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a little about the chemistry of water and its presence on Earth

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So I now know, following my previous post, a little more than I did about how water’s formed from molecular hydrogen and oxygen – you have to break the molecular bonds and create new ones for H2O, and that requires activation energy, I think. But I need to explore all of this further, and I want to do so in the context of a fascinating question, which I’m hoping is related – why is there so much water on Earth’s surface?

When Earth was first formed, from planetesimals energetically colliding together, generating lots of heat (which may have helped with the creation of H2O, but not in liquid form??) there just doesn’t seem to have been a place for water, which would’ve evaporated into space, wouldn’t it? Presumably the still-forming, virtually molten Earth had no atmosphere. 

The most common theory put out for Earth’s water is bombardment in the early days by meteors of a certain type, carbonaceous chondrites. These meteors were formed further out from the sun, where water would have frozen. Carbonaceous chondrites are known to contain the same ratio of heavy water to ‘normal’ water as we find on Earth. Heavy water is formed with deuterium, an isotope of hydrogen containing a neutron as well as the usual proton. Obviously there had to have been plenty of these collisions over a long period to create our oceans. Comets have been largely ruled out because, of the comets we’ve examined, the deuterium/hydrogen ratio is about double that of the chondrites, though some have argued that those comets may be atypical. Also there’s some evidence that the D/H ratio of terrestrial water has changed over time.

So there are still plenty of unknowns about the history of Earth’s water. Some argue that volcanism, along with other internal sources, was wholly or partly responsible – water vapour is one of the gases produced in eruptions, which then condensed and fell as rain. Investigation of moon rocks has revealed a D/H ratio similar to that of chondrites, and also that of Earth (yes, there’s H2O on the moon, in various forms). This suggests that, since it has become clear that the Moon and Earth are of a piece, water has been there on both from the earliest times. Water ice detected in the asteroid belt and elsewhere in the solar system provides further evidence of the abundance of this hardy little molecule, which enriches the hypotheses of researchers. 

But I’m still mystified by how water is formed from molecular, or diatomic, hydrogen and oxygen. It occurs to me, thanks to Salman Khan, that having a look at the structural formulae of these molecules, as well as investigating ‘activation energy’, might help. I’ve filched the ‘Lewis structure’ of water from Wikipedia.

It shows that hydrogen atoms are joined to oxygen by a single bond, the sharing of a pair of electrons. They’re called polar covalent bonds, as described in my last post on the topic. H2 also binds the two hydrogen atoms with a single covalent bond, while O2 is bound in a double covalent bond. (If you’re looking for a really comprehensive breakdown of the electrochemical structure of water, I recommend this site).

So, to produce water, you need enough activation energy to break the bonds of H2 and O2 and create the bonds that form H2O. Interestingly, I’m currently reading The Emerald Planet, which gives an example of the kind of activation energy required. The Tunguska event, an asteroid visitation in the Siberian tundra in 1908, was energetic enough to rip apart the bonds of molecular nitrogen and oxygen in the surrounding atmosphere, leaving atomic nitrogen and oxygen to bond into nitric oxide. But let’s have a closer look at activation energy. 

So, according to Wikipedia:

In chemistry and physics, activation energy is the energy which must be available to a chemical or nuclear system with potential reactants to result in: a chemical reaction, nuclear reaction, or various other physical phenomena.

This stuff gets complicated and mathematical very quickly, but activation energy (Ea) is measured in either joules (or kilojoules) per mole or kilocalories per mole. A mole, as I’ve learned from Khan, is the number of atoms there are in 12g of carbon-12. So what? Well, that’s just a way of translating atomic mass units (amu) to grams (one gram equals one mole of amu). 

The point is though that we can measure the activation energy, which, in the case of molecular reactions, is going to be more than the measurable change between the initial and final conditions. Activation energy destabilises the molecules, bringing about a transition state in which usually stable bonds break down, freeing the molecules to create new bonds – something that is happening throughout our bodies at every moment. When molecular oxygen is combined with molecular hydrogen in a confined space, all that’s required is the heat from a lit match to start things off. This absorption of energy is called an endothermic reaction. Molecules near the fire break down into atoms, which recombine into water molecules, a reaction which releases a lot of energy, creating a chain of reactions until all the molecules are similarly recombined. From this you can imagine how water could have been created in abundance during the fiery early period of our solar system’s evolution. 

I’ll end with more on the structure of water, for my education. 

