John S. Compton

 (source: http://www.cdc.gov/ecoli/)

First and forever a microbial world

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John S. Compton

They are so small, we rarely give them a thought and yet they are out there in numbers too enormous for us to comprehend. In fact, they are estimated to constitute no less than half of the total mass of all life on Earth. So, when you next look out over the landscape covered by plants and teeming with insects, birds and animals, think of the roughly equivalent mass of life that you don’t see. This invisible other half of life is the microbial world, made up of a great variety of microorganisms, so called because they typically measure only 0.5 to 5 micrometres across (that is about one-thousandth to one-hundredth the width of the 0.5 millimeter sized dot atop the letter i).  Although they are nearly everywhere, to see them requires a microscope (although some exceptionally large species are visible to our naked eye, such as Thiomargarita namibiensis, which lives by accumulating spheres of elemental sulphur in its elongate cells in shelf sediments offshore Namibia in southwest Africa).

 

For what they lack in size, microorganisms make up for by their ubiquitous multitudes: 10 to 1000 billion in every teaspoon of soil, a billion or so in every 20 drops (one millilitre) of water, and each of us hosts on the order of 40,000 billion microbes thriving inside our body and out. Microbes have evolved to eke out a living in nearly every habitat on Earth, even those we don’t normally associate with the living world: kilometres below the surface in deep rock fractures, and deep below the surface of massive ice sheets. Microbes can even survive in the vacuum of space, and include those left behind on the Moon by astronauts (most likely in a dormant, resting state). We tend to consider microbes as dangerous and something to kill off indiscriminately with antibiotics and disinfectants. Although some are pathogens, most microbes are benign and many others beneficial, if not essential to our well-being. We are only beginning to appreciate the roles played by the highly diverse microbes that thrive in our gut, our mouths and in every nook and cranny of our skin.

 

 

The bacteria Staphylococcus aureus (colourised from CDC/Matthew J. Arduino, DRPH/Photo Credit: Janice Haney Carr, scale bar is 1 micrometre).

 

 

Escherichia coli (E. coli) bacteria (credit: NIAID, each around 2 micrometres long)

Microorganisms are unicellular, with each individual consisting of a single cell whose features are either relatively simple or complex. Those with generally small, simple cells are referred to as prokaryotes and include two main groups: bacteria and archaea. Their simple cells contain a single, circular loose strand of DNA along with ribosomes housed within a cell wall and membrane. Those with generally bigger and more complex cells in which the DNA occurs tightly coiled within a separate nucleus enclosed by a membrane and, along with ribosomes, contain organelle structures are referred to as eukaryotes. The eukaryotes are thought to have evolved from the merging of different prokaryotes. For example, mitochondria organelles, which act as the energy furnace within eukaryotes, were once separate bacteria that were at some stage taken in by and subsumed by archaea. Bacteria and archaea evolved by around 3.5 billion years ago, while the eukaryotes only evolved later by around 2 to 1.5 billion years ago.  The evolution of eukaryotes was critical to the eventual evolution of all the big, visible organisms like plants and animals whose many cells are eukaryotic.

 

 

Even magnified under a microscope, the many different species of bacteria and archaea can be difficult to tell apart. Some species have many tiny hair-like cilia or long thread-like tails (flagella) to whip them about (see photo top), while others can bind together to form filaments or thin-film colonies. But most individual cells are either spherical to elongate in shape and difficult to tell apart from outward appearances. And this partially explains why archaea were only recently appreciated as being different from bacteria. One way to tell them apart is by what they do chemically, for bacteria and archaea are extremely versatile in the ways in which they metabolise. Some reduce carbon dioxide to methane, others fix nitrogen into nitrate while others convert nitrate to nitrogen, some oxidize sulphur to sulphate while others reduce sulphate to sulphide, and so on...each occupying the chemical niche best suited to their way of life. In essence, bacteria and archaea run most global elemental cycles at Earth’s surface, accelerating the pace of chemical reactions so vital to all life forms big and small. Just how many species there are remains largely unknown, but the application of genetics has facilitated our ability to identify them, with thousands of species typically analysed within any given soil or water sample.

No sex please, we are prokaryotes! Bacteria and archaea reproduce by binary fission, where an individual makes an identical copy of itself and splits into two – a parent and its clone. They can also take up bits of DNA of interest that happen to be floating about in their surroundings or they can transfer specific bits of DNA among themselves. Such horizontal or lateral transfer of DNA helps them adapt to changes and to survive stressful times. They can also shut down and stay holed up as microbial cysts until better conditions return, even if that means remaining dormant for centuries or perhaps millions of years. Although microbes living today are probably not terribly different from the first of their kind that appeared 3.5 billion years ago, they can evolve rapidly. For example, so-called ‘superbugs’ evolve in hospitals by surviving the continuous onslaught of antibiotics and disinfectants.

