Thursday, 27 November 2014

Are we alone?

I recently took a course in cosmology in the hope of trying to fill some voids in my knowledge. We were spared all the mathematics that are needed for a comprehensive understanding, but the excellent tutor certainly put across key points on the age of the universe, its size, its changes through time, and the features of some of its components. My knowledge remains superficial, but it is enough for me to realise that it is impossible to get any real sense of the distances and times involved and humans will never be able to do this as the numbers are so large that we cannot compare them with with anything familiar to us. Another impression that the cosmology course left with me was that some explanations of events and structures are close to being science fiction.

The topic that created most enthusiasm among members of the class was discussion of the origin of life and whether living organisms exist elsewhere. The desire to find organisms has extended to looking for chemicals that may be involved in their make-up and we also make projections about possible habitats; a popular one being to equate finding water on other planets, or in other parts of the Universe, as being tantamount to finding living organisms. We are interested especially in the possibility of intelligent life, with which we can communicate, providing us with a feeling that we are not alone.

It was clear that most of us in the cosmology class had varying views on what we meant by life, with most thinking that it was only possible in a distinct organism, perhaps consisting of one cell, perhaps of several cells. So, is there an agreed definition? As a starting point, I read Schrödinger’s What is Life?, based on a series of lectures he gave at Trinity College Dublin in 1943 [1]. Schrödinger’s discourse detailed the way in which cells, and thus multicellular organisms, were controlled by the physics and chemistry of genes (although the mechanism of control was not known until the structure of DNA was discovered 10 years later). I would like to quote two sections [1]:

What is the characteristic feature of life? When is a piece of matter said to be alive? When it goes on ‘doing something’, moving, exchanging material with its environment, and so forth, and that for a much longer period than we would expect of an inanimate piece of matter to ‘keep going’ under similar circumstances.

The unfolding of events in the life cycle of an organism exhibits an admirable regularity and orderliness, unrivalled by anything we meet in inanimate matter. We find it controlled by a supremely well-ordered group of atoms, which represent only a very small fraction of the sum total in every cell. Moreover, from the view we have formed of the mechanism of mutation we conclude that the dislocation of just a few atoms from within the group of ‘governing atoms’ of the germ cell suffices to bring about a well-defined change in the large-scale hereditary characteristics of the organism.

I am comfortable with Schrödinger’s view that life is a feature of organisms and that the biology of organisms is under the control of what we now know to be DNA. However, we still lack a definition of life and, for this, I turned to Pincock and Frary's The Origins of the Universe for Dummies. Having reviewed complexity, metabolism, development, autonomy and reproduction, the authors write [2]:

Taking all the elements we describe in the previous sections, and all their shortcomings, into account, we can come up with a simple, one-sentence definition of life. (Of course, scientists tell you that this description isn’t perfect, but it serves as a rough definition, at least for now.)

Here’s the working definition, which is sometimes known as the NASA definition of life: Life is a self-sustaining chemical system capable of Darwinian evolution [my emboldening].

There is no mention of organisms here and it is a definition that is difficult for all to accept, as Pincock and Frary anticipated.

It has been pointed out that there is unlikely ever to be agreement on a definition of life. Carol Cleland and Christopher Chyba write [3]:

The philosophical question of the definition of ‘life’ has increasing practical importance. As science makes progress towards understanding the origin of life on Earth, as laboratory experiments approach the synthesis of life (as measured by the criteria of some definitions), and as greater attention is focused on astrobiology and the search for life on Mars and Jupiter’s moon Europa, the utility of a general definition grows. In particular, definitions of ‘life’ are explicit or implicit in any remote in situ search for extraterrestrial life.

Is science making progress towards understanding the origin of life on Earth and do laboratory experiments approach the synthesis of life? I question whether this is so, but, as Cleland and Chyba point out, it depends on the definition used. Does anyone consider DNA to be alive? Isn’t there an elusive essence to life that involves more than the interaction of molecules? Isn’t that what Schrödinger implied?

Cleland and Chyba’s Abstract is worth quoting [3]:

There is no broadly accepted definition of ‘life’ Suggested definitions face problems, often in the form of robust counter-examples. Here we use insights from philosophical investigations into language to argue that defining ‘life’ currently poses a dilemma analogous to that faced by those hoping to define ‘water’ before the existence of molecular theory. In the absence of an analogous theory of the nature of living systems, interminable controversy over the definition of life is inescapable.

