Science Literature

On 11 September 2008, a symposium on the theme "Beyond the Mind-Body Problem: New Paradigms in the Science of Consciousness" was held at the United Nations attended by medical doctors and neuroscientists. The organisers spoke of a search for a more comprehensive perspective on the "self" and the workings of the human mind. The speakers at the conference have been engaged in this search and were ready to consolidate and move on. But in order to develop their thinking, they needed to challenge the prevailing paradigm in neuroscience. "Though much remains to be done, their findings to date have shed a more holistic light on our understanding of the elusive mind-body problem." This holistic view opens up new opportunities for research:

"The symposium will also serve as the occasion for the formal launch of The Human Consciousness Project - a multidisciplinary collaboration of international scientists and physicians who have joined forces to research the nature of consciousness and its relationship with the brain."

Materialist critics say of the new paradigm: "This nasty mind-virus piggybacks on reasonable worries."

The prevailing paradigm in neuroscience is materialism. Everything about the brain is interpreted in terms of physics and chemistry: our sense of free agency, our consciousness, our hopes and our ability to appreciate beauty. Yet this paradigm has only limited results to show for all the effort expended and "scientists have yet to crack the great mystery of how consciousness could emerge from firing neurons". The UN conference set out an agenda for going beyond reductionism. Jeffrey Schwartz warned the delegates that what they were doing would be met with heated opposition, because materialism is deemed by many to be of the essence of science:

"YOU cannot overestimate, how threatened the scientific establishment is by the fact that it now looks like the materialist paradigm is genuinely breaking down. You're gonna hear a lot in the next calendar year about. . . how Darwin's explanation of how human intelligence arose is the only scientific way of doing it. . . I'm asking us as a world community to go out there and tell the scientific establishment, enough is enough! Materialism needs to start fading away and non-materialist causation needs to be understood as part of natural reality."

Sure enough, the event has raised alarm! The New Scientist reported it with the headline: "Creationists declare war over the brain". It has become commonplace for the science media to portray every departure from philosophical naturalism as "creationism" as though that were the ultimate crime for a scientists and no more needs be said. There is evidence that some of the conference speakers have links with the ID Movement, and apparently that is enough to shower derision on them. Since scientists are supposed to be able to grapple with complex issues and think rationally and objectively (rather than emotionally), I do not understand why there is so little outcry against the intolerant attitudes of so many science journalists and writers.

Here are some reactions quoted, described as "the voice of mainstream academia":

Andy Clark, professor of logic and metaphysics at the University of Edinburgh, UK: "This is real and dangerous and coming our way." [. . .] "This is an especially nasty mind-virus because it piggybacks on some otherwise reasonable thoughts and worries."

Patricia Churchland, philosopher of neuroscience at the University of California, San Diego: "it is an argument from ignorance. The fact something isn't currently explained doesn't mean it will never be explained or that we need to completely change not only our neuroscience but our physics."

It is instructive to flag up some of the missing ingredients in this report
1. No interviews with the scientists that were at the symposium are reported. This was noted by Angus Menuge in a letter (unpublished) to New Scientist: "I find it very troubling, that while Amanda Gefter took the trouble of interviewing sources who advocate scientific materialism, she did not interview any critics of that position, instead relying on third-hand reports. This does not seem to reflect journalistic best practice."
2. There was no acknowledgement that ID can lead to new research opportunities. This is perhaps not surprising, because science journalists have been programmed to say that ID closes the door on science. This is bad history, because ID science was the trigger for the time known as the scientific revolution and ever since then ID scientists have consistently demonstrated that ID extends the horizons of scholarly enquiry.
3. There is no acknowledgement that the new paradigm has emerged because of evidence. Materialists cannot allow any evidence to count against their paradigm. They are committed to the principle that all explanations of phenomena have to be formulated by reference to "chance and necessity". Consequently, as in the quote from Churchland above, any hint of evidence against their position is opposed as an argument from ignorance.

