The view that there are macro-properties that do not supervene on micro-features studied by physics is sometimes labelled emergentism. The suggestions is that, where there is no supervenience, macro-properties must miraculously come out of nowhere. But why? There is nothing of the newly landed about these properties. They have been here in the world all along, standing right beside the properties of microphysics. Perhaps we are misled by the feeling that the set of properties studied by physics is complete….The immediate point is that predictive closure among a set of properties does not imply descriptive completeness.
— Nancy CartwrightThe Dappled World

Independence Day 2010

by Tim Gwinn ~ July 4th, 2010

The Declaration of Independence






IN CONGRESS, July 4, 1776.

The unanimous Declaration of the thirteen united States of America,

When in the Course of human events, it becomes necessary for one people to dissolve the political bands which have connected them with another, and to assume among the powers of the earth, the separate and equal station to which the Laws of Nature and of Nature’s God entitle them, a decent respect to the opinions of mankind requires that they should declare the causes which impel them to the separation.

We hold these truths to be self-evident, that all men are created equal, that they are endowed by their Creator with certain unalienable Rights, that among these are Life, Liberty and the pursuit of Happiness.–That to secure these rights, Governments are instituted among Men, deriving their just powers from the consent of the governed, –That whenever any Form of Government becomes destructive of these ends, it is the Right of the People to alter or to abolish it, and to institute new Government, laying its foundation on such principles and organizing its powers in such form, as to them shall seem most likely to effect their Safety and Happiness. Prudence, indeed, will dictate that Governments long established should not be changed for light and transient causes; and accordingly all experience hath shewn, that mankind are more disposed to suffer, while evils are sufferable, than to right themselves by abolishing the forms to which they are accustomed. But when a long train of abuses and usurpations, pursuing invariably the same Object evinces a design to reduce them under absolute Despotism, it is their right, it is their duty, to throw off such Government, and to provide new Guards for their future security.–Such has been the patient sufferance of these Colonies; and such is now the necessity which constrains them to alter their former Systems of Government. The history of the present King of Great Britain is a history of repeated injuries and usurpations, all having in direct object the establishment of an absolute Tyranny over these States. To prove this, let Facts be submitted to a candid world.

He has refused his Assent to Laws, the most wholesome and necessary for the public good.
He has forbidden his Governors to pass Laws of immediate and pressing importance, unless suspended in their operation till his Assent should be obtained; and when so suspended, he has utterly neglected to attend to them.
He has refused to pass other Laws for the accommodation of large districts of people, unless those people would relinquish the right of Representation in the Legislature, a right inestimable to them and formidable to tyrants only.
He has called together legislative bodies at places unusual, uncomfortable, and distant from the depository of their public Records, for the sole purpose of fatiguing them into compliance with his measures.
He has dissolved Representative Houses repeatedly, for opposing with manly firmness his invasions on the rights of the people.
He has refused for a long time, after such dissolutions, to cause others to be elected; whereby the Legislative powers, incapable of Annihilation, have returned to the People at large for their exercise; the State remaining in the mean time exposed to all the dangers of invasion from without, and convulsions within.
He has endeavoured to prevent the population of these States; for that purpose obstructing the Laws for Naturalization of Foreigners; refusing to pass others to encourage their migrations hither, and raising the conditions of new Appropriations of Lands.
He has obstructed the Administration of Justice, by refusing his Assent to Laws for establishing Judiciary powers.
He has made Judges dependent on his Will alone, for the tenure of their offices, and the amount and payment of their salaries.
He has erected a multitude of New Offices, and sent hither swarms of Officers to harrass our people, and eat out their substance.
He has kept among us, in times of peace, Standing Armies without the Consent of our legislatures.
He has affected to render the Military independent of and superior to the Civil power.
He has combined with others to subject us to a jurisdiction foreign to our constitution, and unacknowledged by our laws; giving his Assent to their Acts of pretended Legislation:
For Quartering large bodies of armed troops among us:
For protecting them, by a mock Trial, from punishment for any Murders which they should commit on the Inhabitants of these States:
For cutting off our Trade with all parts of the world:
For imposing Taxes on us without our Consent:
For depriving us in many cases, of the benefits of Trial by Jury:
For transporting us beyond Seas to be tried for pretended offences
For abolishing the free System of English Laws in a neighbouring Province, establishing therein an Arbitrary government, and enlarging its Boundaries so as to render it at once an example and fit instrument for introducing the same absolute rule into these Colonies:
For taking away our Charters, abolishing our most valuable Laws, and altering fundamentally the Forms of our Governments:
For suspending our own Legislatures, and declaring themselves invested with power to legislate for us in all cases whatsoever.
He has abdicated Government here, by declaring us out of his Protection and waging War against us.
He has plundered our seas, ravaged our Coasts, burnt our towns, and destroyed the lives of our people.
He is at this time transporting large Armies of foreign Mercenaries to compleat the works of death, desolation and tyranny, already begun with circumstances of Cruelty & perfidy scarcely paralleled in the most barbarous ages, and totally unworthy the Head of a civilized nation.
He has constrained our fellow Citizens taken Captive on the high Seas to bear Arms against their Country, to become the executioners of their friends and Brethren, or to fall themselves by their Hands.
He has excited domestic insurrections amongst us, and has endeavoured to bring on the inhabitants of our frontiers, the merciless Indian Savages, whose known rule of warfare, is an undistinguished destruction of all ages, sexes and conditions.

