Archive for the ‘chemistry’ Category
more baffling immune system stuff
1RH2 Recombinant Human Interferon Alpha 2b – evidemment
Jacinta: We’ve been mostly educating ourselves via the NinjaNerd YouTube series on immunology, which seems very comprehensive and yet comprehensible, for beginners, and then going to other websites for details. Now getting back to cluster differentiation (CD), a commonly used immunological term. Here’s a useful definition:
The cluster of differentiation (CD) is a protocol used for the identification and investigation of cell surface molecules present on leukocytes. CD molecules often act as receptors or ligands important to the function of immune cells.
Canto: That’s useful indeed. Each CD – 4 or 8 or 25 – represents a cluster of differentiation. Differentiated from other clusters. So back to T regulatory cells, which would be differentiated into those cells that predominantly have CD4 or CD8 molecules, as well as TCRs. All to help suppress auto-immune diseases in particular.
Jacinta: So we have these T regulatory cells, as well as helper and cytotoxic T cells, all created in the thymus essentially, and then they’re distributed to the lymphoid organs – the lymph node locations include ‘the groin, armpit, behind the ears, back of the head, sides of the neck and under the jaw and chin‘. There’s also the spleen and its sinusoidal capillaries, where T cells form a surrounding layer known as the ‘periarteriolar lymphoid sheath’ (PALS), more commonly known as white pulp. A large number of T regulatory cells however remain in a thymus region known as the thymic (Hassal’s) corpuscles. They’re also distributed throughout the body – the tonsils, the respiratory tract and so on. All originating from the red bone marrow.
Canto: Well I’m still a little confused about the difference between the innate and adaptive immune systems and whether there really is any clear distinction between them (I suspect not). My own distinction so far is that the innate system is quick and not very specific and well-attuned, and the adaptive is – everything else.
Jacinta: Well, a bacterial antigen releases endotoxins which causes a massive release of inflammatory cytokines, got that?
Canto: Not particularly. Get this:
Endotoxins (lipopolysaccharides, LPS) are agents of pathogenicity of Gram-negative bacteria, implicated in the development of Gram-negative shock. Endotoxin reacts with lipopolysaccharide-sensitive cells producing endogenous mediators such as tumour necrosis factor alpha (TNFα).
That was my first stop in trying to find out what endotoxins are. Needless to say, it’s meaningless to me. Though I know that ‘endo’ means ‘from within’ as opposed to ‘exo’… I think.
Jacinta; If you look that up you’ll find it’s horribly complex. Okay the bacteria release toxins which release cytokines in reaction. There are many different kinds of cytokines, including histamines, prostaglandins and leukotrienes. Amongst other things these cytokines will impact smooth muscle cells causing vasodilation, increasing blood flow causing heat and redness. Cytokines will also contract endothelial cells, causing fluid leakage and permeability, affecting pain receptors. Bradykinins are also involved in vasodilation and increased blood flow. All this induces swelling and pain. Broadly, the four signs of inflammation are: swelling, pain, heat and redness. That answers a basic exam question. Joint immobility is a fifth sign in some extreme cases.
Canto: I’m looking at a different video, “introduction to the immune system”, because I think we need to stay on the ground floor for a while. I also think looking at language might help. For example, ‘cytokines’ feature heavily, and I was thinking that they were like some kinds of proteins or enzymes, something sub-cellular that could whizz about the body, but then I noticed that white blood cells were called leukocytes, and there were lymphocytes and phagocytes… cells! Like, complex organisms. And ‘kine’, apart from being about cattle, is where our word ‘kind’ came from, as in Kinds of Minds. So ‘cytokines’, methinks, are just the vast array of cells relating to the immune system.
Jacinta: Yes, this is good – a phagocyte is an ‘eating cell’. A lymphocyte is a type of WBC that’s involved in the immune system. T cells are lymphocytes, as are B cells. So, yes, they’re complex, gene-containing thingumies, all of them, and lymphocytes are so called because the lymph system is full of them. But note that ‘cyte’ just means ‘cell’, not necessarily of the white or immune kind.
Canto: So starting again at the beginning, with the innate and adaptive systems. So the innate system is what often causes pains and fevers, that redness and itchiness and raised temperature mentioned before – inflammation. Because of the release of cytokines, as you’ve explained.
