Saturday, March 31, 2012

Earl Scruggs, Rest in Peace

Earl Scruggs, of Flatt and Scruggs, died this last Wednesday.

When I was living in the south I listened to a lot of country music and Grand Old Opry. Flatt and Scruggs were a staple. Earl Scruggs played the banjo. Played it like I'd never heard before. Played it like you have heard since he inspired most of the banjo players across the world.

His web site is here.

Here are some videos from youtube to see what he was like:

A sad week.

Friday, March 30, 2012

Atheists To War!

The Oatmeal is a work of genius. See here.

Stalin's and Hitler's religious views are a matter of conjecture. See here and here.

Thursday, March 29, 2012

Sudden Cases of Inexplicable Political Depression

During the last election cycle I wrote a lot about politics. I haven't so much this time. Mainly because I'm so depressed about it.

Time to share the wealth.

Paul Ryan (R-Wis) has proposed an alternative to Medicare that looks nearly identical to Obamacare. (See here.) Note: Ryancare is touted by Republicans to be completely workable. Yet Obamacare, which functions identically, is touted by those same Republicans to be completely unworkable and unconstitutional. Apparently, something magical happens when you pass sixty.

Now let's add into that a larger look at the Republican budget as a whole. From Ezra Klein:
The Republican plans we've seen share a few basic premises. First, taxes are too high, and must be cut. Second, defense spending is too low, and should be raised. Third, major changes to entitlement programs should be passed now, but they shouldn't affect the current generation of retirees. That would all be fine, except for the fourth premise, which is that short-term deficits are a serious threat to the country and they need to be swiftly cut.

The first three budget premises means that taxes and defense will contribute more to the deficit, and Medicare and Social Security aren't available for quick savings. That leaves programs for the poor as the only major programs available to bear cuts. But now cuts to those programs have to pay for the deficit reduction, the increased defense spending, and the tax cuts. That means the cuts to those programs have to be really, really, really deep. The authors have no other choice.
Given this the Republicans are in the ideological position of having to tax the poor (after all, cutting a subsidy according to Grover Norquist is increasing a tax) for their deficit reduction and spending increases.

Or take it out of Federal workers paychecks (See here.) which will likely increase the cost of government before it decreases it.

On top of that the whole slut shaming of Sandra Fluke (See here) to the sanctioned cold blooded murder of Trayvon Martin (See here and here) just adds to this whole malaise. From what I can tell from the Martin case he was killed purely because he was black. No surprise there.

What's even more appalling than that (unsurprising) fact is the nature of the law in Florida that may well allow Zimmerman to remain uncharged (from here, wikipedia here):
A person is justified in using force, except deadly force, against another when and to the extent that the person reasonably believes that such conduct is necessary to defend himself or herself or another against the other’s imminent use of unlawful force. However, a person is justified in the use of deadly force and does not have a duty to retreat if:

(1) He or she reasonably believes that such force is necessary to prevent imminent death or great bodily harm to himself or herself or another or to prevent the imminent commission of a forcible felony;
The "reasonably believes" as opposed to "reasonably" is interesting here. It means that what the person believes, provided he is within reason, is sufficient for the person to use deadly force. "Belief" and "reason" are both contextual references. Zimmerman believed that Martin was up to no good and followed him. Was it reasonable? According to the 911 transcripts (see here.) Zimmerman followed Martin, classed him with people he clearly thought were undesirable and didn't want him to get away. Was this "reasonable?" Only in a world where black men are scary just by being black. Martin's last conversation suggests he was scared of Zimmerman, of being stalked, possibly of being killed. (See here.)

So here we have a situation created by Zimmerman in which he caused a confrontation, killed a man and then gets off because he might have believed he was in danger. This reminds me of an old joke, a definition of chutzpah: a man who murders his parents and then claims mercy because he's an orphan.

After a while the circuit breaker snaps and I go back to reading comics.

Sunday, March 25, 2012

Biological Revolutions: Go, Go Neurozoa

(Picture from here.)

