Monday, February 29, 2016

Early Origination of Life – Organic Oceans -- Part 2

In part 1 of this subset of posts, the idea was touted that in the early days of planet Earth, there wasn't anything around to consume carbohydrates, and there were a lot of them. They formed a layer on top of the water oceans and lakes and some very interesting things happened, over some tens or hundreds of millions of years. Specifically, some hydrophobic chemicals residing in the organic side of the meniscus between the layers got linked with some hydrophilic chemicals residing on the water side of the meniscus. This particular combination would have no choice but to remain at the meniscus. With enough of them around, and some intermolecular attachment, a membrane could form.

Provided they were stable, these membranes could collect and build up in numbers. One pathway to go forward with a hypothetical method for life origination would have the membranes becoming spherules, and here is some primitive cell. But perhaps life origination theories try to rush too fast to making cells. Maybe there are a few intermediate steps, all reasonable chemically.

What are the possible interactions between a molecule and such a membrane? If the molecule could attach itself to the preferred side of the membrane, then it might do other things. Do you see the looming shadow of the hero of some life origination theories, the Replicator? This is a molecule which makes a copy of itself. Of course, maybe there is a molecule which, when attached to a membrane, can make a copy of itself. Or maybe there is a more complicated set-up, where molecule A, when attached, makes molecule B, and molecule B makes molecule D, which is transformed by something connected to the membrane into molecule C, which is then transformed into molecule A, beginning the whole conga line again. Does such a membrane provide a convenient collection point for a number of molecules, the majority of which just attach and maybe detach later on, and a few which make something else, like serial copies of some other molecule, which begins a series of transformations, mediated by the membrane or various things which have attached to it, into the starting point? If only one of the steps is a one-to-many transformation, such as molecule Z turning some common constituents of the organic ocean into molecule Y's, then there is replication.

On the water side, the ocean would have a lot of ions, sodium, potassium, chlorine, ammonium, phospate, sulfate, calcium, and scads more. Water is a polar molecule and just loves to break up salts and compounds and separate the pair that makes them up. What happens when an ion of some type is blown into the water side of the membrane? Does it alter the membrane? Does it osmose through it and start making changes to things hanging on the other side of it? Does it slip through a crack in the membrane and interact with things from the other side? Does it move some protons around and transfer energy to something on the other side? It sounds like a little chemical laboratory.

What happens if there is some molecule or set of molecules that can reproduce itself? We are talking about molecules which attach to the meniscus membrane, which may provide the mechanism for one or more of the steps of copying, or just to attract some ion to the membrane which can slip through it to be used on the other side. What happens to the copy? Since the molecule or molecules like to attach to the membrane, and one was handy, it would, and this would go on until the attachment points were filled up. Now we have a doubly-thick membrane, formed by the original stuff which was hydorphilic and hydrophobic, like soap, with a second layer of things which can reproduce using the membrane. What can happen with this more complicated membrane?

Perhaps we should consider the options. If some molecule from the organic side attaches, and some ion from the water side sidles through the membrane and makes a change in the molecule, like becoming part of it, we have layering going on without the need for any replication. This assumes there is plenty of that particular molecule in the organic broth. So layers might form, homogenous or heterogenous, and even a third layer or more.

There doesn't have to be just one type of membrane occupying the meniscus region. There could be ten or fifty varieties. If only one is capable of attaching many interesting organic molecules to it, then that one could be the one that initiates life. Suppose it can attach many amino acids, which might have been made by other membranes. They can combine and separate, and do whatever amino acids like to do, until there is one combination which just happens to make copies of itself. So, one of the membranes might serve as a way of speeding up chemical combination, which eventually leads to replication. No cell has been made so far. No membrane has closed in on itself to make an inside and an outside. They have just stayed where their hydrophilic and hydrophobic halves are thermodynamically better off.

It sounds like some chemists could amuse themselves finding out which membranes attract many different types of organic molecules, especially and most importantly, complicated ones. If there are some, we are two steps closer to understanding the origin of life. The first step was having an organic ocean and a meniscus, where certain types of molecules could hang out, and form membranes on the molecular size scale. The second one is having one such membrane serving as a combination zone, where different molecules would be put in proximity, and perhaps would interact.

It is going to take many steps to originate life, but what we see here is a possibility for chemical evolution. Once there is an environment, like a meniscus-inhabiting membrane, where various combinations of attached molecules might occur, the one which replicates the most easily would win out, barring stability problems. The concept of the organic ocean provides both the concentrated environment for such chemical evolution, but also a feedstock which may have plentiful amounts of whatever has to be consumed in such a replication.

There really may be nothing that would prevent some replicator molecule from forming in the liquid ocean itself, except time and probability. Just try to think of two molecules in a dilute solution getting together at the right orientation and joining. Then compare that to a membrane which provides a location for the contact, other feedstock items, some ions to incorporate, some energy to make use of. It could be that no matter how many opportunities for a replicator to form from two component molecules happened in the liquid ocean, the joining never takes place because of some mediation the membrane provides.

Real cell walls do all of the things the hypothetical mensicus membrane might do. The problem for chemistry is simply to show that membranes can form, likely of simpler nature than the phospholipids of a real cell wall, and perform these same functions. How simple can it get?

Sunday, February 28, 2016

Can Only Mammals Become Intelligent?

We know that the intelligent species on Earth, that's us, are mammals and no other class of animals has ever done it, as far as we know. Would intelligent aliens have to be mammals as well, or originated from mammals before they started tinkering with their own genetics? Or are there certain attributes that mammals have which are needed for the development of intelligence, and on an alien world, other types of animals, other classes or even phylae, might become intelligent?

How are mammals unique in connection to intelligence? Intelligence requires a long, extensive learning period, and more freedom from instinctual behavior than non-intelligent creatures. Intelligence is almost synonymous with learning, and how do you induce learning? You have someone responsible for each new creatures learning, and this means parents in the usual case, so far here on Earth. Learning takes years to do, and during that time, someone has to be responsible for that learning, but also for provisioning, sheltering, and in general taking care of the young creature which is learning. How does it develop that the parents of humans put up with caring for youngsters for years and years? They develop a bonding with their young, and that bonding comes from, among other influences, breastfeeding.

No other class in the chordata phylum has such a long period of dependency. What happens in the evolution of mammals is that learning becomes less from genes and more from memes, if that is what you call what any mammal knows and teaches to the next generation. The mammalian class has plenty of species which demonstrate learning, usually by the young imitating their parents or even other elders in the species. Predator mammals teach their young to hunt, by allowing them to accompany the parents on a hunt after a certain level of maturity is reached. Herbivore mammals teach their young to evade predators, starting very young.

Nest building is common among many classes of animals, but little compares with the dams that beavers build. One generation of beavers demonstrates to the next one how to fell trees, now to transport them down to a river, how to block the river flow with a structure made of tree pieces and mud and rock from the river bottom, and how to build a lodge inside the dam with a underwater entrance.

Other nest building, such as with birds, is largely instinctual, but it is obviously not with mammals. With mammals, teaching by demonstration and imitation are the common mode of behavior. There are certainly strong instincts that push a parent to care for a child, but even in this linkage, there is imitation from generation to generation. One parent mammal can rear youngsters, who observe how it is done and this is added to their repertoire of behaviors when their time comes to rear youngsters.

Another aspect of mammals regards the nutrition of young mammals. In other classes, when parents of a species feeds their young, it is from hunted or gathered food. When breast milk is used, evolution has the option of optimizing the contents of the milk to further development in the very young mammal. Evolution has nothing to do with optimizing the nutritional value of whatever happened to be the caught prey or the found food that a parent in a non-mammalian class finds, and so it may be hit-or-miss. But mammals are optimized for this period.

The architecture of the brain of a mammal is different, in that there is very little written into the brain at birth, but there is a large write-space available for learning. During the initial period of a mammal's life, it learns to process sensory inputs, which takes time for repetition and experiment. The same holds for output from the brain for motion and other activities.

Would it be possible to have a different type of creature on a world far from Earth where the young had the ability to learn from imitation, observation, and experimentation for a long period? This is the mandatory requirement for the evolution of intelligence. There has to be some mechanism by which some creatures, likely parents, are involved with the young for a substantial percentage of their lifespan. The mechanism must somehow connect the youngsters with the parents, must make them provide an environment where nutrition, shelter, and learning are available. If it isn't based on the provision of nutrition, what can it be based on?

The brain of an animal which is hardwired to perform certain behaviors, which we usually call instinctual behaviors, has to be formed not of adaptive neural networks which learn by association in layers, but instead of circuits that are genetically programmed. In other words, the genome, when expressed in the brains of the non-mammalian animals, has to produce some associative layers before birth. Many non-mammalian animals are hardly able to learn at all. It would seem that it is an almost exclusive thing, instinctual patterns in the brain laid down by the genes or a largely blank slate of neurons which can record and transform themselves into something which can do the functions that an instinct can, but in many different variations.

