Wednesday, December 30, 2009

touching on the carbon cycle and the long ago

Canto: Okay, before we go on about this, Jass you said that plants emit carbon dioxide in huge amounts by respiration, and then absorb huge amounts by photosynthesis. This idea of being big emitters and big absorbers at the same time is hard to make sense of. Could you explain that a bit more?
Jacinta: Let me briefly explain the carbon cycle. There are two main sources of carbon in our atmosphere, carbon dioxide and methane. Think of the atmosphere, above us, as at the top of this cycle. At the bottom of the cycle, far below us, the earth's crust and mantle contain carbon which is forced upwards and outwards by volcanic and geothermal activity. The other parts of the cycle are the terrestrial biosphere [our territory - though not owned by us, as we share it with other terrestrial animals and plants], the oceans, and underground sediments [in which are found the fossil fuel reservoirs we're so keen on]. Now the terrestrial biosphere and the oceans in particular can be sinks or sources of carbon dioxide, depending on the balance between absorption and emissions. Because it's a bit like profits and losses, climatologists call this the carbon budget [whether of the oceans, or a particular ocean or region, whatever]. And it's always changing...
Canto: Mmm, and some areas, like rainforests, are really big carbon sinks, right? So if all the land was covered in rainforest, would that mean that the amount of atmospheric carbon would be right down? It would all be somehow fixed in the plants and in the soil?
Jacinta: No, I'm not sure about this, but with lots of rainforest, and that means thick vegetation, lots of plants and lots of animal and insects species thriving on them, you'd have lots of respiration, and lots of rotting, because lots of life also means lots of death and decay. In fact, during the early Eocene epoch there was a burst of warming, probably initiated by releases of methane [a much more potent greenhouse gas] into the atmosphere. I won't go into the reasons for that release here, but there was certainly more carbon dioxide in the atmosphere then than there is now. The Eocene became so warm and wet [the ice caps had melted, inundating much of the land, and water was evaporating from the oceans - water vapour is also a greenhouse gas] that vegetation was springing up everywhere - tropical palms in Alaska and Siberia, for example.
Canto: My god! How did they save the planet?
Jacinta: Well, the planet was going along just fine, which doesn't mean we should be sanguine about the current situation. The Eocene saw an absolute burgeoning of life, as you might imagine, though the short sharp warming burst, which lasted only 100,000 years or so [that's only one two hundredth of the whole epoch] caused a mass of extinctions. And if it wasn't the period of the birth of primates, it was the period of their greatest development and success.
Canto: Wow, this long-term view really puts things in perspective. When exactly was the Eocene epoch?
Jacinta: I'll tell you next time. It's worth reflecting on global climate history and the evolution of species. It's a complex but compelling subject.

Sunday, December 20, 2009

a biosphere out of balance?

Canto: There are so many issues around global warming, so many questions to ask. I want to begin with an article I read in a November issue of New Scientist. It was written by Alun Anderson, a former research biologist and editor-in-chief of the magazine. The blurb at the front of the magazine described this piece as 'dispatches from a collapsing ecosystem', but that is very misleading. In fact, Anderson describes a thriving, resurgent ecosystem, that of the Arctic. Polar bears and narwhals and other creatures at the top of the food chain are in trouble there, but killer whales are thriving and taking over at the top. The ecosystem isn't so much collapsing as transforming:
In purely biological terms, the new Arctic will be more productive than the old, because there is more water, open to sunlight for longer, with more plankton growing in it, and more food supports more life. The first signs are already there. After the sudden collapse of the sea ice in 2007, a satellite-borne sensor, measuring the water's 'greenness', showed that the total productivity of the Arctic seas leapt by 40%. That is a big increase. 
These observations underline one particular theme of mine. The 'save the planet' mantra is bullshit. A few degrees of warming is not a threat to our planet. What it does, of course is threaten the biosphere as we know it. It will transform the biosphere, not necessarily for the worse, from a non-human perspective. It will disrupt human activity, though it would be a gross exaggeration, I think, to suggest that it threatens our species' survival.
Jacinta: Yet there are so many unknowns. They say the oceans are becoming more acidic. I don't know if that's directly linked to global warming, but it would presumably be life-threatening to many species. How will this interact with the burgeoning of species, especially in colder regions, due to global warming? But let's get back to the initial question you asked, in the last post. How do we know that greenhouse gas emissions, particularly carbon dioxide, lead to global warming?
Canto: I know that carbon dioxide levels in the atmosphere are continuing to climb, with current levels being at their highest for 650,000 years, but what precisely is the connection between these levels and temperature?
Jacinta: Carbon dioxide levels have remained fairly steady for a long time, with a balance between emissions and absorption helping to maintain relatively stable climatic conditions. As you know, the current level is around 390 ppm, and that's well up on the range in the half million years or more before the twentieth century,  which, according to evidence from ice cores, has been between 180 and 300 ppm. The concern is that emissions are now outstripping absorptions.
Canto: So what, generally, emits carbon dioxide and what absorbs it?
Jacinta: Emissions are measured in gigatonnes. Some 440 Gt of carbon dioxide is emitted annually, about half by plant respiration, and half by consumption of vegetation by microbes and animals. These figures are, incredibly, balanced by the enormous amount of carbon dioxide absorbed annually via photosynthesis. Now, we must look at human emissions...
Canto: Next time.

