Archive for the ‘abiogenesis’ Category
introducing myself to abiogenesis, sort of
Yes, watch out for the creationists and their ultra ultra ultra male god…
So, more sciencey stuff by a non-scientist, this time on how life came about from non-life, and where exactly the boundary lies. I seem to recall, years ago, that Craig Venter, something of a maverick biochemist, or whatever, was competing with the ‘official’, i.e government-funded, program, to map the human genome, and it might’ve come out as a tie, but don’t quote me. And then Venter and Co went on to work on abiogenesis, and then I lost touch…
I was reminded of all this when I watched a video featuring a Christian fundamentalist and biochemist, James Tour (I keep thinking James Tool) and his fight with mainstream biochemists on the difficulty/impossibility of life coming from non-life, because, of course, God – or as Americans like to call him, Guard, because, as we know, Guard blesses America, and safeguards Him (because, as we know America is as fundamentally male as Guard) on an ongoing basis.
In googling Mr Tour, the first thing I came up with was ‘Is James Tour religious?’ The answer, of course, is another question – Do bears shit in the woods?
But let’s not get too lazy by mocking US silliness ad nauseam. In the video, Tour is shown violently lashing out at claims that there is any possible chemical pathway for something living – that’s to say self-sustaining – to have come from something purely chemical, no matter how complex. And yet, in spite of Tour’s noisy, over-the-top attacks on the whole abiogenesis program, presumably because it was ‘playing Guard’, in the end, when talking to a sympathetic and doubtless Christian interviewer, he admitted that we might one day work out the process that sparked life, in spite of its ‘infinite’ (or near-infinite) complexity, because, after all, Guard is infinite (or near-infinite?)….
I suspect he might regret that admission.
So, after all that, how are we going on the abiogenesis front? First, a little history. Spontaneous generation was once considered very much a thing, in the days before microscopes and such, and this is unsurprising, as I myself have seen maggots ‘suddenly’ infesting something rotting in a cupboard in my lazy house-sharing youth. Such situations caused considerable debate in earlier centuries, until better technologies and experiments, in particular the work of Louis Pasteur, finally disproved the concept. But this, of course, left a gap – if there was no spontaneous generation of life, and evolution by natural selection had nothing to say on the subject, then – maybe Guard? Or Guard of the Gap?
But enough of Guard, we already have complex collections of molecules, such as viruses, which seem to bridge the gap between life and non-life through their ability to replicate rapidly under particular conditions – but not independently. According to the RationalWiki on the subject:
Abiogenesis is not a single step event, but a process. Biological life has the properties or capabilities of organization, metabolism, homeostasis, growth, reproduction, response, and evolution.
So, it’s generally considered likely that abiogenesis cannot be sheeted home to one semi-miraculous event – more likely there were various combinatorial chemical developments that more or less succeeded in maintaining the above-mentioned properties. At some stage in this process, a stable life-form emerged that combined these ingredients effectively. This life-form has been dubbed the last universal common ancestor (LUCA).
Three elements appear to be essential – carbon, and hydrogen and oxygen in the form of water. The compounds focussed on by biochemists studying the subject are lipids, which can form membranes, carbohydrates, which can provide energy, amino acids, and nucleic acids (DNA and RNA) for reproduction.
I’m fairly clueless, so I’ll start with amino acids. Wikipedia tells me they’re essential for ‘protein metabolism’, but apparently not all amino acids are involved in this process – far from it. Of the more than 500 amino acids that we know to exist, there are only 22 that are ‘incorporated into proteins’ and into the genetic code of all life. They’re called proteinogenic amino acids, or α-amino acids (alpha amino acids).
