Archive: Mars, Pulsars, DNA, Mammals, More

These articles from late May 2002 still hold interest for CEH readers. What issues from 22 years ago remain the same today?

Note: Some links may no longer work.

DNA Translation Machinery Is the Major Cell Building Project   05/31/2002
“The ribosomal RNA [rRNA] genes encode the enzymatic scaffold of the ribosome and thereby perform perhaps the most basic of all housekeeping functions. However, recent data suggests that they might also control important aspects of cell behavior.” Thus begins a minireview in the May 31 issue of Cell, which says that one of the biggest, if not the ultimate, cellular subsystem is preparing and controlling the machinery to translate DNA into proteins:

An actively cycling eukaryotic cell expends between 35% and 60% of its total nuclear transcription effort in making the 18S, 5.8S, and 28S ribosomal RNAs (rRNA) (Paule, 1998 , and references therein). The 5S rRNA and the small nucleolar RNAs required for ribosome biogenesis, account for another 10% to 20%. Thus, the assembly of the translational machinery occupies around 80% of nuclear transcription in yeast, while in the proliferating mammalian cell as much as 50% is dedicated to this goal. Even relatively small changes in this commitment are likely to have extensive repercussions on the cell’s economy, limiting proliferation rates and perhaps even cell fate. … Though little is known of the changes that occur in vivo, one would suspect that, given the longevity of ribosomes and the highly variable proliferation rates of different somatic cell types, rRNA transcription rates must be regulated over a wide range if neither a ribosome deficit nor an overproduction is to occur.

The minireview by Tom Moss and Victor Stefanovsky, “At the Center of Eukaryotic Life,” goes on to describe many functions of ribosomal RNA, including regulatory functions previously unknown. rRNA molecules appear to silence some genes, a mystery that may be explained by having backup copies available in case damage occurs to the highly active rRNA genes. They conclude, “Recent work argues that the rRNA genes are not simply bystanders in the decisions on cell fate. Understanding the regulatory network surrounding the rRNA genes is then an essential part of understanding cell growth regulation. It may even turn out that the housekeeper is in fact keeping the house.”

Housekeeper? Doesn’t that imply intelligent design? Here is another subsystem that was considered a “bystander” but turns out to be a high-level manager. Without tight management performed by rRNA, the cell would die.

Notice how much equipment and design goes into translation of DNA, which speaks of a language convention (see our May 22 commentary), another indicator of design. Evolutionists imagine all this complex equipment originating from simple RNA ribozymes, which show (under controlled lab conditions) a little activity and replication, but there is a tremendous gap in complexity between artificial ribozymes and the machinery found in single-celled eukaryotes, like yeast. How did yeast figure out it might be good to have hundreds of backup copies, and evolve the equipment to keep them locked up until an emergency? These are capabilities far in excess of what is needed for survival. Yet evolutionists ask us to believe this complexity arose by a process that can’t even add 1.5% length to a bird beak in 30 years. Natural selection, wandering aimlessly in the dark, is wholly incapable of such complex, interdependent operations.

Mouse Genome Released; Overturns Evolutionary Notions   05/31/2002
The full genome of the mouse has been released, and “already long-held notions are being overturned,” writes Elizabeth Pennisi writing in the May 31 online edition of Science. The 1970’s picture of a genome as being a string of genes linked together, for one, has been overturned in the last 30 years as scientists realize that there are long sections of non-coding DNA, parts that have been duplicated or inserted or transposed, and more. Another surprise is that some of these non-coding regions, which evolutionists thought were free to mutate without harming the organism, appear conserved between human and mouse, and that different parts of the genome appear to mutate at radically different rates if animals diverged from a common ancestor. Evolutionary biologists appear to be in for hard times explaining some of the findings. “For one,” writes Pennisi, “it will complicate the work of evolutionary biologists, who often attempt to date when new species emerged using so-called molecular clocks. These clocks depend on the relative number of mutations in a species and are based on the premise that they ‘tick’ at a constant rate throughout the history of the DNA. A number of skeptics have questioned the reliability of these clocks (Science, 5 March 1999, p. 1435), and the new findings could provide them with new ammunition.”

We’ve been reporting this fact for months (see Feb 26 and Oct 1, for instance). The picture is complicated and confusing, certainly not what one would expect if evolution were true. Whatever the genome story is telling, it is not a simple evolutionary tale. “Genomes are evolving in a completely nonuniform way,” complains one biologist, and another mourns that the wide variation in mutation rates in non-coding regions is “a complication we didn’t anticipate.” Maybe it would make more sense if they looked at the genomes with a focus on function rather than phylogeny; i.e., intelligent design instead of evolution.

