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Universal Scholar | December 11, 2017

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The Wrong Stuff

once long ago, she and i dreamed together
of someday touching the stars
out there.
and the Life that dwelt–
but it was alas, the impossible dream
for carbon/water based Life
from a little planet–
like us.


When I was much younger, I was an avid science-fiction fan. I particularly enjoyed stories about space exploration. In these stories Earthlings would discover and colonize earth-like planets. In most stories the colonists would eat native plants and animals. In the more sophisticated stories the local flora/fauna would prove indigestible or toxic, and the colonists would farm Earth-derived plants and animals. In many of the more interesting stories the Earthlings would eventually encounter intelligent alien life forms and interact with them in various ways that ranged somewhere between total war and peaceful cooperation. The local microbial life was generally ignored or treated as harmless due to ‘differences in physiology and biochemistry’. Occasional problems involving local pathogens were resolved by a convenient pill. In the end things would invariably turn out well for the Earthlings. They would triumph in war or turn a profit in peace. They would increase in numbers and influence as they spread throughout the Galaxy. They would leave their mark on the Galaxy — forever.

Unfortunately, in real life, our native Earth bacteria and alien ‘pseudo-bacteria’ would pose an insurmountable problem to planetary colonization or even face to face inter-species socializing. Our bacteria would eat alien carbon/water based life forms alive and their pseudo-bacteria would do the same to us. Any face to face meeting would be mutually suicidal. We dare not visit a world where carbon/water based life already exists and such alien life dares not visit us. In one sense this cloud has a silver lining. We never need fear invasion by extraterrestrials bent on stealing our planet out from under us. We can also discount stories about visits here by little green men who travel in flying saucers. Such a visit would have resulted in the death of the visitors and a raging, uncontrollable pandemic here on Earth. Since the latter has *not* occurred, I can say with confidence that no little green men in flying saucers have ever visited Earth.

Our kind of life — carbon/water based life — is an evolutionary dead end, restricted forever either to the planet where it originated or additionally to cold dead rocks in outer space where native life never arose. Carbon/water based life is just ‘The Wrong Stuff’. To understand why this is so we have only to look briefly at the properties of the bacteria that exist here on Earth and glance at the evolutionary biology that defines us. Then extrapolate just a wee bit.


Meet The Bacteria

What is the composition of life on our little planet Earth? You might find the answer surprising. Suppose we had a giant balance scale, large enough to weigh all the life on our planet. If we put all the animals and plants (including ourselves, birds, weeds insects, worms, yeast, fish, whales, trees and kelp) on one pan and all the bacteria and archaea (which I will lump together here and call ‘bacteria’) on the other, the bacteria pan would weigh out heavier! Most Life on our planet by weight is bacterial! If we look at how many different kinds of living things there are, again the bacteria win. There are more kinds of bacteria than kinds of all other living things counted together! In a sense bacteria own the planet and the other kinds of life here, including ourselves, exist as as their guests? Or perhaps as mere squatters filling the cracks?

As you would expect from their numbers, bacteria are everywhere — in the air we breathe, in the earth we walk on, covering the objects we handle, in the foods we eat and in the water we drink, on our skin, in our respiratory tract and throughout our digestive system, where some of them actually help us process the foods we eat. In fact our gut is the home for hundreds of bacterial species! We carry around with us, in and on our bodies, about ten bacteria for every cell of our bodies! The feces we produce are about sixty percent bacteria by weight — mostly consisting of E coli bacteria. When we test water for fecal contamination we do so by testing for the presence of E coli.

Bacteria are social, they can communicate and co-operate in various ways. For example, there is a process called quorum sensing that permits a bacterium to measure if there are many other bacteria of it’s kind nearby. The result of such a measurement can be a shift in that bacterium’s metabolism, expressed as the pattern of genes currently active. Bacteria of different kinds can co-operate in forming protective structures called biofilms (aka bacterial slime). The bacteria within a biofilm can interact in various ways. The waste produced by one kind of bacterium, can be a nutrient for another. Many kinds of bacteria are motile and can swim along a concentration gradient within the biofilm toward a region richer in a metabolite they need. In a biofilm containing a mixture of bacterial species this can result in the generation of ‘islands’ populated by bacteria of different kinds that support each other metabolically. The dental plaques that promote tooth decay are a form of biofilm that contains and protects many kinds of co-operating bacteria. Bacteria may also compete within a biofilm as they do elsewhere for living space. Some kinds of bacteria produce toxins that incapacitate other kinds of bacteria. We humans collect certain of these bacterial toxins and use them as medicines. We call them ‘antibiotics’.

