Alternative biochemistry

Despite its diversity, all life on Earth displays a remarkable similarity at biochemical level: all the main molecules used in organic processes are built on skeletons of carbon and hydrogen; ions and molecules are dissolved and trasported in water-based fluids; most organism breathe oxygen to release energy from food.

It's still a matter of debate if organic processes can be supported by different biochemical systems. If they can, though, and therefore much wider conditions are suitable to life, potential life-bearing planets become far more common, and their flora and fauna could be much more alien.

Non-carbon basis of biochemistry
Carbon is perhaps the most important element in our chemical makeup, to the point that organic molecules are defined by the presence of carbon atoms in their structure. It has a unique capacity of bonding with many different kinds of atoms, and forming long, stable polymeric chains.

The element most similar to carbon, being right under in the periodic table, is silicon (Si). It has similar bonding property, but less versatility, and, being heavier, has more difficulty forming double bonds. Silicon's closest analogue to hydrocarbons, silanes (SinH2n+2), are highly reactive in water and don't form long chains, while Moreover, most of the complex molecules found in space contain carbon but lack silicon. Also, while ten times less abundant than carbon in the cosmos, it's a thousand times more abundant in Earth's crust, and yet terran life never integrated it in its biochemical processes. Finally, the product of its oxidation, silicon dioxide (SiO2), is a non-soluble solid until more than 1600°C, whereas carbon dioxide is a gas.

On the other hand, silicon dioxide would not be produced at all if silicon life breathed in a reducing atmosphere, containing gases such as hydrogen (H2), hydrogen sulphide (H2S), carbon monoxide (CO) or nitrogen.

Silicon's best chance to form complex, stable molecules is to combine with oxygen in alternate chains (...Si-O-Si-O-Si...), creating silicones, stable even in the presence of oxygen and water. Just under 300-350°C, silicones can form long polymeric structures where carbon cannot, and some silicon-carbon combination last until 500°C: therefore, a silicon biochemistry might outcompete carbon in a high-temperature world.

Similar results can be obtained with other carbon-group elements: namely, germanium (Ge), tin (Sn) and lead (Pb). The Xenology chapters linked at the bottom of the page gives some examples of germanium-, tin- and lead-based organic polymers.

Boron (B) is another possibility: it's even more versatile than carbon, and while its simplest compunds, boranes (BxHy), are extremely reactive in the presence of oxygen, they'd be more stable in a reducing atmosphere. A combination of alternating boron and nitrogen closely resembles carbon, and can form analogues of hydrocarbons such as ethane (C2H6), methane (CH4) and benzene (C6H6).

Less convincing substitutes for carbon can be metal oxides based on magnesium (Mg), aluminium (Al), iron (Fe) or titanium (Ti), which can form stable nanotubes and diamond-like crystals at high temperatures. Both phosphorus (P) and sulfur (S) are able to form long linear chains, but not branched ones, and they need a reducing atmosphere to be stable. Nitrogen (N) can also form long chains in solvents like ammonia (NH3) or hydrogen cyanide (HCN); it always tends to revert to a simple biatomic form, but it can be more stable when combined with carbon, phosphorus, boron or sulfur.

Non-water solvents
It's probably a safe bet to say that life will need a liquid to transport ions and molecules around the body. For terran life, this liquid (called a solvent) is always water. Water does have a number of advantages over other possible solvents:
 * Water has a large liquidity range, which means that can be found in a liquid form in many different conditions.
 * Water is extremely common in the universe (in fact, it's the most common chemical compound).
 * Ice is less dense than liquid water. That allows ice to float and insulate the water below, preventing a whole ocean to freeze.
 * Water is a polar solvent: that allows it to carry dissolved salts. Moreover, it can dissolve proteins, sugars, DNA and oxygen.
 * Water is transparent to visible light, permitting the development of submarine photosynthetical ecologies.
 * Water has a high specific heat and heat of vaporization, which allows it to absorb large quantities of heat, therefore regulating temperature differences.
 * Water is amphoteric: it can work both as an acid and as a base, and is therefore able to participate in a large array of reactions, as a solvent, a reactant or a product.

Besides being abundant, a good solvent should at least have a wide liquidity range and dissolve many different compounds, and preferably it should have a high heat of fusion and vaporization (which would make it more stable when temperature changes), a high dielectric constant (making it a good insulant) and a low viscosity (so that it opposes little resistance to movement). It would likely be a thalassogen, that is, a substance that forms a planet's oceans.

The most likely alternative to water is ammonia (NH3), especially at low temperatures where water is solid. It's able to dissolve most organic compounds, lightweight metals, iodine, sulfur, selenium and phosphorous. It's not as good an insulant as water and it's easy to boil, but it's harder to freeze (it has a high heat of fusion) and it's much less viscous. Its liquidity range is not as wide at 1 atm pressure (-78°C to -33°C), but at a pressure of 60 atm (life on Venus) it boils at 98°C, making it wider than water's range. Alcohols, sugars, fatty acids and amino acid can all be easily solved into ammonia, especially replacing their -OH groups with -NH2. Hydrogen fluoride (HF) is another good possibility. It has the same liquidity range as water and it dissolves polar molecules, just as water does. Paraffin waxes are stable in a HF environment, and the fluorine it contains can be breathed as an oxidant (see "Alternatives to oxygen"). Hydrogen cyanide (HCN) is another good organic and inorganic solvent, with a wide liquidity range, low viscosity, high dielectric constant and specific heat, but it has a tendency to polymerize that could interfere with biochemical processes.

