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 Programming of Life

December 19, 2012

There was a revealing article recently on ScienceDaily concerning a novel approach to determining how life originated. Up until now most scientists have been trying to chemically synthesize the organic compounds integral to the structures of life in hopes of determining how life might have originated through natural processes. To say the least this has been an abysmal failure. There is in fact no evidence that living organisms originated through unguided natural processes. One of the reasons it has been a failure is because scientists have attempted to reconstruct the chemical structures of life, while ignoring the fact that life at its core is an information processing system – something I have been pointing out for years. Now it seems that some scientists are finally coming to the same conclusion:

Now, a novel approach to the question of life’s origin, proposed by two Arizona State University scientists, attempts to dramatically redefine the problem. The researchers — Paul Davies, an ASU Regents’ Professor and director of the Beyond Center for Fundamental Concepts in Science, and Sara Walker, a NASA post-doctoral fellow at the Beyond Center — published their theory in the Dec. 12 issue of the Royal Society journal Interface.

In a nutshell, the authors shift attention from the “hardware” — the chemical basis of life — to the “software” — its information content. To use a computer analogy, chemistry explains the material substance of the machine, but it won’t function without a program and data. Davies and Walker suggest that the crucial distinction between non-life and life is the way that living organisms manage the information flowing through the system.

I for one applaud this change of strategy because at least it acknowledges the right problem. That being said, I am certain they will face the same frustrations those focused on the chemical origin of life have because information systems simply can’t originate apart from the intention of a mind.

Perhaps it will take a few more decades of failure for science to realize this obvious fact.


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.

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.

Fewer People Believe in Evolution

June 15, 2012

One common recent meme articulated by  atheists is the US is becoming more secular while Christianity is fading. There are various polls offered to that effect, and while I don’t disagree that more people are willing identify as atheists, I am not sure that this particularly indicative of the fact Christianity is fading in its influence in the US.

I think better explanation of what is happening is polarization; rather than there being a large middle ground of where people fall on matters of faith, they are being pushed to take sides in what has become a much more contentious discussion about the existence of God and the truth of Christianity. Part of this has to do with the success of more conservative churches and the fading of mainline religious institutions. Part of this has to do with the openness and combativeness of the New Atheists who have no toleration for those they call accommodationists, or those who allow for the notion that religious ideas inhabit a different sphere of thought than science does.

A recent Gallop poll gives some weight to that interpretation. Asking respondents whether they believe human beings have developed over millions of years from less advanced forms of life but God guided this process, human beings have evolved over millions of years from less advanced forms of life but God had no part in this process or whether God human beings pretty much in their present form at one time within the last 10,000 years, the survey found that 6% more people believed in the direct creation of humans than did just two years ago. This would seem to run counter to the notion that the US populace is becoming more ‘secular’ – particularly given the atheist position that God played no part in the development of humans dropped by a point. But the greatest drop was in what I would call the ‘middle’ position, the notion that God guided the development of humans over time. That notion dropped by an amount corresponding to the amount that the full blown creationist position increased. I think this is some indication that the middle ground is evaporating in the wrangling between Bible-believing Christians and the New Atheists.

While I don’t necessarily discount the idea that the U.S. is becoming more secular (the West certainly is to its growing detriment) and I think there are Christian principles that explain why this is so. But the current data suggest something else is going on, and that something else maybe a very refreshing distinction between the Christian and secular position that can’t be compromised away.

Not Your Father’s Evolution

April 10, 2012

SticklebackIt isn’t hyperbole to say that in recent years there has been a revolution in our ability to explore the genome. Though genome sequencing occurred as early as the ’70s, it burst into the national consciousness in 2000 when the Human Genome Project completed its first draft of a complete human genome. Since that time nearly 200 organisms have had their genomes sequenced giving us an ever increasing picture of the diversity of life.

