Mind Science and Society. New course starts August 30th 2021

Year 1

algorithms 4

Requirements satisfied by


linear systems 4

Requirements satisfied by



For those in need of an algebra refresher  ;



science and society 8

For those in need of a calculus refresher


syllabus and sample lecture

Science and Society Summary and Sample

cognitive science 8



logic 4

Requirements satisfied by


biology 4

Requirements satisfied by


linguistics 4

Requirements satisfied by


neuroscience with added material from 8

Requirements satisfied by


and https://www.edx.org/course/neuronal-dynamics

computer science 4

Requirements satisfied by

Year 2


algorithms 4


Requirements satisfied by

science and society 8


Example ressource https://www.coursera.org/learn/emergent-phenomena/home/




cognitive science 8




hardware and operating systems 4


Requirements satisfied by



compilers 4


Requirements satisfied by


computational linguistics 4
Requirements satisfied by

Neuroscience 8

Syllabus and other resources

Neuroscience and Experience Summary and Sample

text analysis and natural language processing 3


Year 3 includes these 8 credit courses in addition to work and/or foreign study experiemce and a project  ;


Requirements satisfied by




syllabus and sample lecture

Biosemiotics/Linguistics Summary and Sample

A cultural component

syllabus and sample lecture using Irish music as an example

Irish Music and Culture Summary and Sample

Year 4 is a year of specialisation where you choous your own subjects more than in previous years. Here are some suggestions  ;


1 Human Computer Interaction: multimodality, enablement, making computers
2 AI ;classical Symbolic approaches versus Subsymbolic and Statistical
3Consciousness studies ; Philosophy of   mind: Classical approaches to mind
and brain, recent developments
4 Computational linguistics ; exemplified in practical approaches to machine
translation and speech processing.
5 Final year project for entire last semester


Language, Vision & Music

What common cognitive patterns underlie our competence in these disparate modes of thought? Language (natural & formal), vision and music seem to share at least the following attributes: a hierarchical organisation of constituents, recursivity, metaphor, the possibility of self-reference, ambiguity, and systematicity.
Can we propose the existence of a general symbol system with instantiations in these three modes or is the only commonality to be found at the level of such entities as cerebral columnar automata?
Cross-cultural experience of these modalities Topics Include: Combinations: language and music; language and vision; music and vision. What can Engineering of software platforms for integrated Intelligent MultiMedia processing of language/vision/etc. tell us?

For example: the use of terms like “interval” and “range” in music.
How is Rhythm important for language, vision and music?
Acoustics: What role does it play in the three modalities? The roles of embodiment and culture in the formation of symbolic apparatus; For example: the use of gesture in face-to-face communication. Emotions: what role do they play in the three modalities? Synesthesia What the visual, musical and linguistic arts can tell us.

What is the developmental relationship between prosody and music? What is the cognitive evidence for the dependence of music on language? Can we speak meaningfully about a semantics of music? Architectures for integration of language, vision and music; what aspects are conscious and what automatic? What aspects are common and what are specific to each? What is the role of modelling creativity? Are the creative processes similar or in what way are they different?

1Neural networks: Bep, Art, Sigma pi, etc.
2Cognitive neuroscience; EEG, Fmri, problems with temporal and spatial
discrimination. Resonate and fire networks
3Consciousness studies ; Philosophy of   mind: Classical approaches to mind
and brain, recent developments

4 Clinical work It is Intended to get psychology certification for the
course that will motivate practical work from “test bashing ” and
elementary first aid to preliminary diagnosis
5 Final year project for entire last semester


Inner and outer empiricism in consciousness research

outer empiricism; the brain as a very noisy and complex system with the skull acting as a very effective barrier to investigation
The notion of a filter; the skull as a low-pass filter
EEG, ECOG, fmri, diffusion tensor imaging, MVPA; advantages and disadvantages
. Using the scalar data from EEG to arrive at a structure for vector data like Bose Einstein condensates
inner empiricism; philosophical issues like Levine’s “explanatory gap”
Subjective states in hemispheric differences, psychedelics. The arts
Combining outer empiricism and inner empiricism

Cognition, computation and consciousness thread

While cognitive science has entered public discourse, there remain fundamental issues about its relation to mind, and – in turn – mind’s relation to the brain. If we accept the computational functionalist metaphor, the details of the biology underlying mental processes become irrelevant. So do issues of subjectivity that lie at the core of being human, and must be finessed away to fit in with computationalism.

