January 28, 2013

Often when I argue that cells are infused with information driven molecular machinery and that this observation constitutes the basis for a readily falsifiable theory on why the cell is the product of the effort of a mind, opponents will accuse me of over-extending the use of the word ‘machine’. That is why I appreciate animations like the one below – it clearly depicts a molecular motor, that has been an integral part of cells since the beginning of life. It is clearly a mechanism composed of multiple integrated and highly interdependent parts that both convert energy into work, and provide the fuel on which the rest of the cell subsists.

The ATP synthase is definitely an information driven molecular machine, and the best explanation of its existence is that it was designed by a mind.


The Ancient Brain

October 16, 2012

One of the major contentions of evolutionary theory is that it explains how organisms become more complex over time. This is a critical aspect because it is unimaginable that complex organisms would spring forth fully formed as the product of natural unguided forces. So evolutionists imagine mutations and natural selection acting in concert to ratchet organisms up the scale of complexity in a step-wise fashion. In this scenario evolution is a tinkerer, not planning, anticipating and directing change but incidentally modifying structures and occasionally stumbling upon beneficial solutions. There are many solid arguments against this idea with more gaining traction all the time, but perhaps the biggest reason to doubt the orthodox evolutionary view is that it simply don’t describe what actually happened in the history of life. There are in fact two realities (amongst others) that weigh against evolution, and they are the evident early complexity of organisms and the enduring stasis of organisms over time. Both are seen in a recent fossil discovery from the Cambrian era:

Complex brains evolved much earlier than previously thought, as evidenced by a 520-million-year-old fossilized arthropod with remarkably well-preserved brain structures.

The remarkably well-preserved fossil of an extinct arthropod shows that anatomically complex brains evolved earlier than previously thought and have changed little over the course of evolution. According to University of Arizona neurobiologist Nicholas Strausfeld, who co-authored the study describing the specimen, the fossil is the earliest known to show a brain.

The researchers call their find “a transformative discovery” that could resolve a long-standing debate about how and when complex brains evolved.

“No one expected such an advanced brain would have evolved so early in the history of multicellular animals,” said Strausfeld, a Regents Professor in the UA department of neuroscience.

Of course no who believed brains developed according to ordinary evolutionary theory expected that an advanced brain would have evolved so early in the history of life and persisted for so long, but the reality poses no problem for those who believe life was intentionally designed. Such unexpected findings are found so often now that one becomes surprised when scientists are surprised – but as long as they cling to decrepit ideas about evolution, they will continue to be surprised at how complexity made an early appearance in earth’s history and persisted through the changing eons – which is exactly what one would expect if they had been engineered to live here on earth to begin with.

Fairness and the Monkey Mind

September 24, 2012

One ongoing contention by atheists is that God is unnecessary to ground morality because humans are naturally social and interdependent creatures who have inherited these characteristics from their evolutionary forebears. As evidence for this contention they often point to examples of certain social behaviors in apes and monkeys, our presumed nearest non-human cousins. We’ll ignore certain nasty behaviors by such animals (and why such behaviors aren’t equally ‘moral’ by this estimation) for now and examine instead a concept that is generally seen as moral in the Christian West – fairness.

In an August post called Where does morality come from? A demonstration with monkeys atheist and evolutionist cheerleader Jerry Coyne (who seems to be a big fan of these sort of studies) attributes the reactions of a capuchin to not receiving a grape in exchange for a rock during the course of an experiment to the monkey’s sense of ‘fairness’, a characteristic he considers to be a basis for morality:

This video is about as powerful a refutation I’ve seen of the notion that our morality is given by God rather than either evolved or a product of our culture. This is taken from a wonderful TED talk by Frans de Waal, primatologist and author of several popular books. His talk is called “Moral behavior in animals”, and is witty and full of insights (you can also watch it here if you don’t have the right Flash player).

Do watch the whole talk, as you’ll learn a lot about “morality” in our mammalian relatives, and there are several nice videos. In the one I show below, two naive capuchin monkeys display what looks for all the world like a reaction to “unfairness” (the video appears about 3/4 of the way through de Waal’s talk). As de Waal notes, cucumbers are okay food for the monkeys, but they really like grapes (de Waal claims that monkeys like food in proportion to its price at the supermarket). A pair of capuchins can see each other getting cucumbers and grapes (they have to give the experimenter a rock before they get a piece of food).