Geftner declares that only the materialist perspective is science in her final paragraph. She also throws out the charge that non-materialists are invoking a "God of the gaps" style of argument:

"What can scientists do? They have been criticised for not doing enough to teach the public about evolution. Maybe now they need a big pre-emptive push to engage people with the science of the brain - and help the public appreciate that the brain is no place to invoke the "God of the gaps"."

This "pre-emptive push" seems to be the only response of the materialists! Shout louder! Put more resources into educating the public! Never admit that non-materialist philosophies can lead to fruitful science! Ignore their claims of arguing from evidence and insist that they are using ignorance to invoke the "God of the gaps"!
In a letter of response to New Scientist, Beauregard and Schwartz write:

"We do not question materialist models of the mind-brain complex merely for ideological or political reasons. We want to move beyond them because we have not found them adequate explanations of mind-brain interactions, nor do they point to useful treatment plans. Your writer's attempt to smear scientists who are looking for new directions, while perhaps entertaining, is a poor substitute for thoughtful coverage of a growing area."

Beyond the Mind-Body Problem: New Paradigms in the Science of Consciousness, September 11th 2008, United Nations, New York.

and

Creationists declare war over the brain
Amanda Gefter
New Scientist, 22 October 2008

See also:

Beauregard, M. and Schwartz, J.M. Non-materialist mind, New Scientist, 29 November 2008, page 23.
Go here for the unedited version.

Menuge, A. Unpublished letter to New Scientist, 26 November 2008.

In an informative essay, Janet Browne reflects on three Darwin commemorations: his funeral in Westminster Abbey, the 1909 centennial and the 1959 celebration. Each grasped the "opportunity to push an agenda, and even to adapt the past, so telling us what we like best to hear".

Nature's contribution to the anniversary preparations (Darwin 200 index here)

Darwin's religious views became known through his correspondence. He was content to be known as an agnostic and his view of God, if he did exist, was that he is remote from this world. Christian reaction to Darwinism ranged from "it is atheism" (Charles Hodge) to "God guides the process of evolution" (Asa Gray). Opposition to the technicalities of the theory came from contemporary scientists who were not persuaded that Darwin had a strong case. After Darwin's death, several colleagues in the Royal Society lobbied to have him buried in Westminster Abbey. This was to make a statement about Darwinism and faith and also to turn Darwin into an iconic figure. Browne writes that this was:

"valuable propaganda at a time when relations between science and religion were intensely fraught. The men of the Royal Society used Darwin's funeral as a way to reassure their contemporaries that science was not a threat to moral values, but rather was becoming increasingly important in the modern world."

By 1909, genetics was revealing that much of the variation reported by Darwin was innate and this was stimulating fresh thinking about biological change. "Thus, new forms could emerge de novo, without selective pressure and adaptive success." At the same time, palaeontologists were reporting lineages that "progressed" and this seemed to inject teleology back into biology. Darwinism was becoming sidelined.

"The 1909 commemorations, organised by a small group of naturalists and Darwin family members from the University of Cambridge, provided a way to reassert the primacy of natural selection against other evolutionary rivals."

A much bigger event was the celebration of 1959. This was the platform where the architects of the "modern synthesis" asserted their supremacy.

"The delegates at Chicago did more than celebrate a new union of the biological sciences. They in effect created modern Darwinism by emphatically rejecting any form of Lamarkism [. . .] The delegates also rejected the idea that the fossil record shows signs of directed evolution, and expanded Darwinian thought to cover the evolution of mind and behaviour. During the conference, Julian Huxley, the grandson of Thomas Henry Huxley, gave a secular sermon in the style of his grandfather, and provocatively declared that religious belief was merely a biological feature of evolving mankind."

