Wednesday, January 30, 2008

The British Centre for Science Education - Revealed

Just a quickie, and to help the search engines out a bit.

I've now finished blogging over at my "BCSE Revealed" blog. The "British Centre for Science Education" has now been pretty comprehensively revealed, I think.

I've now made the complete set of articles available as a website. Please link to it / blogroll it, etcetera, so that others can be helped to find it, and point others to it as need requires.

David Anderson


Sunday, January 27, 2008

Sketching the History

The Last Days of Darwin A Brief History of the Revolution is one of several articles appearing in Salvo Magazine about intelligent design. The following paragraph notes a little known tidbit:

As early as 1951, biophysicist Harold Morowitz was trying to find the cell’s “information content.” He eventually concluded that it was impossible for life to have arisen without some large infusion of information. Not a theist, he nonetheless created space for an Intelligent Designer.

A failure in accounting for the capacity to store and utilize life enabling information is a key indicator for many, if not most IDists, that something is amiss with mainstream thinking. Author James M. Kushiner goes on to note that both Ernst Mayr and Sewall Wright (among many others) believed that gradualism was a central tenet of evolution. But before genomic changes can occur a genome must exist. Yet life appears to have spontaneously emerged without leaving a trail as to what kind of process would have led to its gradual formation.

Kushiner identifies problems with existing evidence and cites the landmark book by Walter Bradley, Roger Olsen and Charles Thaxton- The Mystery of Life’s Origin. This book and Australian biochemist Michael Denton's bestseller Evolution: A Theory in Crisis brought about a subsequent chorus of critcs which solidified intelligent design as part of the analytical landscape. Dembski, Behe et. al. follow. So too do other articles in this issue that are worth reading.


Friday, January 25, 2008

Reductionism vs. Downward Causation

The article Downward Causation contains this quote describing downward causation:

all processes at the lower level of a hierarchy are restrained by and act in conformity to the laws of the higher level

The counterpart of downward causation is reductionism. Quoting from the same article:

Reductionism can be defined as the belief that the behavior of a whole or system is completely determined by the behavior of the parts, elements or subsystems. In other words, if you know the laws governing the behavior of the parts, you should be able to deduce the laws governing the behavior of the whole.

Note the philosophical outlook underlying reductionism. Knowledge about the parts leads to deductions about laws governing the whole. That's the paradigm through which investigations about the origin of life take place. Laws governing chemical reactions of organic compounds yield information from which laws governing cells can be deduced. But if such laws cannot be deduced then what? The "then what" may explain the spinning wheel results accruing from decades of OOL research. Our understanding of the chemical properties of cellular biochemicals provides no insight as to how reactions, involving such chemicals, leads to the formation of cells. Reductionist approaches have not led to progress. More from the same article:

Systems theory has always taken an anti-reductionist stance, noting that the whole is more than the sum of the parts. In other words, the whole has "emergent properties" which cannot be reduced to properties of the parts. Since emergence is a rather slippery concept, which has been defined in many different ways, most of which are highly ambiguous or fuzzy, I prefer to express this idea with the more precise concept of downward causation.

Cells indeed do have properties that are not reducible to the chemical properties of their constituent biochemicals. For example, cellular DNA is able to store genetic information that, when expressed, enables the synthesis of RNA, proteins and cellular structures consisting of proteins. This is possible because of the ordering of nucleotides according to patterns that conform to what are referred to as genetic codes. Yet the codon sequences within DNA do not have to be functionally ordered to retain their chemical properties. Chemical properties of DNA are indifferent to the unique sequencing needed to confer cellular function. DNA is DNA whether biologically functional or otherwise. Ribosome function is not explained by specifically referencing the properties of its individual proteins and RNA. It must be viewed holistically.

Do all systems exhibiting downward causation owe their origin to causes traceable to the properties of their constituent parts? Or does a causal flow downward better account for the origin of systems as well? Michael Behe's irreducible complexity can be viewed as an indicator of downward causality. Downward causality is exhibited in intelligently designed systems. The flow begins with an intelligent plan which, when put into effect, results in an arrangement of parts that make function possible. Technology is created this way.

Reductionists argue that the brain itself (intelligence) lies at the end of a causality trail that commenced with biological systems emerging from simpler biochemical reactions. That however is a belief not sustained by empirical results. When we follow existing causal trails we find no logical barrier to investigating a directional flow downward. Indeed excluding it a priori is a philosophical choice; not an empirical necessity.


