Today’s New Reason To Believe

Posted by Fazale ‘Fuz’ Rana, Ph.D.

[Originally posted on January 10th, 2008]

Kai ABC Proteins Re-invigorate the Watchmaker Argument for God’s Existence

Suppose I discover a Rolex™ watch lying on the sidewalk in front of the Reasons To Believe offices. Without hesitation I would pick it up. My lucky day!

My first inclination would be to keep the watch. But, I would like to think that after the initial excitement of finding such a valuable time piece, I would decide to make a reasonable effort to find the person who lost the watch.

Apart from a sense of right and wrong, my motivation to find the watch’s owner would fundamentally stem from the conviction that the watch didn’t simply come into existence spontaneously from the materials in the environment through the outworking of the laws of physics and chemistry. If it did, why should I feel compelled to try to find the watch’s rightful owner?

But, at some level, I would feel obligated to try to find the owner. Why? Because I know that the watch must have belonged to someone who purchased it with his or her hard-earned money from a store or vendor. More than likely, the merchant got the watch from a distributor; and the distributor from the manufacturer. Ultimately, the watch traces from buyer to manufacturer. The manufacture of the watch, of course, required the work of a watchmaker.

The Watchmaker Argument The reasoning that hopefully would lead me to seek out the watch’s owner undergirds one of history’s best-known arguments for God’s existence: the Watchmaker Argument. This argument was posited by 18th-century Anglican natural theologian William Paley (1743-1805). In the opening pages of his 1802 work, Natural Theology, or Evidences of the Existence and Attributes of the Deity Collected from the Appearances of Nature, Paley sets the stage for his famous Watchmaker Analogy.

In crossing a heath, suppose I pitched my foot against a stone, and were asked how the stone came to be there, I might possibly answer, that for any thing I knew to the contrary it had lain there for ever…But suppose I had found a watch upon the ground, and it should be inquired how the watch happened to be in that place, I should hardly think of the answer which I had before given, that for any thing I knew the watch might have always been there. Yet why should not this answer serve for the watch as well as for the stone; why is it not as admissible in the second case as in the first? For this reason, and for no other, namely, that when we come to inspect the watch, we perceive—what we could not discover in the stone—that its several parts are framed and put together for a purpose, e.g. that they are so formed and adjusted as to produce motion, and that motion so regulated as to point out the hour of the day; that if the different parts had been differently shaped from what they are, or placed after any other manner or in any other order than that in which they are placed, either no motion at all would have been carried on in the machine, or none which would have answered the use that is now served by it…

This mechanism being observed…the inference we think is inevitable, that the watch must have had a maker?that there must have existed, at some time and at some place or other, an artificer or artificers who formed it for the purpose which, we find it actually to answer, who comprehended its construction and designed its use…

For Paley, the characteristics of a watch and the complex interaction of its precision parts for the purpose of telling time implied the work of an intelligent designer. Paley asserted, by analogy, that just as a watch requires a watchmaker, so too, life requires a Creator, since organisms display a wide range of features characterized by the precise interplay of complex parts for specific purposes.

According to the watchmaker analogy:

Watches display design. Watches are the product of a watchmaker.

Organisms display design. Therefore, organisms are the product of a Creator.

The Skeptics’ Challenge

The Watchmaker Argument hasn’t fared well over the centuries. Skeptics often point to David Hume’s critical analysis of design arguments, which appeared in his 1779 work Dialogues Concerning Natural Religion as devastating to Paley’s case for the Creator. Hume leveled several criticisms against design arguments. The foremost, however, centered on the nature of analogical reasoning.

Based on Hume’s arguments, skeptics curtly dismiss the Watchmaker Argument, maintaining that the two things compared—organisms and watches—are too dissimilar for a good analogy. (See pages XX.) Hume asserted that the strength of an analogical argument depends on the similarity of the two things compared, insisting that

whenever you depart, in the least, from the similarity of the cases, you diminish proportionably the evidence; and may at last bring it to a very weak analogy, which is confessedly liable to error and uncertainty.

The merit of the Watchmaker Argument then rests on two questions: Do living systems resemble man-made machines enough to warrant the analogy between the two? If so, how strong is this analogy and, consequently, the conclusion that can reasonably be drawn from it?

