Category: Biology

Life born of Ice…

According to Nordic mythology the Gods were born of the interaction of fire and ice. Considering the chilliness of their northern world I can sympathise. Modern biochemistry is also leaning towards an icy origin of Life – or at least of RNA, Life’s putative precursor…

Did Life Evolve in Ice?

…origins of Life gurus Stanley Miller and Leslie Orgel (sadly late gurus now) were actively researching the idea that the concentration effect of freezing water, via the separating out of solutes, actually improves the production efficiency of long-chain biomolecules. So much so in fact the process can create small chains of RNA. Once a self-replicating ribozyme, or set of ribozymes, formed then Darwinnowing could begin in earnest and launch Life-as-we-know-it.

What’s utterly intriguing is that the process occurs in ice not much warmer than the crustal coating of Europa, making the origin of Life there even more likely than ever. But was that origin independent of our own? The article quotes the minority Archean geological view that Earth was covered in vast ice-sheets after the Late Heavy Bombardment, 3.9 Gyr ago. Problem is there’s also evidence that Earth was very hot for over a billion years from about that time.

Could that be a clue that Life Here actually began Out There?

Paul Davies opines, in his The Fifth Miracle, that Life began on Mars – which was plenty cold enough – and was lofted here via meteorite. Alternatively it might have been lifted electrostatically, since we know Mars has plentiful concentrated electric fields in the form of dust-devils, and bacterial spores can hold a charge. More exotic origins are Bill Napier and Chandra Wickramasinghe’s idea that life began in comets – an even colder site, occasionally warmed via the Sun. Life might have begun even further afield in the Galaxy, but the efficiency of interstellar panspermia is yet to be quantified. Needless to say: if Life began with a chill, then there’s so many more places it might yet be found Out There than we (scientifically) imagined.

BTW A couple of years ago this news appeared: Earth could seed Titan with Life …in which computations show rocks knocked off Earth would reach Titan, but not Europa, at low enough energies for microbes to survive. Of course the same goes for Mars, even more so because its gravity well is much shallower.

UPDATE – Seems Earth really was hot after Life first sprang forth. Studies of heat-related proteins in a large number of microbial species strongly indicates a 30 degree C decline in temperatures from c. 3.5 Gya to 0.5 Gya… Nature Abstract … and the estimated decline matches what has been inferred from oxygen isotope analysis. Seems Earth was HOT ~ +45 C on average in the early Archean. So where did Life get a COLD start???

Early Oceans of Venus – space – 10 October 2007 – New Scientist Space

Venus is currently drier than a bone. But the high deuterium ratio in the atmosphere hints at isotopic fractionation of a LOT of water in the deep past. Enough for a shallow ocean, or perhaps a deeper one with a bit of tweaking. That’s uncontroversial in most planetological discussions, but what is difficult to determine is just how long that primal ocean lasted for. David Grinspoon and Mark Bullock have suggested strongly that clouds would allow an ocean to last at least a billion years or two, making Venus habitable much longer than previous estimates of a mere 0.5 billion years. In that time enough oxygen might have accumulated from dissociation to give life an oxygenic head-start…
Did Venus’s ancient oceans incubate life? – space – 10 October 2007 – New Scientist Space

…theoretically spores from microbes can be lofted into space electromagnetically and because Venus has no observed magnetic field the atmosphere interacts directly with the solar wind. Life could then be blown outwards to Earth, Mars and even a wet, warm early Titan.

Random mutation, directed search

Fortune as ‘randomness’ or ‘chance’ – how the sticks fall – is a big part of biology’s insistence on the non-directed nature of mutation. And I don’t take exception with the idea that what we see in mutation isn’t directed at a solution in a trivial sense. Most mutations seemingly ‘just happen’. A lot of Christians are scandalised by the idea of ‘random mutation’ but biology is revealling more to the story than mere base-pair flips due to chemicals or UV photons.

What seems to occur is genomes in a population under stress collectively perform a search for a viable mutation, and as has been increasingly realised in molecular biology genes seem to be organised to mutate and still remain viable. Parts of genes seem to be able to hyper-mutate in response to external stresses affecting the organism, while other sections seem to resist mutation. In microbes this means the mutations will be inherited, but in multi-cellular organisms the separation of germline cells from soma-line cells is hard to cross. But it does seem to happen. Epigenetic modifications to offspring are being increasingly recognised as caused by the environmental experiences of the mother.