Tuesday, January 22, 2008

Inventions or Discoveries?

(Cross-posted from my new blog: "More Than Words").

There are plenty of things in everyday life we don't think much about - but we ought to!

One thing I am profoundly grateful for, and amazed by, is modern technology. There is such a vast amount of technology involved just in the act of blogging that it is breath-taking

Just to mention a few...

  • The laptop it's typed out on. The processor, the display, the battery (power cuts happen here!), etcetera...

  • Then it gets beamed a short distance through the air to my mobile phone,

  • from where it gets beamed to the nearest mobile tower.

  • Then a combination of fibre-optics and/or satellites get it to blogger, somewhere in the USA, where it is stored on magnetic disks.

  • And then over to you!

I live in Africa, but because of the Internet in many ways the distance feels quite short. I can e-mail video clips and photos, receive e-mails, read the BBC news, send SMS messages, just as when I lived in the UK. If I really wanted to, I could do all of those things on a mobile phone handset costing about £80 (it's probably cheaper where you live!). A tiny thing that fits in my pocket and is so light I don't notice it's there can do all of that. Amazing!

The reason I find it amazing isn't because I think it's magic. I studied scientific subjects at school and university, and as a boy technology was always one of my interests. My understanding of how many of these things work doesn't make them seem less wonderful - it makes them seem far more wonderful. The above list includes the technology involved in electricity, electro-magnetic radiation, satelite technology, magnetism, fibre-optics. When we understand more, we don't marvel less: quite the opposite.

Coming To The Point...

So, what am I saying? Did you notice that I said I was profoundly grateful for these things? Where should that gratitude be directed, exactly?

Often we describe these things as being "inventions". And indeed, in an important sense, they are. There's a big step in between understanding the principles of fibre-optics, electricity, and so on, and then actually putting together all the equipment that uses those principles to make it possible for my thoughts to get out of my head, though the air, and onto your screen. It needed someone to make the long route from A to B.

Fundamentally, though, these things are not inventions, but are discoveries. For the human "inventor", they did not come out of nothing at all, but were a harnessing of things that already existed. In the days when our ancestors did not have electricity, mobile phones or e-mail, the potential for such things were all still latent in the world around them - they just had not been harnessed.

The Big Question

So, is that all just luck? Our "gratitude" is misplaced - a false emotion? We should just be saying, "that's a stroke of fortune"? It is just a wonderful coincidence that such "blessings" (wrong word again!) just "happen" to exist?

Such things are reasons why it's impossible to be a consistent atheist. To have to attribute these things, and many more besides, just to happy coincidence. Let's call it the "good-luck-of-the-gaps" explanation - denying the reality of God, who made all these things for our pleasure and his glory, we have to write off huge areas of human life as being mere fortune. An appeal to "luck", though, is not an actual explanation - it is a confession of ignorance. "Luck" is not a cause or a mechanism - it is a philosophical abstraction. Luck is not a person or mind, and cannot actually do anything.

Such things as the above also make it hard to be an inconsistent theist. By that I mean, acknowledging in our minds the reality of God, but failing to give him thanks or worship with our lives. Technology depends upon minds - human minds which piece it all together, understand it, and manufacture the wonderful little gadgets that result. Much more fundamentally, though, technology depends upon a divine mind. A divine mind, that constructed the creation where all those possibilities have lain latent until a spark of inspiration moved the human inventor to harness them. The enormous potential in the material world for technology speaks clearly of a divine mind behind it. A mind that made it all, and made us so that we might discover and harness it - and give him the praise. We, unless we totally refuse to think about these things, have a corresponding and correct sense that we ought to direct our gratitude and praise somewhere. That's a sense which shouldn't be suppressed, but yielded to.

Much better to live as a convinced worshipper. Or as the Psalmist wrote, 3000 years ago:

O LORD our Lord, how excellent is thy name in all the earth! who hast set thy glory above the heavens.

Out of the mouth of babes and sucklings hast thou ordained strength because of thine enemies, that thou mightest still the enemy and the avenger.

When I consider thy heavens, the work of thy fingers, the moon and the stars, which thou hast ordained;

What is man, that thou art mindful of him? and the son of man, that thou visitest him?

For thou hast made him a little lower than the angels, and hast crowned him with glory and honour.

Thou madest him to have dominion over the works of thy hands; thou hast put all things under his feet:

All sheep and oxen, yea, and the beasts of the field;

The fowl of the air, and the fish of the sea, and whatsoever passeth through the paths of the seas.