Molecular Motors Revitalize the Watchmaker Argument

The discovery of biomolecular motors and machines inside the cell gives new life to the Watchmaker Argument. In many instances, this molecular-level biomachinery stands as a strict analog to man-made machinery and represents a potent response to the legitimate criticism leveled by Hume and others. The biomachines found in the cell’s interior reveal a diversity of form and function that mirrors the diversity of designs produced by human engineers. The one-to-one relationship between the parts of man-made machines and the molecular components of biomachines is startling. Paley’s case for the Creator only becomes stronger with every new example of a biomotor that biochemists discover.

As remarkable as these biomachines are, perhaps none are as provocative as the biochemical timekeeping devices discovered in cyanobacteria.

Paley’s Biochemical Watch

Just as William Paley might have “pitched [his] foot against a watch” while “crossing a heath (field),” Yale biochemist Jimin Wang stumbled onto a mechanical molecular clock inside cyanobacteria (photosynthetic blue-green alga) while performing a structural analysis of the Kai proteins.

The KaiA, KaiB, and KaiC proteins play an integral role in the circadian oscillation that regulates the metabolic processes of cyanobacteria.

The biochemical activity of cyanobacteria varies periodically in response to the light-dark cycle, with certain metabolic activities repressed, or shut down, during the night. The KaiC protein is key to the cyanobacterial circadian rhythm. When its levels are high inside the cell, it represses gene expression. When its levels are low, gene expression is stimulated.

At night, the KaiC protein forms complexes with the KaiA and KaiB proteins. During daylight hours, the KaiABC complexes dissociate. Six KaiC proteins interact to form a ring-like structure. Two copies of the KaiA protein interact to form a structure that operates like a rotor inside the KaiC ring. A spring-loaded mechanism causes the KaiA protein duplex to alternate between two forms (like the opening and closing of a pair of scissors), one that interacts with the KaiC complex channel and one that does not. The KaiB protein functions like a wing nut that fastens the KaiA duplex to the bottom of the KaiC complex.

The KaiA duplex rotates within the channel, with the KaiB wing nut controlling the rotation rate of the KaiA rotor. As the KaiA rotor steps through the KaiC channel, a cam sequentially causes changes to each of the KaiC proteins. This mechanical action causes phosphate chemical groups to attach to the KaiC proteins. When fully phosphorylated, the KaiC complex dissociates. The formation and dissociation of the KaiABC complex regulates the KaiC levels inside the cell, which, in turn, controls the cyanobacterial circadian oscillation.

Once the KaiABC complex is assembled, it’s the mechanical clock-like rotary action of the KaiA duplex within the KaiC channel that controls its stability through the phosphorylation of the individual KaiC proteins.

According to Wang,

The Kai complexes are a rotary clock for phosphorylation, which sets up the destruction pace of the night-dominant Kai complexes and the timely releases of KaiA.

In Paley’s words,

This mechanism being observed…the inference we think is inevitable, that the watch must have had a maker.

Posted by Fazale ‘Fuz’ Rana, Ph.D.

Kai ABC Proteins Re-invigorate the Watchmaker Argument for God’s Existence

Suppose I discover a Rolex™ watch lying on the sidewalk in front of the Reasons To Believe offices. Without hesitation I would pick it up. My lucky day!

My first inclination would be to keep the watch. But, I would like to think that after the initial excitement of finding such a valuable time piece, I would decide to make a reasonable effort to find the person who lost the watch.

Apart from a sense of right and wrong, my motivation to find the watch’s owner would fundamentally stem from the conviction that the watch didn’t simply come into existence spontaneously from the materials in the environment through the outworking of the laws of physics and chemistry. If it did, why should I feel compelled to try to find the watch’s rightful owner?

But, at some level, I would feel obligated to try to find the owner. Why? Because I know that the watch must have belonged to someone who purchased it with his or her hard-earned money from a store or vendor. More than likely, the merchant got the watch from a distributor; and the distributor from the manufacturer. Ultimately, the watch traces from buyer to manufacturer. The manufacture of the watch, of course, required the work of a watchmaker.

The Watchmaker Argument The reasoning that hopefully would lead me to seek out the watch’s owner undergirds one of history’s best-known arguments for God’s existence: the Watchmaker Argument. This argument was posited by 18th-century Anglican natural theologian William Paley (1743-1805). In the opening pages of his 1802 work, Natural Theology, or Evidences of the Existence and Attributes of the Deity Collected from the Appearances of Nature, Paley sets the stage for his famous Watchmaker Analogy.