Bacteria are the prey of a group of viruses called bacteriophage that inject their DNA into a bacterial cell. The virus DNA directs the use of raw materials and machinery in the bacterial cell to synthesize and ultimately release more viruses. If allowed to proceed, this process would prove fatal for the infected bacterium. Some kinds of bacteria have evolved defenses that not only permit them to detect and destroy a novel injected viral DNA but also to recognize viral DNAs they had been exposed to and survived in the past! We humans use parts of these defense systems — bacterial ‘restriction enzymes’ and ‘CRISPR libraries’ — as tools in bio-medical research.

Bacteria fill niches in the environment that one would be hard pressed to recognize as possible niches for Life! There are bacteria that use rather esoteric inorganic chemical reactions involving sulfur or iron as their sole energy source; bacteria that live and are comfortable at temperatures around that of boiling water; bacteria that can live and metabolize, albeit slowly, at temperatures around zero degrees Fahrenheit and bacteria that live in the dark, high-pressure environment of the deep sea floor. There are bacteria that require oxygen, much as we do; bacteria that will use oxygen if available, but can get along quite well without it and bacteria that avoid oxygen completely because it is toxic for them.  Then, there is the tiny percentage of bacteria that have evolved tools that help them evade our immune systems and consequently permit them to parasitize us. We call such bacteria ‘patho-gens’.

If you pick some organic compound ‘out of a hat’ chances are you can find at least one kind of bacterium that can metabolize or otherwise chemically modify it. Bacteria are wonderful organic chemists, something we humans realize and use to our advantage. There are various industrial processes that make use of the biosynthetic and biodegradative abilities of bacteria. Bacteria in the wild are great recyclers. In the woods, forests and swamps bacteria participate in the recycling of everything from animal carcasses and droppings to dead trees and plants. There are bacteria that ‘lock up’ free elements as chemical compounds and others that ‘free up’ elements existing in compounds. At least one species of bacteria is used by us humans to clean up petroleum spills — the bacteria eat the petroleum and use it as a source of energy and raw materials. These particular ‘jack-of-all-trades’ bacteria (aka ‘non-demanding heterotrophes’) will also gobble up gasoline, jet fuel and other hydrocarbons!

There are many different kinds of jack-of-all-trades bacteria and they are widely distributed. Each can metabolize or otherwise modify a range of organic molecules. A mixed cultureof several kinds of these bacteria can function as an opportunistic team that can gobble up the constituents of many mixtures of organic compounds. Jack-of-all-trades bacteria normally live by decomposing and metabolizing the detritus of life. Garbage dumps are a paradise for such bacteria. They are normally not considered pathogens for people with intact immune systems.

Bacteria existed long before we did and they contributed to our ancestry. In very remote times when cells like ours – eukaryotic cells with a well defined nucleus – first arose, one of their cytoplasmic constituents was a kind of bacterium that apparently wandered into the proto-eukaryotic cell and found a home there. That bacterium eventually evolved into the mitochondrion. Eukaryotic cells use mitochondria to extract the energy in food molecules and put it in a form the cells can use. Another type of ‘guest’ bacterium evolved into the chloroplasts that make green plants green and lets them use sunlight as an energy source. A byproduct of this process, oxygen, makes our kind of multicellular Life possible.


A Modicum of Evolutionary Biology

Because of Darwinian Evolution, all Life on Earth is related; we are all members of the same huge family tree. We are all carbon based Life that uses water as a universal solvent. Each of our cells is bounded by a double layer lipid
membrane through which it communicates with its local environment. Early in the course of our evolution, natural selection settled on certain molecules as the building blocks of Life.

Thus planet-wide, our genes consist of essentially the same four nucleotides linked by their phosphate groups to form the DNA poly-nucleotide chains that encode our genetic information. Some of this information is used to determine the synthesis of proteins via an indirect process involving RNA templates called ‘Messenger RNA’.

