that might make us sick or exchange nutrients with us–but they’re also just that–separate organisms. However, as researchers look closer at the relationship between host and microbe, it turns out that things may not be as straightforward as one might learn in a grade school science class. Instead, the crosstalk between bacterial and eukaryotic cells is a complicated web that influences host immunity and even behavior. In the hologenome theory, we might consider our microbes as just another part of us since the microbe-host interactions ultimately influence our fitness in the environment1. So bacteria may not only be their hosts’ roommates but their most intimate confidants, dictating not only when they get sick or how food is metabolized but also more complex social interactions–like their love lives.

In a fascinating paper by Sharon et al. in PNAS2, several experiments demonstrate that mating preference in the fruit fly, Drosophila melanogaster, is mediated by the fly’s gut microbiota. In the initial experiment, lab flies were divided into two groups. One group was fed with starch and the other was fed with a cornmeal-molasses-yeast (CMY) mixture. Then the flies were given a multiple choice mating test where one male and one female fly from each group were placed in a plastic dish and observed over a one hour period for mating behavior. The researchers observed that even after the second generation, the flies preferred to mate with flies reared with the same food source. Preference persisted up to the 37th generation, which was as far as the researchers had tested.

But why on earth would food source affect mating preferences? The gut microbiota was analyzed by 16S rRNA gene sequencing. Flies fed on CMY had a diverse collection of microbes living in their gut. Flies that consumed starch, however, had a collection of gut microbes in which over a quarter of the microbial population consisted of Lactobacillus plantarum. In the next experiment, the flies were fed antibiotics. This abolished the preference and matings became random. Since the antibiotic killed the microbes in the fly gut, it must mean that the microbes were in some way influencing fly mating behavior. In the subsequent test, the flies that had already been treated with antibiotic were fed Lactobacillus plantarum. And lo and behold, the mating preference reestablished itself. Other bacteria, such as Providencia rettgeri and 41 other species, were also tested, but they had no influence on mating preference. So Lactobacillus might be solely responsible for preference.

While analysis of cuticular hydrocarbon levels in the flies show that Lactobacillus may be influencing fly sex hormones, exactly how the bacteria is modulating hormone levels is still unknown. One possible clue might be gleaned from another process that is regulated by hormones–sleep. Trypanosoma brucei is one sleep-altering parasite that infects humans. During an infection, the immune system is triggered. The immune system is known cross-react with hormones. For example, in the early 1990s, a slew of research showed that the immunomodulatory cytokine IL-1 interacts directly with the sleep hormone serotonin3.

Well, what about humans and their gut microbes? No one has yet looked at the relationship of the bugs in human stomachs and human hormone levels, it is interesting that there is variation of gut microbiota between humans due to diet and lifestyle4,5. And while there is the adage that like attracts like that was proven with the Drosophila experiment, we cannot say whether this is a cause or an effect in humans. Or if this even is a significant contributor to human interactions in the first place.

Gut microbes, however, may not be the only ones playing matchmaker. It has already been known for several decades that bacteria cause body odor6. According to Rachel Herz, a scientist at Brown University:

These bacteria feed on the protein on our skin, and as they digest they release gases reflecting their meal. The specific proteins that populate your underarm are genetically determined and reflect your individual MHC gene profile, which is why each of us has a unique smell.

Herz points out that the stuff on our skin includes the chemicals–“quasi-pheromones” such as androstadienone–secreted by our apocrine sweat glands. As the skin bacteria munch and process these chemicals, the gases given off will make us smell either female or male7.

So will the futuristic versions of the little blue pill or love potion number nine be found in the aisles of your local grocery store? Should people pick up a pint of yogurt instead of querying the neighborhood yenta if they want to find their soul mate? I have no idea. On the surface, this seems a bit silly. What we know today is suggestive yet speculative. Your friendly gut microbes probably care less about your love life than your next meal. But it is not inconceivable to think that the human microbiome might become just another one of those dimensions of compatibility an internet dating site might exploit.

* * *

References:

1. Zilber-Rosenberg, Ilana and Rosenberg, Eugene. “Role of microorganisms in the evolution of animals and plants: the hologenome theory of evolution.” FEMS Microbiol Rev. (2008) 32: 723-735. (PubMed)

2. Sharon, Gil et al. “Commensal bacteria play a role in mating preference of Drosophila melanogaster.” PNAS. (2010) 107: 20051-20056. (PubMed)

3. Opp, Mark R and Imeri, Luca. “Sleep as a behavioral model of neuro-immune interactions.” Acta Neurobiol Exp. (1999) 59: 45-53. (PubMed)

4. Ley, Ruth E et al. “Worlds within worlds: evolution of the vertebrate gut microbiota.” Nature Reviews Microbiology. (2008) 6: 776-788. (PubMed)

5. Ley, Ruth E et al. “Evolution of Mammals and Their Gut Microbes.” Science. (2008) 320: 1647-1651. (PubMed)

6. Leyden, James J et al. “The Microbiology of the Human Axilla and Its Relationship to Axillary Odor.” J Invest Derm (1981) 77: 413-416. (PubMed)

7. Herz, Rachel. The Scent of Desire. Harper Perennial: New York, NY. (2007) p 150.