On science and the superhuman.

Experience, Rational Debate; Science Depend On The Supernatural
Posted by William J Murray 

I’m going to lay out three basic arguments for belief in the supernatural. First, science itself would not be possible were it not for the effects of unseen, higher-order supernatural causes. Second, science and rational debate would not be possible unless we all have faith in the supernatural – unseen spirits not bound to material causes. Third, each of us has direct personal experience of the supernatural every waking second of every day.

Let’s first define what “supernatural” means. From Merriam-Webster:

of or relating to an order of existence beyond the visible observable universe; especially of or relating to God or a god, demigod, spirit, or devil.
unable to be explained by science or the laws of nature : of, relating to, or seeming to come from magic, a god, etc.
attributed to an invisible agent (as a ghost or spirit)

1: Science depends on measuring supernatural effects

We call these observable, reliable and measurable effects physical laws, forces and universal constants, but those terms are misleading, much like referring to “chance” as a causal agency. Those terms do not represent causal objects or energies we can point at, but are rather descriptions (or models) of observed patterns of behavior of matter and energy for which there is no known or observable cause. The names of these patterns and models are used as if they apply to causal things, but this is a conceptual error. When we say “gravity causes X to fall”, it is not gravity causing it because gravity is the description of the physics of the event. Something “causes it to fall”, but it is not gravity; it is whatever causes the pattern of behavior we call “gravity”.

What is the “natural world”?

The natural world is the set of phenomena that can be described and predicted according to behavioral and interactive constants. However, those laws and constants do not describe where or how such laws and constants exist in the first place, or what they are, or even how they are affecting physical phenomena. These invisible and mysterious causes are supernatural both by definition and logically because they: (1) necessarily relate to an order of existence beyond the observable natural world (since they cause the behavior that defines what we call “the natural world”, (2) are unable to be explained by science or the laws of nature (since science depends upon observing behavioral patterns, and behavioral patterns cannot explain what causes such patterns in the first place), and  (3) these patterns are attributed to invisible, unknown agents (which we erroneously refer to with objectifying terminology –  forces, constants and laws).

The science of the natural world depends upon an unknown, unseen superset of mysterious agencies causing the predictable, reliable, rationally understandable patterns of behavior we observe and describe as the set of natural-occurring phenomena.

2: Science & rational debate depend upon faith in the supernatural

Conducting science requires one to accept that humans have a free will capacity to identify objective facts about the universe and integrate them into theoretical systems that can be properly verified or disproved via true/false statements about experimental outcomes according to abstract principles assumed to be universally valid.  Logically, this means humans must have a capacity that transcends thought as the mere product of happenstance chemical interactions.  IOW, scientists must have faith that humans have the capacity to override whatever thoughts interacting chemicals happen to produce and instead force them down correct, truthful paths from an assumed objective viewpoint. Such a transcendent observational and willful capacity is necessarily supernatural, as the natural is only capable of producing whatever happenstance thoughts and “wilfulness” interacting chemicals happen to produce.

Rational debate depends upon the same assumption; that humans have some kind of non-physical agency which can supervise and override physical thought processes down paths which are correct according to abstract principles which are considered objectively binding. Such an agency is unseen and would necessarily have the power to intervene in the natural patterns producing thoughts and generating conclusions.

It is only by faith in such a supernatural agency and in the supernatural authority of abstract principles accepted as objectively valid that we can expect to be able to overcome the happenstance course of physical cause and effect in the course of our rational and scientific endeavors.

3: Everyone directly experiences the supernatural daily

Each of us experience ourselves as a seat of consciousness with direct, top-down, intentional, prescriptive control (to varying degrees) over the behaviors of many elements of our bodies and thinking processes.  We don’t know how to make various cellular or chemical reactions occur that are necessary for motion and thought. Somehow, without any technical or mechanical knowledge at all, with no understanding of how to initiate or control any of the various chemical and mechanical resources, simple intention can operate what is probably the most highly advanced and complex piece of equipment in the universe with amazing precision. Like a ghost inhabiting a doll out of a movie, our will alone can set physical forces in motion, control them, and stop them on command – no physics, chemistry or mechanical knowledge required whatsoever.  It is precisely like magic.

Furthermore, our will can instantly access any of virtually countless memories without any understanding whatsoever of how the memory process works or how the data retrieval process works.  We can simply intend to write or say something on a subject and gain immediate access to a seemingly never-ending stream of information corresponding to our intent. We can imagine things that do not even exist in the real world, our minds effortlessly rendering a massive virtual reality for us to experience as we daydream or sleep-dream. We cannot see this agency; we cannot explain how it can immediately differentiate from innumerable, variant intents to magically set billions of cellular processes and chemical interactions on a precise course to find memories, find or generate thoughtful, relevant information, or direct our body to precisely achieve a limitless variance of actions.