In every stage of these Oppressions We have Petitioned for Redress in the most humble terms: Our repeated Petitions have been answered only by repeated injury. A Prince whose character is thus marked by every act which may define a Tyrant, is unfit to be the ruler of a free people.

Nor have We been wanting in attentions to our Brittish brethren. We have warned them from time to time of attempts by their legislature to extend an unwarrantable jurisdiction over us. We have reminded them of the circumstances of our emigration and settlement here. We have appealed to their native justice and magnanimity, and we have conjured them by the ties of our common kindred to disavow these usurpations, which, would inevitably interrupt our connections and correspondence. They too have been deaf to the voice of justice and of consanguinity. We must, therefore, acquiesce in the necessity, which denounces our Separation, and hold them, as we hold the rest of mankind, Enemies in War, in Peace Friends.

We, therefore, the Representatives of the united States of America, in General Congress, Assembled, appealing to the Supreme Judge of the world for the rectitude of our intentions, do, in the Name, and by Authority of the good People of these Colonies, solemnly publish and declare, That these United Colonies are, and of Right ought to be Free and Independent States; that they are Absolved from all Allegiance to the British Crown, and that all political connection between them and the State of Great Britain, is and ought to be totally dissolved; and that as Free and Independent States, they have full Power to levy War, conclude Peace, contract Alliances, establish Commerce, and to do all other Acts and Things which Independent States may of right do. And for the support of this Declaration, with a firm reliance on the protection of divine Providence, we mutually pledge to each other our Lives, our Fortunes and our sacred Honor.

Anticipatory Systems-themed special issue of foresight journal

by Tim Gwinn ~ June 13th, 2010

The journal foresight, an international bi-monthly journal concerned with the study of the future, has published a special issue [1] on Rosennean anticipatory systems. This issue is the result of a 2008 FuMee (”Future Meetings”): Understanding Anticipatory Systems [2].

 

References:

[1] Miller, R. (ed.), Poli, R. (ed.). 2010. Special Issue: Anticipatory systems and the philosophical foundations of futures studies. foresight 12(3).

[2] http://fumee.co.cc/?page_id=7

Louie comments on Venter

by Tim Gwinn ~ June 13th, 2010

Aloisius Louie, author of More Than Life Itself [1], was one of a number of scientists asked to write an article [2] for the Journal of Cosmology commenting on Venter’s recent success in bioengineering [3]. Louie puts the Venter success into proper context:

The important and consequential Venter achievement is an impressive one in technology, but no synthetic life, alas, has been made. An achievement is diminished if it is accompanied by overreaching claims of success, when such hyperbolic ‘accomplishment’ is illusory, and not entailed from what has actually been done.

 

References

[1] Louie, A. 2009. More Than Life itself: A Synthetic Continuation in Relational Biology. Ontos-Verlag.

[2] Louie, A. 2010. “Artificial Claims About Synthetic Life: The View from Relational Biology”. Jrnl of Cosmology. Vol 8. Article 19. 