Thus mutation isn’t guided to a perfect solution – instead genomes seem optimised to allow enhanced rates of variation as a means of searching for a viable solution to a stressor. The collective behaviour of the population seems to work like a “learning machine” – what gets called a perceptron or neural network in computer science – which computes, as a distributed system, a new genome in response to environmental changes. Thus, as Greg Bear fictionalised in “Darwin’s Radio” and “Darwin’s Children”, there is Mind-like behaviour in evolution. There is also a lot of information transfer via viruses and horizontal gene-transfer, much like what Greg Bear imagined.

That’s what our current understanding seems to be telling us – not so much an external Intelligent Designer, separate to the process, but an immanent ‘Mind’ that searches out new solutions through the success or failure of individual genotypes-expressed-as-phenotypes. And that Mind uses more than just base-pair flips and random movements of blocks of DNA during recombination to get things happening. Gene expression can be modified even without changing the genes, mothers can modify the expression of their children’s genes, and there are plenty of other tricks in the Mind’s toolbox.

Of course for a Christian the question arises as to just how that Mind relates to God. I propose we see the natural Minds immanent in the evolutionary process as God’s agents – perhaps even “angels” – but they may not be self-reflective, and may merely be automatons. Programs if you will. But then we are but programs in the wetware we call our brains. We imagine ourselves to be separate individuals, but our minds share a common information sea we call “society” – much like the “pool of genomes” that a species population represents. If we are such tiny sub-programs in something bigger, and yet still conscious, then maybe They are conscious too. If so, then the case for them being Angels is stronger.

If so then we must ask: is the Angel of genus Homo a Fallen Angel? Is that why Satan is called the god of this Aeon and is able to say “all these kingdoms are mine“? Terribly Kabbalistic speculation and perhaps totally baseless, but the more I think on it, the more the idea gains credence. Howard Bloom’s two classic books on the concept of distributed intelligence in evolutionary processes are titled “The Lucifer Principle” and “The Global Brain”, both of which explore the role of hierarchies and social orders in evolution. One particular idea is that we each have our own “Inner Judge” that determines if we’re socially connecting, successfully or not. Failure to connect leads to “condemnation” and a failure to thrive. Recent work has shown that “loneliness” causes changes in our immune systems – we become more vulnerable to illness. People who accept the Inner Judge’s case basically lay down and die. Or actively suicide. All quite irrationally, but seemingly instinctively.

“Satan” means “Accuser” – the Inner Judge’s Prosecutor – and as Jesus put it “he was a murderer from the beginning.” In that light we don’t need to imagine a Devil as something exterior to us. Instead its power is from the evolutionary machinery that makes us NEED to be a part of a bigger social system. But the individual human ego doesn’t accept the condemnation of the Devil lightly – we can either turn to a different archetype (the Self=Christ, as Jung puts it) or we can embrace the Accuser, and accuse society back. People like Anton LeVey and Marilyn Manson consciously sided with the Satanic symbol and point out quite truthfully the flaws and failings of ostensibly Christian mainstream culture.

A great Christian thinker, Jacques Ellul, once pointed out that because Satan is the Accuser in God’s Court, then we must listen to his case against us and answer it squarely. Anything else, especially evasion, is claiming we’re without sin, and thus coming under the power of the Prince of Lies. Satan can only be defeated by truth, because everything else is from him. Knee-jerk reactions by Christians to challenges to their personal cultural idols… it only hurts themselves.

Deep Future for Mankind?

Doctor Who in its last three episodes for the 2007 season presents us with the ultimate fate of humanity. The Universe is collapsing into giant black holes and the last human survivors of the year 100 trillion (or so) have reverted to biological human form. They receive a call to a final refuge called “Utopia” and the Doctor helps them to escape one dying world at least. He notes in passing that the human race reverts to classical form time and time again, even after spending billennia as computer uploads and plasma clouds.

In “The Sound of Drums” and “Last of the Time Lords” we learn that the refugees on Utopia were ‘rescued’ by the Master, made into psychopathic cyborgs and brought back to 2007 to exterminate the current human species, to replace them and make an Empire ruled by the Master. So “We” morphed again.

But what might really happen?

