Archive: Over-Design, Common Descent, Cell Complexity, OOL
These articles from the early days of CEH should still hold interest for today’s readers.
Note: some embedded links may no longer work.
Are Animals Over-Designed? 06/19/2002
Animals appear to have built-in safety factors, or capacities beyond their normal load, such as bones being stronger than their usual needs, peak milk output of mammary glands exceeding a pup’s needs, and an enzyme’s maximum reaction rate exceeding its normal reaction rate. Scientists at the University of California School of Medicine did an experiment to test rats’ ability to process glucose at higher than normal rates, and wrote their results in the June 19 Proceedings of the National Academy of Sciences. They found a 220% safety factor; i.e., rats were able to consume and assimilate 2.2 times as much glucose as their body needs.
This paper by noted evolutionist Jared Diamond and colleagues is listed in the category Evolution, but does it not indicate intelligent planning? Why would natural selection give a rat reserve capacity more than it needs to survive? The authors say their result is at the low end of observed biological safety factors, which can be as high as 700%, and say this observation is “one of the major problems in quantitative evolutionary design” (how’s that for an oxymoron: evolutionary design). They give some possible reasons for this apparent overdesign, but all that can be said is that this finding gives no advantage to evolutionary explanations over design explanations; if anything, it is another problem for evolutionists to puzzle over.
All Wrong: The Classical Darwinian Doctrine of Common Descent 06/18/2002
That’s what Carl Woese of the University of Illinois at Urbana-Champaign thinks, speaking about how the first life originated: “We cannot expect to explain cellular evolution if we stay locked in the classical Darwinian mode of thinking“ Woese said. “The time has come for biology to go beyond the Doctrine of Common Descent.” So is Woese a creationist? Not in the slightest; he proposes that three separate chemical processes led to the origin of life. “His argument is built around evidence ‘from the three main cellular information processing systems’ – translation, transcription and replication – and he suggests that cellular evolution progressed in that order, with translation leading the way.” Woese puts greater emphasis on horizontal transfer of information between living things and non-living precursors. And where did the first information come from? “The pivotal development in the evolution of modern protein-based cells, Woese said, was the invention of symbolic representation on the molecular level – that is, the capacity to ‘translate’ nucleic acid sequence into amino acid sequence.” Scientific American has a summary of the paper that is published in the June 19 Proceedings of the National Academy of Sciences.
Evolutionists are such cheaters. They sneak in information in the unobservable past, when nowhere in the world is information do we see information arising from nonintelligent causes. Woese, like all the others, personifies molecules inventing symbolic representation and translation capabilities, essentially pulling information out of the magic hat. The value of this article is that one evolutionist is telling the others “Everything you know is wrong.” It’s kind of fun to watch them do that to each other.
Woese is just hand-waving out of thin air. He pictures molecules inventing all kinds of capabilities as if they were shipwreck victims landing on an island and figuring out how to work together and build a village and a government. We need to call foul when evolutionists play these games. In reality, this paper is very damaging to the chemical evolutionists. Before he dives into this “murky world of cellular evolution,” as he terms it, he begins: “The evolution of modern cells is arguably the most important problem the field of Biology has ever faced. In Darwin’s day the problem could hardly be imagined. For much of the 20th century it was intractable. In any case, the problem lay buried in the catch-all rubric ‘origin of life’ where, because it is a biological not a (bio)chemical problem, it was effectively ignored.” The problem is not solved by imposing pantheistic wish-fulfillment upon inanimate objects, in contradiction to their own naturalistic premise. Exchanging ignorance for fantasy is not progress; ignorance is the lesser of two evils.
Cell Journal Marvels at Complexity, but Assumes Darwinism 06/17/2002
Book reviews in scientific journals allow scientists to back off from the detail and jargon of a specific paper and comment on the big picture. The June 14 issue of Cell is loaded with book reviews that are a study in contrasts. Details of cellular complexity and design are juxtaposed with simplistic evolutionary explanations. Some examples (emphasis added):
- Standard Textbook: Patrick Williamson reviews the standard text Molecular Biology of the Cell (4th ed., 2002) and refers to the “dramatic complexity of the cytoplasm” that began to be revealed with electron microscopes in the 1950’s. But in the end, he attributes it all “to natural selection in cobbling together solutions to pressing problems using the miscellaneous materials presented by gene duplication and mutation” …
In the past, we have sometimes spoken in deprecating tones of our scientific predecessors “stamp-collecting their way through the characterization of the phylogeny and life histories of the earth’s species. Now, the genome projects have presented us with new sets of stamps to collect, characterize, describe, and explain. Like our predecessors, we can’t usually reduce our insights into a few general principles because of the way organisms have evolved, but we can always anticipate growing satisfaction with the detail and clarity of our understanding of all the many instances we find.
