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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.


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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.


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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.


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Monday, July 30, 2018

Growing Bur Oak Trees 2

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.

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.


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Monday, July 16, 2018

Seashell Simulation

(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?)



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.


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Monday, July 9, 2018

In Miniature

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.

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.


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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 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.


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