January 25, 2024 | David F. Coppedge

Archive: DNA Repair, Cambrian Fish, More

Here are some articles from 21 years ago that became offline during a website upgrade. Some graphics have been added.

Note: some embedded links may no longer work.

DNA Damage Repair Team Hears Alarm at a Distance   01/30/2003
DNA, like a ladder, can break, and when both sides break, it’s serious trouble. Cancer and other lethal diseases can result from these double-stranded breaks, or DSBs, which are “the most deadly” of DNA failures. Most of the time, fortunately, there is a response system called ATM that knows just what to do. It can repair both sides of a broken DNA molecule, quickly and efficiently; when not possible, ATM knows how to throw the self-destruct switch to kill the cell so it won’t become cancerous or otherwise dangerous.

There are many DNA repair mechanisms for many kinds of problems, but most are active during cell division, when there is the highest likelihood for error. ATM, by contrast, works in the resting phase. The heart of the system is a pair of “giant” proteins, normally “locked together in a tight embrace that prevents them from forming any promiscuous liaisons with other proteins” – i.e., their mutual hammerlock keeps them from fraternizing till duty calls. A DSB crisis triggers an alarm; the ATM response separates the repairmen by a process called autophosphorylation, which activates them and puts them to work.

Christopher Bakkenist and Michael Kastan of St. Jude Children’s Hospital in Memphis, Tennessee, writing in the Jan. 30 issue of Nature, found, to their amazement, that ATM can detect the signal some distance away from the problem. A double-stranded break occurring deep within chromatin-wrapped bundle of DNA can get help fast, even if the repairmen are not near. How does ATM differentiate a real crisis from the normal frenzied activity of cell division, transcription, and translation? Danish cell biologists Bartek and Lukas are amazed at the sensitivity of this emergency response system (emphasis added):

“Finally, the sensitivity, extent and speed of the ATM response are truly astonishing. Doses of irradiation that cause only a few DSBs in a human cell activate the majority of ATM within minutes. And induction of just two DSBs per cell is enough to induce the crucial ‘autophosphorylation’ of ATM.

Much remains to be learned about this paramedic team, but one thing is clear: it keeps us alive. “Our genetic blueprint is constantly assaulted by adverse environmental and cellular influences, such as ultraviolet or ionizing radiation and various chemicals,“ write Bartek and Lukas (emphasis added). “Fortunately, these massive attacks on our DNA are largely counterbalanced by promptly deployed, multifaceted surveillance and rescue operations.

Fortunately (evolutionspeak) or should that be providentially (creationspeak)? Notice that ATM is made of “giant” proteins. The bigger the protein, the less likely it could form by chance, and even a small one is astronomically improbable. Yet without ATM and all the other DNA Damage Response team proteins already present, well-trained and effective, would the first hopeful primitive cell survive out of the starting gate? Don’t bet on it.

The Cambrian Explosion: most animal phyla appear abruptly without ancestors at the base of the Cambrian strata. Credit: canbedone (Adobe Stock)

500 Vertebrate Fish Found in Early Cambrian   01/30/2003
Where only one incomplete fossil had been known before, now 500 specimens of early Cambrian agnathan fish of the genus Haikouichthys have been reported in the Jan. 30 issue of Nature. This wealth of new fossils “reveals a series of new and unexpected features that imply a major reconsideration of several features of early agnathan evolution,” says the team of Chinese and European paleontologists. The fish appear to have had eyes, gills, and olfactory organs, and were swimmers. The authors explain the implications (emphasis added):

The possession of eyes (and probably nasal sacs) is consistent with Haikouichthys being a craniate, indicating that vertebrate evolution was well advanced by the Early Cambrian. Although evidently a jawless fish, its precise phylogenetic position is still speculative because this fish shows a puzzling mixture of characters contrary to some previous expectations.

How did this assemblage of fish die? “The specimens may have been buried alive, possibly as a result of storm-induced burial.”