Jacinta: Ah but here’s where it becomes confusing and unhelpful. On a website designed, I think, for high school biology students I found this:
Cytokines…. are a broad category of small proteins that are important in cell signaling. They are released by cells and affect the behavior of other cells. Cytokines include interferons, interleukins, lymphokines, and tumor necrosis factor.
So it looks like you were right in the first place. It is confusing though. Interferons are proteins, as are interleukins, and ScienceDirect, which is generally reliable, says this:
Cytokines, chemokines, and lymphokines are multifunctional immunoregulatory proteins secreted by cells of the immune system.
So we’ve both been confused, and maybe looking at language origins might confuse us more. Best just to accept what the biochemists say.
Canto: So, are we starting again, again? Let’s look at some of the cytokine types. Interferons are as mentioned, signalling proteins. But what, exactly, is meant by signalling, and what exactly is a protein? A chain of amino acids, je crois. So, signalling – that’s about sending and receiving and responding to signs of change:
Individual cells often receive many signals simultaneously, and they then integrate the information they receive into a unified action plan. But cells aren’t just targets. They also send out messages to other cells both near and far.
So far, so obvious. These signals are essentially chemical. Even neurotransmission reduces down to the chemical level. But we’ll stick with pathogens and immunity. Receivers of signals are generally called receptors, and immune-system cells often, but not always, have receptors within or sticking out of the cell membrane.
Jacinta: Interferons are so-called because they interfere with viruses and such. We’ve actually been able to create them in the lab since the 80s for treating some cancers:
Interferons are the frontline defenders in your body. A variety of cells, including white blood cells, produce interferons in response to infection and other stimuli, like cancer cells. They initiate signaling cascades by stimulating the infected cells and those nearby to produce cytokines.
Canto: But are they the frontline defenders? And they’re cytokines themselves, as aforementioned. Cytokine seems a pretty broad term.
Jacinta: Our refined or not-so-refined new definition – cytokines are types of stuff created by a variety of cells as an immune response to pathogens. As to interferons, don’t worry about it.
Canto: Too late, I’m worried. Here’s another quote:
More than twenty distinct IFN [interferon] genes and proteins have been identified in animals, including humans. They are typically divided among three classes: Type I IFN, Type II IFN, and Type III IFN. IFNs belonging to all three classes are important for fighting viral infections and for the regulation of the immune system.
Should we just devote the rest of our lives to interferons and forget the rest?
Jacinta: Everything’s connected to everything else. And we shouldn’t despair – we’ve learned much about the lymphatic system, for example, that we didn’t know before.
Canto: We didn’t know anything before. But yes I’m encouraged. And getting back to language, lymph is apparently Latin for ‘clear water’, which is a good start for thinking about lymphatic fluid, even if it’s anything but clear.
Jacinta: Like sea or river water I suppose. The more you look… Blame all those pesky microscopes and such. Anyway, one video describes the lymphatic system as having three main functions: 1) returning fluid to the heart: 2) helping large molecules (hormones and lipids) enter the blood: 3) immune surveillance.
Canto: Okay let’s look at all that in a bit more detail next time.
reading matters 13: the glass universe
Canto: So The glass universe, published in 2016, has a cute title, referring as it does to the ‘glass ceiling’, another clever term for that invisible barrier up there that appears to prevent women from rising in politics, business and science, but also to the glass photographic plates upon which were recorded the spectrographic signatures of a vast arrays of stars, clusters and the like, in the decades of the late nineteenth century and early twentieth century, by a somewhat less vast array of human computers – the name given to the largely underpaid female stargazers and recorders of Harvard College observatory and elsewhere.
Jacinta: Yes, Dava Sobel, author of the fascinating little book Longitude, as well as Galileo’s Daughter, which is in a stack of books here waiting to be read, has brought to life a group of dedicated women and their male supporters over a period when the higher education of women was just starting to be addressed.