Saturday, December 19, 2009

RNA, complexity, and a change in the weather

RNAP in action during elongation
Jacinta: Right, now I've shown you the chemical structure of one base, adenine. In base pairing in RNA, adenine pairs with uracil, and guanine pairs with cytosine. According to what I've read in Crick, big pairs with small. In DNA, adenine and guanine are relatively big, thymine [and presumably uracil in RNA?] and cytosine are small. Here's a diagram of the chemical structure of uracil:

Canto: Right, only one ring, less components than adenine, certainly. So how and why do these bases pair off?
Jacinta: In DNA the two big and two small base pairs form a neat hydrogen bond. In RNA it's apparently more complicated - there are in fact other base pair bonds - but for our purposes it's the same story. On your comment about rings, yes, the big double-ring molecules, adenine and guanine, are called purines, and the single-ring molecules are called pyrimidines. I could go on, but I'm not sure if mastering all this detail, supposing we can, will get us far in understanding the organic universe.
Canto: Yes, and no. Obviously Darwin didn't know any of this stuff when puzzling over his barnacles and the diversity of species, but that doesn't mean we don't need to know it, or that it's not helpful to know it.
Jacinta: Well I can tell you it gets more complicated, vastly so.
Canto: Okay let's move away from structure and onto function.
Jacinta: In any case let's try to keep it broad. The DNA into RNA thing. An enzyme called RNA polymerase [RNAP], essential to all living organisms, constructs chains of RNA from DNA. Again, this is by no means a simple process, and it is of necessity highly regulated. For example in E coli,more than 100 transcription factors have been found to regulate the activity of RNAP. This enzyme is responsible for many products, including messenger RNA, the non-coding RNA including transfer RNA and ribosomal RNA, and many other recently discovered RNAs. It's an ongoing, burgeoning field of research. Eukaryotic cells have several different types of this enzyme, so it's hard to know where to begin...
Canto: Okay I get the picture, or I get the idea that we're never going to get the picture. Let's just change the subject completely shall we? I'd like to get on something more topical, like our warming planet.
Jacinta: Later, later, Can. Okay, clearly RNA stuff is getting away from us. What's a nucleic acid?
Canto: Something to do with the nuclei of cells, and an acid has a negative charge, a base has a positive charge.
Jacinta: On the right track. The phosphate groups in DNA in normal conditions have a negative charge, that's what makes it an acid, and yes, it's nuclear, except when there's no nucleus. RNA of course is also an acid, very similar to DNA, but without the missing 'oxy' group. The ribose of both these molecules is a sugar.
Canto: Well thanks, I'm definitely learning something here, and we'll get back to it, but i'm wondering if we can explore this more pressing topic next time. Is the rise of carbon dioxide in our atmosphere, presumably due to human activity, the burning of fossil fuel, deforestation and the like, causing the planet's surface to warm, or is the connection between our emissions and warming unproven, as many sceptics are saying?
Jacinta: Okay, we'll get right onto that one, for the sake of our species and many others.

