… the horrid doubt always arises whether the convictions of man’s mind, which has been developed from the mind of the lower animals, are of any value or at all trustworthy. Would any one trust in the convictions of a monkey’s mind, if there are any convictions in such a mind?

I’d say that if his theory was true, horrid was a slam dunk (yes, you are an evolved monkey, no, your thoughts do not mean anything).

But very little in science turned out to be what Darwin or his contemporaries thought.

Non-materialist neuroscientists think that your mind is real and that it helps shape your brain. It is not a mere illusion created by the workings of the brain.

Here are some excerpts from the afternoon panel of the Beyond the Mind-Body Problem symposium (September 11, 2008), sponsored by the Nour Foundation, UN-DESA, and the Université de Montréal. The excerpts feature some interesting exchanges between a number of non-materialist neuroscientists.

Excerpts from the morning panel are here.

Both the morning and afternoon panels were televised and can be viewed here.

The 200th anniversary of the birth of Charles Robert Darwin falls on 12 February 2009. Darwin was arguably the most influential scientist of modern times. No single researcher has since matched his collective impact on the natural and social sciences; on politics, religions, and philosophy; on art and cultural relations, and in ways that the man himself would never have imagined. This Nature news special will provide continuously updated news, research and analysis on Darwin’s life, his science and his legacy, as well as news from the Darwin200 consortium of organizations celebrating this landmark event.

http://www.nature.com/news/specials/darwin/index.html

I wonder if they will also celebrate Alfred Russel Wallace and his Sarawak Law.

People in academia should start insisting on objective scholarship, insisting on it, relentlessly, driving the point home, ramming it down the gullets of the politically correct, making noise! naming names! citing egregious examples! showing contempt to the brink of brutality! The idea that a discipline should be devoted to “social justice” is ludicrous. The fashionable deconstructionist doctrine that there is no such thing as truth, only the self-serving manipulation of language, is worse than ludicrous. It is casuistry, laziness, and childishness in equal parts. Sociology in this country didn’t start with Max Weber. It started with an act of pious charity on the part of Protestants concerned about life in the slums. Today the discipline, if it can still be called that, has returned to sheer sentiment. Only this time the pious are from the puritanical order of political correctness, preying with the rhetoric of Rococo Marxism, which means steering clear of the by-now totally discredited “vulgar Marxism,” all that tired old business of the proletariat, the peasants, the capitalists, the bourgeois elements, the infantile leftists, since all they really care about is preserving Marxism’s greatest joy: the Manichaeistic take on life. Everything is light or darkness! Black or white! No irksome middle grounds or shades of grey! How much simpler the taxing stone-hard task of analysis becomes! He good! He bad! That’s the right idea!  

Note: The Canadian edition of this post here offers promising intellectual freedom updates.

This science article is one those where the researchers variously describe themselves as “stunned”, “amazed”, “surprised” or something else that conveys the notion that theory didn’t predict whatever it is they found. I also watch for discoveries that are described as “unexpected” which conveys the same meaning - the underlying theory of evolution is deficient. Sound theories don’t result in unexpected observations.

Biologists Discover Motor Protein That Rewinds DNA

ScienceDaily (Nov. 2, 2008) — Two biologists at the University of California, San Diego have discovered the first of a new class of cellular motor proteins that “rewind” sections of the double-stranded DNA molecule that become unwound, like the tangled ribbons from a cassette tape, in “bubbles” that prevent critical genes from being expressed.

Read the whole article at the source above. Here’s the revealing part (my emphasis):

What this protein, called HARP for HepA-related protein, did astounded Kadonaga and Timur Yusufzai, a postdoctoral fellow working in his laboratory. The two molecular biologists initially discovered that this motor protein burns energy in the same way as enzymes called helicases and, like helicases, attached to the dividing sections of DNA. But while helicases use their energy to separate two annealed nucleic acid strands—such as two strands of DNA, two strands of RNA or the strands of a RNA-DNA hybrid— the scientists found to their surprise that this protein did the opposite; that is, it rewinds sections of defective DNA and thus seals the two strands together again.

Tunnelling nanotubes: Life’s secret network

New Scientist
18 November 2008
by Anil Ananthaswamy

HAD Amin Rustom not messed up, he would not have stumbled upon one of the biggest discoveries in biology of recent times. It all began in 2000, when he saw something strange under his microscope. A very long, thin tube had formed between two of the rat cells that he was studying. It looked like nothing he had ever seen before.

His supervisor, Hans-Hermann Gerdes, asked him to repeat the experiment. Rustom did, and saw nothing unusual. When Gerdes grilled him, Rustom admitted that the first time around he had not followed the standard protocol of swapping the liquid in which the cells were growing between observations. Gerdes made him redo the experiment, mistakes and all, and there they were again: long, delicate connections between cells. This was something new - a previously unknown way in which animal cells can communicate with each other.

Gerdes and Rustom, then at Heidelberg University in Germany, called the connections tunnelling nanotubes. Aware that they might be onto something significant, the duo slogged away to produce convincing evidence and eventually published a landmark paper in 2004 (Science, vol 303, p 1007).

A mere curiosity?