Greg Benford does quite a good job of imagining how diverse genus Homo might become after a billion years in his “Beyond Infinity” – he has hundreds of human derived species being revived out of gene vaults after a long period of stasis self-imposed by Homo superior. I think self-directed evolution might mean that something like the human form can be retained into an arbitary futurity (like 100 trillion AD), but that by no means implies stasis at the molecular level. I personally can imagine lots of molecular level machinery gradually taking over from old-style DNA/RNA – which is a bit too labile for high radiation environments and odd chemistry. Life extension would demand something more stable since cancer and aging are both caused by breakdowns in DNA/RNA replication fidelity after too many cell generations.

“Smart matter” cellular machines might be required in the long run, addressable by a body’s operating system and able to undergo a degree of “morphing” into useful configurations – we would become our own tool-kits, assimilate silicates and metals, replace calcium minerals with carbon nanotubes, and augment biochemistry with higher energy density power-sources. Technology and biology will merge – if we are to survive in any kind of physicality in the billennia ahead.

That’s how I see our evolution panning out. Frank Tipler, in his “The Physics of Christianity”, believes we will all become Uploads, of necessity – even after the Second Coming of Jesus. Maybe. After all JC said “Flesh and blood can not inherit the Kingdom of Heaven” and “sons of the kingdom will be like the angels, neither marrying nor giving in marriage” – sounds much like a non-flesh based existence to me. But bodies will always be useful regardless of how portable the software we call “the soul” becomes. I think even our Uploaded descendants will still take classical human form as the need arises. There’s a lot of information processing potential in the dimers that make up cytoskeletal microtubules – our bodies are “stupid” because we don’t yet have an interface or an OS that can utilise that power.

How much information is needed for Life?

I’m sick to death of people claiming ridiculous amounts of information in genomes. Pundits with an axe to grind against materialism like to liken the information in a simple cell to the Encyclopaedia Britannica – all of it. But we’ve actually measured the information in microscopic replicating biosystems – viruses, archaea and bacteria – so we have some guide to what’s needed. Biosystems are made of both simple and incredibly complex molecules – and the complex ones, proteins, are encoded as a sequence of DNA. In microbes the DNA is one huge loop – a ring – which tiny molecular machines called ribosomes read and convert the information into proteins. The information itself is the order of amino acids – twenty specific ones in most lifeforms – which make up the protein itself. Once the amino acids are put together into a string connected by chemical bonds the newly made protein then folds up into a shape that lets it do the specific chemistry task that it controls. For many proteins a large fraction of the amino acid sequence can be changed with no change in function or form – most of the action happens in a few small regions. Some protein machines are ubiquitous in function throughout the biological world – cytochrome c for example – but exist in a HUGE variety, with completely different sequences of amino acids.

So how much information will let a biosystem self-replicate? Viruses don’t, though some contain more DNA than the simplest bacteria. But Viruses do self-assemble after their proteins have been made by a host-cell’s ribosomes. In fact many intricate protein machines – which viruses are just one example of – self-assemble from their component proteins, without any apparent molecular “master-builder”. Instead as the proteins jostle around inside their host cell, their specific magnetic linkages will find each other and link up. Brief interactions between the proteins and other unrelated proteins might occur, but in the constant jostling only a proper fit will stick the two together fastly. It’s crowded and busy inside even the simplest cells.

The simplest self-replicating biosystem known is an intra-cellular parasite called Nanoarchaeum equitans a bacterial parasite with a DNA string about 490,885 base-pairs long. A base-pair is the minimal unit of DNA information, which can have four different values (equivalent to 2 bits of computer-style information.) There’s 3 bases per codon in DNA’s “language” so the Nanoarchaeum genome is about 163,000 codons long. A codon is roughly 6 bits. Thus the simplest self-replicator is the equivalent of about 122 kilobytes (1 byte = 8 bits.) There’s 10,000 symbols (including spaces) per page of the Encyclopaedia Britannica – I counted it out of curiosity one day. Each symbol of print is roughly a byte. Thus Nanoarchaeum needs just 12 pages of Britannica to encode its genes.

Taking into account the redundancy of the DNA codon code and the roughly 50%-80% redundancy of amino acid sequences themselves, that means roughly 34 – 13.5 kilobytes of information will code a self-replicating DNA-based cell. Just 3 to 1 page of Britannica.

That’s still a lot of information to “just happen”, but in our ignorance of proto-biochemistry we might be missing the key element that simplifies matters even further.