 

Being the first to live on Earth, bacteria and archaea form the two deepest domains of life, and they are the life forms most likely to endure. Their small size, widespread distribution, genetic diversity and ability to shutdown make them far more likely than other organisms to survive whatever future catastrophes come along. As long as Earth is capable of supporting life it will always include a microbial world. In this sense, the meek shall inherit the earth, if the meekest among us are the smallest and simplest microorganisms. And if life exists on other Earth-like rocky planets orbiting within the wet and warm habitable zone of their stars, it too will most likely be microbial. When considering the abundance and amazing chemical promiscuity demonstrated by the element carbon on Earth, it seems reasonable to conjecture that microbes on other rocky planets are likely to be similar in many respects to our own. It is partly for this reason that we must take every precaution not to contaminate other worlds if we hope to determine unambiguously if life exists elsewhere.

 

 

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Origin of life

How did life first came about? Our planet started out as a molten magma ball too hot for life, but the oldest fossils indicate that life was established soon after Earth had cooled sufficiently to be covered by oceans of water suitable for life. Evolutionary theory allows us to understand how life, once arrived, diversified over deep geological time into the abundant life forms we observe today. However, how life first evolved on Earth remains largely unknown. We have only ever observed life to spring from existing life, and we have yet to find convincing evidence that life exists elsewhere beyond our planet. And although we have extensively modified the DNA of existing organisms, including the synthesis of a simple microbe ( C. A. Hutchison III et al., Science 351, aad6253 (2016). DOI: 10.1126/science.aad6253), we have yet to synthesis life from scratch, from its basic organic molecular building blocks such as amino and nucleic acids.

 

All the diverse life forms on Earth today, including us, appear to be ultimately related to one another and to share a common ancestor. This gives rise to the concept that ‘all life is one,’ which stems from the fact that all life is based on DNA and RNA, the double and single helical molecules that contain the code of life. Similarities in genetic DNA and RNA make-up, as well as the many shared biochemical processes across many different organisms, suggest that we and all other life forms descend from a distant common ancestor. This shared great-great-greatest of grandparents to everything that is living today is known as life’s Last Universal Common Ancestor, or ‘LUCA’ for short.

 

Charles Darwin commented on this profound concept that ‘all life is one’ in his book On the Origin of Species, published in 1859:

 

‘It is a truly wonderful fact - the wonder of which we are apt to overlook from familiarity - that all animals and all plants throughout all time and space should be related to each other…Therefore I should infer from analogy that probably all the organic beings which have ever lived on this earth have descended from some one primordial form, into which life was first breathed.’

 

LUCA is Darwin’s ‘primordial form into which life was first breathed’ and from which all life forms on Earth descended. Hence, the myriad species we see today are each from a long line of descent that includes many now extinct ancestors over the eons of deep geological time and which converge all the way back to LUCA.

 

There have been many ideas put forth on where and how did LUCA evolved, but the upshot is we do not know. What we do know is that LUCA must have evolved sometime between when Earth had first become habitable (4 to 3.8 billion years ago) and the oldest fossil life forms yet found in rocks 3.4 billion years old.

 

 

The earliest fossil evidence of life on Earth comes from organic structures such as these observed in thin slices of rock 3.4 billion years old from Australia and South Africa (image 0.16 mm across, courtesy of Ken Sugitani; K. Sugitani, and others, 2015. Early evolution of large micro-organisms with cytological complexity revealed by microanalyses of 3.4 Ga organic-walled microfossils. Geobiology DOI: 10.1111/gbi.12148)

 

These oldest fossils reveal the overall cell morphologies, but tell us little about the biology of these early organisms. However, they are generally assumed to be representative of the simplest single-celled microorganisms living today. But even the simplest bacteria today include many complex organic structures (DNA, RNA and ribosomes) and intricate biochemical processes that occur within their cell-wall structures. Our general understanding of evolution suggests that the complex biology represented by these fossil organisms evolved gradually over the hundreds of millions of years available from the modification of existing, simpler structures. These first organic structures were not in themselves living entities, but they may have nevertheless evolved as molecules by way of random mutations and natural selection in much the same way that Darwin proposed species do today. These selective forces may have promoted the merging of different ‘molecular species’ in ways that enhanced their mutual stability and replication in what could be viewed as a continuum leading up to the first bona fide life forms, out of which LUCA would evolve to give rise to all life as we know it.

