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Monday, December 15, 2014

Hybrid sunflower roots.

1. Plant 3, roots & tuber.
A few weeks ago, we had a solid freeze and the sunflower season came to an end. I dropped by the old place and dug up my sunflowers to see if any of the F1s had developed tubers. The largest hybrid (plant 3) produced one skinny tuber, while the smaller two plants appeared to produce no tubers at all. This was a disappointment, but a more detailed examination of the remaining plant material led to some positive surprises.

2. Plant 1, seeds.
The first plant looked very much like the Helianthus tuberosus mother, but with more red pigment on the stems. I had assumed this was the result of some recombination of maternal alleles and was at best a control to compare the hybrid plants against. When I looked at the remaining two dried flowers on this plant and found them to be full of seeds (image #2), I realized this plant is likely to also be a hybrid.
3. Plant 3, root bud.

The plant that grew the tuber in image #1 also produced a second type of perennial structure, a new bud growing from the old root crown (image #3). This is a structure that isn't seen in either parent species. This feature has been observed before in crosses of this type, however, so I should have expected the possibility.

4. Plant 2, roots.
The other two plants had mildly-swollen roots (images #4 & #5) that have appeared alive when I checked on them. I don't know if they will show new growth in the spring, or if the roots will at some point finally start to rot.
5. Plant 1, roots.

I'm storing the tuber and all the root structures in a dedicated small cube-fridge over the winter. This should keep them safe from the mice that wander through my basement and allow me to grow at least one of them again next year alongside additional F1s from the ~70 seeds that remain from the first cross.

References:
  1. H. annuss x H. tuberosus : bulbnrose.x10.mx/Heredity/sunflowerXchoke/sunflowerXchoke.html

Wednesday, December 10, 2014

Black Nightshade

I've recently written a new post on the topic of toxicity in this plant that you should also read if you've found this page via search or other methods.



1. Solanum nigrum.
Myths of edibility are much shorter-lived than myths of toxicity. If something is poisonous and you keep eating it, you (or your surviving friends and relatives) will soon learn your error. If something is perfectly edible, but you never eat it for fear of poison, then you will never learn what you're missing.

The common weedy plant Solanum nigrum (Black Nightshade) is a premiere example of this. The berries are routinely considered to be poison, even though there are no recorded fatal poisonings unambiguously associated with the plant.

The berries of every S. nigrum plant I've come across have been very edible, tasting like a somewhat floral and mildly sweet tomato. The ripe berries and green leaves are used over much of the world, with the leaves being used as a pot-herb comparable to spinach. Research has suggested that it might not be a good idea to eat the unripe berries, as they sometimes contain a limited amount of solanine.

Plant poisons tend to be polite, in that they have the trait of tasting poisonous. The putative toxin in S. nigrum is solanine, which has a bitter taste. There are reports of some S. nigrum plants having bitter leaves and unpleasant berries, while others have bland leaves and mildly sweet berries. I suppose I should advise you to not eat the unpleasant tasting plants.

The myth of toxicity of S. nigrum seems to have been spread by the European diaspora. European-derived cultures everywhere seem to think it is deadly poison, even while the natives living in the same places continue eating it routinely. Why would Europeans think this plant is poison?

2. Atropa belladonna; UK range map.
In the UK and much of western Europe, there grows another plant with black berries. This one, Atropa belladonna (Deadly Nightshade), is deadly poisonous, with a long recorded history of deaths… but only in Europe where it grows. In Europe, if you taught children that one black berry (S. nigrum) was edible, but another (A. belladonna) was poison, there would be the risk of them making a deadly mistake in identification. In this context, it is perfectly reasonable for European parents to teach their children that black berries are poison.

A. belladonna has spread to a few other places in the world, but isn't something you will generally run into. If you don't know plants well enough to tell the difference between S. nigrum and A. belladonna, then you really shouldn't be eating anything you find outside. The plants are as distinct as a dog is from a cat. You almost assuredly have experience with identifying those animals, so there is absolutely no way you would mistake one for the other. It still is a good idea to teach children not to eat things you can't identify, but you shouldn't be claiming poison is the reason.

