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Thursday, February 20, 2014

Making My Own Carrots

In 2013 I grew a batch of mixed bed (4ft x 6ft) of several carrot varieties, including a range of different colored forms. I had never grown carrots in my current garden, so I didn't know which varieties would work well and which would utterly fail. My main hope was that several types would prosper and I would get lots of mixed carrots to eat over the fall and winter seasons.

I harvested all the carrots during the second snowfall, digging and cleaning every single plant. There were plenty of largish carrots along with lots of small carrots. The brand of carrot culture that I applied (sow thinly and let the plants fight it out, without intervention) was particularly difficult for some varieties. A short, dwarf-rooted type ("Paris Market") almost disappeared in the resulting jungle. The red ("Atomic Red") variety from the Burpee Kaleidoscope mix tasted great, but performed poorly overall. The yellow ("Solar Yellow") and white ("Lunar White") ones from the same mix, on the other hand, did very well. The orange ("Bambino") and purple-skinned orange ("Cosmic Purple") ones from the same mix, came somewhere in between.

I ended up with several pounds of carrots and have been eating them all winter.



A secondary hope was that I would be able to save some of the largest carrots, those that agreed most with my local conditions and gardening style, for seed growing.   Over several years, this would let me develop a locally-adapted carrot variety of my very own.

Carrots are a biennial plant, producing flowers/seeds during their second year.   Since I wasn't confident in my carrots ability to survive in the ground all through the harsh Minnesota winter, I set some aside in the fridge for growing in the spring. For these, I trimmed the greens short, but left the growth point intact. The roots were then trimmed to fit into a quart-sized ziplock bag in the back of my fridge.

At the beginning of February, I checked in on the stored roots. Several had started to grow new shoots, while several others had rotted to mush. The rot took most of the orange ("Bambino") carrots, so it appears that color will be under-represented in the genetics of my developing population.

I decided that it was time to force the remaining roots, in fear of losing more to rot and so they could get an early start on the growing season. (Admittedly, the desire to see some green growth this deep in winter was a major factor in this decision.) I trimmed all the roots to about three inches long and placed them upright in a wide-bottom glass cylinder. I had enough roots such that they would cross-brace each other and remain upright in this container.

I happened to have a deep purple carrot ("Purple Haze", "Purple Dragon", or something) in the fridge, among leftovers from a farmers' market foray before my own carrots were ready… and I like purple, so I trimmed it like the others and added it to the forcing container.



If I am lucky, the roots will bloom early enough to let me grow the resulting seed this year, having been tricked into living their two year life-cycle in one year. If they don't bloom early, I will have had a nice windowsill plant for most of the winter and will have the seeds for next year.

In either scenario, the resulting next generation plants will contain a mix of F1s from the saved varieties. There are very few wild carrots ("Queen Anne's Lace") around where I live, so I shouldn't have any problems with weedy genetics getting mixed into my carrot population.   The next generation, a few years from now, should then show a riotous mix of traits as the various alleles segregate in the F2 progeny.


Part 2: Carrot flowers.
Part 3: Generation 2.

Sunday, February 9, 2014

Genetics of Squash Shape (2/2)

In my first blog post, I examined a small biology puzzle: the classical model of squash shape genetics (at left) didn't seem to match what I was seeing in my own garden.

The classical model involves two genes ('A' and 'B', respectively).   The dominant allele of both genes must be present (A_B_) to produce a disk-shaped squash.   If one gene is present in the dominant form and the other is in the recessive form (A_bb or aaB_), spherical-shaped squash will result.   If only the recessive alleles of both genes are present (aabb), then elongated squash will result.   After some digging, I found this model comes from a 1927 paper by Edmund W. Sinnott in the research journal, The American Naturalist.

This model predicts that crossing a (AABB) PattyPan to a (aabb) Zucchini should result in (AaBb) progeny plants with disc-shaped squash.   The progeny plants I grew, instead each produced intermediate/elongated-fat squash.   I assumed this meant my original PattyPan squash was a hybrid that contained both recessive alleles (AaBb) and so I then calculated the probabilities of producing (aabb) progeny from crossing the potential male parents (PattyPan and Zucchini) to the female parent (PattyPan).   The best probability I calculated was \( p = \frac{1}{16} \).   I wasn't pleased with this result and decided I needed further data.



