Saturday, February 11, 2006
Biology inspires perceptive machines (PhysOrg]
Biology inspires perceptive machines
Teaching a machine to sense its environment is one of the most intractable problems of computer science, but one European project is looking to nature for help in cracking the conundrum. It combined streams of sensory data to produce an adaptive, composite impression of surroundings in near real-time.
The team brought together electronic engineers, computer scientists, neuroscientists, physicists, and biologists. It looked at basic neural models for perception and then sought to replicate aspects of these in silicon.
"The objective was to study sensory fusion in biological systems and then translate that knowledge into the creation of intelligent computational machines".
Full text at:
--Model of an Internal Evolutionary Mechanism:
Friday, February 10, 2006
[Gen] Science losing war over evolution (Harvard Gazette)
Screening airs evolution versus intelligent design debate
This just in from the front lines of the battle between evolution and intelligent design: evolution is losing.
That's the assessment of Randy Olson, a Harvard-trained evolutionary biologist turned filmmaker who explored the debate in a new film, "Flock of Dodos: The Evolution - Intelligent Design Circus," which was screened Monday (Feb. 6) at the Harvard Museum of Natural History.
Full text at:
Model of an Internal Evolutionary Mechanism
Thursday, February 09, 2006
[PP] Evolution: The Horse Whisperer, Richard Dawkins, and Danish Cartoons
Brief notes from an evolutionary perspective:
In March 2005 'The Guardian' newspaper (UK) printed "The Horse Whisperer is called in to tame children" and said:
"Monty Roberts, the original whisperer who inspired the film and has tamed more than 70,000 wild horses, flew to Britain last week to hold a three-day workshop for Global Education Management Systems (Gems), one of the biggest operators of independent schools in the UK."
Further into the article Monty is quoted as saying:
"It takes a leap of faith because here's a cowboy with ways of working with horses, then he starts talking about children,' he said. 'It's a difficult leap for some people, but not for me.
'I am not for a moment suggesting that animals and humans are the same but, psychologically speaking, their behavioural patterns have more similarities than they have differences."
Why are there more "similarities than differences" - and how does Monty know this?
Monty Roberts has repeatedly spoken of the violence he was subjected to as a child and how his father employed the same brutality against horses. So far so good, but that's only the beginning of the answer - after all, people are people and horses, of course, are horses:
"The neurologist Paul MacLean has proposed that our skull holds not one brain, but three, each representing a distinct evolutionary stratum that has formed upon the older layer before it, like an archaeological site. He calls it the "triune brain." MacLean, now the director of the Laboratory of Brain Evolution and Behaviour in Poolesville, Maryland, says that three brains operate like "three interconnected biological computers, [each] with its own special intelligence, its own subjectivity, its own sense of time and space and its own memory". He refers to these three brains as the neocortex or neo-mammalian brain, the limbic or paleo-mammalian system, and the reptilian brain, the brainstem and cerebellum (see above diagram). Each of the three brains is connected by nerves to the other two, but each seems to operate as its own brain system with distinct capacities."
(From The Triune Brain)
As a rule of thumb, the disruption to internal integrity known as psychological trauma (not to be confused with the popular conception of trauma - see Note 1) gives every appearance of occurring somewhere within the limbic system. An indication of how trauma has been part of Man's heritage since 'before there were words' and the probable basis of Monty's non-intellectual empathy with other animals who have sustained a similar injury.
Like the background radiation from the 'Big Bang', psychological trauma pervades every aspect of human society and its characteristic signature can be found in many cultural institutions - and for the purpose of these notes, specifically Religion.
Scotland's Sunday Herald recently said:
CONTROVERSIAL scientist Richard Dawkins will assert tomorrow evening that religion is a 'virus' that amounts to child abuse.
The new two-part series, to be shown on Channel 4 (UK), will compare Moses to Hitler and claim that God is racist. It will also argue that religion is a 'backward belief system' responsible for terrorism.
The controversial films, which were produced by IWC creative director Alan Clements and written by Dawkins, are a polemic against faith and a stout defence of science.
More controversially, he states 'sectarian religious schools' have been 'deeply damaging to generations of children. 'It's time to question the abuse of childhood innocence with superstitious ideas of hellfire and damnation ,' he says. 'Isn't it weird the way we automatically label a tiny child with its parents' religion?'
