Big history: the role of universal Darwinism, collective learning, & the rise of complexity in the longue durée

This thesis demonstrates how the annaliste school's search for broad trends over a few centuries can be connected to Big History's search for broad trends over 13.8 billion years. The rise of complexity through Universal Darwinism is linked to the annaliste idea of population cycles by the idea of 'collective learning' - which is itself part of the Darwinian process of cultural evolution. On this basis, the macro and micro trends of history are connected. At one end, annaliste population cycles influenced the events of conventional history 5000 to 250 years ago by profoundly influencing the rise and decline of living standards, population numbers, elite incomes, and sociopolitical instability. The Big History concept of collective learning explains both why those population cycles occurred in agrarian civilisations and why there was a transition to the Industrial Revolution, since accumulation of knowledge raised the carrying capacity of the human population, and thus the number of potential innovators. I also examine periods when severe population decline caused accumulated knowledge and the carrying capacity to decline. The carrying capacity has a profound influence on all stages of human history. This work extends the chronology of human history back to 200,000 years of hunter-gatherers and 2 million years of hominine evolution, in which collective learning also played a role in population growth. Collective learning is itself a form of 'cultural evolution', which is in turn a manifestation of the 'Darwinian algorithm'. The latter is a process of random variation and non-random selection that raises the free energy rate density or complexity of certain areas of the Universe: from culture, to biology, to chemicals and minerals, to stellar elements, and the theoretical formation of multiple universes. A portion of this thesis is given over to the role of the Darwinian algorithm in these processes and also to showing how the grand narrative of Big History and even the events of human history are part of the broadest trend of 'rising complexity' in the Universe

Community Police Peacekeeping Amidst Bitter and Divisive Industrial Confrontation: The 1992 APPM Dispute at Burnie

The 1992 Associated Pulp and Paper Mill (APPM) dispute offers a microcosm of 1990s industrial conflict, with large companies attempting to re-establish managerial prerogative through litigation and unions seeing the fight as one of survival.' Also, the APPM dispute presents a microcosm of police-community relations during the processes and procedures of a harsh industrial conflict. It is argued that local and regional factors are vital to the relationship between police and union protesters which in tum can affect the processes and outcomes of an industrial dispute, even one with major state and federal implications. The article is not an analysis of the causes of the APPM dispute but an exploration of the police relationship with the community of striking workers and, as a corollary, with the company. The focus of this paper, the community policing of the 1992 APPM dispute at Burnie, was atypical of the traditional, aggressive and confrontational policing of major industrial disputation in Australian history. Some significant events of this complex dispute have been selected to analyse both police strategy and police-community rapport

JIM JARMUSCH’S MYSTERY TRAIN (1989):

JIM JARMUSCH’S MYSTERY TRAIN (1989)

De Novo Determination of Protein Backbone Structure from Residual Dipolar Couplings Using Rosetta

As genome-sequencing projects rapidly increase the database of protein sequences, the gap between known sequences and known structures continues to grow exponentially, increasing the demand to accelerate structure determination methods. Residual dipolar couplings (RDCs) are an attractive source of experimental restraints for NMR structure determination, particularly rapid, high-throughput methods, because they yield both local and long-range orientational information and can be easily measured and assigned once the backbone resonances of a protein have been assigned. While very extensive RDC data sets have been used to determine the structure of ubiquitin, it is unclear to what extent such methods will generalize to larger proteins with less complete data sets. Here we incorporate experimental RDC restraints into Rosetta, an ab initio structure prediction method, and demonstrate that the combined algorithm provides a general method for de novo determination of a variety of protein folds from RDC data. Backbone structures for multiple proteins up to ∼125 residues in length and spanning a range of topological complexities are rapidly and reproducibly generated using data sets that are insufficient in isolation to uniquely determine the protein fold de novo, although ambiguities and errors are observed for proteins with symmetry about an axis of the alignment tensor. The models generated are not high-resolution structures completely defined by experimental data but are sufficiently accurate to accelerate traditional high-resolution NMR structure determination and provide structure-based functional insights

Folding Dynamics of the src SH3 Domain^†

The thermodynamics and kinetics of folding of the chicken src SH3 domain were characterized using equilibrium and stopped-flow fluorescence, circular dichroism (CD), and nuclear magnetic resonance (NMR) hydrogen exchange experiments. As found for other SH3 domains, guanidinium chloride (GdmCl) denaturation melts followed by both fluorescence and circular dichroism were nearly superimposable, indicating the concerted formation of secondary and tertiary structure. Kinetic studies confirmed the two-state character of the folding reaction. Except for a very slow refolding phase due to proline isomerization, both folding and unfolding traces fit well to single exponentials over a wide range of GdmCl concentrations, and no burst phase in amplitude was observed during the dead time of the stopped-flow instrument. The entropy, enthalpy, and heat capacity changes upon unfolding were determined by global fitting of temperature melts at varying GdmCl concentrations (0.4−3.7 M). Estimates of the free energy of unfolding, ΔGUH2O, from guanidine denaturation, thermal denaturation, and kinetic experiments were in good agreement. To complement these data on the global characteristics of src SH3 folding, individual hydrogen−deuterium (HD) exchange rates were measured for approximately half of the backbone amides in 0 and 0.7 M GdmCl. The calculated free energies of the opening reaction leading to exchange (ΔGHD) indicated that unfolding is highly cooperativeslowly exchanging protons were distributed throughout the core of the protein. The slowly exchanging protons exhibited ΔGHD values higher than the global ΔGUH2O by ∼1 kcal/mol, suggesting that the denatured state might be somewhat compact under native conditions. Comparison of the src SH3 with homologous SH3 domains as well as with other small well-characterized β-sheet proteins provides insights into the determinants of folding kinetics and protein stability

E. coli paired alignments

Multiple sequence alignments used in E. coli gene pair analysis. Each fasta file begins with the E. coli amino acid sequence pair, with other homologous sequences trimmed to match its length. For an interactive list, please visit: http://gremlin.bakerlab.org/cplx.php?mode=ecol

PDB file for PFL Complex

Predicted complex of Pyruvate formate lyase-activating enzyme. Pyruvate formate-lyase (PFL) catalyzes the reaction of acetyl-CoA and formate from pyruvate and CoA in the Fermentation pathway. The PDB file was sampled using the E. coli sequences of PFLA_ECOLI and PFLB_ECOLI

PDB file for TRAP complex

The predicted complex of the tripartite ATP-independent periplasmic (TRAP) transporter. It is composed of three proteins: two integral membrane proteins YIAM and YIAN, and one periplasmic protein YIAO. The PDB file was sampled using UniProt E. coli sequences of YIAM_ECOLI, YIAN_ECOLI and YIAO_ECOLI