The magic of the internet then made its presence known: Ottawa Gardener was forwarded to my original post in a discussion of their recent post.   They had grown Zucchini, PattyPan, and some Pumpkins, then tossed some of the PattyPan squash to their chickens.   The next year when they moved the chicken run, up came a batch of hybrid squash.   Most appeared to be intermediate between the Zucchini and the PattyPan, with a few looking intermediate between the PattyPan and the Pumpkin.   (I've rearranged their photo to make the diagram at left.)

Because there are three potential male parents (and two offspring types), the calculations of probability get somewhat more intricate and I won't go into them here.   The detail I found most interesting was the recreation of the intermediate/elongated-fat shaped squash at the bottom-left.

Upon digging into the research literature further, I found a 1910 paper by R.A. Emerson, again in The American Naturalist.   In this paper, the author describes the result of crossing "White Scallop" (disc) and "Yellow Crookneck" (elongated) squash as being intermediate in shape.   This is contrary to the Sinnott model of shape genetics and is the result that both I and Ottawa Gardener observed in our gardens.

It seems like the Emerson result was never followed up on and the Sinnott result erroneously became the standard model of squash shape genetics that has been used in textbooks ever since.



I'm really happy to know that my garden results are consistent with results from others, but I still need more data.

The simplest model I've come up with requires there to be a third gene (C) that allows the first two genes (A & B) to produce disc-shaped squash.   Sorting out the genetics of a cross involving three genes is much harder than a cross involving one or two genes.   Fortunately, I've got several hundred F2 seeds from the F1 plants I grew.

I plan to grow several F2s this coming year and I've managed to find homes for a few more in others' gardens.   It may take several years of this to collect sufficient data to get an idea of what is going on.

Would you be willing to grow some of my experimental squash seeds, then send me photos/measurements of the fruit that grow?   Get a message to me and we'll work out how to get seeds to you.



Citations and notes :
  1. Emerson RA.   The Inheritance of Sizes and Shapes in Plants.   1910, The American Naturalist 44: 739-746.   (https://archive.org/details/jstor-2455667)
    • "Yellow Crookneck" x "White Scallop" -> F1 "intermediate".
    • This matches the results I found in my garden

  2. Sinnott EW.   Inheritance of Fruit Shape in Curcurbita pepo.   1922, Botanical Gazette 74: 95-103.   (https://archive.org/details/jstor-2470204)
    • Sphere x Scallop -> F1 disc -> F2 (3 disc):(1 sphere).

  3. Sinnott EW.   A Factorial Analysis of Certain Shape Characters in Squash Fruits.   1927, The American Naturalist 61: 333-344. (http://www.jstor.org/discover/10.2307/2456386)
    • Sphere(#103) x disc -> F1 disc -> F2 (3 disc):(1 sphere).
    • Sphere(#22) x disc -> F1 disc -> F2 (3 disc):(1 spheroid).
    • Sphere(#103) x sphere(#22) -> F1 disc -> F2 (9 disc):(6 sphere):(1 elongate).

Part 1

Thursday, January 16, 2014

Mathematical Recreations : Summation of an Infinite Series

My studies in biology have been aided by a solid grasp of mathematics.   I will often mathematically model some system I am working with, to try and predict how it is going to behave.   When I find something that looks mathematically implausible, I like to examine it in some detail to figure out why it looks implausible.

Today I found an article with a video explaining how the sum of all natural numbers is \( -\frac{1}{12} \).
\( \sum_{i=1}^\infty = 1+2+3+4+5+6+7+8+9 … \infty = -\frac{1}{12} \).

Sometimes my impression of implausibility is caused by my limited understanding, but this is definitely not always the case, and I find it worthwhile to explore the source of my unease at a particular statement.


