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Abiogenesis – LUCA, gradients, amino acids, chemical evolution, ATP and the RNA world

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Jacinta: So now we’re thinking of the Earth 4 billion years BP, with an atmosphere we’re not quite sure of, and we want to explore the what and when of the first life forms. Haven’t we talked about this before?

Canto: Yeah we talked about the RNA world and viroids and abiogenesis, the gap between chemistry and biology, inter alia. This time we’re going to look more closely at the hunt for the earliest living things, and the environments they might’ve lived in.

Jacinta: And it started with one, it must have. LUA, or LUCA, the last universal common ancestor. Or the first, after a number of not-quite LUCAs, failed or only partially successful attempts. And finding LUCA would be much tougher than finding a viroid in a haystack, because you’re searching through an immensity of space and time.

Canto: But we’re much closer to finding it than in the past because we know so much more about what is common to all life forms.

Jacinta: Yes so are we looking definitely at the first DNA-based life form or are we probing the RNA world again?

Canto: I think we’ll set aside the world of viroids and viruses for now, because we want to look at the ancestor of all independently-existing life forms, and they’re all DNA-based. And we also know that LUCA used ATP. So now I’m going to quote from an essay by Michael Le Page in the volume of the New Scientist Collection called ‘Origin, Evolution, Extinction’:

How did LUCA make its ATP? Anyone designing life from scratch would probably make ATP using chemical reactions inside the cell. But that’s not how it is done. Instead energy from food or sunlight is used to power a protein ‘pump’ that shunts hydrogen ions – protons – out of the cell. This creates a difference in proton concentration, or a gradient, across the cell membrane. Protons then flow back into the cell through another protein embedded in the membrane, which uses the energy to produce ATP.

Jacinta: You understand that?

Canto: Sort of.

Jacinta: ‘Energy from food or sunlight is used..’ that’s a bit of a leap. What food? The food we eat is organic, made from living or formerly living stuff, but LUCA is the first living thing, its food must be purely chemical, not biological.

Canto: Of course, not a problem. I believe the microbes at hydrothermal vents live largely on hydrogen sulphide, and of course sunlight is energy for photosynthesising oganisms such as cyanobacteria.

Jacinta: Okay, so your simplest living organisms, or the simplest ones we know, get their energy by chemosynthesis, or photosynthesis. Its energy, or fuel, not food.

Canto: Semantics.

Jacinta: But there are other problems with this quote re abiogenesis. For example, it’s talking about pre-existent cells and cell membranes. So assuming that cells had to precede ATP.

Canto: No, he’s telling us how cells make ATP today. So we have to find, or synthesise, all the essential ingredients that make up the most basic life forms that we know cell membranes, proteins, ATP and the like. And people are working towards this.

Jacinta: Yes and first of all they created these ‘building blocks of life’, as they always like to call them, amino acids, in the Miller-Urey experiments, since replicated many times over, but what exactly are nucleic acids? Are they the same things as nucleic acids?

Canto: Amino acids are about the simplest forms of organic compounds. It’s probably better to call them the building blocks of proteins. There are many different kinds, but generally each contain amine and carboxyl groups, that’s -NH2 and -COOH, together with a side chain, called an R group, which determines the type of amino acid. There’s a whole complicated lot of them and you could easily spend a whole lifetime fruitfully studying them. They’re important in cell structure and transport, all sorts of things. We’ve not only been able to create amino acids, but to combine them together into longer peptide chains. And we’ve also found large quantities of amino acids in meteorites such as the Murchison – as well as simple sugars and nitrogenous bases. In fact I think we’re gradually firming up the life-came from-space hypothesis.

Jacinta: But amino acids and proteins aren’t living entities, no matter how significant they are to living entities. We’ve never found living entities in space or beyond Earth. Your quote above suggests some of what we need. A boundary between outside and inside, a lipid or phospho-lipid boundary as I’ve heard it called, which must be semi-permeable to allow chemicals in on a very selective basis, as food or fuel.

