Archive for April, 2013

A couple of yeast walk into a bar…

A couple of weeks ago, the “offbeat news” feeds lit up with the discovery of a Japanese striped beakfish off the Washington state coast. What was surprising about this find was that the fish was in a bait box on a Japanese fishing boat believed to have drifted to its current position following the March 2011 tsunami in Japan.

A picture of the Japanese Striped Beakfish, Oplegnathus fasciatus.

This little guy laughs in the face of tsunamis. Creative Commons image, attributed to user E-190, retrieved via Wikimedia Commons.

The fish has, it seems, generated a lot of publicity for the Oregon aquarium now housing it. But it puts me in mind of another, even more unbelievable journey.

Our story starts around six hundred years ago with some Bavarian brewers of beer. Now, beer has been around since approximately a week longer than there have been humans, or at least humans who farmed barley1. By the 15th century, in Europe2, you could even say they’d gotten pretty good at it. Many of the styles of beer that we’re familiar with today were being produced3, and while yeast wasn’t well-understood by brewers until much later, they knew that adding the dregs of a good beer to newly-cooked wort would make the result similar, and these carefully-tended “starters” became the closely-guarded trade secrets of commercial and monastic breweries.

16th century engraving, by J. Amman, depicting a brewery.

The good old days, where nobody minded if you stuck your hand in the beer.
Public domain image retrieved via Wikimedia Commons.

All that beer had one thing in common: it all used strains of yeast that preferred to ferment sugars under warmer conditions. These so-called “top-fermenting” or “ale” yeasts, nearly always strains of Saccharomyces cerevisiae4, had a tendency to result in a cloudy beer, and to leave behind often-unwelcome5 flavors in the beer through the production of esters if the temperature was too high or not stable enough during fermentation. They also didn’t keep very long, developing a funky, “skunked” taste soon after they were brewed, as undesirable bacteria and yeasts moved in to metabolize sugars and proteins that S. cerevisiae left behind.

The stability problem was helped by the addition of hops, perfected sometime in the 13th century. The mildly antibiotic properties of hops help to keep bacteria and non-brewing yeasts from getting a foothold in the fermenting beer, while allowing the brewing yeast, usually introduced as a well-established colony via a starter, to ferment the wort without competition6. Despite this innovation, however, even hopped beers had a tendency to deteriorate over time, and many people didn’t care for the flavor they imparted to the beer.

Something changed in the late 15th century, though. Those Bavarian brewers I spoke of earlier started making a new type of beer. Brewed in caves, deep cellars, or even under blocks of ice, lager, as the new beer was called, could be fermented at much lower temperatures than previous beers7. Brewing at lower temperatures meant that other organisms were too sluggish to reproduce in the wort to levels that resulted in off-flavors, and caused grain proteins as well as the yeast itself to fall to the bottom of the beer more quickly and completely, resulting in a clearer, more stable brew, with a cleaner taste. These lagers actually benefited from prolonged storage, as long as the temperature was kept low, becoming clearer and cleaner with time, and they were often stored for six months or more8.

A picture of Paulaner dunkel, a dark lager beer.

Today lagers are the most-often drunk beers in the world.
Public domain image retrieved via Wikimedia Commons.

It wasn’t until the 19th century that the fermenting action of yeast would become understood, and the various strains of it used in brewing classified. In 1883, a chemist working for Carlsberg brewery isolated the strain of yeast responsible for lager. He called it Saccharomyces carlsbergensis, but today it is more commonly known as S. pastorianus.

Saccharomyces cerevisiae under a microscope.

Ben Franklin supposedly said beer is proof that God loves us. Does that mean yeast are God?
Public domain image retrieved via Wikimedia Commons.

What happened in the 15th century to cause S. pastorianus to be discovered and rise so quickly to prominence in brewing? For many years, it was believed that S. pastorianus was a hybrid of S. cerevisiae and another strain of yeast (or sometimes two or more). Saccharomyces bayanus, Saccharomyces monacensis, and Saccharomyces uvarum, all used in wine and cidermaking, have each been proposed at one time or another as “second parents” to S. pastorianus, but with the advent of genetic sequencing in the 20th century, it became clear that none of those strains were a perfect fit. Each strain left too many stretches in the S. pastorianus genome that couldn’t be traced to either proposed “parent”, leading some researchers to postulate that another, heretofore undiscovered, strain of Saccharomyces must have been responsible, and others to suggest that the new strain must have undergone a large number of mutations before finding its home in some lucky brewer’s fresh wort.