The provided argument relies on summing a few simple series:
\( S_{1} = 1-1+1-1+1-1+1-1+1 … \)
\( S_{2} = 1-2+3-4+5-6+7-8+9 …  \)

…and then using them to solve the summation of the series of interest.
\( S = 1+2+3+4+5+6+7+8+9 … \)



The first series is known as Grandi's Series.   Because the series continues to infinity, with the sum alternating between 0 and 1 as you add subsequent numbers, the sequence does not converge and therefore there is no meaning to the standard sum for this series.
\( S_{1} = 1-1+1-1+1-1+1-1+1 … \)

However, the Cesàro sum is an alternate methodology where the sum is calculated as the limit of the arithmetic mean of the first \( n \) partial sums of the series, as \( n \) goes to \( \infty \).
\( x_{1} \) = {1}; \( \overline{x_{1}} = 1 \)
\( x_{2} \) = {1, 1-1} = {1, 0}; \( \overline{x_{2}} = \frac{1}{2} \)
\( x_{3} \) = {1, 1-1, 1-1+1} = {1, 0, 1}; \( \overline{x_{3}} = \frac{2}{3} \)
\( x_{4} \) = {1, 1-1, 1-1+1, 1-1+1-1}; = {1, 0, 1, 0}; \( \overline{x_{4}} = \frac{1}{2} \)
\( x_{5} \) = {1, 1-1, 1-1+1, 1-1+1-1, 1-1+1-1+1} = {1, 0, 1, 0, 1}; \( \overline{x_{5}} = \frac{3}{5} \)
\( x_{6} \) = {1, 1-1, 1-1+1, 1-1+1-1, 1-1+1-1+1, 1-1+1-1+1-1} = {1, 0, 1, 0, 1, 0}; \( \overline{x_{6}} = \frac{1}{2} \)
\( x_{7} \) = {1, 1-1, 1-1+1, 1-1+1-1, 1-1+1-1+1, 1-1+1-1+1-1, 1-1+1-1+1-1+1} = {1, 0, 1, 0, 1, 0, 1}; \( \overline{x_{7}} = \frac{4}{7} \)

…which gives us the Cesàro sequence : 1, \( \frac{1}{2} \), \( \frac{2}{3} \), \( \frac{1}{2} \), \( \frac{3}{5} \), \( \frac{1}{2} \), \( \frac{4}{7} \), \( \frac{1}{2} \), \( \frac{5}{9} \), \( \frac{1}{2} \), \( \frac{6}{11} \), \( \frac{1}{2} \), \( \frac{10}{19} \),…

… which alternates between \( \frac{1}{2} \) and a series (1, \( \frac{2}{3} \), \( \frac{3}{5} \), \( \frac{4}{7} \), \( \frac{5}{9} \), \( \frac{6}{11} \), \( \frac{7}{13} \), \( \frac{8}{15} \), \( \frac{9}{17} \), \( \frac{10}{19} \), … ) which converges to \( \frac{1}{2} \).

… so the resulting Cesàro sum is \( \frac{1}{2} \).

There is no sum to this series, only a Cesàro sum.
\( S_{Cesàro 1} = \frac{1}{2} \)



Solving the sum of the second series is a little bit more complicated:
\( S_{2} = 1-2+3-4+5-6+7-8+9 … \)

First add the series to itself:
\( 2S_{2} = S_{2}+S_{2} \)

… but offset each number in the second series by one position:
\( 2S_{2} = (1)+(-2+1)+(3-2)+(-4+3)+(5-4)+(-6+5)+(7-6)+(-8+7)+(9-8) … \)

… which simplifies to:
\( 2S_{2} = 1-1+1-1+1-1+1-1+1 … \)

So, two times our second series gives us our first series.   (Our first series did not have a sum, but we'll go ahead as if it had.)
\( 2S_{2} = S_{Cesàro 1} = \frac{1}{2} \)
$$ S_{2} = \frac{S_{Cesàro 1}}{2} = \frac{1}{4} $$



Solving the third series is then rather simple.
\( S = 1+2+3+4+5+6+7+8+9 … \)

We subtract \( S_{2} \) from \( S \) and then simplify:
\( S-S_{2} = (1+2+3+4+5+6+7+8+9 … \infty)-(1-2+3-4+5-6+7-8+9 … ) \)
\( S-S_{2} = (1-1)+(2+2)+(3-3)+(4+4)+(5-5)+(6+6)+(7-7)+(8+8)+(9-9) … ) \)
\( S-S_{2} = (0)+(4)+(0)+(8)+(0)+(12)+(0)+(16)+(0) … ) \)
\( S-S_{2} = 4+8+12+16+20+24+28+32+36 … \)
\( S-S_{2} = 4(1+2+3+4+5+6+7+8+9… ) \)
\( S-S_{2} = 4S \)
\( S-\frac{1}{4} = 4S \)
\( \frac{-1}{4} = 3S \)
\( S=\frac{-1}{12} \)
And thus, the sum of all natural numbers is equal to \( \frac{-1}{12} \).


So, what's wrong with all of that?

Some basics of series math.

The definition of a series:
\( \sum_{i=1}^\infty a_{n} = a_{1}+a_{2}+a_{3}+ … \)

A sequence of partial sums is associated with each series:
\( S_{k} = \sum_{i=1}^k a_{n} = a_{1}+a_{2}+a_{3}+ … +a_{k} \)

The series \( \sum_{i=1}^\infty a_{n} \) converges to the limit \( L \) iff (if and only if) the sequence \( S_{k} \) converges to \( L \), otherwise it is divergent.

A sum of a series for a divergent series does not exist.

For the series described in the argument:
\( S_{1} = 1-1+1-1+1-1+1-1+1 … \)
\( S_{2} = 1-2+3-4+5-6+7-8+9 …  \)
\( S = 1+2+3+4+5+6+7+8+9 … \)

All three sequences are divergent, so none of them are summable.

Some divergent series can be analyzed by an alternate method to produce a Cesàro summation, but this is distinct from the typical summation used in the described proof and only one of the series is Cesàro summable.

The Cesàro sequence for \(S_{1}\) is {\(1,\frac{1}{2},\frac{2}{3},\frac{1}{2},\frac{3}{5},\frac{1}{2},\frac{4}{7},\frac{1}{2},\frac{5}{9},\frac{1}{2},\frac{6}{11},\frac{1}{2},\frac{10}{19},…\)}. The sequence converges to \(\frac{1}{2}\), so \(S_{1}\) is Cesàro summable.

The Cesàro sequence for \(S_{2}\) is {\(1,0,\frac{2}{3},0,\frac{3}{5},0,\frac{4}{7},0,\frac{5}{9},0,\frac{6}{11},0,\frac{10}{19},…\)}. Since this sequence does not converge, \(S_{2}\) is not Cesàro summable.

The Cesàro sequence for \(S\) is {\(1,2,\frac{10}{3},5,7,\frac{28}{3},12,…\)}. Since this sequence does not converge, \(S\) is not Cesàro summable.


In summary:
\(S_{1}\) is not summable, but is Cesàro summable.
\(S_{2}\) is not summable or Cesàro summable.
\(S\) is not summable or Cesàro summable.

…which makes the argument that the sum of all natural numbers is \( \frac{-1}{12} \) somewhat hard to swallow.   The 'solution' reminds me of the methods used to prove \( 1 = 2 \), which rely on unmanaged infinities hidden away from the reader.

Dealing with series automatically means we're dealing with infinities.   The intuitions developed from working with regular numbers begin to fail when working with infinities.

Some examples :
\(\infty-\infty\not=0\)
\(\infty-\infty=\infty\)
\(\infty-5=\infty\)
\(2\infty=\infty\)
\(\infty^\infty=\infty\)

There are ways to work with infinities, and different infinities have different meanings, but care must be taken that does not appear to be taken in the 'solution' of the sum of the natural numbers that was being discussed.



In particular I distrust the solution of \( S_{2} \) because their method of multiplying the series by two can be done in many different ways to yield unexpected results.

As described above:
\( 2S_{2} = (1)+(-2+1)+(3-2)+(-4+3)+(5-4)+(-6+5)+(7-6)+(-8+7)+(9-8) … \)
\( 2S_{2} = 1-1+1-1+1-1+1-1+1 … \)
\(2S_{2} = nonexistent\)
\(2S_{Cesàro 2} = \frac{1}{2}\)
Shifting over one more:
\( 2S_{2} = (1)+(-2)+(3+1)+(-4-2)+(5+3)+(-6-4)+(7+5)+(-8-6)+(9+7) … \)
\( 2S_{2} = 1-2+4-6+8-10+12-14+16 … \)
\(2S_{2} = nonexistent\)
\(2S_{Cesàro 2} = nonexistent\)
Shifting over one more yet:
\( 2S_{2} = (1)+(-2)+(3)+(-4+1)+(5-2)+(-6+3)+(7-4)+(-8+5)+(9-6) … \)
\( 2S_{2} = 1-2+3-3+3-3+3-3+3 … \)
\(2S_{2} = nonexistent\)
\(2S_{Cesàro 2} = \frac{1}{2}\)
By multiplying each element by two:
\( 2S_{2} = 2(1)+2(-2)+2(3)+2(-4)+2(5)+2(-6)+2(7)+2(-8)+2(9) … \)
\( 2S_{2} = 2-4+6-8+10-12+14-16+18 … \)
\(2S_{2} = nonexistent\)
\(2S_{Cesàro 2} = nonexistent\)
By adding a reversed order copy of itself:
\( 2S_{2} = (1\pm\infty)+(-2\pm\infty)+(3\pm\infty)+(-4\pm\infty)+(5\pm\infty)+(-6\pm\infty)+(7\pm\infty)+(-8\pm\infty)+(9\pm\infty) … \)
\(2S_{2} = nonexistent\)
\(2S_{Cesàro 2} = nonexistent\)

If a series is not summable, then multiplying it by anything is an unreasonable thing to do.   If you choose to go ahead and do so, don't expect the results you get to be coherent.

Friday, December 27, 2013

Rainbow Rose

As children, many people colored white carnations by putting food coloring into the water used to keep the flower fresh.   The technique to make rainbow roses is just a couple steps past those carnations.

The process works because a cut-flower is alive and constantly soaking up water to fuel its metabolism.   Much of the stem is filled with cells specialized to transfer water (and anything dissolved in that water) up (and down) the stem.   Moisture is constantly evaporating from the surfaces of leaves/petals and the force of this pulls water up from the roots (or vase).   The water transporting tissues aren't perfect and there is some diffusion of fluids across the width of the stem, but it is much slower than the fluid travel along the stem.

The base of each petal is fed from a small portion of the stem, including only a small amount of the fluid transporting tissues.   Because the dye is added to a specific arc of the stem and diffuses slowly around it, each petal will end up with a different amount of each dye.

As each petal grows to be much wider than its base, the color it acquired is spread around the arc of the flower to result in the lovely mismatch of colors seen between adjacent petals.



The angle between two adjacent petals around the flower approximates 137.51°, which is the smaller angle generated when the average ratio of adjacent Fibonacci numbers is applied to a circle.   The Fibonacci sequence is generated with a simple formula (ni=ni-1+ni-2; n1=1; n2=1) and just happens to match the arrangement of petals around a flower because it corresponds with the most efficient packing of petal primodia into the limited space of the flower primordium.

You can make your own rainbow roses from a white rose and different food colors.   The process is patented, providing legal protection for the one commercial supplier.



There are numerous vendors on Ebay/Amazon/etc. selling seeds for unrealistically spectacular roses, including a rainbow-rose using the image at right.   Modern roses are the result of centuries of hybridization, resulting in a complex mix of heterozygous alleles for many genes.   This high degree of heterozygosity means that the only way to propagate a specific rose variety is to make (clonal) divisions. Seed grown from a rose will generally not be like the parent plant.   (Wild roses are the exception, as they are relatively genetically homogenous within each species.)

It happens to be that this particular rainbow-rose was created on a computer.   I found the original was a stock photo from GettyImages.   Other rainbow-rose seed sale offers will likely have photos of the real, manufactured, rainbow rose.

It takes several years to grow a rose plant from seed to its first flower.   You will have no recourse with the online markets for when you realize the seed you purchased did not grow into what you were told they would grow into.

Saturday, December 21, 2013

Mystery of the Amazon (2/2)

This mysterious biological structure turned up in the Amazon in the summer of this year. It was discovered by grad student Troy S. Alexander, while he was working in Peru. He posted some of his photos (at left) to Reddit, hoping that someone would be able to help him identify the maker of the structures… but it turned out that nobody on the whole of the internet-aware Earth had seen such a thing. Well… almost nobody. Another Reddit user (Julgr) had photographed (at right) the same structure on the far side of the Amazon in French Guiana.
The best guess that the internet community came to was that the maker was an unknown Cribellate spider and the structure was to protect its eggs.



The widely spaced, though sparse reporting, suggests the spider is widespread in the Amazon region.
The Cribellate spiders fall into 21 families. By filtering for families found in the Amazon, and then for those with maternal behavior which amounts to finding a good place to leave their eggs… I was able to reduce the number of likely families responsible for this structure to the Deinopidae and the Dictynidae.
The Deinopidae are typically long, stick-like spiders. This body form doesn't seem consistent with the size and shape of the structure, so I favor the idea that the creator is a spider from the family Dictynidae.
The size of the structure suggests it was 'designed' to discourage predation by ants, a very common predator of baby spiders.


A research expedition to identify the creature has recently returned from Peru. They found numerous examples to study.

Roughly half of the examples were found on Cecropia trees. Cecropia are a specialized ant-pant, where the tree provides food and homes for the specialized partner ants. The ants' part of the bargain is to keep plant-eating insects (and light-stealing plants) under control.

After routinely checking on the structures they found, three spiderlings were found to have appeared (one per corral). It can be very difficult to identify the adult species from the appearance of spiderlings, as they have lots of growing to do an often will change color or shape along the way.
The researchers posit that it might be a jumping spider (Salticidae family), as it has a prominent pair of forward-facing eyes, even though the eye placement isn't quite right for the jumping spiders.

The Dictynidae (and Deinopidae) also have a pair of prominent forward-pointing eyes. (Example at left : Chorizomma subterraneum) The researchers did find an adult spider (photo at right) near some of the structures. Although the posted photos don't show much detail, this spider is broadly consistent with the Dictynidae.
I await further identification of the spiders, both adults and juveniles, that were found.



An interesting observation made by the researchers is that the central spires appear to contain two eggs. The eggs differ in color, with one being more white and the other being more yellow.
The difference in color of the two eggs and the final hatching of only one spiderling suggests that one of the eggs may have been sterile and would have been used as food by the just-hatched baby.


Part 2

Monday, December 16, 2013

Mystery of the Amazon (1/2)

[1]
Photos of this structure have been bouncing around the web, leading to rampant speculation as to what constructed them. The structures are about 2 cm across and were found on tree trunks and artificial surfaces.

The first images were taken 07June2013 in the Peruvian Amazon by chemistry grad student Troy S. Alexander (Decapod73 on Reddit) and were posted to the Reddit "What's this bug" discussion forum in hopes of finding some clue to the identity of the creature which made them.

Lots of ideas were tossed around. Aliens? Fungus? Moth? Spider? Alien spider? Moth that got lost?

Later in the discussion, user Julgr posted a picture of one of the structures that they had found on a leaf in French Guiana. They had initially assumed it was a peculiar fungus.


[2]
Since the sightings were at both the western and eastern ends of the Amazon rain forest (green in the figure at right), it is possible that they could be found throughout most of the Amazon. The small size of the structures, paired with the rarity of individuals who would both go looking for and report to the wider world about such finds, readily accounts for the sparse reporting so far.

Hopefully, there will be more sightings now that the whole of the world has heard about this mystery of the Amazon.



Following the wide-ranging conversation about this creature eventually led to the BugTracks Blog, where a tentative ID was suggested of a Cribellate spider. This group of spiders produce a characteristically fuzzy type of silk that is seen in this close up of the fence structure.

According to the Wikipedia, Cribellate spiders fall into 21 families, with thousands of species living in a wide range of habitats. Eight families (Austrochilidae, Desidae, Gradungulidae, Hypochilidae, Nicodamidae, Psechridae, Stiphidiidae, & Zoropsidae) have no known representatives in the Amazon region. Two (Amphinectidae & Eresidae) have some representatives in some of the Amazon region, but not covering the sites where the mystery structure has been found. The remaining eleven families (Agelenidae, Amaurobilidae, Ctenidae, Deinopidae, Dictynidae, Filistatidae, Miturgidae, Oecobiidae, Tengellidae, Titanoecidae, & Uloboridae) are found throughout most or all of the Amazon region and are likely candidate families for our unknown spider.

Going through the various Wikipedia pages for each of the families, along with selected google searches, gives some general family trends for maternal behavior. The Amaurobilidae and Miturgidae guard their eggs in a special brood chamber. The Agelenidae, Filistatidae, Oecobiidae, Tengellidae, Titanoecidae, and Uloboridae guard their egg mass in their hunting webs. The Ctenidae carry their egg mass until the brood is about to hatch, then construct a nursery web.

The Deinopidae and Dictynidae spiders hide their egg mass and leave, which is basically the sort of parenting behavior our mystery spider is acting out. Though our mystery spider could easily represent one of the other Cribellate spider families, I'm placing my bet on it eventually falling into either of these. (I might even extend my bet to place it in the Dictynidae, based only upon the typical body form of the family seems more consistent with how I imagine a spider crawling around to make the mystery structure.)

Fortunately, I'm not an arachnologist with his reputation on the line. I can make statements like this and not really be concerned at how they play out in the end.

According to the National Geographic article on the topic, an entomologist will be traveling to the Tambopata Research Center to track down the maker of the mystery during the winter of 2013. We may soon have more data to work with!



Lacewing eggs. [3]
Another topic relates to what selection pressure would encourage the evolution of such a peculiar structure. Ants are a constant threat to small arthropods in most ecosystems and many organisms have evolved mechanisms to protect themselves from them.

Lacewings place their eggs on long silken hairs, out of reach of ants.
Mimetus notius [4]


Other spider species have been noted to construct elaborate egg defense systems.

The mystery structure is the right scale to act as an ant deterrent. The fence-webbing would tangle and trap a single ant trying to climb over (though a swarm of ants would readily overtop the wall). If the fence-webbing is loaded with some scent which ants find irritating, it would discourage any marauding ant from testing the fence.



Moths have also developed some elaborate defense systems (including fences) to protect pupating larvae from ants (and other similar-sized predators).



Urodus sp. [5]
Bucculatricidae [7]
Unidentified moth. [6]

Part 2

Monday, December 2, 2013

The Color of Onions

A friend passed me a link to an EBay vendor selling the "Romanian Rainbow Onion" seen at right.

He and I have on several occasions talked about biologically plausible mechanisms that might result in interestingly colored plants, so he was curious if I thought this onion was a real thing.

I responded strongly to the true blue color depicted in some of the inner rings in particular, as being evidence of fakery. Blue is a fairly rare color in biology and I was quite certain that there had never been an onion with such a true blue color... let alone the beautiful color gradient depicted.

At this point I remembered that modern search engines let you search using an image as the query. The right half of the image at left was found in a Turkish news article talking about European onion imports. The left half of the image is the original rainbow-onion image (after being scaled/rotated/cropped to match the placement of the unmodified onion).

Unfortunately, it seems this rainbow onion is the figment of someone's imagination and modern image editing software.



However, there are biologically plausible mechanisms by which such lovely color gradients could be generated.

www.braukaiser.com/wiki/index.php?title=An_Overview_of_pH[1]
The simplest relies on the interaction between pH the common anthocyanin pigment found in onions, cabbage, and many other plants. Onions generally have a pH on the range of 4-6[2], which corresponds to the purplish shades in the anthocyanin:pH-gradient

There are numerous examples in biology where chemical gradients are generated. Such gradients are critical in developmental biology. It is not inconceivable that an onion could at some point be found (or made) that produced a gradient of pH across the many petiole bases which make up the onion bulb. The gradient that would be produced by this mechanism would not result in the color gradient of the rainbow (ROYGBIV) shown in the original image.

If you want to produce the color gradient of the rainbow, you would have to convince the plant to produce yellow pigments (such as carotenoids) at the appropriate stages of the pH gradient. This more complicated color-gradient system is perfectly plausible in a biological sense, but would be much harder for an agronomist to produce.



It would be far simpler to just make an onion that was entirely blue, by giving it a pH on the range of 8-10. Not only would this be a dramatic color to add to a salad or burger, it would most likely have a very distinct taste. The sharp flavor we experience from onions is due to the presence of sulfuric acid, so by converting the onion to an alkali pH, we would be removing the major flavor component. Without the strong acid component, perhaps more subtle flavors would be revealed.

To breed for a blue onion, you would only have to select the most alkali bulbs each year to produce seeds from. To keep the project from taking a few more centuries than your life will last with modern medicine, I would advise you to find a way to increase the mutation rate of your seeds.