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Monday, December 31, 2018

Biology of Fire

Fire is a part of the natural world. Like everything else in the natural world, living systems have evolved to survive, use, or even require fire. We may have a special relationship with fire, but we're not the only ones with an important relationship with fire. When it's in our control, we see it as a constructive force. When it's out of our control, we see it as a destructive force. And rightfully so, because it's both.

Cropped from image at article.
The recent Camp Fire in California was dramatically destructive, turning much of the community of Paradise into ash. The scale and speed of the destruction was greater than anything in living memory. Over a pair of days, the fire jumped from one building to the next like a living thing. It raced throughout the city, destroying everything as it went. Thousands of people were displaced. There are numerous harrowing tales of narrow escape. Far too many people suffered horrific deaths. In another place and another time, the stories would be handed down through the ages until they became epic sagas.

The trees didn't notice.

The trees remaining standing among all the destruction led some to believe in conspiracy theories. That the buildings were intentionally burned down. That the horrors and escapes were all fiction. That some hidden government agency murdered all those who died. How could all those buildings have burned and missed burning the trees?

Animals can run or hide. Plants have to deal with what comes there way. So. How did they do it?

The trees that so clearly survived this horrific fire had evolved in an environment that included fire. They have thick fire-resistant bark and they shed their lower branches once they get tall enough. They're adapted to survive the sort of ground fire that destroyed Paradise-CA. (Well, the adults are adapted to survive. Any juvenile trees would have been taken out, but the adults will make more.) The structures we built there were not adapted to survive such a fire. Maybe in the future we'll have building codes appropriate to environments where such fires are possible.

So. The trees are adapted to survive fire. Do any plants -use- fire?

I'd have to travel a bit to see a really good example of this. In Australia there is a type of grass in the genus Triodia that is called Spinifex. (There is a different genus of grass with the name Spinifex, so... I got nothing.) During the dry season the grass become so incredibly flammable that it is almost guaranteed that any large area of the grass will burn every few years. The fires burn hot enough to kill off trees and many other plants. The Spinifex survives and readily regrows from underground stems and seeds resting in the soil. Effectively, the grass uses fire to kill off its competition.

Many other grasses seem to have adapted to use this strategy to greater or lesser degrees, but the evidence isn't always so clear-cut.

Ok. The trees survive fire. The grass uses fire. Do any plants -need- fire?

Another tree, the Jack Pine, often definitely needs fire. Its cones are gummed up with so much hard resin that they can't open to release their seeds until they've been burned by a fast, hot fire. After a fire the seeds are able to rapidly germinate into an environment with much less competition. As well, with the reduced level of fuel, the seedlings will likely be protected from another fire until they're large enough to survive it like the adults do. Without fire, the Jack Pine (and other species with serotinous cones/fruit) cannot reproduce. In the absence of some helpful humans who might crack open the cones with power tools, the trees absolutely need fire.

There are numerous fire-adapted ecosystems around the world, with amazing and diverse species that survive, use, and/or need fire for their continued existence. Though plants can't get out of the way of a fire, they're not the only ones with such intricate relationships with it. Animals and fungi deal with fire too. Those sound like later blog posts. Stay tuned.


Monday, December 24, 2018

Mathematical Recreations : Ramanujan's Nested Radical 4

I've previously discussed an interesting math problem posed by Srinivasa Ramanujan way back in 1911.

Over the last three posts on the topic, I've explored my thoughts about this problem and then proved there are an infinite number of valid solutions (any value greater than three).

Since then I've been trying to figure out how to prove all values less than three are not valid solutions. I haven't figured out how to do this yet, but I have figured out how to prove a subset of values are not valid solutions. Any trajectory which reaches zero will then pass to less than zero and be invalid. I might formalize this statement once I've figured out if it can help me finish the overall solution. It might just be a blind alley...

I haven't found anyone else working this problem in the way I have been. The closest I've found has been some comments below a YouTube video where a user talked about calculating through trajectories like I have been. They didn't suggest any sort of general solution to the problem, however.

I did find a mathematical paper using Ramanujan's solution to the problem as part of the title. The authors and reviewers of the paper assumed Ramanujan was correct and didn't test their assumption. I'm considering writing them a letter...


Monday, December 17, 2018

Seed Banks

The largest seed collections are multi-national affairs, backing up national seed collections for large numbers of crop varieties and wild species.
Svalbard Global Seed Vault. The Svalbard global seed vault is designed as a backup for national seed banks. It protects crop biodiversity against regional (and potential global) catastrophes of natural or man-made origin. The facility is protected from many problems that can impact national seed banks by its extreme isolation. Dug into a mountain on an island well north of the Arctic circle, the extreme persistent cold helps to preserve the seeds stored there even with complete power failure. Nations retain ownership of the seeds they store in the global vault. After some event has damaged their local seed banks (or whenever they choose), they can request their seeds back from the vault. Nobody else is given access to the seeds unless the owning nation allows it.
Millennium Seed Bank Partnership. This organization has the goal of banking seeds from 25% of the world's bankable wild species. (Some plant species produce seeds that can't be preserved in a dry state. These have to be preserved through active growth instead of banking.) They focus on species from mountain, dryland, coastal, and island environments that are the most vulnerable to climate change. They also focus on wild relatives of crop species. Their seed collection is used for research, for conservation/restoration projects, and as a back-up for local seed banks (much like Svalbard).
Their overall goal is preservation. Stored crop varieties and species will be maintained (usually in cold storage) in their current form, skipping through time without experiencing any evolutionary changes.

On a smaller scale are local seed lending libraries. Such a library operates by providing seed to members of their local community at the start of the year, then receiving seeds back from those gardeners (that had success) for distribution in the next year. Some growers will ensure their plants are isolated and produce "pure" selfed seed to return to the library. Other growers won't realize they might need to do anything and will occasionally produce hybridized seed to return to the library. Over the scale of many years, the plants that grow from these seeds will be continuously changing. They will be adapting to the local environment and the tastes/favors of the growers contributing seeds back to the library.

Though such a localized variety may have always had the (hypothetical) name "Tomato Alpha", it will be a distinct variety from the "Tomato Alpha" that has been preserved in the seed banks. The common name being applied to what have become multiple different localized varieties will lead to confusion that makes it difficult for people to know what seeds they've received. (This sort of confusion is now seen in tomatoes called "Brandywine".)

Seed lending libraries can't effectively keep an eye out for hybrids (or mistaken identity) in their seeds (nor should they, as this is necessary for developing localized varieties), but they can minimize confusion by ensuring their name is attached to every seed they distribute. "Tomato Alpha, library #1 strain" will be distinct from "Tomato Alpha, library #2 strain" or "Tomato Alpha" (from a seed bank).

Part of my seed-saving philosophy says it is very important for people to save seeds from the plants they grow because it will put incorporate their goals and desires into the future of the plant. This is well captured by the seed lending libraries. I also appreciate the importance of preserving varieties the way the seed banks do because it maintains genetic diversity which can otherwise be easily lost. So, what should we do about the issue of single names coming to refer to multiple varieties?

My personal seed library includes seeds from a variety of sources. I record the variety names for seed that I buy and I'll continue to use the name for seeds I've saved as long as the plants match what the variety is supposed to be. I actively look for hybrids in my garden. If they're interesting, I'll save seeds from them, and then from some of their progeny (etc.). None of these seeds belong to the starting variety, so they get labeled with a description of what the mother plant looked like (since I don't know the daddy) as well as if I know they're F1, F2, etc. Eventually over a several seasons I'll get a better idea of what I want them to be. At the same time their genetics will be stabilizing as they get a better idea of what they want themselves to be. Eventually we'll come to some sort of agreement. I might give them a name at that point, or I might just wait until they tell me what their name is. It might take a while.


Monday, October 29, 2018

Domestication of Yeasts

Saccharomyces cerevisiae is known as the Baker's Yeast. It has helped us make bread, beer, and wine since before recorded history. These days we also use it to make fuel, pharmaceuticals, and for basic biology research. With the innumerable industrial, food, and research purposes we use it for, it is a thoroughly domesticated organism.

With the various mammals we've domesticated, researchers have identified a "domestication syndrome"; a set of features common across domesticated animals. They have shorter faces, milder temperaments, reduced weaponry (teeth, horns, claws), and color changes. In short, they've become cuter. To some degree these are traits that could have been actively selected for, but it turns out that if we only select on temperament, all of the other traits come along for free because all those traits are mediated by the action of neural crest cells throughout the body.