That is, until 2011, when an international group of researchers announced that they had identified a likely candidate for the mysterious “second strain” of S. pastorinanus‘ parentage – in South America. The group isolated and sequenced Saccharomyces eubayanus, a strain of yeast that likes to live on beech trees in Patagonia (and one that’s yet to be found in the wild in Europe despite extensive searching), and found that it possesses genes that represent 99.5% of those found in S. pastorianus and not in S. cerevisiae, making it a compelling candidate for S. pastorianus‘ ancestry.

But how did S. eubayanus find its way into the breweries of Europe from Patagonia? Likely the same way our friend the striped beakfish got to the waters off of Washington: on a boat. One theory is that fruit flies, attracted to barrels of beer or fruit juice on the earliest European vessels to cross the Atlantic to the Americas, brought the yeast with them, stuck to their feet. From there, S. eubayanus somehow found its way into a brewery (maybe through the reuse of barrels or on a person who visited the brewery soon after getting off the ship) and from there into beer, where it got up close and personal with S. cerevisiae, giving rise to a child strain that was perfectly suited for lagering: able to grow and reproduce in much colder temperatures and to thrive on the mix of sugars and nutrients found in beer wort. Now that’s a hell of a journey.

1.A week being about how long it will take to ferment barley and water into something you could call beer, if you were really hard up or had no tastebuds. <<back
2.And quite probably other places, but I’m not familiar enough with the history of beer outside of Europe to say for sure. <<back
3.Some of them by breweries that still exist, and produce beer, even now; the oldest continuously-operating brewery in the world will celebrate its thousandth birthday in 2040. <<back
4.”Saccharomyces” means “sugar mold”. Try not to think about that the next time you’re enjoying an adult beverage. You’re welcome. <<back
5.But not always: the distinctive “banana and clove” flavor of Hefeweizens is a result of esters produced by the yeast used, for example. <<back
6.This was the reason for the creation of the IPA, or India Pale Ale style: it was highly-hopped so as to help it survive long shipping times from England to India during the colonial period. <<back
7.Today beers fermented at higher temperatures are typically called ales, although the term has meant several different things over the centuries. <<back
8.Modern ales usually undergo a period of conditioning as well, but this became possible due to the 19th-century advent of pasteurization and germ-aware sanitation techniques that prevent the beer from becoming infected with undesirable organisms. <<back

Housekeeping…Don’t Eat Me

Clearly it has been too long since I’ve visited the good folks at Science in My Fiction. I’ve forgotten how to insert pictures and videos. Do make with the clickie though folks. You will not be disappointed. I promise. I’ve found you some interesting reading accompanied by cool pictures. Our editor here recommended a few topics for me as I get myself back in the groove. My first choice of those topics was “animal pigmentation patterns.” Of course it was! I love any excuse to talk a bit about my beloved cephalopods.

David Gallo: Underwater astonishments  (YouTube) I’ve enjoyed several TED talks. This one covers several sea creatures but also one octopus in particular that does a stellar job of making like algae. I was hunting a video of one octopus I saw ages ago that kept changing from one thing to another. If you happen to see it or remember it, please leave a link in the comments.

Octopus Escape (YouTube) This is another example of an octopus blending in quickly with its environment. You will see the blanket like spans between its tentacles also change color. Here is a cool article about a blanket octopus (RealMonstrosities). It even has a neat video with it.

When you start looking into camouflage  and more specifically animal coloration, you find a history of study going back hundreds of years.  The Wikipedia articles linked in the previous sentence do a great job of discussing the how, why, types, and applications of the topics. I encourage you to read them and chase down the links. Yes, I will make you tangent hounds yet.  Seriously though, much of what I want to cover in this post involves the new things I learned, some comparisons I had between animals and humans, and some loose story ideas.

