Understanding Levels: Redefining Science in an Emergentist World View

An emergentist world view sets certain challenges to our notion of science and of the kinds of explanations of our world that it seeks. A first is to identify different emergent levels of reality, the living from the non living, the conscious from the non conscious, and within consciousness itself the distinctive emergence of the creative powers of the mind and the freedom of decision making. A scientific explanation of levels will entail an analysis of what is distinctive about the properties and activities on the different levels, the worlds that they operate in and the upward and downward causal relations involved with other levels. All of these feed into a transdisciplinary approach to personhood.


In his DNA, The Secret of Life James Watson formulated his reductionist creed for molecular biology: ‘Life is just a matter of physics and chemistry, albeit exquisitely organized chemistry.’1 Francis Crick went on to ask the further question: What does DNA do in the cell?2 By 1966 it became known that it is involved in the synthesis of the 20 amino acids which in turn manufacture proteins. The genetic code according to Watson brings DNA to life! Red blood cells are produced in the bone marrow by stem cells at the rate of around two and a half million per second. Following Crick and Watson this was interpreted in terms of the active agent DNA synthesizing the haemoglobin in the cells in a most complex and precisely timed switching process. But this basic reductionist strategy of attributing agency to genes, which after all are only chemical molecules, is now being critiqued by some as ontologically and ontogenetically misguided. Alternatively it can be proposed that in the regular manner and precise timing in which we find DNA exquisitely organized in protein synthesis by the cell or more generally the organism we can identify properly biological laws at work. Perhaps Watson in his above remarks is, without recognising it, undermining his very reductionism.

What is distinctive about emergent biological laws is that they are developmental, they are involved in the development of organic life from a single cell to the myriad of body designs and related life cycles that we find in the genera and species of our world. So as well as housekeeping genes involved in protein synthesis there are also to be found in the animal (but not the plant level) the Hox genes that have a fundamental role to play in the development of the emerging body design of the organism, be it a fish, frog, bird or human. These are distributed in a spatial sequence along the chromosome and their switching on and off is precisely synchronised with the development of the body shape along the parallel spatiality of the head to tail body axis. Mutate Hox genes and in many instances you mutate body design. This can lead to the reductionist conclusion that the adult human organism is simply the product of the cumulative switching on and off of the appropriate Hox genes (or more generally the genome) at the appropriate time in the process of development.

But is there not much more to development and evolution than can be learnt by focusing on genes and genomes? Is it not the case that no part of any living unity and no single process of any complex activity can be fully understood in isolation from the structure and activities of the organism as a whole? This leads Jason Roberts in his Embryology, Epigenesis and Evolution, Taking Development Seriously to question why organisms are still ‘so often portrayed as basically or ultimately the product of genes.’3 For him taking development seriously involves critiquing the common notions that genes instruct or program the future organism. Acknowledging that there is general agreement about what must be taken into account in a theory of organism development Roberts concludes his book with the questions: Why, then, have the limitations of genes-plus accounts of interaction not been more widely recognised and appreciated? Why do modern consensus metaphors of genetic programs and primacy persist? Again there is being posed the further question: in the exquisite organisation of the DNA in organic development do we not come to understand the properly biological laws of the organism? In organic development does the organism manipulate the Hox genes or the genes manipulate the organism?

To turn to the field of consciousness studies we find Francis Crick setting a tone with his creed that our joys and sorrows, ambitions, sense of personal identity and free will are ‘nothing more than the behaviour of a vast assembly of nerve cells and their associated molecules.’4 In a debate about dreams at The Science of Consciousness Conference in Tucson in 2006 a neuroscientist was adamant that dreams were just neural noise, a Freudian, that they had all the meaning and significance in a person’s life of Freud’s interpretative analysis. Are the dreams caused by accidental neural processes or does the organism manipulate the neural basis for the dream out of the life context? As biological organisms can manipulate their chemistry why should the stresses and strains of the psychological processes of an organism not be able through their proper autonomy and laws to manipulate the neural structures and processes in the production of dreams? As Lonergan puts it, in the drama of our lives with others can there not occur a ‘subordination of neural processes to psychic determinations.’5 What precisely might be meant here by that subordination of the neural to the psychological?