Is this another puzzle posed by evolution? How did brains which were largely instinctual evolve into ones which were largely non-instinctual? Did the evolution of mammalian milk happen independently of the transformation of the type of brain circuits, or is it related? What is clear is that there is a strong connection between the parents teaching their young for extended periods and the development of the type of brain which can become intelligent. So the question is, does providing milk to young work somehow, via hormonal programming in the mother's brain, to promote long-term care and nurture, which somehow comes to include teaching by demonstration and imitation? Perhaps it is connected with the ability of a more associative and less pre-programmed brain to recognize individual youngsters, and to therefore bond with them in better ways. Perhaps there is a feedback loop, in that if parents have an associative neural network for their brain, the raising of young during the mammalian feeding period induces some patterns which still exist after that period is over, so the simple recognition of their own young creates a desire to nurture. This is, after all, how associative brains work.

Saturday, February 27, 2016

Early Origination of Life – Organic Oceans -- Part 1

Some clever geology has dated the first existence of liquid water on Earth to be about 4.4 billion years ago. Some clever selenology has dated the preponderance of the craters on the moon to have originated before 3.8 billion years ago, meaning the last bits of formation of planets was still occurring then. Life may have originated a million times during the period between 4.4 billion and 3.8 billion years, most of it being extinguished by the next large asteroid making impact. So common dates for the origination of life start around 3.8 billion and go up to 3.4 billion, when there are fossils of some tiny microorganisms.

Many interesting theories have been devised for the origination of life, since Pasteur proved that it didn't just spontaneously form before your eyes. Many of them involve water, with the water being a premordial soup with lots of organics, or being circulated through sea vents so lots of minerals with excess energy would be there, and others. Another theory involves clay, and there are likely many other theories which have not become so popular, but likely most of them involve water.

Since it seems to be very hard to get a cell to form, maybe horizons need to be expanded. Recall that there is a catch-22 going on with cellular life. You need to have some genes and enzymes to make the various organics in the cell, including the cellular membrane, but you need the cellular membrane to hold the genes and enzymes together. Which came first, some DNA, aka the Replicator Theory, or some membranes.

The Replicator Theory says something replicates, and then it gradually makes other stuff which helps replication. This seems quite reasonable, and given the billions of years for evolution to be experimenting with things, something could come out of it. But no one can come up with a Replicator.

It has also been downright difficult to come up with a membrane that is easy enough for a simple replicator to make, or which could accidentally form. Other theories, like the sea vent ones, have energy as the crux of the origination, and some are lumped together as 'metabolism' theories, which says that the first thing which happens is something organic starts absorbing energy from the peculiar water environment at a deep sea vent, or somewhere else interesting.

Sea vents are fascinating places, but no one has found any simple life there, nor anywhere else. It's all gone. So, perhaps analogs of existing places is not the key to figuring out the puzzle of life origination. Instead, let's consider what existed back in the days right after the asteroid bombardment got infrequent enough to allow some calm. Were there a lot of organics around? Nowadays, anything organic is consumed by some organism, but back then before there were any organisms, there were likely a mixture of different organic molecules.

Hark back to the concept of physical chemistry, and recall the concept of miscibility. This simply says that some liquids do not mix together in any proportion. Immiscible liquids can be extreme, and almost none of one kind can intermingle with the molecules of the other kind, and vice versa. Or it can be partial, with some of one kind going into solution in the other, but only a limited amount. The children's chemistry set experiments has the experimenter putting two immiscible liquids together, shaking them vigorously to mix them, and then seeing the utter failure of the shaking to cause the two to mix. You have one solution above another, separated by a liquid-liquid boundary called the meniscus. There are a lot of organic molecules that mix well with water, being miscible, and a lot of organic molecules which do not, and are mostly or totally immiscible. Everyone knows the example of gasoline spilled on a rain puddle. It doesn't mix.

Most simple molecules which do not mix with water do mix with each other, but not all. This means that on early Earth, with organics and water co-existing, there would be pools of each of them. Water forms lakes and oceans, and maybe the immiscible organics did as well. In other words, there on top of the lake or ocean, was a layer of organic molecules. Some other organic molecules are miscible with both, and there is a preference they have which says how much of the molecule is in the water ocean and how much is in the organics ocean, or perhaps the organic layer on top of the ocean. There could be, in our imagination, a lake wholly organic with no water there, but having a whole ocean of organics, like Europa does, seems to be asking a lot. Maybe there were huge quantities of organics back then, but maybe not.

In the organic layer, there is a process of chemical change happening, as some energy source is tapped and different organics are made. Perhaps it is lightning hitting the upper surface. Recall there is no free oxygen, so nothing catches on fire. Perhaps it is a volcano, a meteoroid, our old friend the deep sea vent, or something else. But the organics in the organic ocean are changing, and if something is made which is not miscible in the organic ocean but is in the water ocean, it might migrate, or make a third layer on top. If there were strong winds and waves which made connection between the deeper water ocean and this hypothetical third layer, the third layer would mix in to the water ocean.

Likewise, if something was produced in the water ocean which was immiscible, it might rise up and join with the organics ocean. In both cases, there would be material remaining. if something new that was miscible in the water ocean was made in the water ocean, it would stay there. Likewise for organic miscible new things made in the organic layer.

At the miniscus, things which are in the organic ocean soup are contacting things which are in the liquid ocean soup. Suppose some hydrophobic molecule, miscible only in the organic ocean, contacts some hydrophilic molecule, miscible only in the water ocean, and forms a bond, perhaps with some connection between them that is more tolerant of both. These combined molecules stay at the meniscus, with their orientation being dictated by keeping the hydrophilic one deep in the water ocean and the hydrophobic one up higher in the organic ocean. If the molecule is stable, it would stay there for some time, and perhaps as time progressed, there would be more and more of them. The most stable ones would remain longest, and those, perhaps few types, that were extremely stable might begin to build up their numbers large enough so two would come into contact through horizontal drift. Can they form a linkage of some kind? Given enough permutations, evolution may have found a way to keep two, and therefore many together.

What we have is an elementary membrane. It is not a cell membrane, as there is no cell and nothing to put inside it. But it is a film with the right kind of structure. One of the main stumbling blocks to the origin of life pops out of elementary physical chemistry and considering the different environment of the early Earth. Could the membrane be other than flat? If the molecule comprising one side of the membrane has less cross-sectional area than the one on the other side, there would be a tendency for the membrane to curve, and tend to spherical. At the meniscus, there would be some bubbles of one liquid poking into the other. Perhaps they would close up, and be stable. If so, what would happen if thousands of square kilometers of oceans, plus some lakes, were just full of these microscopic spherules.

Here is a good environment for the replication concept. If one of the trillions of spherules has some DNA, RNA, TNA ,PNA or whatever inside it which is complex enough to make itself and the two components of the membrane, the whole business of life origination may be wrapped up. But still, no one has come up with anything to put inside the spherules yet.

Friday, February 26, 2016

Symbiosis and the Origin of Life

Everyone who works on the origin of life seems to be concentrating on how to get that first cell to form. There are many good suggestions, but as of yet, no experiment that forms one. Maybe the process takes too long. Or maybe that's not the right concept.

In a recent post, the essentials of origination were laid out in clear steps. Basically, there has to be a first something that replicates, and a way for it to get energy and building blocks, the predecessor chemicals that the replicating thing, like a molecule, makes into a copy of itself. At the end of the post, it was discussed that maybe it was a two-stage process, with some molecule or loosely bound group of them that made one component of what another molecule or loosely bound group of them needed. The first one was upstream, and the second one was downstream. Or they both inhabited the same pore of rock face and shared what they received and produced. Perhaps the second one made copies of both the first and second.

This is essentially symbiosis on a chemical level. Symbiosis usually has meant two things living together, like lichen being algae and fungus. The algae are photosynthetic, and produce energy for the combination, and the fungus anchors the combination to some surface. Maybe that is an idea that originated in the chemical world of the deep sea vents. One chemical is good at absorbing energy from the outflux of the sea vent, and another one is good at adhering to a rock surface and holding on to the energy chemical. They are not part of the same molecule, but they are somehow locked together geometrically.

If two molecules can fit together, then neither one has to be able to do everything. They have to be able to exchange energy, or some chemical component, at least in a one-way transfer. In another post it was noted how adhering to a surface in a flow greatly increases the available chemicals. A molecule floating in the stream has a short interval to grab onto whatever it needs, but something attached to a wall with the flow passing it can just wait and grab and wait some more and grab some more.

How might one molecule prevent another molecule of a different type from being dragged away by the flow of the current. If it were shaped like a cage, it might do that. The cage has to have porous walls so that energy-carrying chemicals could get inside, and also there could be no complete interference with the provisioning of chemicals needed to replicate the two molecules.

The type of replication would not have to be the same. The cage-like molecule could just add on holes by extending whatever passes for walls in this molecule, and every once in a while, a piece, capable of extension with the right provisioning, chemical energy source and conditions breaks off and adheres somewhere else. The other one, which might just be a molecule which is metastable, taking energy from some simple chemicals in the flow and then absorbing energy, later to give it to the cage molecule, could be able to reproduce itself or have the cage molecule do it. If there are strong chemical similarities between the cage chemical and the other chemical, there could be some joint mechanism whereby a copy of the second chemical is formed.

