Sunday, January 29, 2012

Biological Revolutions: Abiogenesis Part I

(Picture from here.)

I had planned to have a single blog entry on abiogenesis. But, it’s too big a subject. So, I’m just going to start here and we’ll see how it goes.

Abiogenesis is the process of living systems arising from a non-living environment. We know it happened at least once—since we are, in fact, here. Since there are no fossils of life prior to life, we have to speculate. Luckily, speculation is fun.

At its heart, abiogenesis is process by which complex chemistry that does not involve living systems generates the complex chemistry that does involve living systems. We are chemical systems. The same physical laws that apply to non-living chemistry applies to the chemical reactions that occur inside of us. Glycine derived from lightning striking an oil slick is the same glycine produced by a tomato. The chemical processes in the two cases are different but the end product is the same.

We begin with the nature of the pre-biotic earth. Water. A bunch of organic molecules. Enormous amounts of energy but not too much. There are a lot of volcanoes but the earth is no longer molten. A lot of sulfur, carbon monoxide and cyanide. Things that would kill us quickly and painfully were we to suddenly show up in our time machine.

And most importantly: no oxygen.

Oxygen is great for living systems already here. But it’s absolute poison to any of the self-organizing chemical reactions that might have led to living systems. Free oxygen is a product of living systems. We’ll be talking about that in the entry on the prokaryotic revolution.

Our pre-biotic world is hot, dismal and poisonous.

So: given what we know about chemical processes and the pre-biotic earth, how did we get here?

What is here anyway?

We know what living systems are in that we can point to living systems all around us. While there are a lot of definitions of life floating around, I’d suggest that to get to our sort of living system takes a few pre-requisites:

  1. Containment: creating the enclosed environment in which the chemical processes can occur. Living systems use a cell for this.
  2. Metabolism: deriving additional material by using energy producing chemical reactions to power energy requiring chemical reactions. Living systems use proteins and, to a limited extent, RNA to do this.
  3. Inheritance: one chemical system has to be able to drive the creation of other chemical systems. Living systems do this by reproduction involving DNA.
  4. Coupling: This joins containment, metabolism and inheritance into a package. Inheritance doesn’t do any good if you’re not inheriting the ability to metabolize. The whole DNA-> RNA->protein complex is how living systems do it.
Once you have the package all together natural selection can drive refinement towards an efficient system.

In my opinion, it all starts with containment so that’s where we’ll begin.

Containment doesn’t need a cell. It doesn’t even need a physical barrier. The problem with most of the chemical reactions used by living systems is that without some mechanism to constrain the possibilities the reactions drive away from the goals of living systems rather than towards them. Combinations of nucleic acids tend to hydrolyze as do peptides. These reactions have to occur in an environment where the path is, for example, from nucleic acids to the polymerized RNA or from amino acids towards proteins.

There are a number of interesting speculations on how containment occurred.

(Picture from here.)

Living systems use cells. The three great domains of living systems solve the problem of building cells in two different ways. All use phospholipids, long chains of carbon that have a phosphate group at one end, but use them differently.

In bacteria and eucaryotes cells are enclosed in a phospholipid bilayer. The phosphate group is hydrophilic—it binds easily with water. The long carbon chain is hydrophobic and likes to bind with molecules that are not water such as fats, oils or other long carbon chains. Think of a drop of oil on water. The two keep to themselves.

Phospholipids tend to line up with their hydrophilic end collecting together and their hydrophobic end collecting together. A bilayer membrane is two sheets of phospholipid resulting in phosphate-hydrocarbon on one side binding to hydrocarbon- phosphate. Like a quilt, cloth on both sides but batting in between.

Instead of two layers, Archae have a single layer membrane that have phospholipids at both end. Again, it serves the same hydrophilic-hydrophobic-hydrophilic construction but with a single molecule instead of two.

It turns out that phospholipids will spontaneously form membrane enclosed microspheres called micelles. Phospholipids can be abiotically created given the right starting materials and heat. (See here.)

We need to get pre-biotic systems to this sort of cell structure but containment doesn’t require them. Anything that enables to sequestration of chemical reactions will serve. For example, Sidney Fox took amino acids in solution and let them dry out—like the drying out of a pool. Surprisingly, the amino acids self-organized into long thread-like molecules now called “proteinoids”—essentially, polymerized amino acids. He also found that under the right conditions, these proteinoids would also organize into microspheres: contained bubbles. The bubbles could swell and deflate and even replicate.