O LORD our Lord, how excellent is thy name in all the earth!

(Psalm 8)


Sunday, January 20, 2008

Understanding Downward Causation

This article titled Excursus: Defining Downward Causation, helps to illustrate the meaning of top down or downward causation. The article uses the jaw anatomy of a worker termite or ant to demonstrate the concept of downward causation.

A design construction featuring hinge surfaces and muscle attachments allow for the application of maximum force at a distance from the hinge for a biting or grasping function. Underlying laws of physics are utilized by gross anatomical structures, composed of multiple parts, to accomplish an objective that is beneficial to the whole organism.

Contrast the foregoing with a bottom up effect which can be illustrated by the binding of ATP to a transmembrane protein to facilitate the transport of molecules across cell membranes. The molecular binding initiates a larger biological operation.

The following quoted paragraph from the article (in blue) is instructive:

Downward causation, then, is a matter of the laws of the higher-level selective system determining in part the distribution of lower-level events and substances. "Description of an intermediate-level phenomenon," he says, "is not completed by describing its possibility and implementation in lower-level terms. Its presence, prevalence or distribution (all needed for a complete explanation of biological phenomena) will often require reference to laws at a higher level of organisation as well"

In the case of the termite or ant jaws large biological structures, exploiting higher level physics concepts (Archimedes' levers), control lower level biological functions. Biological explanations for what occurs invoke references to actions controlled by higher level biological organization.

One final point, to be elaborated on in future blogs, concerns the original source of biological organisms. Mainstream biology utilizes bottoms up causal scenarios to explain life from abiogenesis through evolution. Intelligent design is a bit more flexible. Intelligent design can be evidenced in either direction. More on that to come.


Saturday, January 19, 2008

Casey Luskin on Irreducible Complexity

At Telic Thoughts I posted this blog entry centered around an article by Casey Luskin which appeared here. Casey Luskin posted this comment. The following part of it deals with irreducible complexity. Note the reference to empirical evidence cited namely, Scott Minnich's genetic knockout experiments. (The quote appears in blue.)

Raevmo wrote: "Luskin simply asserts IC without any logical arguments or empirical evidence. Overall, Luskin's piece has nothing new to offer."

I reply: These are neither accurate nor fair accusations. This was intended to be a review of the NAS's document, not a presentation of new research. If you have criticisms, then criticize based upon the intent of the document.

Moreover, I gave arguments from Frank B. Salisbury and Øyvind Albert Voie that contend that the cell and DNA-enzyme system are irreducibly complex. Additionally, my response to the NAS observes that "proponents of intelligent design have done experimental tests on the bacterial flagellum showing it is irreducibly complex" and I then cited Scott Minnich's genetic knockout experiments presented at the Kitzmiller trial which show the flagellum is IC. So Raevmo's charges hold no water.


Tuesday, January 15, 2008

Prevention is Better than a Cure

A Model for Basic Eukaryotic Functions points to an often overlooked aspect of DNA repair. There are the familiar DNA repair pathways by which damaged regions of DNA are repaired. But some damage, that would otherwise occur, is prevented by checkpoint or quality control strategies. Such a strategy is found in RNA polymerase which, when encountering incorrect ribonucleotides, is able to remove them. Errors, which would otherwise be evident in synthesized proteins, are avoided through prevention. Preventive measures like this lessen evidence of errors by eliminating them at a stage preceeding gene expression.


Friday, January 11, 2008

Archeological Evidence

During an exchange at Telic Thoughts I made this comment mentioning types of evidence that could be introduced to support Judaism and Christianity both of which which are supported by biblical narratives depicting historic events.

Excavation Opportunities in 2008, at the Bible Places Blog, is a source of information about possible future excavations that could become part of an existing compilation of archeological evidence supporting biblical accounts.


Wednesday, January 09, 2008

Anti-Christian Rhetoric- the Reason

A paragraph from a blog entry at Stephen Jones's CreationEvolutionDesign titled "Q-R" contains a paragraph that I will break down into parts for the purpose of commentary. (Quotes in blue):

"Mistakes peculiar to scientists. Just as there are certain mistakes that a theologian is susceptible to there are ones that the scientist is just as susceptible to in the relationship of theology to science. The first of these mistakes is to have an anti-religious attitude. No system of knowledge can be learned without some sympathy or kindly feeling toward the system- something pointed out long ago by Augustine but never fully appreciated by educators or epistemologists.

