Monday, January 27, 2020

Chromosome Genetics

Knowledge abounds here on Earth about the number of chromosomes humans have and how gender is determined by whether a fertilized egg cell has an XY or XX chromosome pair. It's less well known that cell division includes the opening up of all nuclear DNA pairs and the splitting of them into two batches before replication. Even less well known is how hard it is, given today's technology, to separate chromosomes so they can be accessed individually.

It is not exactly clear if there is any other way of harnessing the protein synthesis control capabilities of DNA so that alien cells might have a different way of doing it. Nor even is it known if there are alternatives to DNA to carry genetic information. Genetics in this area is like exo-planetary studies before any exo-planets were discovered. Everything is speculation.

These two questions are somewhat independent. If an alien planet had non-DNA genomes, that still does not mean that they would not have all the genetic information divided up into chromosomes. The alternatives are to have more than one nucleus in the cell, with perhaps one chromosome in each, or to have one nucleus with only one chromosome pair having all the DNA or its equivalent. Why did Earth evolve multiple chromosomes, or rather, why don't all species have just one large circular chromosome as do many single-celled organisms? What is the evolutionary advantage and would it be universal, meaning on other planets as well?

Among contemporary bacteria, there are some with one, two or more circular chromosomes, some with linear chromosomes, and some with a combination. After billions of years of evolution, the competition for a chromosomal shape has not been won by any arrangement, so for bacteria and other prokaryotes at least, there must be little evolutionary advantage between them. This is not true for eukaryotes, multi-cellular organisms, which all seem to have linear chromosomes. Most eukaryotes also have some legacy circular chromosome material, located in the mitochondria or elsewhere, which reproduce independently of the nuclear DNA during cell division.

One advantage is obvious. To have genetic information for many different types of cells, as well as the signaling information for organizing them, there must be much more information, and a circular chromosome or a single linear chromosome with all this information would simply be too large to fit into the nucleus, or for the meiotic proteins to handle. Having everything in large numbers of diverse mitochondria also seems evolutionarily difficult, for the organization of cell replication. So, using DNA or anything else, it appears likely that alien species will have multiple linear chromosomes.

Alien geneticists may run into the same problem that Earth geneticists have: separating chromosomes is difficult. The processes within the cell are quite complex, and there is not enough information on them to allow them to be replicated or imitated in a genetics lab. Neither have there been any simple mechanical solutions to separating chromosomes. Perhaps we are missing the right discovery. By the time asymptotic technology arrives in the genetics area, however, this problem will have been solved.

It's not clear that the ordering of advances and inventions in the genetics grand transformation will make much difference in how an alien civilization will develop. The end result would be the same. But chromosome separation would allow some cost-savings in making genetic changes to organisms, or to the creation of synthetic organisms. If this cost-savings is large, it would emphasize the possibility of having genetically modified or created organisms throughout the civilization.

All we can do now is map the genome of humans and other organisms, and use that information for diagnoses, or in plant and animal breeding. There is some work being done on inserting novel genes into existing plant and animal genomes, but it is very slow. If it were possible to isolate chromosomes rapidly and inexpensively, this would speed up the process. It would also make the process of genetic modification more certain, as a laboratory could simply work with one chromosome and modify it, without having to worry if the modification methodology would accidentally make a modification in another chromosome, with a similar stretch of DNA.

One interesting question to ask is how would an advanced alien society prepare the genetics of their successive generations of their population. Suppose there is an inexpensive way to separate chromosomes. Then, the alien society could simply decide to choose the best set of chromosomes from the copies available. If there is some optimal set, then all the aliens in later generations would be like clones. Alternatively, if the selection was out of the set of a pair of parents (assuming two genders), a wide variety of individuals would remain, but there would be a trend toward more healthy individuals with better capabilities.

Similarly, if there were pairs of parents with some genetic deficiency in one chromosome, specifically in one of the parents, then that chromosome could be eliminated in the resulting next-generation individual. This would result in the gradual elimination of genetic diseases and other problems, although errors in replication remain possible and there would always be a risk of some new mutation arising.

There are many syndromes which arise because of the improper copying of whole chromosomes, meaning extra copies, and with chromosome separation technology, these would be reduced or eliminated as well. Broken chromosomes could be sorted out as well, and mutations arising from copying errors would be detectable and removable. Reading the genome would be less computationally intensive and less prone to mistakes, if each chromosome was read individually. The current Earth method of batching all the chromosomes together and then sorting them out after all the fragments have been read is clearly something that can be improved on.

The technology to separate chromosomes does not seem to be on the horizon, meaning the old methods would be used here for a decade or so. Microbiological investigation into how to make a cell nucleus separate and then how to create microtubules to reach into the mixture and connect to individual chromosomes needs to be done. Once it is well understood how nature accomplishes this task, it would be more reasonable to expect that genetics laboratories can come up with some combination of biological and physical equipment to accomplish chromosome separation. After this, we might see genetics jump forward very fast in potential applications, and this will give us a much clearer idea of what an advanced alien society might be doing with their own technology in this area.