Liquid hydrocarbons, such as methane (CH4), already known to be present on Titan's surface, lack polarity, so they couldn't dissolve proteins; hower, they could carry non-polar polymers, such as polylipids. Being less reactive and having weaker hydrogen bonds, they'd permit hydrocarbon-life to use hydrogen bonds of its own, especially in a low temperature biochemistry. Lifeforms living in hydrocarbon lakes could gain energy making ethane and acetylene react with hydrogen, reducing them to methane.

This table recaps the main characteristics of some possible solvents, in order of liquidity range (remember that benzene, chloroform and methane are not polar). The values most similar to water are written in bold characters.

Alternatives to other elements
Besides the basic carbon-oxygen-hydrogen combination, terran lifeforms use many other chemical elements in their organic processes, for example phosphorus (part of DNA structure and phospholipids), sulfur (in some amino acids) and calcium (strengthens tissues such as shells, bones and teeth).

There are at least some examples of this elements being replaced on Earth. Discovered in 2001 in Lake Mono (California), the bacterium GFAJ-1 was believed to replace phosphates in its metabolism with arsenates; while biologists do not think this anymore, arsenic (As) could have taken part in the biochemistry of early organisms before being outcompeted by far more common phosphorus; today, some marine algae incorporate arsenic in organic compounds, like arsenosugars and arsenobetaine. Heavier (and therefore less likely) elements similar to phosphorus are antimony (Sb) and bismuth (Bi).

Sulfur is already replaced in many organisms, including animals, by selenium (Se), in form of selenoproteins, while some fungi produce amino acids in which sulfur is replaced by tellurium (Te). The only other natural element in sulfur's same chemical group is polonium (Po).

Calcium minerals (sulphates and carbonates) impregnate animal tissues forming bones and shells, but glass sponges and many diatoms use silica (silicon dioxide), which can form hard, glass-like crystals. Other possible substitutes are metals such as iron or copper (Cu).

Alternatives to oxygen
Also see: Metabolism, Metabolic chemistry

Plants, animals, fungi and most protozoans extract from glucose the chemical energy they need to live by oxidizing with oxygen, thus breaking it up and freeing the energy of its atomic bonds, producing less energetic water and carbon dioxide as waste products.

This, however, is not the rule for all organisms. A large number of bacteria "breathe" different chemicals: they have to be oxidizing agents, that is, chemicals that take electrons away from another reactant:

Other common oxidizing agents include ozone (O3), hydrogen peroxide (H2O2), halogens such as fluorine (F2) and chlorine (Cl2), nitric acid (HNO3), nitrous oxide (N2O), etc.

It's important to remember that the more reactive is a substance (at the top there are halogens, oxygen and the sodium group, see here the strongest shades of red and yellow), the less likely is to find it in nature in a pure form, because it will tend to form compounds. Oxygen is still abundant in Earth's atmosphere only because it's replenished by photosynthesis; an atmosphere rich in halogens or strong acids requires them to be continuously produced by organisms.

Carbon-using alternatives
A great part of organic chemistry is occupied by hydrocarbons, compounds entirely made up by carbon and hydrogen, which can form polymeric chains and combine with oxygen to form carbohydrates. In a strongly oxidant, hydrogen-poor environment, where life still uses carbon as basis of its biochemistry, hydrocarbons may be replaced by oxocarbons. Carbon suboxide (C2O3) is an oxocarbon that can spontaneously polymerize in long chains.

Even with a biochemistry very similar to our own, there are still many possibilities for organic molecules: for example, chirality, the orientation in space of molecules. Sugars and amino acids are asymmetrical, and the two specular forms (enantiomers) have the same chemical properties, as long as all reactants in a reaction change their chirality. Terran life uses L ("left-handed") amino acids and D ("right-handed") sugars. Alien organisms with D amino acids could digest L sugars in the same way we do with D sugars, which they couldn't digest.

Amino acids can also have alpha and beta forms: in the first case, the amino group (-NH2) appears near the end of the carbon structure; in the second case, at the front. Terran biochemistry uses only alpha amino acids, but the difference probably depends only from the way water interacts with the molecules during formation. As in the chirality case, it's likely just a random event during the origin of life that stuck with every organism afterwards.

Alternative nucleic acids
See: Genetics

DNA keeps genetic information thanks to its modular structure: two long polymeric chains made up from deoxyribose (C5H10O4,a sugar with five carbon atoms) and phosphate groups, each holding a large number of interchangeable nucleotides and connected to the other, containing the complementar nucleotides.