Fox found these microspheres in Hawaiian volcanoes. It started another area of speculation involving pumice rafts. Pumice has many pores and tiny chambers. These pores could be partially sealed to provide the environment for early chemical reactions that led to life.

These sound a lot like nanobes or nanobacteria. Both are very small, appear to have reproductive capabilities and are not likely to actually be living systems. They are, however, candidates for protobionts: chemical systems that predate life.

We can, then, have containment with cell structures without actually being cells. This gives us the opportunity for contained chemical reactions without cell membranes. Given, again, that we can get cell membranes spontaneously from phospholipids, what do we put in them?

That's for next time.

Tuesday, January 24, 2012

Lies of the Salamander

The salamander won South Carolina.

I'm no fan of Romney. I think Santorum's an idiot and while I have a fondness for Paul it doesn't make up for any shortcomings of his batshit insane ideas.

But the salamander is a flat out liar.

He's always been a liar. He is lying to you right now. You can tell because his lips are moving. is kind to say he's distorting the truth in this ad. But let's call it what it is: lies. Flat out lies.

So: on the Republican side we have a liar and a cheat, a mediocre and fairly unscrupulous liar, an idiot and a crazy old man.

On the Democratic side we have a guy who's failed at being on the left and has signed into law a bill that should have shamed Dubya.

Hm. Tough choice. But I think I'll stick with the failed lefty.

Friday, January 20, 2012

In Defense of UFOs

UFO bashing is fun and not terribly injurious to one's health, provided the UFOlogists are behind you or in large groups.

But it is terribly convenient.

For my own part I'm in Bill Hicks' camp. Why the Hell would they come thousands of light years and then come down to kick back in Fife Alabama or some such. (See the Relentless clip here.)

Then, I thought. Gee. If we postulated a civilization that had the ability to cross interstellar space, would we even know if they came? After all, it took us thirty four years and millions of dollars to get Voyager up to our own interstellar doorstep. Somebody who could zip down to us for a visit would have presumably much better technology than we do.

So, why is it dismissed so out of hand?

Part of it is, of course, the company the idea keeps. Most UFOlogists would have trouble playing Find Your Foot. But so what? The ideas held by fools need not necessarily be foolish. It wasn't so long ago that the idea of human space flight was considered foolish. And not so long before that the idea of humans being able to survive speeds of a normal train ride was in doubt.

So let's think about it.

Let's say we have a group of aliens, or their envoys, have come here to investigate us. They figured out we have life. They heard the incredible noise we produce. Like the Christmas poem, they've metaphorically sprang to the window to see what was the matter. They don't know us. So they want to check us out.

Granted it's a low probability. We have trouble conceiving the utility of visiting the moon. Anyone that might want to take decades to check us out is beyond our understanding. But we're talking aliens here and their motivation need not be ours.

So they get here. They hide for the same reasons biologists set up blinds: they want to study organisms in their natural habitat. Maybe they take samples. Maybe some of those samples are human. I'd hope they'd figure out that it's unethical to take human samples but since by getting here they've shown their motivations are not ours, it's unreasonable to think their ethics would be like ours either.

Why wouldn't that idea be worthy of investigation?

Imagine, if you will, a grant submitted to the NSF that says something to the effect, "to investigate if there exists possible evidence of earth visitation by extraterrestrials." Would you expect that to be treated fairly? Or better, would you expect it to not be laughed out of the committee?

I could even see possible avenues of research. Let's presume that aliens are bound by the known laws of physics. This means that to visit us they'd have to accelerate to a significant percentage of light speed and then decelerate. That takes energy. A lot of energy. A level of energy usage we can't even approach. So one area of research would be looking for evidence of such energy utilization. Indications of heat or velocity that is of astronomical in scope but local to our region.

Or we could examine transitory phenomena observed in space that doesn't fit what we know-- meteor tracks that don't follow expected trajectories.

We could scientifically evaluate abductees. If these people were abducted and examined, there might be contamination. Even if ET uses similar biology to ours-- DNA and the like-- it won't be identical. Perhaps they use right handed amino acids rather than left. Perhaps start and stop codons don't resemble ours.

I would expect failure of evidence since I don't think we've ever been visited. What bothers me is how we dismiss the idea out of hand without consideration. As if ideas were tainted by those that handled them, housed in a sick bed and ignored ever after.

Thursday, January 19, 2012

Great Moments in Writing

Loren Eiseley's Darwin's Century by way of Faye Flam:
Time, as Humanity had never dreamed lay across that world. It was a world where water wore away the shapes of mountains, and the great bones and carapaces of vanished beasts lay hoar and rime-frosted in deep crevices and canyons.