Lichens are land creatures but there are other examples of symbiosis. Humans, like most animals, are symbiotic with bacteria living in the intestine. They perform various chemical tasks for us, and in return are provided a stable environment, mostly, and a flow of nutrients. A bacteria is immensely more complicated than a molecule which is metastable, but the basic concept of one molecule providing the stable environment and flow of nutrient-containing water is analogous.

One of the big difficulties of figuring out the origin of life is that there are no simple creatures left. Somehow whatever process that originated life is no longer making the very simple things that it used to. Everything seems to have gotten complicated by a few billion years of evolution. Until recently, it was thought that sea sponges were simple creatures, perhaps the fundamental multicelled creature. Then, more examination of them showed they are rather complicated creatures, and their genome is of the same order of complexity, measured by number of genes, as most of the rest of the living things on planet Earth.

One way to express that is to say that any living organisms with DNA coding its genetic structure, gets complicated and there has been enough time for virtually everything we can find to get complicated. No one at any time has found some simple cell, with practically no detailed features, whose cell membrane was encoded by only a short stretch of DNA. Not too long ago, the microbiological community decided that microbes should be divided into two kingdoms, instead of just one. One is the old bacteria, and the newer one was named archaea. Perhaps the name, archaea, was meant to indicate that these creatures were the predecessors of the other kingdoms, but it turned out, they were not.

Some very clever and interesting chemical analysis was done of the cell membrane of archaea, and they were found to have the middle section with the opposite twist of the molecule comprising it that bacteria and higher organisms. It seems like the primitive precursor of everything went along and invented, via evolution, cell membranes, but not one, but twice, the two versions being enantionmers. The two enantiomers would operate the same, and this indicates that there is one good way to make a cell membrane, that works better than any other form, and it just happened that two super-primitive molecular structures came upon this idea, in stereoisomeric fashion.

If it is possible to originate life via a series of simple steps, why is it not being originated now, and producing wonderful evidence showing each step of the way. Perhaps the more developed things just eat the primitive, newly evolved and newly originated stuff, so that absolutely nothing can be found. In other words, nowhere on the world is free from predatory organisms that feast on these primitive structures that would otherwise have begun, all over again, to evolve. Or maybe there is another explanation.

Wednesday, February 24, 2016

Options for the Origin of Life

Around the edges or ends of a word, there are sometimes fuzzy areas, where the definitions are not so obvious. Take 'Life'. What exactly is something, or alternatively, when is something alive? Like most words, there are lots of dictionary definitions for the various uses of the word that exist, but only one relates to the questions surrounding the origin of life. That is, something is alive if it does four things: has the capability for growth, change, reaction to stimuli, and reproduction. Obviously this is not very good.

When the dictionary says growth, it implies under certain conditions. In a mine, a photosynthetic plant doesn't grow, but it is still alive. What that means is that if you brought it out into the sunlight, it could grow. In a mine, a herbivore would not do well, but again, if you brought it out into the sunlight where some plants were growing, it could grow. Things like certain insects which reach a fixed size, and do not add any mass for the rest of their existence aren't dead, so growth isn't necessary anyway. Maybe the dictionary was talking about growth in the past, so if something has a history of growing, even though it had maxed out at the end, it was still alive.

The capability for change is also a bit uncertain. Growth is change, and so those insects we talked about weren't growing nor changing, except they were going to different places, so perhaps that's what the authors of the dictionaries were trying to convey. Plants cannot reach a maximum extent or they are not alive, and everything else can get blown around or walk around or float around and therefore they are alive.

Reaction to stimuli is pretty good. A person in a coma doesn't react to some stimuli, but their lungs would react to a lessening of oxygen in the room, meaning that non-autonomous change is okay in this definitional slice. Tardigrades or other creatures that can survive being frozen don't turn from dead to live every time the temperature fluctuates, so the definition must mean that a there has to be a reaction under some conditions, like unfrozen, rather than always.

Reproduction is a strange one. Old people can't reproduce. Sterile people can't reproduce. Ant drones can't reproduce. This one must mean something a bit exotic, like belonging to a species that can reproduce, even though the individual cannot. So the concept of life is somehow wrapped up in the definition of a species and what belongs to one. Messy!

This means it is going to be hard to talk about the origin of life, as it is not going to be clear just where the boundary gets drawn. As some replicating chemical begins to become more complex, is it alive yet? The exact difference probably does not make much difference to the research being done to investigate how life could spring out of non-life, but instead just makes the terminology tricky.

The first block of options for the origin of life, meaning options in a combinatorial way, relates to how the not-yet-living chemicals that are capable of reproduction, or replication if you prefer, stay in the conditions allowing replication. Just like the plant in a mineshaft, without the chemical flow coming out of a sea vent, the chemical cannot replicate. This is all under the assumption that the current most popular hypothesis of sea vent origination is valid. So here is the molecule, trying to make another molecule. How does it stay in the flow? There are three options. One is that it attaches to a substrate, meaning some particular deposit of minerals at or near the sea vent efflux point. It hangs on there, and materials it needs flow past it. Viscosity is nice, and means that the flow near the surface will be going nice and slow, so some component chemical can be grabbed by the molecule.

A second option means it is in the water, but the water does not move. Why? Because it is trapped by some geometry of the vent, like small deep pores, or overhanging ledges on the outside. Water flows by the outside of the pore, and there is some chemical exchange there, but deeper in the molecule has a residence time more than long enough to replicate. If it replicates enough, it won't matter that some copies slip out the pore opening, perhaps to be decomposed or perhaps to land in another pore. Numbers can still build up to some saturation level, and then a bit of mutation can go on.

A third option also involves being in the water, but the water flows in a cyclic fashion, perhaps a slow vortex somewhere down the sides of the vent stack. Exchange takes place, but just as in the second option, if replication rates beats residence time, the molecule will still build up its numbers.

The second block of options relates to how the energy to generate the replication gets to the molecule which will do it. Two options are immediately obvious. Either there has to be some source of energy, in other words an energetic molecule from the flow, interacting with the replicating molecule and putting it into a metastable state. The metastable state contains some of the energy that the energetic molecule that bumped into it had; the rest might be lost. The other option is that one or more of the components that the replicating molecule will assemble contain the energy needed for the assembly. A subsidiary option is that the molecule, either the one doing the replication or the identical one which is the product of replication, is a lower energy state that the components being separate. This might only be true in the exact location of the replication site, or alternatively everywhere near the vent.

The third option relates to how many pieces need to be assembled to make a copy. This has to do with the richness of the flow that washes over or surrounds the replicating molecule. Is it full of amino acids, or even peptides, or some other carbohydrate? How much building has to be done, and how much was already done by random chemical reactions in the vent flow? The vent flow would be at much higher temperatures, and there could be reactions in that flow during the very long time when it migrates down to the maximum depth and then back up. These reactions could make some handy precursors.

Now everything is nice and tidy for some chemistry to be done. 1) What organic molecules can bond to what mineral surfaces? 2) What energetic molecules can excite a metastate in what organic molecules? 3) Does replication occur in a linear fashion, with components being added linearly and perhaps attached to the end of the replicator, or in a close hugging fashion, the way DNA and proteins hug each other with complementary folding? Is it some combination of that, with multiple bonding sites onto one component, which then linearly attaches to another?

A nasty option, meaning more work to be done before the answer to origination is clear, is about symbiotic molecules. For example, do certain molecules have to be adhering to some part of the substrate to produce a precursor molecule that the actual replicator will use? Instead of the precursors being made in the flow, perhaps there is a tiny, little factory producing them a bit upstream. Figuring that out could be done sequentially, provided that the experiments to find the components needed for replication weren't restricted to only those which were known to be produced in a hot flow of seawater through rocks.

Let's just hope there are labs working on these options, and that someday, soon we hope, results will be announced.

Tuesday, February 23, 2016

Stars Evolve But So What

Like most things, if you keep digging deeper into the details of stars and how they change with time, it gets complicated. Lots of interesting things happen inside a star, as well as outside it. Is there anything here which affects the likelihood of alien civilizations arising?

In other posts, we have already mentioned the short lifetime of hot stars, and how, if life takes the same time on a planet around one of these, the star wouldn't last long enough for a civilization to form. There is some possibility that life might originate faster on such a planet than on ours, or perhaps our planet, Earth, was subject to some difficulties which might not occur in other planets. If this is so, we need to rethink the lack of attention given to planets around hot stars. Once a bit more understanding is obtained about the pathway or pathways by which life can originate, this question can be revisited and answered. For now, the best guess is that hot stars don't host alien civilizations.

As you go down the scale from the largest stars, O class, through B and A, you get to the F class stars. They live long enough for life to originate and do some evolution, but it might be too coarse a measure to say they last long enough. These stars evolve, and change their output flux. What this means is that a planet that was at a nice comfortable radius, where life might evolve if things worked out well, wouldn't be at a nice comfortable radius after the star evolved a billion years or so.

Astrophysicists like to expound on the final stages of a star's life, because it is so interesting and variable. During those stages, which amount to only about 10% of the star's life, it can expand by a huge fraction, explode, collapse, change color, and other things. However, for an alien civilization on a planet orbiting such a star, it is game over at this point. That isn't really very important for figuring out any implications of stellar evolution on an alien civilization. The important part is what happens during the first 90% of its life, when life might be originating and trying to evolve into smart aliens with starships.