Browne points out that "much of what we know about Darwin and Darwinism, including his celebrity status, is the result of the 1959 celebration in Chicago." This created the illusion of a consensus among biologists, but the reality is that many have serious doubts about the efficacy of natural selection to do what Darwinism claims for it. Many also doubt that gradualism is the way evolution proceeds. But the consensus means that doubting Darwin becomes a serious academic crime, for which the guilty get expelled from positions of influence and sometimes expelled even from being able to pursue a career in science.

Browne asks: "Will [the 2009] activities have a veiled agenda, as did those of the past?" The answer to this question must be an emphatic yes! If you don't want your mind to be manipulated, you had better develop your critical thinking skills. For more on Darwin as an icon, go here.

Birthdays to remember
Janet Browne
Nature 456, 324-325 (20 November 2008) | doi:10.1038/456324a

Summary: Anniversaries of Charles Darwin's life and work have been used to rewrite and re-energize his theory of natural selection. Janet Browne tracks a century of Darwinian celebrations.

Ever since the 'anthropic principle' entered the language of science, the case for the universe having the hallmarks of design has become progressively stronger. There is a consensus in the thinking of physicists and cosmologists that far exceeds the alleged consensus about anthropogenic global warming, and also the alleged consensus that natural selection is the mechanism for explaining design in living things. Author Tim Folger elevates the principle to "an extraordinary fact" about the universe:

"Its basic properties are uncannily suited for life. Tweak the laws of physics in just about any way and - in this universe, anyway - life as we know it would not exist."

Is our universe one of an infinite series? (Source here)

Folger's article is based on an interview with physicist Andrei Linde, who says: "We have a lot of really, really strange coincidences, and all of these coincidences are such that they make life possible." Many of these are sketched out for the benefit of readers, and Folger comments:

"There are many such examples of the universe's life-friendly properties - so many, in fact, that physicists can't dismiss them all as mere accidents."

If we apply Dembski's design filter approach, we have three avenues to explore: Law, Chance and Design. Law gets very little attention from Folger, despite the intense search for grand Unification Theories (GUT) or Theories of Everything (ToE). The reason is that GUT have not delivered. We cannot explain why the universe is like it is. No progress has been made in showing why the fine-tuning of fundamental constants should be a feature of the physical world. Indeed, the pendulum has swung away from GUT because of the interest in string theory - which has served to underline how extraordinary the evidences of fine-tuning actually are.

"[Polchinski and Bousso]calculated that the basic equations of string theory have an astronomical number of different possible solutions, perhaps as many as [10 to the power 1000]. Each solution represents a unique way to describe the universe."

This brings us straight to the Chance filter, and there is no shortage of people who are prepared to say how infinitesimally small the probability is for our universe to have the properties it does.

Call it a fluke, a mystery, a miracle. Or call it the biggest problem in physics. [. . .]
"If [dark energy] had been any bigger, there would have been enough repulsion from it to overwhelm the gravity that drew the galaxies together, drew the stars together, and drew Earth together," Stanford physicist Leonard Susskind says. "It's one of the greatest mysteries in physics. All we know is that if it were much bigger we wouldn't be here to ask about it."
Nobel laureate Steven Weinberg, a physicist at the University of Texas, agrees. "This is the one fine-tuning that seems to be extreme, far beyond what you could imagine just having to accept as a mere accident," he says.

Scientists who have adopted the metaphysic of secularism and naturalism have no recourse to Design. According to their reasoning, something remarkable must overcome the mindnumbing improbability of our universe. Physicists with this mindset have given birth to the Multiverse Theory. They

"see only one possible explanation: Our universe may be but one of perhaps infinitely many universes in an inconceivably vast multiverse. Most of those universes are barren, but some, like ours, have conditions suitable for life."

Which thought brings us to the third filter of Design. The argument is not based on ignorance but on evidence. We have good reasons to think that a ToE will never be forthcoming - there is no fundamental rationale for thinking that the universe and matter necessarily have the properties we observe. We have good reasons for thinking that Chance is not the answer, because the only way to persist with this explanation is to postulate an infinity of universes with different properties. We have no evidence to suggest that this option is anything more than science fiction. We have excellent reasons for thinking that Design is the answer because, without setting out to look for designed features, scientists have stumbled across them in abundance. Calling these evidences "fine tuning" points to something substantial. Were it not for the metaphysic of secularism, the design inference would be readily embraced.

