Archive: Clocks, JPL, Smell, Rapid Geology, Mole Rats, Darwin for Kids, ATP Synthase, Golgi, Joy

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

Note: some embedded links may no longer work.

Complexity of Biological Clocks Baffles Researchers   11/16/2001
The entire issue of the November 29 Philosophical Transactions: Biological Sciences of the Royal Society of London is devoted to “Complex Clocks.” Some statements from Fred Kippert’s introduction indicate that molecular biologists, “reductionist by vocation,” have their hands full trying to understand the multiple interacting systems that resist simplistic models.

• The central theme of both special issues is ‘complexity’ – apparently nothing new for biological systems.
• We can now emphasize the complexity of circadian systems as we have recently gained enough knowledge to free ourselves from the inheritance of a past of looking for simple loops and cycles.
• As with any other sensory function, circadian systems need to discriminate between signal and noise. One way of doing so is to ‘probe’ actively for signals, modulating the strength of a given physical or chemical stimulus according to circadian time rather than passively responding to them. This creates ‘zeitnehmer’ (time taker) loops that are both input and output of the clock (an unimaginable complexity for the simple sequential model) which have the interesting consequence of increasing the robustness of the system.
• Another aspect of complexity is the presence of several oscillators in the same organism. Circadian clocks are not confined to the central nervous system but are also present in peripheral organs: examples have been found in invertebrates, like fruit flies and moths, and in vertebrates, like zebra fish and mouse. Peripheral oscillators are self-sustained, as evinced by in vitro studies, but show a great deal of variation in their robustness and responsiveness to external (i.e. light) and/or internal (i.e. hormonal and neuronal) stimuli.
• The physiological implications of relying upon a multi-oscillator system are particularly evident in birds. The avian time-keeping system is the product of the dynamic interplay between anatomically distinct pace-maker components. The flexibility in the interaction is particularly important in helping the circadian system cope with extreme environmental conditions such as those experienced by high-Arctic (low-amplitude light variations in midsummer) or migratory (travel between time zones) birds.

Kippert attributes the origin of complexity in these circadian systems to the environment: the conferees were not “surprised to also find complexity in biological timing mechanisms, considering that they have evolved in response to a complex environment (which we fail to reproduce in our simple artificial laboratory conditions) …. Their contribution brings into focus once again the notion, held all along by the honouree of the conference, that complex environments will necessarily breed complex timing mechanisms.”

He thus falls into his own reductionist trap. The environment no more produces complex systems than horse hair and cat gut produce string concertos. How could rocks, air and sunlight produce complex biological clocks? How could they invent timing mechanisms that allow birds to migrate by the stars and the earth’s magnetic field, and to compensate for solar angle and changing seasonal light, and find their breeding grounds unerringly after thousands of miles of flight? The complex parts of the biological clocks reside in multiple organs and genes, which communicate with each other through feedback loops and compensation techniques. The systems baffle the researchers who try to study them, yet we are told to believe that time, chance and aimless processes of natural selection produced these wonders. Which is more amazing: the clocks, or the evolutionists who attribute them to a blind watchmaker? (See also the Nov. 14 headline on mole rats.)

NASA Center Tolerates the G Word   11/15/2001
Exclusive  The Jet Propulsion Laboratory, a focal point of NASA’s Origins program and search for life, permitted the G word (God), and even applauded it, during an outdoor patriotic celebration Thursday. An ad hoc choir made up of employees, accompanied by JPL’s amateur jazz band, The Big Band Theory, sang and played a mixture of American songs: America, America, God shed His grace on Thee / And crown thy good with brotherhood from sea to shining sea …. Mine eyes have seen the glory of the coming of the Lord / He is trampling out the vintage where the grapes of wrath are stored / He hath loosed the fateful lightning of His terrible swift sword / His truth is marching on. A special third verse was substituted in the finale, Battle Hymn of the Republic, in honor of the victims of September 11:

Now the fateful lightning strikes again across our peaceful land:
New York’s best and finest lie at rest in God’s almighty hand.
As we strive for truth and justice, and for freedom make our stand,
For peace we’re marching on. Glory, glory, hallelujah!  Glory, glory, hallelujah!
Glory, glory, hallelujah!  His truth is marching on.

The program was well received by a moderately large audience in the central plaza, with a huge American flag draped from the 10-story administration building behind the choir.

It was very nice of JPL to stage this performance put together by employees, when a few months ago any event using the G word (except in ridicule) would have been uncomfortable at best. (JPL’s newsletter routinely advertises gay-lesbian support groups and talks by atheists, but squelches announcements by Bible-study groups on campus.)