3. Diospyros texana.
The aversion to black berries has even carried over to entirely unrelated plants, that just happen to have black, round fruit.

Diospyros texana (Texas Persimmon) is a tree that produces perfectly edible black fruit that many (of European cultural extraction) consider to be poisonous, even though there are no toxic relatives or mimics. It has a long history of utilization as a food source by American natives of the arid Southwest, but has in recent times been marginalized to a landscaping plant because of the peculiar attitudes of the now-dominant culture.
4. S. nigrum.



Forms of S. nigrum have been partly domesticated under the name "Garden Huckleberry". These plants have slightly larger berries and a more upright growth form than most of the wild plants. There are red ("Makoi") and orange ("Otricoli") varieties that people might be more likely to believe are edible.

I've collected numerous seeds from a local (Minnesota) form of S. nigrum, with the goal of using them in a mutation breeding experiment. The basic idea is to expose a batch of seeds to some mutagen, like X-rays or some chemicals, and then grow out the resulting plants to look for variations which might be more useful. Larger or different colored fruit are the most obvious things to look for, but other interesting traits may also appear. I would like to use ultraviolet light as a source of mutations, as UV-light is easy to control and keep contained, but I still need to determine if it will work for these seeds.



There are still occasional reports of people eating S. nigrum and experiencing gastrointestinal distress. They could have had a specific allergic reaction to the new food source. For this reason, people should be conservative about eating plants they don't have experience with.

5. Solanine-rich S. dulcamara.
The putative poison found in S. nigrum is the bitter-tasting solanine. It is not entirely clear if everyone can taste this compound. You can experimentally determine your ability to taste Solanine by tasting the very common S. dulcamara (image #5), which has elongated orange/red berries and purple flowers. S. dulcamara is definitely toxic due to the high levels of solanine found in its leaves and berries. For several years, I have been occasionally tasting the berries (looking for a 'sweet' version), but have found very little variation in the amount of poison. If the fruit of this plant tastes sweet to you, then you should have someone else taste it before you really eat any and you might want to avoid tasting wild things like this as a rule.



If you eat some S. nigrum (or S. dulcamara) berries and get sick, you really can't blame me for it. "Some guy on the internet told me it was ok!" won't hold up in court.



References:
  1. Solanum nigrum
  2. Atropa belladonna
  3. Diospyros texana
  4. Solanum dulcamara

Tuesday, December 2, 2014

Nicotine

Nicotine is highly addictive, and not just for us humans.

I observed this black vulture (Coragyps atratus) apparently looking for and eating discarded cigarettes at a roadside park in central Florida. I also noted the same behavior with a different group of vultures at another park during the same trip.

If we were to eat tobacco like this, it would quickly make us sick. Vultures are adapted to eat decaying meat and all the nasty toxins that go with it. Because of this, they have what would be described as an, "iron stomach". I wonder how common the behavior is and if addicted vultures get angry when they haven't had a fix in too long.

Cigarette butts have reportedly been found in the intestines of whales (presumably having been washed out to the ocean and ingested along with their normal food). There are photos of other birds investigating cigarette butts they come across, but I haven't found any reports of any animals actually eating them.

(While trying to find other reports of this behavior, I did find a report of people smoking dried vulture brains. People are strange things.)

Thursday, November 27, 2014

Genetic Assimilation.

1. [source]
Tomatoes sporadically produce fruit with horns, fleshy extensions adjacent to the calyx. Do a web search for, "Devil Tomato" and you will find several like the one in image #1. Generally, there is no evidence for these being the result of a genetic mutation. Rather, they represent the sort of thing that can happen when the normal development program of the fruit is disrupted in some way. Seeds taken from such a horned fruit will be no more likely to produce a plant that has similar fruit than seeds taken from any other fruit on the plant.

2. [source]
 There is a related species, Solanum mammosum, that has multiple such horns (image #2). (Though, there are example plants without horns.) The fruit of S. mammosum are rather toxic, so it wouldn't be a great idea to try and make a hybrid between the species and domesticated tomatoes.

