WHAT IS LIFE? AS A MODERNIST MANIFESTO

The obviously true may be devilishly difficult to define – as best exemplified by Louis Armstrong's famous retort to a naively passionate fan's request for a definition of jazz: ‘Man, if you gotta ask you'll never know.’ It is similarly undeniable that Erwin Schrödinger's What is Life? ranks among the most important books in 20th century biology, but the reasons for its great influence seem oddly elusive. Brevity may be the soul of wit (as garrulous old Polonius told us), and short works are rare blessings in a profession that too often judges worth by literal ponderousness. But What is Life?, in its ninety pages, seems a bit too spare and too elliptical to carry such intellectual weight (though, in a ruthlessly practical sense, such brevity may define the essential differences between attention and oblivion in a profession dominated by doers rather than readers). For example, I think we maybe confident of the correct, if necessarily conjectural answer to an old puzzle in ‘iffy’ history: how would the history of science have differed if Wallace had never lived and Darwin had thereby acquired the leisure to write the many-volumed work he intended, rather than the hurried ‘abstract’ known as the Origin of Species? The answer – since the intellectual world was clearly poised to accept evolution – must be: none whatsoever, except that Darwin would have had the same impact with many, many fewer people having read the book. Moreover, much of What is Life?'s intellectual foundation – Delbrück's early ideas on reasons for the gene's stability – turn out to be quite wrong (see Crow, 1992, p. 238).

Acknowledgements

The original version of this lecture was published in 1993 in the book Man and Technology in the Future, a summary of an international seminar arranged by the Royal Swedish Academy of Engineering Sciences, Stockholm, Sweden.

‘QUO VADIS HUMANITAS?’

We find ourselves in the last decade of this century; no previous century has had such a profound effect on human life. Perhaps no century has produced such a level of apprehension and fear, anchoring them in the consciousness of man. One has become mistrustful. When a discovery becomes known nowadays, the first question is not, ‘Of what use will it be to mankind?’ (as in earlier times) but, ‘What damage will it cause, and how will it diminish our well-being and health?’ Our present state of well-being is bestowed upon us mainly owing to scientific knowledge; this has brought life expectancy up to 75 years, approaching the biologically natural age limit. At the beginning of this century, life expectancy was a mere 50 years and at the beginning of the previous century it was only about 40 years. In developing countries, the curve of life expectancy is also rising, although it lags about 50 years behind ours; meanwhile, our life expectancy is approaching an upper limit. Yet, as never before, we peer apprehensively into the future. This is despite the fact that in the political sector, some of the gravest and most grotesque developments instigated by humanity in this century appear to be in the process of rectification. It is unlikely to be decided in this last decade whether these changes are really for the better.

All living organisms can transmit information between generations. The property of heredity – that like begets like – depends on this transmission of information, and in turn heredity ensures that populations will evolve by natural selection. If we ever encounter, elsewhere in the galaxy, living organisms derived from an origin separate from our own, we can be confident that they too will have heredity, and a language whereby hereditary information is transmitted. The need for such a language was central to Schrödinger's argument in What is Life?: he referred to it as a ‘codescript’. We can make some guesses about the nature of the language. It will be digital, because a message encoded in continuously varying symbols rapidly decays into noise as it is transmitted from individual to individual. It must also be capable of encoding an indefinitely large number of messages. These messages must be copied, or replicated, with a high degree of accuracy. Finally, the messages must have some ‘meaning’, in the sense of influencing their own chances of survival and replication: otherwise, natural selection will not operate.

In existing organisms, there are two such languages, not one. There is the familiar genetic language based on the replication of nucleic acids, DNA and RNA, and there is the even more familiar language, confined to humans, which we are using now. The former is the basis of biological evolution, and the latter of cultural change. In this essay we discuss the origins of both.

In fact, we will not discuss the origin of nucleic acid replication, although this was a crucial step – perhaps the crucial step – in the origin of life.

