h2g2 The Hitchhiker's Guide to the Galaxy: Earth Edition

...here on Earth. Living in the depths of a poisonous California lake. Their DNA is completely alien to anything else on the
http://www.guardian.co.uk/science/2010/dec/02/nasa-life-form-bacteria-arsenic

So, the old adage "life as we know it" has had the goalposts widened somewhat.

This is so fantastic!

I think there might be just about anything out there, considering where stuff lives even on earth.

These bacteria are the est:

<<The Rio Tinto, a polluted, acidic river in Spain, offers astrobiologists a chance to look for exotic life<<


<<Pibernat believes that bacteria living in the river turn this sulfide into sulfuric acid, giving the river its low pH.<<

http://www.astrobio.net/pressrelease/424/life-under-a-spanish-red-river

thats nuff'in, I've got A MIL that can eat anything

...back to an old debate, the question as to whether there can be life of some other kind than 'life as we know it'...

...'life as we know' it can these days be fairly rigorously defined, on a basis of scientific knowledge that for the most part did not exist at the time the debate first emerged, as 'life founded on 'dextro' nucleic acids, founded on the sugars ribose and deoxyribose, forming the links to which nucleotide pairs attaching the two 'rails' of the double helix together are bonded, forming the 'rungs' of the double helix, with phosphate radicals linking the 'rungs', driving a biochemistry founded on 'levo' amino acids and 'dextro' sugars and lipids', or its steroisomers...

Put that way, a micro-organism substituting arsenic for the phosphorus in its nucleic acids is 'life not as we know it', unless one expands the paragraph immediately above to include the phrase: ...and their analogs... .

Presumably the sugars and nucleotides of the nuceic acids of the microorganism remain the same as those of typical nucleic acids and since the microorganism seems able to use arsenic and phosphorus interchangeably, its not something that's really fundamentally different from life as we know it. It is though, if all of this is so, something straining at the limits of the current definition.

This is something that's not completely without precedent. Penicillin, for example, incorporates a dextro amino acid into its structure.




Favorite thought problem: if there were life on Mars stereoisomeric for terrestrial life (levo nucleic acids, dextro amino acids, levo sugars and lipids), how would that effect the Viking bichemical survey results?




It also brings to mind period debates on how life might evolve on a basis of bizarrely alien environments, for example, a chlorine atmosphere, rather than an oxygen atmosphere? Those debates helped to point up a concept that planetary environments are most probably, on a basis of the astrophysics generating the chemical elements in the first place, going have chemistrys closely similar to those which obtain in the solar system, and the point that the evolution of an oxygen atmosphere for the earth was a consequence of the action of life itself.

While a chlorine atmosphere is not impossible, its extremely improbable except in a case where the planet hosting it has oceans of molten sodium chloride overlying a crust saturated in chlorides.

Another popular conception had to do with silicon analogs of the carbon compounds of terrestrial life related to silicones, evolving a 'life' adapted to extremely hot conditions. On the other hand, the hydrosilicon analogs of the petrochemicals and related biochemicals tend to be so explosive that they're likely to be stable only in an extremely frigid environment. Perhaps, if they form a basis of life, on a basis of electrochemical, rather than photosynthetic processes.

Even more extreme concepts have been proposed relating to 'life' coming up in a quantum states in conditions as extreme as the surfaces of neutron stars and helium II seas populated with natural superconductives on objects in the interstellar void.

There was quite a lot of literature on the topic, especially during the 3rd quarter of the twentieth century, relating to 'brainstorming' proposals and rebuttals. The debates helped to clarify concepts as to what life is, and conditions that might be found elsewhere in space.

wow

Afterthoughts:

The phosphate links between the nucleotide pairs carry no information. They are merely structural, so replacement of the phosphorus in them with arsenic may make no difference at all in the protein catalysis produced by the nucleotides.

Though there are only four nucleotides in DNA, with RNA, 'unusual nucleotides', so called, other than the basic four characteristic of RNA, have occasionally been reported.

Also, the uracil-uracil bond allows formation of a nucleotide pair in RNA which contains only one kind of nucleotide, is common in RNA chemistry and makes the coding of RNA much more complicated and less immutable than that of DNA.

Amazing (and makes sense) You explain it well.

This deserves a Guide Entry. "The Chemistry of 'Life As We Know It'

I just realised I (sort of) already knew this - but you helped me link up all the dots - of course Arsenic is below Phosphorous on the periodic table in the same group which is why it acts as a poison. The chemistry is so similar the biology of bodies treats arsenic as it would phosphorous which goes after the Thiamine which regulates metabolism and it'll disrupt the elecro-chemistry of the nerves too.