This growing knowledge has also impacted our understanding of how organisms are related. Unlike previous methodologies which relied heavily on interpretations of morphological similarities to determine relationships between organisms (particularly in the fossil record), methods which were fairly subjective and vulnerable to the predispositions of the person studying the organism, genome sequencing is a much more objective methodology which relies on more rigorous analytical comparisons to determine relationships between organisms. It is also modifying our view on how the genome interacts with the environment and how changes actually occur there.

One such recent analysis of a genome has to do with that of the three-spined stickleback, a species (actually, multiple species) which are found throughout the world in both fresh and salt water habitats. The forms actually vary morphologically depending on the sort of environment they are found in, which presents a significant opportunity to study genetic adaptation to different environments as investigator David Stanley of Stanford explains in the Sciencedaily report:

“The cool thing about these fish is that they’ve colonized a whole series of new environments in the last 10,000 to 20,000 years,” says Howard Hughes Medical Institute (HHMI) investigator David Kingsley of Stanford University School of Medicine. As the glaciers melted at the end of the last ice age, marine sticklebacks ventured into fresh water, settling in rivers, lakes, and streams. The fish adapted to their new homes. Compared with their marine relatives, freshwater sticklebacks tend to be smaller and sleeker, with less bony body armor. The challenges of surviving in new habitats also prompted modifications to their teeth, jaws, kidneys, coloration, and numerous other traits. Moreover, this pattern of colonization and adaptation has repeated itself in several areas where sticklebacks live, including the east and west coasts of North America, western Europe, and eastern Asia. “A world-wide collection of lakes and streams became countless natural evolutionary experiments,”

Many might see in such findings substantive evidence for evolution – and on a small scale, having to do with a variety of variations possible in an organism, they would be right. But these findings are actually quite contrary to the sort of evolution often advocated by Darwinian evolutionists. Instead of incidental mutations coding sequences leading to the production of new proteins (and conceivably, novel structures and systems) the researchers found that the changes were primarily to the same sets of regulatory sequences in separate populations of sticklebacks:

For their latest study, Kingsley, scientists from the Broad Institute of MIT and Harvard, and an international team of collaborators started by sequencing the genome of an Alaskan freshwater stickleback to serve as a standard for comparison. That was an achievement in itself, yielding the first complete stickleback genome sequence. Next, the team followed suit with the genomes of twenty additional sticklebacks from around the world, including ten ocean stickleback varieties found around North America, Europe, and Japan, as well as the genomes of ten freshwater relatives from nearby freshwater locations. They then analyzed the sequences to identify DNA regions that changed whenever the fish made the move from salt water to fresh.

The researchers found 147 “reused” regions in the fish’s genome. That suggests that each time the fish left the sea, variants in this same group of genes helped remodel the fish into forms that were better suited to fresh water, Kingsley says.

While the researchers continue to use the term ‘evolutionary change’, the reality is this is nothing like the sort of change described by the modern evolutionary synthesis, a theory which relies on natural selection acting on genetic mutation. The very fact that the researcher describes these as “key genes that control evolutionary change” contradicts the ordinary notion of evolution itself, which is purportedly an unguided process. If natural selection acting on incidental mutations were actually capable of producing the radically different body plans, structures and systems we find throughout the plant and animal kingdoms, then we wouldn’t expect to see the consistent similarity of genetic modifications that we do with regard to the various populations of sticklebacks. The changes wouldn’t be a matter of merely regulating extant genes, but the origination of new genetic capabilities. As it is, the genetic variation in sticklebacks conforms closely to the expectations we would have if there were limits to evolution as proposed by Michael Behe in his book The Edge of Evolution. Genetic sequencing continues to demonstrate that there are limits to biological variation.

Biologist Francois Jacob famously said, “evolution is a tinkerer, not an engineer”; if that is the case then the various populations of stickleback can’t be said to have ‘evolved’ given that the variations they display appear to be the result of well-designed systems engineered to allow organisms to adapt themselves to a variety of environments.