Archive: Peer Review, Amoebas, Self-Organization, Mars, Stomach Acid, Cholesterol, Junk DNA

Here are some of the stories we were reporting in late November 2001, restored from archives.

Note: some embedded links may no longer work.

Letter 11/22/2001: ’The Perils of Peer Review”, Nature correspondence. Three angry scientists vociferate against the peer review process, comparing it to a religious ritual (or worse, an inquisition):

Your News feature “Peers under pressure” (Nature 413, 102-4; 2001) on the hoary old chestnut of peer review reinforces my decades-old comparison of this ritual to the Latin mass. Obviously many (Protestant?) leaders, including most of the best-known scientists such as Nobel laureates, regard peer-review as a great hindrance to good science (the gospel?). Many excellent journals (churches?), such as the Proceedings of the Royal Society and Proceedings of the National Academy of Sciences managed in my opinion very well without it for a long time. An enormous amount of the best science has been and is being run without benefit of this rubric, as is the worldwide patent system.

After discussing a recent case of dishonesty caused by a scientist’s efforts to hide his work from rivals during the peer review process, they continue their tirade: “Yet this is but a minor defect in the peer-review system. The enormous waste of scientists’ time, and the absolute, ineluctable bias against innovation, are its worst offences.”

And you were taught that peer review was the guarantee of scientific objectivity. We are not here rendering judgment on peer review, but these scientists’s complaints should be taken to heart. It is clear that many of history’s greatest scientists did their groundbreaking work outside the peer review system.  Many creationists today complain that peer review tolerates only naturalistic, evolutionary submissions, and that their work, no matter how empirically sound, is systematically excluded on philosophical grounds.

How the Amoeba Crawls   11/22/2001
Yale scientists have gained new insight into how cells move, reports EurekAlert. They’ve revealed the 3-D structure of seven proteins called the Arp2/3 complex that assembles actin proteins into filaments, which push the front of the cell forward. A similar process (actin polymerization) is involved in white blood cells moving to the site of an infection, and in neurons branching out into the million miles (more or less) of axons and dendrites in the human brain. Thomas Pollard of Yale, co-author of the paper in Science, explains how it works. Chemicals in the environment send messages to the Arp2/3 complex, which in turn cause it to orient the cell and move in a particular direction. He says, “Actin and Arp2/3 complex work like a peculiar motor in a car to make the cell move forward. Rather than turning wheels, the filaments grow like branches of a bush to push the cell forward. Arp2/3 complex is very ancient, having evolved in primitive cells well over one billion years ago.”

How can anyone look at this amazing mechanism, call it primitive and ancient, and say it just evolved? Do you know any other motors that are engineered by blind, undirected, impersonal forces? One of the characteristics that sets life apart from nonlife is its ability to respond to stimuli contrary to what would happen by chemistry and physics alone. The difference is analogous to a man climbing uphill vs a statue of a man falling downhill. To achieve autonomous movement, even the lowly ameba has to have plans and processes. What Darwin did not know, modern biochemistry has revealed: each cell has a detailed DNA code and transcription mechanism that builds precisely-engineered proteins (the Arp2/3 complex), which in turn assemble a motor protein (actin) at the appropriate end of a cell to make it move. An amoeba may look simple, but the simplicity is deceiving; it moves where it wants! Rocks do not do this.

Expert on Self-Organization Agrees Intelligent Design Has Merit   11/20/2001
In a debate 11/13 at the University of New Mexico against William Dembski, Stuart Kauffman “publicly admitted that intelligent design was a legitimate intellectual and scientific project and that research projects like SETI (the Search for Extraterrestrial Intelligence) couldn’t even get off the ground without it,” writes Phillip Johnson in his Weekly Wedge Update for 11/19. Kauffman, well known as a specialist in the theory of self-organization, did not feel I.D. was applicable to biology, but did lay down some boundary conditions for his own theory to work: probabilities that could well bring I.D. into the argument as the only valid approach.

Johnson sees this as a major concession by an evolutionist. Rather than ruling intelligent design theory off the table by fiat, as some evolutionists do, Kauffman was courteous and considered Dembski’s arguments on their merits. Even a local skeptics society seemed to tone down their rhetoric.