How true. One reason that I left a University astrobiology research group was because we all talked about life, but there was no consensus on what we meant. I couldn’t sit back and listen to colleagues talking about the origin of life when they really meant the first appearance of RNA and DNA. I had similar problems when listening to them, and others, saying that life probably originated in hydrothermal vents; that extremophile microorganisms are likely to be found in extraterrestrial habitats with similar harsh conditions to those where these extraordinary organisms live on Earth; etc. While it would be wonderful to find living cells, or conclusive evidence of living cells having been present, on moons or planets elsewhere in the solar system (or elsewhere in the Universe), I’m not expecting such discoveries to be made, as I remain convinced that the first living cell formed on Earth in a once and once only event. Isn't that the best working hypothesis until we can prove otherwise?

[2] Stephen Pincock and Mark Frary (2007) The Origins of the Universe for Dummies. Chichester, John Wiley & Sons.

[3] Carol E. Cleland and Christopher F. Chyba (2002) Defining ‘Life’. Origins of Life and Evolution of the Biosphere 32: 387-393.

Monday, 17 November 2014

“All Nature is marvellous” - Aristotle, Pliny the Elder, and credulity

 The quotation in the title of this post is a translation from Aristotle in On the Parts of Animals, written 350 years BCE. Together with a photograph of a portrait bust, it forms the Frontispiece for Charles Singer’s A Short History of Biology (see above) and Singer, an avid admirer, writes:

The surviving works of Aristotle place him as among the very greatest biologists of all time. He set himself to cover all human knowledge, and succeeded in this vast task in a way which no one has succeeded before or since. He was a deeply original thinker, and he had an unrivalled capacity for arranging his own and other people’s material. To these qualities he added first-class powers of observation and great shrewdness of judgement. No succeeding thinker has exercised so great an influence. [1]

We are left in no doubt as to Singer’s view of Aristotle, his qualities and his importance, but he regards Pliny the Elder, another well-known Natural Historian from antiquity, quite differently. Pliny was Roman and:

..a well-born gentleman, and an able and efficient civil servant. He was a man of immense industry with an enthusiasm for collection. He did not, however, collect natural history objects, but only information or rather misinformation about them. He put together a vast number of extracts from works concerning every aspect of Nature. These he embodied in his famous book on Natural History. Unfortunately, Pliny’s judgement was in no way comparable to his industry. He was excessively credulous. Thus his work became a repository of tales of wonder, of travellers’ and sailors’ yarns, and of superstitions of farmers and labourers. As such it is a very important source of information for the customs of antiquity, though as science, judged by the standards of his great predecessors, such as Aristotle.., it is simply laughable.
  Despite the low quality of his material, Pliny’s work was widely read during the ages which followed. He was the main source of such little natural history as was studied for a thousand years after his time. Many common superstitions have thus passed into current belief from Pliny.
  One idea which comes down to us direct from Pliny is very commonly encountered among ignorant people. It is the belief that every animal, plant and mineral has some use; that is to say, was formed for the benefit of man. [1]

This is harsh criticism, and Pliny does not benefit by comparison with Aristotle. However, it is easy to see that Natural History is very much as Singer describes it. [2] The work is truly encyclopaedic and does not confine itself to plants and animals, but also to many aspects of the physical World.

The idea of the usefulness of plants and animals to humans cannot be laid solely at Pliny’s door. In Genesis 1: 26-29 in The Holy Bible, we read: [3]

And God said, Let us make man in our image, after our likeness: and let them have dominion over the fish of the sea, and over the fowl of the air, and over the cattle, and over all the earth, and over every creeping thing that creepeth upon the earth.. ..So God created man in his own image, in the image of God created he him; male and female created he them.. .. And God blessed them, and God said unto them, Be fruitful, and multiply, and replenish the earth, and subdue it: and have dominion over the fish of the sea, and over the fowl of the air, and over every living thing that moveth upon the earth.. .. And God said, Behold, I have given you every herb bearing seed, which is upon the face of all the earth, and every tree, in the which is the fruit of a tree yielding seed; to you it shall be for meat..

To me, this is as anthropocentric as the writings of Pliny and must have had a considerable effect on how Nature was regarded during the Dark Ages. It is interesting that Singer’s statement about anthropocentricity was made in 1931, at a time when the study of Biology was still strongly influenced by Natural History and it was recognised that having knowledge of plants and animals of all types was important. Since then, we have concentrated more and more on humans, or genetic analogues of our species.