This is going to be a bit long and rambling. The nervous system is not only one of the more interesting innovations in living systems, it's a key discriminator between categories of animals. So we'll have to delve a little bit into taxonomy.

I think of taxonomy as great fun but there are those whose eyes glaze over at the mere mention of clades or kingdoms. I blame bad high school biology teachers.

But enough of that. Let's begin.

As of the last post we now live in a world of single celled prokaryotes, single celled eukaryotes and some multicellular organisms. Some of these are plant precursors, some are fungi precursors and some are animal precursors.

We could make a long and varied collection of posts involving the origin of plants, fungi and animals but we're not going to. Instead, I'm going to attack what I consider one of the salient characteristics of animals: nervous systems.

At the beginning let me be clear. We're talking about all nervous systems: collections of cells that use ionic biochemistry to carry signals across and between them. These are neurons. Brains came later.

So, it's important to first define our terms: what is a neuron?

For once I'm going to quote wikipedia directly. This is a pretty good definition:

"An electrically excitable cell that processes and transmits information by electrical and chemical signaling."
Signaling both within and between organisms and cells has a much longer history than neurons. As soon as cells emitted chemicals there were other cells that understood it. However, neurons are very different. The neuron has a fundamental component architecture:
  • axon: neuron strand that is electrically excitable and carries information to another cell
  • dendrite: section of the neuron that is not electrically excitable but receives signals from another cell's axon
  • synapse: gap between the axon and dendrite where the electrical information is converted to chemical compounds (a neurotransmitter) that cross the gap and cause an electrical potential to occur in a dendrite.
"Excitable" in this context means the cell reaches a certain electrical potential which triggers a chemical and electrical reaction that can propagate across the cell and down the axon.

So, you have our example cell with a dendrite at one end, a cell body and the long thread of an axon leading away from it. At the far end of the axon is the synapse. On the dendrite of our cell are a bunch of synapses from the axons of other neurons. The dendrite is not excitable. The axon is.

An neuron fires and carries a nerve impulse down the axon to a synapse. This synapse releases chemical signals that cross a space between it (the "synaptic gap") and the dendrite of the next cell. The receiving dendrite (our example neuron) raises its potential until it fires the nearby axon material. Then the impulse races away to the next cell.

(The "synaptic gap" is extremely small. So small that it could only be theorized before the electron microscope. Some authorities in the 19th century suggested that the nervous system was one big cell since they could see no gaps between the cells. Santiago Ramon y Cajal put them right and showed the dendrite, axon and attachments between the axons and dendrites. For which he won the Nobel Prize in 1906. From the tiny delay in propagation between nerve cells,Charles Sherrington suggested the junction between nerve cells had a chemical and regulatory aspect. He named the junctions the synapse. For which he won the Nobel Prize in 1921. But the synapse itself was only deduced. It could not be seen until 1954. A good history of the discovery of the neuron is here.)

Like anything else in biology this is a great over simplification. There are synapses between dendrites. This description does not even mention glial cells or myelin. It generalizes the idea of a synapse when the reality is there are many different kinds. It doesn't differentiate a chemical synapse from an electrical synapse, which uses the actual electrical potential to cross a much smaller synaptic gap. Etc. But it is a definition that covers a lot of biological ground and that's why we're going to use it.

Even though there may be a chemical component to the transmission it is local in the tiny synaptic gap. In higher animals there are even enzymes around and inside the gap that destroy the neurotransmitters so that there are no lingering afterimages of the signals.

There are some serious advantages of neurons over general chemical transmission. For one there is separation of signal. If you're receiving chemical signals in a common environment you have to parse out which signals have which meaning-- or, worse, you have to react to all of them. With a neuron you can send separate signals without them competing with one another. You can selectively choose the target of the signal. You can selective choose the source of the signal. You can even encode something about the source of the signal in the frequency or pattern of the impulses.