- Mind Boggling Complexity: Max Gottesman, in a review of Genes & Signals by Ptashne and Gann (2001), slaps his head over the complexity of enzyme actions:
Recall the days of yesteryear when, for biologists, enzymes were enzymes and didn’t need any help in finding their substrates. Alas, those simple times are long gone. Instead we are faced with the horrible realization that proteins rarely see their ligands without being led by the nose to them. So, for example, RNA polymerase once promptly landed on a promoter and revved up to transcribe a gene. It turns out, in fact, that for most promoters, RNA polymerase requires additional proteins just to find the site. And other proteins interfere with its attachment. The number of such auxiliary factors, especially in eukaryotes, is mind boggling … The situation is scarcely better in signal transduction. A hormone can only relay its message to the nucleus via passage through a long series of proteins, most of which have to be spatially constrained to transmit the signal. Even the simple matter of removing a piece of unwanted RNA from a transcript involves the assembly of a dozen or so proteins and RNAs, probably in a configuration that is highly specific. The reason for all this is now quite clear. Transcription cannot be ubiquitous, but is regulated by factors that respond to cellular environment, cell type, phases of the growth cycle, etc. Similarly, transduced signals are not sprayed around the cell, but are channeled toward specific effectors, as determined by the special requirements of the cell at a particular point in time.
- Extreme Life: Thomas Cavalier-Smith takes a hard look at D.A. Wharton’s Life at the Limits: Organisms in Extreme Environments (2002). He likes the treatment of extremophiles and cryptobiotic organisms (those that can go into states of suspended animation), but criticizes his sparse treatment of the origin of life. He believes, contrary to the author, that eubacteria–flagella and all–are our ancestors, not archaebacteria:
The origin of biomolecules is much easier to understand if it occurred in a heterogeneous environment with geothermal activity to condense polymers and numerous small cool pools subject to freezing and drying to stabilize and concentrate them. The breakthrough to the first organisms in which membranes, genes, and catalysts cooperated is also much easier to understand in a cool heterogeneous environment such as polar tide pools (Cavalier-Smith, J. Mol. Evol. 53, 555-595, 2001). It seems much more likely that early proto-organisms were cryptobiotes, able to survive temporary freezing or drying, than thermophiles having to evolve the genetic code and membranes beside oceanic vents in the enormous volumes of the deep ocean, as seems currently popular in some circles.
- Nuclear Pores: Amnon Harel and Douglass Forbes review Nuclear Transport (Karen Weiss, ed., 2001) and note some wonders of the nuclear pore complex:
During the splicing process, mature mRNA, a very large cargo, appears to form a complex with a variety of distinct non-importin beta-type proteins that together mark the mRNA for export and participate in its egress from the nucleus. …
Indeed, it has been very difficult to confirm a specific translocation mechanism for the nuclear pore, which contains multiples of 30-50 different proteins in the final 500-1000 protein nuclear pore complex. - RNA Complexity: Martha J. Fedor reviews RNA (ed. Soll, Nishimura and Moore, 2001) and notes the bewildering complexity of RNA functions in this growing “complicated field”:
The discovery that RNAs could catalyze biological reactions gave a clear indication that RNAs would not conform to the Central Dogma, which dictates that they exist solely to relay information between DNA genes and protein gene products. Over the ensuing decades, RNAs have turned up unexpectedly as key players in myriad cellular activities, both fundamental and exotic. …
A new class of tiny noncoding RNAs (microRNAs) recently was implicated in developmental and spatial regulation of gene expression (Ambros, Cell 107, 823-826, 2001). Really, it would be surprising if nature has stopped here in making use of this versatile macromolecule.