Canto: Yes, it all started with the Drapers, a wealthy and well-connected couple in the 1870s. Henry was a leading astronomer of the day, and ‘Mrs Henry’, aka Anna, a socialite and heiress. Their social evenings were mostly science-focused, with guests including the inventor Thomas Edison, the zoologist Alexander Agassiz, and Prof. Edward Pickering, of Harvard. Henry Draper was working on the chemical make-up of stars, using ‘a prism that split starlight into its spectrum of component colours’, for which he’d won great acclaim, when he died suddenly of a flu-like illness in his mid-forties. His devoted and rich widow, keen to continue his legacy, helped finance, along with Pickering, a continuation of his ground-breaking research.
Jacinta: And so the computers of Harvard College Observatory were born. We need to explain – or try to – the science of spectrographic analysis, but I’d like to first briefly describe some of the women who did this work. They include Williamina (Mina) Fleming, a canny Scotswoman frae Dundee (our birthplace), whose first American job was as the Pickering’s maid but who soon proved her worth as a star spotter and tracker, classifier, and organiser, leading the team of computers in the early decades. In 1899 she was given the title of ‘curator of astronomical photographs’, becoming the first titled female in the university’s history. As such she presided over 12 women ‘engaged in the care of the photographs; identification, examination and measurement of them; reduction of these measurements, and preparation of results for the printer’.
Canto: Far from just bureaucratic work – this would’ve involved a lot of learning and conjecture, noting patterns and anomalies and trying to account for them.
Jacinta: Absolutely. Antonia Maury, Annie Jump Cannon, Cecilia Payne-Gaposchkin, Henrietta Leavitt and the tragically short-lived Adelaide Ames were among the most noteworthy of these computers, and I should stop using the term, because they weren’t machines and they all made lasting contributions to the field…
Canto: And they all have their own Wikipedia pages. What more evidence do we need?
Jacinta: They contributed to academic papers, often without attribution, especially in the early years, and had their findings read out in academic institutions to which they were barred. Over time they became established teachers and lecturers, in the women’s colleges which started to become a thing in the twenties. But let’s get onto the daunting stuff of science. How were these glass plates created and what did they reveal?
Canto: So spectroscopy became a thing in the 1860s. Spectroscopes were attached to telescopes, and they separated starlight into ‘a pale strip of coloured light ranging from reddish at one end through orange, yellow, green, and blue to violet at the other’. I quote from the book. But what these changing colours meant exactly, as well as the ‘many black vertical lines interspersed at intervals along the coloured strip’, this was all something of a mystery, a code that needed to be cracked. Henry Draper had captured these spectral lines and intervals on photographic plates, which were bequeathed to Harvard by his widow. They formed the beginning of the collection.
Jacinta: The term spectrum was first used by Isaac Newton two centuries earlier, and he correctly claimed that this coloration wasn’t due to flaws in glass and crystals but was a property of light itself. The dark lines within the stellar spectra on Draper’s plates are called Fraunhofer lines, after a Bavarian lens-maker, Joseph von Fraunhofer, who built the first spectroscope. He at first thought the dark lines between the rainbow of colours his instrument produced were somehow artificial, but continued work convinced him that they were a natural effect. He gave them alphabetical labels according to their thickness, including the letter D for a double line in the pale orange region. He mapped hundreds of them, though today we’ve detected many thousands of them in sunlight. He didn’t understand what they were, though he realised they were something significant. Later in the 19th century Robert Bunsen and Gustav Kirchov conducted experiments with various chemical elements and found that they burned in colours around those black lines, which we now know as absorption lines.
Canto: Yes, it was Kirchov who connected the colours created by burning elements to the spectral lines that the sun’s light could be separated into, concluding that this great fireball of gases producing white light in the sky was actually a mixture of burning elements, or elements being transformed into other elements. As to the absorption lines, Sobel puts it this way:
As light radiated through the sun’s outer layers, the bright emission lines from the solar conflagration were absorbed in the cooler surrounding atmosphere, leaving dark telltale gaps in the solar spectrum.
These absorption lines, which together with emission lines, are spectral lines in the visible spectrum which ‘can be used to identify the atoms, elements or molecules present in a star, galaxy or cloud of interstellar gas’, to quote from this Swinburne University site.