In a wider context, humans threaten not only each other but, increasingly, the existence of other organisms and the environment. It can be argued that the widespread extinction of plants and animals arises from our belief that they are not important, unless they benefit us directly as crops, saleable commodities, or sources of useful chemicals. It is not the thought of Pliny, or of Jewish and Christian literature, that is driving this attitude, but our politico-economic systems. Singer’s ire is even more relevant now than it was eighty years ago and I wonder if we, like Pliny, are excessively credulous in consuming information conveyed to us about what is really important. It might be suggested that we should return to Aristotelian ideals, reduce our anthropocentricity, and re-examine the view that “All Nature is marvellous” before we become even more destructive. So how can this be achieved in an era of sound bites, reality TV, advertising, and other challenges to our credulity?

[1] Charles Singer (1931) A Short History of Biology. Oxford, The Clarendon Press.

Thursday, 6 November 2014

Darwin’s Dust

During the passage of HMS Beagle through the eastern Atlantic, Charles Darwin became intrigued by dust that accumulated on parts of the ship:

On the 16th of January (1833), when the Beagle was ten miles off the N.W. end of St. Jago [Santiago, Cape Verde Islands], some very fine dust was found adhering to the under side of the horizontal wind-vane at the mast-head; it appeared to have been filtered by the gauze from the air, as the ship lay inclined to the wind. The wind had been for twenty-four hours previously E.N.E., and hence, from the position of the ship, the dust probably came from the coast of Africa. The atmosphere was so hazy that the visible horizon was only one mile distant.. [1]

..Many scattered accounts have appeared concerning the dust which has fallen in considerable quantities on vessels on the African side of the Atlantic Ocean. It has appeared to me desirable to collect these accounts, more especially since Professor Ehrenberg’s remarkable discovery that the dust consists in considerable part of Infusoria and Phytolitharia [the remains of the coverings of single-celled organisms, the latter with siliceous coats].. [1] is a very singular fact, that out of the many forms [of the coverings of single-celled organisms] known to Professor Ehrenberg as characteristic of Africa, and more especially of the Sahara and Senegambian regions, none were found in the dust. From these facts one might at first doubt whether the dust came from Africa; but considering that it has invariably fallen with the wind between N.E. and S.E., that is, directly from the coast of Africa; that the first commencement of the haze has been seen to come on with these winds; that coarser particles have first fallen; that the dust and hazy atmosphere is more common near the African coast than further in the Atlantic; and lastly, that the months during which  it falls coincide with those when the harmattan blows from the continent, and when it is known that clouds of dust and sand are raised by it, I think there can be no doubt that the dust which falls in the Atlantic does come from Africa. [1]

We know from satellite images that considerable amounts of dust are carried out far into the Atlantic, on to South America [2] and, with changes in the jet stream and other meteorological events, to many other parts of the Earth (see image below). It is intriguing to read in Darwin’s report that the dust contains the identifiable remains of “Infusoria and Phytolitharia”. The northern part of Africa, where these aquatic organisms originated, is now desert, but there must clearly have been water present in earlier times and, indeed, a lake covering 350,000 km2 existed in the region 6,000 years ago. [3] It is likely that the remains of cells that Darwin, and others, reported from the Atlantic were originally from this source and we now know that components of the dust include residues from many other algae and animals, including fish, and that these fall into the water, or are carried there by rains, and act as fertilisers. [3] 

Anyone who gardens knows that fish bone meal is a good source of phosphorus for growing plants and it is thus likely to play a similar role when deposited into the oceans, or on to terrestrial landscapes. Recent research by Karen Hudson-Edwards and colleagues [3] has shown that the mineral residues of fish bones allow easier solution of phosphorus than many other bound organic residues that are present in the dust being blown from the Sahara. There is, of course, a finite amount of this material and, in time, it will form a smaller and smaller fraction of that eroded from the region, as the strata containing the organic remains begin to disappear.

Many people are familiar with the idea of fish, and other animals, falling from the sky, having been sucked up by waterspouts from surface waters, [4] but the rain-down of fossilised fish bone meal, and other mineralised plant and animal material, is less well-known. It has been, and continues to be, an important input of fertiliser to both aquatic and terrestrial communities.

[1] Charles Darwin (1846) An account of the Fine Dust which often falls on Vessels in the Atlantic Ocean. Quarterly Journal of the Geological Society 2: 26-30.

[3] Karen A. Hudson-Edwards, Charlie S. Bristow, Giannantonio Cibin, Gary Mason and Caroline L. Peacock (2014) Solid-phase phosphorus speciation in Saharan Bodélé Depression dusts and source sediments. Chemical Geology 384: 16-26.