Friday, December 4, 2009

starting from the base


Canto: You know, just as an aside on this earliest forms of life stuff, it's interesting how the pioneers of modern biology were interested in getting down to the smallest, simplest forms of life, and studying them, to see just how far down they could go, in size, and still find life. I mean they were asking, just how small can a living organism be?
Jacinta: Right, and they were no doubt amazed at the complexity of those little critters, once they developed microscopes powerful enough to detect them and look inside them.
Canto: Well you know Darwin took a microscope with him on the Beagle, a state-of-the-art instrument of the time, and his Beagle notes were more about zoophytes than anything else. Zoophytes were sea creatures - the term is obsolete now - that seemed to have the qualities of plants as well as animals. But he was also intrigued by what he called infusoria, another obsolete term, then given to what we now know are diverse forms of largely water-dwelling eukaryotic micro-organisms. And I'm sure his interest in such organisms ran along these 'how small can life be' lines.
Jacinta: And yet the pioneering microbiologist Christian Ehrenberg considered that there were no 'lower' creatures, and that 'the infusorian has the same sum of organisation-systems as a man'. These were the beginnings of heretical ideas, questioning the role of humanity as the pinnacle of the earth's, or God's, creation. Darwin was definitely being influenced by these new lines of thinking.
Canto: So anyway, we were talking about ribosomal RNA as I recall.
Jacinta: Well you know that the ribosome is the protein-making factory of the cell, right?
Canto: Of course. And so ribosomal RNA is - the RNA in ribosomes, right?
Jacinta: No, it's nowhere near as simple as that, mate. First we know that 'DNA makes RNA makes protein', but it's not a simple process. Certainly rRNA is central to that protein-making process, but there are two other forms of RNA, messenger RNA [mRNA] and transfer RNA [tRNA], that need to be understood and differentiated.
Canto: Yeah, I can see this is going to be horribly complex, but let's just do it. How does DNA make RNA and why does it make these three different types?
Jacinta: Well this first step is called transcription or RNA synthesis. We know that both DNA and RNA are nucleic acids.
Canto: Made up of nucleotides. But what's a nucleotide?
Jacinta: Okay, if you're serious, I'll tell you. A nucleotide has three basic components - a nucleobase, a five-carbon sugar, and a phosphate group [or two, or three]. A nucleobase is involved in base pairing in DNA and RNA. They're often called bases for short. The four bases in DNA are cytosine, guanine, adenine and thymine.In RNA the first three are the same, and uracil replaces thymine.
Canto: Fine, you've named some nucleobases, but what are they?
Jacinta: Well, if you want their chemical structure, you'll find all that here. But aren't we getting a little bogged down?
Canto: No, no, there's no use talking of RNA until we understand the basics, and that includes bases. Let's take it slowly, inch by painstaking inch.
Jacinta: Okay, you're the boss.

Source: Rebecca Stott: Darwin and the Barnacle. Faber & Faber, 2003.

Wednesday, December 2, 2009

more speculations on earth's early days

Canto: Going back to the origin of life on Earth, one of the most interesting pieces of early speculation came from Charles Darwin, who wrote to his friend Joseph Hooker in 1871:

It is often said that all the conditions for the first production of a living organism are present, which could ever have been present. But if (and Oh! what a big if!) we could conceive in some warm little pond, with all sorts of ammonia and phosphoric salts, light, heat, electricity, etc., present, that a protein compound was chemically formed ready to undergo still more complex changes, at the present day such matter would be instantly devoured or absorbed, which would not have been the case before living creatures were formed.
Jacinta: Yes, and much later, in the 1950s, the famous Miller-Urey experiment was carried out to try to reproduce life or something like it out of what were then thought to be the conditions of the primordial Earth's atmosphere, including lots of ammonia and methane.
Canto: In fact, the gases they used were those two plus hydrogen and water. Miller then ran a continuous electric current through this mix, to simulate lightning, again believed to be a common feature of the early earth system. After a week, the finding was that more than ten percent of the carbon in the system [provided by the methane] had been transformed into organic compounds, including amino acids, the building blocks of proteins. It seemed almost absurdly easy, then, to create, from these gases, material which was a giant step along the way towards life.
Jacinta: And was this experiment able to be replicated?
Canto: Oh yes and they have pushed further on. One of the interesting things is that, in the years following this experiment, the scientific consensus regarding the earth's early atmosphere moved away from NH3 and CH4 [ammonia and methane] to CO2, CO and N2 from volcanic activity, with UV radiation reducing the ammonia and methane to a short life span. 
Jacinta: But now things have changed again, and it's believed - by some of course - that Stanley Miller and Harold Urey, together with their brilliant predecessor Aleksandr Oparin, might've been right all along. Studies of the outgassing of chondrites [particular types of meteorite fragments representative of early planetary formation] show a preponderance of just the sort of gasses these early experimenters chose to work with.
Canto: So, just how significant was this work, and is it the only pathway to creating life? 
Jacinta: Well, there's the RNA pathway. Apparently, small segments of RNA can form quite easily, though it's less stable than DNA [they're actually very similar molecules], which makes more sense as info-storage molecule essential to life as we know it, but there has been talk for a long time now of a kind of pre-existing RNA world. Though maybe this thesis is already out-dated.
Canto: I don't know about that. Since the early days after Watson and Crick worked out the structure of DNA, when DNA and proteins were all the go, RNA, especially ribosomal RNA, has come to be recognised as surprisingly multifarious in its functions, both potential and actual. 
Jacinta: Good, we'll have to look more closely into all that next time.  

Friday, November 13, 2009

the oldest photosynthesizing organism

Fig. 1, Origin of life and oxygen evolving organisms based on geological records (from Xiong and Bauer, 2002)

Jacinta: It's probable that photosynthesis evolved slowly, bitsily, growing gradually more sophisticated, more complete - by which I mean growing to be what we recognize it as today. For example, modern organisms use photosynthesis to make oxygen, and starches and sugars, from water, but in earlier environments it's likely that something other than water was used.
Canto: Right, if water can be utilized by some sort of redox reaction, then so can other molecules. But how long has water existed on Earth?

Jacinta: Don't sidetrack me Canto. One of the world's foremost authorities on photosynthesis and its origins is Carl Bauer of Indiana University. In the graphic above, taken from the website of Bauer's lab, he presents an outline of the origin of 'oxygen evolving organisms', by which he presumably means photosynthesizing organisms that generate oxygen.
Canto: Right, so he's taking biological carbon fixation back to 3.8 billion years or so.
Jacinta: At that time, our atmosphere was rich in carbon dioxide. In any case, no matter what molecules were used to produce fuel for metabolism, Bauer has found, through detailed phylogenetic analysis, that Rhodobacter, aka purple bacteria are the oldest lineage of photosynthetic organisms on the planet.
Canto: But they don't 'evolve oxygen' as he puts it?
Jacinta: Right, they're anoxygenic. In fact, there are five known branches of microbes that engage in chlorophyll-based photosynthesis, and only one of them, cyanobacteria, evolve oxygen.
Canto: Can you explain what phylogenetic analysis might be - not for me of course, but for our vast readership out there.
Jacinta: Of course. To examine the phylogeny of an organism, or indeed an organ, is to trace its evolutionary development. The phylogenetic analysis we're talking about here involves molecular phylogenetics. Closely related organisms have similar molecular structures, re their genetic material and their proteins. There's a pattern of similarity to related organisms traceable back in time, revealing a pattern of evolution. There's more to it than that, but it'll do for now.
Canto: So tell me more about these anoxygenic purple bacteria.
Jacinta: Well, Rhodobacter have long been of interest to molecular biologists because of their interesting metabolic processes, and they're the most studied of micro-organisms. They live in water - freshwater or marine environments, and their diverse methods of survival - not just through photosynthesis but through a variety of processes - has made them a favourite for study, due to our own concerns about survival.
Canto: Okay, I'll keep them in mind - but you've pointed out that they're aquatic, which raises the question again - when did water first appear on Earth, and what about non-photosynthesizing organisms that might be older than Rhodobacter?
Jacinta: Yes, all that is interesting, along with the actual origins of these Rhodobacter, and the origins of viruses, which we haven't gotten into as yet. Everybody is obsessed with water as an essential source of life, so that when we look for life elsewhere, we tend to look for signs of water - but it ain't necessarily so.
Canto: Wow, lots to explore there - can't wait for our next little chat!

