Showing posts with label biochemistry. Show all posts
Showing posts with label biochemistry. Show all posts

Thursday, 29 April 2021

H2O by Philip Ball


The 'biography' of water. 

It's not just the school science that Ball tells us such as the hydrological cycle. Ball tells us how water arrived on earth (from the meteorites and comets that coalesced into the earth) and assesses the chances of liquid water on Venus, Mars and the moons of Jupiter. One fascinating chapter considers the various theories of the origin of life and shows how the chemistry of water acts as evidence against some of these theories. He looks at the history of science with regard to water, considering pre-Socratic philosophers up to alchemists and beyond. Two chapters are devoted to the rather odd chemistry of water and the hydrogen bonds that can produce strange results, as well as different types of water. Then he goes back to the role that water plays in living processes One amusing chapter considers some scientific dead ends in which water played a part, including one which initially seemed to validate homeopathy. A final epilogue considers water as a resource and considers the possibility of water wars.

It is an exhaustive, and at times exhausting, study. Ball explains ideas extremely clearly, on the whole, without dodging the difficult stuff. I found his predilection for quoting statistics a little wearisome but my main criticism is that I read it too late. It was only published in 2015 yet it is already out of date in several places. Not Ball's fault!

Ball spends a lot of time and energy trying to impress with very big (and sometimes very small) number but there are also many fascinating moments:

  • "The Polynesian cosmogeny reproduces that of the Old Testament in extraordinary detail: the supreme being Io says ‘Let the waters be separated, let the heavens be formed, let the earth be!’" (Ch 1)
  • "Water on Earth ... nurtured and sustained civilization – yet the fresh waterways that fed the cultures of ancient China and Egypt, Mesopotamia and the Indian continent make up barely a tenth of a thousandth of all the liquid water on the planet. Just about all of the rest is salty, and lethal" (Ch 2)
  • "at a mythological level, the natural waters of the Earth offer humankind a journey into death. The Styx is the conduit to Hades, the Ganges even today a repository of the deceased. The Nile and the Tigris were not only holy in Near Eastern belief but the dwelling place of the dead, ruled by demigods with the power of resurrection. From the association of streams and rivers with death and rebirth comes the Christian practice of baptism." (Ch 2)
  • "The Ship of the Dead is a potent and recurring symbol: the Flying Dutchman, the Marie Celeste." (Ch 2)
  • "In deserts, evaporation is about equal to precipitation and there is essentially no run-off." (Ch 2)
  • "Once mariners considered that there were seven seas to sail: the Atlantic, Pacific, Indian and Arctic Oceans, the Mediterranean and Caribbean Seas and the Gulf of Mexico." (Ch 2)
  • "ninety-five per cent of all land points have antipodes – equivalent points in the other hemisphere – in the sea." (Ch 2)
  • "Because of the fifty-minute difference between a terrestrial day and the lunar rotation period, high tides come twenty-five minutes later on each successive half day." (Ch 2)
  • "in Persian, in which the first word of the dictionary is ab, meaning ‘water’. Herein lies the root of the word ‘abode’, from the Persian abad" (Ch 2)
  • "There is now a rumour, however, that at least some parts of London’s water table are rising again because the big breweries, which consumed much of the water in the city’s aquifers, have moved out of town (or out of business). Londoners are warned of an impending threat of flood rising from the deep, because the capital no longer makes its own beer." (Ch 2)
  • "around six million years ago ... a period of particularly dry climate lowered the sea level and cut off the connection to the Atlantic through the shallow Straits of Gibraltar, leaving the Mediterranean a land-locked sea. Without replenishment from the global oceans, the Mediterranean then slowly dried out." (Ch 2)
  • "The floor of this desert reached two thousand metres below global mean sea level, and the rivers feeding into it from Europe and Africa faced a huge plunge at the dried-up coast, carving great gorges into the rock." (Ch 2)
  • "About five million years ago the dam at Gibraltar seems to have been breached, and the resulting waterfall, as the Atlantic fed back into the dry basin, would have made Victoria Falls look like a leaky tap. The torrent was one hundred times larger than that at Victoria, feeding about a hundred cubic kilometres of Atlantic water into the basin every day to fill up the Mediterranean again in about a century." (Ch 2)
  • "Today around forty per cent of deaths from acts of nature, as well as forty per cent of the societal costs of natural disasters, are the result of floods." (Ch 2)
  • "Egyptian civilization is one of the very few that has no legend of a deluge, presumably because the Nile is so vast that it was always able to act as a buffer against intense meteorological events." (Ch 2)
  • "William Hobbs, who related this tale in 1907, was also moved to speculate that a tsunami might have been responsible for the parting of the Red Sea that allowed Moses and the Israelites to evade their Egyptian pursuers. Later commentators suggested that it was perhaps not the Red Sea that the Israelites crossed but the Sea of Reeds on the Mediterranean coast, and that the tsunami was produced by the eruption of Santorini volcano in the Aegean Sea in the fifteenth century BC – an outburst that may have inundated the northern coast of nearby Crete, triggering the collapse of the Minoan civilization." (Ch 2)
  • "Certain types of phytoplankton produce a gas called dimethyl sulphide (DMS), apparently as a by-product of their metabolism. The distinctive odour of DMS is responsible for the invigorating smell of the coastal sea." (Ch 3)
  • "A fine drizzle consists of droplets of typically 200 micrometres or so across, which reach free fall at a leisurely half a metre or so per second. Cloud droplets about a millimetre across become fully fledged raindrops, heading earthwards with a terminal velocity of about nine metres per second." (Ch 3)
  • "cyclic changes in the Earth’s three orbital parameters, now called Milankovitch cycles, alter the distribution of solar radiation that the Earth receives, and their net effect triggers long-term climate change." (Ch 3)
  • "when dinosaurs were still at large ... the Earth may have been so warm everywhere that no ice sheets existed." (Ch 3)
  • "Medieval shrines to goddesses were nearly always close to wells, springs, lakes or seas;" (Ch 5)
  • "the Lady of the Lake can be identified with Aphrodite, Greek goddess of love." (Ch 5)
  • "Many of the earliest autotrophs seem to have extracted hydrogen from hydrogen sulphide; some very primitive bacteria, called purple sulphur bacteria, still do. Take away the hydrogens and what’s left is sulphur. Many of the bright yellow sulphur deposits in the world today are the waste heaps of primitive autotrophs." (Ch 8)
  • "To early organisms faced with oxygen from water-splitting photosynthesis, it was as though their neighbours had started dumping toxic waste in their back yard." (Ch 8)
  • "Organelles are thought to be the remnants of once fully-fledged prokaryotic individuals, with which the eukaryotes fused in a symbiotic relationship." (Ch 8)
  • "The icefish Chaenocephalus aceratus has refined its oxygen consumption to such a degree that it can make do with no haemoglobin at all: it moves sluggishly enough that the oxygen dissolved in its blood plasma is sufficient to meet its needs. The blood of the icefish is therefore a translucent white." (Ch 8)
  • "Many people perceive something unnerving in human body fluids. Alien abductees seem to regard them as highly prized amongst extraterrestrials, and General Ripper considered his to be the victim of a Communist plot in Stanley Kubrick’s Dr Strangelove." (Ch 8)
  • "Centuries of over-irrigation in the Middle East and in the Indus valley of Pakistan have led to acute problems of salinization, in the latter case giving the region one of the lowest crop productivities in the world." (Epilogue)
  • "Dumping of ‘dung and filth’ into England’s rivers was outlawed in the fourteenth century," (Epilogue)
  • "human excreta can be composted to dark, crumbly fertilizer within a year. There seems to be no strong reason other than aesthetics why compost toilets are not standard items in many modern houses." (Epilogue)