Finally, the system is open ended. With a chemical transmission system each chemical queue represents a single piece of information. Combinations can have meaning but the molecular machinery has to be versatile enough to both sense a particular chemical and that same chemical in combination with other chemicals. The system can't scale up.

But with a neuron not only can you repurpose that dendrite or neuron into a sensor, you can link the nerve cells together. Some cells can be used to process the output of other cells. Or take input from them and transmit it to other locations. No only can you get discrete inputs you can have discrete outputs.

When I first started this series I spoke of a rapid and integrated response. With chemical systems, which are used by fungi or plants, the response is usually specific to a given stimulus and is either specific to that stimulus or general to the organism. With a neuron system you can have integration between stimulus response. With an integrated system you can have the following sorts of stimulus/response patterns.
  • General stimulus causing a general response such as the general withdrawal of a anemone to any touch.
  • Specific stimulus causing a general response such as touching a section of a starfish and causing the starfish to turn towards the touch
  • General stimulus causing a specific response such as many different possible stimuli causing a clam to clamp shut
  • Specific stimulus causing a specific response such as light causing jellyfish to swim away from the surface and darkness causing them to swim towards the surface
All with the same system.

Now, let's talk very briefly about animal divisions. Animals, also Metazoa, are broadly grouped into five groups:
Ctenophora and Cnidaria are also grouped together to form Radiata, the radially symmetric animals.

Porifera and Ctenophora were the first to diverge in the animal line. Bilateria, Cnidaria and Placozoa diverged later. Relationships between these groups reflect not only the evolution that occurred since they diverged from one another but also the common ground between them.
Bilateria, Cnidari and Ctenophora all have nervous systems though those nervous systems are organized differently. Poriphera and Placozoa do not-- which is interesting if Bilateria, Cnidaria and Placozoa diverged from the others later.

Back to the neuron. Consider the evolution of the neuron as the confluence of two distinct components: excitable tissue and the synapse. We need to consider them both.

Excitable tissue really means sodium channels. I could spend and entire post on just sodium channels but I'd rather refer you to this article on the channel itself and this article on how it relates to excitation in the form of the action potential: the electrical impulse that propagates down a nerve fiber. For our purposes, a sodium channel is the enabling technology of the action potential. Evolution can't work with nothing but always works on what's available. Consequently, sodium channels had to be in place prior to the development of the animal nervous system. (A side discussion of the Placozoan Problem can be read here.)

And surprise (see here) it was.

Some gentlemen at Woods Hole have been studying sponges and placozoans. (See here.) Remember, these animals do not have nervous systems. They've also been studying choanoflagellates, a group I mentioned before in the discussion of eukarotes and multicellular organisms. These are single celled organisms with flagella. They are not animals but many researchers have suggested that they serve as a potential source of multicellular life. The gentlemen looked at genetic variations in sodium channels as well as calcium channels, which are thought to be the source of sodium channels.

It turns out sponges and placozoans have genetically similar sodium channels to those used in the nerve cells of animals. In fact, they found homologs following a distinct pattern of relationships not only in mammals but in fungi as well. A graphical representation of these relationships is shown here. Fungi have the calcium channels but not the sodium channels-- no surprise there.

Observe the drawing at left (it should expand if you click it.) The successive branches are interesting. The pattern goes Choanoflagellata, Ctenophora, Placozoa, then a branch including Cnidaria (Medusas and Anthozoans), culminating in the Bilateria, marked here as CNS. While the placement of the placozoans is troubling, the march of that sodium channel right up the chain into animals with distinct central nervous systems is clear.

The precursors of excitable tissue were in place before the animals were.

Dendrites are nesting opportunities for synapses. I'm lumping in the evolution of dendrites with synapses since the synapse makes the dendrite necessary and possible while a dendrite without a synapse makes no sense.

Which leaves us with a synapse.