It is a question that arises in the context of the study of the interaction of emergent levels of activity in the development of a human being. In his electrical stimulation of the cortex while conducting surgery Wilder Penfield observed that the sensory motor action that is so produced was so primitive and lacking in dexterity that it may be likened to the sound of a piano when the keyboard is struck with the palm of the hand.6 The memories so evoked were disjointed, hallucinatory, and difficult to analyse. This posed for him the question: how and from where in the brain did the concert pianist transform that crude action into the subtle, dextrous movements of a Mozart piano concerto? Or a ballerina transform the crude cortical reflex into the graceful points and pirouettes of the Nutcracker Suite? It is significant that he poses the question in terms of the pianist being the agent of transformation. Reductionists would rephrase the question as: how does the brain produce the concert pianist and ballerina?

Similarly in the context of learning a new language as spoken with an extensive vocabulary to be learned and used in everyday and technical situations the question arises: does the brain produce the language user or the language learner transform (subordinate) brain processes in the course of becoming a competent linguist? Clearly we can agree with Jackendoff that the brain will be involved at the speaking/phonetic level in learning a language, and at the sensory motor level in becoming a dancer or pianist.7 But there is also involved the explicitly conscious levels of the use of the senses, imagination and intelligence. One’s senses are unavoidably involved in assimilating the correct pronunciation of a word or the spatial elements in a dance movement. One’s intelligence is involved in understanding the correct meaning of the words spoken and the manner in which they are to be used in conveying meanings in different circumstance. Both of these dimensions are involved in programming the neural level in learning a language or how to play a piano.

The developmental dimension of language learning has recently been taken up by Maryanne Wolf in her Proust and the Squid: The Story of Science and the Reading Brain.  John Carey opens his review with the remark that reading generates thought and gives a sense of inner selfhood. Wolf, who has a core interest in the problem of dyslexia, holds that being talked to, read to and listened to as a child matters hugely. In a home where conversation is valued, a child by the age of five will have heard up to 32m more words spoken than in a more silent household. The later reading skills of a child are known to be related to the frequency with which stories are read to it in the early years.

In this context one needs to consider the formative and personal transformation involved in reading the classics in literature and the sciences. Einstein’s reading of works on Maxwell and Newton transformed his whole scientific outlook. A whole generation of molecular biologists in the making were influenced by Schr�dinger’s What is Life? The great depths of such transformative reading needs to be probed. Further remarks by Carey bring some of our issues into focus:

before a brain can read it must physically rearrange itself. It must create new neuronal circuits to connect the part it uses for seeing with the part it uses for listening to someone talk. Not until it has done this will the brain’s owner realise that the marks on paper present sounds. … Brain scans show that when someone reads an alphabetical language, such as English, specialized parts of the brain’s left hemisphere are activated. But when a Chinese speaker reads Chinese, quite different parts of the brain are used. They are in both hemispheres, and include frontal areas not used for reading by English speakers. Since this proves that the Chinese reader’s brain is connected up differently, it prompts the question whether Chinese thought is different from western thought. Linguists used to argue that there is always a relationship between the language a person speaks and how that person understands the world. This idea fell out of favour under the influence of Chomskyan linguistics and theories of universal grammar. But the advent of the brain scan seems to be reopening the question. What Wolf’s own views are it is impossible to say.8

In this excerpt we can see the problems of the relation between the neural and phonetic/symbolic levels in reading and speaking and the further level of intelligence in which there enters the issue of the relation, central to what language is, between thought, word and reality, the world of the language user. To overlook the thought-reality-world relation and concentrate on the neural and the qualia/phonetic levels of language learning and use is to rob language of its core. It is because of the instrumental nature of the sign that our thoughts can be expressed in enormously different symbol systems.

