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“civilization is a race between education and catastrophe.”
- H.G. Welles

It took life on Earth millions years to figure out how to digest cellulose, the hard wall that makes up the cells of plants, efficiently to get at the energy inside it. In fact, complex lifeforms, such as Cows and Termites, have to take the indirect route of enlisting bacteria in their guts to digest the cellulose for them.

In one of the many many many asides he takes in his book A Short History of Nearly Everything, Bill Bryson talks about plastics being made of hydrocarbons found in oil and natural gas. Although plastics are non-biodegradable, there is a great deal of energy still stored in those hydrocarbons, just waiting for the right lifeform to evolve along and start consuming them.

There is now a continent-sized vortex of the Pacific Ocean swimming with plastic junk. Sea turtles and birds are mistaking plastic bags for jellyfish, ingesting them and dieing. Plastic particles are accumulating in the food chain, appearing, undigested, in the feces of seals and other animals.

Plastic Bag Tree Credit: spike55151

In his book, The Andromeda Strain, Michael Crichton fictionalizes a microbe that mutates to eat rubber. Today, numerous scientists and companies are engineering microbes to eat plastic, or more precisely, microbes with the ability to break down plastics to get at the bounty of hydrocarbons locked up within them.

Companies, like Verde Environmental and WonderChem, produce solutions of microbial cultures that eat oil, slowly. Recently, 16-year-old Daniel Burd, of Waterloo, recently isolated the microbes that eat plastic bags as a Science Fair project, earning him a $10,000 prize and $20,000 scholarship. His discovery may reduce the time it take to degrade plastic bags to just three months. A shovel-full of soil from anywhere on Earth contains millions of the oil-eating Pseudomonas bacteria. It’s just a matter of encouraging these microbes to be fruitful and multiply

The Law of Unintended Consequences comes into play at this point. Algae-like bacteria live in both diesel and biodiesel fuel, clogging up the engines they contaminate. Organisms like these have all ready ruined a large amount of Earth’s underground petroleum, leaving sulfer and methane as byproducts. A quick look at all the modern conveniences requiring plastics that we rely on give us a hint as to the pandora’s box we might be dabbling with here, meaning we might end up needing microbes to clean up the microbes.

“There was an old lady who swallowed a fly…”

The Journal Nature has published an article calling for a Hippocratic Oath for life scientists. Medical doctors have a Hippocratic Oath, which guides their ethics and prohibits them from doing harm, and so do Veterinarians. I am 100% for this, and it appears many others are all ready well ahead on the idea.

GrrlScientist has one version of the Scientist’s Hippocratic Oath:

I promise never to allow financial gain, competitiveness or ambition cloud my judgment in the conduct of ethical research and scholarship. I will pursue knowledge and create knowledge for the greater good, but never to the detriment of colleagues, supervisors, research subjects or the international community of scholars of which I am now a member.

Dr. Gene Weltfish, who teaches anthropology at Columbia, has another version:

I pledge that I will use my knowledge for the good of humanity and against the destructive forces of the world and the ruthless intent of men; and that I will work together with my fellow scientists of whatever nation, creed or color, for these, our common ends.

The Institute for Social Invention has yet another version:

I vow to practice my profession with conscience and dignity; I will strive to apply my skills only with the utmost respect for the well-being of humanity, the earth, and all its species; I will not permit considerations of nationality, politics, prejudice, or material advancement to intervene between my work and this duty to present and future generations. I make this Oath solemnly, freely, and upon my honor.

The Oath of the Scientist from Lucy and Stephen Hawking’s George’s Secret Key to the Universe is my favorite so far:

I swear to use my scientific knowledge for the good of Humanity. I promise never to harm any person in search of enlightenment. I shall be courageous and careful in my quest for greater knowledge about the mysteries that surround us. I shall not use scientific knowledge for my own personal gain or give it to those who seek to destroy the wonderful planet on which we live. If I break my oath, may the beauty and wonder of the Universe forever remain hidden from me.

Not an oath, but the UK government’s chief scientific advisor, Sir David King, hopes the world will adopt the seven principles in the ‘universal code of ethics for scientists’:

Act with skill and care in all scientific work. Maintain up to date skills and assist their development in others.

Take steps to prevent corrupt practices and professional misconduct. Declare conflicts of interest.

Be alert to the ways in which research derives from and affects the work of other people, and respect the rights and reputations of others.

Ensure that your work is lawful and justified.

Minimise and justify any adverse effect your work may have on people, animals and the natural environment.

Seek to discuss the issues that science raises for society. Listen to the aspirations and concerns of others.

Do not knowingly mislead, or allow others to be misled, about scientific matters. Present and review scientific evidence, theory or interpretation honestly and accurately.

Now the AAAS needs to legitimize on of these, or we need to adopt one through populism. : )

Like Thomas Jefferson, I eat a plant-based diet, with occasional meat in small portions. Like most Americans, I have no idea where the food I consume comes from, or how far it had to travel before reaching my dinner plate.

My pickup truck, which gets about 20 MPG. Occasionally On rare occasions, I ride my bicycle to work, but I usually don’t have the time or inclination.

I live alone in a free-standing house. It’s well insulated with energy-efficient windows, but, at around 900 square feet, it’s much more space than I need. Every square foot of space I don’t use eats up electricity in heating and air conditioning.

If every one of the 6.5 Billion people on the planet lived like me, we would need 3.7 Earths to support them all.

3.7 Earth’s to Support a Planet of Ryan Sommas

It takes 16.6 acres of biologically productive land to support my lifestyle. There exists 4.5 acres for each person on our planet.

16.6 Global Acres to Support One Ryan Somma

The average American requires 24 acres, nearly six times our allotment. It takes an immense quantity of resources to support the electricity, running water, roads, infrastructure, and myriad conveniences that go into our first-world lifestyles. There are only 300 million of us living at this 24 acre standard of living, but that’s about to change.

Breakdown of Ryan Somma’s Ecological Footprint

China and India, with their combined 2.5 billion people, are quickly coming into America’s first world standard of living. These countries are now bringing one new coal-fired power plant online every week, further stressing our limited coal and oil resources and contributing to carbon dioxide levels in our atmosphere that are already past environmental sustainability.

Aristotle observed, “That which is common to the greatest number has the least care bestowed upon it,” and we see this fact played out all over the world today. Once the fourth largest lake in the world, the Aral Sea has shrunk to under half its size in the last 50 years since the Soviets diverted the rivers feeding it for irrigation purposes. The Colorado River now often dries up before it reaches Baja, California due to overuse upstream.

We see this same over-consumption of our shared resources repeated in vanishing biodiversity, overfishing, air, water, and soil pollution, traffic congestion, noise pollution, light pollution, radio frequencies, and excessive advertising. This natural tendency of most lifeforms, not just humans, to exploit resources until they collapse, vanish, or are ruined is referred to as the Tragedy of the Commons.

Earth Lights (Click for Larger version) Credit: NASA

The humanist visionary Buckminster Fuller popularized the term “Spaceship Earth” as a means of characterizing our relationship to our planet: inescapable and the only one we have. If its life support systems fail us, then we fail. Our situation is that simple, but understanding how our actions affect our environment is a process of perpetual learning.

You can find out your ecological footprint at ecofoot.org.

Arthur C. Clark’s book 2010 has an early scene that was left out of the movie. A Japanese spacecraft has raced to Jupiter’s moon Europa, ahead of a joint American-Russian expedition, to claim the satellite, and all its water, for Japan. Soon after the craft lands, Earth receives a radio transmission from a lone, doomed astronaut, stranded on the moon after something came up through the ice, attracted by the bright lights, to swallow the expedition’s ship.

Europa’s Thrace Region (Evidence of an Ocean Beneath the Ice) Credit: NASA, Arizona State University

The prolific SF author Alan Dean Foster’s Sentenced to Prism explores a planetary ecosystem of silicon-based life, as opposed to our carbon-based version. Dr. David Brin hypothesized plasma life hidden in our Sun in his book Sundiver, alien beyond understanding. Carl Sagan and Edwin E. Salpeter proposed in a 1976 paper, that an entire ecosystem of gas-inflated organisms could hypothetically exist, floating in Jupiter’s massive ocean of an atmosphere.

Life on Jupiter Credit: NASA

If such speculation seems too implausible to take seriously, consider the many extremeophiles, life forms that thrive in harsh environments, here on Earth. Hyperthermophiles, like those giving Grand Prismatic Spring in Yellowstone Park, survive in 140 degrees C (284 degrees F) temperatures. Acidophiles live in pH of 2 - 3, such as phosphoric acid, which gives soft drinks their fizz and is strong enough to dissolve pennies. There are also bacteria fueled by radiation two miles below ground, taking up to a century to acquire enough energy to reproduce.

Grand prismatic spring, Yellowstone National Park Credit: National Park Service

Recently, scientists have found an entire ecosystem of bacteria eating deep sea rock at fantastic pressures. Entire ecosystems, filled with large, complex animals surrounding sulfur vents also demonstrate that life need not be powered by the sun, as we are through Photosynthesis, but rather chemosynthesis, extracting energy directly from chemicals. Both of these are environments potentially mimic Europa’s oceans, which researchers are currently testing the Environmentally Non-Disturbing Under-ice Robotic Antarctic Explorer (ENDURANCE) probe to explore in the future.

Cryobot Exploring Europa Credit: NASA

In 1976, the Viking spacecraft landed on Mars, where it performed the Labeled Release experiment, stirring a radioactive broth into the Martian soil to detect emissions from any microbial life that may exist there. It found emissions indicative of life, but follow-up experiments were inconclusive, leading to a long-standing debate over what Viking discovered. In the 1990s a Martian meteorite found on Earth yielded fossilized hints of ancient bacterial life on Mars, but this finding also generates more controversy than consensus.

Top: Magnetobacteria on Earth Bottom: Possibly Fossilized Magnetobacteria from a Martian Meteorite Credit: NASA

Astrobiologists hypothesize the myriad ways life unlike our own could exist and thrive on alien worlds. Organisms survive in environments of extreme heat and cold, acid and alkaline, and powered on energy sources solar, radioactive, and chemical here on Earth. For these reasons, the world pays close attention as the Phoenix Mars Lander gathers and analyzes Martian soil samples, seeking water, nutrients, and signs of life.

Is There Life in That Dirt? (From the Phoenix Mars Lander) Credit: NASA

“We’ll never know the worth of water until the well goes dry.” – Scottish proverb.

In November 2007 Georgia Governor Sonny Perdue prayed for rain to alleviate the state’s worst drought in history. Before this last-ditch effort, he had sued the Army Corps of Engineers to cut off Florida’s water supply. Georgia legislator even made an attempt to move their border a mile into Tennessee to claim a critical part of the Tennessee River. The state is still suffering, with water levels at Buford dam droping 15.46 feet between March 2007 and February 2008.

Lake Lanier Oct 2007 Photo by Magician pug

Thankfully, in America we have a fantastic system of governance that allows our states to resolve these conflicts of natural resources in a peaceful, legislative manner. A scarcity of water and other resources has led to conflicts in Africa, including genocide in Darfur.

Africa’s Disappearing Lake Chad Photos courtesy of NASA

In Kazakhstan, the Aral Sea has dwindled down to two smaller bodies of water, both of which could be gone in 15 years. Efforts are underway to save what has now become the northern sea, by damming up water feeding the southern sea, ensuring its doom.

Aral Sea 1989 - 2003 Photo courtesy NASA

Abandoned Ship Where the Aral Sea Once Was Photo courtesy Staecker

In America, Lake Mead and Lake Powell, which supply 22 million people with water in the Southwest, has a 50/50 chance of running dry by 2021, and water levels there have dropped 118 feet. Unless Las Vegas can manage to grow and conserve water and electricity, it soon won’t have either.

Animation of Lake Mead’s Water Levels from 2000 - 2004 Courtesy of NASA

Australia, Great Britain, South America, Southern California and other regions are all experiencing water deficits for numerous reasons from over-consumption to climate change. This is both local to the areas affected and global for the human migrations currently happening and might happen in the near future, which will destabilize other communities with influxes of water-refugees.

Something to keep a wary eye on.

Leah, a gorilla, uses a stick to test the depth of water while wading through it Photo by Thomas Breuer/WCS/PLoS Biology

Like Humans, dolphins, whales, and porpoises are mammals. They are warm-blooded, breath through lungs, and give birth to live offspring; however, they also have fins like fish and live in the sea. The skeletons of these aquatic mammals have finger bones in their fins leftover from their ancestors. Some whales even have a tiny pelvis bone free-floating in their bodies, a leftover from when their ancestors had hind-legs. How did these animals, these cetaceans, whose ancestors obviously once lived on land, find their way back into the sea?

Cetaceans share a common ancestor that “resembled a short, legged wolf with hoof like claws.” It is called a mesonychid, and just as Polar Bears will swim for miles across open sea to find food, or Kodiak bears will fish for salmon in rivers, the mesonychid found its way into the water, only it adapted to stay there, and we can follow the long chain of changing fossils from the mesonychid to our present-day dolphins and whales.

While it’s easy to see the present resemblance between humans and other primates like chimpanzees and gorillas, it’s not so easy to explain why we became so different from them. What happened to our fur? Why do we sweat? Why do our noses look so different from chimpanzees’?

Enter Elaine Morgan’s “Aquatic Ape Theory” of human evolution. The theory proposes that our ancestors spent some portion of their history living in a semi-aquatic environment. Seven million years ago, the Afar depression in Ethiopia flooded to become the Sea of Afar. The skeleton of our Australopithecus afarensis ancestor, “Lucy,” was found in this area, where she lived between 3.9 and 2.9 million years ago. Most fossilized evidence of our evolutionary ancestors comes from this region subsequent to this flooding also.

Sea of Afar Depression Image courtesy NASA

So in the case of humans, we did not run to the sea, it came to us quite suddenly and catastrophically. We were thrown into the deep end of the pool, as it were, and had to adapt with down turned noses to keep the water out, less fur to streamline our bodies for swimming, eyebrows to channel the water away from our eyes, sweat glands to regulate the sudden influx of salt water in our diets, infants that can instinctually hold their breath underwater, enlarged spleens to hold oxygen-rich blood and serve as a biological “scuba-tank” that helps us hold our breath, even the ability to hold our breath, and bipedalism, the ability to walk on two feet, to help us keep our heads above water. Then the waters receded and we were left standing upright on land with much larger brains built from a diet high in fish protein.

Most evolutionary theorists are skeptical of the theory; however, as the Philosopher of Biology, Daniel Dennet observes, this is not because there is any way to prove the theory wrong, only that it seems too “out there” to be plausible. They hold to the “Savannah Ape” theory, which proposes that humans became bipedal running across the open plains and using tools.

Meanwhile, waterfront properties garner the biggest real estate values in human society. Beaches are among the most popular vacationing spots in the world (unlike savannahs). Eating fatty fish, such as mackerel, lake trout, herring, sardines, albacore tuna and salmon, supplies our bodies with omega-3 fatty acids, which help fight heart disease and depression. Scientists are also learning more and more that fish really is a “brain food,” combating mental deterioration in old age.

Perhaps, when we spend a relaxing afternoon fishing, we are getting closer to our true nature than we think?

As the purposes for various genes are identified on a weekly basis in the news, this list will be obsolete in a few months, but I wanted to post this. There aren’t enough plain-English reviews of human genes out there. I apologize if I bullox up something. My criteria was based on the importance of the gene to human beings specifically, novelty, and how well we know the gene does what we think it does.

Click the links for any of the genes listed to learn about how the gene appears to work:

1. FOXP2: This gene may be the most important of all in separating the humans from other primates. FOXP2 is crucial to our ability to talk to the elaborate degree we humans are able. A British family with an abnormal copy of FOXP2 has “immobility of the lips, tongue, and mouth, which makes their speech garbled.”

2. OT: The oxytocin gene is what makes mothers motherly, lovers snuggly, and housepets cuddly. It’s a chemical reward our bodies give us for forming social bonds with one another through physical contact.

Oxytocin Image by Fvasconcellos

3. AVPR1a: One of Homo Sapiens’ strongest adaptations for survival is our social-bonding, our willingness to sacrifice our own well-being for the community and work together for common goals. A variant of AVPR1a appears to have a strong influence on this behavior. Nicknamed the “altruism gene,” it is also found in other species that exhibit strong social bonds. (Another variation of this same gene leads to ruthless behavior, earning it a “ruthless gene” nickname.)

4. SRY: Carried on the The Y Chromosome (often considered a “genetic deadzone”), this is the gene responsible for the masculinization process. Mammals lacking the SRY gene are female; therefore, men are the mutation. This gene is important for sexual dimorphism, as the evolutionary adaptation known as “sex” may allow species to diversify their genes and evolve more quickly.

 
5. OPN1LW: The Gene for Color Vision is found in the retina, and people with color blindness probably have a defective OPN1LW. The evolutionary importance of OPN1NW has downgraded the importance of olfactory genes (the genes for our sense of smell), which have been going dead in our recent evolutionary history, because smell is not as important for survival when you can see in color.

6. RB1: this was the first of the Tumor suppressor genes discovered. The entire Human Apoptosis Gene Array is responsible for killing cells in your body that have gone cancerous before they are able to spread. These genes are like the enforcers for the police-state that makes up your multi-cellular existence.

7. FIT2: This is a gene that many of us would like to knock out the way researchers have knocked it out in animals to prevent fat storage; however, without this gene it’s doubtful humans would have survived this long as fat storage is crucial to surviving times of famine.

In culture, the number of adult neural stem cells triples in the presence of the Sonic hedgehog protein.

8. Sonic the Hedgehog: Cool for being named after a Sega Genesis video game character, but also cool for its importance. Part of the hedgehog family of genes, which are regulators of animal development, Sonic is crucial to the development of neural stem cells.

(Not part of this list is the POKemon gene, found to cause cancer, had to be renamed after a lawsuit by Nintendo.)

9. HAR1F: An important gene separating us from other animals, HAR1 has mutated at an accelerated pace since we split off from other primates a few million years ago. The gene is believed to affect brain development, but more research is needed to understand what it does exactly.

10. Noncoding or “Junk” DNA: It appears that about 80-90 percent of the human genome serves no purpose, and we don’t know why. Are we carrying the “extinct genes” of our ancient ancestors? Are there messages from god written in our DNA, as some creationists want to believe? Are these great genetic deserts a way of preserving our good genes, protecting them by diluting their chance of mutation? There is a genetics joke that Junk DNA actually reads, “this space intentionally left blank.” Junk DNA makes the list for inspiring so much controversy and speculation.

Honorable Mention:

Gene Responsible For Eating Whole Goddamn Bag Of Chips

Note: You can play this post as a mission on PMOG.

If you are reading this, then you are a member of the human race.

You are a member of Kingdom Animalia, meaning you are multicellular, but, unlike plants, your cells do not have a cell wall. You are a member of Phylum Chordata, meaning you have a central nervous system, and Subphylum Vertebrata, meaning you also have a backbone to protect your dorsal nerve cord.

Your warm bloodedness and mammary glands put you in Class Mammalia. Your Subclass, Placentalia, means you were fully gestated inside your mother before birth, as opposed to being grown in a pouch like kangaroos.

Modern and fossil hominid skulls: modern chimp in the upper left-hand corner, then a chronologic sequence of hominids ending with modern humans. Image courtesy NSF (Click for Larger Image)

Like other members of the Order Primates, you have grasping hands, fingers, and both incisors and molars for teeth. Being in the Family Hominidae, you stand upright, have a large brain, stereoscopic vision, and a flat face. Your Genus, Homo, defines you as having an s-curved spine, and your Species, Homo Sapiens, means you have a well-developed chin and high forehead, which provides room for your brain’s frontal lobe, giving you cognitive ability to imagine the future and plan ahead.

There are presently 6.5 Billion beings in this club we call the Human Race. Even though we all share this taxonomic classification, we still exhibit a tremendous amount of diversity in our genes. Unless you have an identical twin, the chances of someone else having the exact same DNA sequence as you is 1 in 6 million, meaning there are in the area of 1083 people on this planet genetically identical to you.

Despite sharing this identical internal genetic code, known as your genotype, your outward expression of this code, your phenotype, is very different. Our DNA gives our bodies a great deal of plasticity when it comes to growing into our environments. All sorts of environmental factors, such as nutrition, climate, your mother’s womb, and physical experiences have all made your personal DNA expression unique.

Even if your genes did express themselves in the exact same way, as they almost do in identical twins, your personal experiences would be unique. Only you occupy the precise space and time in which you currently exist. No one else can occupy your space-time coordinates, and experience the world the way you do.

You will glimpse less than a century of the Universe’s projected googolplex years of life in your own lifetime (one followed by 100 zeros). The atoms that currently make up your body, atoms forged in the centers of stars millions of light years away and billions of years ago, will disassemble. Some of these will find their way into other living things, all of them will continue to venture throughout the Universe in one form or another until the end of time.

But nothing exactly like you will ever experience this Universe the way you are now. You are the Universe observing itself in this momentary flash of consciousness. Savor it.

The Environmental Compliance Division at the Coast Guard base where I work is tasked with cleaning up decades worth of environmental problem areas on base and instituting sustainable operating procedures in the way the Coast Guard serves America. According to ARSC’s newsletter, we “recycled (kept out of landfills) 1330 pounds of toner cartridges in 2007″ and kept 1005 pounds of alkaline batteries from landfills by recycling, five times the amount of batteries recycled in 2006¹.

To clean up past bad practices, the ECD has started planting trees in contaminated areas, which draw pollutants out of the ground and prevent them from contaminating the water table. The fans on short poles visible amid the trees in these photos are drawing petroleum hydrocarbons out of the soil and atomizing them into the air.

Active Phytoremediation Project Area Aircraft Repair & Supply Center, Elizabeth City (Click for Larger Image)

From the information sign in front of this field:

From 1941 until 1991, the surrounding area was used as a fuel farm for aircraft refueling. The fuel farm consisted of multiple underground and above-ground storage tanks which were decommissioned and removed from the site. Evidence of a release was observed during the tank removal activities, resulting in impacts on subsurface soils and groundwater by petroleum hydrocarbons.

Phytoremediation was the selected remedy to control and contain contaminated groundwater migration and to remediate impacted soil and groundwater. Phytoremediation is an innovative and cost-effective technology that refers to the use of plant-based systems to remove, degrade, or stabilize environmental contaminants present in soil and/or groundwater.

Active Phytoremediation Project Area Aircraft Repair & Supply Center, Elizabeth City (Click for Larger Image)

Both poplar and willow trees have been planted across the site to remediate subsurface soils and groundwater. The use of both poplar and willow trees within a phytoremediation plot can capitalize on the favorable phytoremediation potential specific to each species.

The phytoremediation project is being performed in a combined effort with the United States Coast Guard, ARCADIS, North Carolina Department of Environment and Natural Resources, United States Geological Survey, and North Carolina State University.

Wikipedia entry for Phytoremediation.

¹“ARSC Environmental Goals,” The Flyer Volume 1, Issue 2, Feburary 2008.

Recently I needed a way to quickly sort a large dataset on the fly, but the classic bubblesort algorithm was too innefficient. Luckily, a quick google search revealed a Quick Sort v2 Algorithm by Anthony Baratta, who took and modified the Quick Sort Algorithm from 4 Guys from Rolla, who adapted it from an algorithm given in the book Data Abstractions & Structures using C++ by Mark Headington and David Riley, (pg. 586).

Because Baratta’s article was followed with user comments, everyone on the Web was free to contribute criticisms, questions, and, most of all, improvements. Two people posted fantastic advances to the code as well, with one person posting a modification to sort on dates, and another posting a modification to deal with extremely large arrays.

Without these two updates, the original script posted would have left me struggling to overcome these oversights, but thanks to the collaboration and copyleft principles of people online, I can use this code without having to spend days banging my head against my monitor to understand and adapt it.

Like any science, Information Science builds on the knowledge of those before us.

Charles Rosen’s Shakey was an early AI that could move withot bumping into things

Science Fiction is rife with intelligent machines. C-3PO in “Star Wars,” the HAL 9000 in “2001: A Space Odyssey,” KITT from “Knight Rider,” Data from “Star Trek: The Next Generation,” the Terminator, Sonny from “I, Robot,” the agents from “The Matrix,” and the deceptively artificial humans from the movies “A.I.” and “Westworld” are commonplace in our fictional futures.

Video games are filled with AIs who compete against human players. The better the AI, the more challenging gaming experience. Since computers started decisively beating the best chess players on Earth, grandmasters have started coaching competing chess AIs against each other. Artificial Intelligence is already integrated into our interactive entertainment, and holds promise for more real-world applications as well.

But is AI really “intelligent?” The father of modern computer science Alan Turing, described a test for determining a machine’s capability of demonstrating thought: a human judge enters a chat room with a human and a computer program, if they cannot identify which is the human and which is the machine, then the machine qualifies as intelligent. This procedure is known as the Turing Test.

A.L.I.C.E is a ChatBot that holds promise for one day passing the Turning Test. ALICE scans sentences given to it in online chat for keywords and returns one of hundreds of appropriate responses based on the context of the conversation. You can chat with ALICE online at alicebot.org.

ALICE does not understand sentences, it feigns understanding. However convincing, ALICE is not intelligent in any sense, it merely pretends at being human.

Actually understanding the meaning of sentences is an incredibly complex task for computer programs. Consider the following two sentences:

“The cat chased the mouse because it was hungry.”

“The cat chased the mouse because it looked appetizing.”

We can easily deduce that the ambiguous pronoun “it” refers to the cat in the first sentence and the mouse in the second, but consider the wealth of personal knowledge and experience required for our minds to make this distinction. The conundrum in AI development is giving a computer program this level of intuition.

Cyc (pronounced “psych”) is one attempt at a computer program that can actually derive meaning from language. Since 1984, researchers have been plugging facts into this program, trying to teach it common sense. Using facts like “Creatures that die stay dead” and “When Abraham Lincoln traveled to Gettysburg, he took his left foot with him,” Cyc makes its own assumptions about the world.

I visited cyc.com and played the “FACTory” trivia game, where Cyc give the player the assumptions it has made from the facts in its database and asks if they are true, false, or don’t make sense at all. One true assumption Cyc had made was, “Devices are typically located in toll booths,” but I had to think about it. “Condominiums are typically located in modern homes,” was an obviously false assumption, and “Ones are typically located in police stations,” failed to make sense to me or any of the other players either.

At the present moment, Web Developers all over the planet are adding another layer of complexity to the World Wide Web, one that will allow computers to read and process our existing websites. This new layer, called the Semantic Web, holds a great deal of potential for AI development. Already agent programs are running tasks for users on the Internet, retrieving data for them using this new logic layer. Science Fiction has speculated on the possibility of a sentient World Wide Web, maybe the Semantic Web is a step in that direction.

Bees Forsake Their Own Reproduction for the Benefit of the Hive Photo by Todd Huffman

Humans are funny animals. We cooperate at a level of sophistication seen nowhere else on planet Earth. Teachers, food servicers, law enforcement, medical workers, farmers, entertainers, engineers, truck drivers, and a bazillion other specialized laborers make our survival in its present convenience possible. The majority of us would die in a few weeks without our worldwide social support network.

Homo Sapiens behave altruistically toward one another. Human altruism is so strong that it even goes beyond our own gene pool. We are so nurturing that we adopt and care for members of other species like cats, dogs, houseplants, ant farms, hamsters, snakes, lizards, and other pets. We undergo Herculean efforts to save beached, stranded, or wounded whales.

Homo Sapiens care a lot.

We aren’t alone in this regard. In nature, we see cooperation and self-sacrifice everywhere. Primates like Chimpanzees and Gorillas work in cooperative altruistic fashion, as do pack animals. My two pet cats will often spend quality time grooming one another’s fur on the couch, taking turns licking those hard to reach places like on top of the head and chin. Another cat was documented mothering orphaned skunks. It’s obviously natural for members of a species to care for one another, and sometimes even outside their species.

Drone bees work tirelessly to feed their hives, even though they have no hope of reproducing themselves. Their queen, however, shares their genes, and if she survives to reproduce, the drone’s genes will survive as well. Lacking higher brain functions, the altruistic behavior in bees must be instinctual, carried within their DNA. The success of bees is living proof of the success of altruistic genes.

British evolutionary biologist W.D. Hamilton figured out that when an animal’s genetic relatedness to another (r) multiplied by how much altruism would benefit the recipient’s survival chances (B) was greater than the personal cost to survival of the altruistic animal (C), then the genes for altruism would propagate. Expressed mathematically as rB>C, it is known as “Hamilton’s Rule,” and some consider it the E=mc² of biology.

Hamilton’s Rule

The science of Game Theory provides an example of altruism’s strength in numbers. In each round of a game called the “Prisoner’s Dilemma,” two players have the option to either act altruistically or betray the other player. If they cooperate, they both get three points. If they betray one another, they only get one point each. If one betrays and the other acts altruistically, the betrayer gets five points and the altruistic player gets zero.

Scientists have devised all sorts of strategies for winning this game, and those strategies put into algorithms and put into competition on computers. Of all the strategies put into this virtual world, the “Tit-for-Tat” (TFT) comes out on top. This strategy’s first action is altruistic and after that it simply does what the other player did on the previous round, rewarding altruism with altruism and betrayal with betrayal. When TFTs exist in the community, the other more altruistic strategies succeed with them, forming a cooperative community.

Between the success of TFT’s and mounting support for Hamilton’s Rule, we are finding that being good to one another not only makes moral sense, but logical and mathematical sense as well.

Dawkins, Richard, The Selfish Gene, Oxford University Press, 1976.

See also my previous post Nice Guys Finish First exploring the math behind the Prisoner’s Dilema in further detail.

Fossil-hunters once pulled only bones out of the dirt. Then they started pulling up whole skeletons as one big rock, using X-rays and MRIs to catch images of the organs of dinosaurs in the rock. Then they started examining pollen particles accompanying the fossilized bones.

I wonder what important evidence we are destroying today, when we exhume fossils, that future innovations will cherish?

Iron Concretion from a Fossilized Dinosaur Heart

See the complete flickr set here.

“The best road maps to human bodies lie in the bodies of other animals.”
- Neil Shubin

Your Inner Fish

There’s a fascination to tearing apart an old house, tracing its history through what you find hidden behind the plaster. Electrical wires and pipes will run up to the attic and across, instead of taking a direct route through a wall, or worse, run up the outside of the house to enter a second-story bathroom. Awkward plaster intrusions will run between ceilings and walls, where air ducts were added after the house was built. Lead and asbestos hide under new layers of paint and insulation made from safer alternatives. Doors are shaved into rhombus shapes so they can fit into doorframes no longer rectangular from decades of shifting. Bad wall and floor joists are sistered up with new ones for seemingly redundant support. Other times, you just stare at the work of some carpenter long gone and ask yourself, “What on Earth were they thinking?”

The human body is like an old house. Our ancient ancestors started out with one design, a multi-celled organism, which morphed into animals with faces, which morphed into animals with legs and heads, which morphed into animals on two legs and big brains. The end result is a body that has nerves doing loop-de-loos through our body, running absurdly obtuse routes from our central nervous system to the areas of the body they service, holes pushed through muscles to make way for the male’s external sex organs, leaving a weak spot prone to hernias, and flexible throat muscles good for speech, but leave us prone to choking and sleep apnea.

Neil Shubin’s Your Inner Fish is a comprehensive exploration of all our human evolutionary traits, and traces them to our ancient ancestors. I was a bit self-conscious reading this book in public. What would you think of someone intently reading a book titled “Your Inner Fish?” You’d wonder what psychiatrist recommended it, so you could avoid using them.

The book’s title is misleading in scope. This is not just a book about our inner fish, but our inner shark, inner worm, inner moth, sponge, single-celled organism. Haeckel’s Phylogeny Recapitulates Ontology may not be true, to the endless delight of Creationists, but understanding why it isn’t true opens the doors to understanding how different species can all start out looking the same as embryos and yet their organs develop into different specializations.

Several of my grade school teachers would explain the human appendix as once aiding in the digesting of raw meat, like cave people supposedly did. This was wrong wrong wrong wrong wrong wrong. Wrong on soooooo many levels. All my teachers had to do was look inside modern animals with functional appendixes to understand how wrong they were. That’s how we know our ancestors’ appendixes were for digesting cellulose found in plants. Comparative Anatomy is indispensable to understanding why our bodies work the way they do.

Shubin draws this fact out through recounting his adventures in fossil hunting, which sound so interesting that they made me want to go on finds myself. He describes fascinating experiments where biologists patch tissue from one animal embryo to another, producing growths that reveal the purpose of different genes, or scientists evolving algae from single-cell to multi-celluar life in the lab by introducing single-cell predators to their environment, or tying a hair around a newt embryo to cause it to grow into twins.

Shubin’s down-to-Earth, hand-on explorations make this book a gateway for laypeople to the biological sciences. The thrill of fossil-hunting, extracting DNA with common kitchen ingredients, or simply looking at the biology of other animals and appreciating how we relate to them make this book a keeper. It will change the way you look at everything in the Animal Kingdom.