In crossing a heath, suppose I pitched my foot against a stone, and were asked how the stone came to be there, I might possibly answer, that for any thing I knew to the contrary it had lain there for ever…But suppose I had found a watch upon the ground, and it should be inquired how the watch happened to be in that place, I should hardly think of the answer which I had before given, that for any thing I knew the watch might have always been there. Yet why should not this answer serve for the watch as well as for the stone; why is it not as admissible in the second case as in the first? For this reason, and for no other, namely, that when we come to inspect the watch, we perceive—what we could not discover in the stone—that its several parts are framed and put together for a purpose, e.g. that they are so formed and adjusted as to produce motion, and that motion so regulated as to point out the hour of the day; that if the different parts had been differently shaped from what they are, or placed after any other manner or in any other order than that in which they are placed, either no motion at all would have been carried on in the machine, or none which would have answered the use that is now served by it…

This mechanism being observed…the inference we think is inevitable, that the watch must have had a maker?that there must have existed, at some time and at some place or other, an artificer or artificers who formed it for the purpose which, we find it actually to answer, who comprehended its construction and designed its use…

For Paley, the characteristics of a watch and the complex interaction of its precision parts for the purpose of telling time implied the work of an intelligent designer. Paley asserted, by analogy, that just as a watch requires a watchmaker, so too, life requires a Creator, since organisms display a wide range of features characterized by the precise interplay of complex parts for specific purposes.

According to the watchmaker analogy:

Watches display design. Watches are the product of a watchmaker.

Organisms display design. Therefore, organisms are the product of a Creator.

The Skeptics’ Challenge

The Watchmaker Argument hasn’t fared well over the centuries. Skeptics often point to David Hume’s critical analysis of design arguments, which appeared in his 1779 work Dialogues Concerning Natural Religion as devastating to Paley’s case for the Creator. Hume leveled several criticisms against design arguments. The foremost, however, centered on the nature of analogical reasoning.

Based on Hume’s arguments, skeptics curtly dismiss the Watchmaker Argument, maintaining that the two things compared—organisms and watches—are too dissimilar for a good analogy. (See pages XX.) Hume asserted that the strength of an analogical argument depends on the similarity of the two things compared, insisting that

whenever you depart, in the least, from the similarity of the cases, you diminish proportionably the evidence; and may at last bring it to a very weak analogy, which is confessedly liable to error and uncertainty.

The merit of the Watchmaker Argument then rests on two questions: Do living systems resemble man-made machines enough to warrant the analogy between the two? If so, how strong is this analogy and, consequently, the conclusion that can reasonably be drawn from it?

Molecular Motors Revitalize the Watchmaker Argument

The discovery of biomolecular motors and machines inside the cell gives new life to the Watchmaker Argument. In many instances, this molecular-level biomachinery stands as a strict analog to man-made machinery and represents a potent response to the legitimate criticism leveled by Hume and others. The biomachines found in the cell’s interior reveal a diversity of form and function that mirrors the diversity of designs produced by human engineers. The one-to-one relationship between the parts of man-made machines and the molecular components of biomachines is startling. Paley’s case for the Creator only becomes stronger with every new example of a biomotor that biochemists discover.

As remarkable as these biomachines are, perhaps none are as provocative as the biochemical timekeeping devices discovered in cyanobacteria.

Paley’s Biochemical Watch

Just as William Paley might have “pitched [his] foot against a watch” while “crossing a heath (field),” Yale biochemist Jimin Wang stumbled onto a mechanical molecular clock inside cyanobacteria (photosynthetic blue-green alga) while performing a structural analysis of the Kai proteins.

The KaiA, KaiB, and KaiC proteins play an integral role in the circadian oscillation that regulates the metabolic processes of cyanobacteria.

The biochemical activity of cyanobacteria varies periodically in response to the light-dark cycle, with certain metabolic activities repressed, or shut down, during the night. The KaiC protein is key to the cyanobacterial circadian rhythm. When its levels are high inside the cell, it represses gene expression. When its levels are low, gene expression is stimulated.

At night, the KaiC protein forms complexes with the KaiA and KaiB proteins. During daylight hours, the KaiABC complexes dissociate. Six KaiC proteins interact to form a ring-like structure. Two copies of the KaiA protein interact to form a structure that operates like a rotor inside the KaiC ring. A spring-loaded mechanism causes the KaiA protein duplex to alternate between two forms (like the opening and closing of a pair of scissors), one that interacts with the KaiC complex channel and one that does not. The KaiB protein functions like a wing nut that fastens the KaiA duplex to the bottom of the KaiC complex.