As a liquid, water has a structure in which the H-O-H angle is about 106°. It’s a polarised molecule, with the negative charge on the oxygen being around 70% of an electron’s negative charge, which is neutralised by a corresponding positive charge shared by the two hydrogen atoms. These values can change according to energy levels and environment. As opposite charges attract, different water molecules attract each other when their H atoms are oriented to other O atoms. The British Chemistry professor Martin Chaplin puts it better than I could:

This attraction is particularly strong when the O-H bond from one water molecule points directly at a nearby oxygen atom in another water molecule, that is, when the three atoms O-H O are in a straight line. This is called ‘hydrogen bonding’ as the hydrogen atoms appear to hold on to both O atoms. This attraction between neighboring water molecules, together with the high-density of molecules due to their small size, produces a great cohesive effect within liquid water that is responsible for water’s liquid nature at ambient temperatures.

We’re all very grateful for that nature. 

Written by stewart henderson

September 24, 2018 at 10:32 am

Posted in science, chemistry, water

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Always chemical: how to reflect upon naturopathic remedies

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most efficacious in every case

So here’s an interesting story. When I was laid up with a bronchial virus (RSV) a few weeks ago, coughing my lungs up and having difficulty breathing, with a distinct, audible wheeze, I was offered advice, as you do, by a very well-meaning person about a really effective treatment – oregano oil. This person explained that, on two occasions, he’d come down with a bad cough and oregano oil had done the trick perfectly where nothing else worked.

I didn’t try the oregano oil. I followed my doctor’s recommendation and used the symptom-relieving medications described in a previous post, and I’m much better now. What I did do was look up what the science-based medicine site had to say about the treatment (I’d never heard of oregano oil, though I’ve had many other plant-based cures suggested to me, such as echinacea, marshmallow root and slippery elm – well ok I lied, I found the last two on a herbal medicine website).

I highly recommend the science-based medicine website, which has been run by the impressively-credentialed Drs David Gorski and Steve Novella and their collaborators for years now, and which thusly has a vast database of debunked or questionable treatments to explore. It’s the best port of call when you’re offered anecdotal advice about any treatment whatsoever by well-wishers. Not that they’re the only people performing this service to the public. Quackwatch, SkepDoc, and Neurologica are just some of the websites doing great work, but they’re outnumbered vastly by sites spreading misinformation and bogus cures, unfortunately. It’s almost a catch-22 of the internet that you have to be informed enough to use it to get the best information out of it.

As to oregano oil specifically, Scott Gavura at science-based medicine proves a detailed account. I will summarise here, while also providing my own take. Firstly people need to know that when a substance, any substance –  a herb or a plant, an oil extracted therefrom, or a tablet, capsule or mixture,something injectable or applied to the skin, whatever – is suggested as a treatment for a condition, they should consider this simple mantra – always chemical. That’s to say, a treatment will only work because it has the right chemistry to act against the treated condition. In other words you need to know something (or rather a lot) about the chemistry of the treating substance and the chemistry of the condition being treated. It’s no good saying ‘x is great for getting rid of coughs – it got rid of mine,’ because your cough may not have the same chemical cause as mine, and your cough in February 2007 may not have the same chemical cause as your cough in August 2017. My recent cough was caused by a virus (and perhaps I should change the mantra – always biochemical – but still it’s the chemistry of the bug that’s causing the problem), but no questions were asked about the cause before the advice was given. And you’ll notice when you look at naturopathic websites that chemistry is very rarely mentioned. And I’m not talking about toxins.

Gavura gives this five-point test for an effective treatment:

When we contemplate administering a chemical to deliver a medicinal effect, we need to ask the following:

  1. Is it absorbed into the body at all?
  2. Does enough reach the right part of the body to have an effect?
  3. Does it actually work for the condition?
  4. Does it have any hazardous, unwanted effects?
  5. Can it be safely eliminated from the body?

The answer to Q1 is that oregano oil contains a wide variety of chemical compounds, particularly phenolic compounds (71%). It’s these phenolic compounds that are touted as having the principal beneficial effects. However, though we know that there’s some absorption, we don’t have a chemical breakdown. We just don’t know which phenolic compounds are being absorbed or how much.

Q2 – No research on this, or on absorption generally. Topical effects (ie effects on the skin) are more likely to be beneficial than ingested effects, as the oil can maintain high concentration. This would have no effect on a cough.

