Consilient mechanisms biological

The consilient mechanisms in relation to protein-based machines of biology are introduced. Before the four major assertions that... 

A protein-based machine without water as an integral part of its structure could not function by the consilient mechanism. In other words, water is required in at least one of the two states in order to have a movable cusp of insolubility, and in order for competition for hydration to be relevant there must be adequate water present. The first prerequisite, therefore, in addressing the biological relevance of the consilient mechanism is to assess whether or not water exists within or between the changing structural elements of a protein motor during function. 

Immediately below, we note the historical case of oxygen transport by hemoglobin from lungs to the tissues and note how this would be discussed in terms of the consilient mechanism. This was the first biological system appreciated for its positive cooperativity, the cooperative binding of oxygen molecules that is key to successful transport. 

In this chapter we briefly note the improbability of a protein comprised of 20 different amino acids in specified sequence. Then we step through the details whereby a protein of specified sequence comes into being, and, like the accountant, sum up the cost in terms of the biological energy currency, adenosine triphosphate (ATP), that is, in terms of the number of ATP molecules consumed in the production of a protein of unique sequence. Such an essentially ordinary exercise requires inclusion in this book in order to remove unnecessary mystery of protein production, to provide an example whereby molecular machines utilize energy to produce biological structure, and to place in perspective the ease with which new protein-based machines evolve when functioning by the consilient mechanism. 

A Consilient Mechanism Provides a Common Groundwork of Explanation for the Diverse Energy Conversions of Biology... 

To the best of my knowledge, the hemoglobin oxygenation curve is historically the first example of a biologically essential positive cooperativity. Because of this, it becomes an important objective to explore the phenomenology of hemoglobin s positive cooperativity and compare it with that of the consilient mechanism due to an apolar-polar repulsive free energy of hydration (as is done in Chapter 7) and, in fact, to do so for a number of protein-based machines that exhibit positive cooperativity. 

For the universe as a whole, time s arrow points to increasing disorder and uniformity, yet for biology time s arrow points to increasing diversity and complexity of structure and function. We will see how this can be for the structural evolution of the molecular machines of Life. Then we examine how the molecular machines, themselves functioning by the consilient mechanism, facilitate the creation of order. 

More to the point, we now see biology s access to energy by means of the consilient mechanism of energy conversion, combined with readily available mutations to improve protein-based machines, as the source of increased structural order and functional diversity. 

The consilient mechanism was bom out of controlling the hydrophobic association-dissociation of elastic-contractile model proteins to achieve the possibility of some 18 classes of pairwise energy conversions (see Chapter 5, section 5.6). In the process a set of five Axioms became the phenomenology out of which the consilient mechanism arose. For the first time a common groundwork of explanation was able to perform the diverse energy conversions of biology. 

Applying what is now the consilient mechanism for hydrophobic association to the elastic fiber, the prediction became that oxidation of the elastic fiber by a natural enzyme with the biological role of producing superoxide and hydrogen peroxide would cause hydrophobic dissociation evidenced by a swelling and a loss of elastic recoil. A xanthine oxidase superoxide... 

Consilient Mechanisms for Protein-based Machines of Biology... 

A more complete technical description of the consilient mechanisms of concern to biological energy conversion encompasses two distinct but interlinked physical processes of hydrophobic association and of elastic force development. The latter results from a generally applicable... 

On the Relevance of Hydrophobic and Elastic Consilient Mechanisms to Biology s Protein-based Machines... 

This chapter discusses key protein-based machines of biology to demonstrate the relevance of the hydrophobic and elastic consilient mechanisms. The objective in this chapter, therefore, is to investigate selected examples of biology s protein-based machines and to look at the molecular level for a coherence of phenomena with the designed elastic model... 

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