Proteins in turn, are composed of sequences of amino acids linked into polypeptide chains by peptide bonds. There are many different amino acids, but Life here on Earth only uses a pool of about twenty of them out of which all our
proteins are made. We humans require about half of these amino acids as part of our diet – our bodies can’t synthesize them. Proteins are used in our bodies as both structural materials and as the exquisitely specific catalysts called enzymes that implement our molecular biology. In addition to nucleotides and amino acids there is a third class of molecules that shows up everywhere — carbohydrates.

Green plants store the energy they get from sunlight by using it to make glucose out of carbon dioxide and water. They store the glucose compactly as the polysaccharide, starch. Later, when they need the energy, they reverse the process and oxidize some glucose molecules into carbon dioxide, water and *energy* in a form they can use for biosyntheses and other processes. The ‘carbs’ we humans rely on for energy are forms of the sugars and starches produced and stored by green plants. Poly-saccharides, often in combination with other molecules are also used as structural materials. The wood of green plants, the peptidoglycan of bacterial cell walls and the chitin of insect exoskeletons are essentially elaborate co-polymers of glucose, amino acids and other organic molecules.


Now Down To The Nitty-Gritty

I am *not* the first person or even among the first people to recognize the danger of contamination of our Earth by alien bacteria-like life forms acquired in the course of exploring an alien planet. B. Di Gregorio and ‘The International Committee Against Mars Sample Return’ ( called attention to the danger and the mechanism that would implement it almost twenty years ago (ca 2000 CE). What I do here is describe the danger in a way non-biologists can easily appreciate. I also briefly explore a few perhaps non-obvious societal implications of the inter-planetary contamination problem.

Multicellular eukaryotes like ourselves have always had the problem of avoiding becoming food for bacteria. We are a rich source of energy yielding molecules and building blocks that bacteria can use. We rely on system wide defenses to keep bacteria from eating us. Fish, insects, birds, reptiles, mammals and even plants, all have immune systems that protect them from becoming food for bacteria.

As a result of Darwinian Evolution, all immune systems have tools that can recognize patterns in polypeptides and polysaccharides that are characteristic of bacteria. They also have enzymes and other tools that can co-operate to degrade bacterial polypeptides and poly-saccharides, a process that is fatal for bacteria and destructive for their products. These immune functions comprise the primitive ‘Innate Immune System’. Mammals such as ourselves have an additional ‘Adaptive Immune System’ that sits atop of and co-operates with the Innate System. This Adaptive Immune System can *learn* to recognize novel polypeptide and polysaccharide based structures associated with bacteria and also store this information in ways available for future use. Vaccination, for example, is a medical procedure that protects us against infections by taking advantage of the ability of the Adaptive Immune System to learn and store information. Immune systems are the reason jack-of-all-trades bacteria are normally not pathogens for us. These bacteria have not evolved special means that bypass or trick our immune systems. So our immune systems are usually able to quietly destroy them whenever they turn up somewhere where they are not welcome.

There is no reason to assume that the particular building blocks of carbon/water based Life that are universal here on Earth are the only building blocks possible for carbon/water based Life. Given time, and sources of energy, the fecundity of carbon chemistry would be expected to generate a wide variety of organic compounds in the voluminous, watery, abiotic, collection of micro-environments that would characterize a young earth-like planet. And some of these organic compounds may well be potential building blocks of Life under the right circumstances. Assuming that carbon/water based life exists elsewhere in the Universe, we would expect that the building blocks used in any particular instance of Life would reflect physical conditions local to the planet where that Life evolved. We make compatible assumptions about the evolution of Life here on Earth. We search by means of laboratory experiments that model various hypothetical pre-biotic Earth environments to see which ones generate, among other things, *our* building blocks of Life.

It seems reasonable to assume that on an alien planet, where carbon/water based Life evolved, bacteria-like entities would have evolved early and would, as bacteria have here on Earth, provide part of the base for the possible evolution of other forms. Moreover, extrapolating from the bacterial ecology we find here on Earth, we would expect the ecology of the pseudo-bacteria of other planets to be equally rich and space filling. On any planet containing carbon/water based Life the local pseudo-bacteria would be everywhere and among their numbers we would expect to find that, for any specific organic molecule we happen to choose, there would very likely exist some pseudo-bacterium or other that could metabolize or modify it. In short, we should expect to find jack-of-all-trades pseudo-bacteria that as a class are as adept at organic chemistry as the ecologically comparable class of Earth bacteria.