A synapse is an extremely complex structure. It has a transmission end that takes the electrical potential from the nerve cell and translates it into a witches brew of neurotransmitters. These are secreted into the synaptic gap and snagged on the other side. Depending on which neurotransmitter is received and the state of the receiver, the receiving component changes the surrounding electrical potential. When that gets sufficiently high, the electrically excitable part of the nerve cell fires an action potential and we're off to the races.

Tomas Ryan and Seth Grant wrote a terrific review of the research involving the evolution of the synapse in 2009. (See PDF here.) The drawing to the left is from that article. Go ahead. This one should also expand.

This drawing talks about the protiens and associated genes relevant to synaptic evolution. Note: fungi and Choanoflagellates. Poriferans peel off first. Then Cnidaria and Bilatera. This drawing doesn't address Placozoa or Ctenophora. Possibly this particular branch of the research hasn't included those different groups.

What's interesting is the ursynapse, the progenitor of all synapses, falling right between the Poriferans and the Cnidarians-- which exactly follows the Woods Hole research regarding the sodium channels.

There's another way to look at this. That's from the realm of control theory. If we view the nervous system as a controlling mechanism, then it should be amenable to analysis the way we would analyze any other control system. It does (see here) but more interestingly is that it also gives us another perspective of the evolutionary origin of the nervous system.

Animal control systems exist in organisms that reproduce and undergo selective pressure. Selection can then operate on the adaptation of the control system itself. A Swiss/Texas article (see here) suggests exactly in the form of the developing cooperative synaptic networks. Collectively, it is called neuroevolution and it is the assertion of these researchers that it works as well for actual nervous systems as it does for the evolution of artificial neural networks.

Okay. The stage is set for the next revolution. How to organize neurons.

There are two ways: neural nets or rings and the zombie's best friend: Braaiiins.

That's for next time.

Additional reading (some quoted above):
Self-Organization of Neural Systems: artificially modeling the organisms

Wednesday, March 21, 2012

World's Creepiest Hornet

Here is its picture.

Here and here are videos and discussion.

Here is where you run screaming into the night.

Tuesday, March 20, 2012

Drag Queens vs. Chick-Fil-A

Check this out. Chick-Fil-A is known for dump millions into anti-gay groups.
I'd say the Drag Queens win.

Sunday, March 18, 2012

Biological Revolutions: Multicellularity

(Picture from here.)

In our ongoing saga of revolutionary life, we've arrived at a world with both prokaryotes and eukaryotes. All are single celled.

But, when we look around, we see multicelled organisms literally all over the place. From the lowliest parasite to blue whales, multicellular organisms are everywhere.

How did that happen?

Well, that's a complicated question. After all, which one are we talking about?

That's right. Multicellular life forms didn't evolve once. They didn't evolve twice. They perhaps evolved as many as twenty-five times. Animals and plants evolved it separately. Slime molds and algae. Cyanobacteria and myxobacteria-- though multicellularity appears to be more the province of the eukaryotes than prokaryotes.

There are a lot of advantages of being multicellular. Cells can specialize and with specialization comes a higher efficiency at a particular function. Organisms consisting of cells can grow larger. They can exploit different niches, digest different materials. They can employ sacrifice as a tool-- one unit of the organism sacrificing itself for the good of the whole. It's so ubiquitous in multicelled organisms we don't even think about it. Who considers shed skin cells? Dead leukocytes? The discarded cells of the gut? Yet these cells have, in effect, given up their lives on the hope that their genome will be continued by other specialized cells.

These are advantages if the organism is already multicellular. But evolution never works with an eye to the future. The only advantage is current advantage. A What have you done for me lately? sort of world. Thus, the origin of multicellularity must occur in a framework where it is advantageous. Once we have it we can talk about how great it is. But we have to get there first.

Figuring out how this happened is a problem unto itself. By the time multicellular organisms left fossils they were already well established. Whatever happened occurred long before-- some authorities think as much as a billion years ago. Certainly more than 500m years, since that's when we first see whatever fossils there are.

Alright, then. What can we do with living organisms?

Ah. Let me tell you about Volvox.

