Archive: Mutations, Dinosaurs, Water Lilies, Birds, Compound Eyes, More
Here are some of the stories we were reporting in late January 2002, restored from archives.
Note: some embedded links may no longer work.
How Life Defends Against Harmful Mutations 01/31/2002
Different populations have different ways of defending themselves against the destructive effects of harmful mutations, say David C. Krakauer of the Sante Fe Institute and Joshua B. Plotkin of Princeton, in a paper “Redundancy, antiredundancy, and the robustness of genomes” in the Jan 29 Proceedings of the National Academy of Sciences. Although presuming genetic mutations are a source of evolutionary novelty, they explain that damage must be guarded against.
The authors propose that small populations of large organisms (like mammals) use redundancy to maintain fitness: i.e., copies of genes and backup systems. But large populations of small organisms, like bacteria, appear to employ antiredundancy strategies: i.e., they are hypersensitive to mutation, but employ methods of removing harmful mutants:
Assuming a cost of redundancy, we find that large populations will evolve antiredundant mechanisms for removing mutants and thereby bolster the robustness of wild-type genomes; whereas small populations will evolve redundancy to ensure that all individuals have a high chance of survival. We propose that antiredundancy is as important for developmental robustness as redundancy, and is an essential mechanism for ensuring tissue-level stability in complex multicellular organisms. We suggest that antiredundancy deserves greater attention in relation to cancer, mitochondrial disease, and virus infection.
The authors propose a mathematical model for explaining the dynamics of redundancy and antiredundancy in differing populations. Populations exhibiting redundancy have hilly fitness landscapes with steep, narrow peaks. Antiredundant populations have a flat fitness landscape with small peaks, forming a “quasispecies” of mutants with similar fitness.
Although this paper is listed in the category “Evolution,” it is hard to see how it helps evolutionary theory. Whether a population is large or small, it works to shield itself from mutations and achieve stability. The fitness peak concept comes from graphing fitness as the vertical axis on a 3D plot of a population. Evolutionists have been realizing that fitness is not a progressive slope of “onward and upward” improvement, but an undulating landscape with peaks and valleys. A population on a peak is stable, and would actually have to devolve to get off its peak and onto a higher one. This is not evolution in the Darwinian sense. It fits in better with the view that natural selection is a conservative process, allowing enough variation to compensate for contingencies (like mutations) that would otherwise destroy the population. The authors do not describe how “evolutionary novelty” can become established, nor do they provide any example of a beneficial mutation. It appears, therefore, that this paper is promoting a view of life being in a state of dynamic equilibrium, not upward evolution.
Technology Imitates Nature Dept. 01/30/2002: Science News Jan 26, 2002 has a story about how designers are imitating biological cilia, the little beating hairlike projections on many types of cells, to coax micro-spacecraft into position. Unlike the complex biological cilia, the artificial ones are made of silica and powered by electric heaters to make them vibrate at about 60 Hz.
Talk of the Walk of Dinosaurs 01/30/2002
The Jan 31 Nature has two dinosaur articles. A brief communication by four UK scientists determines the gait of theropod dinosaurs from the extensive Oxfordshire trackways. They conclude that the large beasts were able to run and walk, and used different gaits for each, but additional questions are left unanswered:
Furthermore, the anatomical correlations between leg and hip anatomy associated with the adoption of wide- and narrow-gauge gaits are not yet known and we are therefore unable to determine the phylogenetic distribution of these locomotor styles. Nevertheless, the Ardley trackways offer new insight into dinosaur locomotor capacity and will stimulate enquiry into the evolution and biomechanics of large theropod dinosaurs.
Brian Maurer discusses the work of Burness on the size of animals related to land area, asking why dinosaurs grew to be so big:
Dinosaurs present us with a puzzle. In many respects they seemed to be constructed like warm-blooded animals. Their posture indicated they were more active than living cold-blooded vertebrates. They apparently had extended parental care and complex mating rituals. Yet, ecologically, they filled continents as if they were cold-blooded. So what on the surface appears to be a case of convergent evolution between dinosaurs and modern vertebrates may in fact be the result of unique evolutionary events occurring in different ways at different times. Dinosaurs lived in a very different world from any modern animal, and may have interacted with their environment in ways that have no clear parallels among living land vertebrates. The more we study them, the more we get a glimpse into the complex workings of the evolutionary engine.
The references to evolution seem forced. What scientists observe and what they speculate on about family trees and evolution have no necessary connection. Maurer’s comment about the “complex workings of the evolutionary engine” could qualify for Stupid Evolution Quote of the Week. Evolution is a rusting hulk, not an engine.