Secondly, despite billions being poured into it, neuroscience is not progressing quickly. Students are invited to an alternative approach that is rooted in dynamical systems, and ultimately finds a welcoming encompassing formalism in quantum field theory. Indeed, the issue of quantum theory and mind requires a course in itself, as does AI.


Quantum physics and mind

.1. The problem of measurement in Quantum physics and its relationship with observation and consciousness
2. Quantum physics (QP) and its subsets of Quantum mechanics (QM) and Quantum field theory (QFT)
.3. Quantum physics and classical physics
4. Entanglement; the EPR experiment as a reductio ad absurdum of QM. Bell’s inequalities and the consequences of quantum information theory (QIT)
5. QIT and Quantum computing (QC)
6. Measurement, both strong and weak, and determination. Changing the past a la Yakit Aharonov Aspect’s experiment
7. Alternatives to consciousness; QM without observers in decoherence, Bohmian pilot waves, and spontaneous localization, inter alia

Senses, symbols and representations thread

Preceding analysis of mind is a level at which we consider the very act of apprehension of the world, including the systems of signification that constitute cognitive science. On the one hand, the process by which mind intends the world has been successfully reduced to thermodynamics. On the other, the “unreasonable effectiveness of mathematics in the physical sciences” has allowed us humans access to knowledge and technology that is not predictable from our evolutionary origins. We also introduce the students to a level of analysis at which syntax and semiosis itself is seen as being presaged in processes within the cell and the senses.

Deatils of our in-house syllabi

Science and society and cultural studies

Science and society 1 The new biology and (bio)medical science of the 21st century

In late 2019 the existence of a new virus was announced. By the end of 2020 sars-cov-2 had killed millions of people, interrupted the lives of billions, and caused $tens of trillions of economic damage worldwide. Yet that is only the beginning of an incident that will reverberate through the rest of this century, if not this millennium. In particular, the l;ack of a solid paradigm in biology confused the distinction between transmission and infection; the imposition of an inadequate and archaic statistical model internationally by the WHO blinded governments to the fact that the virus was vulnerable and died in predictable fashion in spring with increase in daylight hours; and, capping this comedy of errors, journalists chose to channel government press releases instead of educating themselves.

The many other scientific and associated ethical controversies in current biology are the stuff of daily newspaper headlines. Can we, and if yes, should we clone humans? How easy is it to manipulate development to create new species? Are GM foods really safe? To what extent are organisms the product of their environments and their parental endowments? What really is a gene? Where is the program that determines development? As we develop nano (and sub nano) technology like plasmon rulers to investigate life, are we in danger of losing sight of the still unspecified complex of chemical reactions which produce and sustain life?

It is, paradoxically, a complement to state that biology is in crisis. The word “crisis” in the philosophy of science literature is used to indicate that there is massive opportunity to clean up the MO of the discipline. We therefore start the course with analysis of what a “crisis” in science actually is, with particular reference to the Copernicus/Galileo affair. We then extend the analysis through brief consideration of Quantum mechanics and relativity before resuming the matter at hand; 21st century Biology.

We start the biology with analysis of transcriptional and translational issues in gene expression that, taken together, expose the over-simplifications of the Human Genome Project (HGP) . This new level of complexity allows us to consider more correctly what the consequences are for medicine. Moreover, the biomedical model seems incomplete; its exclusion of social factors from an analysis of health seems incorrect. We give one example of experimental work that proves meditation frees up metabolic energy for the organism.

We end with a thorough analysis of current cutting-edge areas of biology, including ecosystems, before returning to covid-19.