These quotations from Schrödinger were very perceptive, and raised two key questions. The first is whether the development of the egg is computable, and I will suggest that the answer is no, but that it will be possible to simulate some aspects of development. As regards the second question, how genes control development, Schrödinger could not have known that genes exert their influence through controlling which proteins are made, and in this way they control cell behaviour and development.

In posing these questions, Schrödinger was giving recognition to the fundamental importance of development. Development is at the core of multicellular biology. It is the link between genetics and morphology. Indeed much of the genetic information in our cells is required to direct development. Evolution can be thought of in terms of altering the programme of development so that structures are modified and new ones form.

How did we humans come to be so different from other animals? That question could not have even been posed until Darwin showed that our differences from animals had evolved. We were not created different from animals. Instead, we had come over time to be different from them.

Until recently, the question how that had happened belonged to the exclusive province of palaeontology and comparative anatomy. Now, insights are flooding in from many other fields, such as molecular biology, linguistics, cognitive psychology, and even art history. As a result, the problem of the evolution of human inventiveness looks as if it may at last be becoming soluble. It is surely among the most challenging questions in biology today.

Despite Darwin, all of us still lump clams, cockroaches, and cuckoos together under an umbrella concept that we term ‘animals’, and that we contrast with us humans – as if clams, cockroaches, and cuckoos somehow had more in common with each other than they do with us. We thrust even chimpanzees down into that abyss of bestiality, while we stand uniquely on high.

All our unique features are ultimately expressions of our unique inventiveness. Just think of some of the unique forms that our inventiveness takes:

• Unlike any animal, we communicate with each other by means of spoken language and written books.

• We thereby know about things that happened in remote places and at remote past times, such as Schrödinger's 1943 lectures. What animal species possesses any knowledge of what some other individual of its own species on another continent was thinking fifty years ago?

• We depend completely on tools and machines for our living.

Many things in Nature which we thought to be eternal, like the fixed stars, atoms, or quantities such as mass, turned out to be only temporary forms. Now the only thing which is believed to be of eternal stature is the law of Nature. In a contribution to a symposium at the Pontifical Academy of Science on ‘Understanding Reality: The Rôle of Culture and Science’ I tried to explain why I do not think that this is necessarily so and that also the laws may evolve in the course of the history of the universe. Herewith I would like to submit this heresy to a wider scientific public, not as an eternal truth but as a possibility worthy of reflection and discussion.

Today physics knows the laws which describe the material world from the tiny to the vast. That there are no phenomena known which contradict these laws is small wonder since whenever this happened, physics had to adjust them to accommodate also the hitherto unexplained events. The surprising fact is that in this process of gradual extension the laws became both more general and more unified. For instance, quantum mechanics of atomic systems supersedes classical mechanics and incorporates it as a limiting case. Similarly, elementary particle physics contains atomic physics as a low energy limit. This leads people to think that at the top of this pyramid there is an Urgleichung (as it was termed by Heisenberg; now it is called a TOE = Theory of Everything) which contains everything.

Utilisation of nitrogen compounds

Fungi can utilise nitrate, nitrite, ammonia (see footnote, p. 82) and a very wide range of organic nitrogen compounds. Some idea of the diversity of the latter can be gained by reference to an older text such as that by Cochrane (1963), in which the capability of fungi to use a wide diversity of compounds is less taken for granted than is often the case now. The same volume and those of Hawker (1950) and of Lilly & Barnett (1951) give useful information about fungi which are able to utilise:

1. Nitrate nitrogen.

2. Ammonia or organic nitrogen but not nitrate nitrogen.

3. Only organic nitrogen.

At the time the above authors were writing, there was debate about whether or not fungi are able to use atmospheric nitrogen. That debate was prior to the use of 15N for detecting nitrogen fixation. Since the isotope became available, it has been established now that no known fungus is able to fix atmospheric nitrogen (Stewart, 1966). Of course, fungi lichenised with cyanobacteria form organisms that are able to use this source of nitrogen.

The ability to use nitrate nitrogen represents a greater capability on the part of a fungus, for all nitrate users can use ammonia but not all ammonia users can use nitrate. A list of some fungi known to be able to use nitrate is given in Table 6.1. It gives an indication only; to obtain anything like completeness would be impossible.