 

Earth’s surface had an abundance of all the elements necessary for life: carbon, nitrogen, oxygen, phosphorus, etc. It also included organic compounds, such as amino acids, sugar and sugar alcohols, either formed naturally on Earth or delivered by meteorites. Besides water, life forms are mostly made up of amino acids organized into many different proteins, which are the large, complexly folded, three-dimensional organic compounds that make up our blood, muscles, skin, hair, etc. Amino acids existed before life, but how did they become organized into complex proteins under the direction of DNA and RNA housed within cellular membranes?

 

One idea is that early organic compounds may have included simple, self-replicating molecules, with those that replicated the fastest or most accurately persisting instead of perishing. Gradually, compounds as complex as small RNA-type molecules may have emerged whose information-storage capabilities could code for different amino acids in the production of proteins essential for a broad spectrum of biochemical functions. For example, phospholipid protein molecules capable of forming impermeable bubbles may have been precursors to cell membranes providing barriers to the outside world. Over time, incremental Darwinian selection led to improvements in replication and the coordinated merging of different organic structures and protein enzymes into the first simple cellular ensembles capable of extracting energy to grow, replicate and evolve, which in a nutshell is what life does. Of course, much of the above generalized scenario is highly speculative and we are a long way from understanding the many intricate processes by which life arose on Earth.

 

Where on Earth might life have first evolved? A likely ‘primordial soup’ from which life was concocted is in the vicinity of volcanic hot springs located along the axis of the mid-ocean ridge mountain chain in the deep, dark ocean. These volcanic hot springs are called ‘black smokers’ (see image below), because they spew turbulent smoke-like billows of black sulfide particles through mounds and chimney-like columns. The mid-ocean ridge represents the most recently formed oceanic crust. The large temperature contrast between the newly emplaced, hot crustal rocks and cold, overlying seawater drives the intense circulation of seawater through the oceanic crust. Hot, altered seawater is eventually shot back out into the sea via black smoker vents. These and other ocean vents are home to thriving communities of organisms, such as tube worms, clams and shrimp. At the base of the vent food chain are chemosynthetic microbes, which derive their energy from chemical reactions associated with the vents rather than from sunlight energy as do algae and plants living today in the sunlit uppermost surface of the ocean. Support for a black smoker origin of life comes from the fact that some of the most primitive microbes (archaea) live there today in waters as hot as 113°C.

 

NASA/ESA/M. Livio and the Hubble 20th Anniversary Team (STScI)

Is this where life began? Hydrothermal (hot water) vents, such as this one on the Galápagos Rift mid-ocean ridge, are host to a diverse community of organisms (mostly white and red tube worms in the photo above). The vibrant vent community ultimately exists from the energy available from chemical reactions. Some of these reactions are expressed in the precipitation of the dark sulfide minerals that give ‘black smokers’ their name.  (photo from NOAA PMEL Vents Program; source: http://oceanexplorer.noaa.gov/okeanos/explorations/ex1103/logs/july20/media/tubeworms_smokers.html)

 

The mid-ocean ridge forms a long, continuous submarine mountain chain (red) along which black smokers and other vent systems occur. Early Earth is likely to have included a mid-ocean ridge with black smokers, with the continents only forming later.

 

We don’t know how many variations on early life there were before LUCA had evolved. In fact, we know very little about LUCA itself, except that it likely included features of the simplest microbes found today residing in the vicinity of deep, dark ocean vents. Wherever and however LUCA first appeared, its descendants soon ventured out to other parts of the ocean and along the way evolved into many different types of microorganisms. These, in turn, gradually gave rise to the rich diversity of life we are familiar with today in the sea and on the continents.

 

 

©John S. Compton (www.johnscompton.com)

 

Are we alone?

3 March 2016

John S. Compton (www.johnscompton.com)

 

Earth could be considered rarefied if it belongs to a small, esoteric and exclusive group of planets that are rocky, orbit within the habitable zone of their stars and support life. NASA’s Kepler space observatory has now confirmed the existence of at least 2000 planets beyond our solar system (exoplanets). Considering that Kepler has searched within a very small patch of the sky, it is probable that exoplanets are out there in abundance. Some, like the exoplanets Kepler 542b and 186f, appear to be Earth-like: rocky planets up to two times bigger than Earth that orbit within the habitable zone of their star. But whether any of these Earth-like exoplanets also support life remains unknown.

