THe nature of life and its potential to survive

The question we consider is whether such worlds, habitable for a broad range of living things, will ever host complex life, and life that may, like ours, ponder its own existence.. 5, bu

Astronomers’ Universe

More information about this series at http://www.springer.com/series/6960

The Nature of Life and Its Potential

to Survive

ISSN 1614-659X ISSN 2197-6651 (electronic)

Astronomers’ Universe

ISBN 978-3-319-52910-3 ISBN 978-3-319-52911-0 (eBook)

DOI 10.1007/978-3-319-52911-0

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Nikki, without whom this work would not have been possible Her encouragement and ideas have kept the development of this book in motion and made me consider possibilities that would not have otherwise come to mind I am a very lucky man.

Preface

Why is life so tenacious? After all, we find it in virtually every environment Earth can provide Life occupies every niche within each broad canvas of rainforest, clinging to the sides of branches high in the canopy; or lurking under the frozen topsoil of Antarc-tica’s dry valleys Life is found in acidic hot springs and alkaline Rift Valley lakes Life seems boundless

This book explores the nature of life on Earth and questions whether we can extrapolate its terrestrial characteristics to life elsewhere in the universe Here, we assume life is universal, but is this a valid proposition? Is Earth somehow unique in the cosmos—and from our anthropomorphic viewpoint—is intelligent life so incredibly improbable that Fermi’s paradox may be addressed with

an affirmative, “Yes, we are alone”?

In The Nature and Potential of Life, we attempt to apply

what we know about terrestrial life and extraterrestrial chemistry

to extrapolate biology to other worlds, both those we know and those we imagine Although there must by definition be specula-tion, these idlings of the mind are underpinned with solid chem-istry and physics By the end of this book, we aim to demonstrate that not only is extraterrestrial life a certainty in the universe but that intelligent life will, by necessity, arise on particular planets

We conclude our adventure with an exploration of the planets

we have already encountered and those we only imagine at ent Within this fold come the tidally locked worlds of the red dwarfs; these are likely to be the most numerous habitable worlds

pres-in the cosmos The question we consider is whether such worlds, habitable for a broad range of living things, will ever host complex life, and life that may, like ours, ponder its own existence More-over, can life survive the rigors of its environment? Can the uni-verse ever sterilize a planet with a single asteroid strike or a nearby supernova? As we set about terraforming our world into something

a lot less habitable than nature intended, will there ever come a moment when humanity brings about its own extinction?

The Nature and Potential of Life considers biology in all its

complexity, but by grounding it within a solid chemical and cal framework we describe and develop a rigorous set of tools we can use as we probe ever deeper into the cosmos The book is by definition multidisciplinary in nature, but irrespective of your back-ground, whether scientist, layman, or student, you will find some-thing about life that you may not have considered before Enjoy