Introduction

The relationship between fungi and sulphur is intriguing. Though inorganic sulphur at the most oxidised state – sulphate – is the customary source of the element when fungi are grown in culture, it is well known that sulphur-containing amino acids can be used with almost equal facility. In Neurospora crassa, for instance, when inorganic sulphur is lacking, the methionine transport is derepressed (see Chapter 6). Fungi are capable of oxidising inorganic sulphur compounds that may be important in ways other than the provision of sulphate for assimilation. Also fungi can produce volatile sulphur compounds that may be important in the natural environment. Equally, the ability of species to tolerate sulphur dioxide may be important in environments subject to air pollution. Of course the same gas is used also to preserve beverages and food, so that there is an industrial dimension to fungal tolerance of sulphur dioxide. All of the above are considered in more detail in the sections that follow.

The emphasis of this chapter is on inorganic sulphur as the source of the element for a fungus. The evidence from culture studies is compatible with an almost universal ability to utilise inorganic sulphur. As far as I am aware, inorganic sulphur compounds cannot be released from organic sulphur compounds in the external medium of a fungus. Nevertheless fungi contain sulphatases that release sulphate from organic form. An interesting example of this is the utilisation of glucose 6-sulphate by N. crassa (Reinert & Marzluf, 1974).

MONOSACCHARIDE UTILISATION

General features of glucose utilisation in fungi other than yeasts

Almost invariably glucose is one of the sugars most readily utilised by nearly all fungi. This view is supported by the information in Table 5.1, albeit for a minute selection of fungi, although of widespread taxonomic distribution. However, the dominance of growth media based on glucose or glucan as the carbon source adds confidence to the view that glucose is a very important source of carbon and energy for growth. In all probability, almost every fungus metabolises glucose to pyruvate in a manner that is the same or extremely similar to that in Saccharomyces cerevisiae, i.e. by glycolysis or the pentose phosphate pathway/hexose monophosphate shunt. The evidence that fungi utilise glucose in such a manner has been well reviewed by Cochrane (1963), Gottlieb (1963), Blumenthal (1965, 1975) and McCullough et al. (1986). The evidence comes from a variety of approaches but it has to be stressed that it is only for a relatively few fungi that compelling evidence has been accumulated using a majority of the approaches. The effectiveness of any one approach is well discussed with respect to fungi by Blumenthal (1965), but the reader should also consult ap Rees (1974, 1980a, b) for a critique of the same methodology as applied to flowering-plant tissues, in particular with respect to assessing the extent to which the metabolic flux of glucose to pyruvate is via glycolysis or the pentose phosphate pathway.

Introduction

Organic acids are important in fungal nutrition because:

1. They can be a source of combined carbon for growth.

2. They can contribute to the internal osmotic potential.

3. They can contribute to the internal charge balance.

4. They may be involved in the control of internal pH.

5. They can be involved in the loss of protons across the plasma membrane.

6. It has been proposed that the fixation of carbon dioxide into organic acids may be part of the battery of processes allowing a particular species to grow oligotrophically.

7. The production of oxalic acid appears to be important in assisting the decay of wood by fungi (see Chapter 5).

8. Oxalic acid may also be important in reducing the inhibitory effect of too much calcium in the external environment (see Chapter 11).

As well, production of various organic acids, particularly by Aspergillus and Candida spp., is commercially important (Miall, 1978; Mattey, 1992).

Transport

Table 12.1 gives details of those carboxylic acid transport systems that are known to be present in fungi. Except for succinate transport in Neurospora crassa, all the information is for yeasts. The interest in the ability of yeasts to transport carboxylic acids across the plasma membrane is two-fold. First, the ability to use, for growth, carboxylic acids of the citric acid cycle is used as a taxonomic discriminator.