Volvox is a very pretty algae (see the picture above) that congregates in a wonderful hollow sphere. The somatic cells are on the outside. Reproductive cells are on the inside and near the posterior, so they have some limited specialization. The somatic cells have flagella and move the ball around. Some species have actual specialized cells that act as eyespots and cause the ball to move towards the light. How they manage this without nerve cells is a bit of a mystery but they manage. During asexual reproduction the daughter colonies occur inside of the parent colony and then the parent dissolves and the daughter colonies are released. During sexual reproduction male and female gametes are released, join and become new colonies.

A close cousin of Volvox is Chlamydomonas, a single celled green algae. They also have flagella. When they reproduce asexually, they pull in their flagella and then divide within the same cell wall. Sometimes multiple times so that many daughters share the same space. Eventually, the daughters develop flagella and swim away. C. reinhardtii has a sort of sexual reproduction. Normally, C. r. cells are haploid. When stressed haploid gametes develop that can be one or the other of two mating types. These join to form a diploid "zygote" which is dormant in the soil. When favorable conditions occur, the zygote divides via meiosis into haploid daughter cells which then go on their merry way.

What's interesting here is that Chlamydomonas and Volvox share the vast majority of their genetic content. And there is an interesting structural similarity between them in that Chlamydomonas undergoes a division where the daughter cells are packed together and in Volvox the daughter cells don't separate except in reproduction. Could there be a link here?

This represents the "colonial theory" of multicellular evolution. Haeckel came up with this in 1874. The idea is that organisms of the same species could fail to fully separate during division. Most of the time this would be destructive but if other predispositions were to occur at the same time an advantage for the colony would occur.

Interestingly enough, Volvox practices what is called "multiple fission." The nucleus divides multiple times before the cytoplasm divides the daughter cells apart. It's not hard to imagine a cluster of stuck cells resulting from a failure to launch.

An interesting experiment was published this last January. (See here.) Scientists at the Whitehead Institute thought they might be able to force single celled organisms to evolve multicellular behavior. They took single celled yeast and grew it in a test tube. Then, every day they shook up the tubes and pulled out what fell to the bottom and grew that in a new test tube. This went on for a couple of weeks (100 generations) and, sure enough, yeast cells began to show clusters of cells with limited self-sacrifice and specialization.

In the article I read there was no discussion of the heritage of the yeast cells. Could this be a previously evolved dormant property brought to light under extraordinary selection? Or is this the expression of a predisposition of traits towards multicellularity now expressed? I don't know. But it is very interesting.

This doesn't get past the what's-in-it-for-me problem of multicellularity in general. Why should the somatic cells put up with this? Why shouldn't they reproduce on their own? A kind of cellular tragedy of the commons.

In Chlamydomonas the number of cells produced depends on the size of the parent-- a reflection on quality of the environment. Volvox limit the number of cells in a colony. Cheaters are not so favored since the total number of cells limits their advantage. There are mutants where the somatic cells start reproducing but then the colony collapses and sinks. Such mutants are detrimental and are selected against. Volvox manages this by separating cell types very early in the colony's development, limiting the opportunity of mutations to accumulate and have an effect.

However, these mutations are still seen and suggest the opposition has not been silenced. This is not terribly surprising since it's estimate that Volvox evolved multicellularity only 200m years ago. It's probably still having growing pains.

While simple multicellularity (as exemplified by Volvox) has evolved many times. It appears that complex multicellularity is much more rare. Animals. Green plants. Fungi. Algae. Such skills of organization require much more dedication on the part of the workers. The rewards regarding the individual cells don't seem to match what the individual cells have given up.

Whales, squids and redwoods all must face a similar problem: how do you handle revolution in the ranks? Most cells in a complex organism are bound to their role. Each cell is using only that portion of the DNA required by its functionality. Some cells are even barred from reproduction. If that fails, each cell is always on the trigger of suicide (apoptosis) if something should go wrong. Should that fail the secret police (the immune system or its equivalent) are watching. Always watching.