Q3 – According to one manufacturer the oil has ‘scientifically proven results against almost every virus, bacteria, parasite, and fungi…’ (etc, etc, but shouldn’t that be bacterium and fungus?). In fact, no serious scientific research has ever been conducted on oregano oil and its effectiveness for any condition whatsoever. So the answer to this question is  – no evidence, beyond anecdote.

Q4 – There have been reports of allergic reactions and gastro-intestinal upsets, but the naturopathy industry is more or less completely unregulated so you can never be sure what you’re getting with any bottle of pills or ‘essential oils’. As Gavura points out, the lack of research on possible adverse effects, for this and other ‘natural’ treatments, is of concern for vulnerable consumers, such as pregnant women, young or unborn children, and those with pre-existing conditions.

Q5 – At low doses, there’s surely no concern, but nobody has done any research about dosing up on carvacrol, the most prominent component of oregano oil, which gives the plant its characteristic odour. Other organic components are thymol and cymene.

 

So there’s no solid evidence about oregano oil, or about the mechanism for its supposed efficacy. But what if my well-wisher was correct, and something in the oregano oil cleared up his cough – twice? And did so really really well? Better than several other treatments he tried?

Well, then we might be onto something. Surely a potential billion-dollar gold-mine, considering how debilitating your common-or-garden cough can be. And how, if not cleared up, it can leading to something way more serious.

So how would a person who is sure that oregano oil has fantastic curative properties (because it sure worked for him) go about capitalising on this potential gold-mine? Well, first he would need evidence. His own circle of friends would not be enough – perhaps he could harness social media to see if there were sufficient people willing to testify to oregano oil curing their cough, where other treatments failed. Then , if he had sufficient numbers, he might try to find out the causes of these coughs. Bacterial, viral, something else, cause unknown? It’s likely he wouldn’t make much headway there (most people with common-or-garden coughs don’t go to the doctor or submit to biochemical testing, they just try to ride it out), but no matter, that might just be evidence that the manufacturer was right – it’s effective against a multitude of conditions. And yet, it seems that oregano oil is a well-kept secret, only known to naturopathic companies and health food store owners. Doctors don’t seem to be prescribing it. Why not?

Clearly it’s because Big Pharma doesn’t support the stuff. Doctors are in cahoots with Big Pharma to sell attractive pills with long pharmacological names and precise dosages and complex directions for use. Together they like to own the narrative, and a multi-billion dollar industry is unlikely to be had from an oil you can extract from a backyard plant.

Unless

Our hero’s investment of time and energy has convinced him there’s heaps of money to be made from oregano oil’s miraculous properties, but that same investment has also convinced him that it’s the chemical properties that are key, and that if the correct chemical formula can be isolated, refined and commercialised, not only will he be able to spend the rest of his life in luxury hotels around the globe, but he will have actually saved lives and contributed handsomely to the betterment of society. So he will join Big Pharma rather than trying to beat it. Yes, there would have to be a massive upfront outlay to perform tests, presumably on rats or mice at first, to find out which chemical components or combinations thereof do the best job of curing the animals, who would have to be artificially infected with various bugs affecting the respiratory system, or any other bodily system, since there are claims that the oil, like Lily the Pink’s Medicinal Compound™, is ‘most efficacious in every case’.

But of course it would be difficult for any average bloke like our hero to scratch up the funds to build or hire labs testing and purifying a cure-all chemical extract of oregano oil. Crowdsourcing maybe, considering all the testimonials? Or just find an ambitious and forward-thinking wealthy entrepreneur?

Is that the only problem with the lack of acceptance, by the medical community, of all the much-touted naturopathic cures out there? Lack of funds to go through the painstaking process of getting a purefied product to pass through a system which ends with double-blind, randomised, placebo-controlled human studies with large sample sizes?

Permit me to be sceptical. It’s not as if the chemical components of most herbal remedies are unknown. It’s highly unlikely that pharmacologists, who are in the business of examining the chemistry of substances and their effects for good or ill on the human body, haven’t considered the claimed cornucopia of naturopathic treatments and the possibility of bringing them into the mainstream of science-based medicine to the benefit of all. Yes, it’s possible that they’ve missed something, but it’s also possible, indeed more likely, that people underestimate the capacity of our fabulous immune system, the product of millions of years of evolution, to bring us back to health when we’re struck down by the odd harmful bug. When we’re struck down like this, we either recover or we die, and if we don’t die, we tend to attribute our recovery to any treatment applied. Sometimes we might be right, but it pays to be skeptical and to do research into a treatment, and into what ails us, before making such attributions. And to do so with the help of a good science-based medical practitioner. And remember again that motto: always chemical. 