Contents

1 What Is Life? 1

Introduction 1

Beyond the Six Kingdoms 2

How Do Our Genes Work? 7

The Shifting Landscape of Our Genes 9

Genes on the Move 11

The CRISPy Side of Evolution 21

How MRS GREN Became MRS GREEN 22

The Deep Biosphere 25

Life, the Universe and Maybe Everything 29

Conclusions 31

References 32

2 Life’s Grand Themes 35

Introduction 35

The Replication and Transmission of Information 35

The Persistence of Cells 38

Photosynthesis and the Oxygen Revolution 52

Of Peroxides and Perchlorates 59

Sex and Sexuality 62

From Unicellular to Multicellular Life 66

Sensation 68

Neurons, Brains and Integration 70

Are There Reasonable Alternatives to Multicellular Central Nervous Systems? 78

In Silico: The Future of Intelligence Everywhere? 81

The Idea of an Intelligence Window 84

A Few Final Scenarios 90

Conclusions 92

References 95

3 The Origin of Life on Earth 97

Introduction 97

The Dark, Young Earth 97

What Do Astrochemists Know About Life? 104

Southern Fried Chickens and Poached Eggs 115

Before the RNA World 120

The Rise of Modern Genetics from Molecular Goo 126

How Might Life on Earth Compare to Its Rise Elsewhere? 138

The Emergence of Photosynthesis 141

Conclusions 151

References 153

4 Life as the Evolution of Information 157

Introduction 157

The Entropy Illusion 157

The Lady’s Not for Turning—Why Evolution Never Goes Backwards 165

Hypermutation 169

Redundancy and Degeneracy: The Lifeblood of Evolution 171

The Genetic Code 173

Hox Genes 174

Gene Networks and Genetic Learning 177

Redundancy, Entropy and the Major Transitions in Evolution 182

Epigenetics: Add a Dash of Lamarckian Unpredictability 184

Conclusions 188

References 190

5 Life Jim, But Not as We Know It 193

Introduction 193

A Recap 193

Using the Deep Biosphere as a Guide to Alien Life 195

Signs of Life 200

Life Under a Crimson Sun 202

Insurmountable Problems? 202

The Rhythm of Life 208

The Color of Spring 210

ET - From the Familiar to the Sublime 214

Sub-glacial Life 214

Living Rocks 217

The Blob 218

Dustballs, Tumbleweeds and Self-assembling Organisms 219

Planet-Wide Microbial Consciousness 220

In Silico Life: A Reprise 221

Can a Star Be Alive? 222

Nebular Life? 224

Life on Nearby Shores 226

The Signatures of Life 229

Metabolism 229

The Great Pump 230

Biological Impact on Planetary Atmospheres 231

Conclusions 233

References 233

6 Extinction 237

Introduction 237

Humans as Mass Killers 237

The Five Major Extinctions 241

The Ordovician Extinctions 244

The Devonian Event 248

The Great Dying 251

The Fall of Pangaea and the Rise of the Dinosaurs 256

The Rise of Mammals 257

Take-Home Messages from the Mass Extinctions 260

Can Life Be Defeated? 267

Conclusions 269

References 270

7 Agents of Mass Destruction 273

Introduction 273

Our Own Worst Enemy 274

Global Warming 275

Nuclear War 279

Overpopulation 286

Pestilence 292

Collapsing Economies 295

Fashion Bottlenecks 299

What Can the Universe Throw at Us? 302

Ice Ages 303

Near Misses with Black Holes and Neutron Stars 304

Near Misses with Dwarf Stars or Rogue Planets 307

Gamma Ray Bursts 312

Cosmic Collisions with Comets and Asteroids 316

Migrating Mercury 323

Mutually Assured Destruction: Courtesy of the LHC? 324

What Can Science Fiction Tell Us About Annihilation? 329

Wandering Planets: “Earthfall” 329

Death Rays and Antimatter 331

V (1984) 333

Von Neumann Machines 334

Conclusions 337

References 337

8 Ultimately, Can Life Survive? 341

Introduction 341

The Decline and Fall of Life on Earth 342

Tardigrades, Dienococcus radiodurans and Hitching Rides 354

The End of Stars 364

Life Without Warmth 374

Energy, Entropy and Life’s Inevitable Decline 376

Death by Fire 379

Conclusions 382

References 383

9 A Thesis on Life, the Universe and Almost Everything 385

Introduction 385

The Basics for Life and Intelligent Life 385

Oxygenic Photosynthesis as a Rate-Limiting Step 388

Information Entropy, Probability and Time 392

Oxygen’s Role in Expanding Biological Information Entropy 392

Information Entropy in a Changing Environment 394

Plate Tectonics and the Growth in Information Entropy 397

Towards a Mathematical Model for Evolution in a Changing World 404

The Model 409

Information, Information, Information 412

Information, Oxygen, Multicellular Life and the Evolution of Complexity 413

Information, Oxygen and Intelligence 415

Planet A: Aqua-Planet 420

Planet B: A Tidally Locked World 422

Planets C and D: A Young Earth, a Young Mars 424

Information and Extinction 427

Conclusions 432

References 438

Glossary 443

Index 449

About the Author

David S Stevenson completed a Ph.D in molecular genetics from

the Department of Genetics at the University of Cambridge (Hughes Hall College) in 1994 Since then he has worked as a plant molecular biologist, before transferring to teaching at a successful academy in Nottinghamshire Aside from biology and applied sci-ence, he received qualifications in astronomy, planetary science and earth sciences Since 2013, he has published four books with

Springer—Extreme Explosions; Under a Crimson Sun; The

Complex Lives of Star Clusters; and in 2016 The Exo-Weather Report The astronomy magazines, Popular Astronomy, Astronomy,

and Sky & Telescope, have also published a number of his articles

A further book on planetary geology will be completed in 2017.Most recently, Stevenson published a meteorology article demonstrating the successful prediction of winter weather pat-terns in the UK up to six months in advance of winter—ahead of

the Met Office publication in Nature Geoscience Further

peer-review publications covering aspects of planetary science and lution are in preparation

evo-The author lives in Nottingham with his wife, Nikki, and family, without which, he says, none of this would be possible

© Springer International Publishing AG 2017

D.S Stevenson, The Nature of Life and Its Potential to Survive,

Astronomers’ Universe, DOI 10.1007/978-3-319-52911-0_1

1 What Is Life?

Introduction

On the face of it what life is seems fairly obvious If you think

about humans, their pet animals or an animal on a farm, then you know that living things run around, breathe, are conscious (we like to think to varying extents) and are very much tangible things.What about plants? Well, they don’t move much at all; they aren’t warm and fluffy and they almost certainly don’t think much However, they are quite big, they grow and they reproduce when given the chance Bacteria? Hmm, well, they reproduce but are very small They don’t breathe as far as we can see, but then again, neither do plants Fungi? Well, aside from their popularity

at parties,1 fungi spend most of their time looking like a mass of tendrils that extend through whatever substance they are grow-ing on Here, they secrete digestive juices to dissolve the material

on which they are growing They aren’t able to move; they don’t think and don’t appear to breathe Yet, as far as we are concerned, they are alive

How, then, do we define what a living thing is? Why is a cat

alive, but a lump of granite not? Why is a Yersinia pestis bacterium

living but not a crystal of sodium chloride?

Well, you might say living things are complicated, and living things are not Certainly, a bacterium is made up of tril-lions of components, comprised of tens of thousands of enzymes, molecules of fat and carbohydrate, molecules called nucleic acids (which include DNA, or deoxyribonucleic acid) and quintillions

non-of molecules non-of water and other simple substances A rock, by contrast is made up of repeated crystals of silicates and other minerals However, look more closely and things become more complex Take granite It contains quite a variety of minerals: four

1 Why did the mushroom go to the party? Because he was a fungi.

core silicates—quartz, alkali feldspar, an iron-containing mineral called amphibole and another called mica These silicates con-tain silicon and oxygen, with a number of other elements, such as sodium, aluminum and potassium Silicates are fairly large mol-ecules containing hundreds to tens of thousands of atoms arranged

in long chains, much like the molecules we associate with life And, like the molecules of life, these “reproduce” by making copies of themselves

What, then, separates bacteria from lumps of granite? This chapter explores the boundaries between what is alive and what

is not Hopefully, by the end of it, your idea that there is a sharp divide between the living and the non-living will have blurred somewhat You’ll then be on your way to discovering why life is

so adept at surviving in such a wide variety of environments. Beyond the Six Kingdoms

Biologists divide living things into six categories, known as doms: Animalia (animals); plantae (plants); fungi (yeasts and mushrooms); protists (complex but single-celled organisms) and the “bacteria.” Until relatively recently these bacteria were a homogenous group of single-celled organisms that were utterly distinct from the other four groups but were otherwise viewed as rather similar

king-In the 1970s Carl Woese challenged this assertion, basing his contention on the idea that the prevailing view of the bacterial world was flawed Woese observed rather different kinds of chem-istry in two distinct camps of single-celled “bacterial” life Further analysis of the DNA of multitudes of these “bacteria” clearly vin-dicated Woese’s view: the “bacteria”—those microscopic single-celled organisms—were in fact two distinct kingdoms In the end the distinction should have been relatively obvious Woese had realized that those bacteria that lived in the world’s harshest envi-ronments were so different from their more commonplace coun-terparts that they really could not be one and the same kingdom Thus the “bacteria” fall into two broad groups: the Archaea and the Prokaryotes

In general the prokaryotes include those bacteria that we are most familiar with—those that inhabit our bodies, our immediate environment and most of the world around us The Archaea, by contrast, occupy the world’s most challenging or peculiar envi-ronments, such as hot, acidic springs; alkaline lakes; the gastric chambers of cattle; or very saline environments, such as the Salton Sea It may, therefore, be all the more surprising that the group of

“bacteria” that is most closely related to us is the most peculiar Figure 1.1 illustrates this Indeed, some recent analysis suggests that we eukaryotes may just be complicated archaea

In terms of their underlying biology, all living things on Earth share common features They all have DNA as their genetic mate-rial This is their genome They all use proteins to form their inter-nal and external structures and carry out the bulk of the chemical processing that cells need to keep themselves intact and produc-tive Cells also use RNA for a limited but critical repertoire of core chemical reactions, such as the synthesis of proteins and to convey information from DNA to protein

Beyond this are the viruses, which you may or may not decide qualify as living things For now, we can regard them as a sev-enth domain in biology, one populated by a very diverse group of entities that parasitize cells and are otherwise unable to repro-duce without the help of the cells they infect Viruses may have a genome made of DNA or RNA, and some like to use both, depend-ing on which stage of their life cycle you are looking at Many viruses are really rather complex The T-even phages have rela-tively few genes, but structurally would not seem out of place as NASA spacecraft Others, such as the Pox viruses, have a fairly simple structure, but have genes that number close to or greater than those found in simple bacteria Thus, the lines are a little blurred between bacteria and viruses, even at this point

Does this help us answer the question of what constitutes life? Well, no The more you look the muddier the waters become

If, however, we restrict our thoughts to those organisms that are cellular—that is, made up of one or more cells, then liv-ing things can be thought of as cellular structures that contain the information needed to sustain their own survival This is a woolly explanation and is a serious attempt to avoid any conflict

F ig 1.1 This lovely reproduction of German biologist Ernst Haeckel’s

“Tree of Life” was produced in 1879 It graphically illustrates how living organisms originate from smaller branches that ultimately converge in a single trunk

Think of it, if you will, as a compromise between the contrasting behaviors of organisms such as plants and animals and the com-mon, underlying physical structures that comprise them.

