03 September, 2008

The Tangled Bank #113: A Labor Day Carol

Blogging across the parallel universes brings not only rewards but a burden of responsibilities. I learned this to my chagrin one day in 2112, on Tangled Bank #113, a beautiful little terraformed world in Parallel U. Gamma, named in honor of the great Charles Darwin. Certain theories of time travel had recently been overturned. My physicist friend Yoo Chung burst in my door shortly after creating a time travel device that utilized the wormholes he once doubted.

"Dana! Grab your Smack-o-Matic and hurry!" he shouted, arms flailing like dear little windmills. "Darwin never published Origin in Parallel U. Cappa. Now the backward denizens of that universe have stolen a U-Skipper from the anthropologists sent to observe them and are planning to unleash ignorance bombs throughout the multiverse! There's no time to lose!"

I swivelled around without taking my mind from my post-generator. "Yoo. Darling. You created a time machine. We have gobs of time to lose."

His panic faded, replaced by a blank look. "Oh. Oh, right. Okay, when you get around to it."

Persuading a reluctant giant of science to budge might prove a bit difficult, so I called upon our Cephalopod Overlord to marshal an army of arguments for me. Armed with these and my trusty Smack-o-Matic, I marched through Yoo's time bridge and imposed myself upon Charles Darwin and his barnacles.

"What's this I hear about you not publishing Origins, Mr. Darwin?"

Roughly an hour's worth of explaining how a woman in pants waving a monstrous electronic paddle had come to appear in his study ensued before I obtained an answer to my original question. "Well, you see, there's so little interest," he mused, stroking his wild white beard. "Our respective essays were recently presented at the Linnean Society, and the reaction has been anything but thunderous."

"You want thunder, sir, I shall give you thunder." I flourished the Smack-o-Matic. "Behold the Tangled Bank!"

"The which?"

"Something you said once, sir. Your little theory has - will - revolutionize the world. But only if you publish. Allow me to show you the fields of science evolution will impact, and then you can tell me just how not-thunderous the reaction has been."

We began in familiar territory, with biology - but biology as Darwin couldn't have imagined it:

Pharyngula, "Reprogramming the pancreas"

While injecting a person's pancreas with a collection of viruses to rebuild missing cell types might be a little hazardous and crude, there may come a day when we can collect a few cells from an individual by a scraping or biopsy, grow them in a dish to get enough, tickle their transcription factors to cause them to differentiate into the cell, tissue, or organ type we want, and transplant the final, immunocompatible product right back into the patient.

Ramblings, "Biochemistry is worth it"

So then I got to thinking, which is generally a bad sign, and I decided I should take a biochemistry course, since everything I am interested in regarding microbes is on the molecular level.

So that's all well and good, but what makes nonpolar molecules 'hydrophobic?' I undersand why they aren't dissolved like polar compounds, but what makes them 'afraid' of the water molecules and want to 'get away.'

Tonisidaway, "Geography is encoded in the genes"

They report that when a political map of Europe is placed over the genetic map, 50% of plots end up within 310km of the country of origin and 90% are within 700k of the country of origin.

Denialism Blog, "Get ready - flu season is closer than you think"

Small changes occur in the RNA of flu viruses over time, leading to changes in the surface molecules. Even small changes in these surface molecules can change our immune system's ability to respond to an infection.

It's Alive!! "Human parasite's goody two shoes cousin helps coral"

Chromera velia is clearly related to Plasmodium parasites, but rather than being a blood-borne obligate parasite of mammals and insects that rarely sees light of day, it is a plankton-like photosynthesising obligate symbiont of corals.

Biochemical Soul, "Another Step in the Evolution of Humans and Apes from Ancestral Mammals"

One of the most fascinating lines of research within the field of evolutionary biology is the search to find the genes that changed at the split between ancestral mammals and our own closer ancestors, the great apes.

The annotated budak, "Missing in action: Megafauna and seed dispersal in Asia's empty forests"

The study of seed dispersal was a popular discipline amongst late 19th and early 20th century biologists. These included a certain Charles Darwin, who undertook experiments such as feeding seeds to birds, killing the poor fowl and floating their carcasses on seawater for weeks to determine if the seeds would still be viable.

Cheshire, "Environmentally Friendly Pest Control: An Overview of The Sterile Insect Technique"

In many cases, we can use the insects themselves to aid us in their elimination. One method, called the Sterile Insect Technique (SIT) involves using sterilized insects to drive the population down.

a Nadder! "Aliens Among Us"

Some people complain that aliens are very blandly portrayed in books, movies etc. Half are humanoid, often being mere WASPs from another galaxy. The other half are carnivorous plants, slimy blobs etc. They: few portrayals of extra-terrestrial life are truly original.

Not so on Earth.

Agricultural Biodiversity Weblog, "Lost in genebank database hell"

Navigating around germplasm databases can be a frustrating experience. A posting on CropWildRelativesGroup alerted me to a Science Daily piece on tomato genomics which mentioned the wild relative Lycopersicon pennellii (or Solanum pennellii, but I’m not going there, at least not today). But how many accessions of this species are conserved ex situ? And where is it found in the wild?

Darwin had rollercoastered from consternation to wonder to growing delight as we explored the vistas his simple theory had opened in biology. Now, he looked at me expectantly. "Well?"

"Well, what?"

"And where is it found in the wild, then?"

"Oh, that. We don't know. Poor Luigi and Jeremy are still lost in genebank database hell." I gave the Smack-o-Matic an airy wave. "The glory of science, however, is that we can find our way to the truth no matter how lost we get. And, as the Taoists say, getting lost isn't such a bad thing - the journey is indeed the reward. Let's explore the tangled banks of general science and natural philosophy for a bit, shall we?"

Rodibidably, "Defining Science"

The overriding themes on these definitions seems to be knowledge and the search for knowledge. This means that Science is concerned with learning and acquiring information, or knowledge.

A Neotropical Savanna, "Cojoba beans"

Look at how the beans are still attached to the pod, even though they’re not within the pod itself. This appearance might be a way of luring birds to the tree to disperse the seeds (Zuchowski) although few birds seem to be attracted to these beans.

Science After Sunclipse, "An Alloy of Pleasures"

If the Gentle Reader were to deduce a “moral” from the story, it might be that I am a cantankerous individual with an acerbic disposition, and the reader would not be gravely in error. Beyond that, one could say that a science education nearly killed the general-interest bookshelf for me, and what University did not do, the science-blogging world definitely tried to finish.

Chromium Oxide Green, "An arachnid this time!"

The spider had torn off about a third of the flower, and, with its front legs, was spinning the little yellow piece, rotating it, as though she were going to attempt to eat it! It seemed that, with my tapping the web, she had mistaken the flower for a caught insect.

Tethered Cow Ahead, "Similarity Breeds Contentment"

But I leave you with this thought: self-similarity is rife in nature. It is embedded everywhere from the mathematics of fractals to the formation of snow crystals and the songs of birds.

Darwin sighed with pleasure. "What a beautiful sentiment."

"Indeed. It's times like this that I know science is more than theories and experiments. It's something altogether wonderful." I poked him with the tip of the Smack-o-Matic. "And necessary. Consider neurobiology. If we don't understand our own minds, how are we to use them to their fullest potential?"

That One Person Who Likes That Historical Strategy Game, "Big Brains Tell Really Big Lies"

Basically, it turns out that over time, what we know to be a lie can seem to become a truth, as the memory becomes more long-term. The more times we hear it, the more likely it is that at some time in the future we will think it to be true, even if a disclaimer is added every time.

The Evolving Mind, "RP) Gaps in the Brain & a Jack of Many Trades"

Rather than a mono-function corkscrew, human nature is a Swiss Army knife. Any blade currently manifest, endowed in us by “nature,” is one nurture has extended. Plasticity in the brain translates into a great range of potential behaviors and thus flexibility in how an individual or group can adapt to its environment. And environments change.

"That's what your theory has inspired, sir. We now understand our minds in a way we couldn't have done without your enlightening little book."

Darwin rubbed his beard. "This is indeed an inspiration to me. But I feel, Dana, that you are only giving me a part of this story. I've heard rumblings from some of the more superstitious among us. How have they reacted to my theory? Have the objections been overcome?"

"Alas, the traits of stubbornness and willful ignorance are still very much a part of our evolutionary heritage." I shook the Smack-0-Matic. "Hence, this. But while they reject your theory, they're finding it harder and harder to defend against."

Tonisidaway, "Pennsylvania University Museum Exhibition Refutes Intelligent Design"

Using exhibits such as a life-sized transparent model of a recumbent woman, the exhibition demonstrates the features that life has evolved to enable it to survive. The message is that our bodies, being a product of natural selection, are functional, but far from perfect.

Discovering Biology in a Digital World, "Mumps outbreak in Vancouver"

Today, I read that a mumps outbreak is happening in Vancouver, Canada. So far 116 cases have been confirmed.

Why is mumps, a preventable and serious disease, causing problems in Canada?

Submitted to a Candid World, "Our Comment for the 'Provider Conscience Regulation'"

While perhaps to some the regulation’s goals are laudable, by elevating the physician’s conscience above the patient’s health, the PCR evinces a shortsightedness and ignorance of consequences that ought to doom it to failure.

Dubiosity, "The 21-gram soul"

As the story goes, a doctor named Duncan MacDougall proved that the soul exists because he found that people weigh less (about 21 grams) after they die than they did just before death. These results were reported in the New York Times numerous times after the study was performed...in 1907.

I guess science reporting was as crappy 100 years ago as it is now. But, rather than just dismiss this out of hand as we probably should, let's analyze it a bit.

Evolved and Rational, "Is irreducible complexity a problem for evolution?"

An irreducibly complex system is generally defined as a system that loses its function if any one part is removed. If such a system is found, all it would show is that it did not evolve by the addition of single parts with no change in function. However, since this is not the only evolutionary mechanism around, the IDiots who use this argument simply show themselves as ignoramuses when it comes down to how evolution actually works. An irreducibly complex system would not pose a problem for evolution nor justify the design inference.

"You see? Your theory is more than scientifically powerful enough to defeat every challenge thrown at it. And society is better for it - the great advances we've made in medicine, biology, even seemingly unrelated fields like astronomy, chemistry and geology owe a great debt to you."

Darwin's eyebrows rose like caterpillars on a puppeteer's string. "Geology?"

"Indeed."

Outside the Interzone, "98 102 97 88"

Don't think for a second that geology pertains only to rocks.

Reconciliation Ecology, "Holy magnetic cow!!"

Do you think of asking the cow for directions? Why not? For it seems that cow probably knows which way north is!

Chimaera Contemplations, "Delta in distress"

The Sacramento San Joaquin River Delta (Delta) is dying. It has really been dying since 1849, when that historically highly invasive and destructive race of homo sapiens - the white man - discovered gold and started invading the state in large numbers. To be fair, white women started arriving, too.

Tangled Up in Blue Guy, "The Largest Ecosystem on the Planet"

The North and South American continents joined up just three million years ago, but before then there was a chain of deep sea channels from the Pacific through to the Atlantic. Sandwiched between Jamaica and the Cayman Islands is a trench approximately 5000 meters deep (or a little more than three miles,) which has yet to be explored. But that will soon change thanks to the National Oceanographic Centre, Southampton.

"Do you know what they find in those deep sea channels?" I asked. "Life, evolved to tolerate conditions that would kill us in a heartbeat, living off of things we never even considered as food."

"Incredible," Darwin said. He had at some point reached for his pen, and was busy sharpening it. I could see the Smack-0-Matic would no longer be needed. "I knew that evolution was a powerful force, but this is astonishing. And you say that my book will enable us to understand how these things come to be?"

"Not only that," I said, "but it will inspire generations to fall in love with science, and have consequences even for our drinks. Speaking of which, I'm dying of thirst after all of this. I do want you to write this book, but do you think we could go for a beer?"

Beer Science, "Dry Yeast vs. Liquid Yeast"

There are proponents on both sides of the dry vs. liquid yeast debate, both with valid points. Dry yeast is easier to use and can be stored longer, not to mention it’s cheaper. Liquid yeast on the other hand, provides a fresher pitch of healthy cells.

What is a brewer to do? An article appeared last year in the Journal of the American Society of Brewing Chemists that gives me some ideas.


The Off Season Recipe Blog, "A bit of brewing chemistry"

Well, I'd be remiss as a food geek not to make a post about food science, so in response to an open invite to the Tangled Bank, I'll talk a little about beer, corn syrup, and how it all relates to ethanol usage.

This post is about amylases -- enzymes that break down starch into sugar. They are a fairly important class of enzymes, as they happen to be the main enzyme that allows us to convert starches and other polysaccharides into simple sugars such as glucose that allow our bodies to run.

Janne in Osaka, "An Experiment in Coffee Storage"

Science is a method or a way of thinking about things, after all, and it doesn't have to be about complex or esoteric things.

"I can raise a pint to that," Darwin said.

"And after the pint, an inkwell." I sighed. "After which, I shall unfortunately have to leave this Tangled Bank and return. But there will be plenty more Tangled Banks to come, beginning at Science Made Cool, now that you've seen the extraordinary importance of your little book."

5 comments:

Eric said...

Thanks for hosting!

As always- an enjoyable miscellany!

ex animo-
Eric

Jeremy said...

Wonderfully entertaining post, to say nothing of the posts you listed. Who would have thought there would be so much just one week after the previous Tangled Bank?

Thanks.

Irradiatus said...

"a woman in pants"

Hilarious intro!

Well done.

Mike Haubrich, FCD said...

This has got to be one of the most cleverly presented editions of the Tangled Bank I have ever read. Thanks for putting this all together, Dana.

A Free Man said...

Really digging your site, which I found through both It's Alive and Panda's Thumb. Call me a subscriber!

I'm wondering if I could humbly, well as humbly as possible, ask you to have a look at some of my science posts for consideration for #114.

Here's a link to my science writing: http://www.afreeman.org/tag/science/

Best wishes,

Chris