The Biologist Is In: 2018

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.

View from above of neighborhood after a wildfire as burned through. Buildings are burned to ground, but taller coniferous trees remain intact.

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.

References:

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...

References:

https://www.youtube.com/watch?v=r5BGIi84arY

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.

References:

Svalbard Global Seed Vault

Millennium Seed Bank Partnership

Seed Lending Libraries

www.richmondgrowsseeds.org/

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.

Figure showing genome content size of a population of yeast cells. One large peak near the left edge, with a smaller peak at twice the distance along the x-axis. Smaller peaks at 3x and 4x locations.

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.

References:

Domestication Syndrome: http://www.genetics.org/content/197/3/795
Fox domestication: https://blogs.scientificamerican.com/guest-blog/mans-new-best-friend-a-forgotten-russian-experiment-in-fox-domestication/
PhD thesis of Darren Abbey: https://conservancy.umn.edu/handle/11299/185630
Papers with C. albicans flow cytometry analysis:

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.

Three black dry beans, with an almost bluish shine in the light.

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.

Square plastic pot with two bean seedlings.

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.

Mixed dry beans in shades of dark blue, brown, and a color in between that looks like a dark grey..

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.

References:

Nonna Agne's Blue Bean:

Blue Shackamaxon Bean:

https://stores.southgaseedco.com/blue-shackamaxon-pole-bean-seeds-qty-20-very-rare-bean/

Anthocyanins:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5613902/
https://www.frontiersin.org/articles/10.3389/fchem.2018.00052/full
Petunidin: https://en.wikipedia.org/wiki/Petunidin
Delphinidin: https://en.wikipedia.org/wiki/Delphinidin
Malvidin: https://en.wikipedia.org/wiki/Malvidin

Anthocyanins in beans:

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.

References

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.

References:

Monday, September 10, 2018

Botanizing in Hawaii: Solanum linnaeanum

Closeup of flower, leaves, and stem of plant. Flower is pink with four fused petals, forming a square, and has yellow anhers gathered in the center. The leaves are heavily lobed, with long sharp spines protruding from the underside. The stem too is covered in dramatic spines.

Hawaii has a long history of biological invasions. Plants and animals from all over the world have arrived and thrived there under the tropical sun. This can make it somewhat difficult to identify a random plant, because it could literally come from almost anywhere on the planet.

On one of my hikes, I found several plants I immediately recognized a member of the family Solanacea. This is the same family that includes tomatoes, peppers, and eggplants. I was pretty sure it was even a member of the genus Solanum, one of the several species sometimes referred to as "spiny eggplants".

Closeup of a few leaves and two small round fruit. One fruit is entirely brown. The other fruit is pale green with darker green stripes. The leaves are heavily lobed and covered in spines.

I collected a few fruit, intending to secure some seeds for planting back home in Minnesota. A couple days later, while sorting through my collection at a motel, I finally identified the plant as Solanum linnaeanum. Among its various common names are: "Poison Apple", "Devil's Apple", and "Apple of Sodom". They're native to parts of southern Africa, but have naturalized in Hawaii and various other places around the world.

The plant and its fruit are chock-full of toxins. Enough so that very few animals are willing to eat it. At about this point I decided not to take seeds home for garden trials. I do have a few seeds in my collection that come from highly toxic, or otherwise dangerous, plants. I wasn't entirely certain how much difficulty I would have with trying to leave Hawaii with collected seeds. If some official asked me what they were and why I had them, they might not appreciate my responses. So, to limit that risk, I dumped the S. linnaeanum seeds in the garbage.

(Several days later when I left the state, I learned I would have had no trouble at all. Dried seeds in vials didn't concern the USDA officials at the airport at all. Bringing seeds into Hawaii gets their attention, not taking seeds away from Hawaii. Next time I'll be a bit more bold.)