Would this cover all life in the universe, or even all life that has ever existed on Earth? Well, probably not Think about it With the exception of viruses, cells comprise distinct zones, even those

we like to regard as primitive (the bacteria and archaea) The rior of the cell may be subdivided into compartments in all types of organism But this is perhaps most obvious in the eukaryotes, which have clear sub-cellular compartments, each taking care of a different cellular function However, the most obvious distinction between what is cell and what is not is provided by the outer cellular mem-brane, often called the plasma membrane We’d happily state that the region outside of this divide is definitely not alive However, inside, we would have no problem considering the region living.What then of the earliest life on Earth, which was almost cer-tainly not cellular? The membrane that separates the interior and exterior of the cell is comprised of a complex array of proteins and specialized fats, called phospholipids These would not have existed

inte-on the early Earth Therefore, it is thought that nature provided inorganic cages that compartmentalized early life to some extent Life was, therefore, not bound in quite the same way, and living things permeated materials rather than lived within them More

on this in Chap 5, but consider for now that not all living things may have cells, at least not in the way terrestrial life has at present.How else might terrestrial life’s cellular design affect it? In most complex organisms, cells take on specific fates or destinies, dependent on which genes are active within them For example in humankind there are three broad groups of blood cells: red blood cells, white blood cells and the platelets, which are fragments of a larger predecessor cell called a megakaryocyte There are around

200 kinds of specialized cell in the human body, outside the central nervous system, with another 200 possible types of neurons, lurk-ing within it In these complex organisms some cells are involved

in reproduction while the rest work to keep the organisms, as a whole, alive

Thus while few of the cells that fungi, animals and plants have could survive and pass on their genetic information on their own, they can function together to ensure the survival of the

organism as a whole This requires a tremendous amount of nization and cooperation that has taken 4 billion years to evolve Internally, each cell also has its own machinery that keeps it alive and allows it, where relevant, to communicate with other cells around it The real marvel of biology is the manner in which life

orga-is a balance of the cell’s biological prerogative to survive, and the need for it to support, actively, the organism as a whole

Within the cell, there are a number of features common to all life on Earth For example, all cells carry out the process of respira-tion, where glucose or another substances are oxidized (Chap 2) This process may or may not involve oxygen gas, but all of these processes, no matter what cell in which they occur, generates a useful chemical store of energy biologists call ATP, or adenosine triphosphate (Fig 1.2) The chemical energy in this molecule is then used to keep the cell viable, allow it to reproduce and com-municate with its surroundings

Multicellular organisms are composed of at least a few dred cells Each of these cells is “born” from predecessors through one or more processes of cell division The vast majority of cells are able to reproduce through a process called mitosis (Chap 2) Here, cells copy their genetic material and then divide The result-ing cells are identical to one another and the cell from they came This makes these cells clones of one another In multicellular organisms a few cells are allowed the privilege of dividing by

O

P

Phosphate

Mg 2+

F ig 1.2 The structure of ATP Energy is stored in the chemical bonds that

link the phosphate groups together These are shown by wiggles rather than straight lines The negatively charged phosphates are stabilized by a positively charged magnesium ion

another process called meiosis Here, the cells copy their genetic material as before, but then divide twice This leaves each of the four cells that are made with only half the original amount

of DNA This is important because these cells are the gametes—the cells that will come together from different parents through the process of sexual reproduction Through some nifty genetic footwork the DNA in these cells is also jumbled about so that each cell has a distinct combination of genes Through these processes—and the random fusion of different gametes during sex—new and amazing forms of the organism can come about

We call these differences variation

Although only the fungi, protists, animals and plants enjoy the process of sexual reproduction, the prokaryotes and the archaea have some nifty genetic moves of their own that allow them to pass on variation from one generation to another Some of these are downright devious, and we’ll look at them in more detail in Chap 2

For now, we might assume that terrestrial and, therefore, all

life, is cellular, i.e., made up of cells that pass on their tion from one generation to another This is simple, succinct—and quite possibly wrong

How Do Our Genes Work?

Genes have very specific structures If that wasn’t the case they wouldn’t work How they came to be organized this way is one of the key issues in understanding early evolution, for every organ-ism organizes its own DNA in a very similar way and operates its instructions in a similar manner (Fig 1.3) Chromosomes are the broad unit of the genome of an organism These are long mol-ecules of DNA that may be linear or, in most bacteria, circular Along these stretches of DNA are sequences we call genes In prokaryotes and archaea these lie fairly close together, with lit-tle DNA lying between them In most eukaryotes, however, the genes are scattered like so many islands and archipelagos in the vast Pacific Ocean (Fig 1.4) Large sections of DNA do not appear

to code for anything However, in these vast, apparently empty, stretches there are sequences that eukaryotes use to operate their genes There are also a lot of other DNA sequences that make mol-ecules of RNA that the cell uses to control how it works

Protein machines, called RNA polymerases, read genes There are several different types of these, all reading different kinds of genes However, they all do essentially the same thing: make an RNA copy of DNA This RNA copy is known as a transcript, and

it operates in much the same way as a copy of text from a book Although the transcript may be modified in some organisms, essen-tially it is a faithful copy of the instructions laid down in the DNA

Exon Exon Exon

Scaffolding Proteins

Region that is Copied (Transcribed)

DNA Loops

F ig 1.3 The structure of eukaryote genes DNA is coiled around proteins

called histones (not shown) These coils are then organized into loops, bound within a structure called a chromosome Genes form short regions within these larger loops, which are often arranged into organizational clusters

