File under "well said" LXXVI.

 We can easily forgive a child who is afraid of the dark; the real tragedy of life is when men are afraid of the light.

Plato

System's biology:an overview.

 Systems biology can be considered from a number of different aspects.

As a field of study, particularly, the study of the interactions between the components of biological systems, and how these interactions give rise to the function and behavior of that system (for example, the enzymes and metabolites in a metabolic pathway or the heart beats).

As a paradigm, systems biology is usually defined in antithesis to the so-called reductionist paradigm (biological organisation), although it is consistent with the scientific method. The distinction between the two paradigms is referred to in these quotations: "the reductionist approach has successfully identified most of the components and many of the interactions but, unfortunately, offers no convincing concepts or methods to understand how system properties emerge ... the pluralism of causes and effects in biological networks is better addressed by observing, through quantitative measures, multiple components simultaneously and by rigorous data integration with mathematical models." (Sauer et al.) "Systems biology ... is about putting together rather than taking apart, integration rather than reduction. It requires that we develop ways of thinking about integration that are as rigorous as our reductionist programmes, but different. ... It means changing our philosophy, in the full sense of the term." (Denis Noble)

As a series of operational protocols used for performing research, namely a cycle composed of theory, analytic or computational modelling to propose specific testable hypotheses about a biological system, experimental validation, and then using the newly acquired quantitative description of cells or cell processes to refine the computational model or theory. Since the objective is a model of the interactions in a system, the experimental techniques that most suit systems biology are those that are system-wide and attempt to be as complete as possible. Therefore, transcriptomics, metabolomics, proteomics and high-throughput techniques are used to collect quantitative data for the construction and validation of models.

As the application of dynamical systems theory to molecular biology. Indeed, the focus on the dynamics of the studied systems is the main conceptual difference between systems biology and bioinformatics.

As a socioscientific phenomenon defined by the strategy of pursuing integration of complex data about the interactions in biological systems from diverse experimental sources using interdisciplinary tools and personnel.

More on why I.D may already be mainstream.

 

End of the Road for the Intelligent Design Debate?

Brian Miller

This past June, the Center for Science & Culture hosted the Conference on Engineering in Living Systems (CELS). The presenters demonstrated how applying engineering principles and tools to biological research yields profound insights into the operations of living systems and the logic behind their design. This content was fully anticipated by the attendees. The presentation that came as somewhat of a surprise showcased the extent to which the subdiscipline of systems biology has for the last few decades often operated within what is almost indistinguishable from a fully design-based framework. Much of the research within the field has effectively replaced evolutionary assumptions with design-based assumptions, language, and tools of investigation. This scientific revolution, which has only just begun, raises the question of whether the debate over intelligent design has come to an end. 

Changing Assumptions

At a philosophical level, the answer to this question is clearly no. The proponents of scientific materialism still maintain a stranglehold over researchers, so those who openly question the official orthodoxy face the constant threat of secular inquisitors undermining their reputations and careers. In addition, official media outlets and educational institutions continue to feed the public a steady diet of disinformation directed against anyone who speaks honestly about the clear evidence for design in biology. And any material put out by design proponents is immediately met by critics who consistently misrepresent the material’s content and the related science to undermine the authors’ credibility. This practice was well demonstrated by a recent critique of Stephen Meyer’s latest book (here, here, here, here). 

The Tide Shifts

Yet, at a practical level, the tide of the debate appears to be decisively shifting. A review of the journal articles generated by systems biologists reveals how design assumptions increasingly dominate research into the higher-level organization of life. Part and parcel with this trend has been the replacement of the materialist presumptions undergirding biology for the last century with design-based premises:

• Scientists and philosophers of science no longer reject the view that teleology (aka purpose/design) has any place in research. Instead, they explicitly recognize that exploring the purpose of living systems is central to their understanding. 
• Biological systems are no longer often assumed to represent suboptimal design or vestigial remnants of their evolutionary history. Instead, researchers increasingly recognize that assuming optimal design leads to accurate predictions. 
• Biologists no longer assume that biology only marginally resembles human engineering. Many now recognize that the most advanced and effective engineering motifs implemented in human technology are prevalent in life. 

Demise of Reductionism

This transformation in thinking reflects how the philosophical foundation of scientific materialism that has defined science is eroding in the face of the most recent biological data. The traditional approaches implemented in biological research were founded on reductionism — the belief that studying the physical and chemical interactions between biological molecules should eventually lead to an understanding of life’s higher-level operations and organization. This assumption was central to evolutionary thinking since natural selection can typically only operate on single changes to DNA, resulting in alterations of individual proteins or discrete tweaks to biological structures and processes. No evolutionary mechanism can engineer multiple components to seamlessly integrate in such a way as to achieve an overarching goal. 