Jacinta: So we’ll try to keep within the confines of the book, and the scientific developments of the period which these women, in particular, contributed to. So, rather, surprisingly to us modern wiseacres, these revelations about the sun as a super-hot fireball and a producer of elements was a bit hard for 19th century folk to take in, but scientists were excited. Henry Draper described spectral analysis as having ‘made the chemist’s arms millions of miles long’, and in 1872 he began photographing the spectra of other stars. It was long known that they had different colours and brightnesses – called ‘apparent luminosities’ – but spectral analysis provided more detailed data for categorisation, and sets of photographs revealed changes in luminosity and colour over time. Williamina Fleming, Harvard’s principal computer, took charge of Draper’s thousands of plates, which provided the most detailed spectral data of stars up to that time, and was able to analyse them into classes, via their absorption lines, in new and complex ways. It was cutting edge science.
Canto: There was also an interest in throwing more light, so to speak, on variable stars. They were so numerous and complex in their variability that Pickering needed more computers to track them. Lacking funds, he advertised for volunteers, emphasising the role of women in particular, whose effectiveness he’d seen plenty of evidence for.
Jacinta: Not to mention their willingness to work for less, or effectively nothing. These were often siblings or partners of astronomers or other scientists, with unfulfilled scientific ambitions. Later, though, came from the newly created ‘Ladies’ Colleges, such as Radcliffe and Wellesley.
Canto: The Orion Nebula was a particularly rich source of these variable stars, and Pickering found an ideal computer, Henrietta Leavitt, a Radcliffe graduate, to explore them. Within six months, she’d confirmed previous identifications of variables in the nebula and added more than 50 others, afterwards confirmed by Fleming. Then, using a combination of negative and positive glass plates, she found hundreds more, in the Orion Nebula and the Small Magellanic Cloud. As Pickering pointed out, due to the lack of resolution in the plates, this number was likely the tip of the iceberg. In writing up a report of her findings, Leavitt described a pattern she’d found: ‘It is worthy of notice… that the brighter variables [aka cepheid variables] have the longer periods’. This brightness (or luminosity) and its relationship to periodicity (the time taken to go through a full cycle of change) is now known as the Leavitt Law, though of course it took decades for Henrietta Leavitt to receive full recognition for discovering it.
Jacinta: Yes, it’s worth noting that these women worked painstakingly on data analysis, developing new and more rigorous classification systems, studying and theorising about anomalies, and communicating their findings to leading astronomers and researchers around the world. And it’s also worth noting that they were supported and highly appreciated at Harvard by Edward Pickering and his successor as Director of the Harvard College Observatory, Harlow Shapley – though of course there were plenty of naysayers.
Canto: Okay so we’ve spoken of two or three of the computer stars’, and there were many more, but let’s finish with the work of Antonia Maury.
Jacinta: Well we must also mention Annie Jump Cannon (great name), star classifier and photographer extraordinaire, suffragist and generally formidable persona, in spite of being almost completely deaf. She classified around 350,000 stars and contributed greatly to the Harvard Classification Scheme, the first international star classification system. Antonia Coetana de Paiva Pereira Maury (I’m not kidding), a graduate of Vassar College, was a niece of Henry Draper.
Canto: Not what you know but who you know?
Jacinta: It is partly that – and that cliché is worth a whole book to itself – but Maury was no slouch, she was a keen and observant star observer and systemiser. One important discovery she shared with Pickering was one of the first known binary star systems, in the handle of the Big Dipper. This required months of careful observation from 1887 through 1889, as they noted one spectral line separating into two then the lines merging again, then separating, with one line shifting slightly to the red end of the spectrum and the other to the blue. Once they recognised that they were dealing with binary star systems, others were soon found. And once these systems were confirmed, Maury carefully calculated their orbital periods and speeds.
Canto: There were many other important breakthroughs. Spectral colours, as we’ve pointed out, were connected to particular chemical elements, and Cecilia Payne, whose major focus was the measurement of stellar temperatures, found a superabundance in the elements hydrogen and helium, which confounded other experts and soon made her doubt her own calculations. Payne wrote up her findings in the Proceedings of the National Academy of Sciences in 1925, ‘admitting’ that the percentages of hydrogen and helium were ‘improbably high’ and ‘almost certainly not real’.