Interestingly, it appears this species can cross with domesticated eggplant (S. melongena). Doganlar et al. studied an F2 population derived from a cross of the two species in order to map the genomic positions of genes for traits important in domestication. Unfortunately, their paper doesn't have any photos of what the F2 plants looked like. Even with the risk of dragging the toxic traits from S. linnaeanum into the progeny, this would be a fun cross to recreate and explore. The wild species probably has numerous disease/insect resistance traits that would be useful in a garden eggplant, so there is probably value to the experiment beyond simple personal amusement. There's a few online vendors offering seed for this species, so I won't have to make another trip to Hawai'i to start on this project.

References:

Monday, September 3, 2018

Goats of Hawai'i

Group of five goats at the side of a curved road. Three goats are brown and two are black. Behind the goats are piles of dark brown lava stone and scattered clumps of dried grasses.

I visited Hawai'i last year for a horticulture conference. Well, my spouse was attending the conference. I was just going along for vacation. I spent a lot of time driving and hiking during the days when the conference was in session.

Much of the north-west side of the island where the conference was being held is dry-land, with exposed rock from several different ages of lava flows. I came across the bleached bones of pigs and other large animals among the lava, but rarely saw any sizable living creatures.

One day I was driving out to a nearby park to do some hiking and I saw a group of goats crossing the road. I lucked out and was able to capture a few photos like the one above. What immediately struck me about the goats was that they were colored just like many of the aged lava stones I had been seeing the previous few days. They didn't have any of the white markings so common on goats I've seen almost every where else.

It made me think the goats might have been under a pretty severe hunting pressure and that their colors represented adaptive camouflage, protecting them somewhat from visually-hunting humans. If the goats had been resting among the rocks as I drove by, I likely would have thought they too were just rocks.

Goat hunting on the Big Island is allowed year-round in some places, with defined seasons in other areas. There have been intense and largely successful goat eradication efforts in the larger fence-enclosed parks on the island. This represents a fairly high level of hunting pressure, which would definitely be expected to select for traits that help the animals avoid predation.

Unfortunately, I have been able to find no research on the topic of the evolution of wild goats of Hawai'i due to human hunting. This might be a nice topic for a PhD for some motivated student living on the island. Let me know if you come up with anything.

References:

Monday, July 30, 2018

Growing Bur Oak Trees 2

Large acorn cap resting beside a quarter coin for scale. Acorn cap is about three times as wide as the coin. Top half of image shows cap on its side, bottom half shows cap resting upright.

Burr Oak acorn cap.

One of my long-running interests has been domestication of oak trees for food. Now, you can already prepare and eat acorns and there is a long history of native peoples around the world doing so, but rarely does it seem like the oaks have been transformed by the process. What would be ideal is an oak tree that produced very large acorns which were very low in the tannins that make most acorns inedible without intense processing.

Several years back I found a Burr Oak (Quercus macrocarpa) tree with huge acorns littering the ground beneath it. When I broke one open and tasted it... It was straight up sweet. I probably could have taken home a bag full and made a meal from them. Instead, I collected several that looked in the best condition and took them home (to Minnesota) to grow.

http://the-biologist-is-in.blogspot.com/2016/04/growing-bur-oak-trees-quercus-macrocarpa.html

It's now been a couple years and the young trees have not only survived our winters, but they've been thriving. This wasn't a forgone conclusion. The seeds came from trees growing about two thousand miles south of where I planted them. This goes against the general guideline of planting tree seeds collected from somewhere near where you plant to grow them.

Each tree is distinct, with leave size and shape variations. They're all different heights too. I suspect these early differences in growth rate will continue.

Composite of eight images, showing top views (at top) and side views (at bottom) of four young oak trees.

Burr Oak seedlings, each photographed from above and the side.

The trees have only been outside for a couple winters, so it isn't guaranteed that they will survive long-term. Either later this summer or early next year I'll be transplanting the seedlings to cleared spaces in our woods where they can spend the rest of their lives. The local squirrels will be pleasantly surprised in about eight years when the seedlings should start making their first acorns.

References:

Monday, July 16, 2018

Seashell Simulation

Cover image of book, "The Algorithmic Beauty of Sea Shells", with a single large patterned shell at center.

(Book image from large online vendor.)

