Archive: RNA Repair, Diatom Strength, AAAS Superstition

These articles from February 2003 give glimpses into the status of science 21 years ago. What’s new and different now, and what has remained the same?

Note: some embedded links may no longer work.

Cell Repairs its RNA, Too   02/20/2003
The cell has elaborate ways to safeguard its genetic library by repairing DNA, but now scientists are finding the same enzymes can also repair RNA. In the Feb. 20 issue of Nature, Begley and Samson of MIT discuss the findings of Aas et al that RNA methylation damage can be repaired by the same AlkB enzyme that repairs DNA. This is surprising because RNA and proteins were considered more expendable than DNA, but they explain why it makes sense (emphasis added):

Why, though, should it be necessary to repair damaged RNA? The answer could be that although DNA is the final arbiter of genetic information, RNA is essential for the most basic biological processes. RNA-based primer sequences are required for DNA replication; and mRNAs, transfer RNAs (tRNAs) and ribosomal RNAs (rRNAs) are all needed during the elaborate process of protein synthesis. Even the formation of peptide bonds by ribosomes (the cell’s protein-making machines) turns out to require catalysis mediated by rRNAs. Moreover, a battery of small, non-protein-coding RNAs regulates a variety of other cellular processes.

So maintaining RNA integrity is important for proper cellular function. And repairing damaged RNA may be more efficient than destroying it and starting again. Ribosome assembly is a complex, energy-intensive process, and it is not hard to imagine that the thrifty repair of damaged rRNA would be preferable to disassembling or discarding an entire ribosomal particle.

Another surprise is that the repair mechanism seems to be able to distinguish between DNA and RNA, and between toxic methylation damage and normal biological methyl groups attached to some RNAs. Begley and Samson think it not unlikely that DNA and RNA might overlap in other ways, such as in cell signalling.

Update  06/16/2003:  In the June 17 issue of Current Biology, Alfonso Bellacosa and Eric G. Moss from the Fox Chase Cancer Center in Philadelphia remind us that “RNA in a cell is subject to many of the same insults as DNA“ and that “the ‘information content’ of cellular RNA is greater than that of the chromosomal DNA” because almost all of RNA’s sequences have functional significance (messenger RNA and transfer RNA), whereas only 3% of the DNA has coding potential. Since RNA shows significant response to anticancer agents, the authors suppose that newly-discovered RNA repair pathways are important for preventing cancer:

A cell has a great investment in its RNAs – they are working copies of its genomic information. The study of mRNA biogenesis in the last few years has revealed an elaborate surveillance mechanism involving factors such as the UPF proteins that culls aberrantly spliced mRNAs and mRNAs with premature termination codons. There might be a hint that such RNA quality control mechanisms go awry in cancers, just as DNA quality control mechanisms do, where aberrantly spliced transcripts accumulate in a tumor. Now that the gates are open, we may have a flood of studies on the RNome [the RNA genome] stability and cancer.

(Emphasis added in quotes.)

This aggravates the chicken-and-egg problem for evolutionists. In the “RNA World” hypothesis for the origin of life, RNA performed both the information storage and enzymatic functions before these roles were outsourced to DNA and proteins. But how could RNA repair itself? If RNA needs to be protected from damage, the protein repair system would have needed to be there from the beginning. Evolutionists might surmise that different primitive RNAs worked side by side to repair each other, but that strains credibility for a hypothesis already far-fetched.

In typical evolutionary lingo, Begley and Samson blow smoke about what nature produced (emphasis added): “It seems that, for each human protein, parameters have evolved to distinguish between RNA and DNA,” they speculate, and in another place, “It might be that the RNA-demethylation activity of AlkB-like proteins evolved to regulate biological RNA methylation, and that the repair of aberrant, chemical methylation is fortuitous.” Ask them how the cell evolved these things, and you’ll probably get a quizzical look, as if “Why are you asking such a dumb question? I don’t know. It just had to. We’re here, aren’t we?”

Diatoms Can Withstand Huge Crushing Forces   02/19/2003
The intricate silica shells of diatoms provide strength as well as beauty, says Nature Science Update. German marine biologist Christian Hamm and team put pressure on the tiny glass frustrules and measured the pressure required to break them: 100 to 700 tons per square inch. That’s like a dining table strong enough to hold an elephant, explains Philip Ball, author of the news article. The veneer of holes and grooves makes the shells 60% stronger than they would be if featureless. “The diatoms seem to have found a balance between weight, strength and cost of their protective garments,” Ball explains, indicating that they can survive claws and jaws of predators and emerge unscathed from predators’ guts.

Ball quotes Karl von Frisch, Nobel biologist famous for studies on honeybees, as hedging about the aesthetics of the beautiful houses diatoms live in: “I do not want to wax philosophical about so much ‘useless’ beauty scattered over the oceans – Nature is prodigal.” Ball adds in conclusion, “But not so prodigal, it seems, as to create beautiful designs without a sound evolutionary reason.”