See what happens when one of them is given a grape for his rock, and the other a cucumber. Remember, this is the first time these monkeys have been subject to this procedure:

So in the estimation of Jerry Coyne the capuchin’s reaction is an offense to the monkey’s sense of fairness. How does he know this? Because the monkey appears to be reacting in a manner a human might act when they are frustrated by being treated unfairly. And from this appearance he comes to the conclusion that this sense of fairness humans concern themselves with can be understood to derive from our animal ancestors and we can dismiss with God.

Now its possible monkeys have some idea of fairness. It’s possible other animals do. I have a Golden Retriever that gets petulant when I don’t take her with me when I run an errand. The response is similar to that of a three year old that declares it’s “Just not fair” that they didn’t get to go to the park. There is no reason why I as a Christian would deny the existence of such sensations in animals – but is such frustration really the basis for our moral notion of fairness? This is where I think comparisons start to break down.

Fairness in humans of course is a much more idealistic concept than mere frustration at unexpected treatment. We have entire social and political system designed specifically to ensure fairness. We even have symbols of fairness like Lady Justice, a symbol which goes back to the Ancient Egyptians. It is the notion that there is an underlying moral order against which actions should be evaluated without regard for the individual conducting the actions. So the human notion of fairness or the closely related concept of justice is not merely an innate reaction, but a sense that there is way the world ought to be and certain circumstances contradicted this ideal. There is no evidence capuchins are motivated by such ideals.

Of course, Jerry Coyne is inclined to see the rudiments of these ideals in the grasping of a monkey for a grape because he has a belief system which is supported by interpreting monkey responses this way. Though he would call such observations scientific, the reality is such experiments are far from empirical since we have no idea what is happening in the minds of these animals as they react. Both Coyne’s ideas about what fairness is and how he interprets such reactions are highly subjective. Indeed these sorts of experiments have soiled the scientific reputations of other researchers like Marc Hauser who bet his career on interpreting the motivations of monkeys and ended up resigning his position at Harvard due in part to the inherently interpretive nature of such studies.

Atheist tend to cherry pick such studies. Because they have an a priori commitment to naturalism, they are forced to believe that human morality must have been the product of evolutionary development from ape-like ancestors. So any animal behavior that slightly resembles a human action motivated by a moral precept is interpreted as evidence for this notion. Of course, atheists tend to ignore studies that that indicate our presumed ape relatives actually have little interest in fairness, like the one recently published in Biology Letters aptly titled, Theft in an ultimatum game: chimpanzees and bonobos are insensitive to unfairness. In the study researchers set up a scenario where the apes could choose to leave a portion of grapes for the group mates. This is what Professor Keith Jensen, from Queen Mary’s School of Biological and Chemical Sciences observed:

“In each scenario one ape had to choose whether to steal the grapes or leave a portion of grapes for the other. We found that consistently they would steal the food without taking into account whether their action would have an effect on their partner. Neither the chimpanzees nor bonobos seemed to care whether food was stolen or not, or whether the outcomes were fair or not, as long as they got something. Our findings support other studies of chimpanzees but also extend these to bonobos. Both apes have no concern for fairness or the effects that their choices may have on others; in stark contrast to the way humans behave. We can therefore conclude that our results indicate that our sense of fairness is a derived trait and may be unique to the human race.”

Presumed similarities between the behavior humans and apes always lead atheists to conclude they are related, but the opposite is never true – when their behaviors so obviously diverge, atheists never take from that fact that humans have instilled in them something unique that was not merely the result of naturalism.

But then again atheism is never a product of evidence.

The Reality of Biology

August 8, 2012

I have often contended that the most basic components of a living cell are essentially information driven molecular machinery. In other words there are two primary components on the mechanical level – information which contains sets of instructions and machinery to read those instructions and carry them out. And this isn’t a mere analogy – that is actually what we find in the cell in terms of its processes and mechanics. I was reminded of this again when reading comments by geneticist Craig Venter in an article in New Scientist:

“All living cells that we know of on this planet are ‘DNA software’-driven biological machines comprised of hundreds of thousands of protein robots, coded for by the DNA, that carry out precise functions,” said Venter. “We are now using computer software to design new DNA software.”