Introduction

The cell wall, plasma membrane and tonoplast are major barriers to the movement of solutes into and out of fungi. The wall is very much less of a barrier than the two membranes. Nevertheless it cannot be considered solely as a porous structure that allows through it only molecules below a certain size. The wall has other properties that influence the nutritional behaviour of fungi. These properties as well as the porosity of the wall are addressed below. The consideration of membrane focuses on the somewhat scattered information about the lipid part of the membrane; the various transport systems are dealt with in other chapters.

The wall

Introduction

Our knowledge of the polysaccharide composition of the walls in both filamentous fungi and yeasts covers a wide spectrum of taxonomic groupings and for many species there is much detailed information (for reviews, see Farcaš, 1979, 1990; Gooday & Trinci, 1980; Arnold, 1981a; Wessels & Sietsma, 1981; Bartnicki-Garcia & Lipmann, 1982; Bartnicki-Garcia, 1987; Fleet, 1991). On the other hand, we know much less about the other components of the wall. Enzymes are present (see Chapter 2) and polyphosphates can be present (see Chapter 7). Here I concentrate on what we know about the physicochemical properties of the wall of Saccharomyces cerevisiae and other yeasts, drawing attention afterwards to some salient features of the walls of other fungi.

Introduction

Water is required by fungi for growth and for movement of solutes within the mycelium (translocation). Many aspects of reproduction are governed by water availability; for example, spore release and dispersal are dependent on it, as discussed in the classic text by Ingold (1971). In the past 20 years, there has been little to modify what is described there. However, now there is a better idea of spore release in some of the lower fungi (see, for example, Duniway, 1979; Gisi, Hemmes & Zentmyer, 1979; Gisi & Zentmyer, 1980; Money & Webster, 1988, 1989; Money, Webster & Ennos, 1988; Horn, 1989, 1990). Nevertheless, the water relations of basidiospore discharge are still a matter of controversy (Webster et al., 1988; Ingold, 1990; Corner, 1991). In this volume, I consider only the water relations of growth (this chapter) and translocation (Chapter 14). For terminology and background to this chapter the reader is referred to reviews by D. M. Griffin (1981), Eamus & Jennings (1986a), Papendick & Mulla (1986) and Jennings (1990c).

Growth

The general picture

When a fungal cell grows or a hypha extends, it increases its volume. Part of that increase in volume is brought about by the inflow of water. The rate of flow must be such that the pressure generated does not cause the wall to burst (Robertson, 1959, 1965).

Introduction

A living cell must do work to maintain the composition of its internal medium different from that of the external. If that cell is growing, work has also to be done to generate the small but necessary osmotic gradient for the inwardly directed influx of water to take place. In a cell with a wall, such as a fungus, the osmotic gradient is much more significant, in order to maintain the necessary internal hydrostatic pressure for turgor (see Chapter 13). Two important loci for the above work are the plasma and the vacuolar membranes. When work is carried out in moving solutes across these two or indeed any other membranes, we can speak of active transport, i.e. the movement of solutes against their electrochemical potential gradient. Of course, there may also be diffusion of solutes across the membrane, albeit almost always, if the solute is polar, aided by the presence of carrier proteins that overcome the activation energy required by such a solute to enter through the lipid portion of the membrane. When diffusion occurs, it must be down the electrochemical potential gradient. However, it needs to be remembered that if the affinity of such a carrier for the solute on one side of the membrane were to be much higher than on the other or the mobility of solute transfer were to be faster in one direction than in the other – both of which changes would depend on the cell doing work – then active transport would occur (Jennings, 1974).

General

The term ‘growth factor’ has been defined in two ways:

1. A compound that is required for growth in small amounts but excludes those compounds that function as structural material and are not used for energy (Cochrane, 1963).

2. A compound that in minute amounts is necessary for, or stimulatory to, growth and does not serve merely as an energy source (Fries, 1965).