[3] Gibson et al. 2010. “Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome”. Science. DOI: 10.1126/science.1190719

Remarkable: Chitosan could repair spinal damage

by Tim Gwinn ~ April 18th, 2010

From the Journal of Experimental Biology (via EurekAlert!), a very encouraging story entitled “CHITOSAN REPAIRS DAMAGED SPINAL CORD” [1]. The story references a paper published by JEB in January, entitled “Chitosan produces potent neuroprotection and physiological recovery following traumatic spinal cord injury” [2]. The abstract of the paper:

Chitosan, a non-toxic biodegradable polycationic polymer with low immunogenicity, has been extensively investigated in various biomedical applications. In this work, chitosan has been demonstrated to seal compromised nerve cell membranes thus serving as a potent neuroprotector following acute spinal cord trauma. Topical application of chitosan after complete transection or compression of the guinea pig spinal cord facilitated sealing of neuronal membranes in ex vivo tests, and restored the conduction of nerve impulses through the length of spinal cords in vivo, using somatosensory evoked potential recordings. Moreover, chitosan preferentially targeted damaged tissues, served as a suppressor of reactive oxygen species (free radical) generation, and the resultant lipid peroxidation of membranes, as shown in ex vivo spinal cord samples. These findings suggest a novel medical approach to reduce the catastrophic loss of behavior after acute spinal cord and brain injury.

 

References

[1] Knight, K. 2010. “CHITOSAN REPAIRS DAMAGED SPINAL CORD“. J. of Exp. Biol. 213:i-a. DOI:10.1242/jeb.045039.

[2] Cho, Y., Shi, R., Borgens, R. “Chitosan produces potent neuroprotection and physiological recovery following traumatic spinal cord injury“. J. of Exp. Biol. 213:1513-1520. DOI:10.1242/jeb.035162

Paper: "Closure to efficient causation, computability and artificial life"

by Tim Gwinn ~ March 21st, 2010

I missed the publication of this last month. The abstract [1]:

The major insight in Robert Rosen’s view of a living organism as an (M,R)-system was the realization that an organism must be “closed to efficient causation”, which means that the catalysts needed for its operation must be generated internally. This aspect is not controversial, but there has been confusion and misunderstanding about the logic Rosen used to achieve this closure. In addition, his corollary that an organism is not a mechanism and cannot have simulable models has led to much argument, most of it mathematical in nature and difficult to appreciate. Here we examine some of the mathematical arguments and clarify the conditions for closure.

This is a wide-ranging paper which seeks to illuminate and clarify “closed to efficient causation” and its consequences. In the relatively short space of 14 pages, the authors manage not only to delve into some of the mathematical aspects of “closed to efficient causation”, but also counter the arguments of a number of previous critics who had erroneously claimed that “closed to efficient causation” models are simulable.

 

References

[1] Cárdenas,M.L., Letelier,J.-C., Gutierrez,C., Cornish-Bowden,A., Soto-Andrade,J. 2010. “Closure to efficient causation, computability and artificial life”. J. of Theoretical Biology. 263(1):79-92. DOI:10.1016/j.jtbi.2009.11.010.

Systems Biology, Holism and Reductionism

by Tim Gwinn ~ March 13th, 2010

A new paper, “So what do we really mean when we say that systems biology is holistic?” [1] discusses the relationship between holism, reductionism and systems biology.

Although the author does provide a historical overview of various interpretations of ‘holism’ and ‘reductionism’, the end result remains: a lack of clarity, specificity and agreement over the meaning of these terms. In addition, the term ’systems biology’ is arguably equally nebulous.

For my part, there is perhaps nothing more useless in science than arguing between two putatively contrary ill-defined concepts (holism and reductionism), especially if the argument is in relation to how those concepts apply to a third ill-defined concept (systems biology).

Even the author states:

We may not know exactly what modern holism in systems biology is – although we can perhaps generalise that it is usually explanatory ontological antireductionism with some tendencies to epistemological antireductionism - but we do know that it is against reductionism. That might be the end of the discussion, were it not for the fact that it is not entirely clear if we know what reductionism is either.