This is the reason we dare not expose ourselves or our planet to the pseudo-bacteria of an alien carbon/water based world where the building blocks of Life are different from our own. Our immune systems, sophisticated as they are, evolved by a selection process that made them specific for structures composed of thebuilding blocks local to our Earth namely polypeptides and polysaccharides; structures composed of the twenty amino acids or derived from glucose and its stereo-isomers. Our immune systems have evolved over the eons and contain enzymes and other tools that recognize and can deal with elaborate variants of structures composed of these basic building blocks. But there was no selection pressure to evolve tools to deal with hypothetical biological structures that do not exist here on Earth!

Consequently, our immune systems would be ineffective against organisms composed of non-polypeptide, non-poly-saccharide based structures. They would be ineffective against organisms composed of building blocks other than the twenty amino acids and stereo-isomers of glucose.

Notice that the limitations of immune function just considered are *not* reducible to the type of immune learning that occurs when a mammalian immune system encounters a novel *local* pathogen composed of the *building blocks universal here on Earth*. Rather it would be a case where tools that evolved in response to selection pressures provided by structures composed of *one set of building blocks* are now confronted by structures composed of a *different set of building blocks*. An apt analogy would be the futility of trying to compile computer source code written in COBOL by feeding it to a C compiler. Or talking English at someone who only understands Klingon. It just plain won’t work!

What would happen to an alien visitor to Earth whose building blocks were different from ours? Assuming the logic of the alien’s immune system was comparable to our own, its immune system would notice something was wrong when it detected ‘help signals’ emitted by or macro-molecules released by the cells being damaged by invading Earth bacteria. But its immune system would lack the specific pattern recognition tools and pseudo-enzymes needed to detect, classify and destroy the invading Earth bacteria or their products. If the alien immune system possessed pseudo-macrophages they might even engulf some Earth bacteria, but to no avail. They would lack the specific pseudo-enzymes and other tools necessary to dismantle and destroy the Earth bacteria or their products.

There would be a minor evolutionary triumph of sorts for our dying alien visitor in that it would have little to fear from our specialized pathogenic bacteria — the bacteria that normally make *us* sick. These bacteria have tools that assist them in invading specific tissues and evading our immune system in the course of doing this. They are also nutritionally ‘demanding’. They require and expect to find certain specific organic compounds the alien almost certainly will lack. Moreover, our pathogens usually do not have the general purpose tools necessary to perceive the alien’s building blocks as mere organic compounds waiting to be degraded and metabolized. The dying alien need not fear our pathogens.

It is the ordinary jack-of-all-trades bacteria that are invading and which will eventually kill the alien. Mixed cultures of these bacteria, possibly in the form of biofilms, would colonize the alien and simply eat it alive. They would perceive the alien as a water-gel of organic compounds, perhaps a bit more varied than their usual fare. Some of the waste products and other residue of the currently metabolically active bacteria might prove useful to other, initially quiescent bacteria, in the mixed culture and they too would become active and join the party. During the early stages of these activities, while it was still mobile, the alien could be accurately described as a movable feast for the bacteria.

Needless to say, the fate suffered by an alien who comes here would also be suffered by any of us, were we to visit the alien’s home world. The alien pseudo-bacteria would *not* have the peptidoglycan cell wall that our immune system expects and can deal with. Consequently, the Complement System, if invoked, would *not* be effective in breaching it. The catabolic pseudo-enzymes emitted by the alien pseudo-bacteria would *not* be composed of amino acids; they would be polymers of something else. Consequently, the pattern recognition and antigen processing mechanisms of our immune system would *not* be effective in detecting and neutralizing them. Alien pseudo-proteins would *not* be suitable substrates for enzymes that normally process polypeptides into epitopes for antigen presentation to other immune system cells. Consequently, there could *not* be antigen presentation and therefore *no* specific immune response could occur.

Well, you get the picture. Our immune system would *not* protect us from these alien pseudo-bacteria. In fact it could be argued that our immune system would actually *facilitate* the early stages of infection by pseudo-bacteria. For, having kept certain areas of our bodies free of local Earth bacteria, our immune system would thereby allow infection by pseudo-bacteria to initiate there without competition from the otherwise ubiquitous Earth bacteria! Thus in an environment containing pseudo-bacteria, even a tiny bloody scratch or an insect bite would amount to ‘a kiss of death.’

