// Twitter Cards // Prexisting Head The Biologist Is In: July 2018

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.


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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.


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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.


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