DNA sequences that code for proteins

Pol

RNA copy of the gene (mRNA Transcript) Ribosome

Transcription

Translation

Polypeptide (protein) “copy”

of the information in the RNA

F ig 1.4 Terrestrial cells store information in DNA Information is

trans-ferred to another molecule (messenger or mRNA) through the process of transcription These “transcripts” are edited to remove sections of RNA from between the exons, called introns (see Fig 1.3 ) and information is translated into a different language, built from amino acids This happens

in the ribosome

Once the transcript is made, another machine, called a some, interprets the information For although DNA and RNA use essentially the same language, proteins—the workhorses of the cell—are a completely different script RNA and DNA have a lan-guage made up of four simple repeating units called nucleotides However, proteins are assembled from amino acids, and there are twenty or so of these.

ribo-How the ribosome goes about translating the information

is something of a molecular marvel To put it simply, the some reads the information on the transcript in groups of three letters and inserts an appropriate amino acid into the growing pro-tein molecule We look at this in more detail in Chap 3 Thus, although the language is very different, the ribosome effectively makes a protein copy of the transcript

ribo-Now, it isn’t really that simple The genetic code for amino acids is such that, in many cases, there are multiple codes for each

of the twenty amino acids So, were you to try and work backwards from protein to RNA or DNA, you would get an imprecise version

of the original information Imagine having several synonyms for one word, if you don’t know the synonym you can reconstruct the original sentence You can get something like it, but not a precise version In many ways, the ribosome has the toughest job in the cell It has to interpret one code precisely and recreate another molecule with a completely different one based on that original sequence of information That makes it a very complex machine, indeed How it came about is a matter of fierce debate and will be discussed somewhat more in Chap 3

The Shifting Landscape of Our Genes

Many of us like to think of ourselves as a divine creation, fect and made in God’s image Now, God may well exist and have made us in some vast experiment, but irrespective of belief, we are far from perfect Humanity, and living organisms in general, are messy Their genome—the total genetic content of their cells—is hardly made in a functional manner, at least not at a superficial glance Human, plant and indeed all eukaryote DNA is a jumble of genes, defunct copies of genes, bits of duplicated DNA sequence,

per-and an array of bits of bacterial per-and viral DNA sequences Indeed, only around 2–3% of our DNA codes for the cell’s workhorse mol-ecule, protein Meanwhile 50% or thereabouts is made up of pieces

of DNA that can move around, called transposons Quite frankly,

it is a bit of a mess to look at

Yeast has a fairly compact 13.5-million-letter long genome, encoding 5800 genes Of the total length of DNA, approximately half of it codes for proteins Similarly, the fruit fly, Drosophila, has roughly half the number of genes that we have—approximately 14,000 These are snuggly fitted into a genome consisting of 165 mil-

lion letters Turning our attention to plants, Arabidopsis has a

genome that is approximately 125 million letters long It contains

a similar number of genes to us (around 25,000), even though our genome is 24 times larger Maize has approximately 32,000 genes, scattered over ten chromosomes, but its genome is marginally smaller than ours, with a total size of around 2500 million letters, compared to our 3200 million Therefore, there is no direct correla-tion between the number of genes in a eukaryote and the size of its genome Eukaryotes have rather randomly piled on genome weight Differences may be more a matter of chance events than evolution-ary “design.”2 Meanwhile, prokaryotes are really rather functional biological machines with fairly streamlined genomes

What makes humans distinct from say a mouse or a chicken

is the way its 24,000–25,500 genes work and how they ate with one another Human genes are organized in part so that clusters of genes are regulated in functional groups in a manner dictated by the cell’s environment or instructions that have been handed down to it Other genes may appear to be scattered; how-ever, they share common sequences of DNA that allow them to function in the same sort of way, or the same sorts of tissues In many cases, genes are clustered, so that the whole business of coordinating their actions is easier

cooper-For example, we have two proteins that combine to form the oxygen- carrying molecule we call hemoglobin In adults, hemo-globin is produced only in those bone marrow cells that will even-tually form red blood cells Although one of these genes (called the alpha) sits largely on its own, there is a whole group of related genes (beta, delta, gamma, epsilon and zeta) that are clustered

2 By “design” I do not mean intelligent design which is a scientifically abhorrent concept.

along chromosome 11 This beta family produces half the ecules in a hemoglobin protein This is a neat trick, for within this cluster of genes there is one that works when we are an embryo (epsilon), one (gamma) that work near to the time of birth and one that only functions as the principle beta family protein after birth (beta) They all share a common molecular switch on the neighboring DNA that determines which gene works at which time (Fig 1.5) By clustering these related genes together, the cell ensures that they can be switched on and off at the appropriate time Other genes that control development of the organism as a whole—genes that determine where legs, antennae (in insects) and other structures—are often clustered in a similar way.

mol-Within this mêlée of genes and alleged junk there are some interesting surprises, and this brings us to the “seventh” kingdom

of life, the viruses

Genes on the Move

Genes are far from immutable As we gather more and more information about the sequences of our genetic code we can see how organisms are related, how organisms have evolved from

F ig 1.5 The beta globin gene family This cluster (a) of closely related

genes lies on chromosome 11 in humans Each colored box (ε, γ, δ, and β) represents one gene, which fires up (is expressed) at different times in human development Each gene is switched on by looping it to a region of DNA called the locus control region (LCR)

one another, and also how their genomes have evolved in kind Perhaps one of biology’s greatest mysteries is how the DNA has become organized over time As well as the kinds of overt struc-tural organizations that are described above, there is an additional wealth of other structural features These are crucial to the func-tion of the genes that are embedded in the cell’s chromosomes, much like islands in the sea of DNA.

Of these there are two broad groups of structures, one of which might seem rather alien Although the bulk of our DNA is con-tent to stay put, there are large numbers of structures within the eukaryote and prokaryote chromosomes called transposons These sequences of DNA can make copies of themselves and move from location to location—hence the name transposon, derived from

the word transpose, or to move.

There are a variety of different transposable elements in cells Some move by a straightforward cut and paste mechanism, others make a copy of themselves before they move the copy to a new location Still others make an RNA copy of the DNA sequence, which is then reverse transcribed—a DNA copy of the RNA is produced—and it is this DNA copy of the RNA copy of the DNA that is inserted into a new location That all organisms and some viruses have transposons hidden within them testifies to the ancient nature of these mobile DNA pieces It is thought that they originated near the beginning of life itself Sure, more have evolved since, but the underlying principle dates back to the origin of RNA and DNA as genetic material in our cells and every other cell

It is here, in the world of mobile DNA, that we begin to blur the edges of what is alive and what is not What constitutes life? Some of these transposons are distinctly independent entities, or

at least display some of the facets of life—movement, sensitivity, nutrition, reproduction and evolution For, although most trans-posons are restricted to an existence within the cells in which they were “born,” others are able to move from cell to cell In pro-karyotes and archaea this can happen when transposons jump into invading viruses, adding their genetic material to that of the virus Other pieces of DNA, called plasmids, can also collect transposons and move them to new locations This is particularly relevant for

us because many of these transposons host antibiotic resistance genes that are mobilized from cell to cell The ability to move

genes from location to location underpins the spread of antibiotic resistance in many species of bacteria Such resistance is often car-ried on pieces of mobile DNA

