mindlace

It has been far too long since I posted about microbes on this blog. As a brief recap, prokaryotic microbes – bacteria and archaea – outnumber (and outweigh) all other forms of life on this planet by a wide margin. I have long held that those microbes living within the earth – either lithospheric or sedimentary – constitute the largest proportion of these microbes.  I’ve had this opinion since I first wrote a letter disputing the notion that plants were the predominant form of life to the SAT board (at around 16) when they had the temerity to mark me wrong for saying bacteria instead of plants (bacteria and archaea was not an option).

For a long time, this has been in dispute by wiser minds than those assembling SAT tests, but for the most part the question has remained unresolved due to a lack of data. Prokaryotes are nearly invisible to most forms of microscopy, and so systemic reviews of frequency have had to wait for modern rapid gene sequencing and other techniques to arrive.

Research in the 21st August issue of Nature has shed some light on the matter. They were studying microbes that live in deep-sea sediments: microbes that live not on the ocean floor but underneath it, using a drilling vessel that had been repurposed from its original mission of finding more oil.

Data from this paper suggests that there are on the order of a million cells in every cubic centimeter of sediment 500m beneath the sea floor, or more than 50% of all microbial cells on earth. Additionally, the predominant form of these organisms is Archaea.

Now, I’ve already speculated that Archaea pre-dates bacteria and that the nucleus represents a primordial parasitism of an Archaea upon bacterial colonies (many bacteria, despite not being “multi-cellular”, live in aggregates that are, in fact, surrounded by another membrane.) I also believe in xenogenesis; that is, I believe life came to Earth from elsewhere, most likely Mars. Looking through my archives I don’t seem to have come out on this aspect publicly before, but my train of logic is simple:

1. Mars attained the temperatures and pressures needed, particularly surface temperatures around the triple point of water, when Earth was still a sterile molten cauldron. There’s abundant evidence that mars had surface water in its early history.
2. Our best fossil evidence suggests that microbial life arose on Earth practically as soon as the Earth was cool enough to allow liquid water to exist. While the measurement at these deep time distances is subject to wide margin of error, the margin of error is on the order of several million years, which is too short for most known abiotic processes to result in life.
3. Earth was under continual bombardment by fragments of Mars during this time.
4. Therefore, life came from Mars.

More specifically, I think Archaea came from Mars, and that bacteria are the “native’s” way of doing things.

Anyway, the fact that the pervasive form of life in subsea sediments are Archaea leads me to think that my hypotheses still holds.  There’s another issue of Nature that I haven’t quite gotten to yet that has more information about the biotic processes that allow life to continue down there, so watch this space for more microbial meanderings.

Our ancestors were using fire for cooking over a million years ago. This gave us an artifact to compensate for our mutant jaw muscles, which were not as strong as those of our fellow primates. Fire aided our masticatory ambitions as well as our gustatory needs by rendering previously inedible or toxic foods into a feast fit for a king.

With fire, we managed to squeak through the last ice age, and the climate that unfolded before us was like unto a Garden of Eden. Using fire to preserve food, martial game, fire clay and to render deep forest into the more open environment characteristic of the early Fertile Crescent, we began our journey through our species’ logistic growth curve.
Today, we are immersed in the products of fire. By using the products of fire to contain fire we developed cultural artifacts that are the product of temperatures and pressures previously unattainable by Earthly life. Metals, plastics, ceramics, glass; these material products pervade our modern world.

The materials we take from the living world rarely make it into our purview without being touched by fire. The cultural practices that allow a substantial minority of the Earth’s population to live largely free from parasites, malnutrition, and disease were born from fire. The only surcease our kind has known from the unrelenting labour of agriculture has come from ruthless exploitation of others’ lives or the power of fire to toil in our stead.

Fire is not a tender Muse, and our obeisance to her dictates have caused us to repeatedly burn all that we could find to burn. Our initial love affair with Fossil Oil arose from the rapid depletion of another over-exploited resource: Sperm Whales. While themselves the fourth choice, after having extinguished four other species in the North Atlantic, an oil extracted from their fat was the only oil for lanterns if you didn’t want to stoop to burning lard.