Wednesday, November 11, 2009

fixation, redox reactions, nucleotides and more

ATP - see the triphosphate bit?

Jacinta: Okay, so since we're both thoroughgoing obsessional types, we'll have to get to the bottom of photosynthesis, at least to clarify some of the cycles and molecules and such that we referred to last time.
Canto: Great, we're talking the same language. So tell me about this fixing, in relation to carbon dioxide. I'm sure I've also heard of nitrogen fixing...
Jacinta: Well let's not get too sidetracked, but fixation, in chemical terms, means transforming a substance, or molecule...
Canto: Or molecular substance?
Jacinta: Yeah, into a more usable form, like ammonia, in the case of atmospheric nitrogen.
Canto: N2 into NH3, I get it.
Jacinta: Right, though of course much more complicated. And carbon fixation is hideously complicated. The Calvin cycle, worked out many decades ago, basically traces the carbon fixation process. All I can competently say at this stage is that the key enzyme in the process has come to be known as rubisco. I won't say anything more about NADPH - it's essential in the photosynthetic process in chloroplasts. I could say more but it wouldn't make much sense to either of us.
Canto: It acts as a reducing agent, doesn't it?
Jacinta: Yes. You know about oxidation-reduction?
Canto: I know of it. If I was a hands-on biochemist or whatever I'm sure I'd know about it.
Jacinta: Actually redox reactions aren't too difficult to understand. They generally involve electron transfer. The reductant, or reducing agent transfers electrons to the oxidant, or oxidizing agent. So the reducing agent gets oxidized, and the oxidizing agent gets reduced.
Canto: Believe it or not, I follow you. So in the Calvin cycle, NADPH is the reduced form of NADP+, and therefore NADP+ is the oxidized form of NADPH.
Jacinta: You read that somewhere mate.
Canto: Yes but it makes sense all the same. So what's ATP? That's a biggie isn't it?
Jacinta: Adenosine triphosphate is indeed a very important wee nucleotide, the key molecule in cellular metabolism.
Canto: Let's do each other's heads in - what's a nucleotide, and what exactly is metabolism?
Jacinta: Come on Canto, metabolism's just what you think it is - it's the breaking down of food to construct proteins, nucleic acids and so forth. Without which not. A nucleotide is a molecule with a particular structure, found in all cells performing various metabolic functions. They also are the bases of polymeric nucleic acids, as well as being the structural units of DNA and RNA.
Canto: Well read Jacinta.
Jacinta: Well digested encore.
Canto: Whatever you say mate. So, getting back to photosynthesis, how did plants, or bacteria, start getting into this?
Jacinta: You could just as well ask how did more complex organisms start using oxygen and other nutrients to sustain themselves, or how did pre-photosynthesizing organisms, or non-photosynthesizing organisms start utilizing whatever they utilized...
Canto: I could just as well, but I asked about photosynthesis.
Jacinta: Okay, it's known that photosynthesis evolved in bacteria and that it's been going on on our planet for at least 2.5 billion years. As to the how, I'll try to answer that in the next post.

Saturday, November 7, 2009

more on photosynthesis

a simplified version of glyceraldehide [C3H6O3], a triose three carbon sugar used in photosynthesis