I. Introducing Main Concepts of the Course Argument:
We are currently confronted with massive problems of the biosphere. These problems are largely based on the principally reductive nature of our scientific process. In order to overcome these crises we must adapt more synthetic views and methods, which specifically incorporate complexity concepts such as “emergence.” This argument was put forth, for instance, at the end of the book Complexity: The Emerging Science at the Edge of Order and Chaos (1992, Mitchell Waldrop).
1) Complexity theories – key definitions and concepts and their significance. a. Reductionism vs. Complexity – the main paradigmatic shift towards systems b. Significance of this shift in terms of the sciences, technologies, and ethics, and in terms of the connections between science, technology, and ethics.
2) Emergence – the central concept of complexity theories for this course a. Emergence – definitions, ubiquity in different disciplines b. Emergence – as central concept linking: irreducibility of complex parts and whole, self-organization, and adaptation. c. Theories of interdisciplinarity; Unifying theories.
3) Ethics – traditional/ bioethics/ ecoethics a. How complexity illuminates the need for more advanced ethics i. E.g. Climate change scientists claim climate change is “fundamentally an ethical problem.” (Gardiner, Steven M., Ethics, April, 2004.)
4) “Meaning” a. Definition from Religion b. Definition from Cognitive Sciences c. Definition from principal scientific domains d. Challenge: the disciplinary Diaspora and the meaning of “meaning” i. Results in terms of social and environmental degradation, our promotion and our evolving perception of our interlocking biospheric crises. II. Historical Case Study Examples.
5) Evolutionism / Creationism.
6) GMO Example The Ignacio Chapela case; the Arzad Pusztai case.
7) Copernicus/ Galileo III. Contributions from Cognitive Science /Philosophy of Science/ Complexity Sciences & Mathematics.
8) Logical science and meaning a. Meaning – i. Compositional semantics, possible world semantics, and other theories thereof ii. Wittgenstein I and II, Frege, Tarski, Carnap iii. What does brain science tell us? iv. Consciousness and meaning.
9) Biosemiotics – the study of information, codes, and signs in living systems.
10) Math tools, e.g. Wolfram’s web site has many complex system tools IV. Conclusions.
11) Student Presentations.
I. Concluding Discussion.

Science and society 3
Here, the problems faced worldwide are outlined in simple terms. They are split into environmental/demographic and moral/fideistic categories. The rest of the course is essentially a search for knowledge which will help us confront these problems.

Overview of current knowledge – The Natural Sciences
Physics: Introduction to major concepts in classical and quantum physics. The epistemological consequences of the 20th century breakthroughs in QM and general relativity.
Biology: Categories of explanation therein ( teleological, formal causation etc). Basic biological concepts: genetic replication, binding and immunity, intoduction to ecosystems. Status of the concept of “gene” and the theory of evolution. Moral issues in genetic engineering.

Political Sciences: a brief history from Aristotle through Montesquieu and Marx to current issues like communitarianism. Nationalism.
Economics:major concepts and their political manipulation. What is political economy? Alternative models – green model, feminist model, arms economy model
Psychological sciences: distinction between psychology, cognitive science, political influence on progress in psychology and related fields. Ethical and aesthetical theories

