Research Bibliographies, Page 1

This bibliography is like a glimpse into the past, an artefact of my time with BT’s Complex Systems Laboratory. Originally intended for internal use within a research group and later made available to the public, the bibliography has not been actively maintained since 2000.

Artificial Life (General)

Funny to have such a short section here, considering my work is supposed to be primarily artificial life! Please see the other sections for finer characterisations of parts of the field. This category is reserved just for collections, introductions & that sort of thing.

Adami, C. (1998) Introduction to Artificial Life. New York: Springer-Verlag.

This is an outstanding book, particularly for those with an interest in information theoretic or thermodynamic approaches to problems in evolutionary systems. Despite its unsurprising focus on avida, the book remains an excellent introduction to broader issues in artificial life. And despite being called an ‘introduction’, much of the material here is very recent and will be of interest to most professional researchers in the field.

Floreano, D.; J-D. Nicoud, F. Mondada, eds. (1999) Advances in Artificial Life: Lecture Notes in Artificial Intelligence 1674. New York: Springer-Verlag.

This is the proceedings volume for the European Conference on Artificial Life 1999, held at EPFL.

Cognitive Science & Psychology

Like several other sections, it seems bizarre to include a tiny little section on cognitive science when my previous work was so wrapped up with the field! But nonetheless, here it is…

Karmiloff-Smith, A. (1992) Beyond Modularity: A Developmental Perspective on Cognitive Science. Cambridge, Massachusetts: MIT Press.

This book, which introduced the ideas of representational redescription, is still on my list! Notes to follow…

Snyder, A.W. and D.J. Mitchell (1999) ‘Is integer arithmetic fundamental to mental processing?: The mind’s secret arithmetic’, Proceedings of the Royal Society of London B 266: 587-92.

Argues that the remarkable abilities of autistic savants are due to an abnormal ability to access low level levels of neural processing which are present in ‘normal’ individuals but not normally available to introspection. I.e., the neural circuitry responsible for lightning fast mental arithmetic, perfect pitch, artistic ability, and other special savant capabilities may well be present in all normal brains but simply inaccessible. Authors leave open the question of why the brain should be so adept at integer arithmetic, equipartitioning, and similar feats.

Psychobiology & Psychopharmacology

From the standpoint of computational substrates, it’s interesting to consider the relationship between underlying neural functioning and psychopathologies such as depression.

Owens, M.J. and C.B. Nemeroff (1994) ‘Role of Serotonin in the Pathophysiology of Depression: Focus on the Serotonin Transporter’, Clinical Chemistry 40(2): 288-95.

Review of evidence on the role of inhibitory neurotransmitter 5-hydroxytryptamine — 5-HT, or serotonin — and its relevance to depression. Notable results include experimental evidence that a special diet deficient in tryptophan (the central metabolic precursor of 5-HT) and high in neutral amino acids which compete with existing tryptophan for carrier-mediated brain uptake, precipitated a rapid relapse in depressed patients within hours of ingestion. (Who volunteers for these things??) Also discusses, from the transport point of view, the effect of selective reuptake inhibitors in increasing serotonergic neurotransmission and the effect of some amphetamine derivatives, including 3,4-methylene-dioxymethamphetamine (MDMA, or ‘ecstasy’), in creating a large wash of synaptic 5-HT. Also notes that 5-HT transporter mRNA has been observed in areas altogether devoid of serotonergic perikarya as well as the finding that this mRNA expression can apparently be controlled by both nonselective and selective reuptake inhibitors. Interestingly, much of the work on 5-HT transporters is actually performed on platelets, which apparently have identical 5-HT transporter sequences.

Nemeroff, C.B. (1996) ‘The corticotropin-releasing factor (CRF) hypothesis of depression: new findings and new directions’, Molecular Psychiatry 1: 336-42.

Excellent review article on CRF and hyperactivity of the HPA axis. Particularly notable results include notion that elevated CRF levels not only stimulate the HPA axis but also act on extra-pituitary brain sites. Also, evidence suggests that undue stress early in an organism’s life may sensitise CRF neurons, and paraventricular nucleus (PVN) hypothalamic tissue in particular, leading to CRF hypersecretion in response to stresses later in life. This appears linked to an increase in CRF mRNA expression. Selective serotonin reuptake inhibitors appear remarkably effective in normalising ACTH and corticosterone responses to stress, as well as normalising mRNA expression in the PVN and other areas.