There is an initial interval, before planets get formed, when things are very interesting as well. Gas is flowing in toward the central core of a giant cloud of gas, the center of the core is getting hotter from all that kinetic energy of the infalling gas, and pressure is increasing from the increased gravity of the ever denser core. Then fusion igntion starts, and the star changes internally. Exactly how depends on the attributes of the cloud that formed it, but again, this isn't during the period when alien civilizations would give a damn about it. Their planet hasn't even coalesced yet. What does matter is the middle 80% of the life.

Fortunately, it is calm, but unfortunately, not absolutely unchanging. Nowadays, the universe and specifically our galaxy is mostly hydrogen, but with a lot of helium as well. Inside a star, hydrogen is the first element that stars to fuse, and it makes helium. This hydrogen burning goes on, but one slight effect is that the hydrogen fuel gets used up in the core. A little less energy is produced, and it gets a little cooler on the planets. The core becomes more and more helium, and the star compresses some more, and this heats things up and hydrogen in a shell outside the core starts to burn. This is sort of like a charcoal fire that you start at the bottom of a pile of fuel. The bottom gets burning and then the fire moves upwards. This makes more fuel available, and the output increases.

For larger stars, like F class, the 'ash' of the hydrogen burning, helium, can start to burn itself, which is something you wouldn't see in your BBQ pit. But the helium can fuse into carbon, and this opens up a new source of energy, so things can get hotter still.

Small stars evolve differently than mid-size stars, which evolve differently than large stars, even in this middle part of their life, as the types of processes that occur in the different layers of the stars can differ as to which one is more dominant. This is all fascinating, but what matters to the alien civilization on some planet around a star is the output energy, and to a lesser extent, the color.

Stars can grow cooler or warmer, depending on their age, and on the various attributes of the star itself and its prior history. Cooler is not good and warmer might be okay.

If what we guess is the way life originates is accurate, it originates not based on solar heating, but in an environment that is fairly insulated from any stellar effects. A deep sea vent is about the most remote place, other than underground, that you can get from the effects of stellar variation. The temperature there is controlled by the heat from the vent or volcano, and there is a large gradient of temperature. If something is trying to get started as life and it needs to be at 80 degrees C, and the sea vent is at 120 and the ocean is at 20, there is going to be somewhere in between that is 80. If the sun heats up and the ocean temperature goes up to 25, there is still going to be somewhere in the rocks around the vent where things are 80. If the sun cools down and large ice sheets cover the ocean, the ocean water temperature might go down to 0. There is still somewhere on the vent periphery where it is 80. So stellar variation doesn't have much effect on the origination of life as we now envision it.

It takes evolution a really long time to get to chemotrophs, or so we think, and they can happily live around the different sea vents and volcanic areas on the planet, fairly independently of what the star is doing. To make the big switch over to solar power, when chlorophyll is evolved, there has to be a benign surface climate. Somewhere on the surface there has to be open water. This allows free-floating photosynthetic organisms to exist and further evolve.

If the stellar output diminishes at this point, and the open water disappears, this branch of life is going to go extinct. As long as the chemotrophs keep their line of business going however, it can come back for a second try if things warm up again. Warming may be by the star growing warmer or by volcanic activity affecting the atmosphere and generating a greenhouse effect. Color change of the star's output can also have an effect, as the effective albedo of the planet might change, or the transmissibility of the atmosphere could be slightly different with the changed color spectrum.

If the planet was mostly frozen over, with some portion of the tropic area not frozen, and photosynthetic life evolved, and then the sun grew warmer, this would be an open invitation for further evolution of the photosynthetic life, as well as the organisms that would certainly evolve to eat them. A little more warming and some crawling out onto the land surface might happen, and after that, the sky is the limit.

Let's summarize. If some astronomer sees a planet which is in the liquid water zone, LWZ, or even better, in the temperate water zone, TWZ, where water is likely to be between 0 and 33 C, he might think this is a good bet for life, at first glance. If the star has been growing colder, this means the planet was formerly warmer, and possibly not a very good chance for life to have evolved during the last few billion years, on a too hot planet. On the other hand, if the star has been growing warmer, the scenario discussed above, with some virtually independent regions under the ocean evolving life, and then the environment becoming just great for more evolution, he probably has a good bet that life is on his new planet. Do we know how stars evolve? Yes, fairly well, although it is only recently that this has been worked out, and details are still emerging. Then we can use this information to further refine our expectations on all the potential alien solo worlds.

Monday, February 22, 2016

Puzzles in the Origin of Life

Solving the riddle of the origin of life would be a major step forward in the solution of the absent aliens problem. Is it hard to originate life, meaning there are hardly any planets in the Milky Way where it could happen? Then the problem is solved – there never were any aliens. Is it easy to originate life, meaning there are lots, meaning millions, of planets in the Milky Way that possess all the conditions for originating life. Then we have to look for reasons in evolution or the generation of intelligence or civilization collapse or elsewhere in later eras to solve the problem.

Life has two essential attributes. Approximate replication and energy consumption. Life needs energy to sustain a living organism and to build another one. There are two categories, or at least popular science writers like to say there are two categories of theories about the origin of life. One is called the Replicator theory, which has a specific flavor called the RNA world, and the other is called the metabolism theory. The first says that something formed spontaneously which then catalyzed similar things to be formed; this one was promoted in this blog. The second one says there was some energy pathway which existed first and things which could use the energy to build structures formed around the source.

These two theories are the same thing. The replication of the first variety has to be fueled by an energy source, which had to have existed before the replication could take advantage of it. The energy source in the second doesn't become life until there is something which can replicate itself, using that energy. The real questions are in the details.

Once deep sea vents were discovered in 1977, they became a favorite speculation as to the source of energy. Hot fluxes of seawater, having found a way down to very hot layers, would come up with the minerals from deep in the earth. At the vent, they would meet cool seawater, saline, with dissolved gases, and any chemist should be able to come up with a combination that has available energy. Which combination was the one that led to the first replicating molecules or combinations of molecules? We can call that Puzzle number 1.

What was the first molecule that could take advantage of that energy and replicate itself, exactly or approximately? What exactly is replication here? We have a saturated system when the hot vent water is quenched by the cool seawater – things precipitate out. Any supersaturated solution precipitates, and anybody who had a childhood chemistry set knows, chemicals often prefer to saturate onto substrates made up of the same chemical. Do organic compounds do this? Is this replication? If the compound forms a pillar, of the type shown around the sea vents of today, and one piece breaks off to land somewhere else, and begin its own precipitation, is that replication?

If there is no physical connection with the solid structure of the vent, how would chemicals in the ocean stay around the vent, the source of energy, long enough to do any substantial replication. Hot water would rise and move away from the vent. The nature of the connection, however, is still unknown.

Does the available free energy in the vent flow serve to modify such a deposition? If it did, and the rate of deposition increased, it would be something analogous to evolution. We have the interplay of three things here, all the result of the flow out of the sea vents: one is an energy source, one is a mineral source, and one is a set of templates upon which structures can be formed. Puzzle number 2 is the first organic compound or combination of compounds that do the replication. Educated guesses say it might have been RNA, but there are other suggestions as well, GNA, TNA, PNA, and more.

With just these two puzzles solved somehow by nature, the kind of very primitive evolution can continue to find other chemicals and combinations that can take a greater advantage of the energy in the sea vent flow, both quantitatively by replicating, and qualitatively by mutating or simply being modified by chance, into something which makes better use of the energy. A sea vent colony can evolve. Initially autotrophs will be the only things, but then heterotrophs will evolve to consume the hydrocarbon in the bodies of the autotrophs.

So far, there has been no discovery of fossil chemicals buried deep in the sea vent structures, and probably there never will be. With no records, perhaps the DNA of the creatures that live there now may give some clues, but it is not at all clear how to extrapolate back from existing DNA to some pre-DNA molecules, very simple ones at that, which existed at the beginning of life.

Most of us remember when there were no exo-planets known, and a big mystery of the universe was whether they existed, how many there were, and where they were. Then the first one was discovered, and the second, and now thousands are known. Perhaps the same fate awaits us on the origin of life. Maybe there are a dozen different combinations of energy-producing chemical reactions and self-replicating molecules. Perhaps it is very easy for life to form around such a deep sea vent, and it doesn't take many centuries at all to do it.

It would be nice to know if there are lots of ways to originate life, or just one. The author of this blog has suggested elsewhere that going to ten or twenty deep sea vents in all different parts of the oceans and seeing if they have identical DNA coding and genes would tell us a lot about the difficulty of life forming. To date, no one seems to have done this, but the equipment to take samples does exist.

One other item has been plaguing those who think about the origins of life. If life began on a deep sea vent, and was completely dependent on the energy pouring out of the subterranean piping there, how is it going to migrate to the surface? If it doesn't get to the surface, and live there a long, long time, chlorophyll isn't going to evolve, as chlorophyll is a complicated molecule and a lot of intermediate steps need to be taken to get to it. Fortunately, we have Hawaii.