3. [source]
Because there is the developmental potential for horns to be generated in tomatoes, there is the potential for a mutation to emphasize the trait. In the Tomato-TILING project, a few such mutations turned up (image #3). I'm not a professional plant developmental biologist, so I don't expect to get access to these interesting mutant seed lines any time soon.

I like the idea of looking for something that everyone else is trying to avoid. Every tomato breeder I've come across has been trying to breed away from a horned tomato, to produce a more "perfect" fruit shape, so I instead want a tomato that is all horns. I have the mental image of a tomato covered in fleshy projections featuring on a counter in some new science fiction movie.

As the previous examples have certain difficulties as a source for this trait, I've been looking for tomato lines which show a higher rate of these "deformations" to use as starting material in a project to breed a tomato that has the trait more consistently.

A rarely studied evolutionary model called "Genetic Assimilation" describes the process where an aberrant trait produced as the result of some stress is selected for and eventually becomes genetically fixed even without the presence of the stress. This mechanism sounds like Lamarckian evolution, except that it relies on the natural selection and the developmental plasticity of organisms…  rather than the personal experiences and intention of the organism that was favored by Lamark. It works because every trait is impacted by the genetic background, the combination of many subtle influences from other genes throughout the genome.

I frequent the Tomatoville forums, including the "Crosstalk: Tomatoville Research and Development™" forum. I started doing so because people there have a tendency to post lovely photos of the interestingly colored and patterned tomatoes they have been growing. Recently, a user was posted images from the results of a complex cross (["Pink Furry Boar" x "Ananas Noir"] x "Bosque Green Cherry") that they were working with. One of the diverse progeny they grew (image #4) had horns on 4 of the 20 fruit. 20% is a far higher rate than I'd otherwise come across, so I asked for a few seeds.

In a few years, I'll have a better idea of where this project is going. The good thing is that I can eat all the rejects along the way.



References:
  1. Genetic Assimilation:
    1. http://jeb.biologists.org/content/209/12/2362.full
    2. http://en.wikipedia.org/wiki/Genetic_assimilation
    3. http://eebweb.arizona.edu/faculty/badyaev/ecol596e/assimilation.pdf
    4. In tiger snakes: http://blogs.discovermagazine.com/notrocketscience/2009/10/30/big-headed-tiger-snakes-support-long-neglected-theory-of-genetic-assimilation/
    5. In fruit flies: Waddington, C. H. (1942) Canalization of development and the inheritance of acquired characters. Nature 150:563-565.
  2. Horned Tomatoes:
    1. http://www.tomatoville.com/showthread.php?t=34162
    2. https://www.flickr.com/photos/farflung/6462879911/
  3. Solanum mammosum
    1. https://www.flickr.com/photos/30372914@N03/3895429577/
    2. https://www.flickr.com/photos/22012266@N02/7164709249/
  4. Tomato Tiling project
    1. http://tilling.ucdavis.edu/index.php/Tomato_Tilling
  5. Tomato Varieties:
    1. Pink Furry Boar
    2. Ananas Noir
    3. Bosque Green Cherry

Wednesday, November 26, 2014

A Requiem.

Jonathan Abbey, my brother.
I've never really fit in with those around me. I accept this and don't need those around me to think the way I do. All I need is for them to accept me for who I am. I have had the good fortune to find someone to share my life with who does this. Barring some unexpected misfortune, by this time next year, she and I will be married.

The way I think about the world is very rarely linear. This has caused conflict between me and my academic advisor, as she wants me to construct lists of what I am working on and how I will set about completing then. I generally think in images, patterns, and relationships. When I am working hard on a puzzle, I tend to see my thought processes as some form of abstract math, even though I don't always have the vocabulary to convey that math to those around me. There are conceptual problems that I've thought about for a while and came to solutions that I'm absolutely certain are true, but I don't yet know how to show them to anyone else. Sometimes, I don't even have a glimpse of how to explain.

