Archive: DNA, Insects, Human Body, Fossils

These articles from March 2003 are useful for comparing what science was saying 21 years ago with discoveries since then.

Note: Some links may no longer work.

DNA Repairmen Can Back Each Other Up   03/21/2003
The DNA Damage Response team has many specialized technicians, but now scientists have found some of them can fill in for a fallen comrade. Amundsen and Smith of the Fred Hutchinson Cancer Research Center, writing in the March 21 issue of Cell first set the stage for the story:

Faithful repair of broken or damaged DNA occurs by homologous recombination. This process requires a series of enzymes, collectively forming a “recombination machine,” that act on broken DNA. At least three broad classes of activities—helicases, nucleases, and synapsis proteins—constitute parts of this machine and can be provided either by one complex protein or by several separate proteins.

They describe two team members, RecBCD and RecF, that act independently under normal conditions.  “But recent analysis of an E. coli mutant that lacks RecBCD nuclease activity,” they announce, “normally required for that pathway of recombination, provides a striking example of how functional parts from these two recombination machines can be interchanged.”

Their minireview entitled, “Interchangeable Parts of the Escherichia coli Recombination Machinery,” also describes how the machines work.  They feel this is probably not an isolated example of interchangeable roles: “Perhaps in wild-type cells also, there are situations of altered DNA metabolism not yet recognized in which activities from the two recombination machines interchange to maintain chromosomal integrity.”

See also our 07/26/2002 and 01/04/2002 headlines on DNA Damage Response.

Why would natural selection maintain interchangeable parts, or keep a specialist trained on a job it normally doesn’t have to do? These little molecules are incredible. They’re like paramedics trained on each other’s tasks, so that the CPR operator can do the gauze if the bandage doctor is out of commission at the moment, so that the cell doesn’t bleed to death for lack of technical skill. Imagine little robots able to find and repair DNA; it’s uncanny. They know just what to do, and they’re on call 24 x 7. Amazing.

In this paper, you can find the words machine or machinery 42 times, repair 17 times, but not one mention of evolution, nor any conjecture on how this complex, redundant, mechanical system emerged. The logical conclusion is left as an exercise.

Insects Evolved Six Legs Multiple Times   03/20/2003
Scientists have always believed the insects evolved from a single common ancestor, but now Francisco Nardi and an Italian team have thrown a “naked fowl” (plucked chicken) into the works, says Richard Thomas in the March 21 issue of Science. Nardi claims that hexapods (six-legged critters) are not monophyletic (one common ancestor) but paraphyletic (two or more common ancestors). He bases his team’s conclusion on mitochondrial DNA sequences from Collembola, a group of wingless arthropods including springtails, assumed to be ancestral to the insects.

“This in turn suggests,” comments Thomas, “that today’s terrestrial hexapods are products of at least two independent invasions of land and that some of the features shared by all hexapods have arisen convergently.” He warns that many arthropod experts will not be convinced by these data. “Systematics is a very contentious field, so we can count on criticisms about the small number of species, the single data type, and the method of analysis,” he says.

For a layman’s level report on this story, see Nature Science Update.

Similarities between molecular trees and morphological trees seem to be the exception rather than the rule. Molecular comparisons have thrown a monkey wrench into the assumed family trees of most groups (see the recent example with mammals). This all seems like such a waste of time. Evolutionists are just playing connect-the-dots games, based on evolutionary assumptions, with way too many dots and way too many assumptions. But this is what evolutionists like: a good wrestling match, where they can argue with each other endlessly without ever having to know the truth. Prehistory is unknowable by definition, because it is hidden in the unobservable past: unless, of course, a credible Eyewitness told us what really happened.

Ready-Mix Patch Kit Stands Ready To Repair Your Body’s Brick Walls   03/19/2003
You’ve probably used those packets with two compartments that do something when the dividing membrane is broken, allowing the components to mix: instant heat, instant cold, instant glue, or instant light. Your body has something like that to repair its tissues. Tissues are the webs of specialized cells that distinguish us multicellular organisms from the rest, and the bulk of tissues are composed of epithelium. Epithelial cells line up in tightly-knit ranks forming the lining of most organs, the lungs and windpipe, the digestive tract, and the skin. Because they are subject to injury, these membranes must have a means of repairing themselves quickly. So they have a kind of ready-mix patch that works only when two components combine. But the system must work flawlessly, or a disaster can result.

Keith Mostov and Mirjam Zegers talk about this in the Mar. 20 issue of Nature, “Cell Biology: Just Mix and Patch,” reporting on work by Paola Vermeer and company in the same issue. Epithelial cells have two linings. Consider the respiratory tract as an example. One lining, the apical side, faces the airway. The other, the basolateral side, lines the other end and the neighboring cells. These two linings are segregated by a kind of O-ring seal that makes a tight fit between neighboring cells. Scientists recently found that the basolateral membrane has one component of the patch, called erbB2, and the apical side has a matching component called heregulin. Normally kept apart, they can be brought in contact when a breach occurs in the epithelial tissue. Together, they activate a complex series of steps leading to cell division and presto! the gap is filled in with another snug-fitting cell, and life goes on.  It is essential these active ingredients don’t mix at the wrong time. Too much cell division and you know what happens — cancer. Science Now has a news write-up on this story, and its discovery that is “so beautifully simple.”