In all likelihood, the pseudo-bacteria and their pseudo-tools would be completely invisible to an Earthling’s immune system, since at its most fundamental level our immune systems ‘see’ in terms of specific receptor target complementations that would be lacking here. Thus only the damage wrought by the invaders should be visible to it. That immune system therefore, would probably devote its remaining life to cleaning up the cellular and molecular debris left by the pseudo-bacteria. This would be debris composed of structures of the *local Earth building blocks* possibly haptenized by small pseudo-bacterial molecules. The jack-of-all-trades pseudo-bacteria that comprise the invading mixed cultures — possibly in the form of pseudo-biofilms — would probably perceive us in the same terms that Earth bacteria would perceive aliens; as large water-gels of organic molecules. Each of the diverse kinds of pseudo-bacteria in the mix would grab whatever it could use. For these pseudo-bacteria it would be a happy time; a feast in fact. There would be energy and raw materials for all! For an Earthling though, it would (alas) be the end of the road.

But hark! We need not travel to an alien’s home planet to be served up as a feast! Remember the dying/dead alien visitor to Earth we conjectured earlier? It would be expected to have on and in its body a rich collection of pseudo-bacteria from its home world. And among these would be jack-of-all-trades pseudo-bacteria that would delight in feasting upon us! Thus a subset of the pseudo-bacteria carried by the now defunct alien visitor would infest native Earth multicellular eukaryotes — indiscriminately. We are after all, all composed of the same kinds of (yummy) organic molecules. It would mark the beginning of the end for all of us! Humans and their ancient enemies the rat, the cockroach and the bedbug, would be infested together and eventually, perish together — along with cod-fish, cows, dogs, dung-beetles, llamas, ants, whales, sparrows, squid, butterflies, frogs, pussy-cats and elephants. Green plants would of course, suffer a similar fate.

For we are all distant cousins, and we would, perhaps, finally cluster together and mourn together beneath our now ragged banner:

‘Polypeptides and Polysaccharides –- Forever!’



1) Thus, we can never visit any place off planet that is really interesting. And other intelligent carbon/water based life-forms can never visit us. We would be like matter and anti-matter. We would begin to annihilate each other on contact. We could only communicate electronically, at safe distances.

2) In the absence of immune systems capable of countering them, an influx of alien jack-of-all-trades bacteria-like entities would clear a planet of its multicellular Life. The bacteria-like entities would drive ALL the native multicellular Life to extinction!

3) Carbon/water based life-forms are an evolutionary dead end! They are restricted to their little planets until their suns finally go BOOM, as ours will do in a few billion years, putting an end to our solar system, our planet, our species and everything it has accomplished over the course of its existence! It would be as if we had never existed!

4) But there may be a way out for us! The current generation of experimental neurophysiologists is beginning to analyze the mammalian brain in a promisingly competent manner. If this continues, we can expect to understand enough of the molecular biology and topology of the mammalian brain in sixty to one hundred years to allow theoreticians to abstract its logical structure from the experimental data. This in turn would eventually permit the construction of truly intelligent machines – Androids, capable of learning as we do and of appreciating and practicing science and the arts. Androids, potentially capable of greater than what we currently call ‘human intelligence’!

The crucial question under this scenario would be: how would we perceive such beings? Would we see them as potential slaves? Or servants? as militarily or technologically advanced cultures have viewed *other peoples* in the past? If we follow this route the consequences would be tragic, as they have been in the past. Or would we be enlightened enough by then to see androids as progeny. As *our children*, whose synthetic brains preserve modes of perception, emotion and thought that we recognize as human because we modeled them after idealized versions of ourselves?

In this sense we would be able to travel to any place in the Universe that we had the technology to get to. Our synthetic progeny would not suffer the limitations of carbon/water based Life. They could explore the Universe and occasionally return home and show the ‘stay at homes’ what they found — out there. As their progenitors we would ultimately survive through them.

Well, at least its a thought. Can *YOU* think of a better alternative? I can not.

J. G. Kurjian
in memoriam
(5/13 – 12/15)