Irish Cultural Studies
Irish music presents perhaps a unique example to the world. Originally a “high” art form, it was forced underground by colonial forces and preserved orally for hundreds of years. Only in the past fifty years or so has a nascent self-awareness allowed it to develop further. Yet Irish music based on traditional sources has failed to maintain the breathtaking development of the years 1960-1985. Having considered the history , this course looks at some techniques and projects that might redress this problem. First of all, the use both of modern and pre-Famine Gaelic poetry as song lyrics is examined. Counterintuitive techniques which work well, such as the use of 12:8 rhythms to complement this poetry are examined in conjunction with developments of techniques pioneered by groups like Clannad in masterpieces like “Fuaim”. (Beidh mioneolas a lorg ar shaothar Nuala Ní Dhómhnaill. ) Nuala Ní Dhómhnaill’s work with groups like Kila and others will be examined, and the use of classical and jazz techniques to set this music will be examined in detail. The extension of the chordal accompaniment pioneered by the likes of Donal Lunny to jazz will be the next topic. Finally, the crossover between jazz scatting and Irish lilting will form the basis of practical exercises. © 2005 Melanie O’Reilly and Seán O Nuallain
COURSE TITLE: “Irish Song and Music – from Sean-Nos to Jazz”.
COURSE DESCRIPTION: 1. Discipline or subject area: Celtic Studies 2. Position of course within subject area: While “Celtic” is a rather nebulous term, it is possible to discern a code of music that is specifically Irish. In this course, we examine the harmonic, rhythmic and melodic techniques that historically have characterised Irish music. Students will be encouraged through praxis to create in the field. 3. Intended audience: The students should have an interest in one or all of the following: Ethnomusicology, Irish studies, post-colonial studies, gaelic linguistics.
COURSE OBJECTIVES: When students have completed this course, they will: – Understand the distinction between diatonic and modal music. – Understand the composition techniques used by the Irish masters of the 17th century like O Cathain and the later development in O Carolan. – Distinguish between the classical period of Irish music and later imports such as the reel. – Recognise the main harmonic patterns now used (Dorian, Ionian, Myxolydian,and Aeolian) and their contrast with their diatonic counterparts – Understand the use of microtonality in “sean-nos” and be able to evaluate theories of its origins. – Be able to lilt (sing) simple tunes. – Understand the use of syllabic poetry, both in the classical period and as used in song lyrics, and contemporary use of blank verse. – Follow the recent development in Irish music by Donal Lunny in Emmet Spiceland, Planxty, the Bothy Band, Moving Hearts, Coolfin and others such as Clannad. – Be aware of the socio-economic context of the current recent stasis in the music development.
PREREQUISITES: Students should : -Be able to read music, or show a willingness to learn -Show a willingness to learn the basics of the Irish language -Be open to post-colonial theory -Be other than tone-deaf.
1. Gaelic poetry as song lyrics ; the classical period of syllabic verse. Later development O Rathaille, Mac Gearailt, Ni Dhomhnaill.
2. The Classical period of Irish music. In 1621 Donncha Mac Tadhg built a harp customised for European music. What musical system did the Irish masters use?
3. Later Imports: Reels, single Jigs, slip jigs, hornpipes,. Rhythmic patterns in these and the 1970’s Balkan fusion.
4. The Celtic Revival: the tension between classical and populist, manifested in President Hyde versus O Riada and O Gallchoir.
5 The late 20th century boom: Planxty, Clannad , De Dannan, Moving Hearts, Deiseal.
6. Current Stasis: Irish culture and neo-liberalism.
7. New directions: –
a.) Nuala Ni Dhomhnaill and Celtic Jazz.
b) Clannad, Enya, and Celtic World music.
METHODS OF INSTRUCTION. Students will read and discuss material in class and over a bulletin board and do practical exercises.
COURSE GRADE The students will do one practical project and one written exam, each worth 50%. Both must be passed
CORE MATERIALS: O Nuallain (2002) : “On Tonality in Irish Traditional Music”. Benjamins, in McKevitt et al eds “Language, Vision and Music”. O Tuama and Kinsella 1981 “ An Duanaire”-Poems of the Dispossessed”.-Mountrath Dolmen. Brendan Breathnach -1971 Reprinted 1993- “Folk Music and dances of Ireland”, Cork Mercier Press.
Arts Council of Ireland (2004), “Towards a policy for the traditional Arts . 70 Merrion Square, Dublin 2, Ireland ISBN 1-904291-09-0 Asch, R. (ed) (1993).
Three Nations: A Common History. Castle, G. (ed.) (2001)
Postcolonial Discourses Oxford: Blackwell Coogan, T. (2000) De Valera London: Random House De Paor, L. (ed) (1986).
Milestones in Irish History, Cork: The Mercier Press. Donoghue, D. (1986).
We Irish, New York: Knopf. Ellis, D. S. (1999).
“More Irish than the Irish themselves,” History Ireland, Vol. 7, No1, 22–26. Hamilton, H. (2003).
The Speckled People, London: Harper Perennial. Ignatiev, Noel (1996),
“How the Irish became white” London: Routledge. Lee, J (1985) Ireland 1912–1985. Cambridge, England Cup. Murphy, J (1986) Litton, H. (1998).
Irish Rebellions 1798–1916, Dublin: Wolfhound Press. Mountrath, Dolmen Press. —