Mars May Have Enough Water to Flood Planet   05/30/2002
The BBC News reports that Mars may have enough ice locked up in the soil (see May 28 headline) to have flooded the planet in the past. The article states, “The underground ice solves one of the deepest and longstanding mysteries about the Red Planet: where did the water go?”

Observation 1: Mars has no liquid water now, but could have had a worldwide flood in the past. Observation 2: Earth has a surface 70% covered by liquid water and could have had a worldwide flood in the past. Skeptic: Noah’s Flood is just a legend. Where did the water come from? Where did it go?”

How Did Uranus and Neptune Form?   05/30/2002
The June 2002 issue of Sky and Telescope NewsNotes section, p. 20, laments the problems of explaining the ice giants: “Pity Uranus and Neptune. Not only do they evade the naked eye and underwhelm the telescope, no one can even explain why they exist.” The three leading proposals all have problems:

1. Core Accretion, the standard model, would take too long. Rocky accretions that would build up enough gravity to collect gas would take hundreds of millions of years, but accretion disks around other stars don’t appear to last that long.
2. Disk Instability, a model proposed in the March 2002 Icarus might only take a few hundred years for blobs of gas to decouple and ice particles to settle in. Then a nearby hot O star might blow away the gas atmosphere in a million years. Other planetary scientists are glad to see an alternative to core accretion, but think this model is contrived and depends on unlikely timing.  The Icarus article begins, “The robustness of the current theory of the origin of the Solar System deteriorates sharply with increasing distance from the Sun.” It claims core accretion has a hard enough time with Jupiter and Saturn, but “The problems facing the formation in situ of the ice giant planets, Uranus and Neptune, by the core accretion mechanism are even more severe” because not only would they take too long to form, but any accumulating material would have been ejected into cometary orbits. “Ice giant planets cannot form in the standard model,” they affirm, and therefore propose their alternative. Hal Levison, however, is skeptical that the solar system could form so near a hot star.
3. Migration, in which Uranus and Neptune would form at Jupiter’s distance then migrate outward, does not account for the compositional differences between the gas giants (Jupiter and Saturn) and the ice giants. This model is proposed in the May Astronomical Journal.  Hal Levison explains what he calls his “fairy tale” migration theory in the June 2 Astrobiology Magazine; where he calls his and the other theories “crazy.” He concludes, “We have to start thinking of alternatives. Probably there’s a method for their formation that no one has even thought of yet.”

Other puzzles about these ice giants, Uranus and Neptune, include their ring systems (which appear young and tenuous), their strange moons like Miranda (which has composite terrains with sharp edges and one of the highest cliffs in the solar system), Ariel (whose canyon floors appear to have been resurfaced by a fluid), and Triton (a large body that orbits retrograde and, though -391^oF, has active geysers, a fresh-looking surface and complex terrain). In addition, there are the extremely high winds on Neptune (fastest in the solar system), the oddity that Uranus is tipped on its side, and the magnetic fields which are highly inclined from the poles and offset from the center of mass. Compare the head-scratching and hand-wringing in this story with the neat, computer graphic simulations of solar system evolution seen on educational TV shows and diagrams in textbooks. Time to face the real worlds.

Membrane Channels Are Doorways to Health – or Death   05/29/2002
The latest issue of Neuron, May 30 has an essay about membrane channels and their importance. The authors of “Channels Gone Bad” begin,

Channels regulate ion flow across membranes and are an essential component of cell function. Indeed, nearly all cell membranes contain ion channels, proteins with diverse roles, and sometimes highly complex behaviors. Channels are activated and inactivated by many signals and their function regulated by countless processes. Yet, beware of the aberrant channel. Channels that open when they shouldn’t, channels that do not open very well or at all, channels that stay open too long, misplaced channels, lack of channels, too many channels; all these scenarios can have disastrous consequences.

They describe some of the horrible consequences of mistakes in the genes that code for these complex proteins: cancer, numerous types of disease, and death.

Published the same day, the May 30 Nature has a report on how ion channels open and close their gates, and features two more papers on this subject by the pioneer in this field, Roderick MacKinnon of the Howard Hughes Medical Institute: the crystal structure and gating mechanisms and conformational changes of potassium ion channels. The papers contain detailed pictorial models of how the channels and their selectivity filters attract and transmit the correct molecules rapidly and accurately, but repel interlopers.