"I don't think that the multiverse idea destroys the possibility of an intelligent, benevolent creator," Weinberg says. "What it does is remove one of the arguments for it, just as Darwin's theory of evolution made it unnecessary to appeal to a benevolent designer to understand how life developed with such remarkable abilities to survive and breed."
On the other hand, if there is no multiverse, where does that leave physicists? "If there is only one universe," Carr says, "you might have to have a fine-tuner. If you don't want God, you'd better have a multiverse."

Design theory provides the best match with empirical science. If you have any doubts about the pervasive influence of secularisation within contemporary science, this multiverse debate should make the issues clear. Folger's article is very significant for spelling out the thinking of some of the leading figures in the scientific world. For a 2002 comment making the same point, go here. For a recent 2008 comment on these issues, go here.

Science's Alternative to an Intelligent Creator: the Multiverse Theory
Tim Folger
Discover Magazine online, November 10, 2008

First para: A sublime cosmic mystery unfolds on a mild summer afternoon in Palo Alto, California, where I've come to talk with the visionary physicist Andrei Linde. The day seems ordinary enough. Cyclists maneuver through traffic, and orange poppies bloom on dry brown hills near Linde's office on the Stanford University campus. But everything here, right down to the photons lighting the scene after an eight-minute jaunt from the sun, bears witness to an extraordinary fact about the universe: Its basic properties are uncannily suited for life. Tweak the laws of physics in just about any way and - in this universe, anyway - life as we know it would not exist.

In a short article, Bruce MacFadden of the Florida Museum of Natural History suggests that museums can effectively increase public understanding of evolution. Taken at face value, this objective is shared by ID scientists - the main issue relates to content. What is meant by increasing public understanding of evolution? What messages will be communicated to the public? It is clear from MacFadden's article that Darwinism is perceived as capturing the essence of evolution - and this is where the problems start.

Without the connecting lines, would people discern evolutionary links? (Source here)

Apparently, visitors to museums are more likely to "accept evolution" than the general public. Whereas 33% of the US population "rejects the tenets of evolution" but the figure is only 10% for museum visitors. The fuzzy meanings attributed to the word "evolution" make these figures difficult to interpret. For example, ID scientists have no problem accepting that Darwinian mechanisms exist in nature, but typically deny that these mechanisms have anything to do with the origin of phyla, classes, orders and families. Furthermore, there are at least two possible reasons for the survey findings: museums may be doing an effective job of communicating Darwinism already; and, people may be voting with their feet and sceptics may not enjoy visiting museums where an evolutionary story intrudes on the pleasure of seeing the collections.

The understanding of museum visitors was probed in one survey: 95% understood the concept of superposition in geology, 80% were able to recognise that the geological column represents a time line, but only 33% gave the "correct" answer to a question about natural selection.

"[W]ith regard to understanding mechanisms of evolution within a species, a scenario was presented in which successive generations of cheetahs are able to run faster; only one-third of respondents correctly attributed this to natural selection."

The problem with this example is that the natural selection explanation has not emerged from observation but it is inferred from theory: it is another of the "just-so stories" proposed by Darwinists. Cheetah design affects many different aspects of the animal and some of these are likely to be affected by natural selection. However, whether this is the complete story remains an open question. The "natural selection" answer may be the right one, but any confidence in its correctness comes from dogma, not empirical science.

We are given an insight into the thinking of exhibit designers when we read: "The challenge, however, is to find novel interpretive strategies that will attract the public to learn about more challenging concepts such as natural selection". Clearly, the emphasis is not on the collection, but the accompanying message. And in the case of evolution, the public need more exposure to natural selection as a creative force.