Cognitive science

Cognitive Science 1
To provide the students with an understanding of the
field of cognitive science and related disciplines.
As a result of the course, students should:
Understand cognitive science in its relation to computer science and philosophy
Understand the nature of computational models of mind.
Understand in outline the physical and psychological process inherent in human memory, language and vision.
Be sensitive to similarities and differences between human cognitive function and computer processing.


Cognitive Science and related disciplines:
Brief history of philosophical and psychological
approaches to mind:
Empiricism versus idealism from the pre-Socratics onwards.
Cognitive science as a possible resolution of these opposing viewpoints.
Audition, memory, language and vision:
Human physiological and psychological processes.How these are approached from the computational perspective.
Thinking and problem-solving: convergent versus divergent problems.
The work of Bartlett and Piaget.
Different approaches to learning from behaviourism to cognitivism.
Introduction to Connectionism: History of the area from McCulloch and Pitts through to Minsky. The revival in the 80s. Connectionism as an alternative, and as a complementary paradigm to conventional AI. Its use for cognitive modelling.
The computer and the mind: the treatment of emotion, consciousness and voluntarism in a computational framework and consequent limitations of that framework.


Bolton, N (1972), The Psychology of Thinking, T+A Constable Ltd.
Copleston, F (1962) A history of Philosophy, Image Books.
Gardner, H. (1985) The Mind’s New Science: Basic Books
Johnson-Laird (1993) The Computer and the Mind: Fontana.
McClelland, J. and D. Rumelhart (1986) PDP: MIT Press.
McTear, M. (ed) (1988) Understanding Cognitive Science: Ellis Horwood.
Miller (1966)Psychology: The Science of Mental Life: Penguin.
Nadel (ed) (2002) Encyclopedia of the Cognitive Sciences
O Nuallain (2003) The search for Mind. England: Intellect
Ornstein (1972) The Psychology of Consciousness: Freeman.
Stillings, N. (1988) Cognitive Science: An Introduction: MIT Press.
Thines (1977) Phenomenology and the Science of Behaviour, Unwin.
Wilson and Keil (eds) (1999) MIT encyclopedia of the Cognitive Sciences

Cognitive Science 2 : Cognition and consciousness

As a result of this course, students should;

Acquire sensitivity to the distinction between Cognition and consciousness
Acquire an overall view of the areas involved;
Become aware of the continuity of the current research with precedents in history
Know the basic arguments in the philosophy of mind from Plato through Descartes, Berkeley, Hume, Kant, Levine and such popular putative contributions as that of Chalmers.
In the absence of any certain conclusions about the nature of subjective experience , which this course dues not claim to give, be able to evaluate the many current and future claims that will be presented to them proposing a direct link from neural fact to subjective experience

This course starts with a barrage of questions about the relationship between Cognition and consciousness

Cognitive science
Definitions of Cognitive science (CS) – is it about mind, cognition, consciousness, knowledge, or what?
2. What is its relationship to its constituent disciplines?
3. Culture: what is its relationship to the real world?
4. What, if anything, can it tell us about ourselves?
5. How therefore should we pursue it?

Does mind include consciousness? Should CS therefore be able to tell us something about ourselves?
Definitions of mind vary greatly from Nous through the scholastics to restricted computational definitions
Does it include the Freudian and computational unconscious?
What definition of C shall we use – a workspace one or another computational one, a purely neural one a la Walter Freeman, or shall we attempt to detail mechanism, going into quantum mind?
Given that the vast majority of neural processes are unconscious, what risks are involved in reducing CS to phenomenology?