The Hawaiian Island chain, starting with the Midway islands, is what a deep sea vent might grow up to be. The Midway islands are small little atolls, and there are reefs that never made it to the surface. But they are volcanic in origin, meaning that some hot water had to come out of them, a la deep sea vents. It seems that the source of the heat, a magma flow deep in the mantle, has been migrating along a fairly straight line, leading to larger and larger islands, with the finale being the island of Hawaii, at the southeast end of the progression. Each of these were once completely underwater. Some still have active volcanic flows. Once such a flow gets to with a few tens of meters from the surface, all those solar photons, chock full of available energy, are available, and once whatever chemotrophs there were evolve the capability of using this source of energy, they can cut themselves free and float through the oceans, spreading the seeds of life everywhere.

Trying to figure out the exact steps that evolution or the chemical pre-evolution discussed above took is like trying to figure out what automobiles were designed, and perhaps mocked up, before a new model was formed. There are few records of these trials, and probably no records of the intermediate steps. They weren't the million-seller successes, and so there aren't any left around to find and examine. The best bet is laboratory experiments, and these are costly and probably take a long, long time. Once we figure out how to do simulated chemical experiments, things should be quicker, but until that happens, the puzzles are likely to remain unsolved.

Sunday, February 21, 2016

Life in Solar Systems with Hot Jupiters

Many of the exo-planets first found were hot jupiters, planets with mass similar to our Jupiter's, but with an orbital radius more like Mercury, with some even closer in. These were found by the velocity method, where the spectral lines of the star were observed with very precise spectroscope, and periodic fluctuations in the wavelengths were found. These fluctuations were correlated with what there would be if a large planet were orbiting close to the star, causing it to be moving around the common center of mass.

The prevalence of hot jupiters in the initial tallies of exo-planets was attributed to the selection effect. Spectroscopes were just good enough to detect the motion of the star when a large planet was causing it to move, as there are various noise effects in the data, plus some instrumental accuracy to worry about. There is no doubt that the selection effect was a fact, and as spectroscopes became better and better, and at least local noise was tamped down, many more planets of smaller size and larger orbits, mostly both, were discovered, thus validating the suspicion of the selection effect. However, there are solar systems out there with hot jupiters in them, and the question is, are there planets there, and if so, could they support life?

Where do they come from? Humor aside, the common theory of origin of these planets is that they were formed out further in their solar systems, and then they migrated in. They migrated in because they lost angular momentum, but it is not so clear why they would, in a system where everything is orbiting around the same central mass, with the same velocity vs. radius curve. They would have to be born in close, as a hot jupiter, to have the star's tidal pull grab it and drag it in closer. So perhaps an alternative explanation is that they were born in closer, about where they were observed.

When a cloud of gas starts condensing to form a solar system, it has some angular momentum. It keeps that angular momentum all through the condensation process, with the star and the planets sharing it. Perhaps some gets lost when the solar wind picks up enough power to push out some of the remaining gas, but by and large, the planets and star inherit it. Angular momentum is just a measure of how fast the gas cloud was rotating. Some clouds should be rotating faster than others, in other words, there is a distribution of angular momentum, or better put of the angular momentum divided by the total mass of the cloud. At the upper end of the distribution, things are merrily whirling around, and the gas cloud starts forming planetesimals out far from the star. But at the lower end of the distribution, there isn't much whirling at all, and the gas keeps falling directly into the star. If there was virtually no angular momentum, all the gas would fall into the star, and there would be no planets. Do we know how many stars have no planets – not yet, so this avenue does not provide clues. But assuming the distribution doesn't have some minimum to it, there will be gas clouds condensing with little angular momentum. These can form hot jupiters, as all the gas gets in pretty close before the little angular momentum it has provides enough centrifugal force to counteract the centripetal force of the central star.

If this concept of formation is correct, it would mean that there wouldn't be much mass left out far beyond the hot jupiter to form other planets. It's all heading inward. But there might be enough for some other planets to form close in near the star. These would likely be smaller planets. At this point in the data collection efforts on exo-planets, it is not clear if many stars with hot jupiters have other planets. At least one is known, but not a lot.

The stars that form hot jupiters seem to be preferentially F and G stars, which is reasonable because of the mass involved. K stars are smaller, and red dwarfs, M stars, much smaller, and if the planetary mass is proportional to the total mass, there isn't much around for a jupiter-sized planet.

F and especially G stars are ones which are expected to have origin planets, provided a lot of conditions are met. One of the easy to check ones is the orbital radius. Is the planet in the LWZ, the liquid water zone? Recall that it is not enough that a planet is sitting in the LWZ, but that longevity of that location is important. Life doesn't form overnight, and a planet has to sit for a long time in the LWZ in order to let life get started.

If a hot jupiter is in the same solar system, this means that there is a source of angular momentum near the star that is much greater than tidal effects. What this source means is that a coupling of angular momentum out from the hot jupiter to the outer planet, over a billion years or so, might move it either into the LWZ or out of it, or even through it. This means the planet is not a candidate for life to evolve there, or if it did, that it would be snuffed out by the radial migration of the planet.

The coupling of angular momentum to an outer planet happens by an analogous mechanism to tidal effects, which means it is a second-order effect. Second-order effects are weak, but sensitive to the mass of the hot jupiter and the outer planet. It is easy to understand. Suppose you are on the outer planet and are watching the hot jupiter orbit around the star, your sun, in close. When the hot jupiter is on the approaching side of its orbit, it is trying to slow your planet down, assuming you are both orbiting in the same direction and roughly the same orbital plane. When the hot jupiter is on the receding side of its orbit, it is trying to speed your planet up. The two effects are almost identical, and so each orbit of the hot jupiter has an averaging effect.

Your planet is trying to speed up the hot jupiter during its approaching phase and slow it down during its receding phase, and this means that, ever so slightly, it is going to be spending less time on the approaching phase than the receding phase, so the net effect of the approaching phase will be just a bit stronger. Your planet is going to go in toward the star. With luck, the effect will not be enough to move your planet out of the LWZ or perhaps, with a lot of luck, the star might be losing a bit of its energy as it gets older and the hot jupiter might just be keeping you in the LWZ.

It is hard to say whether solar systems with hot jupiters should be taken off the list for doing the very precise and very expensive work of looking for some clues for life there. What can be done is some good simulations of the effects to see just which ones of them have planets moving out of the zone during a period of interest, or whether they were just pulled into it. Simulations of planetary motion is so well figured out that it can be done easily – wasn't it Galileo or one of his successors that first did it?

One thing that is fortunate is the selection effect. Solar systems with hot jupiters are hard to miss, unless the orbit of the jupiter is almost perpendicular to the line of sight from here to there, and that is not very likely, given that the dominant source of all the angular momentum comes from galactic rotation. That means looking perpendicular to the galactic disk might be problematic, but most stars aren't in that direction anyway.

Saturday, February 20, 2016

Recognizability and Clones

When the first starship to visit Earth lands somewhere and the aliens get out, what would we see? Would they all look alike, as in some science fiction movies? Alternatively, if we ever get our act together and build a starship, go out to some planet we know has an alien civilization on it, and start walking around the downtown of one of their cities, are we going to feel surrounded by clones? Every one of them looking alike?

Cloning will certainly be possible, assuming the aliens we meet have passed through the genetic grand transition, which is just a name for the short interval of time in which genetics gets figured out and all kinds of possibilities are added to the civilization's menu. They could certainly clone things, and aliens as well, and it would be done with more finesse than we do it. We are struggling with mastering the intricacies of cell and embryo growth, as well as gestation. They will have left that all behind. So cloning all the next generation of aliens would be a very inexpensive way to keep the population renewed. Just split an embryo a few times, until there was a quorum of cells that could grow, put them all into some sort of gestation apparatus, and out comes the clones. This is a concept that has occurred in science fiction, but does it make sense from what we can figure out about aliens?

Suppose you were in charge of making decisions on the composition of the next generation of aliens? Would you say: “We need some diversity here” and decide that some would be healthy and live long lives, and others would be chronically unhealthy and live short and unpleasant lives. Even if you had no sympathy for those you were creating, the civilization would fire you, because you were increasing the burden of health care costs by a huge amount. So both from the grounds of sympathy and the grounds of cost and efficiency, you would decree that the whole generation you were planning would be just as healthy as they could be. You would not try to sneak in some genetic diseases, or some predisposition to whatever illnesses aliens could still get. You would instead see that they were set up with a great set of genes and were as immune to everything known to the medical field in the civilization.

That was easy. Now you think about making some diversity by having some dumb aliens and some smart aliens. Your sympathy starts kicking in again, and you wonder why you would wish dumbness on any part of the next generation. You also know that smart people make less demands on the civilization's services, and are immune, to misuse the word, to fraud by those smarter than they are. So, everybody gets to be smart, and that's another box checked off. Now you move to physical qualities, such as athleticism. Some of the next generation are going to be ill-coordinated and clumsy, with bad eye-hand coordination and no stamina or endurance? No, they are not. Everybody gets to be athletic. How about ugly? How many ugly people in the next generation? Zero. You can move through all the functional attributes and decide that these will be set to the best available.

Is there a loophole? You could deprive everybody of something, so you have one faction of dumb people and one faction of ugly people and one faction of clumsy people and one faction of unhealthy people and so on? Why bother? Why would the civilization want to pick up the cost of these deprivations and what good could it possibly serve? Could you come up with a reason for unhealthy people? No. And the same for the other attributes.