ID scientists have their own take on this. We need more and better teaching about evolution. We need to help students recognise what natural selection can and cannot do. This means that empirical studies of natural selection in action are valuable. Visitors to exhibits should be encouraged to develop a critical mind, and to ground thinking on hard data rather than on ideology.

I bounced these ideas off a friend whose career has been in musuem practice. He thought it was worth emphasising the importance of both context and evidence:

"While art and aesthetics are generally regarded as largely self-interpreting, this is not so with natural and human history. The evidence is the same. There may be selectivity in displaying it. But a very high proportion of the message is communicated by a different medium and the effectiveness of that medium is all important. Consider also the implications of displaying a homological series (as with MacFadden's horses) or a comparison of genomes without supplementary interpretation. In exercising their imagination, visitors may be influenced by their particular world-view but without the associated evidence, are unlikely to come to well-founded conclusions."

How should publicly-funded museums construct their exhibits? There is a strong case for requiring the self-appointed Darwinian guardians of science to engage in constructive dialogue with other scholars who do not share their confidence in the conceptual model provided by Darwin. There are some important issues to consider, including:

* Encourage critical thinking vs Provide packaged answers
* Reflect controversies in science vs Promote "consensus" science
* Major on displaying collection vs Major on communicating a story

Many scientists today are honest about the way secularisation has influenced the science community. They regard secularisation as an essential characteristic of science, whereas others of us regard secularisation as an unwelcome intrusion that is ultimately destructive of science. Since public money funds many research programmes and also many museums, and since a large proportion of the public have a theistic worldview, there is an urgent need for a broader-ranging debate over these issues. At present, it looks very much like a one-sided discourse about how the 'public understanding of science' can be aligned closer to that of the secularisers. Is it really the task of museum staff to put visitors right when they point out that the exhibited materials do not justify the accompanying commentary?

"Realizing that evolution is potentially a controversial topic, some institutions such as the Australian Museum communicate an explicit policy statement about the role of evolution as part of their mission. Other institutions, such as the Museum of the Earth in Ithaca, New York, provide training to communicate a consistent policy and content about evolution, as well as prepare docents and staff 'on the floor' on how to respond to controversial questions from visitors."

Evolution, museums and society
Bruce J. MacFadden
Trends in Ecology & Evolution, 23(11), November 2008, 589-591

Abstract: Visitors to natural history museums have an incomplete understanding of evolution. Although they are relatively knowledgeable about fossils and geological time, they have a poor understanding of natural selection. Museums in the 21st century can effectively increase public understanding of evolution through interactive displays, novel content (e.g. genomics), engaging videos and cyberexhibits that communicate to a broad spectrum of society, both within the exhibit halls as well as outside the museum.

Quote from Michael Lynch:

"It has long been clear that much of what we see in biology cannot be explained in terms of natural selection alone, yet we continue to witness an unwarranted proliferation of adaptive stories, in some cases extremely bizarre ones, to explain every aspect of existing and extinct biodiversity. What needs to be accomplished will take more than 12 months. More realistically, it will require the education of a new generation of scientists in the basic principles of evolutionary theory that have emerged since Darwin."

Source: Darwin 200: Great expectations, Nature, 456, 317-318 (20 November 2008) | doi:10.1038/456317a

The biological world is full of remarkable nano-machines, each of which is breathtaking in complexity and elegance. Some are particularly worthy of note because they encapsulate design principles which we can appreciate relatively easily. Such is the case with the circadian clock of the prokaryotic cyanobacterium Synechococcus elongates. An informative review article about this subject has been recently published.

The cyanobacterial circadian clock elements
"The clock is composed of three proteins, KaiA, KaiB and KaiC, that together form a circadian clock. At the beginning of the cycle, KaiA (at the top) stimulates the large KaiC hexamer (center), which then adds phosphate groups to itself. Then, as KaiC fills itself up with phosphates, it binds to KaiB (bottom), which inactivates KaiA and allows the phosphates to be slowly removed. As the number of phosphates drops, KaiB falls off and KaiA can start the cycle again." (Source here)

"Cogs and Gears: The Kai Proteins"
The three Kai proteins make up the cogs and gears of the clock. The core is made of KaiC proteins, which alternate between two states: hypophosphorylated and hyperphosphorylated. The other two proteins promote changes between these states in a highly organised manner, based on reactions at specific sites - known as T432 and S431.