Wednesday, January 18, 2012

Much Ado about Methane

Real Climate article Much Ado About Methane gives a real analysis of the methane release in the arctic.

But if you want to see lakes explode, check this video here.

Tuesday, January 17, 2012

Book View Cafe News

Irene Radford re-releases her master-work series Merlin's Descendants through the Book View Cafe

Beginning with Guardian of the Balance 978-1-61138-138-2 $4.99 $3.99

Exclusive to the Book View Café, an introductory price reduction
Caught between her beloved father, the Merlin of Britain, and Arthur Pendragon, the old ways and the new, Wren must find a way to balance the forces of Chaos with peace. She nurtures the land and the people, creating a haven for anyone displaced by the turbulence. And for the safety of all she must guard her heart against the deep love she shares with Arthur, a married king who holds the future of all the Britains in his hands and his sword.

Sunday, January 15, 2012

Biological Revolutions of the Mind: An animal perspective.

(Picture from here.)

I've been thinking about the long view recently. Specifically, the age of life on this planet. Wikipedia's timeline of evolution is interesting but it compresses as it approaches us, in effect giving the same weight of the rise of complex cells to the rise of insects. This tends to trivialize the magnitude of complex cells.

I think we can consider a few points in the timeline as truly revolutionary:
  1. Abiogenesis revolution: the rise of living systems. Most of these are likely extinct.
  2. Prokaryotic revolution: bacteria and the like. About 3.8 billion years ago.
  3. Eukaryotic revolution: complex cells such as found in amoebas and human beings. Say, 2 billion years ago
  4. Multicellular life: About 1 billion years ago.
  5. Neurozoan revolution: Anything with a nervous system. This allows integrated system response to local stimulation. Somewhere between 1 billion and 600 million years ago.
  6. Cognozoan revolution: Centralized response driven life forms. Life forms with brains or central nervous systems (CNS.) Say 600 million years ago.
Neurozoan appears to be the invention of John Opie (2010.) Lots of animals have nervous systems and no brain-- hydras, for example.

Cognozoan is my own. Do you like it?

I do not use the term "revolution" lightly. While nothing really compares in scale to the abiogenesis revolution, each of these so-called revolutions changed the landscape of earth. Once we had prokaryotes we had the ability have true inheritance via DNA and variability in metabolism. We got photosynthesis and an oxygen atmosphere. Once we had eucaryotes we could have fungi-- which pretty much created something called "soil." All complex life forms from trees to sea anemones are multicellular. I suspect the roles of predator and prey, as we know them, originated here.

Neurozoans: all free living animals. Period. Full stop. End of story.

Once we introduce cognozoans, we have abstract behavior. Mating dances. Specialized predator/prey strategies. Fish. Crabs. Beetles. Starfish. Squids. Anything with a CNS. Most animals past the size of mesozoans have a brain. One could venture a guess that a central processing system is required beyond a certain level of behavioral complexity.

While this is an animal centric perspective I may be addressing some plant concerns as well.

I'm going to be going over these revolutions in the next few weeks and talking about them one at a time. Each of them is worth a blog entry of their own.

This is going to be fun.

Thursday, January 12, 2012

Arisia Schedule

I'm doing Arisia this year. Here's my schedule:
  • Friday 7pm: The Future of Bioetichs as Portrayed in Film, Alcott
  • Sunday 10am: Trash to Treasure! — Fast Track 1
  • Sunday 4pm: A "Self" or "No Self?" Neuroscience in SF, Independence (3E)

Sunday, January 1, 2012

Anatural Selection

I've been talking about "natural selection" a lot. Natural selection is defined to be the differential success of reproduction between related organisms based on the context of that organism's reproduction.

I use the word "context" precisely here. We like to think about natural selection by way of success in foraging or in evading predators or being predators. But differential reproduction covers a lot of ground. The context of the peacock is how pretty that male's tail looks to Lady Peacock.

Biologists like to talk about how such secondary sex characteristics show fitness but it ain't necessarily so. "Fitness" is a long term view of things-- it's a biological form of "Mister Right." But Lady Peacock isn't so much interested in Mister Right enough as much as she's interested in Mister Right Enough.

For example, let's consider bettas, or Siamese Fighting Fish. Male bettas display to one another to show dominance and to get the attention of females. A common biology demonstration is to create a model that stimulates bettas to display. It's not hard by alteration of color and shape to get a model that triggers a stronger display in a female or a male than an actual male betta. Betta display is costly in that it takes energy to display and fight and bright displays attract predators. So bettas are in a continuous mini-max race to woo their mates and not cost their own life while doing so.