Canto: I believe fatty acids formed the first membranes, not phospho-lipids. That’s important because we’ve found that fatty acids, which are made up of carbon, hydrogen and oxygen atoms joined together in a regular way, aren’t just built inside cells. There’s a very interesting video called What is Chemical Evolution?, produced by the Center for Chemical Evolution in the USA, that tells about this. Experimenters have heated up carbon monoxide and hydrogen along with many minerals common in the Earth’s crust and produced various carbon compounds including fatty acids. Obviously this could have and can still happen naturally on Earth, for example in the hot regions maybe below or certainly within the crust. It’s been found that large concentrations of fatty acids aggregate in warm water, creating a stable, ball-like configuration. This has to do with the attraction between the oxygen-carrying heads of fatty acids and the water molecules, and the repulsion of the carbon-carrying tails. The tails are forced together into a ball due to this repulsion, as the video shows.

fatty acids, with hydrophobic and hydrophilic ends, aggregating in solution

Jacinta: Yes it’s an intriguing video, and I’m almost feeling converted, especially as it goes further than aggregation due to these essentially electrical forces, but tries to find ways in which chemical structures evolve, so it tries to create a bridge between one type of evolution and another – the natural-selection type of evolution that operates upon reproducing organisms via mutation and selection, and the type of evolution that builds more complex and varied chemical structures from simpler compounds.

Canto: Yes but it’s not just the video that’s doing it, it’s the whole discipline or sub-branch of science called chemical evolution.

Jacinta: That’s right, it’s opening a window into that grey area between life and non-life and showing there’s a kind of space in our knowledge there that it would be exciting to try and fill, through observation and experimentation and testable hypotheses and the like. So the video, or the discipline, suggests that in chemical evolution, the highly complex process of reproduction through mitosis in eukaryotic cells or binary fission in prokaryotes is replaced by repetitive production, a simpler process that only takes place under certain limited conditions.

Canto: So under the right conditions the balls of fatty acids grow in number and themselves accumulate to form skins, and further forces – I think they’re hydrostatic forces – can cause the edges of these skins to fuse together to create ‘containers’, like vesicles inside cells.

Jacinta: So we’re talking about the creation of membranes, impermeable or semi-permeable, that can provide a safe haven for, whatever…

Canto: Yes, and at the end of the video, other self-assembling systems, such as proto-RNA, are intriguingly mentioned, so we might want to find out what’s known about that.

Jacinta: I think we’ll be doing a lot of reading and posting on this subject. I find it really fascinating. These limited conditions I mentioned – limited on today’s Earth surface, but not so much four billion years ago, include a reducing atmosphere lacking in free oxygen, and high temperatures, as well as a gradient – both a temperature gradient and a sort of molecular or chemical gradient, from more reducing to more oxidising you might say. These conditions exist today at hydrothermal vents, where archaebacteria are found, so researchers are naturally very interested in such environments, and in trying to replicate or simulate them.

Canto: And they’re interested in the boundary between chemical and biological evolution, and reproduction. There are so many interesting lines of inquiry, with RNA, with cell membranes….

Jacinta: Researchers are particularly interested in alkaline thermal vents, where alkaline fluids well up from beneath  the sea floor at high temperatures. When this fluid hits the ocean water, minerals precipitate out and gradually create porous chimneys up to 60 metres high. They would’ve been rich in iron and sulphide, good for catalysing complex organic reactions, according to Le Page. The temperature gradients created would’ve favoured organic compounds and would’ve likely encouraged the building of complexity, so they may have been the sites in which the RNA world began, if it ever did.

a hydrothermal vent off the coast of New Zealand. Image from NOAA

a hydrothermal vent off the coast of New Zealand. Image from NOAA

Canto: So I think we should pursue this further. There are a lot of researchers homing in on this area, so I suspect further progress will be made soon.

Jacinta: Yes, we need to explore the exploitation of proton gradients, the development  of proton pumps and the production of ATP, leaky membranes and a whole lot of other fun stuff.

Canto: I think we need to get our heads around ATP and its production too, because that looks pretty damn complex.

Jacinta: Next time maybe.

 

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Written by stewart henderson

July 29, 2016 at 8:51 am

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