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.

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.

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.

starting from the base

adenine

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.

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.