Topic 1

Historical aspects: Plato, Aquinas, Descartes, Locke, Berkeley, Hume, Kant, Husserl, Levine; the advent of cognitive science and its related/constituent disciplines. Other theories of consciousness; conscious inessentialism in Lashley and Jackendoff. Fodor versus Descartes on modularity. Freeman, Suppes; consciousness as a sample. Piaget and other cognitive theorists
Topic 2
Global work space theory. We now have quite an array of evidence for widespread recruitment of brain regions for conscious, but not very similar unconscious sensory input. What implications are there from such a phenomenon? If one believes there is axonal broadcasting of visual input, for example, when it becomes conscious, does that imply some sort of loss in the information being broadcast?
Topic 3
Edelman, involving the dynamic core hypothesis. Llinas and the thalamocortical system. In-depth discussion of brain theories that address similar problems in similar ways. Detailed, critical discussion of recent work by (a) Walter Freeman, advances a strong case for a particular nonlinear dynamical model based on EEG, the notion of an AM phase wave packet; (b) Tononi and Edelman, involving the dynamic core hypothesis; (c) Llinas and Pare, on the thalamocortical system. Tononi’s later “Inegrated information” theory; Orch OR.
These models all aim to deal with a sizable body of brain evidence. So they are biologically plausible to a considerable degree. Are they computationally functional as well?
Topic 4
The interaction of spatial and temporal codes. Topographic maps that go point-to-point into higher-level maps and retinotopic mapping from the retina to LGN, from there to V1, and in the other “V areas” up to IT. The spatial resolution of those maps decreases as they become more abstract and object-like. But at the higher levels we also see more integration of multiple “features?” How do these spatial maps interact with spectral codes?
Topic 5
Multimodal mapping. Spatial location and information integration. What other binding mechanisms are there? ;Filling ; mechanisms and change blindness. Again, spatial location is a great way to integrate information from separate sense modalities. Sound and visual input from the same perceived location in space will tend to be experienced consciously as the same event, providing the two sensory inputs occur within about 100 ms of each other. How are we to understand that? Multimodal mapping has to involve at least two competing ingredients: (a) integration of senses across an accurate spatiotemporal representation of the world (b) separation of the senses, so that we can distinguish between the sight of a bird and the sounds it makes. How do we cover both of these competing objectives?
Topic 6
The contrastive approach in consciousness studies. We know that a lot goes on without consciousness. For example, the cerebellum is mostly unconscious. Yet in many animals it has a similar number of neurons as the cerebral cortex. What is the difference? What happens with the brain goes to sleep, and the waveforms become slow, large in amplitude and regular, rather than fast, low in amplitude and irregular? Consciousness is a very specific brain phenomenon.
C in spiritual disciplines. Summary and conclusions; student presentations

Texts – Copies of “The search for mind” and “Two sciences of mind” will be distributed on registration See also the cognitive science program on universityofireland.org

Neuroscience 2

Executive summary

This course makes the radical claim that dynamical systems theory provides solutions to problems plaguing neuroscience, rather than simply attractive models. It starts with the microscopic level, that of single neurons. A biologically realistic neuron model as a harmonic oscillator is shown to allow neurons do pseudo-Fourier transforms. While it is already known that spike timing becomes naturally causal in this model, we have also implemented a C++ simulation and are developing a Matlab equivalent showing that it can operate on a raw power spectrum, and learning can be formulated as adjustment of delays. In short, the neural code at the microscopic level is, as Karl Pribram thought, the Fourier transform.

The mesoscopic level caters for the missing piece of “intentionality” ie how mind “intends – points to – things in the world. It is argued that nonequilibrium thermodynamics provides a good model here. The vocabulary of dynamical systems, starting as we already have with the periodic attractor of the harmonic oscillator qua pendulum, is proposed as a first approximation for what we need to do at the mesoscopic level. We then argue, following Freeman and Vitiello, that quantum field theory (QFT) provides a more elliptical, encompassing and veridical formalism as dynamical systems engage with the highly dissipative system that is the brain and its environment. The exquisite fit between QFT and the Freeman observations will occupy much of this course.