A few more Cool Cell Tricks were reported recently:

• Cells have an exquisite toolkit for dealing with iron. Three New Zealand scientists writing a Perspective special feature in the Proceedings of the National Academy of Sciences describe a family of proteins called transferrins that clamp around iron and delicately transport this very toxic atom to wherever it’s needed in the cell. The clamp has a hinge that opens the structure and disgorges the iron when it is safe to do so. Another protein called hemopexin transports heme by holding it in the center of a four-part structure.
• Another Special Feature in the same issue talks about nitrogenase, which we discussed Sept. 6, 2002. Two Harvard chemists attack this puzzling molecule with the zeal of Captain Ahab pursuing Moby Dick (this is actually how they end their article), but in spite of the best efforts of scientists for decades, “Few problems in bioinorganic chemistry have proved as challenging and refractory.” They speak of techniques this molecule uses that are “biologically and chemically unprecedented,” and marvel like Scotty and Captain Kirk aboard an alien ship trying to figure out a novel dilithium crystal reactor. Hidden inside the inner sanctum of this molecular machine is a secret method for separating nitrogen atoms at room temperature that is the dream of agricultural chemists, because artificial nitrogen fixation (e.g., fertilizer making) is costly and energy intensive. “The synthetic problem of nitrogenase, nevertheless, remains unsolved,” but they think we’re getting warmer.
• Current Biology for March 18 has a quick guide to a very versatile gene called APC (adenomatous polyposis coli), without which we either die or get colon cancer. It moves all over the cell, in and out of the nucleus, even riding the intracellular railroad. APC has many jobs. It’s a potent tumor suppressor, it regulates gene transcription, and it has a role in “maintaining adherens junctions, and also helps to tether mitotic spindles to the cortex and to orient them in the epithelial plane. In mammalian cells, APC has been implicated in cell migration. APC also helps safeguard the fidelity of chromosome segregation in mitotic cells.”

Wow; a multi-talented kid. It appears to be essential for cell survival, too. Maybe we should celebrate national APC appreciation day. But it appears we would quickly run out of days if we gave equal time to nitrogenase, erbB2, hydrogenase, the nuclear pore complex, ATP synthase, etc. etc.

It is so much more fun to see these things as engineering marvels instead of lucky rolls of the die. You don’t have to worry so much about how Lady Luck could win against impossible odds. Instead, you can just enjoy the talent show.

Tank-Like Reptile Goes Extinct Twice   03/19/2003
If paleontologists at an Australian museum have a specimen classified correctly and their dating is right, they have an extraordinary tale of resurrection to explain, says Nature Science Update. An animal went extinct, then showed up alive and well 115 million years later, then went extinct again. The animal is a dicynodont (see article for artist reconstruction), a mammal-like reptile that looks like a monster out of Star Wars with the body of a hippo, the beak of a turtle, and the tusks of a walrus. The curators re-analyzed fragments of a skull in the Brisbane collection of the Queensland Museum. How the dating was arrived at was not explained.

Update 04/01/2003: The April issue of Geology asks, “Has the utility of Dicynodon for Late Permian terrestrial biostratigraphy been overstated?” Authors Angielczyk and Kurkin lament the uncritical use of these bones to correlate geographically separated beds (emphasis added):

Our analysis includes two species referred to Dicynodon that occur only in Russia and the type species that occurs in southern Africa.  Our results suggest that these three species do not form a clade to the exclusion of all other dicynodonts; the alternative hypothesis of a monophyletic Dicynodon is more weakly supported. Although preliminary, our analysis challenges the use of Dicynodon for biostratigraphic correlations between Russia and South Africa, and we urge caution in using this taxon to correlate other widely separated basins. This study also emphasizes that without phylogenetic information, there is no guarantee that named taxa represent biologically real entities, and the uncritical use of named taxa can easily lead to spurious biostratigraphic correlations.

In other words, assuming that similar looking bones belong to the same genus, or that they evolved from a common ancestor, and then using them to tie together a story of global extinction, is not necessarily supported by the evidence.

Geologists and paleontologists come up with stories of world-wide extinctions due to meteorite impacts that make for good TV animations, but are they based on “uncritical use” of evidence? When the uncritical use of evidence leads to contradictions and absurdities, who is heeding the call to be cautious, so as not go build a story on “spurious biostratigraphic correlations”?

This is not an isolated case; there are dozens of living fossils of creatures long thought extinct that are doing just fine today. If this poor dicynodont survived the first extinction, how did it get along on its own 115 million years? Maybe it died of loneliness. Funny that the story is flexible, but the dates are not. You can fit any miracle – even resurrection – into a timeline that is not open to challenge.