Now I have no doubt Venter thinks this software and machinery evolved. Given that he isn’t a theist, he has to believe this. But that fact is irrelevant to the point that he has correctly identified the essential nature of life and how it operates. He has not only identified it, but he has put that knowledge into practice by programing the software and using it to operate the machinery of the cell showing further that cellular systems are not merely analogous to information systems but in fact are information processing systems.

This fact should be the greatest cause of skepticism of materialism and naturalism when we come to understand that there is not a single shred of evidence that such systems can come about through unguided processes. The only known and demonstrable way to develop machinery which processes information is through planning, design and application of the knowledge of such systems. It might have been possible before we ourselves developed such systems to imagine they could originate from natural processes, but now that we have been engineering such sophisticated technology ourselves for decades such a belief is no longer an intellectually valid option. And given that the knowledge gained by our own development is applicable to the technology found in the cell tells us that they share a common original mechanism.

Now one could still imagine that life developed through a series of incidental modifications to these core systems to develop the diversity we see on earth today. One could also look at the similarities contained within the software that operates all of life and imagine that the systems all share a common origin at some point at time. I think there are better explanations, but an intellectually honest person could imagine these things. What one could not claim and be a person of intellectual honesty and or understanding is that the system of software and requisite machinery originated apart from the knowledge necessary to build such systems. To believe such a thing would be to ignore everything we know about information processing, software development and machine engineering

In other words, that one could only believe life originated as the result of unguided mechanical processes is by neccesity a tenet of utterly blind faith.

A Primer on Intelligent Design

July 16, 2012

*This post was originally published June 8th, 2006*

I mentioned in an earlier post that I had long been interested in the science of life and its origins and I have spent a number of years exploring the intersection between science and faith. In recent years the conversation has centered primarily on Intelligent Design, a theory much talked about in the media, courts, schools and scientific circles. To that end I wanted to give those unfamiliar with the ins and outs of the issue an overview of the discussion to date.

Below are a series of questions and answers about Intelligent Design. I attempted to be as even-handed as possible though I readily acknowledge that in general I support intelligent design as a scientific theory.

What is Intelligent Design (ID)?

Intelligent Design is the scientific theory that states that certain features of the universe and of living things are best explained by an intelligent cause not an undirected process such as mutation and natural selection. It is a theory promulgated to answer this question, posed by William Dembski, an originator of the theory of ID, and one of its primary proponents:

Can objects, even if nothing is known about how they arose, exhibit features that reliably signal the action of an intelligent cause?

That question can be asked by anybody regardless of metaphysical belief; and the answer, presumably, wouldn’t require a particular belief either.

To that end, two main criteria have been proposed to determine the earmarks of intelligent activity in the formation of an object (or organism) – they are irreducible complexity, and specified complexity.

Irreducible complexity is drawn from a statement by Charles Darwin:

“If it could be demonstrated that any complex organ existed which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down.”
–Charles Darwin, The Origin of Species: A Facsimile of the First Edition, Harvard University Press, 1964, p. 189

Thus Michael Behe describes an irreducibly complex system this way:

“A single system which is composed of several interacting parts that contribute to the basic function and where the removal of any one of the parts causes the system to effectively cease functioning”
–Michael Behe, Darwin’s Black Box, p. 9

In simpler terms if you have a mechanism (for example, a mousetrap) you can only reduce that mechanism down to a certain number of parts before it ceases to function in any useful way. In biological terms all the parts to a irreducibly complex biological system must be in place at once in order for it to function in any useful way and confer a survival advantage to the organism. Thus, such systems could not be formed by a series of gradual modifications as required by Darwinian evolution.

In the case of specified complexity, developed by William Dembski, the idea really centers on information patterns. If a pattern is both specified (that is fits a defined arrangement) and complex it is a reliable marker of intelligent activity. Thus a mountain side may be complex, that is made up of a variety of materials, but it isn’t specific in its arrangement. A crystalline structure like a diamond might be specific because its structure is organized in uniform a pattern but they aren’t complex.