Evading all the safe guards must come as liberation albeit at the cost of the organism.

Is cancer the price we pay for the majesty of our organization as we suppress the relic desire of our cells for their old single celled freedom?

Additional reading:
From Simple to Complex, The Scientist

Wednesday, March 14, 2012

Moebius Dies

Jean Giraud, the comic artist known as Moebius, died last Saturday. I first ran into his work in the old Heavy Metal magazine. Subsequently, I hunted it down for several years. You can see how his work influenced such people as Sam Kieth, Richard Corben, Geoff Darrow and Mike Mignola. If you've seen The Fifth Element you've seen his style on the big screen.

He had a lovely, clean style where the lines would draw your attention to one place only to find the narrative action in another. Note the picture above. It was a curious style that I loved.

Look up Jean Giraud in Google and pick images. You'll see many many wonderful things.

A sad day.

Official Website: be prepared for French.
Good biography. And another one here.

Monday, March 12, 2012

Me and Mike Mignola

Back in 2006 I got a chance to meet Mike Mignola at a SFWA party. The picture at left showed up recently at Library Thing. Mister Mignola is an outstanding artist. I follow two of his works pretty religiously: BPRD and Hellboy. Oh, heck. I follow pretty much everything he does religiously.

See? I wasn't lying. I really met him.

Why we need wrists

Here's a video of Boston Dynamics' "Cheetah", a running four-footed robot.

Note how the feet touch the ground. Without a wrist, the straight leg nearly has to drag the ground when it is pushing off. Further, as the angle steepens between the leg and the ground there's 1) more opportunity to slip and 2) reduced ability to push off.

Here's a real cheetah. Here's a picture of cheetah anatomy. Note how the forelegs are kept straight and the paw is kept bent. Cheetah's run on their fingers (paw) bending at the metacarpals. A human hand is organized differently. Hold out your hand. The fingers are the carpals. The bones of the back of the hand are the metacarpals. The metacarpals join back to the wrist. The foot organization is similar.

Now, look at the anatomy image of the cheetah. It's "fingers" splay out in front if it. The metacarpals bend upwards and are supporting weight directly into the wrist. When the cheetah moves, the "finger" stretch out flat-- the paw-- the metacarpals stiffen and the fingers act to grab the ground. The wrist stiffen as well and the whole arm moves back. Then, when the paw comes back up the wrist and metacarpals unlock and the whole assembly swings up and out of the way so that it can be brought forward.

The same motion in the back.

Here's Boston Dynamics"Big Dog." It has a wrist but instead of metacarpals it has a pole and no paws (no fingers.) Better than the BD cheetah but still a long way to go.

Sunday, March 11, 2012

Biological Revolutions: Eucaryosis

(Picture from here.)

In the last post we talked about the world prokaryotes made.

Now we're going to talk about eukaryotes, bequeathed to us in part by the prokaryotes.

Essentially. you can consider eukaryotes as defined by their use of membranes. Think of prokaryotes as a bag of chemicals that mix, mix, mix and the resulting chemistry is what drives their lives. (Not to denigrate bacteria. The metaphor is intentionally oversimplified.)

In eukaryotes that bag is subdivided into smaller bags inside the larger one. There's a bag for DNA material (the nucleus.) A bag for energy production (the mitochondria.) A bag for photosynthesis (the chloroplast.) These are called membrane bound organelles: they're boundaried by membranes and look like little organs. The defining structure is the nucleus. Eukaryotes may or may not have the other organelles.

Right from the beginning we can see that there's a sort of specialization of the cell structure of eukaryotes. It's interesting that the more highly organized collections of cells on the planet (kelp, oaks, starfish, dolphins, us) are all made of cells that began with internal specialization.

The fundamental theory on how eukaryotes evolved were from a union between two prokaryotes creating the Last Eukaryotic Common Ancestor (LECA.) The question is how this happened.