Where we humans do extremely foolish things, such as use antibiotics to boost the growth of farm animals rather than restrict their use to killing our pathogens, we invite natural selection to

do its worst Most antibiotics come from microbes Bacteria and fungi use them to kill competitors, but this requires that they also have their own resistance genes Otherwise they would kill them-selves when they made their antibiotic Therefore, nature is set up

to help us and hinder us in equal measure Use an antibiotic too widely, or use it in isolation, and we encourage the survival and reproduction of those bacteria that allow them to hold the resis-tance gene, or encourage the spread of rare microbes that carry mutations that allow survive Worse still, most antibiotic resis-tance genes are carried on those mobile pieces of DNA, the trans-posons, and these transposons may be loaded within other mobile pieces of DNA called plasmids All of these pieces can move from cell to cell and species to species, taking the antibiotic resistance gene, or genes, with them Our generic use of antibiotics merely enhances the spread of these resistance genes Where they confer

an advantage to the cell, the cell that has them will survive and pass on its cargo of mobile and other DNA when antibiotics are present Those that don’t, perish That is all there is to natural selection

With antibiotics used to fatten up farm animals we are dering a vital resource and perhaps setting ourselves up for a grand catastrophe in the future At the time of writing, the power of the final—last resort—antibiotic had just been overcome by one vari-ety of bacteria in the feces of farm animals in China Given mass transport of humans, commodities and farm products it will only

squan-be 3 years squan-before many life-threatening infections squan-become able with our current range of antibiotics What a waste

untreat-More generally, when transposons move from location to location they can disrupt the function of genes by splitting them

in two Indeed, many years ago researchers used this property to

identify the function of genes in the plants Arabidopis and maize

It has been used extensively by others to identify genes in pretty much every organism you can imagine

One might, then naively, assume that these pieces of mobile DNA were bad—passing their cargo of genes from location to location, cell to cell, and on occasion, from organism to organ-ism However, natural selection is the mother of invention As well as allowing some cells to gain new features, such as antibi-otic resistance genes, transposons can also rearrange the regula-tory pieces of genes that control how they work This property has given mammals one of their core characteristics: the ability to feed their young.

All female mammals lactate, or produce milk This is a fairly odd feature in animals Think about it Females secrete a watery solution of proteins and fats and that is the only food their young can digest for several weeks or months No other class of organ-ism does this Other animals—reptiles, insects, amphibians and the others—all are able to digest food obtained from their environ-ment, such as leaves Mammals have specialized organs, which

we call breasts in humans and udders in most other mammals

In turn, these only produce milk after a successful pregnancy has advanced to a late stage and in its immediate aftermath As with nearly everything on the mammalian front, the monotremes, such

as the duck-billed platypus, have a halfway house They do not develop “breasts” or equivalent structures Instead, they secrete milk from their abdomens, effectively from sweat glands, indicat-ing how the process came about Monotremes aside, the nearest organisms you can find in the animal kingdom that also produce food from their bodies are scaly bugs These invertebrates produce

a nectar-like solution that they feed the ants that protect them from predators

The secretion of milk requires an instruction that signals the glands responsible to do so only at the correct time This is a hormone called prolactin In primates and many other mammals there is one copy of this gene, but it codes for two different func-tions One coded form of the gene controls the production of milk, and this form of prolactin is secreted from the pituitary gland The other coded form is active and produces prolactin in tissues, such

as the lining of the uterus Here, it appears to be essential for the success of pregnancy It turns out that the instructions that direct the second uterine function are contained within transposons that are inserted close to one end of the prolactin gene Different trans-

posons are inserted into this part of the gene in different mals However, by doing so, each transposon has inserted a new set of instructions that have helped revolutionize mammalian life

mam-on Earth For without the insertimam-on of these pieces of mobile DNA, humans and many other mammals would not be able to maintain successful pregnancies

If we describe transposons as pieces of DNA that can copy themselves but, by and large, stay within the cells in which they originate, we can conveniently separate them from the viruses Again, these can be descriptively reduced to pieces of genetic mate-rial that can copy themselves Now, in both instances “copy them-selves” is a little bit of a misnomer Strictly speaking it means that the machinery within the cell that they inhabit can be usurped to copy them They can’t copy themselves without outside help.Now, viruses are simply a step up the ladder They are mobile pieces of genetic material that, in this case, can jump between cells rather than simply within the chromosomes of the cell they begin in There are a huge variety of viruses out there in the world Some have DNA genomes, some have RNA Some kill the cells they infect, others simply corrupt the cell and steal its resources to finance their own replication Some viruses insert copies of their genetic material into the chromosomes of the host cell, while many more simply pretend they are part of the cell’s genome and get copied by proxy

Eukaryote viruses tend to manipulate the infected cell out directly killing it Death is often a secondary consequence of the indirect damage they cause, rather than as a direct result of a frontal assault Viruses that infect bacterial cells almost always kill their host cell when they replicate The difference in strategy

with-is a consequence of the structure of the cell Bacteria have an outer wall, and this must be disrupted to let the progeny viruses out When this happens, the cell takes in water, swells up and bursts Bacterial viruses also tend to chop up the cell’s genetic material

to release resources that it can use Meanwhile, eukaryote viruses convince the cell to manufacture what it needs and tend to block the cell carrying out its normal functions

Beyond this, the viruses are also of key importance in tionary terms For while many viruses cause much suffering to the organisms they infect, viruses are also agents of innovation This

evolu-is most obvious in bacteria—the prokaryotes In most cases, as we’ve stated, infection is followed within 30 min or so by death; however, it is not always this way To get an idea of how the differ-ent paths emerge it is worth taking a quick peek at how infection unfolds.