Friday, January 17, 2020

Mineral Planets

Let's use the term mineral planet for planets that an alien species could turn into a sustainable habitat. These are a far cry from an origin planet, which is one which could give birth to life by evolving its own first cells. It is a far cry from a seedable planet, which is one which could not evolve its own starting cells, but which could take a seed of some sort of cells and have them multiply and eventually evolve into something interesting, like an alien civilization. Instead, a mineral planet is one where an advanced civilization could establish mines and habitats, on the surface or below it, and thereby produce enough resources, energy and minerals, to sustain an alien colony without any continuing support from the home planet. It has to persist for a long period. 

There may be very few origin planets in the galaxy, and somewhat more seedable planets, and maybe a huge number of mineral planets. One implication of such a lopsided ratio would be that mineral planets can be stepping stones for an alien civilization to cross the galaxy. Note that some or all alien civilizations may adopt the goal of seeding as many seedable planets as they can, following a philosophy that life is its own goal, and that just like planet-bound species try to disperse as much as they can, alien civilizations try to spread life as much as they can. Traveling 300 light years from a civilization's origin planet to the nearest seedable planet might be simply too much to do, and so finding a network of mineral planets in the general direction of that seedable planet would allow them to gradually work their way over to it, and when close enough, to accomplish the seeding effort with more payload and duration in orbit that they could have if they had to travel 300 light years.

Reliability might play a role here. If a speed of 1% of the speed of light is used as a guess of the maximum speed the civilization might attain with its colony ships, this means 1000 years of reliability is necessary to go to the nearest mineral planet, but 30000 years would be necessary for the closest seedable planet. If the probability of enough equipment lasting 1000 years can get raised to 98%, a risk the civilization might be willing to take, the same equipment has a probability of the same quorum still working after 30000 years of travel of only 55%.

Monitoring a seedable planet is also easier from 10 light years away than 300. It might be that seeding a planet is necessarily a very chancy situation, and multiple visits are the only way to accomplish it and verify that it has been accomplished in such a way that a billion years of evolution or two can follow without total extinction. Maybe seeding can only be handled by landing a small colony on the planet, and staying there for a long period. This could also be accommodated better from a nearby solar system than from a distant one.

Is there anything which can be credibly said about the prevalence of mineral planets? The formation of stars seems to leave a disk of matter revolving around it, which can turn into planets. This is a matter of the disposition of angular momentum, and how hard it is to collect it all in a central body. Everywhere we look we see planets, and our ability to find them is not so great right now, so there are probably many more per cubic light year than we have discovered in our locality. If there are several planets on the average per star, how likely is it that at least one of them is a mineral planet?

To be a mineral planet, the planet has to be mineable and habitable. Planets too close to the star are too hot on the surface to establish a colony, and the temperature below the surface would be higher than the average temperature at any latitude. The orientation of the planet would indicate the spread of temperatures over the planet, from pole to equator, and indicate if there was any latitude above which a colony ship could land and stay without thermal damage. Phase-locked planets provide a different criteria, but if the north pole of a non-rotating planet is designated as the closest-to-star point, then again, there may a latitude beyond which the ship could land.

Too much atmosphere would interfere with colonization, and planets might be excluded on this basis. Since smaller planets cannot long hold onto the atmospheres they have at formation, size is an indicator of this problem. The maximum size depends on the distance from the star, as it is easier to hold onto an atmosphere if the planet is far from the star and the atmosphere is very cold. Cold gases evaporate much more slowly.

Another question to be asked is the radiation level. If the star is a very active one, the colony ship would not even be able to come in close to it, unless some sort of shielding was build into the hull. Perhaps advanced engineering could figure out a way to get a mine dug, and alien colonists down into the mine without receiving too much radiation. Once under the surface, all the radiation is absorbed before reaching them. This is an interesting project to be considered.

With all these factors eliminating candidates, how much might be left? Our surveys of exo-planets are too limiting to calculate this number, but it might be that 90% are no good, meaning one in three stars, of middle class, has a candidate. There is more to being a mineral planet that simply being mineable with a surface not too lethal. There has to be the right mix of minerals.

An alien body has certain needs for elements, and alien technology has a different set of requirements for elements. Together they comprise the shopping list of elements, or rather minerals from which the needed minerals can be extracted. Some small molecules might also be extracted, principally water and carbon dioxide, maybe some others. The distribution of elements on a planet is a result of the original composition of the gas cloud, which comes from the effect of nearby supernovas in the cloud's history. Then there is the condensation question and the diffusion question, with minerals forming as elements and condensing into dust, and then being filtered by the solar wind and light output from the star over millions of years. After that, when the planet forms, geology plays a role in determining which minerals are at the surface.

The only planet we have any experience with is Earth, and it can provide us with a model problem. Suppose there was a planet in a state just like modern Earth but without any atmosphere, without any fossil fuels, no life, and of course no people, meaning no mining. Could an alien colony ship find the right minerals, in accessible form, so that it could produce a sustainable colony here? Perhaps U-235 is the key. We can mine uranium ore, refine it, enrich it, build a reactor, and extract more energy than was needed to construct the reactor and keep it fueled. Alien reactors should be even more efficient in the use of fissionable and fertile fuel than ours are, as we have had only a few decades of experience with fission power. Perhaps the guess of one solar system in three having a mineral planet is not too far from the truth.