Now that patriots and Christians have had the stage for a few minutes, we would like to see if the Darwinists can come up with something better that will stir the hearts of the those who borrow God-words when terror strikes, but otherwise have no use for them: O ugliful for stinking slime that sees beyond the years / Thy bubbling hydrothermal vents give rise to blood and tears …. Gory, gory evolution; Gory, gory evolution; Gory, gory evolution; ‘Tis ruthless stumbling on.

Honey, You Smell Good; Let’s Evolve   11/15/2001
According to Nature Science Update, evolutionists have a new twist on sexual selection. By studying sticklebacks (a small fish), researchers at Max Planck Institute in Germany think that the females can smell which males have a better immune system. They mate with the ones with the best MHC gene complex (involved in immunity) to get a better chance of having offspring that will survive. “The reporter hints that this effect may also work in humans: “In 1995, the famous ‘sweaty T-shirt’ study showed that women prefer the smell of sweat from men whose MHC genes are dissimilar to their own, hinting that the odour warns women not to mate with close relatives.”

Don’t tell this to the deodorant companies. If you mask your B.O. you may be hindering evolution. How are little fish-brains supposed to understand genetics, or care whether their kids have kids? As usual, the disclaimers are at the very end of the article, after the confident headlines have done their bluffing: “How humans, mice and sticklebacks detect MHC profiles using body odours is a mystery. ‘We don’t know whether the odour differences are directly from MHC or from different bacteria living on the animal’s skin….’”

Coastlines Evolve Quickly   11/15/2001
In a letter to Nature, three geologists propose that large-scale coastal landforms like capes and cliffs can form rapidly as a result of instabilities when the angle between shore and surf reaches a certain point. “Wind and wave data from this area [Carolina coastlines] support our hypothesis that such an instability mechanism could be responsible for the formation of shoreline features at spatial scales up to hundreds of kilometres and temporal scales up to millennia.”

That’s millennia as in thousands, not millions, of years.

Blind Mole Rats Keep Biological Clock Running   11/14/2001
A paper by Israeli scientists in the Proceedings of the National Academy of Sciences finds that mole rats in Israel that have lost their sight due to living underground in the dark are apparently still able to maintain circadian rhythms. Expression of genes thought responsible for circadian rhythms are enhanced, and the harderian gland is substantially larger: “The expression of Clock and MOP3 [possible circadian rhythm genes] in the harderian gland of Spalax is remarkable and should be emphasized: the harderian gland of Spalax is tremendously hypertrophied, occupying the entire eye-socket, whereas the eye is degenerated (0.7 mm in diameter), subcutaneous, and embedded in that huge harderian gland. It was previously suggested that the harderian gland of Spalax is a possible photoreceptor and photoperiodic organ.” They conclude that “The mosaic evolution of the Spalax eye, harderian gland, and brain, and its circadian genes provides a dramatic model of tinkering evolution at both the molecular and organismal levels. From an evolutionary perspective, the genetic basis of circadian rhythms in blind subterranean mole rats may be different from that of strictly diurnal or nocturnal and sighted mammals.”

This paper is listed under the category Evolution but really proves nothing. The mole rats are still mole rats, they have the same organs (whether enlarged or atrophied), and have no new capabilities. Both creationists and evolutionists accept that gene expression and phenotype can be influenced by environmental factors. The paper, furthermore, is filled with wiggle words like might, may, possibly, and could, and evolutionary puzzles: the genetic phylogenies are mixed up (some of the mole rats’s genes are closer to humans than to other rodents); the authors characterize the development as “mosaic evolution” (what on earth is that?) and convergence (definition: multiplied miracles), and it is not clear whether these genes or the harderian gland are associated with circadian rhythms in the first place. The authors claim this is a “dramatic model of tinkering evolution at both the molecular and organismal levels,” yet leave you wondering, “so where’s the evolution, and who, pray tell, is doing the tinkering?”

For a creationist perspective on degenerative structures like the de-evolution of eyes in blind cave fish, see this article by Carl Wieland.

Darwin for Children   11/14/2001
Evolution-based books for children are nothing new; The Water Babies, The Land Before Time and even Berenstein Bears help predigest Darwinian concepts for young minds. Now, in his new book Animal Baby-Sitters, Cornell biologist Paul Sherman explains for children “a mystery that has puzzled evolutionary biologists for years – why some animals postpone breeding in order to stay home and help their families – may actually make good evolutionary sense.” His research has studied how the offspring of scrub jays, crows and naked mole rats help the population reproduce by ensuring the survival of the next generation. So it’s not really altruism, but an indirect application of good old Darwinian survival of the fittest. According to the report in UniSci International Science News, The authors are betting that some of their young readers will be intrigued by animal stories about behaviors that pose many questions and offer some – but not all – of the answers.  “It’s never too early,” Sherman says, “to get children hooked on the magic and mysteries of behavioral biology.” 