In this context Crick, like Watson, also adds, for him, a quite problematic remark: ‘Our wonder and appreciation (of the explanatory quest) will come from our insights into the marvellous complexities of our brains, complexities we can only glimpse today.’9 In this he admits that the eventual solution to the currently unsolved problems will come through a combination of our wonder and insights. In a similar vein Pinker has remarked that it will take an unborn genius – a Darwin or Einstein of consciousness – to come up with a flabbergasting new idea that suddenly makes it all clear to us.10 What is also interesting is that in very many case studies of great scientific insights there is identified an element of the presentation by the imagination of the elements of the unsolved problem to our mental striving. As Watson cannot answer and avoids the question as to how the chemistry of life is so exquisitely organized, so Crick and Pinker are left with a conscious mental residue, the wonder and leap of insight of the discovery process which will resolve and clarify all that is confused and incomprehensible in consciousness studies at the moment.

But once that admission has been made about the source of the breakthrough it brings with it some unpalatable consequences for reductionists. It involves the recognition that there is a distinct form of first person consciousness, the scientific form of consciousness that studies the neural correlates of the visual consciousness of others. Called simply human intelligence it can be argued that that form of consciousness does not reduce to anything else but explains everything else. It is fundamentally accessed, not through fMRI scans or the like but through narratives of scientific discovery. Until such narratives of discovery have been composed the insight experiences involved in the discovery process remain in the dark, unknown. Once such narratives of discovery have been recognized for what they are, objectifications of the first person consciousness of the research scientists exploring a particular domain, a reductionist world view is undermined.


David Chalmers has forcibly argued that the qualia of the experiential, the awareness of purple or the sound of the spoken words, are irreducibly different from the correlative neural processes in the brain.11 In his review of reactions to Chalmers’ In Search of a Fundamental Theory Robert Almeder singles out Sydney Shoemaker, one of philosophy’s most insightful of materialists.  Shoemaker ‘believes that if Chalmers’ arguments succeed, his achievement will be enormous, for he will then have succeeded in overthrowing materialist orthodoxy that has reigned in philosophy of mind and cognition for the last half century.’ Although skeptical about the arguments he acknowledges that they express clearly and forcefully widely held beliefs.12

I would now like to suggest that Chalmers has not gone far enough with his assertion of the irreducibility of the dual properties of the neural and qualia. Effectively it overlooks further components in consciousness, notably the performance of problem solving and resolution by means of insights, aha or moments when something clicks and one can go on with things, around which exactly the same arguments can be made. Such insight experiences are now slowly being recognized as foundational for creative mathematics and science. In can also be argued that there is an even greater irreducible qualitative difference between the wonder and moments of breakthrough that come in insight problem solving, and experiential visual experiences and their imaginative counterparts in and through which the elements of the problem to be solved are presented.

James Watson’ book, The Double Helix is not directly about the molecular biology of the cell but, as the subtitle of the book makes clear, it is ‘A Personal Account of the Discovery of the Structure of DNA.’ Among others, two things are happening in Watson’s narrative of discovery. Firstly, there is an account of the actual problem content. There the emphasis is on the chemical properties of DNA. It would eventually find its objectification in the short paper sent to Nature in April 1953. Secondly, there is an emphasis on how those properties were discovered. There the emphasis is on the first person consciousness of the scientific researcher which finds its objectification in his 1968 book. It is addressing, not the question about the hereditary ode in the cell but about how he, with Crick and others as human beings, discovered it. Clearly there is the dramatic interaction of the small group of scientists involved in the process which, rightly, has fascinated many. Our present focus brackets that drama to address the question: What does the narrative of discovery teach us about the mental powers or processes which make the breakthrough? Where and from what sources and emergent levels in us do scientific discoveries come?