 

Written by stewart henderson

August 24, 2018 at 10:18 am

an intro to chemistry for dummies by dummies

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orbitals – one day we may understand

Jacinta: Well, in ‘researching’ – I have to put it in quotes cause what I do is so shallow it barely counts as research – the last piece, I came across a reference to Philip Ball’s choice of the top ten unsolved mysteries in science, at least chemical science.

Canto: Philip Ball, author of Curiosity…

Jacinta: Among other things. His list was published in Scientific American in 2011, the official ‘Year of Chemistry’ – which passed unnoticed by supposedly scientific moi. The actual article is largely unavailable to the impoverished, but at least I’ve been able to access the list here. So I thought we might have fun discussing it in our quest to self-educate autant que possible before we die.

Canto: Yes I don’t know enough about chemistry to say whether this is a bog-standard list or an eccentric one, but there are no quibbles about the first mystery – the origin of life. But have we already covered that?

Jacinta: Not really. Ball’s mystery number 1, to be exact, is ‘How did life begin?’ – by which he presumably means life as we know it. And, as Jack Szostak puts it, the answer lies with ‘chemistry plus details’. Putting the right chemistry together in the right order under the right conditions, which they’ve managed to do in a ‘small way’ in the lab, synthesising a pyrimidine nucleotide, as noted in our last post.

Canto: Yes it seems to me we’re never going to solve this mystery by somehow stumbling upon the first life on Earth, or even a trace of it. How will we ever know it’s the first? Then again creating different kinds of conditions – gases and pressures and molecular bits and pieces – and mixing and shaking and cooking, that may not solve the mystery either, because we’ll never know if it happened like that, but it might show how life can begin, and that would be pretty awesome, if I may use that word correctly for once.

Jacinta: Usage changes mate, live with it. So what’s Ball’s second mystery?

Canto: ‘How do molecules form?’ Now we’re really getting into basic chemistry.

Jacinta: But isn’t that a known known? Bonding isn’t it? Like O² is an oxygen atom bonding with another to create a more stable configuration… I don’t know.

Canto: Well let’s look into it. What exactly is a chemical bond and why do they form? Molecular oxygen is common and stable, but what about ozone, isn’t that just oxygen in a different molecular form, O³? Yet in different molecular form, oxygen has different qualities. Ozone’s a pungent-smelling gas, whereas standard oxygen’s odourless. So why does it have different molecular forms? Why does it have any molecular form, why doesn’t it just exist as single atoms?

Jacinta: But then you could ask why do atoms exist, and why in different configurations of protons and neutrons, etc? Best to stick to how questions.

Canto: Okay, I’d like to know how, under what conditions, oxygen exists as O³ rather than O².

Jacinta: So we have to go to bonding. This occurs between electrons in the ‘outer shell’ of atoms. In molecular oxygen, O2, the two oxygen atoms form a covalent bond, sharing four electrons, two from each atom. The water and carbon dioxide molecules are also covalently bonded. Covalently bonded molecules are usually in liquid or gas form.

Canto: What causes the atoms to form these bonds though?

Jacinta: There are two other types of bonds, ionic and metallic. As to causes, there are simple and increasingly complex explanations. I’m sure Ball was after the most complex and comprehensive explanation possible, which I believe involves quantum mechanics. For a very introductory explanation to the types of bonds, this website is useful, but this much more complex, albeit brief, explanation of the O2 bond in particular will leave you scratching your head. So I think we should do a sort of explication de texte of this response, which comes from organic chemist David Shobe:

If you mean the molecule O2, that is actually a complicated question.  It is a double bond, but not a typical double bond such as in ethylene, CH2=CH2.  In ethylene, each carbon atom has a sigma orbital and a pi orbital for bonding, and there are 4 electrons available (after forming the C-H bonds), so each bonding orbital (sigma and pi) has 2 electrons, which is optimal for bonding.  Also, since each orbital has a pair of electrons, one gets a singlet ground state: all electrons are in pairs.

In O2, there are 1 sigma orbital and 2 pi orbitals for bonding, but 12 valence electrons.  Four electrons, 2 on each oxygen atom, are in lone pairs, away from the bonding area.  This leaves 8 electrons for 3 bonding orbitals.  Since each orbital can only hold 2 electrons, there are 2 electrons forced into antibonding orbitals.  This is just what it sounds like: these electrons count negatively in determining the type of bond (technical term is bond order), so 2 sigma bonding electrons + 4 pi bonding electrons – 2 pi antibonding electrons, divided by 2 since an orbital holds 2 electrons, equals a bond order of 2: a double bond.