Now about the title of the post,  when you visit the animal coloration article, the first thing you see is the spotted finned and tailed, striped oriental sweetlips fish hanging out while two  striped cleaner wrasse clear off parasites. According to the article, the sweetlips’ spots signal sexual maturity. While  “the behaviour and pattern of the cleaner fish signal their availability for cleaning service, rather than as prey.” So much of this leaves me wondering exactly how. In human behavior, uniforms often help convey our participation in a specific profession.

The concept of mimicry was one I recalled from middle school science. In Batesian Mimicry, harmless species imitate the harmful ones. In Müllerian Mimicry, the harmful creatures look like each other. Think bees and wasps here. In everyday life you can convert this to think of various law enforcement agencies resembling each other. Not that they are harmful, but the uniforms are meant to convey authority.

I learned that some frogs change their skin color to regulate body heat. There has to be something here to work with. While others have use melanin to tint their bodies to protect from sunburn. Sound familiar?

Here are three new things I learned from How Animal Camouflage Works (HowStuffWorks):

Chameleons might not only change their color to match their environment and as a matter of signaling, but also to broadcast their mood. My clothes, my hair style, my makeup often are affected by my mood. I wonder what it would be like if I could choose to shift my skin color and hair color by my mood. I wonder what it would be like if these parts of me gave away my feelings. Now imagine what that would be like in the political and diplomatic arenas. I read an anthology a while back about alien life. It had more than one story in which a person communicated with another by changing the tones of their skin.

Nudibranches change their color gradually thanks to a change in diet. I love pizza. I had bad acne as a teenager and young adult. Make of that what you will. I can assure you I turned red while deciding to share it.

Some fish change their appearance by released hormones that react to a change in environment. I know some couples start to look alike after being together a while. I really don’t think I’ve taken on the appearance of the cities I’ve lived in. It could be interesting though. I mean think about the folks that get painted up to support their local sports teams. On a scarier note, I am back to thinking about hormones that can change the way you look without your input on the matter.

One more article for the road: Why do some organisms glow? ( one also includes a cool video. This has to be one of my favorite aspects of this topic. I have always been fascinated with deep sea creatures. I am thinking of covering this topic separately in my next post. Interested? Leave me a comment. Also, share with me some stories in which camouflage played a role. Does this post inspire some story ideas for you? What neat things did you learn from making with the clickie?

Thanks for reading; it’s so nice to be back.

*All links are to Wikipedia unless otherwise noted.



Just when you think you’ve got it figured out: vertebrates use red blood with hemoglobin. The hemoglobin carries oxygen in the bloodstream. Even some invertebrates use hemoglobin, although not octopuses: they have a blue copper-based compound in their blood instead.

And then there’s the icefish. These fish have no hemoglobin, or anything else to bind oxygen in their blood. Instead, they have clear plasma. Because they live in very cold areas, and have very low metabolisms, icefish can get away with having oxygen simply dissolve in their blood.

Scientists have known about the icefish and its clear blood since at least 2006, but it wasn’t until recently that a specimen has been kept in captivity. The Tokyo Sea Life Park has a mating pair of ocellated icefish. Not only do these deep-water Antarctic fish have clear blood, they have no scales.

Just another example of evolution disproving what we think we know, and laughing at our generalizations. There are certain physical and chemical laws involved, of course: this strategy may save the fish the metabolic cost of maintaining hemoglobin and red blood cells, but would only work for a lethargic fish in cold, deep waters.

Sniff-less in Science Fiction

It’s springtime in the Northern Hemisphere, so much of my attention has lately been on my nose. Working in the garden exposes me to an array of allergens, and like anyone who enjoys examining most of their experiences through the lenses of science and fiction, I began searching for interesting nose-related research. Because the end of winter and the onset of allergy season also coincide with the return of my interest in social contact, I’m in the mood to share the highlights of my search.

What does nose science have to do with writing science fiction? Plenty! My simple search for sniffles-related research turned up several worthwhile writing prompts within the study of the sense of smell.

