Tuesday, October 30, 2007

Different Approaches to Tracing Causal Trails

Top-Down Causation by Information Control: From a Philosophical Problem to a Scientific Research Program is a paper having implications for intelligent design. The paper contains this insightful paragraph:

Many scientists consider `top-down causation’ not to be real: they believe it is just a complicated way of describing things that in the end confuses the real causal patterns, which are believed to be bottom-up only (see Fig. 1a). It is also assumed that phenomena that are not easily understandable in a bottom-up way today, will be so understood in the future. This approach has been extended to all natural systems thanks to the huge success of the reductionist methodology in physics and, in recent decades, in molecular biology and neuroscience. As in Francis Crick’s famous dictum: "You, your joys and your sorrows, your memories and your ambitions, your sense of personal identity and free will, are in fact no more than the behavior of a vast assembly of nerve cells and their associated molecules" [Crick 1994]. The emphasis in the phrase “no more than” is a denial of the reality of anything additional to the pure assembly of cells and is therefore also a rejection of top-down causation.

What strikes me about this is two things. First, I think it is accurate with respect to the type of causality scientists consider to be "real." Secondly, the consideration of what is "real" is strictly philosophical. In other words it is not dictated by nature. Instead it is the chosen lens through which humans have decided to view nature.

Top-down causation is, of course, a natural part of the universe and is frequently observed on this planet. Homes and machines are constructed using this approach. So are many other things. It is the type of approach used by intelligent beings and is therefore a marker of purposeful, intelligent causality. You can see now why its consideration has been excluded from determinations of physical causes. You also might suspect that this exclusion has hindered our understanding of life's origins.

The challenge for IDists is to construct a methodology and apply it to test hypotheses related to the origin of life. OOL is a field noted for its lack of plausible details about how life came about. It has utilized a bottoms-up approach to no avail. It's time for change.

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Wednesday, October 24, 2007

Crystal Arguments

The following exchange occurred in the comment section of a blog entry posted by Mike Gene. Part of the exchange is reproduced here for the purpose of commentary as it entails a flawed argument frequently employed against intelligent design. There are variations of crystal arguments which are arguments by analogy seeking to explain how biological complexity could be generated from laws of nature. The biological complexity referred to is that of an initial genome. My comments appear in green while those of the other commenter are in red. The follow-up commentary is in blue.

Bradford: The ateleologist would proceed to argue that the dice were fixed as a consequence of some natural force of nature. Perhaps the ends were eroded or the faces were indented in six places on each side by some mechanism.

Most scientists understand that humans act with purpose, and that dice are human manufactured devices that should be "fair", but are often tampered with to gain advantage over adversaries. Think Bradford! It is your knowledge of humans and dice that allows you to consider cheating to account for skewed distributions.

A more appropriate example might be water forming ice. Perhaps it is Jack Frost who carefully weaves beautiful and intricate crystals on the windowpane, or perhaps there is some underlying property of water. Making that scientific determination requires forming and testing valid hypotheses.

Indeed it is my knowledge of humans and dice that allows for a conclusion of cheating when skewed distributions are observed. It is important to note that accurate conclusions are pegged to correct assessments of contingencies inherent to the situation at hand. But would one infer that an intelligent designer was a necessary part of a hypothesis involved in the explanation of snowflake patterns or the beauty of frozen ice on a windowpane? No. But why not?

While the patterns themselves can be complex and beautiful they are made possible through a change in one variable- temperature. The temperature leads to an appearance that is a property of water under conditions that can be specified. Causality is determined. Given the properties of matter (in this case water) and the environmental conditions, snowflakes or ice will form; along with the complex patterns in the snowflakes or ice. Complexity is predictable and linked to the properties of matter and weather conditions. It is our scientific knowledge that allows us to make accurate predictions that complex patterns will arise.

Contrast this with nucleic acids; biochemicals organisms utilize to store information used to code for proteins and RNA and the related functions these encoded end products enable. Like water nucleic acids have chemical properties. Unlike water the chemical properties of nucleic acids do not reveal the conditions of a prebiotic environment that would lead to the unique sequencing patterns enabling the synthesis of functional proteins and RNA. But is that because we simply have not determined what those conditions are or do the chemical properties of nucleci acids and the nature of encoding systems signal that environmental conditions alone are insufficient to account for biologically functional nucleic acids?

