The Biologist Is In: November 2019

Thursday, November 28, 2019

Fava Beans

Cluster of brown/purple flowers on a fava bean plant.

[Photo from link.]

I've eaten fava beans (Vicia faba) from time to time, but I've never grown them. I was recently perusing some postings from blogs I occasion and found an interesting post. The post contains a wonderful series of photos of fava bean flowers in the author's garden, ranging in shades of red/pink and brown/black. A forum discussion revealed that these variations were the result of crossing the varieties "Crimson Flowered" and "Red Epicure". After searching around a bit, I found that for the vast majority of fava bean varieties the flowers are only red/pink or brown/black.

The flowers are impressive enough in the garden already. Some improvement in flower size or color range would be awesome. My biology background leads me to think of at least two strategies.

Hybridize F. faba with related species with different flower colors.
Find rare varieties of F. faba with different colors.

1. Hybridization? I like this strategy generally, but the usefulness of the strategy depends on the plant being worked with. It turns out that there are no known species which can be used to produce hybrid seed with V. faba. There is some research looking into why crosses don't work. F. faba as seed parent crossed with V. galilaea and V. johannis both appear to result in fertilized eggs. F. faba as pollen parent crossed with V. bithynica also appears to result in fertilized eggs. The fertilized eggs don't seem to result in viable seeds, however. There is some later developmental failure which interferes with the cross. It might be possible to use embryo rescue to allow some of those crosses to grow up. This is well outside my skill set for now.

Variously colored fava means laid out in a grid, 11 beans wide and 6 beans tall.

[Photo from link.]

2. Finding old/rare varieties relies on such varieties still existing. The internet provides us with an amazing ability to find things, so long as someone, somewhere has put it online in some form. The image at right and others suggest there's a great deal of genetic diversity around, which might include interesting traits impacting flower color. The task of getting seeds to trial may be rather involved, but it is definitely a way forward.

References:

"Crimson Flowered": www.thompson-morgan.com/vegetables/vegetable-seeds/pea-and-bean-seeds/broad-bean-crimson-flowered/4772TM
"Red Epicure": davesgarden.com/guides/pf/go/40640/
misc: www.heritageharvestseed.com/beansbroad.html
misc: prseeds.ca/seed_categories/beans/favas-broad-beans/

Thursday, November 21, 2019

The Color of Onions : The Whims of Genetics

I've previously posted about what might go into changing the color of onions (the-biologist-is-in.blogspot.com/2013/12/the-color-of-onions.html), but now I've gone and done an experiment. It was an accident, really, but many useful experiments start out as accidents.

We planted out a batch of "red" onion seedlings this last spring. We got them in a trade from someone who had started them. We got a pot of onion threads, and they got a couple squash babies in return. I'd never grown onions before, so I just put them (along with several types of decorative onions, hoping the deer would leave them all alone) into a raised bed that I had recently cleared. I watered the babies a few times when I noticed the soil was dry. I never fertilized or amended the soil. I basically ignored them. In retrospect, this is not the way to get those luxuriant onions you see in the store. Somehow, almost all the plants survived and produced bulbs. Inch-long bulbs, that is.

I pulled each onion as its leaves died down. They got cleaned, dried, and then left alone on the kitchen windowsill. After too many had accumulated, I moved them to a spare drying rack left over from an ongoing tomato-jerky experiment with a food dehydrator. A couple days later, I happened to notice that one of the bulbs was a much darker color than all the others. An early thought was that this was the color of some mold infesting the bulb, but on close examination there didn't seem to be anything wrong with it. It definitely was a darker shade.

I started looking at the color of the collected onions. One stood out as being more red than the others... actually red instead of that purplish color that "red" onions typically are. Another was a rich purple color.

12 vials in a row, filled with clear colored liquid going from red at left, to blue, green, and then yellow at the right.

www.braukaiser.com/wiki/index.php?title=An_Overview_of_pH

Since "red" onions are colored by anthocyanins that change their color depending on pH, we can estimate the pH of the cellular structures where the pigment is found. The red bulb approaches a pH of 2, while the purple bulb approaches a pH of 5. If we could drive the pH further to the right by the same interval, we'd get a pH=8 onion that looked blue.

I was planning to save the color outlier bulbs (red, purple, dark) to grow the following year for seed. Unfortunately, they didn't survive the winter. I was pretty sure they wouldn't survive outside, but I didn't think about how best to get them to survive inside.

I may re-do this initial experiment next year. Onions with unexpected colors would be fun.

References:

Thursday, November 14, 2019

Biology of Blue

Two plants on the forest floor, with broad oval leaves growing from the base and a thin stem topped with dark blue berries.

Blue-Bead Lily (Clintonia borealis)

Blue is very hard/expensive for biology to produce.

Blue light is higher energy than other visible frequencies, so chemistry to absorb everything else but pass/reflect blue light is ... tricky.