Did you know that the vibration of scent molecules may have as much to do with the detection and identification of different odors as their shapes and surfaces? Apparently, even we weak-nosed humans can tell the difference between molecules that are identical except for a feature as tiny as how their atoms transfer electrons. Where’s the story idea in that? Well, if your main character has a device or an ability to change the way their body odors, maybe they can escape the police. Or affect their perceived age.

Why do we humans have such a comparatively weak sense of smell, anyway? One reason is that, unlike other mammals, it seems that our olfactory bulbs don’t continue making neurons after birth. For the sake of a story, one could speculate about how changed a character’s experience of life might be if they were born with anosmia or hyposmia and later developed a keen sense of smell. Or vice versa; a character with hyperosmia might find a coworker’s perfume so antagonistic that they develop scent-cancelling ‘white odor‘ nose plugs, sell the idea for a fortune, and retire from the cubicle farm.

But what if your main character’s odor issues don’t live in their nose or their brain, but in other organs or their blood? What if exposure to scent molecules triggered unusual experiences instead of the full body yummy feeling most people get from eating or drinking something they like, or the visceral disgust we get when we ingest something foul? To me, that smells like a reasonable science-basis for ‘magic’ potions.

Which reminds me of reading The Scent of Magic by Andre Norton. That was years ago, but it was the first and remains the most memorable use of olfaction I’ve read in a piece of fiction. If anyone can recommend other or more recent stories that put the nose to the literature stone, I’ll be grateful. In the meantime, I’ll amuse myself with more sniffing science.

Further adventures in chemistry

I’m sure you’re all familiar with the endochronic compound thiotimoline, first reported by noted biochemist Dr. Asimov. No? His original publication on the subject is a model of scientific writing, as is apparent in this excerpt from “The Endochronic Properties of Resublimated Thiotimoline” (Asimov, 1948).

It has been long known that the solubility of organic compounds in polar solvents such as water is enhanced by the presence upon the hydrocarbon nucleus of hydrophilic – i.e., water-loving – groups, such as the hydroxy (-OH), amino (-NH2), or sulfonic acid (SO3H) groups. Where the physical characteristics of two given compounds – particularly the degree of subdivision of the material – are equal, then the time of solution – expressed in seconds per gram of material per milli-liter of solvent – decreases with the number of hydrophilic groups present. Catechol, for instance, with two hydroxy groups on the benzene nucleus, dissolves considerably more quickly than does phenol, with only one hydroxy group on the nucleus. Feinschreiber and Hravlek in their studies on the problem have contended that with increasing hydrophilism, the time of solution approaches zero. That this analysis is not entirely correct was shown when it was discovered that the compound thiotimoline will dissolve in water – in the proportions of 1 gm./ml. – in minus 1.12 seconds. That is, it will dissolve before the water is added.

Not current on your organic chemistry? Then just read the final sentence of the above excerpt, though I do recommend making an attempt at the full paper linked above.

Dr. Asimov went on to publish several more studies on the subject, including “The Micropsychiatric Applications of Thiotimoline” (Asimov, 1953) and “The Marvellous Properties of Thiotimoline” (Asimov, 1957).

Other scientists have picked up the topic, expanding greatly on the potential applications of this compound.

A 1989 letter to the British Medical Journal clarifies the history of thiotimoline research (Croall, 1989).

A researcher at Sun Microsystems has been pursing the use of thiotimoline for debugging computer systems (Davidson, 2001):

We have used thiotimoline to build a silicon debugging platform that works as follows. We apply a functional test to two units under test (UUTs) running in lockstep. When the test system detects an error in unit A, a signal alerts special equipment to add water to a thiotimoline sample. Exactly 1.12 seconds before the water is added, the thiotimoline dissolves. This action triggers the sending of a signal, which travels to unit B and stops its clock after a programmable number of cycles. The 1 s between the addition of water and the thiotimoline’s dissolution is far longer than the error latency.

“Yet Another Application of Thiotimoline” appeared in the same journal, IEEE Design & Test of Computers, in the subsequent year (Nelson, 2002). The author proposes a thiotimoline-based keyboard to help overcome writer’s block.

Dr. Asimov himself returned to the study of thiotimoline in 2007, to propose an application in the social sciences: using a telechronic battery to prevent election fraud.