Now, yeast don't have neural crest cells, but they're still domesticated. It didn't evolve to have a more amenable temperament, but it did evolve to grow rapidly in the amenable conditions we provide for them. There's a different sort of "domestication syndrome" that it would have developed along the way. Any trait or ability it needed to live as a wild yeast, but did not need to live under our care, would be lost. This would happen because any lineage that dispensed with those traits would be able to grow faster without the energy drain they represent.

So. What traits would yeast lose under domestication? It's not entirely clear. We can't just look at the cells and see a difference. Nor do we exactly have the wild progenitor yeast around to make comparisons with.

Here we're going to take a bit of diversion.

My first major project in grad school was to figure out how to use flow cytometry to determine the genome size of a different yeast called Candida albicans. In the past, This analysis had proven difficult to do with this yeast for others. This difficulty had been generally blamed on the organism's ability to grow either as independent yeast cells or as elongated hyphal cells that get all tangled up in each other.

I started with protocols developed for S. cerevisiae. At three months in, I was testing yet another protocol variation and the data that came out of the experiment looked like the figure at right. Previous data had much broader, indistinct peaks. (I'm sure I have some of those early figures around somewhere, but I'm not going to spend a bunch of time digging for them.) I was amazed and quickly set up a repeat of the exact same experiment. It failed miserably.

I had made a mistake somewhere in the protocol which made things work. Because it was a mistake, it wasn't written down in my lab notes. You can only write down what you know you're doing.

It took me another frustrating month to figure out what it was I had done wrong. I had used way too much EDTA in the buffers for processing the cells. With this improved protocol, I could get good flow cytometry data from even the most difficult hyphal-growing strains of C. albicans. This disproved the previous theory as to why this species was difficult to work with while doing this assay.

Subsequently, the protocol proved effective with every random yeast species I was able to acquire for testing. I never tested them with the original S. cerevisiae protocol for comparison. In retrospect, I consider this to be an oversight.

The flow cytometry protocol has since then been used in numerous papers from several separate labs. The flow cytometry protocol and analysis tools I developed become the second chapter in my thesis. The idea of wrapping up the material into a paper did come up after I graduated, but I really didn't have the time/energy to dedicate to the process. Researchers should probably cite that chapter, but I know that thesis chapters tend to only get cited rarely. If you are interested in all the details, you are welcome to have a read.

I pretty quickly developed a working theory about what was going on. EDTA binds to divalent cations (Ca2+ and Mg2+) in solution, locking them up so other enzymes don't have access to them. Many enzymes require certain levels of these ions to function normally. For whatever reason, the endogenous nucleases of C. albicans were much less sensitive to low levels of divalent cations than those found in S. cerevisiae. Now, I couldn't think of any way to test this theory. I wasn't in a biochemistry or structural biology lab, so the techniques that would have been useful were well outside our wheelhouse.

This uncertainty has stuck with me for the roughly seven years since then. Just a couple days ago, I developed an idea that in some sense explains the results. Domestication.

S. cerevisiae is a thoroughly domesticated species. It hasn't had to fight for what it needs, so it could very well have evolved enzymes that are used to easier environments with more consistent levels of necessary ions. I strongly suspect the flow cytometry protocol for S. cerevisiae only works because of the domestication syndrome of traits found in S. cerevisiae.

I'm not sure how one would test this theory, but it sure seems to make sense of the observations so far.


Monday, October 1, 2018

The Color of Beans

I've been looking for some blue-colored beans for several years. Its easy to find beans in a range of colors (red, pink, white, yellow, green, black), but blues are a rarity in beans. Early on I found an Italian bean called "Nonna Agne's Blue Bean", but the only seller in my country was out of stock. Sometime along the way I received an offer of some French heirloom blue beans via a facebook connection, but no seeds ever appeared. (She offered them for free, so I can't complain too much.) Blue beans are around, but they're rare.

Last year I received some beans from an online collaborator after I had mentioned my interest in blue beans. She said one of her plants that season had turned out to be an unexpected hybrid that produced blueish seeds. The three seeds that arrived are shown at left. To my eye they were basically black, but with maybe the slightest blue cast. I wasn't optimistic, but after the difficulty I'd had finding blue beans I was going to give them a try.