It is the latter condition and it is our knowledge of chemistry, biology and encoding symbolism that allows for a correct inference of intelligent design. Like the example of dice and humans, it is our knowledge, not our ignorance, that makes possible an accurate conclusion. While determinism marks the physical process that results in crystalline formation a functional sequencing of nucleotides is contingent on an existing biological condition that confers selective value to the sequencing. That condition being an availability of amino acids corresponding to codons and of proteins to the nucleic acids containing the codons. This is irreducible complexity on a most basic biological level.

The biological utility of codons lies in their symbolic nature. The symbolism is as real as the amino acids composing proteins synthesized in accordance with the identity and order of the codons. It's contingency all the way and a contingency whose logic lies in the existence of a larger replicating biological system- the cell. Crystals provide evidence of the molecular properties of their constituent substance. Functional nucleic acids provide evidence of an already existing cell replete with the proteins they code for. That's a problem for those seeking to convey the idea that life was generated like crystals.

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Friday, October 19, 2007

Anti-ID Propaganda

Chuck Colson authored the linked article with the title, What Darwinism Can't Do, which begins with these two paragraphs:

The intelligent design (ID) movement has been accused of a lot of things over the years. Among the mildest of those accusations is that ID is just religion masquerading as science.

Anyone who could seriously think that, cannot be paying attention. Intelligent design, as defined by the Discovery Institute, teaches simply “that certain features of the universe and of living things are best explained by an intelligent cause, not an undirected [random] process such as natural selection.” That’s it. It does not attempt to define or describe that cause. Most scientists who subscribe to intelligent design do believe in some form of evolution. And some of them are not even believers in the Bible—they are secularists. They simply believe that Darwinism does not have all the answers, especially about how life originated. (Darwin himself never pretended certainty on that.)

The religion masquerading as science charge sometimes arises from opportunism and other times from ignorance. The arguments used by IDists are based on scientific data related to biological organisms, their cells, cellular systems and biochemicals. The arguments arrayed against ID positions similarly reference the same things. When one examines actual ID position papers and critical reactions to them, one thing one does not find is exchanges over religious principles. That is telling. Although the religion card is played often, actual concepts advanced by IDists such as irreducible complexity, front loading, CSI and design arguments based on the coding nature of DNA, spark intense scientific debates rather than exchanges over religious issues.

The best forum for exchanges between IDists and their detractors is Telic Thoughts and it is also an internet site which features the comments of a number of scientists who believe in evolution and intelligent design but not necessarily in the Bible. Yet the worn out and discredited charges about religion persist. Propaganda machines have a momentum of their own.


Sunday, October 14, 2007

Guest Post of Thought Provoker

Thought Provoker, the internet moniker of an individual I first encountered at Telic Thoughts, is hosting this guest post. Sometimes referred to as TP, Thought Provoker has previously authored guest posts at Telic Thoughts. Guest posts are the brainchild of Mike Gene and it looks like I have gone into the adoption business.

TP has his own blog appropriately known as Thought Provoker. Guest posts of TP at Telic Thoughts can be viewed here.

The usual disclaimers apply. This post reflects the views of TP and not anyone else at Intelligently Sequenced. As is the case with all ideas we may agree or disagree with points made in the essay. TP's post follows:

Allow me to introduce myself. I am Thought Provoker. Bradford has been kind enough to offer to allow me a Guest Post on Intelligently Sequenced. This is remarkable because, more often than not, Bradford and I have disagreed in Telic Thoughts. I think this speaks highly of Bradford.

I won't guarantee everyone will agree with my post but I offer it in an attempt to provoke constructive thinking by suggesting a new choice in approaching Intelligent Design. I call it the Third Choice.

The Third Choice is primarily a model offered by the scientists Penrose and Hameroff that I have tailored for use as an ID hypothesis. Sir Rodger Penrose is famous for modeling Black Holes along with Stephen Hawking. Penrose joined forces with Dr. Hameroff who has studied cellular biology and made the study of consciousness his life's work. They call their model the Orchestrated Objective Reduction model of consciousness (Orch OR for short).

This post will be a very brief introduction/summary. I would suggest visiting www.hameroff.com for more details. However, even though it is a summary some non-trivial subjects have to be addressed first, including cosmology and quantum physics.