Water Lilies: the Missing Link? 01/30/2002
A press release by the National Science Foundation argues that water lilies may be a missing link. The origin of flowering plants, Darwin’s “abominable mystery,” has long been a problem. Since all angiosperms have triploid endosperm but water lily endosperm is diploid, it may be represent a precursor to the divergence of angiosperms from gymnosperms. This is the theory of two Colorado biologists writing in the Jan. 31 Nature, who admit (emphasis added):
Recent phylogenetic hypotheses suggest far greater evolutionary distances between flowering plants and all other extant seed plants than had previously been imagined. Thus, the task of determining the homologies and evolutionary histories of defining angiosperm characters, in essence solving Darwin’s “abominable mystery”, appears as daunting as ever. If diploid endosperm represents the ancestral condition for flowering plants, a key intermediate condition in the early evolutionary history of angiosperms has been revealed. … The presence of diploid endosperm in an early angiosperm lineage brings us one step closer to bridging the substantial gap between flowering plants and their seed plant ancestors.
There is no way to prove this is a transitional form. Water lilies are doing just fine today with their diploid endosperm. The NSF project officer gloats that “This is a significant first-time discovery because now we are a big step closer to understanding the evolution of flowering plants.” Notice his bluffing exaggeration (“a big step closer to understanding the evolution”) compared to the measured optimism of the authors (“one step close to bridging the substantial gap”). In actuality, due to other major problems with evolutionary theories about the origin of plants that keep mounting in biochemistry, they are taking only small steps north on an iceberg speeding south.
Birds Evolved Flight Out of Love 01/29/2002
A UC Davis biologist, discontent with both leading theories of the origin of bird flight, presented his own: parental care. EurekAlert says that James Carey finds flaws with the two leading theories: (1) the top-down theory (that wings grew as lizards jumped out of trees) would predict wings between front and hind legs. (2) The bottom-up theory (that wings started out as insulation or insect swatters) would predict that each stage must be advantageous, but no intermediates are found. So he presents a new theory: that reptiles, tenderly caring for their eggs, found the trees a safer place. The report summarizes:
In time, these early ancestors of birds developed more advanced techniques for caring for their young. They started to feed their young in the nest, pumping liquid food or placing small food items in their mouths. They also began to produce fewer and more dependent offspring and smaller eggs, and began nesting in bushes and then small trees to better protect their offspring from predators.
Gradually the forelimbs of these creatures became feathered and even more elongated, enabling them to better manipulate their eggs and to “parachute” from their tree nests to a soft landing. Later they would develop the ability to glide and eventually fly by flapping their wings.
Writing in the German journal Archaeopteryx, Carey “also discusses why flying dinosaurs with non-feathered membrane-like wings, such as the pterosaurs, became extinct. He suggests that they perished, not because they were out-competed by birds but because they lacked the sophisticated parenting skills needed to cope with a changing environment.”
Did you know there was a whole journal dedicated to Archaeopteryx, the discredited link between reptiles and birds? We’ve said it before, and we’ll say it again: evolution is not a scientific theory, but a game for storytellers who amuse themselves by competing for who can tell the biggest whopper. The only thing worth noting in Carey’s ridiculous speculation is how he trashes the other two leading theories for the origin of bird flight.
[Note: A year later, the WAIR model was proposed by Ken Dial. It rose and fell. Evolutionists still cannot explain the origin of powered flight.]
Briefly Noted 01/29/2002
Gleanings from the Proceedings of the National Academy of Sciences Jan 29 online preprints (emphasis added in quotations):
- Biochemistry: A team describes a Human Elongator Complex that helps in the DNA transcription operation. The introduction states, “The formation of a transcription initiation complex at a particular promoter is a complicated and highly regulated process. However, the establishment of a transcription initiation complex seems much simpler than the process of transcription elongation with respect to the chromatin impediment, where the elongating polymerase has to traverse a nucleosome approximately every 200 base pairs.” They describe how human Elongator performs just this function.
- Biochemistry: A team from the Netherlands describes a second endonuclease enzyme that aids in DNA excision repair (see our Jan 4 headline on DNA Damage Response). This enzyme they named Cho is even more effective than UvrC and appears to come into play when the other repair enzymes are unable to complete the job: “If, however, a specific lesion remains because UvrC is not able to induce 3′ incision as argued above, a replication block at this damage to which UvrB will probably remain bound will trigger the SOS response, resulting in expression of the Cho protein. The Cho protein in its turn will attempt to incise the preincision complex. When this incision is successful the UvrC protein will induce the second incision and the repair process can be completed. … Taken together, the combined action of UvrC and Cho broadens the substrate range of nucleotide excision repair in E. coli. ” E. coli, is, of course, a lowly bacterium, mindless of these fail-safe mechanisms taking place within its interior.
- Fossils: Symbiotic bacteria and protozoa have been found in the gut of a remarkably preserved termite preserved in Miocene amber presumed 20 million years old. The organisms “markedly resemble” those in living termites.