We experience this self-will as transcending mere physical causation from a higher order of existence, being able to direct the matter and energy of our bodies at will.  We have power over our physical and mental nature exactly like a supernatural ghost in a machine, capable of the most wondrous and amazing feats of physical complexity, creativity and computation without any understanding of how any of it is physically initiated, maintained or controlled.

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That all of these things are considered “mundane” hides their astounding, miraculous, supernatural nature.

On asking the right questions.

Foundational Question: Is Intelligent Design Science?

Steve Laufmann

Editor's note: Mr. Laufmann is a consultant in the growing field of Enterprise Architecture, dealing with the design of very large, very complex, composite information systems that are orchestrated to perform specified tasks in demanding environments.

It's long been said that the path to the right answers lies in asking the right questions. Better questions tend to yield better answers. Not-so-good questions may yield little, or even hide the answers. Some questions illuminate, others obfuscate.

Intelligent design provokes (at least) two foundational questions. I'll briefly address the first of these here, and the second in a subsequent article. First:

Is Intelligent Design Science?

This question is central in the ongoing debate about ID. It's argued about often, sometimes loudly, and occasionally well. Because the topic has been covered thoroughly in this forum and others, I'll present here just five observations about how this question is asked, debated, and answered.

1. The answer is yes, intelligent design is science, though not everyone knows it yet.

However, the reasons behind this are understood neither widely nor well. In my experience there are two common areas of misunderstanding:

First, many people try to apply demarcation criteria that are not appropriate for historical sciences. Demarcation criteria, such as observability, testability, falsifiability, predictive capability, and repeatability, do not generally apply to the causes of unobserved and non-repeatable events in the past. This is as true of the random events in Darwinist theory as it is for the actions of an intelligent agent in ID. Further, philosophers of science have largely abandoned demarcation criteria because there are too many exceptions to such rules.

Second, relatively few people are versed in the methodological nuances of historical sciences, so fail to properly apply these to ID.

2. The dispute over ID has more to do with the definition of science than with any particular scientific merits of ID.

A central question lies at the heart of the origins debate: Are unintelligent causal forces capable of producing the complex orchestrations of information and processing machinery that we see in biology? These orchestrations occur at multiple levels, from molecular machinery within a cell to complex body subsystems (like the skeletal or circulatory systems) to the human mind.

Darwin's proponents argue that the answer is yes, unintelligent forces can do all the necessary work. ID proponents argue the other way. (See "Evolution's Grand Challenge" for my take on this question.)

As historical sciences, both Darwinism and ID deal with past events in space-time history. All historical sciences apply a similar rational process to infer the best explanation (cause) for observed outcomes (effects).

The rules are the same. The process is the same. The reasoning follows a similar path. Clearly, there is methodological equivalence between Darwinism and ID. How then can the Darwinian view be science while ID is not?

3. Most of the fireworks around ID are due to a conflict of worldviews.

In what way does ID offend? Put simply, the problem lies in the answers ID is willing to consider, and with the philosophical implications of those answers.

Many scientists, and a good number of laymen as well, conflate science with materialist philosophy. Many go further and conflate materialist philosophy with rationality.

By remaining open to the possibility that an intelligent, purposeful cause was involved in the history of life, ID presents an affront not to science, but to the presuppositions of materialism.

4. The question about ID as science is asked by different people for different purposes.

Some people genuinely want to understand ID, and whether and how it fits into the objective study of the natural world.

There are good answers for such people. (See the links below for helpful resources.)

A second class of questioner is less interested in a productive discussion. For this person, questions about the scientific bona fides of ID can be used to hold at arm's length any serious conversation about detectable design and intelligent causation.

Once science, materialism, and rationality become conflated, the definition of science can function in two important ways: (a) as sufficient warrant to disregard the claims associated with ID, or (b) as a bludgeon to beat up anyone who seriously entertains ID or associates with its proponents, especially those that otherwise look like perfectly respectable scientists.

One strategy that's proven fairly effective is to label any proposal that dares to challenge a strictly materialistic perspective as "pseudoscience." Once it's tagged with a derogatory label, all related questions can be safely ignored. These tactics are so well rehearsed that they've become pro forma, often a matter of unconscious habit, among the most committed materialists.

It's essential, then, to discern the motives behind the question and to respond accordingly. The first class of questioner sincerely wants to understand how all this fits together. The latter doesn't understand how all it fits together and doesn't want to.