Does it cost more money to have a good gene in some place on some chromosome instead of a bad gene, so that you could save a bit on the cloning costs? No, the quality of the gene does not relate to the cost of installing it. It might be even cheaper to have all of the next generation have the same set. So, you are well down the road to calling for clones.

Then it dawns on you that if everybody is identical, it is going to be pretty hard for one alien to have a friend. Everybody looks alike? Here on Earth identical twins sometimes have the problem of not being recognized. On the alien world you are on, it would be a million times worse. So, perhaps you can make some differences that are not functional, do not cause any costs to the civilization, and still allow recognizability.

Perhaps some of the next generation would have deep voice and some would have high voices. And why stop there, as a voice box in an alien would likely not make a single frequency, but a combination of them. So, voices could fairly simply be made quite different, and recognizable. If there are many genes for the vocal system on an alien, there would be a large number of combinations. Related to this is the differences in speech patterns, such as more or less aspiration with certain sounds, assuming they have aspiration. Slower or faster pronunciation of certain sounds would be a difference. Tone shifts would also be. The number of possibilities for unique voices skyrockets. So there is no problem with making aliens recognizable from voice.

The same holds for appearance aspects. Even staying away from anything not attractive, there are many varieties and options in features, pose, stance, motion details and so on. Gait can be different without being caused by unhealthiness or unathleticism. Eye motion, eye size, eye color, and habits of looking can be different. The list of attributes that can be diverse without passing the lines that were set on intelligence, healthiness, and so on is very large and even with a population in the billions, individuals could be both unique and recognizable by others.

So when aliens come to visit us, we can expect to recognize different ones. This does not even extend to wearing different clothing habitually or any other external, added items, such as coloring, fur or hair decorations, clothing decorations, and so on. There is no recognizability problem.

The loss of individual identity is not a factor in the aliens refusing to allow the genetic grand transition to happen. There may be other reasons, but this is not one of them. As noted elsewhere, the conquest of genetics will make the conquest of robotics seem more or less inconsequential in comparison. Some of the aspects of this transition are mentioned here, here, here, here and elsewhere in this blog.

Friday, February 19, 2016

The Onset of Scarcity

In some other posts, it was discussed that scarcity issues are a tremendous peril for alien civilizations. Star travel is not a solution for shortages on the home planet, as the cost of shipping something over light years distance is ‘astronomical’ (Sorry, I had to say that.) Local interplanetary shipping may help postpone the inevitable shortages a bit, but even that is costly in terms of energy usage. This problem limits what an alien society can do and for how long it can do it. It produces a short window of time in which the alien civilization can do star travel, for example to colonize another planet somewhere else in the Milky Way. If they miss the window, the resource shortage prevents them from having a second chance. Like all conclusions in this blog, it needs to be looked at again and again, for exceptions or omissions, but for now it seems that this is one of the most likely reasons there are no aliens visiting us.

There may be a little bit of misconception about what actually happens to curtail the civilization’s living the high life for ever and ever. What happens is the cost of extracting resources gets higher. These costs can be tabulated in terms of two things: energy and resources themselves. As the mines have to be dug deeper or ores shipped farther or more ores dug up to be processed, more energy is needed. This is no big deal if you assume there is infinite fusion energy around. Just build another reactor. Problem solved.

No. There are connections. To build another reactor, you need resources, which are getting more and more scarce. So there is a Catch-22. You need resources to build a reactor to get more power and you need more power to get resources to build the reactor. This smells like some square law thing, meaning that things get worse really fast near the end.

To try and understand the processes, let’s build a model. Before doing so, remember that modeling is just another language, like French or Russian, except it is a language of mathematics. What is nice about languages of mathematics is that you can intersperse it with English to make everything clearer, which is particularly hard to do with French or Russian. Spoken languages are meant to be done independently, but mathematical languages are meant to be used with a spoken language. That’s just nice, and everyone should have the right to be taught, properly, how to speak some mathematical languages, like modeling.

That being said, I will reveal the secret behind the curtain of modelers. Modeling is just a way of communicating ideas. A model proves nothing. It is just a tool to try and put numbers into some concepts. You can make a model do anything you want it to, just like you can use English to say anything you want to. To try and convince someone of some idea because it has a model portraying it is deceptive. Models are not science, they are a language of mathematics, no matter how complex they are or who creates them. They convey the ideas of the author, just like an essay does.

I like simple models, because simple models help people understand the interplay of ideas that are quantitative. So, here we will use the maximally simple model.
Consider an alien planet, which at time zero has 500 units of resources. For simplicity, we only think about one resource. It has cities, full of citizens, which depend on the resources and the energy which is produced in their power plants. Let’s just consider averages. At time zero, the city needs 1 unit of resources to get it to time one, and 1 unit of energy from the power plant. The power plant produces its own energy, but in the standard design of the power plant, it needs 0.04 units of resource per year to produce one unit of power. This is averaged over its lifetime, and most of the resource usage comes at the construction phase. Recycling is already figured into these numbers, which are only the net amounts, or the recycling losses, if you prefer.

Resources, net of course, come from some resource extraction operations, like mining, and they need some power to do their job, which we take as 0.1 units to begin. They also consume some resources, which starts as 0.04 as well. This means that, for the one city to function for one unit of time, 1.1 units of energy have to be generated, and 1.14 units of resources are consumed in each unit of time. If resources were like tomatoes on supermarket shelves, all equal and all waiting to be picked up, this model would function linearly, and the last resource would be used up in 500/1.14 units of time, where we are taking 500 as the measure of total resources available on the planet.

But resources get harder to extract and process and make available as there are less and less of them. This means that the power needed and the resources lost in gathering a unit of resources gets larger and larger as the remaining amount diminishes. How fast? For the simplest model, suppose it is inversely proportional to the amount. So, when there are 250 units left, it takes 0.2 units of energy to extract and prepare one unit of resources, plus 0.08 units of the resource itself. Here’s what happens:

What happens is that cheap fusion power just keeps being used to extract more and more resources, which do not go to the city, but to the resources extraction operations and power plant construction, and the city is oblivious of the changes, until near the end, when the power a new plant can provide does not return enough resources to enable its construction. Buried in the assumptions are that fusion fuel is inexpensive, virtually inexhaustible, and it does not negatively impact anything at all. Quite a nice package: cheap fuel, as many reactors as necessary, and resources that go on and on until they don’t.

Never forget by this time, the alien civilization is quite smart, and they wouldn’t be fooled by the seeming unchanging life they lead. Furthermore, they have mastered artificial intelligence, and one would hope the master computer network, or whatever embodies their AI, would tell them that they have only a certain number of time units (maybe these are years or decades) before some resource shortages hit them. Even if there is no visible sign of any resource shortage in the cities, somebody would notice the gradual change in the composition of the infrastructure, meaning more reactors and mines every unit of time.

There is little they can do, other than colonize. Being smart and all, they are already recycling as best as anyone could. The home world is headed back to living on renewable resources, as there won’t be any other ones. This means no industrial equipment, as it all uses resources, except for what can be made out of grown materials and powered by natural forces, such as rain, tides or wind. No hope for visiting Earth if they didn’t make the voyage before the last bit of time, when shortage actually start looking like shortages, and cheap deuterium doesn’t ameliorate it any more.

Thursday, February 18, 2016

Are Ice Ages Necessary for the Evolution of Life?

Life has a great impact on the composition of the atmosphere of Earth. It is also true that the atmosphere of Earth has a great impact on life on the planet. It could be said that the two, the atmosphere and life, are an interacting system. If someone in the astronomy business is going to go out and make estimates of what planets among those newly discovered ones might have life, they should certainly incorporate this system into the conceptualization.

The simplest phenomenon is the greenhouse effect, controlled by the well-known greenhouse gas, CO2. If plants start doing photosynthesis, and in so doing produce some CO2, which gets into the atmosphere, some heating may occur. A planet with no greenhouse gases whatsoever has its temperature set by two things, the input solar flux from the star it orbits, and its own internal heat, seeping up to the surface. The internal heat comes from the formation of the planet, when the kinetic energy of the gas, caused by gravitational attraction, is converted to heat when the gas condenses onto the proto-planet. It takes a long time for this heat to dissipate.

A planet with greenhouse gases simply has an atmospheric layer blocking much of the heat from radiating away from the planet. In its place, the cold upper parts of the layer radiate much less energy. The right gases do not interfere with solar energy, which has a higher temperature than the absorption bands of the gases. Another way to say this is that the LWZ, liquid water zone, which some astronomers like to dub the habitable zone or the Goldilocks zone, moves further away from the home star.

Another interesting part of this system is the oceanic circulation. Depending on where the continents are, there could be more or less warm water from the tropics moving toward the poles to warm them. On a planet with a lot of this circulation, polar ice would be smaller than otherwise. If something happens over the eons to reduce the circulation, which might be atmospheric greenhouse gases, there would be more ice. Ice is bright and shiny, and reflects solar photons back into space more than does rock or ocean. So, as ice cover increases, a feedback effect happens and things get colder, meaning more ice. Ice age!

Volcanic activity is another player, as it dumps large amounts of greenhouse gas into the atmosphere. An ice age might be terminated if sufficient volcanic activity occurs, but this might mean a basalt flood to get the quantities high enough.