I've decided it's about time I did a book review. The book is probably not going to already be on your reading list. You are likely to have never heard of it and if you brought it up at a party, I don't expect you'd see a glimmer of recognition among your conversational targets. That said, I think it is a important book because it approaches an interesting topic in biology in a different way than most biology books and in doing so may reach an audience which normally wouldn't connect with biology books.

The book is: "The Algorithmic Beauty of Sea Shells", by Hans Meinhardt (ISBN 3-540-44010-0). I own a copy of the third edition in English. The first version was printed in 1995 in Germany.

At first glance, the book appears to be about how the patterns on sea shells are formed. The book talks very little about molluscs, however. In the first chapter, Meinhardt introduces us to the idea of dynamical systems and how they're involved everywhere in the origin of patterns in the world we live in. From sand dunes to fern leaves, everything we see is a snapshot of a dynamical system. He then goes on to introduce seashell patterns as the history of a complicated dynamic system that played out over the life of the animal.

Chapters 2-9 develop an increasingly detailed mathematical model describing more and more complex patterns found on seashells. You don't have to be able to follow the math to follow the discussion. There are lovely photos and images from the author's computer simulations at every turn. However, if you are interested in the math, the essentials are laid out for you to explore. This detailed mathematical description of the biology is what is often lacking in biology books and what may attract the interest of people who normally would shy away from the "soft-science" that biology is often perceived to be.

Chapter 10 discusses efforts to mathematically model the shapes of seashells. Again, the math is only written out lightly and there are numerous figures illustrating the efforts that have come out of the research into the subject.

Chapter 11 introduces a computer program the author wrote to generate the many simulations illustrated throughout the book. The software comes with the book in the form of a CD-ROM and can can be run on any modern computer using DOSBox, an emulator of the DOS operating system on an x86 computer. This chapter can be entirely ignored if you're not interested in the software.

Chapter 12 takes the lessons learned in chapters 2-9 and applies them in a simplified way to the more complicated biology that is responsible for how plants, animals, and other organisms develop. If you're interested in how the bones of chicken wings (or our arms) are laid out, this is the chapter that might gain your interest. The topics discussed here are much less worked out than the detailed analysis of how seashell patterns are formed.

When I first came upon this book, I was already a biology student at university who also did extensive computer programming. and math. The book spoke to me in a way that no biology book had done before. If you are interested in math as applied to biology, or in how you can convince computers to do complex math, this book will probably be of great interest to you. If you are interested in the complexities of biology and how we can approach the beginnings of an understanding about them, this book will probably be of great interest to you. If you have no interest in math or biology, then this book will probably not be for you. (Also. What are you doing here at this blog?)

Simulation image of complicated shell-inspired pattern, with white/black/red/green colors.

I found the software included with the book to be clunky and slow. It is written in basic and run through a slow interpreter. I decided it would be fun and educational to re-implement the software in a faster language. I was using Turbo Pascal and so began writing. After several years, during which many other things took up most of my time, I had written a program which replicated much of the original software.

The figure at right is from my own software. It takes about 1% of the time to compute as it did in the original program, so it is much easier to play around with generating many different versions. Unfortunately, my program isn't yet complete. There are numerous simulations where my output doesn't quite match the author's. Whenever I am able to dedicate some time to working on this project, I find I am able to resolve more issues, but it will still take some time yet before I am "done".

Eventually, I'd like to write up a detailed description of what I learned while re-implementing the software. If I found the time, I'd like to extend the software in new directions. I've done some initial work towards simulating more realistic 2d clusters of cells, but without any of the complicated math needed for pattern generation. I'd like to explore the evolutionary dynamics that can lead to complex pattern formation. (Things like the various forms of mimicry and what not.) For now, I've put up the various figures I've generated at my Flickr account.

References:

Monday, July 9, 2018

In Miniature

Balcony railing planter with several miniature tomato plants.

My unnamed micro-tomato variety.

I've been growing miniature-sized tomato plants for several years. They first got my attention because I could grow them in a balcony-railing planter right outside my kitchen. Soon after I decided I wanted to breed new varieties that could grow in the same tiny spaces. A few years in, I'm stabilizing one new micro-tomato variety that produces larger fruit than any of the varieties I started with. (Later on in the growing season, I'll be able to illustrate the size difference in the fruit.)