Pretty good ITIWBS but there are a few slight misunderstandings in there.

D-amino acids (or dextro as you call them) are spread widely throughout life. So it is not unusual at all to find them - in fact *all* bacteria have them in their cell walls and this is why penicillin contains a residue of one.

What you don't find is D-amino acids being coded for by the genetic code. DNA contains coding regions that are code for protein sequences. There are 20 amino acids that are in the genetic code - the so called 'canonical' amino acids and all chromosomally encoded proteins are constructed from them.
Finding a genetic code for new amino acids - that *would* be a stunning discovery.

It is perfectly possible and in fact very common for other amino acids to be biosynthesised in cells, including opposite configuration D-amino acids. They just aren't coded for by DNA and are much less common than their canonical counterparts.


The unusual RNA nucleotides are much more common than you might imagine. There is a type or RNA called transfer-RNA (or t-RNA). It's job is the translation of nucleotide into protein. On one end of a t-RNA molecule is an 'anti-codon' this is three nucleotide recognition sequence that binds to the DNA codon for a specific amino acid. On the other end of the t-RNA molecule is attached that very amino acid which is then incorporated into a growing protein chain on a cellular machine called a ribosome.
Anyway, cutting to the chase, their are 20 t-RNA's - one for each canonical amino acid but in t-RNA you will find many unusual nucleotides that are not A,C,T (or U) or G. So actually these 'unusual' nucleotides are quite ubiquitous in t-RNA. This leads many people to believe that t-RNA is a relic of an ancient life form that had many more nucleotides than exist today.


Personally, although this is a very interesting piece of work, it is to my mind not all that much of a revelation (Bah Humbug I know ). That bacteria can live inside of rocks and in ice and stuff is well known and of course such things that live on the extreme will naturally have survival skills that we haven't yet imagined. It doesn't make them aliens.
As you observe, arsenate is very similar chemically to phosphate. I would say though that it won't be anywhere near as stable. Plus arsenic isn't very abundant. Hence the useage of phosphate and not arsenate generally.

Interesting stuff anyway

Thank you, Orcus, for your more detailed treatment on unusual nucleotide bases and D-amino acids. You've covered a number of points I didn't know about and provided a number of useful starting points for further study. I haven't done any very intensive study on this since the middle 1980s, comparing DNA codons with RNA codons.

I agree, by the way, that RNA is more primitive than DNA, which probably arose as mutation of RNA on the basis of loss of an oxygen atom, and persisted and eventually became dominant in molecular evolution on account of its greater stability and immutability than that allowed in RNA biochemistry.

I would consider, on a basis of that, a discovery of nucleic acids founded on sugars other than the ribose and deoxyribose group a more fundamental departure from conventional genetics than substitution of arsenic for phosphorus in the structural elements of the double helix. In such a case, one might expect an entirely new range of information carrying nucleotides bonding to the alternative sugars.

A point of clarification with respect to the thought problem related to the Mars and Viking lander experiments. What I was suggesting there was a biochemistry founded on D-canonical amino acids.

The findings with the studies on the Murchison meteorite certainly suggest that terrestrial biology hasn't exhausted all the possibilities that might evolve in natural biochemistry.


http://www.google.com.au/imgres?imgurl=http://www.daviddarling.info/images/Murchison_meteorite.jpg&imgrefurl=http://www.daviddarling.info/encyclopedia/M/Murchison.html&usg=__V_JrlVP6MvcnN8GABIob4724XVo=&h=232&w=300&sz=44&hl=en&start=0&zoom=1&tbnid=gDQuhN9-N9RHGM:&tbnh=148&tbnw=191&prev=/images%3Fq%3DMurchison%2BMeteorite,%2Bimages%26um%3D1%26hl%3Den%26lr%3D%26sa%3DX%26biw%3D1280%26bih%3D595%26tbs%3Disch:1&um=1&itbs=1&iact=hc&vpx=144&vpy=89&dur=3131&hovh=185&hovw=240&tx=130&ty=110&ei=_hr5TNadBIiWsgOu4ay0Aw&oei=bBr5TLTSApPGsAPi_sHQAg&esq=25&page=1&ndsp=18&ved=1t:429,r:0,s:0

Oh I'm sure it's perfectly possible for life elsewhere to be right-handed rather than left handed. Assuming there was no 'creator' then symmetry must have been broken at a very early stage of development of the molecules of life. There is no great reason for the bias to the L-forms other than a random event at the beginning of things. No reason at all why it might have occurred the other way elsewhere I think.

