Mad Prime

I made this picture today in the new version of Inkscape, making extensive use of the new thin/thicken tool.

While reading up on giraffes and acacias on the internet, I noticed that the acacia featured in the original Science article wasn't in Wikipedia at all - not even a stub! The acacia, Acacia drepanolobium (Whistling Thorn) has a ton of info about it lying around on the internet, so it definitely deserves a wikipedia entry.

I found a creative commons photo on Flickr and the photographer, Martin Sharman, graciously changed the licensing on the photo to allow for commercial usage so I could use it in the wikipedia article. So I made the article, and I think the subject is pretty cool - this tree has a neat symbiosis with several species of ants, check it out.

The first known example of parasite induced fruit mimicry: Scientists report (in the April issue of American Naturalist) the discovery of a parasitic worm that infects ants and turns their butts bright red -- so they resemble berries. The parasite also changes their behavior, causing them to wave their butt around in the air. A bird spies the "berry", eats it up and is infected. Bird poop is fed upon by the ants, completing the parasitic cycle.

Science magazine had an article exploring a paradoxical observation: acacia trees fenced off and protected from herbivores seem to be less healthy. It turns out the acacia trees are usually in a symbiotic relationship with a species of ant that protects them. When nobody's munching on the trees, they stop providing for the ants and the symbiotic relationship breaks down -- in a way that's actually worse, in the end, for the acacia.

Then I started wondering, tangentially, if giraffes and acacias coevolved tallness. So I googled around... what I actually found was some surprising controversy regarding the evolution of the giraffe's neck.

Everyone pretty much assumed they evolved tall necks to reach more leaves, but in 1996 a couple of guys proposed that the neck was actually a product of sexual selection. Turns out that the males use their necks as weapons when fighting each other. Check out this crazy youtube video. (url: http://www.youtube.com/watch?v=C7HCIGFdBt8 )

The argument they had against the feeding hypothesis was that giraffes spend a lot of time browsing at or below shoulder level. In 2007 another group published a study which found that higher quality biomass was available to giraffes higher up, due to competition with other foragers at lower levels. In the end I think I'll stick with the tall-to-reach-leaves-hypothesis, but I thought this video of fighting giraffes was too awesome not to share.

I've done it myself, using Exploratorium's online recipe.

As Schrödinger so famously demonstrated, whenever one is illustrating fundamental scientific principles, the optimum choice for such an illustration is a cat. In that spirit, I'd like to present one of my favorite examples of how fundamental biology phenomena are visible in our everyday life.

Some background: Gene copy number is important. Variations in gene copy number are, perhaps, a subtle sort of problem -- having 50% more or less copies of a gene available for expression is conceivably a minor thing in the biochemical world, where feedback loops regulate gene expression to increase or decrease as necessary. (That's why so many disorders are recessive; as long as one functional copy of a gene exists, things seem to work fine.) Nevertheless, the duplication or deletion of entire chromosomes has a severe effect. Within the autosomes (non-sex chromosomes), no cases of chromosome loss are viable. The only extra chromosome that is mild enough to be viable in humans is trisomy 21, which causes Down syndrome. Chromosome 21 is the smallest autosome.

Because of this, when it comes to the sex chromosomes, mammals are faced with a copy number problem. Males (XY) have only one copy of the X chromosome, while females (XX) have two. The ways biology addresses this issue is called "dosage compensation". In mammals, dosage compensation is achieved by randomly inactivating all but one X chromosome in all cells. Thus, regardless of an animal being male or female, only one X chromosome is active in any given cell.

This X-inactivation occurs early in embryonic development. Once a cell has decided to inactivate a given X chromosome, that decision is inherited by all its daughter cells. As a result, female mammals exist as a "mosaic" of X-inactivations -- in their bodies, whole patches of tissue have one or the other X inactivated.

An interesting consequence of X-inactivation is that, unlike genes on other chromosomes, only one allele of a gene on the X chromosome is expressed in any given cell. This phenomenon is easily visible in tortoiseshell cats -- tortoiseshell coloration arises from X-inactivation, so these cats are almost always female. The coat color gene, which has alleles for orange or black coats, exists on the X chromosome. Because of X-inactivation, only one of the two genes is active in various patches of skin, giving rise to a pattern of orange and black patches. Since the process of X-inactivation is random, this pattern of patches is random.

I love this example of X-inactivation so much, I added a picture of a kitty to the wikipedia page on X-inactivation. It's always cool to have a everyday visualization of what would otherwise be an abstract genetic and developmental phenomenon.

Sometimes mother nature inspires engineering. Sometimes especially hard problems are solved by organisms in ways we might not have imagined on our own. Bugs seem like unlikely muses, but they've inspired many an engineer.

Recently Science Magazine posted a news item about a synthetic lens that behaves much like an insect eye. The problem was this - how to create a very small camera that captures a wide angle light? A fisheye lens would be the obvious solution, but those are hard to create on a small scale.

Drawing inspiration from insect eyes, Jeoung, Kim, & Lee have created artificial compound eyes:

Now, I'm not clear on how detectors are set up to receive light that's captured by the polymer, but the pictures sure look cool.

Multi-directional vision isn't the only the only thing we have trouble miniaturizing - sound localization has also been difficult to miniaturize.

Humans seem to use the difference between the ears in volume of sound and time it takes to arrive to localize sounds. This was first described by Lord Rayleigh as the "duplex theory of localization".

But this system can't work for flies. With the speed of sound at 350 meters per second, a half a centimeter seperation of ears - huge in the world of bugs - only nets a 15 microsecond difference. Humans, with 20 centimeters of seperation between the ears, enjoy 600 microseconds. Now, human reaction time is at best around 300,000 microseconds; it's amazing that 600 microseconds is enough to be preserved by carefully timed propagation through axons, but 15 microseconds is simply lost to neuronal noise.

But bugs can find noises! Ormia is a parasitic fly that likes to lay its eggs on grasshoppers, and it has ears that are a scant half millimeter apart. And yet they can localize sound as well as humans. They need to, to find the chirping male grasshoppers that will host as food and home to their parasitic children.

They accomplish this trick through linking the ears' oscilliatory motions. This results in vibration differences - in both level and timing - between the two ears, caused by small differences in the timing of the sound's arrival.

This clever solution has inspired engineers to create Ormia-based miniature directional microphones.

Finally, bug brains. Now, it's true that bug brains aren't very big, but bugs have interesting swarm properties. And when it comes to making robots, the simplest behaviors of living things are the most realistic thing we could try to imitate. No one falls for a talking pseudo-human robot, but a robotic bug really looks alive!

I heard about BEAM robots (Biology Electronics Aesthetics Mechanics, or something like that) from an article on Make magazine's blog. While BEAM philosophy isn't necessarily about bugs, that's what these things look like.

The bugbots at the Maker Faire were solar-powered. Sunlight doesn't give enough energy to continuously drive a motor, but capacitors can collect the energy to a critical point and release to create bursts of action. The bugs hop around in the sunlight, some of them attracted to it - moving towards their food source!

I really want to build one of these solar bugs. They sell kits at www.solarbotics.com and a lot of community (advice, guides, designs) exists at the solarbotics-hosted community at www.solarbotics.net.

I've been getting my little science news snippets these days from Science Now news (Science Magazine, unfortunately restricted access) and Nature News (unrestricted access). I look around for other news sources, I know there's a ton out there. Today I looked at Seed magazine's news.

The top article at the time was this one: "Junk (DNA) In The Trunk".

The article's opening paragraph...

"Finding a function for the 98.5 percent of our DNA that doesn't encode for proteins - sometimes known as "junk DNA" for its jumbled, illegible arrangement - became a little less elusive last week. Geneticists from Johns Hopkins published an innovative way of using zebrafish embryos to test the purpose of non-coding human DNA sequences in the March 23rd online issue of Science Express."

Oooooh, how mysterious! We don't understand 98 percent of our DNA!

Actually, it's not.

It's not a mystery.

It's a bunch of repetitive elements, parasitic self-propagating sequences that occassionally, in frenzied bursts of self-centered replication, manage to insert copies of themselves all around the DNA. They're called transposons. 72% of our DNA is composed of retrotransposons, LINEs, and SINEs, three varieties of selfish, self-propagating junk.

This is just bad reporting. People should not propagate the mystical idea that there's vast tracts of presumably functional DNA that remain a mystery to scientists. It doesn't need a function! We're pretty sure it doesn't have much function. This sort of thing is vexing enough when it takes the form of science fiction but it's totally unacceptable in science reporting.

Of course, the reporter did not actually get any facts wrong. He simply missed the point.

This really is something interesting here. Transposable elements have been a great tool for analysis of transcriptional promotion for Drosophila, and zebrafish is an animal much more relevant. What we really care about here isn't the junk. We care about transcriptional regulatory elements, those small regions preceding genes, and maybe a few small distal elements, that determine when a gene is going to be expressed.

So, yes, there are interesting noncoding portions, but to conflate that with the 98.5% number and the term "junk DNA" is going to propagate the ignorant characterization of this stuff as being of mysterious function, when we're pretty damn sure it ain't.

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... And, as if the world conspires to drive me apoplectic, Chris sent me a link to this article about the in silico simulation of a virus. But... what's the point? I mean, sure, it's an impressive computational feat, but what did they learn? The article failed to report on the results!

Here it is, in a quote from Nature News:

"The model also shows that the virus coat collapses without its genetic material. This suggests that, when reproducing, the virus builds its coat around the genetic material rather than inserting the genetic material into a complete coat. "We saw something that is truly revolutionary," Schulten says."

See, that's an interesting result. The LiveScience reporter missed it.

Science reporting shouldn't just be about mysteries and pretty toys. I wish science reporters didn't keep misunderstanding science and missing the point of research -- not just for the layman's sake, but mine too, because I like reading about this stuff.

I was listening to the Long Now lectures again, this one by Michael West on the subject of human life extension. I can't say much of it stuck with me, but there was one topic that really caught my attention. And that was this: Ancient Greek had two words for life -- "bios" for the life of an individual, finite and mortal, and "zoe" for the infinite and general phenomenon of life.

He applies this language to the contrast between the somatic tissue of our bodies and the germ line tissue of our gametes. The gametes are immortal, an unbroken line that extends back to the first life from which we all descended. They've never died. But every time they move through a new generation a set of cells is created to house and protect this royal lineage -- our bodies. Thus, the body is the "bios", the somatic mortal tissue of finite span. And that cycle of embryonic stem, germ stem, and gamete cells is the "zoe", the immortal life that is unbroken.

After hearing that, of course, I thought Zoe was pretty much the best name ever to give one's daughter. There she is, made from your immortal fragment, the part that can live on.

To my dismay, Chris pointed out that there's already someone named Zoe Ball, a somewhat famous person. I was crushed. (I even whined about changing our last name.) Anyway, I'm passing along the name to you guys, in case you get any daughters and don't know what to call them.