Breeding a plant to be shorter can allow it to direct more of its resources into producing the fruit or seeds we're interested in rather than the stems we find less useful. This reallocation comes at the cost of the plant being overgrown by weeds much easier, so the plants require our assistance to do well.

Efforts in the 1930s-1960s to breed wheat, barley, rice, and maize into shorter, more productive versions is part of what we now refer to as the Green Revolution. Though changes in crop production systems and agricultural inputs also were also developed during this period, the alteration of plant structure through breeding efforts is considered to have been a major factor responsible for increasing grain production during that time period.

There are efforts to produce dwarfed tomato varieties for field production, such as the Ground-Dew and Ground-Jewel varieties from the University of Minnesota. These are a size up from the micro varieties I've been working with.
Right now I have eleven plants of my micro-tomato variety growing in a two square foot planter. A single normal sized plant will occupy a much larger space. It will be interesting to compare the production of my micro plants vs. an individual normal sized plant in my garden by the end of the growing season.

Even if the micros can produce more mass of tomatoes for a given area than a normal sized variety, it doesn't necessarily mean such a small variety would be useful for field-scale production. In a small planter, I can keep ahead of weeds to a degree that would be cost-prohibitive in a field situation.

Until recently, I hadn't thought about growing miniature versions of other crops. A few days ago I learned of a corn variety called, "Mini-Maize". It, like the first micro-tomatoes was bred for use as a research plant. The smaller size and shorter life-cycle allows more plants and more generations to be grown in the limited spaces available in a research biology lab. A plant biology researcher I interact with occasionally on Twitter has offered to send me some seeds for this corn, so maybe I'll be adding this crop to my balcony garden.

Extremely dwarfed sunflower plant with single flower at top.

Unknown dwarfed sunflower mutant.

A few years ago I found this photo of a mutant sunflower that came out of some research program. I haven't been able to find any detailed description of it, nor can I currently find where the photo came from. Like the other dwarfed crops I've mentioned, I can imagine this plant might be more efficient at seed production with respect to area. I can also imagine how any weed pressure at all might negate those gains. I'd really love to have seeds from such a plant, as I can easily imagine growing them on a windowsill.

What is it that makes a plant dwarfed? The classical story is of hormone production or response. Gibberellins are one group of plant hormones that , among other roles, are responsible for stem elongation. If a plant produces lower levels of these gibberellins, or the receptors that allow cells to respond to them, then the plant will have shorter stems than usual.

This can potentially happen without reducing the size of other plant parts, resulting in short plants with normal sized leaves and fruit. This ideal reallocation of energy resources in the plant to our goals doesn't always happen. In the real world, the fruit or seed cluster size is often reduced somewhat along with the overall size reduction because of a link between gibberellins and meristem size. A smaller floral meristem results in a smaller flower and then fruit. Recent research suggests stem elongation and fruit size are regulated by gibberellins via different pathways, so we may be able to resolve the issue in the future and thus further increase crop productivity.

References:

Mini-Maize: http://www.genetics.org/content/early/2016/07/15/genetics.116.191726
Tomatoes:

Micro-Tom: https://www.totallytomato.com/P/00468/Micro+Tom+Tomato
List of ten micro-tomato varieties: https://www.renaissancefarms.org/seeds/10-varieties-of-miniature-dwarf-tomatoes-under-8-inches-tall/
Ground-Dew and Ground-Jewel: https://mnhardy.umn.edu/varieties/vegetables/tomatoes

Dwarf Millet: http://www.caes.uga.edu/newswire/story.html?storyid=4701&story=Dwarf-millet-discovery
Green revolution:

Biology of dwarfed plants:

http://lifeofplant.blogspot.com/2011/03/hormones.html

Atkinson et al. "Ears, Shoots, and Leaves." Nat Plants. 2017 Sep;3(9):686-687. doi: 10.1038/s41477-017-0010-z (Pubmed link.) (Sci-hub link.)