Rosen’s work arises during the discussion, but the author appears to misstate Rosen’s view:

Although neo-reductionism has had a low profile among systems biologists and biologists in general, a new kind of holism, Relational Biology, has attracted attention, mostly among those who are dissatisfied with traditional molecular biology but also sceptical about the explanatory capabilities of modern versions of holism. Developed over some years by Robert Rosen and a small band of disciples, relational biology does not dispense with the hierarchy of the Vienna Circle, but rather inverts it. Rosen, based on some earlier similar ideas by Elsasser, claimed that physics, by virtue of its application to homogeneous molecular structure is in fact not the fundamental science, but actually a special case. Biology, as the science of the complex, is the lowest level in the layer model.

The notion of a hierarchy (and its inversion) is unhelpful with respect to understanding Rosen’s view, nor did Rosen argue that biology was more fundamental than physics. Also, “Biology, as the science of the complex” can be a somewhat confusing phrasing.

Rosen realized and proved [2] (and Louie proved in even more detail [3]) that if all the models of a given system are simulable (i.e. Turing-computable) then the analytic models of the system coincide with the synthetic models of the system. That is, all the information one can have about such systems can be found in its synthetic models alone. Moreover, the entire collection of these synthetic models can be combined into one model, which is called the largest model of the system. As an immediate result of this coinciding, the properties of such systems are entirely fractionable and can thus possess no “emergent” properties. Rosen defined this class of systems to be the class of mechanisms or simple systems.

By contrast, the class of complex systems are those systems which possess at least one nonsimulable model and, as a consequence, possess at least one analytic model which does not coincide with a synthetic model. That is, there is at least one model (i.e., analytic model) of the system which describes properties of the system for which there is no corresponding model of an assemblage of parts of the system (i.e., synthetic model). In simpler terms, in such a case the system possesses properties which cannot be described by an assemblage of the properties of its parts.

This means of classification allows for a precise definition of ‘emergent property’, if one so desires.

It is important to point out, as Rosen did repeatedly, that complex systems can still possess many analytic models which coincide with synthetic models: “The failure of a system to be a mechanism does not at all mean that has no mechanical models; indeed, in some sense, these form a subcategory of the category of all its models.” If this were not the case, then all the obvious successes of reductionistic-oriented science to date would not have been possible. Thus one must be careful when stating that biology is “the science of the complex”.

As a corollary: the existence of an abundance of simple models in a system cannot, by itself, logically entail that simple models alone are exhaustive of all models of the system

The class of organisms, Rosen argued persuasively, form a subset of the class of complex systems; however, organisms are not the entire class of complex systems.

Rosen also proved that the very structure of the Newtonian paradigm (and its quantum mechanical variant) is such that it inherently treats physical systems as simple systems: that is all that this paradigm can encode (or “see”) about any system, simple or complex.

 

To put all this together, in the Rosennean picture:

  • The class of all natural systems can be bifurcated into two non-intersecting subsets: simple systems and complex systems.
  • The class of organisms are a subset of the class of complex systems.
  • Modern physics is founded on a paradigm which can treat systems only as simple systems.
  • Therefore, physics needs to alter/enlarge its paradigm if it is to more fully model  complex systems, such as organisms.
  • Necessarily, some of those models will be nonsimulable.
  • Likewise, systems biology will need alter/enlarge its paradigm to embrace nonsimulable models.

 

So, there is no “hierarchy” in the Rosennean view, nor is biology in any sense more fundamental than physics. Instead, the complex system nature of biological organisms is symptomatic of the need for more encompassing approaches in both biology and physics. As Rosen said, “Perhaps the first lesson to be learned from biology is that there are lessons to be learned from biology.” [4]

 

References

[1] Gatherer, D. 2010. “So what do we really mean when we say that systems biology is holistic?”. BMC Systems Biology. 4(22).DOI:10.1186/1752-0509-4-22

[2] Rosen, R. 1991. Life Itself: A Comprehensive Inquiry Into The Nature, Origin, and Fabrication of Life. Columbia Univ. Press

[3] Louie, A. 2009. More Than Life itself: A Synthetic Continuation in Relational Biology. Ontos-Verlag.

[4] Rosen, R. 2000. Essays on Life Itself. Columbia Univ. Press.