However, there are *two* pi antibonding orbitals with the same energy.  As  a result, one electron goes into each pi antibonding orbital.  This results in a triplet ground state: one in which there are two unpaired electrons.

That may be more answer than you wanted, but it’s what chemists believe.

Canto: Wow, a tough but interesting task. So a very good place to start is the beginning. By double bond, does he mean covalent bond?

Jacinta: Well according to this clearly reliable site, ethylene, aka ethene (C2H4) is the simplest alkene, that is an unsaturated (??)  hydrocarbon with double bonds – covalent bonds – between the carbons. So I think the answer to your question is yes… or no, there are triple covalent bonds too.

Canto: Okay so I’d like to know more about what a covalent bond is, and what valence electrons are, and then we need to know more about orbitals – pi and sigma and maybe others.

Jacinta: Well guess what, the more you dive into molecular bonding, the murkier stuff gets – until you familiarise yourself I suppose. There are different types of orbitals which lead to different types of covalent bonds, single, double and triple. The term ‘covalent’ means joint ownership, sharing, partnering, as we know, of valence. So how to describe valence? With great difficulty.

Canto: Just watched a video that tells me that covalent compounds or molecular compounds only exist between non-metallic elements, whereas ionic compounds are made up of non-metallic and metallic elements, and ionic bonds are quite different from covalent bonds. And presumably metallic bonds join only metallic elements. Don’t know if that helps any.

Jacinta: Well yes it does in that it tells us we really need to start from scratch with basic chemistry before we can get a handle on the molecule problem.

Canto: Okay, time to go back to the Khan academy.

Jacinta: Yes and we’ll do so always bearing in mind that fundamental question about the formation of molecules. So our chemistry lesson begins with elements made up of atoms so tiny that, for example, the width of a human hair, which is essentially carbon, can fit a million of them.

Canto: And the elements are distinguished from each other by their atomic numbers, which is the number of protons in their nuclei. They can have different numbers of neutrons, but for example, carbon must always have six protons.

Jacinta: And neutral-charge carbon will have six electrons buzzing about the nucleus, sort of. They keep close to the nucleus because they’re negatively charged, we don’t know why (or at least I don’t), and so they’re attracted to the positively charged protons in the nucleus.

Canto: More fundamental questions. Why are electrons negatively charged? Why are positively charged particles attracted to negatively charged ones? And if they’re so attracted why don’t electrons just fall into the nucleus and kiss their attractive protons, and live in wedded bliss with them?

Jacinta: Let’s stick to how questions for now. Electrons don’t fall into the nucleus but they can be lost to other atoms, in which case the atom will have a positive charge, having more protons than electrons. So with the losing and the stealing and the sharing of electrons between atoms, elements will have changed properties. Remember oxygen and ozone.

Canto: So it’s interesting that, right from the get-go, we’re looking at that ancient philosophical question of the constituents of matter. And though we now know that atoms aren’t indivisible, they do represent the smallest constituents of any particular element.

Jacinta: But as you know, that smallest constituent gets weird and mathematical and quantum mechanical, with electrons being waves or particles or probability distributions, with the probability of finding them or ‘fixing’ them being higher the closer you get to the nucleus. So this mathematical probability function of an electron is what we call its orbital. Remember that word?

Canto: Right, that’s a beginning, and it gives me an inkling into types of orbitals, such as antibonding orbitals. Continue.

Jacinta: We’ll continue next time. We’ve only just entered the darkness before the dawn.

 

http://solarfuel.clas.asu.edu/10-unsolved-mysteries-chemistry

https://www.factmonster.com/dk/encyclopedia/science/molecules

https://www.quora.com/What-type-of-bond-do-2-oxygen-atoms-have

https://chem.libretexts.org/Core/Organic_Chemistry/Alkenes/Properties_of_Alkenes/Structure_and_Bonding_in_Ethene-The_Pi_Bond

https://en.wikipedia.org/wiki/Unsaturated_hydrocarbon

Written by stewart henderson

May 23, 2017 at 1:27 am

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

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chemical-evolution-1

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.

 

Written by stewart henderson

July 29, 2016 at 8:51 am