While disagreeing with Dawkin's perception of how evolutionary changes occur, and aware of the fact that a 'deeply' held belief in aetheism/science can be the other side of the coin to fear of believing in a God of psychological origin (rather than any 'other kind' - if such exist), the above observations hold an uncomfortable truth.
From Channel 4's own page on the program:
In addition, though religions preach morality, peace and hope, in fact, says Dawkins, they bring intolerance, violence and destruction.
Again from a psychological perspective: 'morality' is needed to compensate for the ongoing presence of maladjustment to a compounded trauma within individuals so that they can then co-exist as a group, 'peace' means suppression and internal 'soothing' of the wound (hence the 'sing-song' voice often employed during church services), and 'hope' promises a future free from internal reactions with one's own wound (often caused by other people outwardly expressing the presence of theirs). Unfortunately the hope proferred can only be realized in some kind of 'afterlife'.
In short, and at best, Religion can be seen as an archaic form of therapy. At worst, the surface veneer may easily be broken down and lead to events like those which promped the writing of these notes: people have died over the publication of cartoons!
It is very telling that no God does its own killing...
There is more at issue with Islam here than with the cartoons published in Jyllands-Posten or with the principle of 'freedom of speech'. I for one feel an obligation to those people, who in the Society I live in, once suffered during the process of separating Church from State - the ugliness of the current pedophile scandal in the Roman Catholic Church is but an echo of how much worse things once were.
Finally, and in a related vein, an item from today's Daily Telegraph (UK):
Two hundred years after Anglican reformers helped to abolish the slave trade, the Church of England has apologised for profiting from it.
Last night the General Synod acknowledged complicity in the trade after hearing that the Church had run a slave plantation in the West Indies and that individual bishops had owned hundreds of slaves.
It voted unanimously to apologise to the descendents of the slaves after an emotional debate in which the Archbishop of Canterbury, Dr Rowan Williams, urged the Church to share the "shame and sinfulness of our predecessors".
Physicists question whether there are "universals" in biology. One reason is that the prevailing theory of biological evolution postulates a random walk to each new adaptation. In the last 50 years, molecular genetics has revealed features of DNA sequence organization, protein structure and cellular processes of genetic change that suggest evolution by natural genetic engineering. Genomes are hierarchically organized as systems assembled from DNA modules, which themselves generally constitute systems at lower levels. Each genome is formatted and integrated by sequence elements that do not code for proteins. These formatting elements constitute codons in multiple genetic codes for distinct functions such as transcription, replication, DNA compaction and genome distribution to daughter cells. Consequently, the genome has a computational system architecture. Proteins are systems composed of functionally distinct domains connected in polypeptide chains. Whole-genome sequencing indicates that rearrangement of genetic modules plus duplication and reuse of existing genomic systems are fundamental events in evolution. Studies of genetic change show that cells possess mobile genetic elements and other natural genetic engineering activities to carry out the necessary DNA reorganizations. Natural genetic engineering functions are sensitive to biological inputs, and their non-random operations help explain how novel system architectures can arise in evolution.
Technorati tags: genome system architecture, signal transduction, cellular computation, natural genetic engineering, mobile genetic elements,dna, biology, evolution, shapiro
Wednesday, February 08, 2006
STEPHEN JAY GOULD AND RICHARD C. LEWONTIN
REPUBLISHED FROM THE ORIGINAL WITH THE KIND PERMISSION OF THE ROYAL SOCIETY OF LONDON: GOULD, S. J. AND LEWONTIN, R. C., 'THE SPANDRELS OF SAN MARCO AND THE PANGLOSSIAN PARADIGM: A CRITIQUE OF THE ADAPTATIONIST PROGRAMME,' PROCEEDINGS OF THE ROYAL SOCIETY OF LONDON, SERIES B, VOL. 205, NO. 1161 (1979), PP. 581-598.