Imagine that you are a single-celled organism, perhaps an

E.coli bacterium on a human’s skin or a cyanobacterium in the

oceans You’re going about your daily life, metabolizing this and that when along comes a virus It attaches to your cell wall and then begins to drill a hole through it Once the passageway has been opened, the virus injects its cargo of genes, much like a nurse administering a vaccination In most instances, within a few min-utes, you’ve had your life put on hold while the virus gets your cellular machinery to construct a set of enzymes These special-ized proteins then fatally set about chopping up your chromosome into handy sized pieces, while your cell’s machinery makes hun-dreds of copies of the invading virus Less than 30 min after the virus punched a hole through your cell wall and membrane, you explode, scattering the newly born viruses into what was your sur-roundings This process is called lysis, and, let’s face it, it is a bit grim

However, not every cell faces this fate A very small minority

of viruses infect a cell that, for want of a better expression, is not very happy Maybe it does not have sufficient nutrients to repro-duce, or perhaps there is some sort of toxin present in the cell’s sur-roundings In such a situation it is not in the virus’s best interest to get the cell to manufacture more copies of the virus Reproduction may be weak or impossible, and this would likely allow the cell to stop the virus in its tracks with one of the defensive systems that exist in the cell Therefore, the virus switches to a new mode of operation Using a surprisingly simple set of biological switches, the virus can sense the cell’s distress Now, not wishing to add to the woes of the cell, the virus holds off committing its host cell

to its ruinous path, and it sits tight in the cell The virus thus becomes part of the cell This process is called lysogeny In this state, the virus only gets its genetic material copied when the cell duplicates its own DNA Typically, the viral DNA is inserted into the DNA of the cell (into its chromosome), so that the process of replication affects the virus as well as the cell

However, should things improve in the cell the virus can sense the change in cellular fortunes and change tack once more, killing the cell and spreading to infect new host cells There is a catch, though Any mutation that affects the ability of the virus to escape will allow the virus’s genes to become a permanent addi-tion to those of the cell Through this mechanism bacteria can gain genes from other cells Although this process is quite rare, it does happen.

Now, if you imagine that the chance of this happening are about as likely to win the lottery, then yes, you’d be right Indeed, lottery odds are better by a factor of about 100–1000 Only one

in every few hundred million to few billion cells gets to keep the virus that has infected it Poor odds, maybe, for the individual cell, but with over one billion bacteria per milliliter of sewage, in real-ity, that’s rather a lot of possibilities for the population as a whole

In the oceans, there are millions to hundreds of millions of teria per milliliter of seawater On your skin there are at least a few hundred thousand bacteria per square centimeter—even if you wash fairly often In your digestive tract there are trillions of bac-teria, all of them vying for your body’s waste Therefore, overall, there are many opportunities in nature for bacteria to acquire and transmit genes This is where evolution through natural selection

bac-is often mbac-isunderstood

People think of organisms in isolation Small numbers are easier to handle than large ones If there was more chance of a bad event—such as a gene disruption—happening than a good one, surely all organisms would suffer deleterious events and suc-cumb If this were true, evolution would be a dead duck However,

we aren’t talking about one man becoming the Hulk We’re ing about a billion organisms each experiencing its own singular event Some are bad and the organism suffers, while some are good and the organism benefits Most, incidentally, have no effect what-soever On a population scale, evolution is perfectly reasonable Evolution is not reasonable on the scale of an individual—except when we consider cancer To these singular topics, we will return

talk-in Chaps 4 and 9, when we look at natural selection and its sequences in more detail

con-Do viruses provide any benefit to humans or are viruses all bad for us? Well, for the most part viruses do not confer any real

benefit, certainly on the timescale of a generation However, over longer evolutionary time there are some subtle reimbursements For example, take the Epstein- Barr virus (EBV), the cause of glandu-lar fever In most instances, glandular fever is annoying but hardly life threatening There are a few weeks of feeling awful, but over-all, the infected person is unaffected in the longer term However, look beyond this, and this Herpes family virus appears to hold one significant benefit for its host After the disease has run its course, the virus lies dormant in a population of white blood cells It is said to be “latent.” This latent infection is life-long and in most instances does not produce a recurrent disease However, research

by Erik Barton and colleagues (Washington University Medical School) showed that the persistent infection causes a continual, low-level stimulation of the host’s immune system Perhaps, and somewhat bizarrely, this confers resistance of the host to bubonic

plague (Yersinia pestis) and a fairly common, and an often ant, form of food poisoning caused by Listeria monocytogenes bac-

unpleas-teria Quite why the protective effect only works for these two types of bacterial infection is unclear

Some viruses that afflict humans also transfer genes from son to person Some Herpes viruses contain human genes that are involved in the control of cell division This benefits the virus

per-as they can tell the cell to manufacture all the goodies the virus needs to reproduce when it infects the cell Other, fairly distant relatives of HIV contain a variety of similar genes that cause cells

to become cancerous upon infection Perhaps the most famous is the Rous Sarcoma virus, or RSV for short This was the first virus discovered, shortly after the turn of the twentieth century Indeed,

it was the virus’s capacity to cause cancer in chickens that led to its identification Fortunately, for us, most of these retroviruses infect birds and other mammals, but spare humans and most other primates

The transport of genes, from organism to organism via viruses, is called transduction Transduction is one of a variety

of methods that organisms use to move genes Collectively, these methods are known as lateral, or horizontal, gene flow These processes appear to be very prevalent in nature, although there

is some debate over how long term the effects of these processes are For example, while we can detect a lot of gene flow between

organisms, how much of this DNA is retained after such sions remains unclear Eukaryote cells such as ours show quite a lot of viral and bacterial DNA dotting our chromosomes Yet, the picture is not quite as clear as you might think Eukaryote cells contain two ancestral bacteria: mitochondria and chloroplasts These structures carry out respiration and photosynthesis, respec-tively Although each retains a small, residual chromosome, most

incur-of the genes required for their function now resides in the nucleus

of the eukaryote cell This is an ongoing process, and genes can be detected that are moving into the nucleus even now

The problem is, as this mitochondrial and chloroplast DNA

is effectively bacterial, distinguishing the fingerprint of additional incursions from other bacteria is rather tricky Much of the bacte-rial DNA you detect is likely to be from these organelles, rather from fresh invasions At the time of writing there is a growing buzz regarding the draft DNA sequence of the cutest and most resilient multicellular organisms on Earth, the tardigrades These little animals will be given a section all to their own, in Chap 7

However, the issue here is how much DNA do they have that is bacterial in origin?

When DNA is sequenced from an entire genome, the DNA is shredded into pieces and sequenced in chunks The original DNA sequence is then assembled using computer programs However,

if the DNA contains a lot of contaminating sequences then these can get mixed up with the DNA of the organism that you are interested in Now, the draft sequence of the tardigrade genome

is 18% bacterial DNA Research indicates that this DNA helps these tough little cookies survive in extremely harsh conditions However, perhaps more likely, these bacterial DNA sequences are just contaminating molecules from bacteria that were living on the tardigrade’s surface or digestive tract With better resolution of the DNA sequence, this problem should be resolved

Beyond the kingdom of animals, lateral gene flow also forms the bedrock of gene technology in plants Our use of the

Agrobacterium to infect and genetically modify plants is simply

us usurping the process that nature invented and bacteria use to get food from infected plants We might like to think we are the masters of gene technology, but Mother Nature has been doing it for far longer

Terrestrial organisms have evolved under the backdrop of gene flow Consequently, most organisms that we are aware of have evolved systems that partly defend them against the influx of new and potentially harmful genetic material In eukaryotes there are various detection and defensive systems that involve the mol-ecule RNA (ribonucleic acid) For example, when you are infected with influenza virus, the virus delivers a package of eight RNA chromosomes to the infected cell These contain the instructions for taking over the cell and manufacturing the key components of the new virus particles.