The study of nature and the natural laws which govern it is not intrinsically anti-Christian. However superfluous philosophical assumptions can become part of the "system of knowledge" associated with science. For example, science entails the study of natural phenomenon. The sympathy or kindly feeling referred to by Augustine is, of necessity, focused on the assumption that what we test must conform to predictable natural laws. The universe of science is natural and the philosophy of naturalism a predictable outgrowth of this. But if the belief that reality is confined to nature gains the sympathy of a student, opposition to any doctrine encompassing a wider view of reality it is the next step in a progression of thinking. Naturalism precludes God and miracles become equated with mythology.

Dogmatists study science as well as theology. The evangelical indicates that man is a spiritual rebel and his spirit of rebellion is reflected in all his activities. Unregenerate man opposes the doctrines of creation, sin, redemption, and eschatology. A man may be religious and yet anti-Christian. Opposition to Christianity at the level of science is in many instances simply localized or vocalized opposition to Christianity in general.

Cherry picked scientific data become the club and public forums, hosting exchanges about the origin and diversity of life, the arena for bashing Christianity and all that is associated with it including Christians in such forums.

Therefore anti-Christian man takes pleasure in making the gap between science and Christianity as wide as he can make it, and will heartlessly ridicule any efforts at reconciliation. In this instance, the gap between science and Christianity is in reality the gap between faith and unbelief." (Ramm, 1954, p.38).

This is why you will often see critiques of Noah's flood and other biblical incidents at sites said to be focused on evolution and intelligent design. Belief and unbelief is the real dividing line for most.


Thursday, January 03, 2008

Contrasting Views on the Nature of Causality

I previously blogged about the paper Top-Down Causation by Information Control: From a Philosophical Problem to a Scientific Research Program which is authored by G. Auletta, G. F. R. Ellis, FRS, and L. Jaeger. Differences between the perspective of mainstream biology advocates and Intelligent Design supporters ultimately come down to differences in perceptions of causal patterns.

The causal contrast pits emergence theorists, who believe complex biological systems self-assembled from simpler components, against top-down theorists who view causality as flowing from a direction of higher complexity to lower level components. Emergence theorists think basic forces evidenced in physics and chemistry ultimately account for causal pathways to complex biological systems like cells and cellular structures. A top-down approach to cellular information systems cites their function as an indicator of a different causal reality.

Conspicuously the origin of life is absent from the category of documented emergent phenomenon. Emergent theorists look for chemical outcomes that generate cellular hardware associated with information storage and the biochemical synthesis of encoded end products. Emergence advocates look to chemistry for solutions on how information was initially generated.

While top-down theoreticians are free to view coded information abstractly as represented by biochemical symbols (codons) coding for chemical properties (amino acid side chains) that determine protein function, emergent theorists are constricted to viewing abstractions only as useful cognitive tools that do not reflect causal realities. It is as if we are to ignore the possibility that symbolism implies intellect and tuck the idea away in a mental category reserved for apparent realities rather than actual ones. There is precedent of course for suspecting that our senses may not accurately convey reality. What IDist, with any significant experience observing internet exchanges, has not come across the flat earth argument aimed at clueless rubes by their sophisticated critics.

The appearance of a flat earth is a sensual feedback phenomenon (sensual perceptions being consistent with the extrapolation) while symbolism is imputed based, not on a visual picture, (my cat views the same screen as me without a recognition of the symbolism of the words) but rather based on a capacity to correlate a visual object with a concept. Symbols retain their physical nature while conveying a concept to those with an understanding of the encoding convention rules. So emergence demands that a process, not influenced by the input of a mind, generates the hardware, symbolism and rules by which a coding system functions. Paradoxically it also requires intellects to discount an option having the earmarks of reason embedded in the designated cause (a symbolic code) in favor of an option (emergence) that requires a belief that nature mimicks reason through a mindless chemical process.

Top-Down Causation by Information Control: From a Philosophical Problem to a Scientific Research Program focuses on what are called functional equivalence classes of operations in an effort to establish an experimental basis for determining causal flow. In biological terms higher level signals that influence action on a lower level would indicate information control. As the authors state: "A key issue here is that of equivalence class of lower-level operations, ...where operations occurring in biological systems can be considered as coordinated space-time pathways of physical-chemical interactions. The criterion for an equivalence class of operations is the outcome that an operation brings about: if two different operations give the same outcome, they can be considered equivalent. Thus, what is of concern here are functional equivalence classes (sets of operations that produce the same outcome)."

I'll explore specific biological testing possibilites in future posts.