// Twitter Cards // Prexisting Head The Biologist Is In: 2013

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)

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.

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.

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.

Wednesday, November 27, 2013

Genetics of Squash Shape (1/2)

In 2012, I saved some seeds from a "Patty Pan" squash I grew in the garden.   This spring, I grew three of the saved seeds and had two survive to maturity.   I was expecting the plants to produce the flying-saucer shaped fruit that the "Patty Pan" squash is known for, so I was surprised to see what developed.   The fruit from both plants was elongated and grew in yellow (later maturing to orange).

I decided it was time to investigate the genetics of squash fruit shape.   I recalled seeing this figure in some ancient genetics text book explaining the common shapes of squash as being due to two interacting genes and eventually I found a version of it.   The "Patty Pan" squash shape is caused by having a dominant allele for each of the two genes, while the elongated "Zucchini" shape is caused by being homozygous recessive for each of the two genes.   A squash with a spherical/pumpkin shape has a dominant allele for only one of the two genes.

Since my "Patty Pan" squash produced elongated children, it had to carry a recessive allele for each gene, thus it had the genetic composition of (AaBb).   I didn't control the pollination which led two the seeds I grew, so the father is unknown.

The first model for this cross is that the pollen came from a male flower on the same plant.
(AaBb) x (AaBb) -> (aabb)

Both pollen and egg had to carry recessive versions of each gene.   A quarter of the egg and pollen cells would be double-recessive (or double-dominant), so the probability of this cross resulting in the observed progeny would be 1/16.   The probability that two progeny would have the double-recessive trait is (1/16)^2 = 1/256.   This is not exactly a likely probability.
The second model for this cross is that the pollen came from a male flower on a nearby "Zucchini" squash I was also growing.

(AaBb) x (aabb) -> (aabb)

A quarter of the egg cells and every pollen cell would be double-recessive, so the probability of this cross resulting in the observed progeny would be 1/4.   The probability that two progeny would have the double-recessive trait is (1/4)^2 = 1/16.   This is also not exactly a likely probability.

A third model is that the classical story of squash shape is wrong for the genetics I am playing with.   Generally, I would consider this also to not exactly be a likely probability.

To discriminate between the three models, I need more data.   Right now there are too few data points to be certain and unlikely events happen all the time.

I still have six viable-looking seeds from the parental "Patty Pan" squash and this season I saved almost every seed from a fruit each of the two progeny plants.

Next year, I plan to grow out the six remaining first generation seeds and as many of the second generation seeds as I can find homes for.   I expect I will be sharing lots of squash with everyone I know.

Part 2