At the time, it was not clear whether these structures were anything more than a curiosity seen only in peculiar circumstances. Since their pioneering paper appeared, however, other groups have started finding nanotubes in all sorts of places, from nerve cells to heart cells. And far from being a mere curiosity, they seem to play a major role in anything from how our immune system responds to attacks to how damaged muscle is repaired after a heart attack.

They can also be hijacked: nanotubes may provide HIV with a network of secret tunnels that allow it to evade the immune system, while some cancers could be using nanotubes to subvert chemotherapy. Simply put, tunnelling nanotubes appear to be everywhere, in sickness and in health.

“The field is very hot,” says Gerdes, now at the University of Bergen in Norway.

It has long been known that the interiors of neighbouring plant cells are sometimes directly connected by a network of nanotubular connections called plasmodesmata. However, nothing like them had ever been seen in animals. Animal cells were thought to communicate almost entirely by releasing chemicals that can be detected by receptors on the surface of other cells. This kind of communication can be very specific - nerve cells can extend over a metre to make connections with other cells - but it does not involve direct connections between the interiors of cells.

Quite different

The closest animal equivalents to plasmodesmata were thought to be gap junctions, which are like hollow rivets joining the membranes of adjacent cells. A channel through the middle of each gap junction directly connects the cell interiors, but the channel is very narrow - just 0.5 to 2 nanometres wide - and so only allows ions and small molecules to pass from one cell to another.

Nanotubes are something different. They are 50 to 200 nanometres thick, which is more than wide enough to allow proteins to pass through. What’s more, they can span distances of several cell diameters, wiggling around obstacles to connect the insides of two cells some distance apart. “This gives the organism a new way to communicate very selectively over long range,” says Gerdes.
It is a previously unknown way in which cells can communicate over a distance

Soon after they first saw nanotubes in rat cells, he and Rustom saw them forming between human kidney cells too. Using video microscopy, they watched adjacent cells reach out to each other with antenna-like projections, establish contact and then build the tubular connections. The connections were not just between pairs of cells. Cells can send out several nanotubes, forming an intricate and transient network of linked cells lasting anything from minutes to hours. Using fluorescent proteins, the team also discovered that relatively large cellular structures, or organelles, could move from one cell to another through the nanotubes.

Read the whole article here.

The money shot for us is the last section titled (my emphasis below the title):

Unbelievable

Their work, published in May, shows that nanotubes are not just an artefact of the methods used to grow cells in culture, as some have suggested. And what they have seen is spectacular: some of the longest tunnelling nanotubes ever observed, more than 300 micrometres long, connecting dendritic cells in the cornea (The Journal of Immunology, vol 180, p 5779). “We can see them their whole course, spindling all the way through the cornea,” says McMenamin. “It’s fantastic.”

“I’ll bet you that within weeks to months, people will start noticing them in other tissues. It’s just a case of how you look,” he adds. “You’ve got to know what you are looking for. It’s a bit like being a good bird-watcher. A hundred people will see a flock of seagulls, and it’s only a very good bird-watcher who will spot this one tern flying in that flock.”

Gerdes, meanwhile, continues to marvel at what is unravelling before his very eyes. “Whatever one can think of has been done by nature,” he says. “It is unbelievable what the cell is able to do.”

Now here’s an exchange that caught my attention:

“The way biology works is different from mathematics,” said Mark Gerstein, a bioinformatician at Yale. “If you find one counterexample in mathematics, you go back and rethink the definitions. Biology is not like that. One or two counterexamples — people are willing to deal with that.”

More complications emerged in the 1980s and 1990s, though. Scientists discovered that when a cell produces an RNA transcript, it cuts out huge chunks and saves only a few small remnants. (The parts of DNA that the cell copies are called exons; the parts cast aside are introns.)

Actually, the biologists flatter themselves. They underbussed vast discrepancies between their belief system and the evidence - along with lots of people who insisted on discussing their implications - until finally, the system is collapsing in the gene’s “identity crisis” (Zimmer’s phrase).

Thomas Kuhn was right. Old paradigms don’t get disproven; they collapse from their own unworkability.

One thing about this article, it is mercifully free of rubbish about evolution.

We actually don’t know what most of the stuff in the genome does. So why not wait until we do know before we begin to describe its history? That will save a lot of rewrites down the road, maybe inconvenient ones.

(Note: Re the business about cutting out huge chunks and saving only a few small remnants … Brings back memories. We textbook editors used to do that when we were racing a deadline. We would copy a whole chapter from the master copy of the manuscript to date, and then select only a few pages for which final revisions had been ordered. Then we just recycled the rest of the pages of the chapter. Wasteful? Yes, of paper. But not of time. Under deadline panic, the most important quantity was time, not paper. And we knew from experience that our method was slightly faster. So I would recommend caution to anyone making claims that such methods show that the system cannot be the product of design.  When we editos did it, that’s precisely what it was - design.)