Everyone who lacked the mixed fortune of living near a gasworks was utterly dependent upon them for light. The first binary communications medium, the telegram, had dramatically shrunk the world; if you didn’t burn the midnight oil, the other guy would, and by the 1855 whale oil was going for the 2003 equivalent of over $1500 a barrel. The extraction of kerosene from fossil oil freed us from burning whale fat.

By the turn of the 20th century, internal combustion engines dramatically increased our appetite for oil; the newly developed spark engine delivered more horsepower but demanded a less viscous fuel than the rapeseed and peanut oils used in early diesel engines. By this time, ‘crude’ oil was already being distilled into different fractions, and a fraction that was slightly more viscous than kerosene was adopted for internal combustion engines.

Today transportation fuels dominate our consumption of oil, and in the largest markets it has surpassed the use of all other fossil fuels. We now sit perched somewhere near the peak of oil production, and the consequences of continued fossil fuel use will make the mere extermination of whales seem quaint.

Some hold out the hope that another energy supply will come to surpass oil, or more broadly combustion; Photovoltaic Solar, Nuclear, Wind, Hydroelectric and Geothermal sources have all been mooted. Using these sources will allow us to reduce our use of fossil fuels, particularly coal, as point sources. None can provide the portability, stability, and ease of use that has made oil the number one source of energy.

I apologize for the lack of posting; I’m frantically trying to get my projects done in time for the end of the semester. After that, I’ll have a good deal to say. In the meantime, you can get a snapshot by checking out my comment on Glen Barry’s post where he rightfully dismisses current biofuel production approaches. Unfortunately he has little to offer beyond the “keep the darkies from breeding and turn out the lights” theme that has been unwisely promulgated for the last thirty years by ecologists.

While I understand that extremely serious problems lead people to propose drastic solutions, every time I hear this argument it sounds like a sanctimonious relative hectoring people for their scandalous enjoyment (energy consumption) and filthy minds (reproduction).

When are people going to realize that telling people to stop fucking and raising children is a sure-fire way to be ignored, or worse, have your very real concerns dismissed?

And can we please knock off this more-eco-than-thou crap where we try to convince people they need to stop [insert energy-using-activity here]? The problem is not energy. You would think that ecologists, of all people, would realize that (practically) all power comes from the Sun, and that it’s going to keep pumping out billions of times more watts than we can possibly use for the next five billion years.

Yes, we currently utilize the Sun’s energy in the most catastrophically stupid manner imaginable, but the problem is the means, not the end. Drive around in your HumScalade all you want- just don’t fuel it with the bones of our ancestors. Sheesh.

I am disturbed that none of my professors have bothered to mention Rosalind Franklin’s contribution to “Watson and Crick’s” description. Who did more real science, the person who actually showed the structure or those who drew the obvious inferences?

Their description contains the following assertions: DNA is double stranded in antiparallel sequences of four nucleotides bonded to each other by hydrogen bonds, producing two complimentary base pairs that provide a basis for accurate replication. It is telling to note the mistake in assuming it is the pairing that provides the basis for accurate replication. In the same paper they deny the existence of RNA as a coding molecule: “it is probably impossible to build this structure with a ribose in the place of the deoxyribose”. Additionally they assert that there are two hydrogen bonds in each base pairing, further revealing their ignorance in chemistry. Anyone who had done basic denaturing experiments of the sort used in discovering the five purine and pyrimidine variants a full half-century before Watson & Crick’s paper would have seen that one of the pairings has a different energy.

The double helix portion is what Watson got from seeing Franklin’s innovative X-ray crystallography, and the rest of the paper could have been written by anyone who was able to add two and two together.

Luckily, Crick was available to do the tedious math and dash a paper to publication without even mentioning Franklin by name, only a quick falsehood asserting they hadn’t seen her work, which clearly showed the double helix, before publication.