Notice the words magic and mystery, and they told you evolution was scientific fact. No, evolution is a set of magical tales, mystery stories and what-if conjectures that can explain anything and everything, even opposite things, so long as no God is involved. Get ’em “hooked” on the magic while they’re young; the sorcerer needs new apprentices.

Body’s Energy Motor Takes Breaks   11/13/2001
The Proceedings of the National Academy of Sciences has another new paper about ATP synthase, the ubiquitous motor protein of all life. Japanese scientists have found that it pauses for several seconds between its rapid rotational cycles, for causes not yet known. The pauses appear to be related to the presence of ADP-Mg.

If you’re not yet excited about ATP synthase, here are a couple of good reasons to learn about it: (1) It’s running your body right now.  Trillions of these exquisite little motors are providing the energy for everything you do, and yes, the biologists call them motors, even describing their parts as rotors and stators. These incredibly tiny molecular machines are almost 100% efficient. Scientists are astounded at these motors; one of its discoverers, Nobel laureate Paul Boyer, calls ATP synthase “a splendid molecular machine.”Scientists only began to understand it within the last seven years. (2) ATP synthase is a prime example of why chemical evolution is a dying theory. All life, even the simplest bacteria and blue-green algae, have them. These motors are far too complex and perfect to arise by chance. The DNA that codes for them is also far too complex and perfect to arise by chance. Neither would emerge from the primordial soup by itself, but both need each other. Are we staring at prima facie evidence for God?

There’s a lot of material out on ATP synthase, both lay articles and detailed scientific papers; use your favorite search engine and learn about those little motors inside you. Here is a list of scientific papers to get you started.

Cell’s Golgi Body Recycles Itself Continuously   11/12/2001
The Golgi apparatus, a maze of channels near the nucleus of a cell whose function was mysterious a few decades ago, is gradually revealing its secrets. Scientists at Virginia Tech and Heidelberg have found that the proteins making up the apparatus are constantly being renewed, according to EurekAlert. One of the scientists describes what the Golgi body does:

The Golgi apparatus is a complex organelle. It is involved in the processing of proteins destined for either secretion or for the outer surface of the cell. Traditionally, scientists have looked on the Golgi apparatus as a fixed structure that processed proteins in an assembly-line fashion.

The organelle is a cup-shaped arrangement of layers of flattened sac-like membranes that’s located in a characteristic place near the cell’s nucleus. Proteins are processed through the layers of the Golgi apparatus, with enzymes in each layer causing modifications as the proteins proceed through the layers, finally to be shuttled into vesicles that take them to the cell’s surface.

Vesicles are bubble-like containers that bud from the Golgi apparatus and transport proteins to the cell’s surface membrane. The vesicles themselves are made of proteins, which are absorbed by the surface membrane when they have completed their mission. Proteins are delivered to the Golgi apparatus for processing in vesicles that bud from the endoplasmic reticulum. Therefore . . . there is a constant flow of materials from the endoplasmic reticulum through the Golgi and to the cell’s outer surface.

The new “central finding” about the Golgi body is that it is “not a fixed structure, but that every component of it is recycled through the endoplasmic reticulum. This recycling allows the replacement of frayed proteins, acting as a kind of quality control to ensure the structure can perform its function.”

Update 01/11/2001: More on the Golgi apparatus in Science, “the central protein sorting station of the cell,” especially how it creates protein vesicles for transport: a very complicated series of steps involving enzymes and lipids working together.

If you drew pictures of cells in biology class years ago, just about all your teacher and textbook knew about the Golgi body was its name. Now we are seeing that it is a key processing site for proteins built by the ribosomes, and part of a complex assembly line with quality control built in. All these operations require energy that is generated by the ATP synthase motors, and everything is orchestrated by the master control library in the nucleus.

Articles like this usually hasten to discuss how we might use this knowledge for medicine or pharmaceuticals, but almost never ask the obvious question, How did these complex factories arise? They just assume they “evolved” somehow. Surely more biochemists somewhere are beginning to have serious doubts that all this complexity could be the result of blind, purposeless, random collisions of molecules.

A Merry Heart Prevents Heart Disease   11/12/2001
Researchers at Johns Hopkins have found that a positive attitude is the best prevention against heart disease, according to EurekAlert. Even individuals with a family history of heart disease were only half as likely to have a heart attack or chest pain requiring surgery if they had a good attitude. The power of positive thinking was strong even when traditional risk factors like cholesterol, weight and smoking were taken into account.

Sir John Herschel once said that all scientific discoveries seemed only to confirm the truths come from on high, and contained in the sacred writings. Three thousand years ago, Solomon said “A merry heart does good like a medicine” (Proverbs 17:22; see also Eccl. 5:18-20).