The system might function like this. Chemotrophs come into existence in the deep ocean by rifts, where there is good chemical energy flowing into the ocean. They could care less about ice cover. But in some shallower areas, given enough time, the various steps along the pathway to photosynthesis can be taken, and then CO2 is made. Photosynthetic organisms break their connection to the shallows, and spread through the seas. Now CO2 gets significant enough to have an effect, and less ice for a while. Then ocean circulation takes a hit, and the ice cover albedo feedback brings back the ice age.

Volcanoes step in, and the ice retreats, and life spreads to the land, where more CO2 is made, even more efficiently than in the ocean. Now the ice age cycle is somewhat reduced, but still goes on.

Regrettably for Earth science, figuring out geological evidence for ice ages is difficult and their extents and even durations are still controversial. Since we have not yet figured out the evolutionary pathways for life from some self-reproducing chemical up to ourselves, we have difficulty in coming up with an integrated picture of this system. And this does not even count the difficulties in figuring out the locations of the continents at any given epoch of geological time, much less the oceanic circulation.

Is there anything that can be usefully extracted from what we do know, or can estimate, about the life-atmosphere-ocean-volcano system that will provide a narrower window for finding planets that might have evolved life? Note we are not looking for intelligent life here, so radio waves and lighting are non-starters. Note that greenhouse gases have effects when they are very low in concentration, so observing the constituents of the atmosphere during a transit, as we are now learning to do, would not tell us about their presence or absence. If we did find, for example, a large fraction of an atmosphere was CO2, this would probably be an indicator that life was not present, rather than the other way around.

Perhaps the most visible possibilities are the polar caps. At this point, seeing an exo-planet as a single pixel is an amazing accomplishment. Seeing it as a 10x10 image will require bigger instruments, which may not even have been thought of yet, to say nothing of being checked for feasibility or, gasp, cost. However, if we did see a polar cap, perhaps by looking at multiple transits on planets with significant obliquity, this would be a red flag for a solo planet. Maybe we could name it Peary or Shakleton.

The other side of this nudge upwards in understanding would only come from a better balance of funding for other critical areas of research. Astronomy gets a large share of public research monies because their launches and instruments take a lot of money, and frankly, because they excite and interest a large number of taxpayers. But learning better about where our continents were two billion years ago, or how to derive some overview of ancient oceanic circulation, or for that matter, what are the essential steps in the evolution of life, would have a large payoff for the big picture of where life could be in the Milky Way, as well as better understanding of our own little Earth.

I would be the last person to suggest that money be taken away from our astronomical probes and instruments and diverted to geology or ancient biology, as those probes and instruments are necessary for our steps forward and, honestly, exciting and interesting, but instead some other source should be found so we move forward with a balanced portfolio of science projects, all pertaining to the question of where aliens are hanging out.

Wednesday, February 17, 2016

The Big Memes in an Alien Civilization

This blog is interested in why aliens have not paid a visit to us here on Earth, but it was soon realized that since we understand very little about what are the real possibilities for alien civilizations in the Milky Way, our speculations about why aliens are avoiding us lack a solid footing. The blog is designed to try and rectify that, by thinking through just what type of civilizations might have emerged on other planets.

Since star travel is the core idea for aliens visiting Earth, some of the posts here have discussed alien memes relating to star travel. Alien civilizations were divided up into categories based on what choices they had made relative to colonizing other planets or otherwise traveling through the Milky Way. It was realized early on that there is no purpose that any alien civilization could find from physics or astronomy or biology or anything else, and they would have to make a decision based on something inherent in their own civilization. But once they passed the genetic grand transition, and bestowed a universal high intelligence on all of their members, the idea of figuring out something and making it stick, generation after generation, would not work. Reason and rationalism does not come up with the answer to questions which have no answer. The only way out of this dilemma was to have a decision based on the earlier phase of the history of the alien civilization, before mass intelligence started to erode anything that was not based on reason. Back in those early days, if there was a person or group who had influence over a substantial part of the population and who had goals for having his/her/its civilization travel to the stars, there was a way to do it.

If you want to make rational citizens believe and support something arbitrarily chosen, you have to make them believe it, deeply, before they become rational. The only avenue for embedding star travel memes into the alien civilization is to make it part of the training for young aliens. Rationality comes later, and neural associative networks do not have erase buttons. What goes in early stays in.

Star travel is a large subject for memes, but there are larger ones. Other posts have indicated the role that resource scarcity would play in how an alien civilization’s history plays out, and there are two choices that the society has to have made in order to determine its response to scarcity. One relates to the choice of three things: population, duration of the society, and living standards. For a finite stash of resources, a combination of the population count and the translation of living standards into a resource consumption figure show how long it is before scarcity takes its toll on the civilization and they must say goodbye to their golden age. Half the population and double the duration. Drop living standards so that half of the resource consumption is needed and again, the duration is doubled.

Again, physics and chemistry and other sciences provide no answer to the question of how much population should be maintained. There is nothing that can be gleaned from genetics or astronomy about how well the alien civilization should treat itself. These are arbitrary choices, and in analogy with the star travel choice, have to be made prior to the dispersal of the advanced intelligence genes to the whole population. There is no value that can be compared between an alien living at some living standard and two aliens living at half that living standard. Which is better? Neither.

Another choice is analogous to this one, but centers on the individual level. With genetics at the end of its progress, where everything that can be done is understood and can be done by the civilization. They can design the genetic code of the citizens to give them, say, fifty years, or a hundred, or a hundred and fifty. What this means is that the birth rate of new aliens has to be adjusted inversely to adhere to the proper population count. Nothing in science or anywhere else tells the civilization that two aliens living for fifty years is worth more or less than one living for a hundred years. Each generation can rethink the choice of inherent lifespan, but if it is written into their memes, it is much harder to promote a change, especially since there is no rational reason to choose one or the other.

How the choice of lifespan is accomplished is not defined. Old age could suddenly set in at forty nine or thereabouts, or healthy adults of age fifty could voluntarily choose not to live any longer to make space for new aliens. The method the society chooses does not change the mathematics of the choice. This is the way memes are implemented in a civilization. They are interpreted to provide the details of the implementation. There is nothing but rationality once the memes are chosen. Figuring out the best coding of genes to promote early and sudden aging is an engineering question, and can be figured out and put to the test, either simulated or real-life. Only the memes themselves are arbitrary. A society full of brilliant members would not miss any opportunity to improve their science or engineering if some small gap were found.

There are a thousand choices that derive from the selection that the memes make. Every detail of life can be put under the microscope of reason and examined to see if it contributes to satisfying the memes or if there are different details which might do it better. Once memes are set, the whole civilization can make all the choices it needs to make in order to define just how they live their lives, how they govern their society, how they impose the mandatory needs of society such as recycling on every citizen, what they allow for travel, and so on and so on.

The two memes discussed here, population count and living standards for one, longevity of individuals for another, together with the star travel meme, serve to specify many of the choices that an alien civilization has to make. Perhaps there would be a science meme. There may be more, and perhaps a complete set has five or ten or more, but these choices are not large in number like a thousand and even a hundred or two seems like overkill.

There is a problem that the society faces if the initiators of the meme set did not figure out in advance how to deal with any conflicts that arise. Direct conflict is not possible and could not even begin to be taught in standardized training, but minor conflict in some situations could occur. Prioritization or interpretation would have to be done to deal with such conflicts. Otherwise the concept of memes providing the fundamental basis of the alien civilization falls apart, under the scrutiny of countless brilliant minds.

Monday, February 15, 2016

Does Transportation Degrade Recycling?

The exhaustion of resources appears to play a large role in reducing the number of alien civilizations which might be touring the galaxy at any one time, and so thinking through how bad it has to be would be useful in gaining a better appreciation of the impact. A recent post discussed construction of the large arcologies needed for very high levels of recycling. But simply living in an arcology of that size implies there would need to be transportation of some kind. Would that be the worst sector for recycling losses? Assuming there is more than one arcology on the alien planet, would transportation between cities be a worse loss that transportation within the city?

An earlier post, dedicated to obtaining reasonable limits on population for an alien civilization living on one planet, with all of them at a high standard of living, as measured in energy consumption, came up with a population limit of 10 billion, divided into a thousand cities of 10 million citizens each. The cities were, for the purpose of getting some idea of the scale, 10 km by 10 km in footprint, and were 100 stories high. Travelling 10 km by walking, or whatever aliens use as a substitute for walking, seems like a time-consuming thing, if done frequently, so some method of speeding up transportation would be needed for this. Vertical elevators seem to be a reasonable choice, but if there were ramps, small vehicles could be used. Horizontally small vehicles would work, or some sort of tram system would as well. Ten kilometers is not long enough to require high-speed transportation, so anything imaginable would work, and not much volume inside the arcology would be necessary for it. Furthermore, short distances like that would allow even batteries from our era to be used, to say nothing of what might be developed after a thousand more years of science. So, electricity can be used, which sets a bound on how much recycling losses might be caused. If something is more efficient, relative to recycling, that would lower the bound even more.