 

The discovery of these distant rocky exoplanets, along with our Sun’s four inner rocky planets Mercury, Venus, Earth and Mars, suggests that rocky planets are not rare. However, they tend to be small and difficult to detect. Rocky planets are unusual in that they concentrate all the heavies, those elements heavier than the two lightest elements hydrogen (H) and helium (He). Most of the atoms in our solar system, as well as our universe as a whole, consist of H and He, with H making up 73% and He 25% of all atoms. All the other elements known on the periodic table make up the remaining 2%. These heavies were forged from H and He within large stars or during the explosion of large stars (supernovas) since the big bang 13.7 billion years ago. Because large stars are relatively rare, not much of the original H and He that formed at the time of the big bang have managed to be forged into the heavier elements.

 

H and He are great for making stars but it is difficult to imagine how they could ever form the building blocks of life. Life as we know it requires elements such as carbon, oxygen, nitrogen, phosphorus, sulfur and a whole host of trace metals and other elements. So, the key initial step in making a living planet is making one that, like the rocky planets, concentrates the heavies. But all we need to do is look at our rocky planet neighbours to realise that the other critical factor for life is that the planet orbits within the habitable zone. Venus is too hot and Mars is too cold, but Earth is ‘just right’ – neither too hot nor too cold for liquid water to exist in abundance. Earth, the ‘blue marble’ planet (see image above), is unique among our solar system’s rocky planets, with our big blue ocean and swirling white clouds indicating that we orbit within our Sun’s habitable or just right ‘Goldilocks’ zone. There have been recent discoveries of planets from other solar systems that appear to orbit within their star’s habitable zone, but whether they too are blue marble planets is more difficult to discern (see image below).

 

The ideal rocky exoplanet, one that may support life, would be the same size or up to twice as big as Earth and orbit a star similar to our Sun as does the best candidate, Kepler 542b. Size matters because a planet needs to be big enough to retain an atmosphere of gases heavier than H and He. Like a child’s helium balloon, Earth’s initial H and He gases floated off into space, eventually joining up with their multitudinous kin residing in our Sun. However, the heavier gases, including water vapour, were retained and once conditions had cooled enough this water vapour rained out to form the oceans. And it was soon after the oceans formed that life was established on Earth. It is the presence of life that may or may not be the most rarefied aspect of our planet. Besides extraterrestrial visitors or communiqués from outer space, how might we detect life on other planets? What features could we look for uniquely associated with life?

 

Earth can also be thought of as rarefied in terms of its outermost layer, its atmosphere. While iron sank to the core, the lightest elements buoyantly made their way to the surface to form Earth’s atmosphere - its most elevated and lofty, least dense layer composed of a thin mix of gases. Earth’s atmosphere initially had no oxygen gas (O2), but today oxygen gas is abundant making up 21% by volume. The oxygen gas content increased as a by-product of photosynthesis, the process by which algae and plants use sunlight energy to combine carbon dioxide (CO2) and water to grow. It is thought that it was the rise in oxygen gas to threshold levels, for example, that allowed for the rapid evolution of animals during the Cambrian explosion 541 million years ago. And life as we know it, based on carbon and photosynthesis, seems the most likely for other rocky worlds given that their chemistry would be similar to ours and life arose here so soon after it was possible.

 

Currently we are unable to see potential Earth-like exoplanets well enough to know if they are blue marbles having oxygen-rich atmospheres. However, far more powerful space telescopes are in the works and these might be able to provide the first solid evidence for life elsewhere. If we could find evidence for life on just one other planet the implication would be that Earth is not rarefied after all. In that case, the equation: ‘chemistry (of a rocky planet) plus energy (from its star) plus time equals life’ just may apply, and we would be only one of many, many living worlds in our universe.  Given how science has humbled our rarefied views of our place in the universe in the past (for example, Earth is not the centre of the solar system; we are not separate from but are in fact related to all other organisms on Earth), it should not come as too big a surprise to learn that we are not alone. Of course, Earth is special and its particular life forms are undoubtedly unique in many respects, but it seems likely that there are many other worlds out there, equally alive and special.

 

 

An artist’s interpretation of a ‘blue-marble’ exoplanet (Kepler 186f) (NASA Ames/JPL-Caltech/T. Pyle).