However, when the viruses are copying their RNA somes, they make stretches of double-stranded RNA—regions where the RNA molecule is paired with complementary mole-cules These molecules are recognized by machinery within the cell that activate a system that shuts down the production of new viral chromosomes (Fig 1.6) Moreover, a chemical called inter-feron is also produced that alerts nearby cells, including immune cells, to the infection

chromo-Neighboring cells can be made resistant to the incoming virus, while the immune system begins a systematic hunt through your infected tissues that ultimately leads to your recovery If that seems

a little perfect, well it is If it were all that happened then you would probably never fall ill with influenza However, influenza is

Processing of transcript to make crRNA (CRSPR RNA) CAS III

DNA virus

CAS III selectively attacks virus DNA or related RNA molecules using crRNA as a guide

F ig 1.6 RNA interference and CRISPR These two related processes are

used by eukaryotes (left) and prokaryotes (right) to target and switch off

(silence) the activity of genes

engaged, like many other viruses, in an evolutionary game of cat and mouse It carries machinery specifically designed to disable that resistance system In the end some (rather a lot) of cells do become infected, and you do get ill, long before the immune sys-tem comes to your rescue.

The CRISPy Side of Evolution

Well, technically, not CRISPy but CRISPR, or Cas9 Repetitive Interspersed Sequence Resistance This rather catchy acronym describes a system bacteria use to catch, degrade and utilize DNA acquired from invading bacteriophages (bacterial viruses) When viruses invade bacteria, as we’ve seen in most instances they set about the destruction of the bacterial chromosome and the assem-bly of new viruses Now, although this sounds like a one-sided battle, it isn’t quite that clearcut Bacteria can and do fight back Bacteria carry a set of enzymes that can chew up DNA, and they can do this in a very specific manner

Now, while some of these systems are quite general, there exists another very specific system, called CRISPR, which not only chews up DNA from the incoming virus it inserts it into a cassette of genes This has two effects on subsequent viral inva-sions Firstly, the bacterium can use RNA copies of the viral DNA chunks to direct enzymes to chop up the DNA of the incoming virus It can also use the RNA copies to stick to viral messenger RNA and prevent it from translating and directing the assembly of new viral proteins This stops the virus from producing those that

it needs for its replication and gives the bacterium enough time to then chew up the viral DNA with enzymes Figure 1.6 illustrates this and the related process, RNA Interference (RNAi, for short).Although this is great news for the humble bacterium, it has proved to be even more profitable for us While CRISPR took over a decade to reach widespread use following its discovery, it is now the darling of the genetic modification business CRISPR-based tech-niques, including the potential use to modify human embryonic DNA, have taken the biotechnology world by storm At the time

of writing (January 2016) there were over 489 families of patents in effect Now, this is not a count of individual patents but rather a

measure of the groups of patents based upon the application they are pursuing At the beginning of 2016 there were over 2400 pat-ents linked to this technology and the number of patent families was increasing at a rate of five-fold over the preceding 18 months

No other biological technique has exploded onto the scene with such rapidity and promised so much

What is CRISPR, and why is there so much fuss around it? CRISPR is related to the various systems that are employed by our cells to annihilate RNA viruses, regulate our transposable ele-ments and control the development of tissues and organs Together they form a family of RNA-based molecular switches that control the activities of all life on the planet The CRISPR system is used

by bacterial cells to annihilate incoming bacterial viruses, but the manner in which they do this (Fig 1.6) has made it applicable to the manipulation of DNA in general For this reason, most bio-tech and molecular biology labs will be using such technology to carry out manipulation of cellular activities or development From

a biological perspective, the similarity between CRISPR and the RNA-interference systems in eukaryotes suggests a common evo-lutionary origin for these regulatory mechanisms

Life has come a long way since it began, probably rather cariously, 4 billion or so years ago Although it was undoubtedly simple and rather functional in its earliest days, it has bifurcated and evolved new functions that fit with its spread to more chal-lenging and diverse environments However, does this bring us any closer to deciding what life really is? Is a molecule of DNA alive?

pre-Is a molecule of DNA that can direct its own duplication alive?

Or is a virus, with a more complex package of genes, alive? What makes a bacterium living but not a virus, or would you describe each as living? That brings us to a middle-school favorite: MRS GREN, who I might now rename MRS GREEN

How MRS GREN Became MRS GREEN

Around the age of 10–12 British students are taught that life can be thought of a set of skills that all living things share These skills are movement, reproduction, sensitivity, growth, respiration and nutri-tion, or MRS GREN for short On their own, each of these attributes can be identified in most, but not all, living organisms Humans

and animals in general show all of these features, while plants don’t, but show most Plants, for example, generally do not move All living things sense their environment in some regard We have five senses that we use on a daily basis: sight, sound, taste, hearing and touch Plants sense light, gravity, touch and water Bacteria and other microbes—and this is a generalization—can taste their sur-roundings and in many cases also respond to light and heat.

Asteroids are not, generally, thought of as living, but they also respond to gravity, heat and light, the latter two through the Yanofsky effect Thus, as asteroids have the same number of the attributes of living things as bacteria, does that make them as liv-ing? Certainly, you’d be hard-pressed to get an astronomer to say

an asteroid was alive What then defines living organisms? This

is the problem facing biologists and their astrobiological brethren Clearly, if you have a problem defining terrestrial biology, then how are you going to stand a chance defining extraterrestrial life? Could you ever hope to identify it, unless it was coincidentally like ours?Let’s try again to define life There are certainly some shared features among all living organisms, and one of these is not cov-ered by the original MRS GREN definition: evolution

From a biologist’s perspective, how would we define life? Well, for one thing, living organisms have an integrated set of biochemi-cal reactions that sustain them We refer to this as metabolism Although nature is festooned with chemical reactions, metabo-lism, as a tightly interwoven set of reactions orchestrated by pro-teins and RNA molecules, is a uniquely living quality

Now, although not all life in the universe may use our set of proteins and RNA, it will have a metabolism of sorts This can be distinguished from other chemical processes by the nature

tool-of the organization Living things build or obtain the basic set tool-of chemicals they need for their survival They are not simply lying around The formation of crystals from a molten brew of silicates doesn’t qualify, as it is a stochastic process based on the abundance

of different chemical elements in a mixture Granite does not nize its formation, nor do the organic compounds in the atmo-sphere of Titan This is essentially a random process However, the formation of fatty acids, or proteins, or indeed any other mol-ecule you care to describe in a living organism, is manufactured by design (and, again, I am not implying intelligent design)

orga-Metabolism is thus a unique feature of life

The ability to reproduce is generally thought of as a living process However, as crystals can grow by the addition of repeti-tive sequences of ions and other chemical elements, one would argue that non-living things can reproduce.