Two of those three beans sprouted. This was kinda a dramatic time, as those two sprouts could easily have died and then another possible blue bean lead would have gone nowhere. Fortunately, both plants thrived.

A few months later I had a small pile of new beans. When I started shelling them I was very pleased to see some distinctive blue color. As the beans age and dry down, they start to produce some tan pigment which muddies up the pretty blue.

Next spring I'll plant enough of the more blue beans so I can grow enough to make a few meals of them. Right now I have too few to make a meal and have enough for planting.

How did I know that the biology of bean color should be able to produce a blue bean? The red color of beans is due to a group of biological pigments called anthocyanins. This same group of compounds is also responsible for the rare blue pigments we see in biology.

An analysis of black beans showed most of the anthocyanins to be delphinidin (at 56%), with lesser amounts of petunidin and malvidin (26% and 18%, respectively). Delphinidin and malvidin are responsible for blue color in various flowers. The petunidin is described as having a dark-red/purple color. All together, this suggests that black beans really are just super-dark blue beans. This is corroborated by references I've heard of black beans crossed to white beans sometimes producing distinctly blue beans in among the progeny.

So, why are blue beans so rare? I got nothing that explains it. Blue is such a lovely and generally rare color that I would have thought people would have been growing blue beans as much or more than the now-common red beans. Maybe I can help rectify the situation in time.

As I was writing this post I decided to look around again for vendors selling blue bean varieties. I found a European vendor that seems to have stock of the Italian "Nonna Agne's Blue Bean". I also found another unrelated blue variety called "Blue Shackamaxon Pole Bean". I might think about ordering some of each, but it'd be more fun to make my own now that I've got a start at it.


Monday, September 24, 2018

Botanizing in Hawaii: Hawaiian Pepper

Closeup of a pepper plant branch. Several leaves hang down, with a few small elongated peppers and small whitish flowers raised above the leaves.
One of the plants I really wanted to find on my trip to Hawaii is known as the Hawaiian Pepper. This semi-wild pepper plant is generally referred to as a type of Capsicum frutescens, though you will often find references to it as different varieties of C. annuum. The ancestors of these chiles were first introduced to the islands around 1815, but they have since been integrated into the local culture and are often described as native. The small size and non-aggressive growth of the plants has allowed them to integrate into the island ecosystem without being too disruptive. Like other wild peppers around the world, birds also help distribute the seeds.

You can order seeds for it (I have no affiliation with the linked company, but found them via a quick search.), but I wanted to find the species growing wild on the islands.

Wider view of a whole pepper plant, with dried grass and shredded wood mulch around the plant.The plants I found were... not exactly growing wild. As I walked along part of the resort where we were attending a conference, I glanced through a gap in some hedges and saw the characteristic look of chile plants. When I walked around behind the hedges, I found what looked like a little guerrilla garden someone had setup outside the watered and maintained landscaping of the resort. There were several Hawaiian Pepper plants of about the same age/size spaced about the area. I suspect someone who works on the resort planted them and would go by every now and again to tend to them.

I collected a few dried pods that had dropped to the ground around the plants. I didn't grow any this year, but I did send some seeds to a collaborator out in California. (They're on twitter as @ChaoticGenetics. Go check them out!) Last I heard the plants were growing well.


Monday, September 17, 2018

Botanizing in Hawaii: Railroad Vine

Green vines stretched out across the pale sand. There are a few pink flowers along the vines at left.
This is a plant that I knew from my childhood visits to the south Texas shore. Railroad Vine (Ipomoea pes-caprae) is a cousin of the common Morning Glory vine that is specialized to live on beach-side sand dunes. Its seeds are salt-water tolerant and are distributed widely by ocean currents. It grows on tropical and sub-tropical beaches worldwide. On Hawai'i, we only found it growing in one location. Most of the beaches we visited were too rocky for it to prosper.

Closeup of a pink flower with leaves around it.
Closeup of a single leaf. The leafe looks something like a round paper plate folded in half, with a stem at one end.The flowers seemed to wilt under the intense sunlight. If we had found them earlier in the day, they probably would have looked more like my childhood memories of them.

The leaves are thick and smooth, with a major crease down the middle. My recollection is that the common name, "Railroad Vine" has to do with the plant's habit of growing long strait vines along the sand, with evenly spaced leaves.