An adaptationist programme has dominated evolutionary thought in england and the united states during the past forty years. It is based on faith in the power of natural selection as an optimizing agent. It proceeds by breaking an organism into unitary 'traits' and proposing an adaptive story for each considered separately. Trade-offs among competing selective demands exert the only brake upon perfection; nonoptimality is thereby rendered as a result of adaptation as well. We criticize this approach and attempt to reassert a competing notion (long popular in continental europe) that organisms must be analyzed as integrated wholes, with baupl�ne so constrained by phyletic heritage, pathways of development, and general architecture that the constraints themselves become more interesting and more important in delimiting pathways of change than the selective force that may mediate change when it occurs. We fault the adaptationist programme for its failure to distinguish current utility from reasons for origin (male tyrannosaurs may have used their diminutive front legs to titillate female partners, but this will not explain why they got so small); for its unwillingness to consider alternatives to adaptive stories; for its reliance upon plausibility alone as a criterion for accepting speculative tales; and for its failure to consider adequately such competing themes as random fixation of alleles, production of nonadaptive structures by developmental correlation with selected features (allometry, pleiotropy, material compensation, mechanically forced correlation), the separability of adaptation and selection, multiple adaptive peaks, and current utility as an epiphenomenon of nonadaptive structures. We support darwin's own pluralistic approach to identifying the agents of evolutionary change."
Tuesday, February 07, 2006
The innovation triad: an EvoDevo agenda (Journal of Experimental Zoology)
This article introduces a special issue on evolutionary innovation and morphological novelty, two interrelated themes that have received a remarkable increase of attention over the past few years. We begin with a discussion of the question of whether innovation and novelty represent distinct evolutionary problems that require a distinct conceptualization. We argue that the mechanisms of innovation and their phenotypic results - novelty - can only be properly addressed if they are distinguished from the standard evolutionary themes of variation and adaptation, and we present arguments for making such a distinction. We propose that origination, the first formation of biological structures, is another distinct problem of morphological evolution, and that together with innovation and novelty it constitutes a conceptual complex we call the innovation triad. We define a problem agenda of the triad, which separates the analysis of the initiating conditions from the mechanistic realization of innovation, and we discuss the theoretical problems that arise from treating innovation as distinct from variation. Further, we categorize the empirical approaches that address themes of the innovation triad in recognizing four major strands of research: the morphology and systematics program, the gene regulation program, the epigenetic program, and the theoretical biology program. We provide examples of each program, giving priority to contributions in the present issue. In conclusion, we observe that the innovation triad is one of the defining topics of EvoDevo research and may represent its most pertinent contribution to evolutionary theory. We point out that an inclusion of developmental systems properties into evolutionary theory represents a shift of explanatory emphasis from the external factors of natural selection to the internal dynamics of developmental systems, complementing adaptation with emergence, and contingency with inherency
Full text at:
--Model of an Internal Evolutionary Mechanism
Monday, February 06, 2006
New theory could have implications for cancer research (PR + Article)
1) Molecular Evolution (News Item) The findings, reported in the June 24, 2003, issue of the Proceedings of the National Academy of Sciences USA (PNAS), undercut the widely held view among scientists that evolutionary breakpoints - disruptions in the order of genes on chromosomes - are purely random. Apart from its implications for evolutionary theory, the study could have major implications for medical research related to diseases such as leukemia, which are caused by clinical (rather than evolutionary) chromosomal breakpoints.
Researchers from the University of California, San Diego (UCSD) Jacobs School of Engineering have uncovered evidence that major evolutionary changes are more likely too ccur in approximately 400 'fragile' genomic regions that account for only 5% of the human genome.
2) Human and mouse genomic sequences reveal extensive breakpoint reuse in mammalian evolution
[Pevzner & Tesler, PNAS, June '03]
The human and mouse genomic sequences provide evidence for a larger number of rearrangements than previously thought and reveal extensive reuse of breakpoints from the same short fragile regions. Breakpoint clustering in regions implicated in cancer and infertility have been reported in previous studies; we report here on breakpoint clustering in chromosome evolution. This clustering reveals limitations of the widely accepted random breakage theory that has remained unchallenged since the mid-1980s. The genome rearrangement analysis of the human and mouse genomes implies the existence of a large number of very short "hidden" synteny blocks that were invisible in the comparative mapping data and ignored in the random breakage model. These blocks are defined by closely located breakpoints and are often hard to detect. Our results suggest a model of chromosome evolution that postulates that mammalian genomes are mosaics of fragile regions with high propensityfor rearrangements and solid regions with low propensity forrearrangements.