So aliens could putter around the city in small electric vehicles, small enough to fit inside an elevator, and get from one corner of their city to another in some minutes. An arcology is necessarily designed to minimize transportation, so the average trip would be much less that this, and likely most trips would be short walking distance ones.

Other transportation within the city might involve heavy loads being moved from one part of the city to another. There would be large load corridors, and the same argument about the maximum distance being short enough for electric power, and the usual distance being short as well, indicate that there is no need to consider than transportation within the arcology would be a large sink for recycling. Vehicles and elevators and trams all wear out, leaving some residue in the environment, which would be the largest recycling burden. Just to get some ballpark estimates, consider a typical vehicle which is in constant use for its lifetime, running at 10 km/hr 12 hours a day, meaning 120 km per day or 40 thousand km/ year. If there were tires on it, and they wore out at these low speeds after 160 thousand km, tire wear might be 10% of the weight of the tire, meaning tread loss, over four years or 2.5% over one year. This compares with 0.1% as a target. If this is the most significant loss that the vehicle suffers, and tires are 3% of the total weight, the vehicle is suffering a 0.08% total annual weight loss.

It is, of course, not the same thing to lose tread as to lose metal parts of the vehicle, and lumping them all together may be an illegitimate way of figuring out overall recycling capability. One cannot make new tires from old metal parts of the vehicle. Can future technology make tire tread that lasts ten times as long as we do? Can tires be dispensed with and some levitation be used instead which has very low recycling losses? Can tires be made of other materials which share the composition with body parts? Compare these engineering challenges with the effort needed to solve them. An advanced civilization mastering all technology that is physically possible and which recognizes that high recycling rates are necessary for its survival would likely figure out how to beat this loss. The fact that we might find a 2.5% loss when a 0.1% is desired seems a solvable problem, given the long time and large effort available to solve it.

This leaves intercity transportation as a possible recycling sink. The previous post indicated a thousand cities might be a reasonable estimate, and if the planet has a good fraction of its surface as area where cities can be built, they could be separated by up to half the circumference of the planet. Maybe 20 thousand km is a reasonable number for coarse estimating of the maximum travel distance.

If there were a large amount of travel on the planet, then it would be useful to see if the level of recycling losses on this longer distance transportation would necessarily much higher than some target figure like 0.1%. If there were very few trips, the losses would not significantly degrade the overall recycling rate of the alien civilization. So the first question is, in such an advanced civilization, what is the demand for long-distance travel.

There is no business travel, as there is no business, as everything is automated and done just the same this year as for the last hundred years. There is personal travel, but without migration, such things as face-to-face renewal of acquaintances would not necessarily occur between cities, but only within cities. Why would there be migration? There is no job-seeking which draws people from one city to another. Work is voluntary and occasional. Educational training would be transmissible from one city to another, with no need to go from one to another to be trained; and training in all cities would be optimized back in the days of the grand transitions. No city would have a monopoly on one type or even any better training or education than any other. There seems to be virtually no need for intercity travel for personal reasons.

This leaves tourist travel. The cities are all the same, but unless the planet has been engineered to be uniform, there would still be interesting places to go, where natural sights were the best. This could involve a large amount of travel, especially considering that there is no employment obstructing the use of time. The other side of this coin is that professional media experts could go to all of these, and record the absolutely best views at the best time of the day or year, and make them available to everyone. Going to a nature site would result in a poorer view of whatever is there, and not in all seasons, and not when the fauna is present, and so on.

What about relaxation? Perhaps the alien citizens like beaches, or mountaintops, or rivers or something else to simply go and relax there. Or perhaps relaxation is totally understood since the neurological grand transition, and relaxing is best done in a chamber best suited for it, with the environment chosen, the scenery chosen, special foods or drinks chosen, breezes chosen, motion chosen, and whatever else that could aid in relaxation already there.
What about competitive travel? Wouldn’t one city’s best athletes, debaters, poets, musicians, artists, and all the other things they might compete at which we don’t have a clue about, all want to go to the intercity competitions? The numbers are what make the difference here. A single person or team from each city doesn’t add up to much travel.

So far, travel numbers are low, and that means that even if recycling losses are worse in intercity transportation than elsewhere, the total isn’t going to be affected much. If that were all the possible losses, recycling would not be significantly degraded by transportation.

That isn’t all the possible losses, however. Generating new resources involves transportation of significant materials around the planet. Mining sources are not uniformly spread around the crust. And as far as mining goes, transportation is only one source of recycling losses connected with it. It deserves a separate post.

Sunday, February 14, 2016

Transitioning to Arcologies

Point 1: Resource exhaustion has been singled out as an important factor in determining how many alien civilizations are present at any time in the Milky Way. Point 2: Recycling of resources is an obvious way to extend the usage period of a planet's resources and would be adopted by any intelligent species facing resource exhaustion or possibly long before it became a significant problem. Point 3: Raising the recycle rate very high, or in other words, reducing the depletion rate to a very low value requires much of an alien civilization, and living in arcologies appears to be the living arrangement most conducive to low depletion rates.

Question 1: If an alien civilization evolved into a living arrangement nothing like an arcology, would it be possible for them to transition into ones rapidly enough to put low depletion recycling in place before shortages cripple the living standard?

In more basic terms, if A has to happen to prevent civilizational collapse, but B, which is not-A, is the existing situation, and if there is no path from B to A, then collapse will happen. Is there a way for an alien civilization to move the entire population, except for some small numbers, into arcologies, organize the necessary recycling, and live according to the conditions this imposes? If not, we have a stronger answer for why there are no aliens visiting Earth.

Can such an arcology be built and would it stand up to time and be usable for long periods of time? Consider the structure itself first. If it is built for a finite period of time, like a century, and then is expected to be abandoned or simply demoed, then the mass of the building is not being recycled. This does not have to be the process, however. If the building is thought of as a piece of equipment, the same principles of recycling might be imposed on it as are imposed on other complex items, such as transportation vehicles or systems, computing systems or networks, power generation and distribution facilities, utility infrastructure and so on. These principles start with the object being designed to be decomposable into parts which are themselves either also separable further or are amenable to recycling by themselves. For example, electrical and fluid and information transmission services inside the arcology would have wiring, piping, cabling or whatever that can be taken off the arcology, either for repair or replacement, or when the structure itself is being recycled. Instead of being cast into a structure, these transmission systems would be removable whenever necessary. Moreover, each part of the transmission system would be removable and could be taken for recycling.

The structure itself is subject to the same rules. The building has to be capable of being disassembled. A large explosive demolition is not what one would see. Instead, the same process of construction would be repeated in reverse for deconstruction. This may seem strange or impossible, that buildings larger than our skyscrapers and much more versatile in the interiors, containing all that the civilization needs and permitting all that it wants to do to be done inside, could be disassembled like a Lego block structure. Yet even here, in the primitive backwater called Earth, some steps have been taken in that direction, perhaps enough to indicate that disbelief is not necessary.

A Chinese company, Broad Sustainable Building, has figured out a process of building skyscrapers out of prefabricated parts. This is not the same thing as designing a building to be taken down, but the concept of building huge buildings, for example, BSB's 30 story hotel/office building, was put up in 15 days by fabricating a huge number of identical pieces in factories, testing them there, and then assembling them onsite. The details of the design are not completely clear, but with removable fasteners between parts, the concept of deconstruction seems quite reasonable. The breakthrough implication for an recyclable arcology is not in the speed with which construction can proceed, but the demonstration of the concept that large buildings can be put together out of pieces, assembled like, yes, Lego blocks.

The Chinese company, BSB, did not design their components to be recyclable and neither did they come up with the concept of pre-fabricated skyscrapers for the purpose of someday recycling them. There is no impetus on Earth at this point to do this, and no profit in it and no purpose for it at this time. But this methodology is a step toward the recyclable arcology that demonstrates that safety and stability concerns, structural integrity, and many design features can be accomplished with a building that consists of fairly small components. They did not stop at 30 stories because of some strength limitations and plans for higher buildings, using the same methodology, have been done.

An arcology that was sufficiently wide, and 30 or 40 or 50 or 60 stories tall would certainly be sufficient to house a city's population. BSB has never displayed for much wider cities and there is a good reason for that. Cities on our planet are divided into blocks, some square and others irregular, with roads between them, and it is a much more difficult thing to obtain planning approval to make these transit corridors disappear and be replaced with a single large imposing building. It certainly has been done, but BSB is building pre-fabricated buildings in part, perhaps a large part, because they are less expensive, and so building ones to match all or part of a city block is quite to be expected. The expansion in footprint is something that is not without issues, but they do not detract from the concept of a decomposable building of recyclable parts.

There is no reason to think that an alien civilization would build a city as an arcology, live in it for a century or two, and then move onto another one while taking the old one down and recycling the parts. There are many reasons why a different strategy would be adopted. The different strategy is to have a large arcology, part of which can be disassembled without greatly disrupting the life within the city, and then reassembling it out of renovated parts. Imaging a large arcology, one percent of which was under reconstruction at any time. This means that all of the city would be renovated every century. Of course there are questions of how to route traffic if there is constant changes of construction areas, how to re-route utilities and so on, but they do not seem insuperable, simply something a good computer could figure out.

There are other issues about transitioning to arcologies, but they will have to wait to another post.