In his early years Watson was influenced by his reading of Schr�dinger’s What is Life in which it is speculated that the key to hereditary processes are locked up in an aperiodic molecule. In 1944 Avery identified DNA as the possible molecule involved. Watson became excited when Maurice Wilkins introduced him to an X-ray diffraction picture of DNA and the discovery that genes could form crystals. This was followed by an introduction to the alpha-helix by Linus Pauling from Jean Weigle. His first approaches to Max Perutz about joining him in Cambridge were unsuccessful but Watson persisted. There followed, in the fateful collaboration with Francis Crick, an at times painful period of learning from his mistakes. Early in 1953 after, yet again, his scheme had been torn to shreds, this time by the American crystallographer Jerry Donohue, he found himself forced to take on board the corrections. He was so fearful at this time that they would lead him, yet again, to another cul-de-sac, that he put the required steps on hold until the following day.

When I got to our still empty office the following morning, I quickly cleared away the papers from my desk top so that I would have a large flat surface on which to form the pairs of bases held together by hydrogen bonds. Though I initially went back to my like-with-like prejudices, I saw all too well that they led nowhere. When Jerry came in I looked up, saw that it was not Francis, and begin sifting the bases in and out of various other pairing possibilities. Suddenly I became aware that an adenine-thymine pair held together by two hydrogen bonds was identical in shape to a guanine-cytosine pair held together by at least two hydrogen bonds. All the hydrogen bonds seemed to form naturally; no fudging was required to make the two types of pair bases identical in shape. Quickly I called Jerry over to ask him whether this time he had any objection to my new base pairs.13

Donohue said no, and the rest is history.

In his account of the content of the discovery in his book, DNA: The secret of Life, Watson refers to the understanding involved as ‘the insight that made it all possible.’14 What the event teaches us is that once the correct imaginative presentation of the elements of the problem of the base relations is in place the image causes the insight. The fact that the base structures as he now understood them were spatially complementary meant that they could hold together a two chain helix with no irregularities in it. The unzipping and re-zipping of that double helix could in turn be the ground of the hereditary mechanism which they were in search of. After many false starts and oversights Watson now communicated the content of his insight to Crick, and later the staff of the Cavendish and King’s College, inviting them to test it and see if they could find any flaws. Although Crick would not give his approval to the overall structure of DNA until the 1980s the base structure stood up to the test. None were forthcoming.

The content of insights, of eureka moments or discoveries in this sense are always communicable. When the peer group associated with the problem shares an understanding of what conditions a solution must fulfill then the content moves out of its solitary genesis and becomes a part of the understanding of the group. In many cases a new insight can require an intellectual conversion, that is to say a difficult change in ways of thinking about the problem in the group. Still, the communicative nature of the formulations of insights and its rapid entry through the revisions of text books into the educational process reveals that the cultural activity and collaboration that is scientific research and its communication breaks free of the slow process of biological evolution and adaptation. In this sense insight events are at the heart of cultural evolution.

Towards the end of the 1950s three French researchers, Jacques Monod, Fran�ois Jacob and Arthur Pardee, found themselves drawn into an intriguing puzzle concerning the genetics of cell metabolism. In the course of nurturing the bacterium Escherichia coli on a mixture of two sugars, glucose and lactose, it was found that it stopped growing for about an hour and then resumed, absorbing the lactose. As the growth rate differed from the sum of the individual growth rates it was clear that the organism was digesting them sequentially. Monod, Jacob and Pardee would meet in Monod’s office each day ‘thinking up hypotheses, possible regulatory mechanisms, and inferring from them the results we could expect from the projected experiment.’15 Leo Silzard, ‘a truculent character crackling with insight and cleverness’ held a theory of generalized repressing, Monod of generalized induction. It took a winter of experimenting, the PA JA MA experiments, to decide the matter.  