Weirder things might be needed. Physicist Paul Davies has speculated that backwards causation might cause the past to be at least partially determined by the future – thus biochemistry was arranged to be consistent with the existence of Life by the (future) observation that Life exists. Else there would be no observation for that “consistent history” to ever happen. This occurred not by design, as in engineering by an external god, but by an inner mathematical consistency that insists the Universe is observed and thus observers should exist.

The self-referential nature of that idea gives me a headache, but check out Davies “The Goldilocks Enigma” (called “Cosmic Jackpot” in the USA) for a fuller discussion. There’s a whole barrel of mysteries as to how proteins do what they do and we might find some pretty wild quantum effects are necessary for life itself.

Ask yourself: if you were a god how would you do it? Can Life be designed?

Plasma life

New research on plasma crystals raises the prospect of inorganic helices encoding genetic information…

‘It might be life Jim…’, physicists discover inorganic dust with life-like qualities

…for a long time I have pondered the possibility that UFOs – unexplained ones, not the mundane sort – are caused by coherent plasma structures that we can call “alive” though not ‘organic’. Work on plasma crystals seemed a way for plasma beings to have some sort of stability though made out of a medium in continual flux like plasma, and now this new work has confirmed my suspicions.

If plasma beings – which I call “plasmons” even though that means something else in optical physics – exist how would they manifest to us? Balls of glowing light are one possibility – their raw physical natures concentrated and leaking visible energy. They might also, after co-existing with us for millennia, know how to manipulate our perceptions magnetically, via fine-scale magnetic-field variations around our skulls to excite our neurones. Plasmons might then appear in whatever form the brain dredges up to explain the imperfect firings of neurones – could religious, paranormal & UFO visions result from plasmons trying to communicate with us? Being plasma they could have existed almost from the dawn of time, spanning the cosmos, perhaps even playing a role in the creation of life on “cold matter” worlds like our own.

Think on it.

Human Hibernation gets closer

Discover Magazine’s May 2007 edition has an amazing up date on work being conducted into induced hibernation in mammals. In recent years news arose of dogs and pigs being aroused from a death-like state after several hours, and of mice being induced to go into metabolic slow-down by breathing the right concentration of hydrogen sulphide. As the Discover article relates the work has gone further with dogs and pigs being put into hibernation by hydrogen sulphide and the amazing story of a Japanese man, Mitsutaka Uchikoshi, who went into a hypothermic torpor for 24 days after being knocked unconscious.

Naturally the first thought for the medicos working with this surprise mammalian ability is the preservation of a patient’s life when they’ve suffered major injury. If they can be suspended in a low metabolic state, then transfers from incident site to an ER becomes infinitely easier, giving the victim a much needed time-extension. Also many different major surgical procedures would become much less risky if a patient’s blood pressure, heart rate and so forth can be slowed to a crawl.

Of course, for a space-minded thinker, the next questions are:

  • just how long can the suspension last?
  • how much can physiological requirements be reduced?
  • how easy is it to induce and revive from?
  • does it reduce radiation damage?
  • could it be used as a step towards total biostasis?

    • In fiction there’s a long tradition of suspended animation, either through extreme metabolic reduction and/or cryopreservation. The new prospect of a natural suspended animation in all mammals is a rather exciting step forward for the credibility of the concept. Another curious prospect is based on the observation that mice which have had their metabolisms reduced, but not all the way into torpor, are able to breathe an atmosphere with a much lower oxygen content than what would otherwise kill them. Perhaps this provides a way to allow people to adapt to non-standard atmospheres?

    James Blish’s 1965 novel, Welcome to Mars, uses just such a plot device to allow the protagonist to breathe the thin Martian air – as thickened by being at the bottom of Hellas. Unfortunately for Blish’s story a few weeks later Mariner 4 showed the Martian atmosphere was less than 1/10th of the expected density. Still he did correctly predict that there would be plenty of impact craters and what “canals” (channels) that existed would be geomorphological in origin. He also predicted a frozen sea of ice, which Mars Express potentially has discovered.

Alternative-style “proteins”

For several years molecular biologists have been fiddling with the machinery of Life, trying out its capabilities. Now a new kind of “protein” made from beta-amino acids (different to our alpha-aminos by having an extra carbon) have been synthesised and seem able to mimic regular proteins… Chemists show that nature could have used different protein building blocks. All this research, plus work on alternative coding systems in DNA, enable molecular tailoring of bacteria to specific tasks – like making gasoline out of sunlight and carbon dioxide, or making amorphous carbonia out of the world’s excess cee-oh-two.