Is there anything else that is uniquely biological? Well, yes: evolution Only living things can evolve—although our computer systems may soon emulate this, and thus might, one day, be con-sidered alive An organism in isolation does not evolve Cats do not morph into dogs while you try and coax them from the garden fence However, the error-prone system of copying DNA and RNA means that it is an icy day in hell when an organism copies all of its genetic material without a mistake Evolution, through natural selection, is thus a natural outcome, which we will explore more closely in Chap 4 However, the principle is sound Although a crystal of quartz will remain quartz when melted and refrozen, DNA alters when it is copied Thus, the organism that contains this DNA is forced to change as well

What does this mean for life? Well, in isolation, this tion includes viruses and transposons However, given that these

defini-do not metabolize (at least not in isolation) they cannot (strictly speaking) be considered living things They are components of life, and they lurk in a gray area between living and non-living They influence life but are not alive themselves Think of viruses and transposons as part of the metabolic toolbox, but not the full works Therefore, they do not qualify as life, while cellular organ-isms (on Earth) do And, yes, there are some complex viruses and some simple bacteria, but without a capacity to metabolize such entities should not be considered living

Now, if you are a microbiologist, you will probably shout out the name of some of those “gray area” bacteria For example, the mycoplasmas cause disease in humans and are intracellular para-sites They have around 300 genes a piece, which is insufficient to allow them to live independently of our cells Indeed, they have roughly the same number of genes as Pox viruses Where would we put these? Well, we can gnash our teeth a bit and put them with the living organisms, as they can produce all the material needed

to replicate their genetic material They can also carry out ration However, they can’t do all of the other necessary tasks Given that they can replicate their genetic material and respire

respi-we can comfortably put them with living things No virus can respire No virus encodes all of the genes needed for their repro-duction; some encode none at all Although the sizable Pox virus has a few important genes needed for replication, it hasn’t got the full complement, nor does it respire Therefore, one would argue that mycoplasmas are living but Pox viruses are not.

Thus, to sum up, if we look at all of the criteria that might

be considered common, yet unique, to all life on Earth we are left

with two principles: error-prone reproduction leading to evolution and respiration By respiration, we include a varying proportion of other metabolic pathways that the organism needs for its survival

We can’t say that every living thing must make all of its ents, for if we do most animals are clearly insufficient, as most take in ingredients in their diet We humans do not make our own food—only plants do Nor do we make a lot of the basic ingredi-ents needed for our survival This includes the full complement of amino acids and our vitamins We cannot internally synthesize six

ingredi-of our amino acids Moreover, obviously, vitamins are only mins to us because they cannot be made in our bodies Vitamin A,

vita-C, D, E, F, K, and the multitude of B vitamins are all chemicals our bodies need to operate certain chemical reactions and, by defini-tion, must be consumed in our diets Clearly, we’d be hard-pressed

to consider humanity as non-living So, we can lump mas with humans, but keep viruses and transposons separate The former are alive and the latter not

mycoplas-Now, can we extend this idea to life elsewhere in the verse, and will this concept allow us to identify alien life should we encounter it? Hopefully, the answer to both of these questions is yes. The Deep Biosphere

uni-Deep, in the dark Cueva de Villa Luz cavern in Mexico, hang ing infestations known as “snottites.” These dripping stalactites are living sculptures made of a community of bacteria and archaea Living in an atmosphere that would be lethal to us, these cells derive energy from the conversion of gaseous hydrogen sulfide to sulfuric acid This turns the water into dilute battery acid with a

drool-pH of zero Toxic volcanic gases seep through cracks in the ground

and are absorbed by the oozing microbial mass Water percolates down through cracks from above, and the bacteria hang suspended from the walls in these dripping seepages In an environment of utter blackness, limited oxygen and toxic gas, life thrives.

The predominant cells inhabiting a similar cave in Italy go by

the glamorous name of Acidithiobacillus thiooxidans Although

not quite a name that slips off the tongue, this organism may be rather important, helping produce the acid that eats away lime-stone in many cave systems across the globe

Acidithiobacillus and many other species of bacteria and

archaea have made a living in many obscure environments How

is this possible, given life’s prerequisites?

For example, all life must respire Respiration provides the energy needed to keep the wolf from the door Most of the life that

we see uses oxygen to power the process of respiration However, the life we see around us is but a thin, shimmering veneer on a deep, dark ocean of life Most of the life on our planet lurks beneath the surface of the soil (Fig 1.7)

a

b c d

e

f g

In the immediate depths, the soil is richly permeated with copious numbers of different species of organism The roots of plants intimately interweave with the hyphae of countless mutu-alistic fungi These serve to increase the surface area of the roots, enabling the plants to draw water and minerals from the soil In turn, plants deliver the fruits of photosynthesis to the fungi.

This oxygen-rich domain soon gives way to a deeper layer of anaerobic life Thanks to the action of various respiring organisms living near the surface, oxygen concentrations rapidly fall within a few centimeters in the topsoil Below this zone, bacteria resort to using nitrates to respire, but otherwise keep up the general sem-blance of the life that lives above These bacteria return nitrogen

to the atmosphere from the dead and decomposing material left on

or near to the surface of the soil

Deeper down, where there is effectively no free oxygen, life has to come up with different ways of respiring Within the crust

of Earth, organisms are still abundant, but given the absence of organic material or oxygen, they have adopted rather interesting means of producing energy and synthesizing those useful chem-icals needed for life The most minimalist of them all use the following ingredients: carbon dioxide (as carbonate ions), water, ferrous ions, plus an admixture of other ions such as nitrates, sulfates and phosphates These deep biosphere organisms use heat from the planet’s interior to power their internal chemis-try Ferrous ions are oxidized to ferric ions (rust), while water is split to release hydrogen This, in turn, chemically reduces carbon dioxide to useful organic material All other ions involved in the functioning of organic molecules of life, such as nitrates, are simi-larly processed (Chap 2

There are a vast variety of species of bacteria and their distant cousins, the archaea, that constitute this hot, deep bio-sphere Most live at temperatures we would find intolerable and use an underlying biochemistry that we would find alien Yet, on top of this there are clear common themes: the use of a common genetic material, the use of RNA to deliver and process informa-tion, the use of proteins to form structural features and carry out the bulk of the cell’s internal chemistry, and the use of carbohy-drates and fats to form structural components such as the cell membrane