The lovely blue feathers of the Blue Jay (Cyanocitta cristata) and Eastern Bluebird (Sialia sialis) have no blue pigment in them. The vibrant blue so often seen in dragonflies is produced without any blue pigment. Even the blue color we see in the eyes of some people has no blue pigment. These and many more examples of blue in biology all are referred to as structural colors instead.

Structural colors are produced by the presence of microscopically fine structures that interfere with light. The blue of some human eyes is caused by very small particles of melanin (a brown pigment), for example.

Molecular structure diagram, illustrating the general structure of flavones, with three six-carbon rings.

Flavone structure.

Some blue berries, like those of Marbleberry (Pollia condensata) are blue due to a structural color. Others, like the Blue-Bead Lily (Clintonia borealis) I photographed in northern Minnesota (at top-left) have a blue flavinoid pigment. The flavinoid pigments are derived from or structurally similar to flavone (at right).

Some insects (like the Lycaenid butterflies) are blue due to flavoniods like kaempherol. Some of the more common flavinoid pigments are the anthocyanins responsible for the red/purple/blue colors seen in fruits and other plant tissues. Different compounds in the group have various modifications to the basic flavone structure. Those modifications impact the stability of the ionic form of the molecules at different pH levels, as well as the specific frequencies of light that are absorbed.

I don't have a solid grasp on the physics that leads to all the differences in color, but the following quote from this paper seems to be illustrative.

"Confining electrons to a smaller space makes the light absorbed bluer and if they move around in larger space the light absorbed is redder."

When the light absorbed is bluer, the light transmitted (and thus observed) is redder, and vice versa. Thus, when electrons are more de-localized, the molecule will have a more blue color. Conversely, when electrons are more restricted, the molecule will have a more red color.

In the structure of lycopene, responsible for the classical red color of tomatoes, electrons are restricted to travel within very localized regions of the molecule.

Molecular structure figure, single enlongated carbon chain with double and single bonds.

[From Madu & Bello, 2018.]

Compared that to the anthocyains, where the electrons are de-localized into aromatic carbon rings. Here the electrons are much more free to occupy larger spaces. The molecules often absorb more red and appear bluer.

Molecular structure figure, illustrating the basic structure of anthocyanins.

[Modified from Khoo et al, 2017.]

One of the anthocyanins that is more stable at higher pH is called delphinidin. It is responsible for the clear blue color found in delphiniums and can also be found in various purple plant materials. The exact shade it presents us with depends on the specific pH of the cell and the association of the delphinidin with various molecules or ions in ways far more complex than I've been able to become clear about with my readings so far.

So. Why does biology often go with structural colors, when there are commonly available molecules which produce the color? Two partial answers that come to mind are:

It may be that the flavinoid blue pigments are more energetically expensive to produce than other pigment types.
It may be that structural blues are very easy to come by on accident (like iridovirus infection of isopods).

Evolution is a tinkerer, not a planner. It can be very hard to ever answer questions of "why" in biology. It is far easier to answer questions about "how" or "what". In the end, biologists often have to say, "I really don't know. Do you have any ideas about how we might find out?"

References:

Structural color:

Bluejay color: https://dnr.wi.gov/wnrmag/html/stories/2003/feb03/jays.htm
Eastern Bluebird color: https://academic.oup.com/beheco/article/14/6/855/269116
Dragonfly color: https://jeb.biologists.org/content/207/22/3999.long
Human eye color: https://www.sciencealert.com/science-how-blue-eyes-get-their-colour
Bluebead Lily:

Butterflies:

https://link.springer.com/article/10.1007/BF01880094

Marbleberry (Pollia condensata):

Anthocyanin pigments:

Chemistry of colors:

https://www.ias.ac.in/article/fulltext/reso/006/03/0066-0075

Lycopene structure:

http://ijsrch.com/IJSRCH18322

Iridoviruses: https://link.springer.com/chapter/10.1007/978-3-642-70280-8_4

Thursday, November 7, 2019

Botanizing in Alaska: Alpine Blueberry

Small blueberry bush with unripe green berries.

The Alpine Blueberry (Vaccinium uliginosum) grows throughout Alaska. I took this photo during midsummer. The berries ripen during fall, so I didn't get any on the trip when I took the photo.

The ripe berries are well-regarded by humans and bears alike. Both can be found collecting them along roadsides in the fall. Ideally not in the same place at the same time, but you have to keep aware of your surroundings while berry picking in case you're lucky/unlucky.

On a more recent trip than when I took this photo, I was lucky enough to find plenty of ripe blueberries to pick as well as a black bear filling itself on blueberries. I was especially lucky in that the two of us were picking berries in different places.

Within each berry are several tiny seeds. The seeds need a period of cold moist stratification before they will germinate effectively. I'll be planting a batch of seeds in a pot outside to see if I can get any plants to grow next year.

References:

Bog/Alpine blueberry: