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
• www.croptrust.org/what-we-do/svalbard-global-seed-vault/
• en.wikipedia.org/wiki/Svalbard_Global_Seed_Vault
• Millennium Seed Bank Partnership
• en.wikipedia.org/wiki/Millennium_Seed_Bank_Partnership
• www.kew.org/science-conservation/collections/millennium-seed-bank/about-millennium-seed-bank
• Seed Lending Libraries
• www.richmondgrowsseeds.org/

Significantly Fuzzy and Uncertain Math

I was always a very smart student, but I wasn't always a very good student. During lessons over the years, there would occasionally be little pieces that I would miss. Well, I either missed them or they simpler weren't taught. One of the earliest ones was about what the point of remainders were in doing division. I never once remembered a math teacher saying the remainder was the numerator and divisor was the denominator. When the schoolwork moved past remainders, I had to basically learn the math all over again because there was no apparent connection between what we were doing with what I had been taught before. Years later I was puzzling over what the point of that early math had been and I made the connection, filling in the gap in what I was taught. If someone is trying to teach me something and I can't integrate it into the knowledge I already have, it has always been extra difficult.

In high-school, I was taught about significant figures. Our pre-calculus teacher got in an argument with a student (not me) one day. She was adamant that, "0 was not the same as 0.000", but she didn't explain why. I always had the hardest time keeping the rules for significant figures straight during calculations. It was only in college that I finally understood that significant figures represent the level of uncertainty in a measurement. The idea that a numerical measurement was a distinct concept from the number that described the measurement was something of a novelty to me.

---

Those significant figures rules?

1. For addition & subtraction, the last significant figure for the calculated results should be the leftmost position of the last significant figure of all the measured numbers. Only the position of the last significant figure matters. [10.0 + 1.234 ≈ 11.2]
2. For multiplication & division, the significant figures for the calculated result should be the same as the measured number with the least significant figures. Only the number of significant figures matters. [1.234 × 2.0 ≈ 2.5]
3. For a base 10 logarithm, the result should have the same number of significant figures as the starting number in scientific notation. [log₁₀(3.000×10⁴) ≈ 4.4771]
4. For an exponentiation, the result should have the same number of significant figures as the fractional part of the starting number in scientific notation. [10^2.07918 ≈ 120.0]
5. Don't round to significant figures until the entire calculation is complete.

---

Lets see if we can convert these basic rules into something with a more statistical flavor. First we should define a way of writing uncertain numbers. lets define an example number 'x', which has a measured value of '2' and an uncertainty of ±1. If we consider the measurement to fit the Gaussian assumption, then that uncertainty would be the standard deviation.

x = (2±1)

If we add these two measurements together, with all their uncertainty, we'd expect an average value of 4 with some unknown standard deviation.

(2±1) + (2±1) = (4±[?])

---

[from link.]

We'll need to take a step back at this point. If you
If you go explore the topic of "fuzzy mathematics" on Wikipedia, you'll find some abstract discussion of set theory rather than something that seems like what we've been talking about here. If you do some searches for "fuzzy arithmetic", you'll get into a realm of math that is between the abstract set theory and something closer to what I'm looking for.

If you dig even further, you'll find Gaussian Fuzzy Numbers (GFN). This sounds very much like the sort of math I want. Two GFNs are added together to generate a new GFN in a two step process. The means of the two numbers are added to make the new mean. The standard deviations are added to make the new standard deviation. In the above notation, this would be:

(2±1) + (2±1) = (4±2)

This is a pretty straightforward rule, but it doesn't feel like it has the statistical flavor that I'm looking for.

---

Method 1

How can we derive the standard deviation produced by adding two uncertain measurements? After thinking about it a bit, I thought of two methods to estimate what the value would be.

My first method basically simulates two uncertain measurements. I created a set of several thousand random samples within each initial Gaussian distribution, then iterated every possible pairwise addition between the two sets. I then calculated mean and standard deviation estimates from the set of pairwise additions. I repeated this estimation process a few thousand times and calculated the average values for the mean and standard deviation. With enough repetitions of this process, the estimates began to converge.

(2±1) + (2±1) = (3.9998±1.4146) ≈ (4±sqrt(2))

Method 2

That approach to estimating the new standard deviation takes a lot of calculations. My second method is much more efficient and converges faster. I started with two Gaussian curves, sampled at some high density. I then iterate through every combination of one point from first and second curves. For each combination, the two x-values were added to make a new x-value. The two y-values were multiplied to make a new y-value. (The y-values are probabilities. Multiplying the two probabilities calculates the probability for both happening at once.) Plot all those x/y value pairs (in light blue at left) and the envelope (or outline, roughly) of those points (shown in red) describes the same curve we calculated more roughly with my first method. I fitted the Gaussian distribution function to this curve to get the numerical estimate for it's standard deviation.

(1±1) + (1±1) = (2±1.4142) ≈ (2±sqrt(2))

---

That seems a nice and simple relationship, but it is distinctly different than Gaussian Fuzzy Number calculation described previously would indicate. It took some further digging before I found a document on the topic of "propagation of uncertainties". The document included a nice table with a series of very useful relationships, describing how Gaussian uncertainties are combined by various different basic mathematical operations.

From these relationships, we can short-circuit around all the iterative calculations I've been playing with. If we have measurements with a non-Gaussian distribution, it might still be necessary to use the numerical estimation methods I came up with.

---

Lets compare the three methods for tracking uncertainty through calculations.

Significant figures: (1±0.5) + (1±0.5) = (2±0.5)
Gaussian fuzzy numbers: (1±0.5) + (1±0.5) = (2±1.0)
Propagation of uncertainties: (1±0.5) + (1±0.5) = (2±0.70711)

The significant figures method underestimates the uncertainty through the calculation, while the Gaussian fuzzy numbers approach overestimates the uncertainty. Both these methods do have the advantage of being simple to apply without requiring any detailed computation. However, the errors would probably accumulate through more extensive calculations. I'll have to play around with a few test cases later to illustrate this.

---

I didn't like significant figures when I was first taught about them. The rules struck me as somewhat arbitrary and the results didn't fit at all with my expectations of how numbers should behave. The lessons were always a stumbling point for me because of this disconnect.

Over the years since, I had occasionally played around with how to do it better. It was only recently that I figured out how to derive the solutions I described above and realized propagation of uncertainties was what I had been searching for. Those high-school lessons would have been so much more effective had they included the real math instead of assuming I couldn't handle the concepts.


References:

• https://en.wikipedia.org/wiki/Significant_figures#Concise_rules
• Fuzzy mathematics: en.wikipedia.org/wiki/Fuzzy_mathematics
• Fuzzy arithmetic:
• reference.wolfram.com/legacy/applications/fuzzylogic/Manual/9.html
• reference.wolfram.com/legacy/applications/fuzzylogic/Manual/10.html
• www.slideshare.net/MohitChimankar/fuzzy-arithmetic
• fuzzy.cs.ovgu.de/ci/fs/fs_ch04_arithmetic.pdf
• link.springer.com/chapter/10.1007/3-540-32371-6_3 
• Calculating uncertainty:
• www.wikihow.com/Calculate-Uncertainty
• Propagation of uncertainties:
• virgo-physics.sas.upenn.edu/uglabs/lab_manual/Error_Analysis.pdf

Science Outreach

Though I haven't been writing much here lately, I have been active with another modern form of science outreach. You can follow my Twitter feed @thebiologistisn for links of interest, observations, and other short-form expressions that don't really fit here on my blog.

The topics covered will be pretty much the same as here. Though you will probably get more of a hint about my political stances, as Twitter's soundbite format is so fitting to politics.

I have connected the blog with my Twitter feed, so new posts here will be automatically linked there. This will make it easy to keep track of when I post. It will also make it easy for you to ask me questions about the topics I discuss, unlike here.

Have a wonderful holidays. I'll be back to [more or less] regular updates before long.

"Invasive" Squirrels

Range of American Red Squirrel (Tamiasciurus hudsonicus).
Range of Eastern Grey Squirrel (Sciurus carolinensis).

There are two native tree squirrel species in Minnesota. The Eastern Grey Squirrel (Sciurus carolnensis) would be familiar to almost anyone living in the eastern half of the USA, while the American Red Squirrel (Tamiasciurus hudsonicus) would be familiar to many people living in the north-east corner of the country (as well as most of Canada).

I happen to live in the native range of both species. I see them routinely in our yard... especially around the bird-feeder. The Greys climb down from above and snack directly from the feeder, while the Reds seem content with grabbing the seed spilled to the ground by avian visitors.

The Reds are about half the size of the Greys, but are much more feisty. We've watched single Reds aggressively attack single Greys, leading to the inevitable retreat of the larger Grey. The reds are generally more feisty, including in the intensity of their scolding calls when we scare them away from the porch.

The Greys make treetop nests out of leaves and branches. The Reds make homes of old woodpecker nests, burrows, or gaps in human establishments. We had to partially deconstruct a rear porch ceiling to discourage investigations by one Red, but most are content to reside in the piles of old wood just inside the edge of our woods.

---

What got me thinking about squirrels was a discussion with my wife and a third party. The third party referred to the red squirrels as invasive. Both my wife and I responded that they actually were native to the area. Later I realized that the root of the disagreement likely came down to different definitions of the word "invasive". We were interpreting the word in the context of the red squirrels being native. The third party might have been thinking of the word in the context of the red squirrels invading human structures. I don't know that this was their meaning and I don't expect to bring up the subject again with them, but this realization helps reinforce the need to be clear on what are meant even by terms in common use. (I previously posted a more extended conversation about the meanings of "diversity" in biological contexts.)

If you find someone saying something that at first strikes you as absurd, it may be because they're using words differently than you are. Don't simply discount them as being incoherent. Try to determine what they mean, not just what they say. Once you've gotten through the barrier caused by sharing the same language, their experience may help expand yours.


References

• Tamiasciurus hudsonicus: en.wikipedia.org/wiki/American_red_squirrel
• Sciurus carolnensis: en.wikipedia.org/wiki/Eastern_gray_squirrel
• the-biologist-is-in.blogspot.ca/2015/03/biological-diversity.html

The Impermanence of Being (a Fossil)

A fossil you find may have existed hidden away underground for millions of years, but they have a very short lifespan once uncovered and exposed to the elements. Rain, snow, wind, animals, plants, and people (not just collectors) all wear away at exposed fossils that are almost invariably fragile. Within a relatively few years of becoming exposed, they crumble away to unrecognizable gravel. Good fossil exposures are transient things.

Because of the temporary nature and physically limited size of fossil sites, many fossil-hounds develop a habit of being somewhat vague when describing where they've found a really nice specimen (at least until they have gotten to know you well). If you widely spread the news about some interesting site you found, you're more likely to find the site completely picked over the next time you visit. These days, I can imagine fossils being quickly stripped from a site for sale online. I don't have a problem with someone selling fossils, but I would definitely despair at finding an interesting site emptied between one visit and the next. Much of the value of an interesting fossil in the context. (The geologic era, what species were found with it, etc.) This information can easily be lost if a site is picked over with too much haste.

The former fossil site, now a movie theater.

I recently checked in on a site where I once found numerous wonderful fossils. The site was directly behind my high-school in San Antonio, Tx. Thanks to GoogleMaps, I now know it to be the parking lot for a movie theater. I have no problem with telling the wider world exactly where the site is located. There is no further damage over-exposure can do to it.

Previously, there had been a wide, flat hilltop covered with multi-pound specimens of Exogyra ponderosa (a reef-forming oyster), along with the numerous shells from several smaller relatives. The fossiliferous layer was the very top of the hill, so one could walk along and easily visualize how the ecosystem was organized back in the Cretaceous era when this hilltop was the floor of a shallow sea. Though all the animals had been extinct for 60 million years, the fossils were comprehensive enough to clearly be a well-populated oyster reef. The site was impressive. I expect ecological studies could have been done there. The nearby area of undeveloped land probably contains fossils, since much of Cretaceous limestone does, but the oyster reef did not extend into that area. The reef no longer exists and only the few fossils remaining from the site in the hands of collectors like myself (and the biology teacher who pointed me towards the site) are evidence for it having ever existed.

A ~6in long Exogyra ponderosa from the oyster reef.

I always meant to spend more time exploring the area, but the classes and drama of high-school always seemed to get in the way. When I graduated and moved on to college in Austin-Tx, my parents moved out of state. I no longer had any connection to the neighborhood. It wasn't until years later, when I too had moved out of state, that I got my first car and with it the freedom to go wandering around looking for fossils and the like.

Now I have other fossil sites to visit and keep quiet about. (For example, where I found another mollusk... the-biologist-is-in.blogspot.com/2014/05/a-gastropods-lesson.html).


References:

• fossillady.wordpress.com/tag/exogyra-ponderosa/
• www.wikiwand.com/en/Exogyra

The Messy Science of Tardigrades

[Image source.]

Recently there has been some controversy in the news about the evolution of genomes in tardigrades. In particular, one recent paper claimed to see evidence for large-scale horizontal transfer of genes from bacteria/etc. into tardigrades, while another recent paper claimed to see no evidence for horizontal transfer.

The meat of the issue comes down to exactly how each group assembled the genomes they analyzed and published about.

Group 1:

1. Illumina-seq (shotgun sequencing) with paired-ends.
2. Notice lots of bacterial, etc. genes.
3. Re-sequence genome using PacBio extremely-long-reads.
4. Validate presence of bacterial/etc. sequences in tardigrade genome.
5. Publish paper!

Group 2:

1. Illumina-seq (shotgun sequencing) with paired-ends.
2. Notice lots of bacterial/etc. sequences.
3. Filter out bacterial/etc. sequences before constructing final genome.
4. Publish counter-"paper"!

The first group first sequenced with paired-end reads using Illumina technology, then did re-sequencing using the extremely-long-reads of PacBio technology. This two-method sequencing allowed them to more reliably validate if the bacterial/etc. sequences were actually found contiguously in the DNA of the tardigrade or not. Any artifacts from one technique would likely not be found in the second independent technique. Any results shared between them thus have a higher confidence. The PacBio sequencing wasn't as comprehensive as the Illumina sequencing, so there wasn't complete validation of all cases of horizontal gene transfer. There is the potential that they've over-estimated the level of horizontal gene transfer. However, their methodology would allow them to see the difference between massive horiztonal gene transfer in the tardigrade's evolutionary history vs. the presence of contaminating DNA in the sample being sequenced.

The second group didn't put the same level of rigor into their sequencing. They used Illumina technology (as the first group), followed by intensive filtering of sequences which seemed to have an origin from contamination. They argue the bacterial/etc. genes seen in the first group's genome assembly were due to contamination. However, their result is exactly what would be expected from their methodology whether there was actually massive horizontal gene transfer in the tardigrade's history or not. I'm not convinced that their method would have been able to tell the difference.

---

A detail of the first group's results that lends credence to their interpretation over that of the second is that the bacterial/etc. genes found in the tardigrade's genome were not simply a random selection of genes as would be expected from a contamination origin. Instead, they were a selection of genes involved in DNA repair and stress response. These are exactly the sort of genes that would be expected to favor the survival of the tardigrades that had incorporated them.

Another section of the first group's results which were overlooked by the second was that the bacterial/etc. genes found in the tardigrades show evidence of having evolved inside the tardigrades for an extended period of time. The bacterial/etc. genes show a shift in the codon usage to be more like that of native tardigrade genes. As well, the bacterial/etc. genes have gained introns (something not found in bacteria). Both of these classes of changes would be very unexpected in a scenario where contamination was the source of the DNA.

---

The first group probably over-estimated the level of horizontal gene transfer in the tardigrade. The second group probably under-estimated the level of horizontal gene transfer in the tardigrade. So...  what is going on? This entire event shows very well how science is done in real life. Someone will have an interesting result. Someone else will produce an apparently contradictory result. Over time, the new results get closer and closer to telling us what the reality is.

The real world is messy. Science is, at its best, an attempt to understand what is happening in the world. It isn't telling people what should be, or what might be, but what actual is. The apparent uncertainty seen in regards to the tardigrades may confuse people who might be used to watching fictionalized representations of science that always seems to get everything right on the first try, or those who trust in science to get the right answer without realizing the extended process that getting the right answer can be. In the end, it is a good thing. All the interest the results in these papers has produced will likely inspire more research to be done which will add further clarity to what is going on in these interesting little creatures.


References:

• Tardigrade controversy: english.netmassimo.com/2015/12/05/two-sequencings-of-tardigrade-dna-give-contrasting-results/
• Paper 1: "Tardigrades are really strange."
• Boothby TC, Tenlen JR, Smith FW, Wang JR, Patanella KA, Nishimura EO, Tintori SC, Li Q, Jones CD, Yandell M, Messina DN, Glasscock J, and Goldstein B (2015). Evidence for extensive horizontal gene transfer from the draft genome of a tardigrade. Proc Natl Acad Sci U S A. pii: 201510461. [Epub ahead of print] [PMID 26598659]
• Paper abstract: www.pnas.org/content/early/2015/11/18/1510461112.abstract
• Commentary: motherboard.vice.com/read/newly-sequenced-tardigrade-genome-shows-theyre-even-weirder-than-we-thought
• Paper 2: "Not so much."
• Koutsovoulos G, Kumar S, Laetsch DR, Stevens L, Daub J, Conlon C, Maroon H, Thomas F, Aboobaker A, Blaxter M (2015). The genome of the tardigrade Hypsibius dujardini. [doi: http://dx.doi.org/10.1101/033464]
• Full paper: biorxiv.org/content/biorxiv/early/2015/12/01/033464.full.pdf
• Commentary: motherboard.vice.com/en_uk/read/a-new-analysis-questions-how-much-foreign-dna-tardigrades-actually-have?trk_source=recommended
• Good discussions:
• www.homolog.us/blogs/blog/2015/12/06/chimeric-pacbio-reads-and-tardigrade-controversy/
• whyevolutionistrue.wordpress.com/2015/11/27/the-weird-genome-of-water-bears-tardigrades-more-than-a-sixth-of-it-was-swiped-from-distantly-related-species/
• www.igs.umaryland.edu/labs/hotopp/2015/12/05/quick-look-at-the-two-manuscripts-on-tardigrade-lgt/
• www.genomicron.evolverzone.com/2015/12/the-curious-case-of-the-tardigrade-genome/
• Bdelloid rotifer genome: phys.org/news/2012-11-dna-ingesting-tenth-quirky-creature.html (Another interesting case suggestive of extensive horizontal gene transfer.)

Pain

You think you know pain. You've experienced pain all your life. You just might have probably broken a bone, or given birth, or been [mildly] electrocuted...  some of the more physically painful events that a person might think of experiencing.  If you're really unlucky, you may even now be living through the intractable, unending, pain that can be caused by cancer or some other disorders.

Some rare few people have no comprehension of your experience. They have a disorder called Congenital Insensitivity to Pain, or CIP. The disorder interferes with their ability to feel any pain. Not having to feel pain might sound like a nice idea, but pain is your body's way of telling you that something is wrong. Pain can get out of hand at times, but without it...  life gets difficult.

You learned a hot pan from the stove was not to be touched, because it hurt. You learned to take care while running, because it hurt when you fell. When you accidentally bite your tongue or cheek, it hurts and you [try to] avoid it again. Without pain, you would never learn any of those lessons. You would be severely burned, or break bones, or bite through your cheek and tongue. Pain is important, because it helps you learn to keep from damaging yourself as you go through life. People with CIP have very difficult childhoods, with their bodies experiencing damage at levels a typical person could never imagine.

---

Geneticists have studied families with high rates of CIP and have identified several mutations in the gene SCN9A. This gene encodes the voltage-gated sodium channel Nav1.7, critical for the normal transmission of signals along pain-responsive nerves. The same ion channel is responsible for the transmission of signals along olfactory nerves (Ahn et al 2011; ), so patients with the disorder also have an impaired sense of smell.

Researchers recently replicated one of these mutations in the laboratory mouse (Minnett et al, 2015). The resulting mice had no reaction to stimuli that should have caused a great deal of pain, without causing actual physical damage, like electro-stimulation. The mouse showed increased endogenous opiod activity. The introduction of the opiod antagonist Naloxone resulted in restoration of the mouse's ability to feel pain. A human subject with a similar mutation of SCN9A also showed a restoration of the ability to feel pain when treated with Naloxone, for the first time in their 39 years of life. The researchers are using their new knowledge to develop a treatment for intractable, chronic pain. The treatment would mimic the effects of the SCN9A mutation, by using a low dose of opiods paired with an Nav1.7 antagonist. This should allow for the effective management of pain with low doses of opiods, so avoiding the potentially-lethal side-effects associated with high-dose opiod pain-management therapy.

Not all cases of congenital insensitivity to pain are due to mutations in SCN9A. I found a paper (Manfredi et al, 1981) which describes a patient who had no pain response, but did not have an impaired sense of smell. This ability to smell indicates the patient had a functional SCN9A gene. The patient was also described as not showing a restoration of pain sensation upon treatment with Naloxone. My reading of the 2015 paper suggests the authors didn't realize that Naloxone would restore pain sensation in their patient. It looks like they missed this critical knowledge that was known in the 1981 paper when they were doing their literature research for the project. The 1981 patient may have a mutated NTRK1 gene, another known cause of congenital insensitivity. The state of research in 1981 didn't involve the intensive genome sequencing needed to identify mutant genes, so it remains unclear.

---

Did you catch the problem in this story?

The 2015 paper indicated the patient had never experienced pain until the researchers realized that Naloxone might be a treatment for their disorder. The 1981 paper described an interesting patient with congenital insensitivity to pain who, surprisingly, didn't respond to Naloxone. Naloxone has been known as the treatment for this disorder for more than thirty years.

The patient described in the 2015 study has lived through 39 years without a medical professional giving them the known treatment for the disorder that resulted in them experiencing the extreme physical damage that the disorder leads to. The treatment could have normalized their pain responses and prevented the damage. Because of the diversity of underlying biological causes to different cases of CIP, Naloxone treatment may not work, but it is readily tested and has minimal side-effects.

This disorder impacts maybe 100 people on the planet. It receives very little research attention, even though it is a relatively charismatic disorder, so it is understandable that critical knowledge might occasionally be forgotten or not communicated to those who should know it. That the re-found knowledge of the 2015 paper is being used to develop a treatment for the intractable pain experienced by many people across the world is a wonderful thing. It really could improve the lives of millions of people by removing their chronic pain without needing powerful and dangerous drugs. However, It still makes me very angry that the patient in the 2015 paper wasn't given appropriate treatment for most of their life with the disorder.


References:

• www.nbcnews.com/id/6379795/ns/health-childrens_health/t/rare-disease-makes-girl-unable-feel-pain/
• en.wikipedia.org/wiki/Congenital_insensitivity_to_pain
• motherboard.vice.com/read/people-who-dont-feel-pain-are-helping-us-find-better-pain-meds
• www.sciencedaily.com/releases/2015/12/151204090034.htm
• Minett MS, Pereira V, Sikandar S, Matsuyama A, Lolignier S, Kanellopoulos AH, Mancini F, Iannetti GD, Bogdanov YD, Santana-Varela S, Millet Q, Baskozos G, MacAllister R, Cox JJ, Zhao J, and Wood JN (2015). Endogenous opioids contribute to insensitivity to pain in humans and mice lacking sodium channel Nav1.7. Nature Communications 6: 8967. [PMID 26634308] [Link]
• Manfredi M, Bini G, Cruccu G, Accornero N, Berardelli A, Medolago L (1981). Congenital absence of pain. Arch Neurol 38 (8): 507–11. [PMID 6166287]
•  Ahn AS, Black JA, Zhao P, Tyrrell L, Waxman SG, and Dib-Hajj SD (2011). Nav1.7 is the predominant sodium channel in rodent olfactory sensory neurons. Mol Pain. 7:32. [PMID 21569247]
• NTRK1:
• www.ncbi.nlm.nih.gov/gene/4914
• www.ncbi.nlm.nih.gov/pmc/articles/PMC3087230/ 
• Treatment: neurosciencefundamentals.unsw.wikispaces.net/Congenital+insensitivity+to+pain
• Incidence:
• ghr.nlm.nih.gov/condition/congenital-insensitivity-to-pain
• www.orpha.net/consor/cgi-bin/OC_Exp.php?Expert=88642

Transgenic Sweet-Potatoes

One of the first tools available to biologists seeking to make transgenic plants was a natural bacteria called Agrobacterium. The bacteria infects plants and induces the production of auxins and cytokinins, plant hormones that together trigger the growth of a disordered plant tissue called a gall. The gall provides nutrients that the bacteria then uses for its own growth. The bacteria pulls off this trick by inserting genetic information into plant cells. It can do this because it carries a plasmid that can function both in its own cells and in the cells of a plant. When the bacteria infects the plant, the plasmid is transferred into the plant's cells. Once there, the plasmid integrates into the genome of the plant and activates. The bacteria are natural genetic engineers.

Genetic remnants can be left behind whenever the bacteria does this trick and nowadays we can do genome sequencing to find such remnants. Kyndt et al found remnants of this process in sweet-potatoes (Ipomea batatas). In particular, they found such a fragment inserted into an intron of an F-box gene in the sweet-potato genome. Interestingly, this interruption is found in all domesticated sweet-potatoes they examined and not in wild related species.

The insertion contains multiple complete genes and results in the interruption of the F-box gene. F-box genes are generally involved in protein degradation and in plants they're involved in the regulation of development during growth. It isn't clear that the insertion they found results in a change in the development of the plant associated with domestication, however. They are still working on this.

Oh yes, did I mention they found this fragment in all samples they examined of domesticated sweet-potatoes? This means that every single sweet-potato is a transgenic organism, a GMO. We didn't make it a GMO, but there is no way around it, every sweet-potato is a GMO.

Every sweet-potato is a GMO.

Are you against GMOs? Then don't eat any more sweet-potatoes. Are you actually against the business practices of Monsanto surrounding their GMO and herbicide products? Then rail against those business practices instead of the red herring that GMOs are in the overall story.



References:

1. Agrobacterium: en.wikipedia.org/wiki/Agrobacterium
2. Kyndt et al, 2015: m.pnas.org/content/early/2015/04/14/1419685112.full.pdf
3. F-box genes: en.wikipedia.org/wiki/F-box_protein
4. Red herring: en.wikipedia.org/wiki/Red_herring

Biological Diversity

In recent conversations I've had with biologists at a plant breeding symposium at UMN and other local events, I've come across people using the term "diversity" in rather distinctively different ways.

---

A researcher was described how low diversity soybeans were, as an argument for the fast-neutron mutagenesis project he was working on to develop new useful diversity. I didn't believe soybeans to be a low diversity crop, as there are so many wild and weedy forms available in the center of diversity for the species in China. He then made some comment about the limited diversity brought to the United States from Asia...  which made me wonder why he would limit himself to what is locally available, when strains from the whole world are available with some effort.

The closing keynote speaker was later discussing his 34 year career of soybean breeding and started off by describing the great diversity available in soybeans for breeders to work with. I then realized that the first researcher and I had been using different measures of diversity. He was using "diversity" to mean what was commonly available locally (definition #1 below), while I (and the keynote speaker) were using "diversity" to mean the range of genotypes available worldwide (definition #2 below).

Population genotype structures:
Local: AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAABB
World: AAAAAAAAAAAAAAAAAAAAAAAAAAAAABBCDEFGHIJKLMN

1. Range of genotypes locally available. The population approximates just genotype A, so under this definition the crop species has a very low diversity.

2. Range of genotypes in a species. The population includes 14 distinct genotypes (ABCDEFGHIJKLMN), so under this definition the crop species has a very high diversity.

---

At another event, a speaker was talking about how some regions of the genome for his study plant species had very low diversity and that this indicated recent introgression from a related species because the rest of the genome had a very high diversity.

I commented that I would have to look into the math behind it to better grasp what he was talking about.  He shrugged off the need for this and said the region was determined as having low diversity using a hidden-markov-model (HMM) approach.

I pondered on his statement. The HMM approach is used to identify transitions between states as you move along the axis of a dataset. In the case of the speaker's research, the HMM would calculate the most probably coordinates in the genome for transitions from high diversity to low diversity and back. Unfortunately, this still doesn't explain what he meant by "diversity". As the speaker was talking about a region of the genome having lower diversity than average for the species(individual?), there are two ways I can interpret his use of "diversity".

3. The amount of heterozygosity within an individual. A highly inbred individual will have a very low "diversity", while a highly outbred hybrid individual will have a very high "diversity".

4. The variation in haplotypes across a population. Haplotypes are distinct coordinately traveling regions of genetic information. The more haplotypes in a region, the more diverse the population is. A You would need to sequence a relatively large number of individuals to get a glimpse at the sort of data this analysis would require.

I have the feeling he was using "diversity" to mean a change in some measure across the genome of an individual (definition #3 above), rather than a measure of the population of the species (definition #4 above).

If he meant "diversity" like definition #3 above, then I would interpret a region of the genome with much lower level of heterozygosity to indicate a recent loss-of-heterozygosity (LOH) event, such as a damaged chromosome region being repaired by replacement with sequence from the intact other homolog to the chromosome. If he meant "diversity" like definition #4 above, then I would interpret such a region to indicate a recent selective sweep. In neither case does the data suggest to me there has been an introgression from an unspecified near relative with a higher propensity to self.

I really wish I had been able to get more clarity from the speaker about what he meant. I also wish he hadn't dismissed my interest in his project so quickly.

---

The meaning of even commonly used words can drift between different groups of speakers. In science it is very important to be clear in what you mean by the terms you use, even for the words that don't seem to be jargon.


References:

1. HMM: en.wikipedia.org/wiki/Hidden_Markov_model
2. Haplotypes: en.wikipedia.org/wiki/Haplotype

Publish or Perish

Most of my biology-focused posts have been about topics related to garden projects I've done or have been thinking about. The subject of gardening does account for much of the biology I spend my free-time thinking about, especially now in the middle of a winter-bound Minnesota. It is also far easier to examine the growth and interactions of living things in the garden than it is to go on expeditions or develop lab protocols to explore the diversity of biological topics.

I've avoided talking in detail about the biology I do at work because the work is on-going and to publicize it here might detract from the process of publishing the work in more formal contexts once the projects reach usable conclusions. Sometimes a key result can be quickly replicated once the idea behind it has been developed, so talking about results too early can be asking for some competitor to beat you to publication. I've defended my thesis and dealt with graduate school bureaucracy sufficiently to be awarded my PhD. I can now refer to myself as "Darren Abbey, PhD" in professional contexts. (I can also refer to myself as "The Doctor" (Dr. Who?) in certain social contexts.)

Along the way, I've written or contributed to several research publications. The following list is the publications I've been received name credit for my contributions, from oldest to most recent.

1. Gale CA, Leonard MD, Finley KR, Christensen L, McClellan M, Abbey D, Kurischko C, Bensen E, Tzafrir I, Kauffman S, Becker J, Berman J. (2009) SLA2 mutations cause SWE1-mediated cell cycle phenotypes in Candida albicans and Saccharomyces cerevisiae. Microbiology. 155(Pt 12):3847-59. [PMID: 19778960]
    
2. Forche A, Abbey D, Pisithkul T, Weinzierl MA, Ringstrom T, Bruck D, Petersen K, Berman J. (2011) Stress alters rates and types of loss of heterozygosity in Candida albicans. MBio. 2(4). [PMID: 21791579]
    
3. Abbey D, Hickman M, Gresham D, Berman J. (2012) High-Resolution SNP/CGH Microarrays Reveal the Accumulation of Loss of Heterozygosity in Commonly Used Candida albicans Strains. G3 (Bethesda). 1(7):523-30. Erratum in: G3 (Bethesda). 2(11):1473. [PMID: 22384363]
    