Intelligence allows for patterns that are both specified (organized in discernible pattern) and complex, like written languages, computers codes and machines. In short, it allows us to discern the degree to which intelligence played a part in the formation of Mount Rushmore versus the natural formation of a cliff wall.

These two criteria form the basis of intelligent design theory.

Does ID disprove evolution?

ID is primarily a criticism of evolution on one specific point; primarily that undirected causes such as mutation and natural selection aren’t sufficient alone to account for the current genetic diversity we see in biological systems. Beyond that it allows for other evolutionary concepts such as common descent, adaptive radiation and natural selection.

Intelligent Design also acts as a critique of the natural origin of life and the universe though this is not a criticism of evolutionary theory per se  because evolutionary theory isn’t an attempt to explain the origin of life and the universe.

Is ID Creationism?

No – ID and Creationism have fundamentally different goals; creationism attempts to reconcile the narrative of Genesis with scientific theory while ID simply attempts to answer this simple question – Can objects, even if nothing is known about how they arose, exhibit features that reliably signal the action of an intelligent cause? Of course, creationists often find the information ID provides as useful (just as they sometimes find the information provided by other sciences as useful) but this doesn’t make ID and creationism the same thing.

Is ID science?

This depends how one defines science. If the standard definition is used that science is any idea arrived at through hypothesis, repatable observation, investigation and testing  then yes, ID qualifies as science.

If one adds the current addendum that all explanations must be the product of wholly natural phenomenon (that is, non-intelligent, or non-directed forces) as does methodological naturalism, then ID wouldn’t qualify as science. If methodological naturalism is a required assumption of science, then science itself conceivably prevents us from answering fundamental questions about the origin of the universe, life and the origin of species by dismissing viable explanations.

Didn’t the court rule ID wasn’t science?

In the Kitzmiller v. Dover case Judge John E. Jones III ruled that ID was not science and as such could not be taught in the science classroom. If one holds that courtrooms are where science is conducted, then yes, at least in the Middle District of Pennsylvania ID is not science,; though of course the court also ruled ID may be true.

It should be noted that to this day, evolution is the only scientific theory which requires court protection from detractors in order to maintain viability.

Aren’t all supporters of intelligent design Christians?

No, actually a number of them aren’t; among non-Christian ID supporters we have Anthony Flew (Agnostic), Michael Denton (agnostic), Mustafa Akyol (Muslim), Slade Gorton (Jewish). Of course, whether or not they are Christian is rather irrelevant; one could safely say 95% of atheists are evolutionists of one stripe or another, but that doesn’t really say anything about whether or not evolution is the best explanation for the existence and variety of life on earth.

Does ID hurt science or science education?

I have always been perplexed by this idea; that somehow if ID were accepted as a viable alternative to evolution that all critical thinking would end. This runs counter to two obvious facts, the first being that historically science in large part is the product of a Christian culture that had no problem reconciling the existence of a Creator with natural exploration. In fact many great scientists among them Newton, Kepler, Bacon, and Pascal were notable commentators on theology as well as scientific icons.

The second obvious fact is that the debate between evolution and intelligent design is perhaps one of the most vibrant scientific discussions of the twenty-first century. It has driven an interest and exploration into origins and genetic capability, and the very structure of life. There is really only one side who wants to shut down discussion in the debate, and that side isn’t supporters of intelligent design.

I hope this helps further the discussion now going on about Intelligent Design both for supporters, critics and the casual observer.

Did We Evolve To Argue?

August 30, 2011

File this one under ‘Stuff I Wanted to Blog About This Summer but Didn’t Find the Time’.