Consequently, as long as the display does not impair their ability to reproduce it helps it. You could argue a "fitness" representation to this but I think it's reaching.

However, selection happens everywhere: politics, palate, fashion. The survivability of the apple is based on how well it tastes to humans. The success of dogs and cats depends on how much they engender caring emotion from us. The prolific triumph of raccoons, rats and cockroaches in the urban environment rests solely on their amazing success in exploiting what we choose to cast aside.

But this is not limited to organisms. Objects, too, can be selected for or against. Religion, car styles, hairdos, family size, presidential politics, all respond and change over time. They survive or don't based on the our ability to adapt them to changing cultural shifts of context.

These cultural artifacts are called memes and selection and modification of memes have been demonstrated. They "evolve."

I think memes are analogous to viruses in that they are packaged bits of information that have an affect to a target system.

(You can extrapolate from that idea that I don't think viruses are alive and you would be right. I think of viruses as biochemical systems that can undergo selection but are not, in and of themselves, alive. I think of it more as complex biochemical poisoning where the poison catalyzes the production of more poison.)

Virus reproduction is extremely interesting. For example, some viruses bring along their own polymerase to enhance the environment where they are produced. Some don't. Replication of living systems have mechanisms to prevent error. Viruses depend on error to introduce variation-- they are indiscriminate in the assembly of the virus product allowing selection to weed out those virus fragments that are not infective.

As I talked about in the Signs of Life entry, living systems have a certain constancy level required for viability. Viruses also dance to this constancy/variation tune. Some are quite constant, one generation to another, some are quite variable, some have parts that are variable and constant in the same virus. You can have two related viruses attack a single cell at the same time and the resulting virus has DNA from both.

Ideas and institutions have similar behaviors.

Even small ideas can have significant staying power if they can be abstracted beyond the context of their birth. There are scores passed on emails that talk about the excesses of congress or the president or Wall Street. They sound just plausible enough to be passed on. I have read emails talking about Obama that were originally credited to the Carter administration. I've read emails dissing congress I'm convinced were originally popularized by Mark Twain. These memes have thoroughly transcended the original context of their birth.

As viruses require living organisms to propagate, memes recombine. I have seen religious rituals in Mexico that clearly derive from both the original Mayan religion and the Catholic tradition. The Christmas tree does not originate from Christianity though it has been associated with the Christian holiday.

There are natural boundaries to memes that consist of such things as culture and language. Memes that have shed enough of the original context down to the bare essentials have managed to cross these barriers. Hatsune miku, for example, is a Japanese phenomenon I spoke of a while back. It has not crossed the walls of culture terribly efficiently. Pokemon, however, did.

One of the interesting things about memes is how we modify them intentionally. Pokemon is a good example of that. But nothing compared to Bill Bright 's Four Spiritual Laws. Bright boiled down Christian theology into four principles: 1) God loves you 2) Man is sinful and separated from God 3) Christ is the bridge between holy God and sinful Man 4) You need a personal revelatory experience with Christ to bridge the gap.

By abstracting the evangelical problem to its most simple term, Bright created an elegant evangelical solution: present the dilemma, propose a solution and explain the solution's implementation. This meme was simple enough and divorced enough from its original context it could easily jump cultural and language barriers-- though not without its detractors.

Like viruses, memes require active human participation to be reproduced and transmitted. An idea unpropagated is no different from a crystallized virus: inactive and unchanging.

The evolution of memes can proceed quickly or take generations. "All your base belong to us" came, went, came back and is now pretty much gone. Lolcat has a surprising longevity. Zoroastrianism had a good run of close to 2,000 years. Christianity and Hinduism are with us yet, though I think neither of them reflect their original founders all that much.

A question I hear about biology a lot is why is it so complex? Physics and chemistry are complex but nothing like biology.

One of the reasons I think is that in physics and chemistry fundamental laws and principles have been established and verified. Atomic theory covers most of chemistry and physics rounds out the rest. In physics, there are a collection of basic principles that govern such things electrical and mechanical phenomena. While there is much we do not know, we would be inordinately surprised to find fundamental conflicts. E.g., the OPERA neutrino experiments.

We do not have the fundamental laws and principles of biology. We know some things. We understand the principles of selection. We know that heritage shapes the subsequent modifications of organisms. But we have no mathematical model that can predict these things. Without the underlying model we fall back into studying individual examples and hope from them to discover the fundamentals.

Given the apparent resemblance of principles between, say, selection of inherited traits and selection of inherited religious principles, I think we might find out more than we expect.