Canto: So is it to be photosynthesis today?
Jacinta: Maybe. Not all life depends on photosynthesis, you realize.
Canto: Uhh, yes of course, but tell me what photosynthesis is, then I can be clear about what it is that life doesn't entirely depend on.
Jacinta: Well, most people know that the oxygen around us, the oxygen we breathe, that we depend upon, has been produced by microbial and planktonic life, in the oceans mainly. Now this oxygen is a kind of waste product of a process that transforms oxides into sugars by means of sunlight. What's really important about photosynthesis, apart from its obvious importance for us, is that it's a process that creates 'food' from the most ordinary, inanimate chemicals around - carbon dioxide and water. Did you know that water was an oxide?
Canto: No. I knew that it contained oxygen, though.
Jacinta: Well there you go. Would you like a glass of dihydrogen monoxide?
Canto: You can't get rid of me that easily. Okay, so your plankton or whatever takes a ray of sunlight, or a photon or whatever, and synthesizes sugars out of carbon dioxide or water. That's as clear as mud.
Jacinta: Well, I seem to remember that the exact mechanisms were worked out only quite recently. Let's take plant photosynthesis. Light energy is absorbed by proteins containing chlorophyll...
Canto: Hang on, hang on - absorbed? What's this absorbed? Is that where a miracle occurs?
Jacinta: A miracle is just something we haven't examined sufficiently.
Canto: Oh how prosaic, how materialist.
Jacinta: Okay I'm not sure if absorption is a technical term but sunlight excites molecules, and I presume that's the key. The excitation results in electron transfer reactions. Chlorophyll is involved, absorbing the light due to its pigmentation, and promoting electrons to higher energy levels, creating free energy.
Canto: The electrons then release energy in returning to their stable or ground state.
Jacinta: Too right. When an electron goes into a higher energy state, the molecule it inhabits is said to have a higher reduction potential, so that it tends to donate electrons. That's how light energy becomes chemical energy, apparently.
Canto: How?
Jacinta: Get an education Canto.
Canto: No I think I understand.
Jacinta: Well what follows is very complex and I can't say I fully understand it myself. Electrons are donated to electron acceptors in an electron transfer chain. There's a whole heap of them, and what results at the end of this chain is a reduced molecule called NADPH. This molecule, along with ATP [which is also produced through this process], is involved in the Calvin cycle which fixes carbon dioxide into triose sugars.
Canto: What? Do you really know what you're talking about Jass? What's this thing called 'fixing' I've heard so much about? What are these molecules? What's a triose sugar?
Jacinta: Okay, you’re right, I’ve not got my head around those details, but there’s so much to explore in this universe, mate. I’ll answer your questions, but I’m also interested in pre-photosynthetic life, and much else besides.
Canto: I can’t wait.

Monday, November 2, 2009

cyanobacteria, meteorites, fossils and photosynthesis

Canto: I'm still wondering about life.
Jacinta: There's a lot to wonder about.
Canto: Well, bearing in mind those rough and ready rules, what is the earliest form of life we know of?
Jacinta: Nobody knows. There are big arguments about the status of viruses, but the earliest candidate we know of, I mean the earliest fossil, was some sort of prokaryote, something like a modern cyanobacterium.
Canto: But it's unlikely that the earliest fossil was the earliest life form. I mean, I know very little about cyanobacteria, and obviously prokaryotes are much less complex than eukaryotes, but even one of those things couldn't have just - spontaneously generated. There must've been precursors.
Jacinta: Surely, but it's worth thinking about timelines here. The earliest prokaryotic fossil - the oldest know fossil of any kind - dates to 3.8 billion years ago. The earth was formed 4.6 billion years ago, and clearly it would've taken some time for it to be ready to sustain life.
Canto: Not so fast about that. We always think of life as we know it,we of little imagination. Look at the archaea so recently discovered. If life can thrive in hot volcanic springs, that certainly extends the range of possibilities.
Jacinta: Good point, but there's another interesting thing about this 3.8 billion date. Have you heard of the Late Heavy Bombardment?
Canto: Come on, forget about Armageddon, this is getting interesting.
Jacinta: No, really, what astronomers call the LHB took place just about 3.8 billion years ago - a heavy shower of meteorites in this region. All our evidence is from the Moon, which as you know is almost as pock-marked as Manuel Noriega's mug. Being a more or less dead rock, the Moon still bears the scars, whereas Earth's surface is shifting and spewing and subducting all over the place, so there's no direct terrestrial evidence of this shower, but it's a reasonable assumption...
Canto: Aha! Life from outer space.
Jacinta: Yes, well, that's one of many hypotheses. It's all very speculative.
Canto: Okay, I won't get carried away. Tell me about this cyanobacteria.
Jacinta: Uhh - do you mean the earliest fossils or cyanobacteria in general?
Canto: Dunno.
Jacinta: Well, cyanobacteria are mainly associated with marine environments, and they're also known as blue green algae. 'Cyano' comes from the Greek for 'blue'.
Canto: Right, as in Cyano de Bergerac, the guy with the big blue nose.
Jacinta: They've been around for a long time, engaging in what's called oxygenating photosynthesis to help transform our planet's atmosphere into something habitable for big beasties like ourselves.
Canto: Wow, photosynthesis, tell me about photosynthesis. But first, you mentioned blue green algae. Now, I would've thought algae were eukaryotic. 
Jacinta: Ah yes, nomenclature and taxonomy, always fraught. The term 'blue green algae' came in long before those distinctions were made and so it has stuck. As to photosynthesis, that's one of those key and fateful processes that link the organic to the inorganic and make our fragile biosphere such an astonishing place.
Canto: You're astonished eyes delight me Jacinta, let's shore up our fragile relationship for a while before you reveal all.
Jacinta: Okay, let me reveal all before we begin. Symbiosis here we come.