There was an interesting article in the New York Times last June titled, Reason Seen More as Weapon Than Path to Truth which describes a theory by Hugo Mercier and Dan Sperber, researchers in the cognitive sciences. The theory basically states that human reason evolved to “help us convince others and to be careful when others try to convince us”, not necessarily to discover the truth or accuracy of a belief. I find the idea fascinating because it underlines one of the fundamental flaws of the belief that human cognitive mechanisms are solely the product of evolutionary processes   – namely if our ability to think was the product of evolution alone, then there is no reason to believe that our beliefs are particularly rational. This has been articulated thoroughly by Alvin Plantinga, but here the authors take it in a different direction:

Other scholars have previously argued that reasoning and irrationality are both products of evolution. But they usually assume that the purpose of reasoning is to help an individual arrive at the truth, and that irrationality is a kink in that process, a sort of mental myopia. Gary F. Marcus, for example, a psychology professor at New York University and the author of “Kluge: The Haphazard Construction of the Human Mind,” says distortions in reasoning are unintended side effects of blind evolution. They are a result of the way that the brain, a Rube Goldberg mental contraption, processes memory. People are more likely to remember items they are familiar with, like their own beliefs, rather than those of others.

What is revolutionary about argumentative theory is that it presumes that since reason has a different purpose — to win over an opposing group — flawed reasoning is an adaptation in itself, useful for bolstering debating skills.

Mr. Mercier, a post-doctoral fellow at the University of Pennsylvania, contends that attempts to rid people of biases have failed because reasoning does exactly what it is supposed to do: help win an argument.

“People have been trying to reform something that works perfectly well,” he said, “as if they had decided that hands were made for walking and that everybody should be taught that.”

This theory, like others based on the assumption that human cognition evolved naturally is as likely as any other speculation about the development of human reason. If it’s true, it means atheists are as presumptive in their ideas as Christians, and as likely to cling to their beliefs regardless of the evidence to the contrary. This renders the notion that they have come to their beliefs in a more ‘rational’ manner moot, as in reality they simply were convinced by a skilled debater, and are simply now following their propensity to defend their beliefs. The idea that there is truth or reality to be discerned is moot – we are all mere products of our cognitive development. There is no basis for an atheist to argue that he or she can rise above this.

Indeed the only confident and consistent way to argue for the ability to discern truth is if one believes one has been given cognitive equipment to do so; this could only be the case if a designer of human minds actually exists.

Of course if atheists are correct, then what is true about this matter is an argument we can never have.

Laetoli Footprints Keep on Walking

July 28, 2011

I have written previously about the Laetoli footprints and what they tell us about the history of humanity. Like all good science, there has been further research on the subject that confirms my original contention – that at a time when our ancestors were supposed to be the small, ape-like Australopithecus afarensis, something very like a modern human was walking around. From the article:

Quite remarkably, we found that some healthy humans produce footprints that are more like those of other apes than the Laetoli prints. The foot function represented by the prints is therefore most likely to be similar to patterns seen in modern-humans. This is important because the development of the features of human foot function helped our ancestors to expand further out of Africa.

 “Our work demonstrates that many of these features evolved nearly four million years ago in a species that most consider to be partially tree-dwelling. These findings show support for a previous study at Liverpool that showed upright bipedal walking originally evolved in a tree-living ancestor of living great apes and humans. Australopithecus afarensis, however, was not modern in body proportions of the limbs and torso.

“The characteristic long-legged, short body form of the modern human allows us to walk and run great distances, even when carrying heavy loads. Australopithecus afarensis had the reverse physical build, short legs and a long body, which makes it probable that it could only walk or run effectively over short distances. We now need to determine when our ancestors first became able to walk or run over the very long distances that enabled humans to colonise the world.”

In short, what scientists have long contended to be our primitive ancestor, Australopithecus afarensis, can’t have made those footprints, and thus is unlikely to have been our ancestor.

This fact demonstrates a few problems with evolutionary paleontology – the first is that many evolutionary trees are constructed on presumptions about what think our ancestors must have looked like. Australopithecus fit the image of an ape-like intermediary, and so scientists held it up as ‘proof’ of that ancestry. The problem is, absent genetic evidence, such contentions are always guesswork, guesswork that we now know to be wrong in this instance.

It also demonstrates that our paleontological record of human history is still very incomplete. Obviously something else existed at the time of Australopithecus which made those footprints – yet we have no fossil record of such a creature other than these footprints. This tells us that the story of our biological ancestry is still largely unknown, despite assurances from evolutionists.

Obviously, as someone who believes humans are the product of design, I have no problem with an ancient human with the modern ability to walk upright.