The KaiA duplex rotates within the channel, with the KaiB wing nut controlling the rotation rate of the KaiA rotor. As the KaiA rotor steps through the KaiC channel, a cam sequentially causes changes to each of the KaiC proteins. This mechanical action causes phosphate chemical groups to attach to the KaiC proteins. When fully phosphorylated, the KaiC complex dissociates. The formation and dissociation of the KaiABC complex regulates the KaiC levels inside the cell, which, in turn, controls the cyanobacterial circadian oscillation.

Once the KaiABC complex is assembled, it’s the mechanical clock-like rotary action of the KaiA duplex within the KaiC channel that controls its stability through the phosphorylation of the individual KaiC proteins.

According to Wang,

The Kai complexes are a rotary clock for phosphorylation, which sets up the destruction pace of the night-dominant Kai complexes and the timely releases of KaiA.

In Paley’s words,

This mechanism being observed…the inference we think is inevitable, that the watch must have had a maker.

Breakthrough May Revolutionize Stem Cell Research

Originally posted on July 19th, 2007

I have always wanted to have my cake and eat it too, but alas, that have-it-all scenario is not possible. Or is it? Breakthroughs by scientists from Kyoto University in Japan and MIT and Harvard University in the US now make it possible to generate embryonic-like stem cells (ELSCs) without destroying human embryos. These research teams produced ELSCs from mice adult skin cells. Neither eggs nor embryos were necessary.

The biomedical community hopes that embryonic stem cell research (ESCR) will lead to techniques that can generate replacement tissues from embryonic stem cells (ESCs). They claim that implanting replacement tissue derived from ESCs into damaged and diseased organs provides the means to treat and possibly cure many horrendous diseases and debilitating injuries. Unfortunately, in order to harvest stem cells from human embryos, the embryo must be destroyed.

In addition to ethical concerns, use of ESCs is riddled with several serious technical problems. Perhaps the largest hurdle facing this biotechnology is rejection due to genetic mismatch between the ESCs and the patient. This problem is identical to rejection that can occur after organ transplant procedures. If the donor and recipient are not compatible, the recipient’s body rejects the organ. It’s almost certain that the recipient’s body will treat genetically incompatible ESCs as foreign material and reject the cells before they can deliver any promised benefit.

Both research teams were able to transform skin cells called fibroblasts into ELSCs by transferring four genes into these easily isolated cells using a retrovirus as a carrier. The ELSCs can develop into all the different cell types in the human body, just like ESCs. ELSCs don’t raise any ethical concerns, however, since they derive from adult cells, not embryos. Biomedical applications of ELSCs won’t be frustrated by rejection because the fibroblasts used to produce them can be taken from the patient.

At this point, it is not clear if human fibroblasts can be coaxed to form ELSCs. Safety concerns are also a factor. Researchers are troubled by the use of a retrovirus to introduce genes into the fibroblast. They are also cautious because one of the transforming genes is involved in tumor formation. Still, the initial results are exciting and future work should address these potential pitfalls.

The discovery of methods to generate ELSCs from adult fibroblasts augments exciting advances already taking place with adult stem cells. These cells can be readily isolated from adult tissues like scalp, dental pulp, bone marrow, the olfactory bulb, the umbilical cord, and the placenta. No embryos are destroyed and no human life is lost in the process of isolating adult stem cells.

Numerous new discoveries indicate that several types of adult stem cells behave like embryonic stem cells. Under laboratory conditions these adult stem cells can be coaxed to develop into a wide range of cell types that are suitable for use in tissue replacement therapies. An increasing number of biomedical researchers are focusing their efforts on adult stem cells. The number of papers published in scientific journals on adult stem cells and their potential as therapeutic agents is growing week by week. Use of adult stem cells in tissue replacement therapies has an added advantage. Adult stem cells do not suffer from the problems associated with use of embryonic stem cells, like rejection and tumor formation.

As biomedical applications for adult stem cells (and hopefully ELSCs) matriculate to clinical applications, treatments for diseases and injuries that cause dreadful human suffering will be available without requiring the destruction of human embryos. That prospect leaves a good taste in my mouth.

Now if only someone could come up with cake that can be eaten without causing weight gain…

For more information on stem cell research see “A collection of interview questions posed to, and answered by, Dr. Fazale “Fuz” Rana.â€?