Nemeroff, C.B. (1998) ‘The Neurobiology of Depression’, Scientific American 278(6): 28-35.

Excellent review article describing the chemical pathways implicated in depression, ranging from norepinephrine and other monoamines, to serotonin (produced in neurons projecting from the raphe nuclei to many areas, including those which affect the release of norepinephrine), to hormonal disturbances in the HPA (hypothalamic-pituitary-adrenal) axis and the stress-diathesis model, which predicts that early childhood stress can permanently increase CRF gene expression. For more details, see Owens and Nemeroff (1994) and Nemeroff (1996).

Cryptography and Cryptanalysis

Bennett, C.H.; G. Brassard and A.K. Ekert (1992) ‘Quantum Cryptography’, Scientific American 267(4): 26-33.

Very straightforward survey of quantum key distribution techniques based on the pioneering work of Bennett and Brassard, recently (1989) demonstrated in a working device at IBM’s Thomas J. Watson Research Center. Additional comments on Ekert’s work and also on the use of similar methods for discreet public decision making based on securely held private data.

Shamir, A. (1999) ‘Factoring Large Numbers with the TWINKLE Device’, extended abstract, Dept. of Applied Mathematics, The Weizmann Institute of Science.

Describes a fascinating and ingenious GaAs-based ultra-fast optical implementation of the sieving process used in the QS (Quadratic Sieve) and NFS (Number Field Sieve) algorithms for attacking product of primes style public-key cryptography systems such as RSA. The author suggests the relatively inexpensive device could improve the efficiency of the NFS algorithm by two to three orders of magnitude, increasing the size of factorable numbers by 100 to 200 bits. “The main practical significance of such an improvement is that it can make 512 bit numbers…[used in many e-commerce applications]…easy to crack” (p. 2).

Dynamics and Self-Organisation

Also see the section on neural networks and that on Benford’s Law under Information Theory.

Bak, P.; C. Tang and K. Wiesenfeld (1988) ‘Self-Organized Criticality’, Physical Review A 38(1): 364-74.

This and a short 1987 account by the same authors (Physical Review Letters 59: 381) are the original sources for the phrase ‘self-organised criticality’. Despite a great deal of hype which later accreted around the phrase, this original article is rigorous and free of hyperbole, offering an account intended to link nonlinear dynamics, the appearance of scale-invariant spatial self-similarity (i.e., fractal structure), and 1/f noise, or ‘flicker noise’ in a robust way. The essential dynamical property of the systems considered is the presence of many metastable states.

Garfinkel, A. (1987) ‘The Slime Mold Dictyostelium as a Model of Self-Organization in Social Systems’, in Yates (1987), pp. 181-212.

Fascinating account of aggregation in slime mold Dictyostelium, which self-organises from single-celled amoebae into multicellular colony, which then undergoes cellular differentiation and moves as a whole over macroscopic distances. (For the full story on slime molds, see Loomis 1975.) The paper describes and critiques various attempts to model the self-organising behaviour of Dictyostelium using field models and individual cell models, neither of which have been particularly successful. Includes interesting comments on the crucial role of entrainment in self-organisation (both in terms of frequency and in terms of phase — the latter also being known as ‘phase locking’, or ‘synchronisation), including some architectural preconditions for entrainment to occur (p. 195, for instance). (See Winfree 1980 for discussion of biological phase entrainment examples and Glass and Mackey 1979 for a simplified model of phase locking entrainment under the action of a sinusoidal stimulus.) This is an incredibly interesting account of self-organisation; latter parts of the paper, extrapolating to the emergence of social structures, are somewhat less rigorous.

Glass, L. and M.C. Mackey (1979) ‘A simple model for phase-locking of biological oscillators’, Journal of Mathematical Biology 7: 339-52.

Simple model of biological phase entrainment due to sinusoidal stimulus.

Loomis, W. (1975) Dictyostelium discoideum: A Developmental System. New York: Academic Press.

Background on slime mold with amazing life cycle summarised & analysed in Garfinkel (1987).

Winfree, A. (1980) The Geometry of Biological Time. Berlin: Springer-Verlag.

Discussion of phase entrainment in cricket chirping, firefly flashing, glycolitic oscillation in yeast cells, and eclosion cycle coherence in insect populations mentioned in Garfinkel (1987).

Yates, F.E., ed. (1987) Self-Organising Systems: The Emergence of Order. London: Plenum Press.

This collective volume brings together several early perspectives on self-organisation from physicists, biologists, chemists, and others.

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