A key concept to understanding the Third Choice is to realize General Relativity is the observed reality. Special Relativity is NOT reality. It is incomplete. There is a single, inertial frame of reference. This means our universe exhibits Minkowskian Geometry (not Euclidean Geometry). From Einstein’s Ether: Why did Einstein Come Back to the Ether?...
"In (1905) Einstein constructed a relativity theory that was based on the assertion that the ether was superfluous. In 1908 Minkowski formulated the theory of the “absolute world”. The nineteenth century ether no longer existed. A new kind of ether (space-time) came into being. One could keep on maintaining the ether, and at the same time strip it of the notion of absolute rest. Einstein seemed to agree, and after 1916 he returned to the ether. In 1920 he combined Minkowski’s absolute world concept and Mach’s ideas on rotational movements…"

Minkowskian Space-time is reality. Three dimensional Euclidean Geometry is not. Calculating Minkowskian distances ("dl") adheres to the following equation...
dl^2 = dx^2 + dy^2 + dz^2 - dt^2
Photons (traveling at the speed of light) have a Minkowskian distance of ZERO. Quantum "paradoxes" like GHZ states are trivial to understand for photons since they can be anywhere and anywhen instantly.

This provides an understanding of how any and all quantum effects can be interconnected regardless of distances in space-time. Hopefully, it can be understood that they not only can be interconnected but that they are interconnected.

While there may be resistance to the implications of this, the alternatives are not that attractive. Either we continue to wait for physicists to come up with a better idea (they have been waiting for eight decades) or we embrace a metaphysical concept called Many Worlds.
Once it is realized that quantum effects are interconnected, it is a short hop to realizing there is no such thing as randomness. A lack of randomness wasn't a problem when Newtonian Physics was king. The only possible sources for randomness are quantum effects and conscious decisions.

If quantum effects are interconnected, their randomness is an illusion. Quantum effects are non-deterministic but they are also not random. What if consciousness is also interconnected with quantum effects?

This would explain quantum physic's measurement problem. The observer doesn't "randomly" decide which measurement to take. Conscious decisions are interconnected with the quantum effects being measured. The implication of this is that the appearance of randomness in living organisms is a direct artifact of quantum effects.

Sounds good in theory, but is there evidence of life even using quantum effects?
"Early in 2007 a team of Berkeley Lab and UC Berkeley researchers identified quantum mechanical effects as the key to the astonishing ability of photosynthesis to utilize nearly all the photons absorbed by the leaves of green plants. Now a different team has found new evidence that points to a closely packed pigment-protein complex of the photosystem as the key to those quantum mechanical effects.
How nature manages to pull off this stunt was a long-standing mystery until the spring of 2007, when a study led by Graham Fleming, Deputy Director of Berkeley Lab and a UC Berkeley chemistry professor, found the first direct evidence of what he calls a 'remarkably long-lived wavelike electronic quantum coherence.'"

While it is tempting to end the discussion here, quantum based photosynthesis doesn't explain how consciousness is interconnected to quantum effects (the final piece to solve the quantum measurement problem).

Single-celled organisms avoid obstacles and predators, find food and engage in sex. How are they able to accomplish this? An obvious presumption is that the cell's cytoskeleton performs the combined function of skeleton, muscle and nervous system. The cytoskeleton is made up of microtubules and actin. Microtubules (MTs) are made up of tubulin dimers that have two states, alpha and beta. If the alpha and beta states of these small tubulins (8 nm by 4 nm by 5 nm) can be in quantum superposition, it would provide an explanation for how the actions of living organisms are directly interconnected to quantum effects.

It is reasonable to presume that tubulins are capable of being in quantum position since similar sized fluorofullerenes exhibit quantum behavior. link

However, this is once again a situation where something can happen but it is questionable whether it does happen. DNA provides another possible example of life directly using quantum effects. A scientist named Patel has pointed out the search function inherent in the DNA is a quantum process requiring superposition link

Life's direct dependency on quantum physics has become obvious in the case of photosynthesis. It is also likely for DNA. While the case for microtubules is harder to make right now, too many observations are explained by it to dismiss it out of hand, IMO.


Saturday, October 13, 2007

An Ongoing Effort to Detect Intelligent Design

Radio telescope array dedicated to astronomy, SETI is the title of a University of Califorina at Berkeley news item which provides information about a new radio telescope that will gather astronomical data and also search for extraterrestrial intelligence. Of course if extraterrestrial intelligence were found mainstream thinkers would view this as confirming their preconceptions about design rather than illustrating how efforts to detect design can yield productive findings.