Frank Ryan, Darwin's blind spot: evolution beyond natural selection. Thomson Texere, 2003


Tuesday, October 27, 2009

life with c & j

Canto: Hi, what's new?
Jacinta: Well I've been wondering about life, in a shallow sort of way.
Canto: What brought that on?
Jacinta: Some reading, of course. What else? Sparks to brighten the imagination.
Canto: To set it aflame.
Jacinta: The analytic imagination.
Canto: Bien entendu. So what about life?
Jacinta: Well, questions lead to more questions. What's the most basic form of life you can think of?
Canto: Hmmm. A virus? A chromosome? Is a chromosome alive? Remember the selfish gene theory? Was it a theory? To be selfish you have to be alive, don't you?
Jacinta: That's a lot of questions. Well done. Generally, I'm not sure that genes are considered to be alive, though they're obviously essential components of life. As we know it.
Canto: Probably depends which microbiologist you're talking to.
Jacinta: They've developed rules about what constitutes a living entity. Or someone has. But rules are made to be broken.
Canto: Let's hear them.
Jacinta: Well, first [but not necessarily first], such an entity has to metabolize. That's to say, it has to absorb something and burn it as fuel to maintain and grow itself. I mean, to provide it with energy. Which rules chromosomes out, maybe?
Canto: I haven't accepted any rules. Anyway, what is a chromosome? Tell me that.
Jacinta: Shit Canto, you gorgeous thing, don't sidetrack me. Let's just spell out these rules first, okay. The second rule is that life has complexity and organisation.
Canto: Right. No living thing that we know of, none that is uncontroversially accepted, prokaryotic or eukaryotic, is simple.
Jacinta: Absolutely. Bacteria are anything but simple. Third rule, but they're not in any order. All living entities reproduce.
Canto: That's almost too obvious. They produce again. Not quite the same as replicate. They don't produce replicas.
Jacinta: Well, near enough.
Canto: Near enough, indeed. Like two circles, neither of them exact.
Jacinta: Exactly. Fourthly, living entities develop. They grow, they absorb, they move, they struggle and suffer.
Canto: Death?
Jacinta: Let's not go there. Fifth, they evolve. That brings us back to those imperfect reproductions of course.
Canto: Like Chinese whispers, they change with changing conditions. They adapt. They want to preserve their identities and they strive for something fresh.
Jacinta: Worth exploring, but not now Canto, not now. Last rule, living entities are autonomous. They're not directed by or entirely dependent on any other living entity.
Canto: Ooh, that's a tricky one. Remind me never to make babies with you Jacinta. You'd see it as a living entity and therefore autonomous, and I'd be stuck with all the feeding, arsewiping, example-setting, obstacle-reducing, etc etc.
Jacinta: As if. But you're right, this is the most troublesome rule, and maybe the weakest. Where would a bacterium be without a colony - or an ant, for that matter?
Canto: A rough and ready set of rules.
Jacinta: Makeshift.
Canto: A starting point. So what is life?
Jacinta: I'm not sure, but here's to it loverboy.

Peter Ward, Life as we do not know it: the NASA search for [and synthesis of] alien life. Viking, 2005