Chemists Dispute Claim of Life in Martian Meteorite   11/20/2001
Since the high-fanfare announcement of possible microscopic evidence for fossilized life in Martian meteorite ALH 84001 by a NASA team in 1996, the three major lines of evidence have been slowly eroded.  Now, scientists at Arizona State University take the last remaining claim down another notch. They argue that the magnetite crystals that were alleged to be the work of bacteria are too indistinct for such a claim to be made, and that NASA was selective in its observations, ignoring 73% of the other magnetite crystals in the rock.

Like Carl Sagan used to say, extraordinary claims require extraordinary evidence. Next time you hear a claim about the discovery of extraterrestrial life, remember ALH 84001.

Cholesterol Builds Better Brains   11/20/2001
90% percent of your brain is composed of glia cells, not involved in thinking like the neurons, so less interesting to researchers. But now neuroscientists have found that they secrete a molecule with a bad rap – cholesterol – that is essential for the formation of synapses (connections) between neurons. Cholesterol may clog arteries, but it is vital in cell membranes. The team had two big surprises: first that cholesterol was so essential to synapse formation, and second that the lowly glia cells produce this vital substance. “We were definitely shocked,” said one investigator. Source: Science News 11/17/2001, p. 309.

Here again, an important function is discovered for cells thought to be mere scaffolding. Over and over, scientists find that every player has its role, often essential, to the success of the play. It reminds us of the Apostle Paul’s body analogy of the church in 1 Corinthians 12, which we might update as follows: “But now indeed there are many members, yet one body. And the eye cannot say to the hand, ‘I have no need of you’; nor again the neurons to the glia, ‘I have no need of you.’ No, much rather, those members of the body which seem to be weaker are necessary.”

How Did Cell Nucleus Evolve?  Nobody Knows   11/19/2001
In a new Explore feature, Scientific American investigates current thinking about how eukaryotic cells evolved a nucleus, and concludes that no theory currently explains all the facts. Some think that early cells developed a symbiotic relationship with bacteria or archaea, but the nucleus has unique features that are not present in either assumed progenitor. Every theory has serious objections. One biochemist admits, “We really probably don’t have any idea what happened. It does seem like, whatever happened, it was probably very complicated and not very sensible.”

Not sensible to naturalistic philosophy, that is. This is what happens when scientists feel obligated to explain life by materialistic means. This article makes a good case study for how a theory can sound plausible at first glance, until nasty details get in the way.

Wonders Within 11/19/2001: “Why don’t our digestive acids corrode our stomach linings? Scientific American describes the complicated chemistry that your stomach performs to keep its hot potato – hydrochloric acid, HCl – from burning itself. Biologist William K. Purves of Harvey Mudd College explains why the stomach needs the acid in the first place:

In summary, HCl in the stomach lumen accomplishes four things. It helps break down ingested tissues for attack by digestive enzymes; it provides the correct pH for the action of those enzymes; it converts a catalytically inactive proenzyme to an active enzyme (as we just saw); and it destroys invading microorganisms in the stomach contents.

The proenzyme he refers to is like a chain saw with a blade guard; if let loose in the cell that manufactures it, it would be dangerous. After release into the stomach, the HCl dissolves away the blade guard so that the chain saw goes to work on the food, not on the stomach. Later, as the food moves on to the next processing station (the small intestine), the HCl is no longer needed, so the pancreas neutralizes the caustic acid which has ten times the acidity of lemon juice.

Just thought you’d like to know. Aren’t you glad you don’t have to operate this system in manual mode after every meal?

Your Non-Essential Genes Protect You   11/23/2001
Scientists at the National Institutes of Health have been scanning through 3,760 non-essential genes in yeast and finding them not so useless after all. So far, they have found 107 that apparently protect from radiation and toxins in the environment. Non-essential genes are ones the organism can live without – grow and develop into maturity without apparent harm. When danger lurks, however, these genes are switched on and provide protection. Since these genes in yeast and mammals are similar, they expect similar protection is afforded humans by these “non-essential” genes.  (Source: EurekAlert.)

Whatever happened to “junk DNA”? The more we learn, the more we find out “God don’t make no junk.”