As things clarified, the excitement grew. There is in research a unique moment: when one suddenly sees that an experiment is going to overrun the landscape. It is the moment when the facts combine to indicate a new and unforeseen direction. When the change taking place is due more to a feeling, to a premonition, than to the chilly facts of logic. Where the dream of novelty suddenly takes on consistency without being fully assured of becoming reality.16

There follows in Jacob’s memoir The Inner Statue a wonderful account of the distinction between what he terms day science and night science. Day science is the science of the organized textbook such as we find in Essential Genetics: A Genomics Perspective by Daniel Hart and Elizabeth Jones. It has the majestic arrangement of a Bach fugue or French garden. Night science, on the other hand, ‘wanders blindly. It hesitates, stumbles, falls back, sweats, wakes with a start. … At the mercy of chance, the mind frets in a labyrinth, deluged with messages, in quest of a sign, of a wink, of an unforeseen connection. Like a prisoner in a cell, it paces about looking for a way out, a glimmer of light.’17 Jacob’s account of the struggle of night science to emerge into the light of day science in his memoir, The Statue Within simply has to be read to complete the picture of science.

At the end of an afternoon on a Sunday in Paris late in July 1958 Jacob and his wife, Lise decide to go to see a film that failed to engage. Perhaps because of this a current of images and thoughts took over Jacob’s idle mind.

I am invaded by a sudden excitement mingled with a vague pleasure. It isolates me from the theatre, from my neighbors whose eyes are riveted to the screen. And suddenly a flash. The astonishment of the obvious. How could I not have thought of it sooner. Both experiments – that of conjugation done with Elie on the phage, erotic induction; and that done with Pardee and Monod on the lactose system, the PA JA MA – are the same. Same result. Same conclusion. In both cases a gene governs the formation of a cytoplasmic product, of a repressor blocking the expression of other genes and so preventing either the synthesis of the galactosidase or the multiplication of the virus. In both cases, one induces by inactivating the repressor, either by lactose or by ultraviolet rays. The very mechanism that must be the basis of regulation. But there is more.18

His wife discerns that he has had enough of the film and they leave and on the boulevard Montparnasse he tells her that he thinks he has grasped something of significance. Later, in their house, he tries to no avail to communicate the importance of the moment.

Only in September does he get to discuss it with Monod, the two faces of whose character he etches with artistry, the charming and the dogmatic/domineering. There follows over time a long conversation between them, Jacob trying to change Monod’s ideas, a task that he admits was not easy. Jacob liked his hypothesis, not just because of its simplicity but for a ‘crazier reason,’ effectively the imaginative source of his insight.

Some weeks earlier, I had observed my son Pierre playing with a model electric train. The train had no rheostat. Nevertheless, Pierre could vary the speed of the train by manipulating the switch, making it oscillate faster or slower between start and stop. Then why not a similar mechanism in the synthesis of proteins?19

Reminiscent of the attitude of some to the spatially structured model building of Crick and Watson, Monod considered this ‘argument’ a bad joke. Involved is the presentation to Jacob’s senses and imagination of the imagery of a switch which, transferred, caused in him an insight into a possible explanation of their experimental observations. As their conversation continued and eventually engaged with a wider group, Monod came to change his mind. The switch, central to Jacob’s insight was to become a foundational category of developmental molecular biology.

 To grow on a sugar, the bacterium had to have a particular enzyme to degrade it. Monod found that the bacterium did not have the enzyme initially. It first produced one kind of enzyme to metabolize one of the sugars, and then produced a different kind to metabolize the other. It seems that the bacterium responded preferentially to one of the sugars to produce an appropriate enzyme not initially present while at the same time inhibiting the production of an enzyme to metabolize the other sugar. In this the organism was physiologically adapting itself and changing the proteins it produces in accordance with its environment. They had discovered the fact that the parsimonious bacterium adjusted its metabolism according to the food supply.