An important study, designed for the more intelligent general reader. April 2021



This review was written by

the author of Bally and Bro, Motherdarling 

and The Kids of God

Wednesday, 25 May 2016

"Life on the Edge" by Jim Al-Khalili and Johnjoe McFadden

This book is about Quantum Biology.

The essential thesis of this work is that life is too ordered to have developed by chance from the random fluctuations of thermodynamics. Each living cell requires the coordination of a number of organelles; even the molecules of RNA which might have formed the first replicating molecules are highly complex and ordered. Enzyme processes which are the fundamental processes of life are carefully structured, although the language that this book uses (the enzymes unzip, cut, select etc) tends to prejudice one's thinking towards assigning a purposeness which the enzymes may not possess. Instead of thermodynamics, the authors propose that life requires the more ordered processes of quantum physics.

The two effects they believe are most useful to life are quantum tunnelling and quantum entanglement. Quantum tunnelling makes use of the wave nature of particles; since the particle wave means that the particle is delocalised in space it has a possibility that it is on the far side of an energy barrier so that it can react even when the energetics suggest it won't. The delocalisation also makes possible 'quantum search': instead of randomly trying out one combination after another you can explore all possibilities at the same time.

But the problem with quantum effects is that they are on a very very small scale and that the waviness feature can be disrupted by 'measurement' which in practice means interaction with another particle. Given how busy and crowded and hot the inside of a cell is, it seems surprising that there isn't a permanent state of decoherence. But these authors suggest that the cell uses tricks to ensure coherence for long enough for the necessary actions for life can take place; in one occasion they suggest that this takes place by a synchronising of oscillations within the cell which is the same thing as is suggested by Stephen Strogatz in Sync.

This is a serious scientific book and they provide great evidence for what they are suggesting. But at the end I was unsure how important it all was. There are electrons and protons inside the molecules that make up cells and these very tiny particles inhabit the quantum universe and follow quantum rules. So it is surely inevitable that the chemical reactions that make and are used by enzymes utilise quantum mechanics, after all, chemistry is all about electron transfer. There surely is no dispute about this. I think what they are suggesting is that the fact that quantum physics underpins the chemistry means that the odds on the spontaneous generation of life are much better than they first appear.

OK. It is obviously harder than we first thought to create life. Even the simplest organisms we know have extraordinarily complex internal structures. If it is too difficult to create complex molecules by random reactions then we are left with the possibility that life wasn't generated in the early history of this planet but was either created or arrived from elsewhere (although this still begs the question of how it arose elsewhere). But if quantum effects makes it too easy to create complex molecules than why was life apparently only created once? (These authors seem to suggest that the complex molecules somehow competed and only one life form remained after natural selection had taken place but if it really is that easy to create complex molecules why has this process only happened when the earth was very young?) In the end you have to assume that there is only one type of life that is viable but that it is relatively easy to spontaneously generate this form. After all, astrobiologists tell us that there are very few elements which have the appropriate reactions so that it is almost certain that only carbon-based life forms can exist in this universe.

This was an incredibly well-written book with lots of lovely asides (mostly about the bizarre life histories of the scientists mentioned) and it explains some really difficult stuff superbly well. I am not sure to what extent I was convinced by the thesis but it was great fun reading it.

May 2016; 433 pages