The “delicate filigree coating” in the shells provides strength and beauty. Why must these attributes be mutually exclusive? Gothic cathedrals were ornate but also structurally sound, and medieval chain mail provided protection as well as a display of artistic craftsmanship. There is no reason to exclude “useless” beauty in the design of diatoms if they were created, and there is no reason for evolution to evolve beauty for microscopic organisms who only need to survive. Look at the star-shaped example in the article and consider that this is just one of many thousands of geometrical shapes produced by these tiny algae.

Who is there to appreciate these things if not man? Diatoms surely could not care what they look like (ever seen a diatom looking at itself in a mirror?). Nor would evolution care to produce five-pointed stars and triangles and spheres with “lacework veneer of holes and grooves … more intricately tooled than the finest suit of medieval armour,” as Philip Ball describes them, if durability were the only factor being winnowed by natural selection. Consider also the wonder of how these single-cell plants undergo division and produce identical copies of themselves and their shells. No Gothic cathedral can do that!

Frisch and Ball cannot get away from personifying Nature for “her” ability to create beautiful designs, prodigal or not. And they fail to provide a “sound evolutionary reason” for why or how impersonal laws and natural selection could combine strength and beauty into such miniature works of art. Instead, it would seem the Creator hid a million wonders for humans to discover, some that awaited the invention of the microscope and telescope, to demonstrate His power and wisdom, His care for even small things, and the inability of human nature philosophies to explain them. Wouldn’t that fit perfectly with what Psalm 96 says:
“Oh, sing to the LORD a new song! Sing to the LORD, all the earth.  Sing to the LORD, bless His name; Proclaim the good news of His salvation from day to day. Declare His glory among the nations, His wonders among all peoples.
For the LORD is great and greatly to be praised; He is to be feared above all gods. For all the gods of the peoples are idols*, But the LORD made the heavens.  Honor and majesty are before Him; Strength and beauty are in His sanctuary.”

*e.g., Mother Nature, or Natural Selection.

AAAS Compromises with Superstition   02/16/2003
According to EurekAlert, the American Association for the Advancement of Science has a new way to help native American students learn science: listen to them and learn from them. These students often find Western science difficult to reconcile with their cultural beliefs. A tribal college in Washington invites native American elders to give lectures, and takes students on field trips into their own communities. “The idea, according to speakers at the AAAS Annual Meeting, is that the students learn more if they have a cultural context for their studies, but also that native American culture and its integrated view of the world may have much to offer Western science” (emphasis added).

It is one thing to be a good listener, but it is another to act on bad advice. Most native Americans are wonderful people, and they do have some things to teach westerners, but their traditional philosophy of nature is poison to science. If the AAAS thinks that listening to the spirit of the coyote is going to help them understand the world, science will take an about-face.

This editor once heard a Park Ranger at Navajo National Monument explain that in Navajo culture, it is taboo for a child to ask questions. When the parent or shaman is ready, he will tell the child what to believe. Some northern California Indians were afraid to enter the redwood forests, and some Wyoming tribes afraid to enter the geyser basins, for fear of evil spirits. The great goal of a young Indian was to go on a vision quest, empty his mind, and learn from the spirits what to do. How can anyone learn science without renouncing such blatant superstitions? At a time when Christians are routinely bashed by certain establishment scientists (especially anti-creationists), why does native American religion get such good press, and such politically-correct deference, especially from the AAAS, whose mission is to overcome superstition?

This is by no means a blanket condemnation of native American thought – there is enough evil and stupidity to go around in any culture, because all are in rebellion against their Creator – but the gentle, environmentally-conscious, harmonious depiction in Dancing with Wolves with its anti-Western undercurrent was distorted with half-truths and whitewash. Suffice it to say the native Americans did not invent modern science. Believers in the Judeo-Christian Scriptures did, based on their belief in a law-giving God, linear time, and a universe that was other than God (see our chapter on the rise of modern science, with disclaimers and definitions). Does the AAAS feel kinship with native Americans because of a common pantheistic world view, that invokes emergence and self-organizational principles to explain the origin of life, and game theory to explain the interactions between species?

Here’s what we suggest. Yes, listen to them, visit their lands, strive to build bridges and relationships, and avoid unnecessary confrontation. That makes sense with any culture. But don’t compromise truth with superstition. Statements like the following are just patronizing:

He [a tribal professor] notes that physics, mathematics and astronomy use the circle to represent periodicity. “In other contexts, it represents balance, wholeness, perpetuity and non-linearity.”

That is not going to help a student do math. The AAAS could learn from missionaries who understand cross-cultural ministry. They know it is important to build relationships, spend time and listen when making contact with another culture. One must build trust, establish common ground, and understand the other person’s point of view. It is even helpful to build from their vocabulary and traditions rather than jump in with foreign words and concepts. But a good missionary will not compromise the message; she or he knows the people need to repent of their false beliefs and believe the truth. Native Americans, for all the richness their culture brings, need to repent of anti-scientific superstitions. The spirit of the coyote is going to keep them in darkness.