A third example of an insight/eureka moment has to do with Crick’s engagement with the question, what is the function of DNA in the cell, what does it do? It was acknowledged that it produces proteins, made up of the then 20 known amino acids. This led to the further question, how does DNA code onto the 20 amino acids in the manufacture of proteins? Centrally his book, What Mad Pursuit, A Personal View of Scientific Discovery, is an account, not just of the solution to the problem of protein synthesis in cells, but of how he and Brenner, with the help of Gamow, Jacob, Marshall Nirenberg and others, came to make it. It opens up for us the creativity of the discovery process. As with the problem of the structure of DNA the quest for an understanding of its role in protein synthesis went through many frustrating moments. Through learning from the errors Crick and Brenner entered progressively into the details of the problem but eventually found themselves stuck. Crick recalls waking up on Good Friday morning 1960 in a state of utter darkness and confusion.

In the afternoon Fran�ois Jacob presented a seminar in Cambridge which included an account of an experiment, thought up in Paris, but carried out in Berkeley by Arthur Pardee and Monica Riley concerning gene enzyme relations. In the course of a cross examination it became clear to Crick and Brenner that they would have to accept the results of the PM JA MO experiment. But if they accepted their result then it seems to indicate an oversight in their own work. What alternatives did this leave? At this point Sydney and Francis leaped to their feet shouting. And intense discussion followed. According to Crick, both of them had seen the solution to their problem. The messenger RNA was different from ribosomal RNA. It was the Volkin-Astrachan RNA for the phage infected cell. According to Crick, ‘Once this key insight had been obtained, the rest followed automatically.’20

Volkin and Astrachen has shown that their RNA, unlike ribosomal RNA had the same composition as DNA and quickly renewed itself. This clearly suggested its relevance for protein synthesis. Crick later described the impact of the moment.

It is difficult to convey two things. One is the sudden flash of enlightenment when the idea was first glimpsed. It was so memorable that I can recall just where Sydney, Fran�ois, and I were sitting in the room when it happened. The other is the way it cleared away so many of our difficulties. Just a single wrong assumption (that the ribosomal RNA was the messenger RNA) had completely messed up our thinking, so that it appeared as if we were wandering in a dense fog. I woke up that morning with only a set of confused ideas about the overall control of protein synthesis. When I went to bed all our difficulties had resolved and the shining answers stood clearly before us. Of course, it would take months and years of work to establish these new ideas, but we no longer felt lost in the jungle. We could survey the one plain and clearly see the mountains in the distance. … The new ideas opened the way for some of the key experiments used to crack the genetic code ….21

In 1966, largely thanks to the further insights of Marshall Nirenberg and others, and the results of an enormous parallel experimental programme, Crick would finally put the finishing touches to the code structure for protein synthesis.

Further accounts of moments of insight of enormous scientific importance are narrated by Kary Mullis in his Nobel lecture and Craig. J Venter in his book, A Life Decoded, My Life My Genome. The problem which had exercised Mullis for some time had to do with producing a significant quantity of identical DNA from a small initial sample. On a night drive from Berkeley to Mendocino he found his mind in overdrive. Suddenly there occurred what he referred to as three eureka moments out of which was born the technique known as PCR, the polymerase chain reaction. It is one of the basic tools of current molecular biology. After an initial research career dealing with adrenalin Venter dedicated his later adult life to the problem of sequencing an entire genome including the human. After a long period of wrestling with the details of the problem the brainwave ‘all of a sudden it came to be at thirty-eight thousand feet over the Pacific Ocean: I was using the right sequencing technique but on the wrong DNA.’ Venter goes on to recall how when, on the next day he shared his eureka idea with his lab collaborators he was met ‘with a brick wall of skepticism and doubt.’22 The consensus was that there was a high likelihood of it failing. Mullis had a somewhat similar experience.

Insights such as those illustrated are not just isolated moments. Rather they are prepared by a long pre-history involving a mastery of the problem as problem and which usually involves the making of many mistakes. Neither are they marginal or peripheral to science but are definitive in their content of the core of molecular biology. Once they have emerged their consequences for future science and he future manipulatio

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