One idea suggests that Eukarya originated when a bacteria engulfed a member of the Archaea. (See here.) Three bacteria have been implicated:
  • Planctomycetes: a phylum of aquatic bacteria. These reproduce by budding.
  • Verrucomicrobia: a recently described phylum of bacteria found in aquatic and soil environments. They are often parasitic and found in eukaryotic hosts. They may be relatives of both Chlamydiae and Planctomycetes.
  • Chlamydiae: intracellular pathogens found in a wide variety of hosts. All known species grow by infecting eukaryotic cells.
These are collectively called PVC and are not to be confused with sewer pipe.

The archeon in question may be something called thaumarchaeota, a newly proposed phylum containing only four species. These are chemotrophic organisms and may play a role in biogeology but it's too soon to tell. The thaumarchaeon provided a number of necessary proteins absent in other phylums of the Archaea and Bacteria. The PVC donated donated another of other chemicals involved in, for example, membrane chemistry that is necessary for a nucleus.

This process is called endosymbiosis: a symbiotic relationship with something inside. This isn't hard to think about. We do this all the time with the bacteria in our gut. Cattle absolutely require endosymbiosis to survive. Endosymbiosis was a possibility as soon as there were organisms that had an inside and an outside-- remember containment?

It's also quite likely that there were archaic viruses that also injected their fair share into the LECA. One scenario is the addition of these viral proteins accelerated the eukaryote drive towards complexity.

But it's never simple. There are six major eukaryotic supergroups. (See here.) If LECA was the sole ancestor of all the supergroups we'd expect there would be a lot of common ground between them. There is, of course. But there are some interesting distinctions.

The mitochondrion is a little organelle that has its own DNA and ribosomes-- this fact is the source, in fact, of the idea that eukaryotes derived from a prokaryote swallowing a neighbor. It reproduces along with the rest of the cell but does it on its own, separating its own DNA and creating daughter mitochondria. Its ribosomes are larger and more complex than ribosomes of prokaryotes. From this we can infer that LECA's mitochondrial ribosomes were also larger and more complex. LECA is the ancestor of the eukaryotic supergroups.

But the ribosomes of the supergroups are quite varied and diverse-- more than we would expect. More, in fact, than the ribosomes in the main cell or bacteria or chloroplasts. (See here.) One possibility is that viral invasions added or altered DNA differently in the mitochondria in the different supergroups. (See here.)

It gets even more interesting.

Gemmata obscuriglobus (a member of Planctomycetales) lives in fresh water and reproduces by budding. Its nuclear material has a double membrane the resembles a eukaryotic nucleus. This psuedonucleus suggests a bridge between prokaryotes and eukaryotes. (See here.) In addition, G. o. can perform endocytosis.

Endocytosis is the process of cells engulfing material and ingesting. Bacteria and Archae don't do this. Instead, they pull material into the cells through pores. G. o. appears to be able to ingest material by enclosing it in a membrane and bring the enclosed material into the cell.

Maybe G. o. is just a curiosity. Except it appears to use a set of proteins to do the job similar to the ones used by eukaryotes. Similar proteins have been found in other members of the PVC tribe.

Complicating this is the role of viruses, some of them very, very large. The Mimivirus has more DNA than a bacteria and about half that of a eukaryotic cell. Further, Mimivirus contains coding for several common proteins to the three domains of life: Bacteria, Archaea and Eukaryota. Some have considered viruses as the source of Eukarota in that a large virus could hijack a cell but get stuck before it is able to create more viruses. Instead, the cell divides using the virus DNA instead of its own. Since the virus has its own membrane it, in effect, becomes the nucleus of the cell. The other organelles were then engulfed via endocytosis.

Regardless, there's no doubt what happened next.

We few, we happy few, we band of brothers

The eukaryotes were born.

Saturday, March 10, 2012

This is how your mind works

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

Sunday, March 4, 2012

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.

Friday, March 2, 2012

Strange Things

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

Thursday, March 1, 2012

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.