A number of similar polymers with different structures are known: TNA replaces deoxyribose with threose (C4H8O4), a sugar that has only four carbon atoms; HNA uses hexitol (C6H8(OH)6), which has six. GNA doesn't use sugars at all, but glycol (C2H6O2); PNA, even more different, has a compound similar to an amino acid linked to phosphate groups linked by peptide bonds. None of this polymers exists in nature, but they've all been produced in a lab (also see). PNA could even combine with DNA to form a triple helix structure; it's thought to be a possible precursor to RNA in early life.

Alternative photosynthetic pigments
Also see: Photosynthesis, Metabolic chemistry

To absorb light, photosynthetic organisms use pigments that reflect light of a specific wavelength, and therefore colour (and this is the visible colour of the organism), and absorb the rest. On Earth, they absorb mostly visible light, thanks to a variety of pigments.

The most important are porphyrins, simple ring-shaped molecules, extremely stable, with a single metal atom in their centre. All green plants use chlorophyll, a green porphyrin with a magnesium atom, with two forms: chlorophyll a absorbs better purple and orange light, while chlorophyll b absorbs mostly blue and yellow light. Some bacteria use zinc- and copper-based porphyrins, and there is the possibility of porphyrins with nickel, cobalt or manganese atoms.

A different but still common kind of photosynthetic pigments is carotenoids, which in turn comprehend carotene (a hydrocarbon) and xanthophyll (made up from carbon, hydrogen and oxygen). They both absorb the more energetic blue-violet part of the light spectrum, so carotene appears orange and xanthophyll yellow; they're present in many vegetables, and xanthophyll is the chemical that makes an egg's yolk yellow.

Phaeophytin is derived from chlorophyll that lost its magnesium atom when treated with an acid; it appears dark blue and it's present in many algae and bacteria; most bacteria and some algae also use phycobiliproteins, which include blue phycocyanin  and orange-red phycoerythrin.  Halobacteria use another protein, bacteriorhodopsin, to absorb green light (it looks purple) directly to move protons with solar energy, without it taking part in true photosynthesis.

As a simpler alternative, some metal oxides, such as zinc oxide (white), titanium oxide (white) and tungsten oxide (light yellow) appear to be able to capture and store energy when exposed to light and take part in oxidation-reduction in a similar way to chlorophyll; silicon and germanium, instead, could convert light in electric energy as they do in photovoltaic cells, splitting water molecules through electrolysis (see here).

Here there is a collection of graphs that shows the most common wavelengths produced by different stars, in different environments. Whatever these wavelengths are, the plants likely won't be of that colour, because that is the wavelength they will want to absorb, rather than reflect. The peak of light in each situation is summarized in the table below; wavelengths are measured in nanometres (see here for detail on star classes and definition of Ms, Ls and AU). The table assumes a planet with an Earth-like atmosphere. Compare to the table the values of peak absorption of the most common photosynthetic pigments, which will have to be as close as possible to the value in the table:
 * Pheomelanin: 330 nm (ultraviolet) - colour: reddish brown
 * Eumelanin: 340 nm (ultraviolet) - colour: black or dark brown
 * Clorophyll a: 430 nm (blue); 680 nm (red) - colour: green
 * Chlorophyll b: 450 nm (blue); 660 nm (red) - colour: green-yellow
 * Carotenoids: 480-520 nm (light blue to green) - colour: orange or yellow
 * Phycoerythrin: 500-580 nm (green to orange) - colour: orange-red
 * Bacteriorhopsin: 570 nm (green) - colour: purple
 * Phycocyanin: 620 nm (red) - colour: blue

Alternative blood pigments
Also see here.

All terran organisms having more than a few cells need a fluid transporting molecules around the body, that is, blood. While a liter of seawater at body temperature cannot carry more than 5 cm3 O2, adequate pigments can have a carrying capacity fifty times higher, by binding oxygen to metallic atoms. Most animal groups use hemoglobin, a porphyrin very similar to chlorophyll with an iron atom at the centre; it can simply bind to oxygen in the respiratory system, thanks to its high pressure, and then release it in the tissues.

Since iron oxide is red, hemoglobin (and the cells that contain it) colour blood red; it's been suggested that red has such a connotation of danger and emotion to humans because it's the colour of blood. However, different pigments are found throughout the animal kingdom that use different metal, ad therefore have a different colour: for example, hemocyanin, the second most common blood pigment, contains copper, and makes blood blue.

In Earth-like conditions, hemoglobin is still the most efficient oxygen carrier known, though it could be outcompeted by others if other metals are more abundant or the organisms that develop them happen to have other evolutionary advantages. As discussed here (also see the last picture here), anyway, at lower concentrations of oxygen (px < 0.02 atm) hemocyanin is actually more efficient than hemoglobin. Chlorocruorin and hemerythrin are never really competitive, while Vaska's complex is more efficient than several forms of hemoglobin at px < 0.02 atm and px > 0.2 atm. Coboglobin is roughly at par with hemoglobin, and slightly more efficient with px < 0.05 atm. Still, in favourable condition (high atmospheric pressure, high concentration of oxygen, high temperature) a very efficient transport of oxygen might be unnecessary, so minor pigments could thrive anyway.