Mike Gene authored this comment at Telic Thoughts. It contains the following quote:

In abstract world of logic, perhaps this is the way it should be. But in the real world, reductionism is played against vitalism. Non-teleologists believe that if something is explained by physicochemical processes, non-teleology has been supported. This is because they think teleology is supposed to come with forces distinct from physicochemical.

Very true. Most IDists do not dispute the linkage of a result to a physiochemical cause. Neither do they believe that evidence of such is ipso facto evidence for non-teleology. No wonder productive dialog is difficult.

Monday, October 08, 2007

The Rad54 Gene

A Science Daily article with the title Gene For Neat Repair Of DNA Discovered, describes a gene which enhances the efficiency of DNA repair. Less efficient repair of damaged DNA in somatic cells can lead to cancer. It also leads to genetic diseases in germline cells. The gene in question goes by the name Rad54. As the article notes the Rad54 gene prevents mutations by enabling more precise repairs.

DNA repair is so critical that organisms have multiple mechanisms to accomplish it. Some act as redundant back-ups but when all else fails the ultimate solution - cellular suicide- can be an effective strategy. Cellular suicide is known as apoptosis and involves its own mechanisms and signaling pathways. It is also the ultimate back-up system.


Thursday, October 04, 2007

'The Case for the Real Jesus': A Book Review

Lee Strobel has written a new book called 'The Case for the Real Jesus.' It is a fitting sequel to his prior best seller 'The Case for Christ.' The book focuses attention on six challenges to Christianity that have been prominently publicized in recent years. The challenges involve rehashing old objections that have been answered previously. However, new generations tend to forget both the objections and the answers that overcame them.

Strobel repeats a pattern established with 'The Case for Christ' by interviewing reknown scholars and getting their responses to the six challenges. The six are as follows:

* Alleging that there are plausible ancient manuscripts providing different views than the four gospels

* Allegations that the church tampered with biblical texts and therefore the texts cannot be trusted

* New refutations of the resurrection

* Christian beliefs were actually copied from pagan religions

* Jesus was an imposter and did not fulfill messianic prophacies

* People are best advised to pick and choose that which they wish to believe about Jesus.

The interviewed scholars did a thorough job of debunking each challenge. Craig A. Evans, PhD in biblical studies and prolific writer and editor of more than 50 books, was questioned about the claim that our understanding of Christianity would change if certain ancient manuscripts were incorporated into what the church considers canonical writings. One manuscript specifically mentioned was the so called Gospel of Thomas. Critics have dated the writing of the "Gospel of Thomas" to around the middle of the first century. This would lend support to a number of arguments they make based on this assumption. Unfortunately that also seems to be the motive for the dating of Thomas.

The Evans interview, in many ways, paralleled the results of other interviews by bringing forth decisive evidence against charges that the church ignored plausible early writings that would have changed the nature of Christianity. An objective scholarly analysis would date Thomas to at least a century later than the time frame provided by critics. An examination of the actual evidence is revealing. Evans disclosed the facts that are downplayed or ignored by those touting Thomas as a canonical candidate. Evidence indicates that Thomas was written no earlier than the latter part of the second century which contrasts with dating from the middle of the first century proposed by critics. The reasons:

* More than half the New Testament writings were referred to or paralleled in Thomas including 14 or 15 of the 27 New Testament books. Some of this material was not recorded until the last decade of the first century. Evans, a noted New Testament scholar, was unaware of a single Christian writing prior to the year 150 that referenced as much of the New Testament as Thomas.

* Thomas was written in a number of languages which include Syriac- spoken in Syria. Syrian Christians did not have access to the four Gospels in their own language until the year 175 when a blend of the four Gospels known as the Diatessaron was recorded in Syriac. The content of Thomas reveals familiarity with the Diatessaron particularly its material arrangement and order. In addition only the Syrian church referred to Thomas as Judas Thomas; the name used in the Gospel of Thomas. Values of the Syrian culture of the second century- its ascetics and anti-commercialism, its mysticism and its elitism are all evident in Thomas.

* Most striking though are 114 sayings that appear in Thomas. Their order does not appear noteworthy in Greek or Coptic but in Syriac there are catchwords that act as memory aids. The catchwords link the sayings together. A word in one saying is indicated by the preceeding saying and so on.

Similar devastating refutations of revisionist Christian history are evident throughout 'The Case for the Real Jesus.' Strobel's other interviews reflect the knowing scholarship evidenced by Evans which contrasts with the selective use of evidence by church critics. Strobel has authored another fine Christian apologetic.

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