- Evolution: A team of geneticists writes that “mtDNA from fossils reveals a radiation of Hawaiian geese recently derived from the Canada goose.” The surprising and unexpected results lead them to postulate a case of convergent evolution.
- Evolution: Biologists from Utah have found a gene for gamma-carboxylation, long thought to be a vertebrate specialty involved in blood clotting, in a marine mollusc Conus. The gene had remarkable similarity to its human counterpart, and to a gene in Drosophila (fruit fly) whose function is unknown:
The unexpected conclusion that emerges from our study of the Conus gamma-carboxylase gene is that all eight introns in the human gene, corresponding to the Conus genomic interval analyzed, are evolutionarily ancient, older than the Cambrian explosion (~540 million years ago) when the molluscs and chordates are first detected in the fossil record. This finding raises the intriguing question of whether most introns in other human genes have a similarly ancient lineage. Our results suggest that Drosophila (and perhaps, other insects) may not be the appropriate invertebrate standard for evaluating whether vertebrate introns are likely to be relatively recent or more ancient than the Cambrian explosion.
Surprises, always surprises, for those who think evolution explains everything.
“a case where commonly used methods of historical inference are positively and significantly misleading.”
Compound Eyes Evolved Multiple Times 01/29/2002
The molecular phylogeny wars are heating up again. Todd Oakley, biologist at Duke university, writing in the Jan 29 preprints of the Proceedings of the National Academy of Sciences explains three reasons biologists have assumed that compound eyes had a single origin: (1) detailed similarities appear between diverse groups, even at the gene level; (2) the number and arrangement of cells in the eyes of diverse groups are similar; and (3) the neural circuitry is the same (conserved) across diverse groups of arthropods. These would seem conclusive, but Oakley argues based on molecular evidence that compound eyes evolved multiple times separately. The abstract states (emphasis added):
Eyes often take a central role in discussions of evolution, with debate focused on how often such complex organs might have evolved. One such debate is whether arthropod compound eyes are the product of single or multiple origins. Here we use molecular phylogeny to address this long-standing debate and find results favoring the multiple-origins hypothesis. Our analyses of DNA sequences encoding rRNA unequivocally indicate that myodocopidsthe only Ostracoda (Crustacea) with compound eyes are nested phylogenetically within several groups that lack compound eyes. With our well-supported phylogeny, standard maximum likelihood (ML) character reconstruction methods significantly reconstruct ancestral ostracods as lacking compound eyes. We also introduce a likelihood sensitivity analysis, and show that the single-origin hypothesis is not significantly favored unless we assume a highly asymmetric model of evolution (one favoring eye loss more than 30:1 over gain). These results illustrate exactly why arthropod compound eye evolution has remained controversial, because one of two seemingly very unlikely evolutionary histories must be true. Either compound eyes with detailed similarities evolved multiple times in different arthropod groups or compound eyes have been lost in a seemingly inordinate number of arthropod lineages.
If his multiple-origin hypothesis is true (and he sounds confident it is), then other ways of inferring evolution are all wet: “Our molecular phylogeny clearly indicates that myodocopids are monophyletic and are nested within several groups lacking compound eyes. ased on this phylogeny, methods of character reconstruction significantly favor the independent origin of myodocopid compound eyes, constituting the strongest phylogenetic evidence to date for multiple origins of arthropod eyes. If this is not an independent origin, and compound eyes were actually lost many times, then this is a case where commonly used methods of historical inference are positively and significantly misleading.” (Emphasis added).
The gullibility of evolutionists is positively and significantly astounding. Of course eyes are more easily lost than formed. Why is that hypothesis hard to believe, unless it fits in with creationist principles? Instead, in order to rescue evolution at all costs, he is more willing to believe that organs that gave Darwin “cold shudders” evolved multiple times. Read Michael Behe’s description of vision, then realize that Oakley assumes that a naturalistic miracle occurred not just once, but numerous times, resulting in structures that are nearly identical!
This story illustrates two things: (1) the growing tension between molecular phylogenies and morphological phylogenies (genes vs looks), and (2) the dogma of Darwinism. Evolution is a fixed parameter that must not be challenged, questioned, or doubted, no matter the evidence.
The Mathematical Equations of Political Corruption 01/28/2002
A Polish team of physicists and economists has concluded that political corruption, resulting in wealth accumulating in the hands of the super-rich, follows the same power laws that polymer molecules obey. Nature Science Update comments on the theory in Physical Review, “Wealth condensation in Pareto macroeconomies.”
How can this theory have any validity when they left out the primary factors: sin, greed and personal responsibility? This is scientism run amok. Some scientists think you can analyze anything according to mathematical equations, even the fortunes of evil dictators. Let’s see them apply the same methodology on themselves; how about a paper on “The dynamics of implosive logic collapse in naturalistic hypotheses.”