Thursday, April 5, 2018

The Naming of Things

If you've been following me here for a bit, you've probably noticed I'm interested in plant breeding (especially garden veggies). My main goals are to have healthy plants that grow and produce well for me with minimal inputs in my short-season climate. The measure of, "tasty" I go by is what tastes good to me and my family, with what other people consider tasty (when I occasionally do taste-tests) held to a lesser significance.

Two large cherry sized, blocky, white tomatoes. They're sitting on a notebook with a sketched map of the garden, showing where all the plants are and which plants were grown from the same batches of seed. There is a blue pen pointing at the specific plant which produced the fruit.

From 2017, with garden notes.

I've been working with tomatoes for several years and have developed some more fine-tuned ideas about what I want the plants to become. One of my lines, seen at right, is approaching stability. That is to say, most plants from one year to the next produce very similar fruit. The fruit are blocky, large-cherry sized, white (well, paler than yellow) in color, and have a very thick outer fruit-wall (not the skin). They've tested well with people in and outside my immediate family, so I've been thinking about the possibility of distributing their seed in the future.

A few dozen of the large white cherry tomatoes sitting on a white plastic cutting board.

From 2016.

In my personal notes, I've been using the rather uncreative name of, "Abbey White" for these tomatoes. It is sufficiently descriptive to let me know what I'm talking about in my notes, but it isn't a name I expect to attach to the variety when/if I start distributing it. I could easily adjust it to, "Abbey's White", but I'm not sure I want to go with that either.

In the forground is a ceramic bowl filled with diced white tomatoes. In the background is a large wooden cutting board covered in white, yellow, and orange tomatoes (as well as a few green tomatilloes).

From 2016.

"Wait. Tomatoes are red, right!?" A white tomato might seem kinda unusual, but it's just one of a very wide spectrum of colors that tomatoes can be found in. (Check out these companies I have no affiliation with: Artisan Seeds, Baker Creek Heriloom Seeds, TomatoEden, and SeedSavers Exchange. There's so much more diversity in color and taste available if you're willing to grow tomatoes from seed.) My tomatoes tend to be any color but red. Red fruit that have turned up in my garden have tended to have a taste I didn't favor, so over a few years I stopped growing as many red tomatoes. I expect I'll need to bring in some new genetics before I can grow red tomatoes that will taste good to me.

While I was thinking about how to go about naming this variety (and others in the future), I came across twitter user @JanelleCShane. She's been playing with Recurrent Neural Networks (basically a type of AI (specifically a type of machine learning)) trained on diverse datasets, like fruit names (or knitting patterns (or Irish melodies)), so I tweeted:

I actually will need some names for a few new tomato varieties I'm working on. This might be an interesting experience approach to coming up with names. https://t.co/TGFYDcUeBb
— Darren Abbey, PhD (@thebiologistisn) March 8, 2018

(I only later noticed my garbled grammar.) I was somewhat surprised when she responded back, asking if I had a list of tomato variety names she could train her AI with. I didn't, but I was pretty sure I could pull one together pretty quickly from online resources. After some looking, I found several sources ([1], [2], [3], [4], [5], [6]) with large lists of tomato variety names. To avoid spending too much time gathering the names, I wrote web scrapers to process each source and output text files with lists of names. In total, across the six sources, I collected 11,719 distinct tomato variety name strings. Some may represent extinct varieties. Some are in other languages. Some are numerical codes. There's also capitalization and spelling variations. I threw them all into a file that Janelle could use to train her AI.

Have a look at her blog post on the tomato name trained AI at: http://aiweirdness.com/post/172622965862/tomatonames

So. What did the trained AI come up with? Well, at first the AI got overly fascinated with the numerical code names in the training dataset. It produced lots of new "names" that would be quite not useful for naming a new variety. Janelle stripped out most of the code names from the list and trained the AI again.

This time there were some really good results, some really wrong results, and all sorts of weirdness in between. I've highlighted some of my favorites from each category.