 

©John S. Compton (www.johnscompton.com)

 

Deep Time/Big History

Image of Carina Nebula from NASA/ESA

5 February 2016

John S. Compton (www.johnscompton.com)

 

Where did you come from? Like many questions, the answer depends on the timeframe. At the one, most recent extreme is the seemingly straightforward response that you came from your mother, grown in the space of nine months from one of her eggs fertilized by one of your father’s sperm. At the other, most distant extreme is the origin of the many atomic elements that went into making you. The carbon, nitrogen, oxygen, and other elements that make up your complex organic compounds were made long, long ago from the fusing of lighter elements in the interior of enormous stars and as these stars blew asunder in enormous explosions (supernovae, supernovae, such as the one pictured above, the Carina Nebula) since the big bang 13.8 billion years ago. So, in this sense, it would be correct to say we come from ancient star dust. But what about the intervening time that separates these two extremes? How is it that the minute, elemental bits of star dust once made were able to assemble eventually into something as miraculous as you or any other living life form on Earth? This is the realm of deep time or what has become known as ‘big history,’ covering all events prior to the written word 5000 years ago.

 

And it turns out, it took a long time and a lot had to happen before anything even remotely resembling us lived on Earth. Hence, from the perspective of deep time we are a very late arrival. There are many ways to try and understand just how recent our arrival is – such as the arrival of our species (Homo sapiens) seven and a half minutes before midnight on the 31 December relative to a start of the big bang on January first of that same year.  Farming only arrives around 20 seconds before midnight, written history 10 seconds before and Edison's first commercial light bulb literally in the final wink of an eye (300 milliseconds) before the end of an all-time-encapsulated-in-one-year timeframe. But whatever device is used, deep time remains a difficult concept for most of us to grasp fully.  Even in the course of our lives our perception of the passage of time changes, from the agonising wait for our birthday as children to the speed at which the years appear to fly by to an octogenarian.

 

The figure to the left provides a graphical representation of deep time from the big bang to the present day, a span of 13.8 billion years.  More recent times are expanded successively in the columns from right to left. The second column on the right represents the classic geologic timescale, with the major ancient past epochs of the last 540 million years, including, for example, the Cambrian when trilobites crawled about and the Cretaceous when dinosaurs ruled. The third and final columns to the left represent the last three and the last half million years, respectively – the time span over which our human (Homo) lineage evolved. The last three million years, and particularly the last million, are demarcated by a wiggly line that represents fluctuations in climate from cold to warm and back again. These climate wiggles are important to our evolution because they are believed to have played a decisive role in shaping who we are.

 

Climate change in many respects was the ‘master variable’ because climate ultimately determines the types of habitats our ancestors adapted to in order to survive - the types of food on offer, the other animals we shared our habitat with, the frequency of fire, the severity of seasonal differences, just to name a few.  All of these factors influenced how our features were selected for over time. But is deep time still relevant to us today? For some among us, curiosity and a wanting to know how it happened is ample justification for learning about our deep past.  Most of us love stories and what better story is there than our big history, writ large over millions of years? So many things could have happened differently from the way they did, and yet the unique events that did unfold are what ended up shaping us into who we are today.  If we are to understand ourselves in the deepest sense, we need to know our deep past.

 

We forget most of our past but embody all of it.

 

(Quote from John Updike in his Introduction to Rabbit Angstrom)

 

We do quite literally embody our past – from our cellular functions, to upright walking, to our unusually large brain – these and all of our other features have origins rooted in our deep evolutionary past, origins that link us in many respects to all other life forms on Earth. There are many events that shaped each of our individual lives that we have forgotten and there are many events in the deep past that shaped who we are today that are unknown to us. But for some of these past events we have bits of evidence preserved in the rock and archaeological records that allow us to speculate on our big history; to tell the story of how it happened that we came to be.

 

©John S. Compton (www.johnscompton.com)

 

 

 

 

 

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image of deep, geological time from big bang to the present day from John S. Compton website

Figure of deep (geological) time from big bang to today.

(Big bang image from NASA/WMAP Science Team; timescale adapted from Walker, J.D., Geissman, J.W., Bowring, S.A., and Babcock, L.E., compilers, 2012, Geologic Time Scale v. 4.0: Geological Society of America, doi: 10.1130/2012.CTS004R3C. Marine oxygen isotope records are from Lisiecki, L. E., and M. E. Raymo, 2005. A Pliocene-Pleistocene stack of 57 globally distributed benthic d18O records, Paleoceanography, 20, PA1003 (doi:10.1029/2004PA001071).

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© John S. Compton