We’ve reported several interesting discoveries recently about these amazing channels. Here is another complex function – active transport – that would have had to be operational early on in chemical evolution, independently of the origin of the genetic code, translation mechanism, and reproduction, to allow nutrients to enter and waste to exit. So many precise parts would have had to come together simultaneously to evolve a living cell, that it is incredible to believe it could ever happen by chance. Not only are these channels precision engineered gates, this article shows that small abnormalities wreak havoc. Read our previous entries about potassium channels, chloride channels, and water channels and stand in awe of the wonders within your body keeping you functioning right now without your conscious thought or control.

Pulsar Ages Are All Mixed Up   05/28/2002
The June issue of Sky and Telescope is on newsstands, and its NewsNotes highlights what it calls “The Pulsar Age Crisis.” Findings that some appear older than previously believed, and one pulsar perhaps 15 times younger than earlier reported, “undermine a seemingly secure corner of astronomy.” Age-dating a pulsar by the amount of proper motion from the center of the supernova remnant often disagrees wildly from estimates of its spin-down time, the previous standard of dating. One astronomer comments, “These results make people aware of the uncertainty, especially in the case of young pulsars, and of the assumptions that go into the age estimates.”

At least they’re honest about it, but this was one of the “secure corners” of astronomy; what confidence do we have that the proper motion technique is any more reliable? Those rely on assumptions, too.

Mammal Family Tree A Conflicting Tangle   05/28/2002
An international team of zoologists publishing in the May 28 online preprints of the Proceedings of the National Academy of Sciences examined the mitochondrial DNA of 60 mammalian species and tried to construct an evolutionary family tree. Although some relationships were listed as “strongly supported,” their article mentions a number of controversies in the ranks, and their resulting tree seems to break other pet theories, as these excerpts indicate [emphasis and bracketed words added]:

1. The phylogenetic position of Pholidota has been a matter of debate. A sister group relationship between Xenarthra and Pholidota in a basal position in the eutherian tree has been proposed (e.g., ref. 12). However, other authors (13) have challenged this proposal.
2. Despite the anticipated close relationship between Dermoptera and Primates, the grouping of Dermoptera within the order Primates as the sister group of the Anthropoidea is highly unexpected. … [later in paper] The position of Dermoptera within Primates as the sister group of Anthropoidea is highly unexpected, even though there are morphological arguments in favor of a close relationship between the two orders (44).
3. The traditional order Lipotyphla splits into three lineages: Erinaceomorpha, Tenrecomorpha, and Soricomorpha. On the basis of their separate phylogenetic positions [i.e., assumed evolutionary ancestry] and the depths of their origin, each of these lineages is recognized as having ordinal status.
4. Consistent with other mtg studies (10, 11), the ML amino acid analysis did not favor a monophyletic Rodentia but rather split the order into two groups, one with myomorph rodents and the Taiwan vole, the other consisting of the two hystricognaths and the dormouse and the squirrel.
5. The support for branch K (African clade) is conclusive but the relationships between the aardvark, the elephant shrew, and the tenrec remained largely unresolved.
6. The relationship between Carnivora and Perissodactyla (40) was morphologically unexpected, but this relationship has been generally supported in subsequent molecular studies.
7. The relationship between artiodactyls and cetaceans [whales] was recently addressed in two morphological/paleontological studies (51, 52). The conclusions of these studies were inconsistent. Gingerich et al. (51), in agreement with molecular results, concluded that cetaceans have their origin within Artiodactyla, whereas Thewissen [a leading theorist on whale evolution] et al. (52) inferred that Artiodactyla and Cetacea were sister groups. Test of the latter phylogeny relative to the best mtg tree found the latter relationship as highly improbable (Table 3). Although the morphological conclusions may initially seem incongruent, both might be correct if Archaeoceti is paraphyletic. Archaeocete paraphyly has been suggested (53-56) and it is possible that the study by Thewissen et al. focused on taxa that do not form a monophyletic group together with extant cetaceans.
8. The amino acid analyses reconstructed trees that were largely congruent irrespective of the method used. In comparison, the nucleotide trees differed considerably depending on the analytical approach used.
9. The mtg results challenge several traditional or semitraditional morphological hypotheses for eutherian relationships… [six examples cited]
10. Finally, the pinniped results lend no support to the morphological hypothesis of a sister group relationship between Odobenidae and Phocidae to the exclusion of Otariidae (21), underlining the problems associated with basing phylogenetic conclusions on anatomical features that may have strong adaptive values.
11. The suggestions of a Cretaceous origin of eutherian orders have been met with suspicion by many paleontologists. It has been argued that the molecular estimates suggesting early origin of eutherian orders are artifactual and caused by accelerated molecular evolution at the Cretaceous/Tertiary (K/T) boundary or immediately thereafter (63). However, a post-K/T acceleration of this kind would actually have an opposite effect, as calibration points such as A/C-60 (the split between ruminant artiodactyls and cetancodonts 60 MY B.P.) (58), placed within the postulated window of accelerated evolution, would tend to shrink the estimated datings of earlier divergences. Furthermore, comparisons between estimates based on eutherian calibration points of different ages do not suggest any effects of this kind (49).
12. If the proposed relationship between the zhelestids and the heterogenous eutherian group is phylogenetically correct, the zhelestid fossils support mtg analyses that place primate origin and divergences much deeper than commonly conceived (2, 19, 49, 58, 59).
13. The trees reconstructed in the real data studies and the mtg analyses show pronounced similarities when they are viewed as unrooted.
14. The capacity of mt rRNA genes for resolving ordinal mammalian relationships may be more limited than generally believed (e.g., ref. 68). Only the stem regions of the mt rRNA genes seem to carry a useful (albeit marginal) phylogenetic signal and inclusion of the other parts of these sequences may increase the background noise and promote the selection of the wrong signal (20).
15. One of the main differences between the mtg results and the recent mt/nuclear studies (7) is related to the position of Erinaceomorpha, which in mtg analyses (both amino acid and nucleotide) has a basal position in the eutherian tree. This finding is inconsistent with nucleotide analyses of nuclear sequences, which preferably place Erinaceomorpha with Soricomorpha in a less basal position.
16. As is evident from the branch lengths in Fig. 1, the mt evolutionary rate of the anthropoids is fast compared with other eutherian lineages.
17. Superficially, the trees shown in Figs. 1 and 2 may appear strikingly different. … Independent of analytical method, all amino acid analyses placed this point on the branch leading to myomorph rodents and the vole, whereas ML nucleotide analysis placed it on the short Xenarthra branch, alternatively on the branch leading to the African clade. However, as a result of the short branches separating basal eutherian divergences, an mtg amino acid tree with the root placed on the African clade branch is not statistically refuted under a rate heterogeneity model when Erinaceomorpha is excluded from the data set (Table 3).
18. The current mtg analyses and the recent mt/nuclear studies identify different rooting points in the eutherian tree. It is as yet not clear whether this inconsistency is related to the OG or to the eutherian data sets, or both.  Whatever the reasons for this discrepancy, it is evident that the establishment of the rooting point of the eutherian tree is of paramount importance to the discussion of eutherian evolution, both molecular and morphological.

We apologize for the length of this entry, but sometimes the devil is in the details. We wanted our readers to experience the sweating that goes on behind closed academic doors trying to put together an evolutionary tale for the textbooks and media sound bites. Does anyone feel confident that evolutionists have a consistent story here? That this paper makes things better? That evolution just jumps right out of the data? That they are making progress? Ever since Linnaeus, morphology (outward appearance and skeletal structure) has been the gold standard for establishing taxonomy, and ever since Darwin, morphology has been the basis for building family trees (phylogenies). But now that we have means of comparing genes, mitochondrial DNA and proteins, the picture is more confused than ever. Old favorite groupings are out, and strange bedfellows are in. The PBS Evolution series boasted about the clear family tree of whales, but this is contradicted in quote 7 above. Quote 13 seems to say that the data only match when unrooted; i.e., not having a common ancestor – so where is the evolution?

The tweak space here is considerable. When genetic relationships don’t match, the evolutionists invoke their hand-waving ideas of parallel evolution (paraphyly); i.e., that different groups that look very similar had the same sets of accidents on different paths, or convergent evolution, that totally different lineages converged on the same appearance. When those fail, they can fall back on rate heterogeneity, another fudge factor that supposes different genes mutate at different rates.

A creationist would expect similarities between similar types of animals. For evolutionists, molecular phylogeny has clearly not been the proof they expected. Remember articles like these the next time you see one of those nice, neat-looking family trees that look so solid. The inside is full of termites, and the outside is a facade.