The Good,	the Weird,	and the Wrong.
Floranta Sweet Lightning Speckled Boy Flavelle Market Days Fancy Bell Pinkery Plum Mountain Gem Garden Sunrise Honey Basket Cold Brandy Sun Heart Flaminga Sunberry Special Baby Golden Pow	Birdabee Sandwoot Bear Plum The Bango Grannywine Sun Burger Bungersine First No.4 Smoll Pineapple The Ball Golden Cherry Striped Rock Eggs Old German Baby Frankster Black Bumbertime Adoly Pepp Of The Wonder Cherry, End Students Small Of The Elf Champ German Ponder Pearly Pemper Green Zebra Pleaser Flute First	Speckled Garfech Green Dork Cluster Gall Shirve’s Gigant Bullburk Giant Ballsteak Black Crape Brandywine, True Grub Caraball Ranny Blue Ribber Roma Wasting Star Scar Giant Bug Beauty Banana Placente Bananana Stoner Speckled Bake Ruck Green Boor Wonder Bagg Sun Bung Bellende Shart Delight Solad Piss

There were also a collection that would fit perfectly among the real tomato names, though they'd be kinda strange in other contexts.

Matt's Sandwich
Indigo Tree
Striped Hollow Potato Leaf
Lelly's Yellow Stuffers
Terra Pink Strain
Greek Boar
Ton's Oxheart
Babla's German Paste
Mortgage Lifter, Honey Blues

I really like when the AI tried to name a tomato after a person. It didn't have enough examples for real human names, but it gave it a good solid try.

Matt's Sandwich
Lelly's Yellow Stuffers
Ton's Oxheart
Babla's German Paste
Shirve’s Gigant Bullburk

Amusingly, the AI came up with an existing name that wasn't in the training dataset. "Sunberry" is the name of another fruit. It's a close relative of the tomato, so I think I'll call that a positive score for the AI.

Do any of these names fit my tomato? I'm not sure. I do rather like, "Flavelle" and, "Mountain Gem". I'll probably have to let the ideas ferment a while before I come to a decision.

I have recently seen a tomato that the name, "Speckled Garfech" would be perfect for. It came out of someone else's breeding program, so I won't share a photo. Imagine a yellow/orange striped tomato covered in green spots.

Two photos combined. The top half is a photo of a large yellow ceramic bowl filled with small cherry tomatoes. The cherry tomatoes area a mix of white and pale orange with a pink blush on one end. The bottom half is a photo of a closeup of a single larger tomato that is white with pale dark stripes. There are smaller red tomatoes and other items in the background.

From 2017.

I've got a couple more tomato lines that I'd like to stabilize (photographs at right). The upper photo shows a mix of small, very sweet cherries in pale-yellow/white with a pink blush on the bottom end of some. I'll be growing seeds from the ones with the blush. I expect the same phenotype will turn up next year, but I'm also sure there are lots of recessive alleles still hiding in them (for larger fruit, other tastes, and not having the blush).

The lower photo is of a larger, meaty white with pale stripes. This one is a bit further along already thanks to some lucky genetics, even though this phenotype only appeared in the last year. The fruit color, size, and shape are all due to recessive alleles, so those traits should already be stable. The stripes, flavor, and plant growth details probably won't be stable yet. I'll be growing several seeds from this fruit this year to find out.

References:

Tomato seed sources:

Tomato variety databases:

Collected tomato variety name list:

https://t.co/04VTFXlp0m

en.wikipedia.org/wiki/Web_scraping
LSTM Neural Network:

www.seedsavers.org/sunberry-organic
Some of Janelle Shane's AI work:

Tuesday, March 20, 2018

Genetics of Male-Sterile Plants

Male sterile plants are an incredibly important piece of classical biotechnology. (To be clear, they're not the result of "genetic engineering".) They allow the efficient production of hybrid varieties, which dominate the corn, rice, sunflowers, etc. markets because of their high productivity (due to heterosis, hybrid vigor) and consistency (due to genetic uniformity).

Without male-sterile genetics a seed producer has to prevent pollen from one parent from being transferred to the other parent, somehow. This is time-consuming and arduous work (like detasseling corn), or was simply impossible (like with wheat). With male-sterile genetics there is no pollen to worry about in one parent, so there is no need for intensive efforts to prevent pollen transfer. All a seed producer has to do is grow the male-sterile plant inter-cropped with the intended pollen-donor, then collect seeds only from the male-sterile plant. Every seed will be a hybrid. It's as simple as that!