That will finally bring us to the macro level, at which we experience, talk to each other, and do math. It is argued that formalisms that cater for co-ordinate free flows are more appropriate here than any others

As a result of this course, students should;

-know the essentials of neuroscience, including the perhaps more veridical theories of neural function and communication that may currently be emerging from such areas as non- linear systems, quantum field theory, and analysis of subthreshold neural oscillations

This path through the material may be diverted at any point by students’ questions!
Topic 1
Neurophysiological plausibility: assessment of conventional neural networks, the integrate and fire paradigm, and approaches built on subthreshold resonance. Introduction of the resonate and fire (RFNN)paradigm; vocabulary of non-linear systems to be used in the course. The Hilbert transform as superset of the Fourier transform; its applicability to brain function.
Topic 2
RFNs continued Continuation of analysis of the work of RNF theorists like Izhekevich, Reinker and Doris. Axonal versus dendritic communication. The FM radio analogy pioneered by Izhekevich, Doris and Freeman. Pellionisz and Llinas on tensors in the work popularized by Churchland.
Topic 3
The vocabulary of dynamical systems
Meaning as AM in the work of Freeman. In the first place, it is worth noting that Walter’s is a thoroughly neurobiological account. While much of his vocabulary draws on his considerable math and engineering background, he eschews the cognitive and symbolic lexicon. Thus, there is no reference to grammars, to Piagetian formal operations, to phenomena/conscious experience or the like; the goal is consistent with Occam’s razor.

Thus, we find references to perception-action cycles, to phase transitions, to attractors, and to the propagation of entities instate-space. Methodologies recommended include diffusion tensor imaging, nonequilibrium thermodynamics
Topic 4
. Quantum field theory (QFT) as a more elliptical language.
Topic 5
Conclusion, and student presentations

Texts and other material
Students are recommended to prepare themselves with “The search for mind” and “Two sciences of mind” which will be distributed beforehand. A primer on dynamical systems like “Does God play dice?” by Ian Stewart is recommended as background reading.
It is worthwhile to familiarize oneself with the first two lectures of
Matlab and its free emulator Octave are used a lot in neuroscience;
universityofireland.org features useful pointers toward prerequisites, and access will be given to other online tutorials on registration

Cell language and biosemiotics

Course objectives When students have completed this course, they will: – Understand the essentials of linguistics theories. – Understand the classical theory of gene expression and the challenge emerging from evo-devo (evolutionary developmental biology), among other areas. – Understand the relationship between code and context in biological and human-made systems.

Gene expression; The work of Avery, Schrodinger, Pauling, Franklin and Crick in determining the structure of DNA. What is biosemiotics? Major theoriticians – Barbieri, Sebeok, Emmeche, and others. Code and context. Apoptosis, sugar, and sequence code. Sign, meaning, and interpretant/adapter. Organic “information” and “meaning”. Parallels between gene expression and NL production: the lexicon, syntax, semantics, and “context” in each case.

Classical linguistic and semiotic theory. Saussure, Peirce, and the emergence of the field of semiotics. Generative Grammar. Outline of alternative formalisms; Categorial grammar, lexical-functional grammar, HPSG, functional-unification grammar, and so on. Compositional semantics. Limitations of linguistics theories in relation to neuroscience Jacob, Monod, and the existence of regulatory genes. Alternative splicing, metabolic context, and other issues suggestive of fruitful links with linguistic theory.
The parallels between genome and language at various levels of cellular functions. The surprising parallels with linguistic theory,in particular the “bionoetics” of Piaget and Wittgenstein’s two periods. Fodor’s “language of thought”

Evolutionary developmental biology. The discovery of hox genes, the homeobox, and the consequences for evolutionary theory. Hox genes and chemical gradient; the notion of a genetic “toolkit”. Organism-environment coupling the work of Kaufmann and others in considering the system at the “edge of chaos”

Copyright © 2020, 2021 Sean O’Nuallain