Jacinta: Yes, it’s well worth noting that the knowledge we have of stars today, which seems almost eternal to us, is in fact very recent. The book also covers the dispute between Harlow Shapley and Edwin Hubble – with many on either side of course – as to whether other galaxies existed. That dispute was only resolved in the thirties, and now we count other galaxies in the trillions. So the period covered in Sobel’s book was a truly transformative period in our understanding of the universe, as well as transformative in terms of women’s education and women’s participation in the most heavenly of all the sciences.
Canto: Whateva.
References
The glass universe, by Dava Sobel, 2016
https://science.nasa.gov/astrophysics/focus-areas/what-are-galaxies
https://en.wikipedia.org/wiki/Annie_Jump_Cannon
https://en.wikipedia.org/wiki/Antonia_Maury
https://en.wikipedia.org/wiki/Williamina_Fleming
reading matters 7
She has her mother’s laugh, by Carl Zimmer , science author and journalist, blogger, New York Times columnist, etc etc
content hints – inheritance and heredity, genetics and epigenetics, Darwin and Galton, the Hapsburg jaw, eugenics, Hugo de Vries, Theodor Boveri, Luther Burbank, Pearl and Carol Buck, Henry Goddard, The Kallikak Family, Hitler’s racial hygiene laws, morons, the five races etc, Frederick Douglass, Thomas Hunt Morgan, Emma Wolverton, PKU, chromosomal shuffling, meiosis, cultural inheritance, mitochondrial DNA, Mendel’s Law, August Weismann, germ and soma, twin studies, genetic predispositions, mongrels, Neanderthals, chimeras, exosomes, the Yandruwandha people, IVF, genomic engineering, Jennifer Doudna, CRISPR, ooplasm transfers, rogue experiments, gene drives, pluripotency, ethical battlegrounds.
about ozone, its production and depletion
People will remember the ‘hole in the ozone’ issue that came up in the eighties I think, and investigators found that it was all down to CFCs, which were quite quickly banned, and then everything was hunky dory….
Or that’s how I vaguely recall it. Time to take a much closer look.
I take my cue from ‘An ancient ozone catastrophe?’, chapter 4 of David Beerling’s The emerald planet, in which he looks at the evidence for a previous ozone disaster and its possible relation to the great Permian extinction of 252 millions years ago. I’ll probe into that matter in another post. In this post I’ll try to answer some more basic questions – what is ozone, where is the ozone layer and why does it have a hole in it?
Ozone is also known as trioxygen, which gives a handy clue to its structure. Oxygen can exist in different allotropes or molecular structures which are more or less stable. O3, ozone, is much less stable than O2 and has a very pungent chlorine-like odour and a pale blue colour. It’s present in minute quantities throughout the atmosphere but is most concentrated in the lower part of the stratosphere, 20 to 30 kilometres above the Earth’s surface. This region is called the ozone layer, or ozone shield, though it’s still not particularly dense with ozone, and that density varies geographically and seasonally. Ozone’s instability means that it doesn’t last long, and has to be replenished continually.
In 1928 chlorofluorocarbons (CFCs) were developed as a seemingly safe form of refrigerant, which, under patent as Freon, came to be used in air-conditioners, fridges, hair-sprays and a variety of other products. As it turned out, these CFCs aren’t so harmless when they reach the upper atmosphere, where the chlorine reacts with ozone to form chlorine monoxide (ClO), and regular O2. This reaction is activated by ultraviolet radiation, which then breaks up the unstable ClO, leaving the chlorine to react with more ozone in a continuing cycle.
By the eighties, it had become clear that something was going wrong with the ozone layer. Studies revealed that a gigantic hole in the layer had opened up over Antarctica, and without going into detail, CFCs were found to be largely responsible. There was the usual fight with vested business interests, but in 1987 the Montreal protocol against the use of ozone-depleting substances (ODS) was drawn up, a landmark agreement which has been successful in starting off the long and far from completed process of repair of the ozone shield.
As a very effective oxidant, ozone has many commercial applications, but the same oxidising property makes it a danger to plant and animal tissue. Much better for us to keep most of it up above the troposphere, where its ability to absorb UV radiation has made it virtually essential for maintaining healthy life on Earth’s surface.
So here are some questions. Why does ozone proliferate particularly at the top of the troposphere, in the lower stratosphere? If it’s so reactive, how does it maintain itself at a particular rate? Has the thinning or reduction of that layer seriously influenced life on Earth in the past? From my reading, mainly of Beerling, I think I can answer the first two questions. The third question, which Beerling explores in the above-mentioned chapter of his book, is more speculative, and more interesting.