This Science Daily story describes a paper from the latest PLOS Biology, on the role of ORFans in generating species-specific traits in animals. Konstantin Khalturin and his co-authors at the Christian-Albrechts-University in Germany note the “substantial fraction” of ORFans — genes without known homologs — in every genome thus far sequenced, and argue that the origin of unique morphologies may rest in part with these unique genes:

Understanding the molecular events that underlie the evolution of morphological diversity is a major challenge in biology….All genome and expressed sequence tag (EST) projects to date in every taxonomic group studied so far have uncovered a substantial fraction of genes that are without known homologs. These ‘‘orphans’’ or ‘‘taxonomically restricted genes’’ (TRGs) are defined as being exclusively restricted to a particular taxonomic group. For example, analysis of the phylum Nematoda has identified more than 20% of genes that were nematode-unique TRGs. The draft genome of Ciona intestinalis revealed that nearly one-fifth of the genes were orphans. A comparison between the genome sequences of Schizosaccharomyces pombe and Saccharomyces cerevisiae showed about 14% of the predicted proteins to be unique to Sc. pombe and 19% unique to Sa. cerevisiae. In Drosophila, TRGs include indispensable regulators of development such as bicoid and spätzle. Recent comparative data on the genomes of 12 Drosophila species revealed that about 2.5% of genes are not present outside of the genus Drosophila and, therefore, have most likely arisen de novo. An even larger proportion of lineage-specific genes have been detected in the genome of Tribolium. In bacteria, the cumulative number of orphans identified does not appear to be leveling off, although hundreds of complete genome sequences have been already analyzed. (p. e278, reference numbers omitted)

In their paper, Khalturin et al. examine the role of ORFans in specifying unique anatomical features of two species of the freshwater polyp Hydra. The paper is open access (God bless PLOS; long may it prosper), so go check it out.

To anyone who wishes he or she was born in the 15th century, to take part in the great voyages of discovery: ORFans represent our biological New World. The open vistas of science never end.

(That’s the sort of thing cheerleaders say, you know.)

Indeed, the extraordinary social skills of humans, compared with other primates, may be honed by constant practice with imagined or absent partners.

We now know that human brains have a set of security and precaution networks dedicated to preventing potential hazards such as predation or contamination. These networks trigger specific behaviours such as washing and checking one’s environment. When the systems go into overdrive they produce obsessive-compulsive pathology. Religious statements about purity, pollution, the hidden danger of lurking devils, may also activate these networks and make ritual precautions (cleansing, checking, delimiting a sacred space) intuitively appealing.

How does this help us understand why people spend their Friday night driving aged parishioners to holy hours or refuse to save their lives during a Rwandese massacre by abandoning fellow believers to their fate? Something is obviously missing from his explanation.

One thing missing is accuracy about obsessive-compulsive pathology. An obsessive-compulsive disorder (OCD) sufferer knows that her obsessive compulsions are nonsense. That is, she knows that her son will not die if she fails to count all the windows in her apartment building all over again. But due to bad brain wiring, she feels the fear. (See The Spiritual Brain, pp. 129-30.)

Indeed, encouraging the patient to substitute thinking for feeling is the basis of a successful non-materialist treatment for obsessive-compulsive disorder, pioneered by Dr. Jeffrey Schwartz. So OCD would explain religious ritual only if the typical worshipper felt an inner compulsion to engage in the activity while believing it useless - not a common scenario, and hardly a convincing basis for a theory of religion. That anyone would advance such an explanation in a science journal shows how limited the appetite for accuracy is in this area.

 Read all here:

See also at MercatorNet: The payoff for straining the brain - how focus and sleep really do improve your academic performance

What is also noticeable about the events surrounding Michael Reiss is the lack of comment and support for him from organisations who hold to a theistic evolution position such as the UK based Faraday Institute (FI) and Christians in Science (CiS). A word search on the CiS website for ‘Reiss’ reveals only one entry in an article (in the School Science Review - see below) merely as a mention of Reiss’s book under ‘Further Reading.’ On the FI website no results for Reiss were found.

One may wonder why there is such silence from CiS and FI when Reiss (who is a theistic evolutionist who held an important position at the Royal Society) was recently treated so unjustly at the hands of some Fellows of the Royal Society. The article by Michael Poole and comments in the postscript of Denis Alexander’s book Creation or Evolution give some clues. Both quote Augustine, and use it to infer that creationists and intelligent design supporters are ‘disgraceful’, ‘dangerous’ and therefore an embarrassment to the gospel. This gives the appearance that some leaders in CiS and FI do not share Reiss’s calls for respectful dialogue, but instead wish to isolate IDers and creationists by misrepresenting their arguments and disrespecting their worldview. Poole’s article has a prominent place on the CiS Home page and he seems to be the spokesman on education policy within the CiS.

I would love to be proved wrong on this, so perhaps if I have misunderstood the silence on Michael Reiss by CiS and FI then I offer my apologies in advance, but they need to demonstrate their support for Reiss and his call for respectful dialogue in the classroom through written articles on their websites to remove doubt.

Mike Poole on the CiS website ‘Creationism, Intelligent Design and Science Education,’ SSR, (90) 330, p. 123-130, Sept. 2008
See also Science and Values

Update: The previous title to this post raised questions about whether I booted DaveScot. That is not the case. DaveScot resigned as moderator, but he remains a friend to the site.