The same question can thus lead to very different conversations. Yet both are worth the effort to engage.

5. Whether ID is science is, at some level, merely a category question.

Consider the origins question from another perspective: What actually happened in space-time history?

If the ID hypothesis is correct and an intelligent cause intervened in the course of past events, but consideration of this possibility is not science, then by this definition science is incapable of fully addressing the question of origins. As a category of investigation, then, science becomes less interesting and it's likely that a new category will be invented that will look just like science, but without the presuppositional baggage of materialism.

If science, or at least biology, is to remain relevant into the next century, it must come to terms with the growing body of evidence that demands a new look at the causality behind biological information and the biological machinery that processes that information. Biologists may well need to acknowledge that they've conflated science with their philosophical prejudices, rethink those cherished 19th-century presuppositions, reconsider the causal mechanisms they're open to, and follow the evidence wherever it leads.

This is a practice that was once called "science."

Caught in the Vortex

ID can easily get caught in the vortex between competing worldviews. While ID may not align with a person's presuppositions, that may have more to do with his view of the universe than with the universe itself.

But the questions persist, and the growing body of evidence is real. The gaps in materialism's explanatory capability are growing, and will not disappear merely because materialists wish them to do so.

Since what we really want to know is how these things came to be, it seems only reasonable to remain open to all likely explanations, at least until they can be discarded based on scientific, rather than philosophical, grounds.

Biology offers profound mysteries ripe for exploration. Given how little we really know about how life works, much less how it came to be, it seems only prudent to keep our options open and follow the data. And to ask good questions.

For a more thorough treatment of ID and science, see the following resources:

• "How Can We Know Intelligent Design is Science?" by Casey Luskin
• Signature in the Cell: DNA and the Evidence for Intelligent Design, by Stephen Meyer
• "What's the Mechanism of Intelligent Design?" by Ann Gauger
• "Answering a Common Complaint: Does Intelligent Design Require Faith?" by Casey Luskin
• "Why Intelligent Design Is Science: A Reading List," by Casey Luskin
• "More on How We Can Know Intelligent Design Is Science," by Casey Luskin

In a subsequent post, I'll look at a second foundational question, which has the potential to yield still more interesting answers.

It's irreducible complexity all the way down.

Local Fitness Landscape Mapped Out for Green Fluorescent Protein
Cornelius Hunter


Proteins are a showstopper for evolution. Proteins consist of dozens, hundreds, even thousands of amino acids and, like most machines, they don't work very well until most of the parts (amino acids in this case) are in place. Half of the amino acids don't give you half the function of a protein. You can read more about this here and here. Now a new paper in Nature, "Local fitness landscape of the green fluorescent protein," reinforces the problem of protein evolution.

One approach to studying how evolution could create new protein designs is to start with some sort of random sequence of amino acids, see how well it works, and try to evolve it to obtain a protein. This is difficult because the protein design space is astronomically huge and proteins are sparse within that space. Any random sequence of amino acids will merely give you junk. Furthermore, the fitness landscape is flat and doesn't provide the guidance evolution needs to move toward functional proteins.

Another approach is to start at the end and work backwards. In other words, start with the finished product -- a functional protein -- and see what the fitness landscape looks like as you swap in different amino acids. This is difficult because, unfortunately for evolution, the fitness landscape drops off precipitously as you move away from the native protein design. Modifying only a few percent of the amino acids leads to a rapid loss of function.

The new paper takes this second approach. It uses a bioluminescent protein known as the green fluorescent protein, taken from the jellyfish Aequorea victoria. It is a wonderful study that systematically mapped out the protein's function (as measured by the protein's fluorescence) for a total of 51,715 different protein sequences that are nearby the native sequence.

The results confirmed what earlier studies had indicated: the protein function drops off dramatically with only a relatively small number of substitutions. But the study also explored the effect of multiple substitutions. It is well known that the effect of two substitutions, for example, is not always simply the sum of their individual effects. They can interact with each other in either positive or negative ways. This is referred to as epistasis.

The new study found that negative epistasis was strong and prevalent. As one of the researchers explained:

We were really surprised when we finally had a chance to look at exactly how the interactions between mutations occur. We also did not expect that almost all the mutations that are only slightly damaging on their own can destroy fluorescence completely when combined together.

It was well understood that evolving a protein is an astronomically unlikely event, and these results indicate it is even more difficult. Those negative results, however, are not reported in the paper. Instead, the paper discusses possible ways that one green fluorescent protein, found in one particular species, may have evolved into other green fluorescent proteins, found in other species. The implications for the initial evolution of a protein are ignored.

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