4. Hickman MA, Zeng G, Forche A, Hirakawa MP, Abbey D, Harrison BD, Wang YM, Su CH, Bennett RJ, Wang Y, Berman J. (2013) The 'obligate diploid' Candida albicans forms mating-competent haploids. Nature. 494(7435):55-9. [PMID: 23364695]
    
5. Abbey DA, Funt J, Lurie-Weinberger MN, Thompson DA, Regev A, Myers CL, Berman J. (2014) YMAP: a pipeline for visualization of copy number variation and loss of heterozygosity in eukaryotic pathogens. Genome Med. 6(11):100. [PMID: 25505934]
    
6. Ford CB, Funt JM, Abbey D, Issi L, Guiducci C, Martinez DA, Delorey T, Li BY, White TC, Cuomo C, Rao RP, Berman J, Thompson DA, Regev A. (2015) The evolution of drug resistance in clinical isolates of Candida albicans. Elife. 4. [PMID: 25646566]
    

I've also got a couple others in the pipeline. For one I'm looking for a target journal, for the other I'm still deciding exactly how to present the results. I'll let you know more details once they're further along the way to publication.

The projects a grad student works on depends on a mix of the lab they end up in and their personal style of problem solving. I ended up in a Candida albicans lab and brought to it a heavy computational approach. The mix between the two is the realm of computational biology, the topic I find myself most connected to.

The academic life can readily be described as, "Publish or Perish". With six name papers from my time in grad school, I've done alright. Now I just have to figure out the next step.

GMO labeling : The right to know what is in our food.

Sometimes biology intersects with political-charged topics that engage large-numbers of people. In the USA, there has been recent activity around the labeling of foods made from genetically modified organisms (GMOs). The following video epitomizes one viewpoint on the subject.

http://www.upworthy.com/a-14-year-old-explains-food-labeling-in-language-even-condescending-tv-hosts-should-get-3?c=reccon3

---

One of the major arguments presented in the video is that people have the right to know what is in our food. Because of this, GMO foods should be labeled.

I think this is a wonderful idea!

However… there's a big problem. People think they know what is in regular crops, while they think they don't know what is in GMO crops. Can you list the compounds found in the last organic heirloom tomato that you ate? Do you know what is in "natural" corn? How about the poisons found in the various types of beans that people eat? How about the poisons sprayed on any crops (even organic) that you might find in the store? The reality is that people, in general, have no idea what is in any of the food they eat.

A second problem I have is that the GMO-labeling ideas being pushed will do nothing to assist people in knowing what is in their food. If you're eating a tomato which included a gene from a fish and the label only says the tomato has been altered with a certain form of technology, then the label does nothing at all to inform you about what you're eating.

We do already have an established method for indicating the presence of small amounts of diverse substances in our food that can be utilized for labeling GMOs: the ingredients list. If your tomato product also includes some fish genes, then the ingredients list for the tomato should include the fish (and any bacterial) genes that are found in it. Finding an ingredients label on a single tomato will discourage those who aren't interested in purchasing GMOs, but will allow those who are interested in learning what is in their food to be able to easily educate themselves.

So far, no organization is pushing for such an educational labeling idea. The people pushing for GMO-labeling don't want honest and educational labeling. They're pushing for labels to inspire fear, uncertainty, and doubt (FUD) about GMOs.

I think such a labeling system should also be extended to indicate what chemicals were sprayed on the fruit and thus are likely to remain on the fruit. This issue doesn't involve GMOs, but these chemicals are something we do know with certainty are poisons...  and yet there is no push for this information on labels.

---

I am a biologist, so I realize my perceptions of this subject are likely to be distinct from those of most people.

I agree with the reasons stated for GMO labeling, but I am totally against every GMO-labeling proposal I have so far heard being discussed because they don't help attain the goal of the stated reasons.

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
• en.wikipedia.org/wiki/Solanum_nigrum
• www.liseed.org/solanunusual.html
• black: www.rareseeds.com/garden-huckleberry/
• red: www.flickr.com/photos/sugans_shutters/10223815933/
• orange: www.rareseeds.com/otricoli-orange-berry/
2. Atropa belladonna
• en.wikipedia.org/wiki/Atropa_belladonna 
• www.lmarrick.com/ancient-anesthetics-belladonna/
• www.brc.ac.uk/plantatlas/index.php?q=plant/atropa-belladonna
3. Diospyros texana
• en.wikipedia.org/wiki/Diospyros_texana
• www.texasbeyondhistory.net/st-plains/nature/images/persimmon.html
4. Solanum dulcamara
• en.wikipedia.org/wiki/Solanum_dulcamara

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