Who Am I Supposed To Believe? A Recognized Scientist At A Major Research University In The Field For Four Decades Or Simps?

Forty years' experience as a bacterial geneticist has taught me that bacteria possess many cognitive, computational and evolutionary capabilities unimaginable in the first six decades of the twentieth century. Analysis of cellular processes such as metabolism, regulation of protein synthesis, and DNA repair established that bacteria continually monitor their external and internal environments and compute functional outputs based on information provided by their sensory apparatus. Studies of genetic recombination, lysogeny, antibiotic resistance and my own work on transposable elements revealed multiple widespread bacterial systems for mobilizing and engineering DNA molecules. Examination of colony development and organization led me to appreciate how extensive multicellular collaboration is among the majority of bacterial species. Contemporary research in many laboratories on cell-cell signaling, symbiosis and pathogenesis show that bacteria utilise sophisticated mechanisms for intercellular communication and even have the ability to commandeer the basic cell biology of 'higher' plants and animals to meet their own needs. This remarkable series of observations requires us to revise basic ideas about biological information processing and recognise that even the smallest cells are sentient beings.
  
Especially when his paper supports his contention in way the old mechanistic biologists can't respond to.
  

1. Introduction

The philosophy of microbiology is not well defined, at least for practicing microbiologists like me. If we think about it, I suppose most microbiologists see microorganisms as constituting a special branch of living organisms. Some, like myself, appreciate microbial virtuosity and emphasize the essential role microorganisms play in maintaining the biosphere and carrying out the bulk of energetic and microchemical transformations on the planet (Lovelock & Margulis, 1974; Lento & van Oijen, 2002). Others follow conventional wisdom and think of microbes as ‘lower’ forms of life, simpler and less capable the eukaryotes because of their smaller size and apparent lack of internal celluar structure. The conventional wisdom is an extension of the mechanistic views that came to dominate biological thought in the early years of the twentieth century. The idea is that microbes, particularly prokaryotes, exemplify the basic properties of living cells reduced to their simplest configurations. The goal of researchers who subscribe to this view is to find or construct the minimal living organism (Luisi et al; 2006).

Molecular biology came into being on the promise of confirming mechanistic views of life by defining how living cells worked at a physico-chemical level (Judson, 1979). Ironically, molecular biology has uncovered a vast realm of complex intracellular machinery, signal transduction, regulatory networks and sophisticated control processes that were unanticipated in the early days of this new approach to life (Alberts et al.; 2002). Increasingly, computational rather than mechanical models are invoked to account for the operation of subcellular systems, the cell cycle, cellular differentiation, and the development of multicellular organisms (Bray, 1990, 1995; Gearhart & Kirschner, 1997). 

James Shapiro, goes on to contend that:

 

 

. . . we are witnessing a major paradigm shift in the life sciences in the sense that Kuhn (1962) described that process. Matter, the focus of classical molecular biology, is giving way to information as the essential feature used to understand how living systems work. Informatics rather than mechanics is now the key to explaining cell biology and cell activities. The traditional mechanistic view held that the structure of biological molecules determines the actions of cells in some kind of linear fashion. But today we know that biological molecules change their structures as they interact with other molecules and that these internal structural changes contain information about the external environment and conditions within the cell. As illustrated below, we have abundant results showing that what a cell does is a function of the information it has about itself and its surroundings (i.e. about past molecular interactions). Much contemporary research aims to understand how cellular processes are controlled adaptively to guarantee survival and reproduction in response to the millions of molecular events that occur in each cell cycle. This informatic approach is richer than a mechanistic one because it allows us to discuss complex, non-linear, goal-oriented processes with all kinds of feedbacks and decision points (See O’Malley & Dubpre, this section, for further discussion about the inadequacy of mechanistic thinking).

Which certainly is why his colleague and old-fashioned materialist ideologue, Jerry Coyne, has raged and raged against James Shapiro without really addressing what he says - he KNOWS, GODDAMNIT that this can't be true because of his faith in what I referred to the other day as that hold-over of late 19th century materialism into modernism.  Only, in physics, in biology, etc. that materialism can't explain what scientists have observed when they looked hard and deep into their fields, even starting out with, as Shapiro notes, "the promise of confirming mechanistic views of life."

Every dominant ideological framing of the past has fallen due to the internal skeleton it was based on proving inadequate and failing.  In the social-science, that has happened so regularly in just the 20th century, that people don't notice that the stinking, dead carcasses pile up a lot higher than the current occupant of the field.  The same is true, in a slower rate of attrition, in real biology.   If Shapiro is right, and he makes a very good case in his paper that he is,  this is big news.  Only, as Planck said, progress for biology, in general, will probably depend on the devotees of old-fashioned mechanistic biology to die off, too.  It will take stupid people with college-credentials who haven't looked at anything to do with current science since the 1960s longer to die off, the popular (mis)understanding of science is thoroughly stuck in the 19th century because it was so easy to describe with physical models.  Which scientists who should have known better encourage because they love that paradigm as well.  

Of course, what they really get stuck on was mentioned in passing by Shapiro, something I'm not sure even he understands the logical implications of nature exhibiting "goal-oriented processes" something which has been a taboo in biology since the publication of On the Origin of Species and which was imposed on science, without any evidence, by force of materialist-atheist ideology.  

This exposure of the enormous complexity of the "simplest" organisms which must provide the great ideological scientific effort of abiogenesis its modeling for the "first organism" makes the hurdles of those who claim it life arose by random chance processes ever higher.   Every complexity in these 'simplest' organism, every aspect of their metabolism and reproduction and interaction with other organisms which gain in complexity only adds to the improbability of it ever having happened by random chance events working on molecules in the early Earth or any other place in the universe. 

Only, you have to read the paper to know that.  I know Simps didn't and neither did his tag-team buddies at the Eschaton "brain trust" as they love to call themselves. 

I was a fairly good student of biology back in the 1960s, two of my teachers tried to get me to change my major.  Only, when I look back, so much of what I was taught has now been shown to have been rather naive or just wrong.   If that was where my thinking about it stopped, what I got A's for then would be laughably inadequate now.   What it seems to me is that even as they are faced with evidence that should have led them to abandon their ideological framing decades ago, they can't admit that it doesn't work, anymore.  It's no different from those who can't give up their literalist 6-day creation beliefs.  Just more respectable in academic culture.