"[T]he KaiC phosphorylation cycle comprises four consecutive steps: (i) T432 phosphorylation, (ii) S431 phosphorylation, (iii) T432 dephosphorylation, and (iv) S431 dephosphorylation. This information provides the framework for a reanalysis of the Kai protein structures, suggesting how the in vitro clock might work."

"Why Biological Time Does Not Run Backward"
Research has identified numerous subtleties in the details of the phosphorylation reactions. These suggest reasons why the cycle only works in one direction.

"Overall, the structural information on the phosphorylation events at the KaiCII subunit interfaces and the inter- and intrasubunit interactions formed by the phosphorylated residues indicates that the number of hydrogen bonds increases as first T432 and subsequently S431 is phosphorylated. This progressive increase in molecular interaction would make the reverse reactions unfavorable, causing a built-in ratcheting mechanism that drives the KaiC oscillator unidirectionally."

"How Does This in Vitro Clockwork Tick?"
The researchers found that the protein assemblage could be made to function outside the cell. They have demonstrated that the circadian oscillations keep to time and provide the cell with a clock that does not get swamped by metabolic noise. Conseqently, even cell division does not disrupt the time-keeping: the daughter cells adopt the same time as the parent.

"The unexpected demonstration that KaiC's phosphorylation status continued to cycle when the three Kai proteins are combined in a test tube and ATP was added to provide energy shows that circadian oscillations are not absolutely dependent upon transcriptional and/or translational feedback."

The authors of the review paper set these fascinating details in an evolutionary context, but it should be pointed out that the research is about the operation of the clock, not its origin. Like so many other studies of this type, the evolutionary comments are a veneer on good science: they do not emerge from the research itself. Here are examples:

"The benefit of a clockwork that is imperturbable even when buffeted by the massive intracellular changes of cell division could have provided an evolutionary driving force for convergent circadian clock mechanisms among diverse organisms.
We now recognize KaiABC as a dynamically oscillating nanomachine that has evolved to precess unidirectionally and robustly."

It has not escaped the attention of ID scientists that this nano-molecular clock is the biological equivalent of Paley's watch. It has cogs and gears, it has a 1-way ratchet, it ticks accurately - and it is integrated into the transcription and translation feedback system of the cell. All this can be found in cyanobacteria that are often portrayed as examples of what "primitive" cells look like. Finding this molecular clock leads to a strong design inference, as is traced out by Rana here.

Structural Insights into a Circadian Oscillator
Carl Hirschie Johnson, Martin Egli, Phoebe L. Stewart.
Science 322, 31 October 2008, 697-701 | DOI: 10.1126/science.1150451

Abstract: An endogenous circadian system in cyanobacteria exerts pervasive control over cellular processes, including global gene expression. Indeed, the entire chromosome undergoes daily cycles of topological changes and compaction. The biochemical machinery underlying a circadian oscillator can be reconstituted in vitro with just three cyanobacterial proteins, KaiA, KaiB, and KaiC. These proteins interact to promote conformational changes and phosphorylation events that determine the phase of the in vitro oscillation. The high-resolution structures of these proteins suggest a ratcheting mechanism by which the KaiABC oscillator ticks unidirectionally. This posttranslational oscillator may interact with transcriptional and translational feedback loops to generate the emergent circadian behavior in vivo. The conjunction of structural, biophysical, and biochemical approaches to this system reveals molecular mechanisms of biological timekeeping.

See also:

Rana, F. A Biochemical Watch found in a Cellular Heath, Reasons to Believe, January 10th, 2008