Crick is so blinded by the power of simple math that, in 1961, he announces at his Nobel Prize speech: “In all probability, therefore, codons do not overlap”, implying 64 amino acids. If Crick had taken the time to read the most highly cited paper in publishing history, already a decade old by the time he took his trophy, and stooped to testing his theory using the protocol described therein, he would have saved himself the embarrassment.

So the woman who did the real work gets no recognition, while the man who lifted her research, made some basic and false inferences, established a false and misleading Dogma that gets taught to gullible graduate students to this day, and for this he gets a Nobel?

Thanks to our inestimable leader, the topic of making fuel from corn and other cellulose sources has received renewed airplay. Unfortunately it suffers from the same problem as every other time this has been discussed: Cellulose is an incredibly long-chain hydrocarbon that looks very little like the alkanes that predominate in fuel oil. For reference, existing gasoline consists of 7-11 carbon hydrocarbons. Because cellulose is almost all sugars, it has to be degraded almost down to nothing, aka ethanol. By the time you get to ethanol, you have not only broken the expensive 1,4 bond between individual sucrose molecules, you’ve also broken the 6 sugar beta-glucose subunits into three pieces. Needless to say, most of the energy in this process has gone to whatever organism or chemical operation you used to break it down that far.

This is why most traditional ethanol producing factories start from the corn kernels from which they can get free, or more cheaply linked, polysachharides. Which is fine, except for the fact that the ears represent a fraction of the mass of the corn plant, and the sugars represent a fraction of the mass of the ear. Additionally, it takes 125 days or so before a corn plant is ready to harvest, so even if you could theoretically get energy from the entire corn plant, you would get 79 * 10¹⁵ Btu out of the entire US corn harvest, which would fall short of our current energy demands by over 10 billion Btu/annum.

This problem persists with all macroatomic plants: the bits that are easy to degrade are a small fraction of the plant, and the rest is mostly cellulose.

If you switch to prokaryotes, however, the situation is much better. Take Anabaena, a filamentous bacteria that is incredibly common. In the right conditions, you can get exponential growth that covers the surface of your medium within a month. The bulk of anabaena consists of a polysaccharide mucilage, phospholipids (fat), and peptidoglycan. Peptidoglycan consists of polysaccharides connected with small proteins. We are awash in enzymes that will degrade these molecules; even our tears contain peptidoglycan degrading enzymes.

The phospholipids can be broken down into hydrocarbons (fatty acids) and glycerine fairly easily, using processes similar to those used to make soap. The peptidoglycans can be degraded with the aforementioned enzymes, and the (cheaply linked) polysachharides can be degraded any number of ways.

All this means more of Anabaena can be cheaply utilized to make gasoline-like substances. Even using batch methods, it can be harvested almost 12 times a year and will give you a much larger annual yield than the same acerage devoted to corn. Furthermore, I just picked Anabena because it is very common; there are literally millions of species of bacteria and other microorganisms out there, some of which most certainly are made up of molecules even more amenable to this form of transformation.

Furthermore, breeding bacteria is a process that takes months, not years, so we can selectively breed whatever strains we’re using for more optimal yield.

The general idea that living biomass is the most likely replacement for fossil biomass is dead on: the notion that it will come from plants or other macroorganisms is absurd.

I had the privilege of listening to Dr. Bhattacharya speak about the evolution of the chloroplast a few days ago. It inspired this notion in me: what if the nucleus was originally a parasitic archaeon that infected bacterial colonies?

One of the main tricks that he mentioned was the acquisition of a sugar transporter by the chloroplast/cyanelle/cyanobacteria within the eukaryotic cell; i.e. they changed to release some of the sugar that their photosynthesis generated into the cell.

The other point was that gene transfer seems to always go from the organelle to the nucleus; in at least one species of algae there’s no single chromosome left in the chloroplasts, just 14 single-gene plasmids.