There have only ever been a few people that I looked to as role models, for inspiration. Athletes, artists, politicians, and other people who arguably have large positive (or negative) impacts on the people of the world have never felt like role models to me. The people I have ever felt this sort of connection with, that remind me of how I see and want to see the world around me, I can count (in no particular order) on one hand.
  1. Albert Einstein.
  2. Richard Feynman.
  3. Stephen Hawking.
  4. Jonathan Abbey.
None of them were biologists. Perhaps this shouldn't be a surprise, as I often don't fit the standard model of a biologist all that well. They all shared a clarity and depth of thought that I aspired to.

The first three are names you are probably familiar with. Well, you're probably familiar with them if you've had a long-running interest in science and how the universe works. Einstein and Feynman died before I became aware of them and I don't expect to ever meet Stephen Hawking. (I wouldn't know what to do or say if I did.) It was only when I started learning about how they came to the discoveries they're known for that I started looking to them as role models.

Jonathan Abbey was the older of my two older brothers, my parents' first child. A few weeks ago, he died unexpectedly. The proximate cause of his death was cardiac disease, atherosclerosis. This is what is colloquially referred to as "hardening of the arteries". The ultimate cause of his death was his inability or refusal to keep to the schedule for his medication. He had type-1 diabetes and ankylosing spondylitis, two auto-immune diseases which amplify the effect of high blood-pressure on the damage to cardiac arteries which causes atherosclerosis. He went to the emergency room in the week before with chest pain. They gave his heart a clean bill of health and sent him home.

He spent a great deal of time thinking about thinking (meta-cognition). He encouraged me to pursue a PhD and was very proud of the work I have been doing when I last visited with him. He lamented his own choice of not pursuing a higher academic degree for himself. His professional work involved designing and managing very complex systems. He liked video games, music, and poetry as hobbies. He spent time thinking very deeply about people and how the world works. He pursued knowledge and argued vehemently against "belief". He strongly felt that what was real, what was verifiable, was most important. He was a good father, but maybe not so good of a husband or boyfriend. Many people who knew him thought he was a genius. He was my brother and I'm having a hard time dealing with his passing.

I've gotten past the shock. I've gotten past the sporadic moments of denial. I've even gotten past the moments of anger. I never really went through a bargaining stage. Now, I mostly just feel old. I think this is a mix of depression and acceptance.

I don't believe in a soul or an afterlife and neither did he. Attempts to comfort me by saying, "he's in a better place", in any form or variation are misplaced. Such efforts will anger me, even if not obviously so. If I know you, they will discourage me from interacting with you in the future. If I don't know you, I'll just delete your comment and maybe ban you.

I'm in the very final stages of completing my PhD in the department of Genetics at the University of Minnesota. By the time I post this, I'll have handed off my written thesis to my committee for review. In another two weeks, I'll defend my thesis and be done with it.

I'm sad that my brother won't get to know.

Monday, November 17, 2014

What is a chicken?


We refer to them by the species name Gallus gallus domesticus, but there was a time before they had any connection to us. The wild species is Gallus gallus, also known as the Red Jungle Fowl, and it can still be found running around the wilds of south-east Asia.

There is genetic evidence that modern chickens arose from multiple independent domestication events. The diversity of alleles found in domestic chickens encompasses those found in wild populations of G. gallus spread through India (G. g. murghi), Burma (G. g. spadiceus), and Tailand (G. g. gallus). This is best explained by the early incorporation of Red Jungle Fowl from different regions into the common pool of chickens being cared for by people.

It turns out that there are three other related species of jungle fowl (grey, Ceylon, and green) roaming the area of south-east Asia. A trait found in domesticated chickens that causes yellow skin on the legs and feet is due to an allele which shows most similarity to an allele found in the Grey Jungle Fowl.

A. Green stars indicate putative domestications.
B. Domesticated chicken.
C. Red Jungle Fowl. (Range in red in A.)
D. Grey Jungle Fowl. (Range in grey in A.)
At least four different populations across two (of what we consider) separate species contributed to modern domesticated chickens.

How could the process of domestication start in multiple places at the same time? Well... it can't, but it can happen close enough in time to be indistinguishable to modern researchers.