I didn't know about that meteorite, thanks for that

The unusual nucleobases in RNA by the way are called pseudouridine , dihydrouridine, inosine, ribothymidine and 7-methylguanosine.
Not that I copied that list from wikipedia or anything

Afterthoughts on post 12:

In eukaryotic reproduction, in the process of meiosis, germ cells carrying one half of the chromosomal mass of the parent cell being generated, producing 'haploid' sets of chromosomes, the two haploid sets of chromosomal alleles stay together as distinct sets from generation to generation, so that, for example, the X-group of chromosomes one inherits from ones' mother is still essentially the same set she inherited from her mother, etc., while the X-group or Y-group one inherits from ones' father is the same group of chromosomal alleles he inherited either from his mother or his father respectively. This was established by means of radioactive tracer experiments in which a radioactive oxygen isotope was introduced into one of the two sets of chromosomal alleles of a laboratory culture of micro-organisms.

This leaves a problem accounting for apparent 'crossover' traits, traits that originated with one parent being transmitted in the complementary set of chromosomal alleles.

In the process of mitosis, replication of the chromosomal masses, the DNA molecules actually split in two along the line of the bonds between the complementary nucleotides of the nucleotide pairs, so that temporarily the DNA double helix becomes two single helixes. Since there is only one possible nucleotide complement for each of the DNA nucleotides, the information carried by the missing half of the double helix is reproduced with great fidelity in the copy. RNA is much less immutable this way, much more prone to variation.

Sometimes a filament of a single helix, especially near the end of the DNA molecule, may break off, carrying away half of the genetic information coded on it. In such a case, the missing half of the DNA information is still regenerated on the fragment, which can then drift to another chromosomal body, even into the opposite set of alleles, and eventually embed itself there, carrying the information coded on to an entirely different chromosomal mass than the one it originated in, while the fragmentary filament that remained attached to the parent chromosomal mass simply regenerates the original code. One of the two mitotic copies will, of course be a little shorter than the other.

The fragment moving from one chromosomal mass to another is called a 'transposon'.

Recombinations of transposons are an important process driving natural evolution.

The process is also important in context of recessive vs. dominant traits. An allele coded by only one copy of an allele on a single haploid set of alleles is a 'recessive'. It becomes manifest only when a matching allele on the complementary set of haploid alleles is present. If there are two or more copies of the same allele on the same haploid set of alleles, then it is a 'dominant' gene. 'superdominants' have been reported, for example, with the genes coding for sperm production with rats and human beings, where there are eight copies of the gene.

In an opposite way, reflecting the unequal division of genetic material resulting from fragmentation of the chromosomal DNA, the process can account for the phenomenon of 'replicant fade' twins. For example, with alley cats, if the female has only three fertilized eggs, she may and usually will, if conditions are good, throw of an identical twin of one of the zygotes, which will usually be less robust and less prominently marked than its identical twin. (There are other processes which can contribute to this phenomenon.)




[I originally got on to this doing horticultural work in my garden, working with ornamental indian corn, using a breeding technique where inbreeding and outbreeding were simultaneously being maximized, reintroducing all of the ancestral strains and a like number of neophyte strains into the population with each succeeding generation, conserving one (and the same) transposon in each generation, replicating an approach pioneered at Texas A & M, where transposons were originally discovered. (Mutation mink in the fur trade was similarly developed.)

So, my interest is that of the hobbyist. I'm currently developing some similar efforts involving some other plants in my garden, with a restriction to traditional horticultural techniques.]

An update on Marias' post 4,

http://www.astrobio.net/exclusive/3698/thriving-on-arsenic




[A recurring bug that's recently affected myself and a number of other h2g2 researchers, broken links relating to search items remaining in the cache when posts a link to h2g2.

Important always to check the link on preview and posting. The link that previews is not necessarily the link which will post. Possibility of a broken link apparently increases every time its copied or previewed. It took an editorial intervention to fix the problem when this came up recently in Peer Review.]

Sounds complicated. I shall now recite Vogon Poetry.

Wow, cool. Reading that article I happen to know Steve Benner, although he probably doesn't know me. He was my boss's PhD supervisor.

I'm looking forward to the articles coming out where they analyse the structure of arsenous DNA and other biolmolecules from this organism grown on a solely arsenic envornment. Should be interesting.
I think this guy has found his career changing moment.

The paper has been getting a fairly hostile reception, I've been reading.

http://rrresearch.blogspot.com/2010/12/arsenic-associated-bacteria-nasas.html