There is an ongoing controversy over the origin of the nuclear pore complex, a remarkably complex “gate-keeper” that sits around holes in the nuclear membrane and controls what molecules can and can’t enter and leave the nucleus. It seems reasonable that a parasitic archaea would find controlling such things to be a selective advantage.

Basically the picture I’m painting is this: there are a lot of specialized bacteria, that do all sorts of interesting chemistry, often times in colonies that may even be membrane bound. By entering the colonies and releasing membrane translation proteins that cause the release of useful material (ATP or Sugar), you ensure your dinner; by translocating interesting genetic tricks from the organelles to the nucleus, you feed your grandchildren.

The way to falsify this prediction would be to do a systematic cross comparison of the cladistics of whatever dna-bearing organelles we can find, and see if there are similar patterns of heredity. If we were to find evidence that other organelles have ancestral prokaryotic cousins, it would be additional circumstantial evidence for this notion.

This reminds me that I need to look into why chromosomes are perpetually condensed in some species of algae, particularly the ones that don’t have histones. It would be nice, for example, to know how the heck they get transcription done.

Nature Mill makes an indoor composter. It makes me think that an indoor gas-generation device could work.

In a lovely paper, Geoffrey Grinstein and Ralph Linsker write about synchronous activity in scale-free networks. Scale-free (also known as “small world”) networks have the property that no node is greater than N hops from any other. These gents show that this topology can persist over a node-set of arbitrary size. This handily mitigates a concern of mine regarding the scalability of various Distributed Hash Table algorithms I’ve been pondering.

Another upshot is that I need to think of some kind of experimental protocol that would allow me to assess the topology of biofilms’ chemical networks.

In other topology news, the evolutionary tree is looking bushier every day.

I was reading last week’s science (it’s finals, I’m a little behind). I particularly enjoyed the discussion about Nature’s Rotary Electromotors – (PDF version). While I sort of knew this abstractly, the article really brought home to me that ATP Synthase is a mechanical motor; its rotation smooshes ADP + P (actually PO₄^3-) together and makes them into ATP.

It’s interesting, to me, that we essentially engage in the combustion of sugar to drive a rotary engine. Amusingly, the ATP synthase movies I linked to above remind me of the Wankel Engine. It also suggests that we’re going to have a rough time ever getting past light -> hydrocarbon -> mechanical energy through combustion -> electricity/chemical potential as the chain of work for artifacts that have to move about and carry their own energy supply.

Science had a number of interesing articles in the Dec 24th issue, but one in particular – Toward a Systems Approach to Understanding Plant Cell Walls (full pdf) stood out.

I’m interested in utilizing bacteria to replace other processes, and one relatively simple example is using bacteria that produce cellulose and other polysaccharides to make paper-like sheets or possibly wood or ceramic-like structural material.

Firstly, it illustrates that the cell wall is a pretty complex place, with four or five major polysaccharides operating in concert to make the wall. Additionally, extensive regulatory control is necessary to allow the cell to expand. This suggests to me that it may not be simple to use bacteria to create load-bearing structural materials.

However, paper is already put through a good deal of processing to simplify its structure, so it seems possible that bacteria could be used for this purpose. Evidently a number of bacteria, including e.coli, generate cellulose as an adhesion mechanism.

Given my utter lack of lab experience, for the moment it seems like it could be possible to culture large amounts of bacteria in a bioreactor and then deposit them in a sheet on a surface that would trigger adhesion. Possibly they would have to be bred to overproduce cellulose, but the general approach should be straightforward. Ideally, the inputs and outputs of this process would require substantially less net energy than raising trees for 20 years and then chopping them down.

One thing I need to constantly be on the lookout for, as I begin lab work, is ways to simplify the cultivation techniques. Eventually it should be possible to have a clay pot bioreactor tended by hand or driven by a small motor, or something to that effect. The only way biologically based artifacts are going to make a difference to the worlds poor is if they can participate in the production process.