It is a common pattern in domestication for the idea of domesticating an animal or plant to spread faster than the newly domesticated organism can spread. This results in multiple independent domestication of a single species, or of similar species, found across a wide area.

Cattle appear to have been domesticated two or three times (from Bos tauros, B. indicus, and possibly B. africanus). Sheep and goats appear quite distinct to us now, but when they were domesticated, they were very similar creatures.

Chile peppers have been domesticated at least five times (Capsicum annum, C. chinense, C. frutsecens, C. bacatum, C. pubescens). Squash were domesticated at least five times (Curcurbita pepo, C. moschata, C. maxima, C. mixta, C. ficifolia). Carrots (Daucus carota), parsnips (Pastinaca sativa), celery (Apium graveolens), parsley (Petroselinum crispum), Dill (Anethum graveolens), and chervil (Anthriscus cerefolium) all belong to the family Apiaceae and look very similar in their wild state.

So.  What is a chicken?

It is an example of how the rapid spread of ideas through human culture impacts the process of wild things becoming integral to our civilization.



References
  1. http://en.wikipedia.org/wiki/Red_junglefowl
  2. Multiple domestication : http://www.biomedcentral.com/1471-2148/8/174
  3. Hybrid between red and grey jungle fowl : http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000010 
  4. Cattle : http://archaeology.about.com/od/domestications/qt/cattle.htm
  5. Chile peppers : http://archaeology.about.com/od/cbthroughch/qt/Chili-Peppers.htm
  6. Squash : http://en.wikipedia.org/wiki/List_of_gourds_and_squashes
  7. Apiaceae : http://science.jrank.org/pages/1240/Carrot-Family-Apiaceae-Edible-species-in-carrot-family.html

Tuesday, November 11, 2014

Evolution

While thinking about the evolvability of different artificial life simulations, as discussed some in my last posting, I realized that it would be helpful to talk about what is required for a system to evolve. It comes down to four basic traits.

1. Reproduction: Some unit in the system has to reproduce. This unit could be bacterial cells in your gut, or it could be numerical representations in a computer. (Even fire can be described as reproducing when it spreads through a house or forest.)

2. Inheritance: During reproduction, each new unit in the system has to gain traits from its parent(s). The traits could be hidden, as in recessive alleles, or it could be obvious, as in dominant alleles. The number of parents can be one or more than one. (We have two, but maybe some aliens have three or more.)

3. Mutation: At some point in the reproductive cycle, there has to be the potential for changes in the traits (mutations) that are inherited.

4. Death: Death is generally required to remove individuals from a population, thus freeing up room for the next generation. However, there are scenarios where death isn't required. If the population is continuously expanding into new territory, the front-line sub-population can evolve over time without individual death. In this case, the older organisms being left behind fills the same role of actual death.



It is relatively easy to prove mathematically that a system with these four traits will experience evolution.

Lets give it a go in a simulation that has a maximum population of four organisms represented by letters and driven by the following rules.
  1. Reproduction with inheritance: A -> AA; B -> BB
    • A or B can duplicate.
  2. Mutation: A -> B.
    • A can mutate into B.
  3. Death: A -> A 
    • Only A can die.
We start the simulation with "A" .

"A" -> "AA" -> "AAAA" -> "AAAB" -> "AAAB" -> "AB" -> "AABB" -> "AABB" -> "ABB" -> "ABBB" -> "ABBB" -> "BBBB"

This may not look like the sort of math you are familiar with, but it is math nonetheless. Math is the manipulation of abstract symbols that represent precise concepts with the extremely rigid rules of logic. 2+2 always equals 4. A system with the described traits will always experience evolution.

Now, this little toy system I've described has an extremely low evolvability. The starting state of the system ("A") does meet the four requirements and thus evolves. However, once the system has reached the final state ("BBBB"), it no longer meets the four requirements and thus cannot evolve further.



If you argue that life doesn't evolve, then you are logically arguing that life does not meet one of the four requirements discussed above. Unequivocally, life meets the four requirements.

Life evolves. The math doesn't provide any other possibility.