Full text at:
Model of an Internal Evolutionary Mechanism
The findings, reported in the June 24, 2003, issue of the Proceedings of the National Academy of Sciences USA (PNAS), undercut the widely held view among scientists that evolutionary breakpoints - disruptions in the order of genes on chromosomes - are purely random. Apart from its implications for evolutionary theory, the study could have major implications for medical research related to diseases such as leukemia, which are caused by clinical (rather than evolutionary) chromosomal breakpoints.Full text at:
Biological Networks: The Tinkerer as an Engineer (Science)
This viewpoint comments on recent advances in understanding the design principles of biological networks. It highlights the surprising discovery of "good-engineering" principles in biochemical circuitry that evolved by random tinkering.
Full text at:
Model of an Internal Evolutionary Mechanism
Sunday, February 05, 2006
The above link will take you to my main website where you'll find articles on Psychology, Social Psychology, various evolutionary topics, archives (such as Lamark's "Zoological Philosophy") and sundry other stuff.
If you want to go directly to the "Model of an Internal Evolutionary Mechanism (based on an extension to homeostasis) linking Adaptive Mutations to the Baldwin Effect" page then click here.
The model is derived from 'anomalies' found below the level at which psychological trauma occurs: this is different to the popular conception of trauma - see Trauma: A Simple Internal Model
It has been several years since the pages were published on the web and it wasn't until about 6 weeks ago that I suddenly found I now have time to take up the reins again! At the moment, I'm busily researching a rewrite of the proposal (although the core concept will obviously be unchanged) and I thought that creating a blog would make the process more enjoyable - providing anyone reads it of course... :)
In addition to occasional personal posts this blog also contains auto-added entries (all with 'evomech' in the title) from the Evolution: Where Darwin meets Lamarck? discussion forum.
Don't be deterred if the papers from the forum look too technical (a lot of them make my eyes boggle), there's plenty of other stuff in the message archives - just pick and choose the bits you like!
Researching the possibility of an internal mechanism - particularly when its non-intellect based and therefore testable - necessarily raises the question "If an internal mechanism exists, then why hasn't it been found before?".
The subjective answer is because of 'cultural conditioning'. Consequently, the posts I make to evomech are a combination of topics containing the 'homeostatic signature' that I'm looking for and those in which the exploration of natural realities appears to be in conflict with cultural conditioning - to illustrate the basic problem see An Error In Associating Lamarck With 'Adaptive Mutations'?
Any feedback would be welcome, you can add a blog comment to this post, visit the main web site's Guestbook, or email direct
I'm out of time for now but one final (deletes "plea for help") point: As an independent researcher my resources are very limited and I often have difficulty in obtaining papers (for example, see Wanted: 'Obscure' 1889 Paper on Trilobite Eyes & The Fibonacci Series) - if you can help then please do!
The control of body size in insects (Dev Biol)
Control mechanisms that regulate body size and tissue size have beensought at both the cellular and organismal level. Cell-level studieshave revealed much about the control of cell growth and cell division,and how these processes are regulated by nutrition. Insulin signalingis the key mediator between nutrition and the growth of internalorgans, such as imaginal disks, and is required for the normalproportional growth of the body and its various parts. Theinsulin-related peptides of insects do not appear to control growth bythemselves, but act in conjunction with other hormones and signalingmolecules, such as ecdysone and IDGFs. Size regulation cannot beunderstood solely on the basis of the mechanisms that control cell sizeand cell number. Size regulation requires mechanisms that gatherinformation on a scale appropriate to the tissue or organ beingregulated. A new model mechanism, using autocrine signaling, isoutlined by which tissue and organ size regulation can be achieved.Body size regulation likewise requires a mechanism that integratesinformation at an appropriate scale. In insects, this mechanismoperates by controlling the secretion of ecdysone, which is the signalthat terminates the growth phase of development. The mechanisms forsize assessment and the pathways by which they trigger ecdysonesecretion are diverse and can be complex. The ways in which thesehigher-level regulatory mechanisms interact with cell- and molecular-level mechanisms are beginning to be elucidated.
Full text at:
For Nijhout's latest paper (Jan '06) - see:
and a '98 paper:
Model of an Internal Evolutionary Mechanism