But what exactly is an amino acid? Obviously it’s an acid, which we tend to think is something negative that breaks down and destroys stuff. But then amino makes me think of animation, in a scrambled sort of way. I mean, life? They are described as organic molecules, or organic compounds after all. Why? Apparently, for many biochemists an organic compound is one containing carbon. The proteinogenic amino acids are the ‘raw material’ assembled by our ribosomes (by the ribosomes of all living cells?) into the multitudinous peptides and proteins that do so much mysterious work throughout our bodies. I’m getting most of this from Wikipedia, a fantastic resource that just keeps getting fantasticker. It’s article on abiogenesis is itself virtually book-length, and the links take you to dozens of other useful and lengthy articles.
So how did amino acids come into being? Before ribosomes, the amino acid-making machines in our cells, came into being, that is. Well, first we needed the elemental ingredients, and they existed billions of years ago, at the Earth’s formation, and even before the Sun had coalesced into the star we know today. In a PubMed article abstract, ‘The origin of the biologically coded amino acids’ (that’s to say the proteinogenic ones), the problem/solution is put this way:
The types of amino acids produced depend on the conditions which prevailed at the time of synthesis, which remain controversial. The selection of the biological set is likely due to chemical and early biological evolution acting on the environmentally available compounds based on their chemical properties. Once life arose, selection would have proceeded based on the functional utility of amino acids coupled with their accessibility by primitive metabolism and their compatibility with other biochemical processes.
So, before there was biological evolution there was chemical evolution, which also may have been a matter of fits and starts. For example, some have speculated that carbonaceous meteorites raining down on the early Earth may have provided a spark, or a boost. These speculations are forward-looking from the non-living, in a sense, while another approach is backward-looking from known candidates for LUCA. Here’s how Wikipedia puts it:
It appears there are 60 proteins common to all life and 355 prokaryotic genes that trace to LUCA; their functions imply that the LUCA was anaerobic with the Wood–Ljungdahl pathway, deriving energy by chemiosmosis, and maintaining its hereditary material with DNA, the genetic code, and ribosomes. Although the LUCA lived over 4 billion years ago (4 Gya), researchers believe it was far from the first form of life. Earlier cells might have had a leaky membrane and been powered by a naturally occurring proton gradient near a deep-sea white smoker hydrothermal vent.
I won’t pretend I understand all that, but prokaryotes are unicellular organisms, and anaerobic respiration utilises ‘electron transport chains’ other than – and less efficient than – oxygen. The Wood-Ljungdahl pathway is, inter alia, a proposed mechanism – still controversial – for the anaerobic prokaryotic life found at deep sea alkaline hydrothermal vents, in the late 1970s.
The key problem, it seems to me, is that of effective replication, way back in the day. DNA and RNA are both very complex molecules, and so they didn’t just spring into existence. The Wikipedia article articulates the problem in a sentence that’s easy to simply overlook:
Prebiotic synthesis creates a range of simple organic compounds, which are assembled into polymers such as proteins and RNA.
We’re still quite a way from understanding that ‘assembly’ stage, though we’ve managed a bit of prebiotic synthesis, but there’s no reason to assume that we can’t work it all out. Now if we could find simple, perhaps differently-organised life or proto-life on other planets or moons…
That’s astrobiology, apparently. And Wikipedia can explain it all better than me, so excuse my laziness.
The 2015 NASA strategy on the origin of life aimed to solve the puzzle by identifying interactions, intermediary structures and functions, energy sources, and environmental factors that contributed to the diversity, selection, and replication of evolvable macromolecular systems, and mapping the chemical landscape of potential primordial informational polymers. The advent of polymers that could replicate, store genetic information, and exhibit properties subject to selection was, it suggested, most likely a critical step in the emergence of prebiotic chemical evolution. Those polymers derived, in turn, from simple organic compounds such as nucleobases, amino acids, and sugars that could have been formed by reactions in the environment. A successful theory of the origin of life must explain how all these chemicals came into being.
Hoping to write about this more in the future, exploring any new developments, if any.
References
https://rationalwiki.org/wiki/Abiogenesis
https://en.wikipedia.org/wiki/Abiogenesis