The second definition clearly encompasses a broader range of compounds than the first. Fries (1965) in amplifying his definition pointed out that it includes certain organic compounds, e.g. amino acids, nucleotides, fatty acids. These compounds would not be covered by the first definition because they or carbon skeletons based on them are incorporated into structural material. Equally, the compounds are usually required at higher concentration (10–1000 pg cm−3) in contrast to 0.01–1 pg cm−3, the concentration at which vitamins (the bulk of those compounds embraced by the first definition) are required by fungi. By vitamins I mean those compounds as understood by other biologists to come under this title, i.e. the compounds have a catalytic function in the organism as a coenzyme or constituent part of a coenzyme.

Nevertheless, it is difficult to make a clear separation between the two categories. Cochrane (1963) pointed out the arbitrary nature of the definition that he used. Thus, riboflavin is included under it but one cannot separate adenine's cofactor-like role in ATP from its part in nucleic acids.

Introduction

Magnesium, calcium, iron, copper, manganese, zinc and often molybdenum are required by fungi for growth. The order approximates to the concentration required in a normal growth medium. Magnesium is required at c. 10 M, while molybdenum need only be at true trace concentrations, namely c. 10 M. The latter element is required by those fungi utilising nitrate (see Chapter 6). Cobolt will be needed by those fungi that synthesise their own vitamin B12 (Fries, 1965), whereas nickel is required by those fungi exhibiting urease activity (Hausinger, 1987). The list might be longer but rigorous evidence for inclusion of other elements is not easy to obtain. Trace contaminants of reagents by a suspected element make it difficult to demonstrate that it is required for growth. Molecular biology and enzyme studies are likely to prove more revealing.

Copper and zinc can be toxic at concentrations higher than those required for growth. Since other multivalent metals can also be toxic, this chapter deals with the avoidance of toxicity. I have refrained, except in certain instances, from listing the role(s) of these various elements in fungi. To give a proper indication of the function of an element requires the provision of biochemical information beyond the scope of this volume.

Transport of multivalent metals (other than iron) across the plasma membrane

Specific systems

At its simplest, uptake of a multivalent metal by a fungus is biphasic; there is an initial rapid phase, which is believed to reflect binding to the wall, followed by a second, slower phase (Figure 11.1)

As far as I am aware, there has only been one other book about fungal nutrition. This contrasts very markedly with the large number of books devoted to the nutrition of higher plants. Here, we have a coherent field of study, well established through the need to understand how plant yield might be increased through the provision of inorganic nutrients. The economic benefits of an effective fertiliser regime for an agricultural or horticultural crop have been an important driving force for establishing plant nutrition as an identifiable discipline in plant physiology. But this identity for plant nutrition is aided in general germs by the fact that the higher plant has a specific organ, the root, for absorbing nutrients and the effectiveness of that organ can be determined by observable responses in other parts of the plant, such as change in shape and colour.

Fungal nutrition is clearly about what kinds and amounts of nutrients will support growth or bring about differentiation, whether it be secondary metabolism on reproductive structures. However, to focus on fungal nutrition thus described would be to produce recipes and little else. This book is about the nutrition of fungi as a web of processes, attempting to provide a mechanistic basis for the subject.

Introduction

It is a truism to say that for a heterotrophic organism the rate of nutrient uptake governs the rate of growth. For a fungus, there is a need to supply not only the nutrients from which the polymeric materials of the organism are built but also the inorganic ions that act as cofactors and the nutrients that either directly or indirectly help to generate the internal solute potential. Thus, the rate of functioning of those processes at the plasma membrane will be an important determinant of the rate of growth. At its simplest, the processes at the plasma membrane or indeed any other membrane can be described in terms of two characteristics, namely: (a) the affinity constant, KT, of the transport system (equivalent to the Michaelis constant, Km, but not in a strictly formal manner); and (b) the flux, the number of moles of solute transported per unit surface area of membrane per unit time (mol cm−2 s−1). Assessment of the affinity constant makes assumptions, albeit very rudimentary, about the mechanism of transport, i.e. that there is a transporting molecule to which the solute first binds before crossing the membrane. This is true for many solutes but is not necessarily obligatory. The determination of the flux of a solute, however, makes no presuppositions about the mechanism of transport. The net flux is the difference between influx and efflux, and the flux determined for one of these directions is the sum of those processes acting in that direction.