More commonly today, systems biologists reject this reductionist approach since it has failed to yield any significant understanding of the complex organization of organisms. Instead, they have learned that they must look at life as a collection of integrated systems composed of integrated components where the whole is greater than the sum of the parts (aka holism). In other words, Michael Behe’s concept of irreducible complexity has implicitly become a central tenant of the field. Researchers would rarely use such language or acknowledge the implications, but this conclusion is unmistakable. 

Virologist Derek Gatherer comments, 

The broadening of molecular biology into systems biology has created a situation where researchers have a vague inkling that their underlying philosophy is in need of refurbishment, and holism appears to offer much of what is wanted.

Similarly, philosopher of science Michel Morange describes critiques of the traditional approach to biology in his provocatively titled article “The Death of Molecular Biology?” He asks,

[D]oes it mean that molecular biology is dead, and has been displaced by new emerging disciplines such as systems biology and synthetic biology? Maybe its reductionist approach to living phenomena has been substituted by one that is more holistic…Some even consider the age of molecular biology as having been a period of extreme misorientation of biological research, an error that it is high time to repair.

Explicit Design Language 

Many systems biologists have replaced reductionist approaches with design-based methodologies. Science philosopher P. A. Braillard comments,

More and more scientists are claiming that systems biology constitutes a fundamental change or even a revolution in the life sciences…. Although some aspects of systems biology fit the mechanistic framework, explanations used by working scientists do not always correspond to the traditional definitions of mechanistic explanations provided by philosophers. … I refer to this kind of explanation as design explanation.

Philosophers and complexity theorists Pam Mantri and John Thomas are equally candid about both the need for and the resistance against this trend, 

Unfortunately, research in the world of modern biology is currently divorced from that of design-theory. Yet each discipline could benefit from studying the other. From a design perspective (and subject to environment/precedent constraints), form seems to be following function (e.g., the elbow joint of the fore-arm for bringing food to the mouth). The fundamental problem associated with design in biology, is that of agency. … In this paper, we try to bridge the seemingly insurmountable gap between design-theory and biological “designs,” without getting derailed by “intelligent design” polemics. 

Mantri and Thomas desperately attempt to reframe “design-theory” within the confines of evolutionary assumptions, but their efforts amount to little more than invoking such phrases as “stigmergic teleology” and “emergence” without providing any substantive details of what such concepts would look like in an actual evolutionary scenario. 

Given this trend in the increasingly explicit use of design language, a key question is how long biologists wedded to scientific materialism can argue that life looks like a duck, swims like a duck, and quacks like a duck, but it is actually a cat. 

A Human of the gaps argument?

  A party of biologists studying a troupe of macaques that have colonised an abandoned scrapyard stumble across a functional refrigerator,one of their number suggest that members of the macaque troupe  may have inadvertently assembled the device while playfully tinkering with the available scrap.His colleagues naturally pour scorn on the idea maintaining that despite the isolated state of the location it is far more likely that humans are responsible for both the manufacture and the transport of fridge to its present location.

  They voice the opinion that monkeys simply lack the intellectual wherewithal to ever(even with all the time and luck in the world) produce even a suboptimal  refrigerator.

  Would our lone dissenter be justified in referring to such reasoning as a human of the gaps argument?

In the beginning of what?

  John1:1The BibLE"At first there was the word,and the word was where(the) God was,and the word was God ."

On the face of it this does appear to be referring to the absolute beginning of the creation spoken of at proverbs8:22_30. As indeed does 1John1:1,Revelation3:14.

Our Socinian friends assure us however that this is  merely a reference to the beginning of the new creation see 2Corinthians5:17

John1:14The BibLE"And the word became flesh and abode among us and we saw his glory,glory such as that of an only Son from the Father,full of grace and truth."

 How could John1:1 possibly be a reference to Jesus becoming the beginning of the new creation when ver.14 speaks of him as becoming flesh. Surely the beginning of the new creation would speak of flesh becoming spirit not the other way around 

John3:6,7The BibLE "What is born from flesh is flesh and what is born from spirit is spirit. Do not wonder at my telling you 'you must be born over'"

Even worse than I thought.

  Trinitarians are now telling me that each member of their trinity is equal to the entire trinity.

If this turns out to be a majority opinion .It would mean that the trinity is an even more egregious violation of the principle of occam's razor than I previously thought. For in Christendom's trinity one would have an example of a whole that is less than the some of its parts

 Psalms83:18KJV"That men may know that thou, whose name alone is JEHOVAH, art the most high over all the earth."

Thus not even the trinity as a whole would correspond to the JEHOVAH of psalms 83:18 in as much as each of his/its three constituents would be equal to him/it.