Most male-sterile mutations can be found in cytoplasmic DNA. The mutations can be found sporadically or generated by various experimental methods. With cytoplasmic-male-sterile mutants, all progeny of the plant will also be male-sterile. Once they have been found, they can be introduced into any variety (with some effort) by traditional breeding methods.

At the top are two circles. Yellow at left, with a female symbol beside it; pink at right, with a male & female symbol beside it. Immediately below them, halfway betwen, is another circle representing a hybrid of the above circles. This one is half yellow and half pink, to illustrate the genetic contribution from the parents in the top row. There is only a female symbol beside this circle. There are eleven further circles below. Each is placed horizontally halfway between the previous hybrid and the original pink circle. In each subsequent hybrid circle, the proportion of yellow (as a pie diagram slice) is reduced by half. All the subsequent hybrid circles only have the female symbol beside them. The very bottom circle is filled entirely in pink, representing a male-sterile version of the original [pink] variety.

Fig 1.

We start with a target variety (pink in diagram at left) that produces normal pollen and a source variety with a cytoplasmic-male-sterile trait (yellow in diagram at right). We cross the two varieties, with the first variety as the pollen-donor. The resulting seeds all carry the male-sterile trait, but only 50% of their genetics are like the target variety.

We cross the resulting plants back to the target variety and the new seeds will share 75% of their genetics with the target variety. If we do this backcross again, the next generation will be 87.5% identical to the target variety. (Then 93.75%, then 96.875%, then 98.4375%.) Each generation brings our male-sterile plants closer and closer (by 50% of remaining difference) to our target variety. Eventually the only difference between our target variety and the male-sterile plants is the male-sterility trait itself.

At this point, we've made a male-sterile version of our initial target variety. It can then be used in making large numbers of F1 hybrid seed. As long as the original target variety is maintained, the male-sterile version of that variety can also be maintained by continuing to cross with it.

The figure was drawn from a vague memory of a similar figure illustrating conversion of a sunflower variety into a male-sterile version. I saw the figure years ago and I think it was associated with some USDA research. I wasn't able to find it while writing this, but I'll add a note here with the citation/link if I come across it later. The original author/artist deserves the credit for the method of visualizing the illustrated concept.

(The figure also illustrates the process of introducing any single dominant trait into a target variety via recurrent back-crossing, with dominant-carrying individuals chosen at each generation. With recessive traits, it is more complicated.)

Fig 2.

Less commonly, a male-sterile mutation can be found in nuclear DNA. These are also called genetic-male-sterility and are harder to work with because they're usually recessive. With recessive traits (male-sterile or otherwise), you have to do test selfings every two generations in order to be sure you can re-capture the double-recessive individuals for the next back-cross generation.

In the figure at right, I have each circle labeled with their genotype with respect to the recessive male-sterile trait. ("msms" is the genotype corresponding to the male-sterile phenotype.) Each circle is filled in yellow and pink to represent the contribution from the genomes of the initial strains, as in the previous figure.

As a result of the additional complexity of maintaining and using male-sterile traits caused by nuclear mutations, very few varieties have been developed using them. (A couple are mentioned in [link].) As soon as a cytoplasmic-male-sterile trait is found or made for a species, it would become the trait of choice by seed producers.

The utility of any male-sterile trait is limited to those who are trying to produce large numbers of consistent F1 hybrid seed. These traits would be neutral or positive for home gardeners who don't save seed from year to year. (Positive because they're cheaper to produce than regular F1 seed.) Anyone who saves seed from year to year, from home-gardeners to amateur plant breeders like myself, would probably find the traits annoying and want to avoid them.

With the small number of plants in each generation that I have space to grow for most of my projects, I really don't want a few (or most (or all)) of them to be partly sterile. Fortunately, like any other negative trait, you can select against it if it does turn up in your plant breeding projects and it will soon cease to be a significant issue for you.

References: