This is how your mind works

This is your mind. This is a hive of bees. Can't tell the difference?

See here.

Shoes for Industry No More

Peter Bergman of Firesign Theater died last night. News here.

I quickly found the following videos:

Everything You Know Is Wrong

Nick Danger

Top Secret Government UFO Warning

Frank Zappa and Firesign Theater

Don't Crush That Dwarf, Hand Me the Pliers

Waiting for the Electrician or Someone Like Him

I think We're All Bozos on This Bus

Revenge of the Non-Smokers

Dear Friends

TV or Not TV

Let's Visit the World of the Future

And many others

Evolution of a Video

Tyler Rhodes wanted to make an evolution video.

See how he did it and the video itself here.

Very very cool.

Biological Revolutions: The Prokaryotes Change the Earth

(Picture from here.)

Last time we talked about the origin of the prokaryotes.

Of course, there are wrinkles and wrinkles in that story. For example, there's now some evidence that modern double-membrane Gram-negative prokaryotes formed as a union between an ancient antinobacterium and an ancient clostridium. If this is true, it suggests the idea that eukaryotes formed from the union of ancient prokaryotes has merit since it happened before.

But we're not going to talk about that.

We're going to talk about how once they originated prokaryotes changed the world.

Prokaryotes are responsible for the origin of all modern biochemical pathways. These pathways are often divided into these two groups:

• Heterotrophs: cannot fix carbon (turn CO2 into long chain organic molecules) but use available organic carbon for growth and energy.
• Autotrophs: produces complex organic molecules from simpler organic molecules. They can fix carbon.

"Troph" from the Greek for nourishment. "Hetero" meaning different from self. "Auto" meaning self. "Heterotroph" then means deriving nourishment from others and "autotroph" means deriving nourishment from one's self.

Autotrophs make their own food. There are gradations between them. Autotrophs depend on additional material that they can use to fix carbon-- some metals, CO2, etc.

Heterotrophs would include organisms that consume complex or simple organic materials from the environment and other organisms or their remains.

Here, as is always the case, the definitions get fuzzy. There are chemotrophs: obtain energy by the oxidation of chemicals in the environment. The chemical sources can be organic molecules (chemoorganotrophs) or inorganic molecules (chemolithotrophs.) Are these heterotrophs or autotrophs? People have classified them based on the material being consumed. Chemoautotrophs are those that use the energy from energy rich but simple materials such as hydrogen sulfide (H2S) and fix CO2 into more complex organic molecules. Chemoheterotrophs cannot fix carbon; they have to consume organic molecule precursors to generate more complex molecules but still use H2S (or its equivalent) for energy. Some bacteria get energy from the oxidation of iron (rust) or manganeze.

You would think that phototrophs would be more straightforward. After all, they use light for energy, right? Again, like chemotrophs, it can get more complicated. You can use light for energy but lack the ability to fix carbon and be a photoheterotroph or use light for energy and fix carbon to be a photoautotroph.

Given the above, we have several biochemical pathways that are uncovered: deriving energy from chemical sources, deriving energy from chemical sources, generating complex organic molecules from simple ones and combusting organic molecules to get energy. All of these pathways originated in the prokaryotes. You can say that the first impact of the development of prokaryotes was on themselves.

But wait. There's more.

Prokaryotes originated this far from complete list:

• Nutrient recycling
• Decomposition
• Disease
• Oxygen production
• Oxygen consumption
• symbiosis
• endosymbiosis
• biological diversity and "species" boundaries
• non-reproductive genetic exchange

They were also responsible for the origination of eukaryotes-- which is us. They could survive without us-- and in fact did for a couple of billion years. We could not survive without them.

In short, prokaryotes invented our world. We just happen to live in it.

It gets better.

The period of time when prokaryotes ruled the earth is called the Proterozoic eon. It had three subdivisions:

1. Paleoproterozoic: 2.6-1.5 billion years ago. Cyanobacteria evolved along with photosynthesis. Biochemical pathways evolve or are perfected.
2. Mesoproterozoic: 1.6-1 billion years ago. Multiple changes in geologic chemistry. Rise of oxygen and oxygen geology. Eukaryotes appear. Multicellular organisms appear.
3. Neoproterozoic: 1-.54 billion years ago. Severe glaciation ("Snoball earth".) First multicellular fossils.

Probably the biggest and most obvious change from the Proterozoic eon is the Oxygen Catastrophe. Cyanobacteria invented photosynthesis about 2.6 billion years ago. This was an enormous selective advantage: to fix CO2 with nothing more than a photon. No need for H2S or the organic leavings of other organisms. Just clear sunlight.

Fixing CO2 involves taking the carbon and attaching it to a pre-existing carbon chain. It uses water releases the two oxygen molecules. The general reaction can be described in this way:

2n CO2 + 2n DH2 + (energy) -> 2(CH2O)n + 2n DO

where D is an electron donor. In the case of photosynthesis this results in

2n CO2 + 4n H2O + (photons) -> 2(CH2O)n + 2n O2 + 2n H2O

Water participates in and is cause by the reaction so the net result is

2n CO2 + 2n H2O + (photons) -> 2(CH2O)n + 2n O2

Essentially, for every fixed carbon you get a molecule of O2. That's a fair amount of oxygen essentially for free since the organism doesn't have to pay for the photons. Consequently, cyanobacteria prospered. Half a billion years later we can see oxygen in the geologic record in the form of iron oxide. It reaches about 5% of the atmosphere (modern O2 is near 20%) and stays there for a billion years. Then, about a billion years ago it zooms to 35% of the atmosphere, crashes down to about 20% and oscillates around that point until the present day.

Why the lag?

Well, there are a lot of opinions about it. One idea is that there were geologic and tectonic changes that occurred to promote the retention of oxygen in the atmosphere. After all, there were chemical reactions on the land and in the ocean that consumed oxygen as quickly as it was produced. One obvious one is the transition of iron to iron oxide but there are many others. This covers a lot of ground but not all.

There's also a hypothesis about a nickel famine. Methanogens (organisms that produce methane) Methane is a big trap for oxygen. UV takes methane and O2 and transforms it to CO2. Modern methanogens require nickel for chemosynthesis. As the earth cooled nickel would have been less available. If the ancient methanogens also required nickel (likely) when the supply ran out they would have reduced their production of methane enabling oxygen to start to dominate the atmosphere.

Another idea is that oxygen itself had to be present to retain oxygen. When enough oxygen is in the atmosphere the ozone layer is formed. Ozone is O3- and produced when high energy UV strikes O2. It has the effect of shielding the earth from UV. Once this is in place the methane cannot transform into CO2 and no longer acts as an oxygen sink.

Regardless, O2 ran wild. It shot over modern levels and then dropped back to "normal"-- likely because organisms that used oxygen caught up with the supply. With oxygen, aerobic metabolism became possible. Aerobic metabolism (also invented by prokaryotes) gives you much, much more bang for the same amount of material than anaerobic metabolism. It made all of the complex organisms possible. It made specialization possible. Heck, it made size possible.

It also changed the very earth.

Prior to the oxygenation of the earth there were about 2,000 minerals found on earth. Afterwards, there are 2,500 additional ones. There's more organized carbon in the earth from fossil uptake during tectonic changes. There are structural changes in the very rocks themselves from the buried fossils-- half of the American south is built on limestone which derives from fossil shelled animals.

And at some point around a billion years ago two unrelated prokarotes got busy with one another and the eukaryotes were born.

Strange Things

Thirty years ago the Bulgarians built a monument shaped like a flying saucer. (See here.)

You can't make this stuff up

You can't make this stuff up. I mean, I wish I had. But I can't.

• Rick Santorum channeling Steve Jobs.
• Judge Richard Cebull (appointed by G. W. Bush to Montana federal district court) forwarded mail to Barack Obama that seems to compare blacks to dogs. It was okay because it was "anti-Obama."
• Sam Brownback, Governor of Kansas, is going to sign the state's anti-abortion bill. One of the neat bits in it is a provision that allows doctors to withhold information from patients.
• Art Jones, a Republican candidate running for congress in Illinois says the holocaust never happened. It is "the blackest lie in history."
• Rush Limbaugh, aging, fat, drug addict radio personality, said that Sandra Fluke, the woman Issa would not allow to testify in favor of contraception coverage (apparently men that didn't want it were qualified) a slut and a prostitute. He was roundly applauded by his listeners.
• Oklahoma has passed a bill that declares a zygote a person. Soon to follow: life begins at ejaculation.
• Roy Blunt, Republican Senator from Missouri, added an amendment to the Senate transportation bill to allow employers to deny coverage on anything they want based on anything they might believe. It's actually going to make it to a vote. Roy Blunt has been voted "Senator with the Creepiest Picture in Wikipedia" three years running.
• Gordon Warren Epperly filed a lawsuit in Alaska saying Obama could not be a candidate and cannot be president because he's not white.

Most Disturbing Plumbing Commercial Ever

Here. How did this ever get on screen?