This can’t be good news for evolutionists, even though they try to put a happy face on it, saying the discovery may “extend further our knowledge of their earliest evolution.” But what evolution? They used to claim no fish were found till the Devonian, as if that somehow muffled the Cambrian explosion a little bit. But now, here you have advanced features in vertebrate fish right in the early Cambrian, and evidence that supports flood burial. Don’t tell the creationists.

A Picture Is Worth 1,000 Blurs   01/30/2003
Have scientific illustrations gone too far? Julio Ottino of Northwestern University, in an editorial in the Jan. 23 issue of Nature, cautions fellow scientists to be honest in their illustrations. Compared to old issues of scientific journals, there has been an explosion of color figures recently, partly due to new and easily-accessible illustrating technologies. Flashy artwork and image processing can give pure speculation a look of reality. While Ottino supports the use of illustration as a long-standing and essential part of science, giving impetus to the scientist’s imagination, there is no substitute for raw data and rigorous analysis.

He suggests some guidelines: within reason, “A sensible first rule would be that pictures must not be divorced from science and scientific plausibility.” You can color molecules but not picture miniature space shuttles flying among red blood cells.  Aesthetically, pictures should not be unnecessarily gaudy. Everyday phenomena should not be wantonly extrapolated to micro or mega scales.

Finally, scientists publishing figures as part of their research papers should always ask some general questions. What is the point of the image? Is the objective to teach, to excite or to show how things could be? How can this objective, whatever it might be, be made clear to the viewer? There are many new tools for making beautiful drawings, but if good use is to be made of them, scientists and artists should collaborate closely. Going all-out with computer-generated images without asking questions like those discussed here may be a perfect example of confusing progress with progression.

“Figures influence people,” he says, “sometimes unconsciously.” Scientists are people, too, and are not immune.

He should have drawn examples from evolutionary biology, such as those Jonathan Wells exposed in his book Icons of Evolution. How much of the success of the theory of evolution derived from graphics, considering that Darwinists have long used visualization to misrepresent, distort, lie, whitewash, distract, and propagandize? In Cosmos, Carl Sagan morphed outline figures from goo to you by way of the zoo, nonchalant about the missing transitional forms that vastly outnumber known living and fossil types. It continues today. The La Brea Tar Pits museum has a mural, not untypical, showing an evolutionary continuum from molecules to an astronaut.  NASA Educational Programs illustrate DNA coming out of stellar explosions. A recent educational TV channel used computer graphics to show a scaly dinosaur running along the ground, holding out its arms, sprouting wings and feathers, and taking off into a flying Archaeopteryx – all within 10 seconds. Leading scientific journals like Nature have not hesitated to portray, on the cover, artists’ renditions of feathered dinosaurs and half-ape human ancestors. Though illustrations are attention getting and usually helpful in science, only facts count. Pictures don’t lie, but liars use Photoshop.

Heliconius butterfly (Illustra Media)

Iridescent Wings and Scales Play Tricks with Light   01/29/2003
“Photonic crystals” sounds like something out of Star Trek, but butterflies use them to create those shimmering colors that sparkle on the wings, says Physics News Update. Not made out of pigments or minerals, photonic crystals are precisely aligned series of bumps or holes that cause light to refract particular wavelengths. Birds use similar light tricks, says Elisabeth Pennisi in the Jan. 24 issue of Science. They use closely-packed collagen fibers, sometimes in hexagonal arrays, to intensify certain wavelengths by backscattering. These techniques allow birds and butterflies to produce much brighter colors than could be achieved through pigmentation.

Did birds and butterflies really figure out optical nanophysics just to get a mate? How come other birds and moths are dull colored, then? Why would the mate care about iridescent color – does a bird or moth have aesthetic values? How could two very diverse groups develop similar technology? Let’s hear some detailed analysis instead of the usual vacuous ungod-of-the-gaps generality, “natural selection did it.”

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