Sidney Chapman, a brilliant geophysicist and mathematician of the early twentieth century, essentially answered the first question. He realised that ozone was both formed and destroyed by the action of sunlight, specifically UV radiation, on atmospheric oxygen. He calculated that this action would reduce and finally stop at a point approximately 15 km above sea level, because the reactions which had produced the ozone higher up had absorbed the UV radiation in the process. No activation energy to produce any more ozone. That explained the lower limit of ozone. The upper limit was explained by the lack of oxygen in the upper stratosphere to produce a stable layer – for production to exceed destruction. This was interesting confirmation of observations made earlier by the meteorologist and balloonist Léon-Phillippe Teisserenc de Bort, who noted that, contrary to his expectations, the air temperature didn’t fall gradually with altitude but reached a point of stabilisation where the air even seemed to become warmer. He named this upper layer of air the stratosphere, and the cooler more turbulent layer below he called the troposphere. It’s now known that this upper-air warming is caused by the absorption of UV radiation by ozone.
Our picture of ozone still had some holes in it, however, as it seemed there was a lot less of it around than the calculations of Chapman suggested. To quote from Beerling’s book:
… there had to be some as-yet unappreciated means by which ozone was being destroyed. The fundamental leap required to solve the problem was taken comparatively recently, in 1970, by a then young scientist called Paul Crutzen. Crutzen showed that, remarkably, the oxides of nitrogen, produced by soil microbes, catalysed the destruction of ozone many kilometres up in the stratosphere. Few people appreciate the marvellous fact that the cycling of nitrogen by the biosphere exerts an influence on the global ozone layer: life on Earth reaches out to the chemistry of the stratosphere.
Now to explain why the hole in the ozone shield occurred above the Antarctic. My understanding and explanation starts with reading Beerling and ends with this post from the USA’s National Oceanic and Atmospheric Administration’s Earth System Research Laboratory (NOAA/ESRL).
The ozone hole over Antarctica varies in size, and is largest in the months of winter and early spring. During these months, due to the large and mountainous land mass there, average minimum temperatures can reach as low as −90°C, which is on average 10°C lower than Arctic winter minimums (Arctic temperatures are generally more variable than in the Antarctic). When winter minimums fall below around −78°C at the poles, polar stratospheric clouds are formed, and this happens far more often in the Antarctic – for about five months in the year. Chemical reactions between halogen gases and these clouds produce the highly reactive gases chlorine monoxide (ClO) and bromine monoxide (BrO), which are destructive to ozone.
Most ozone is produced in the tropical stratosphere, in reactions driven by sunlight, but a slow movement of stratospheric air, known as the Brewer-Dobson circulation, transports it over time to the poles, so that ozone ends up being more sparse in the tropics. Interestingly, although most ozone-depleting substances – mainly halogen gases – are produced in the more humanly-populated northern hemisphere, complex tropospheric convection patterns distribute the gases more or less evenly throughout the lower atmosphere. Once in the stratosphere and distributed to the poles, the air carrying the halogen-gas products becomes isolated due to strong circumpolar winds, which are at their height during winter and early spring. This isolation preserves ozone depletion reactions for many weeks or months. The polar vortex at the Antarctic, being stronger than in the Arctic, is more effective in reducing the flow of ozone from tropical regions.
So – I’ve looked here briefly at what ozone is, where it is, and how it’s produced and destroyed, but I haven’t really touched on its importance for protecting life here on Earth. So that, and whether its depletion may have had catastrophic consequences 250 million years ago, will be the focus of my next post.
References
The Emerald Planet, by David Beerling, Oxford Landmark Science, 2009
a little about the chemistry of water and its presence on Earth
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.
Always chemical: how to reflect upon naturopathic remedies
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:
- Is it absorbed into the body at all?
- Does enough reach the right part of the body to have an effect?
- Does it actually work for the condition?
- Does it have any hazardous, unwanted effects?
- 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.
an intro to chemistry for dummies by dummies
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
Abiogenesis – LUCA, gradients, amino acids, chemical evolution, ATP and the RNA world
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
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.