- Molecular Machines: Ishii and Yanagida review Biology at the Single Molecule Level (ed. Leuba and Zlatanova, 2001) and show that the discovery of molecular machines is forcing a paradigm shift:
The history of science has shown that new concepts frequently emerge and interpretations of the data become modified as more sophisticated and accurate measuring systems are developed. New data allow us to emphasize different aspects of biological systems and to reveal aspects of those systems that had not previously been unveiled. …
As nanotechnologies have expanded, many researchers have realized that the laws that govern materials of nanometer size are very different to those applied to macroscopic machineries with which we are more familiar. Nature, however, has already developed and utilized nanotech. Life is full of nanomachines, and their functions are very different from artificial nanomachines. … Researchers now know that protein molecules are more complex than the simple design the DNA information implies. Studying the mechanism underlying protein functions is intriguing, and prerequisite are the techniques that allow us to monitor the dynamic structure of protein molecules and directly detect the functions of proteins.
- Homology and Evo-Devo Richard R. Behringer in “Hand of man, wing of bat, fin of porpoise” reviews The Evolution of Developmental Pathways by Sunderland (2002). He thinks Evo-Devo is the wave of the future:
Biologists have always been fascinated by the astonishing diversity of metazoan life that has evolved on Earth. It is now evident that extant species have evolved from common ancestors through genetic changes that are acted upon by natural selection. In The Origin of Species (1859), Charles Darwin discussed the “law of embryonic resemblance.” He and others before him had noted that plants and animals within the same great classes, though morphologically diverse in their adult forms, were remarkably similar in their embryonic forms. For example, the limbs of vertebrates, including “the hand of a man, wing of a bat, and fin of a porpoise,” are morphologically and functionally distinct, yet they all develop from morphologically identical limb buds in their embryos. Darwin suggested that the embryos of different species provided a glimpse of a common parent for the different classes of organisms, supporting his concept of descent with modification. Thus was born the field of evolutionary developmental biology.
He goes on to discuss the various controversies, questions, problems and conundrums in the field of evo-devo, but concludes it has a bright future thanks to television:
Finally, the current movement in the Evo/Devo field suggests a bright future. That future may be driven by those children who watched natural history programs on television and have been inspired to pursue studies and careers in biology. I predict that these young biologists will not be satisfied studying a handful of primary model organisms. I suspect that these enlightened individuals will have broader interests and will be naturally attracted to the Evo/Devo field to reveal the “hidden bond” described by Darwin that exists between common ancestors and current species.
- From Cytoplasm to Cytoskeletons Don Ingber in “Putting the Cell Biology Establishment on the Stand” reviews Cells, Gels and the Engines of Life by Pollack (2001). He slays the dragon of misconceptions that the cell is simply a bag of fluid:
While our knowledge of the molecular widgets that comprise living cells has exploded beyond our wildest dream, our understanding of cell architecture and the relation between structure and function still remain rudimentary. For example, one mainstream cell biology textbook defines the cell as “a small membrane-bounded compartment filled with a concentrated aqueous solution of chemicals,” like a balloon filled with molasses. In fact, many biologists who work with molecules in isolation still share this view, as do virtually all lay people, including the congressmen and women who decide which science projects the government will invest in. Pollack views this image as a dragon that must be slain and I cannot agree more. The living cell is a chemo-mechanical machine and it uses all forces and devices at its disposal-physical as well as chemical and electrical-to carry out its miraculous tasks. The reality is that the cytoplasm is a molecular lattice, known as the cytoskeleton, that is permeated and insufflated by an aqueous solution. The different molecular filaments that comprise the cytoskeleton-microfilaments, microtubules, and intermediate filaments-position the cytoplasmic organelles. But this is not a passive support system. The same scaffolds orient many of the enzymes and substrates that mediate critical cell functions, including signal transduction, glycolysis, protein synthesis, transport, and secretion; analogous insoluble scaffolds mediate RNA processing and DNA replication within the nucleus. This use of “solid-state” biochemistry greatly increases the efficiency of chemical reactions because they are no longer diffusion limited, and it provides a means to compartmentalize different cellular activities. The cytoskeletal system also can dynamically grow and shrink within different microcompartments as a result of the action of specific molecular regulators. … Indeed, it is through these varied functions of the cytoskeleton that living cells can exhibit behaviors that are far beyond anything observed in man-made materials. The abilities of a cell to move its entire mass upstream against the flow of blood or contract against hundred pound weights are two simple examples.
He critically examines Pollack’s attempt to pull a simpler, unifying framework out of the new complex picture of cell processes.
Two things should be clear from these examples: observational science reveals bewildering complexity and design in the cell; Darwinian stories, however, are just glittering generalities and personification fallacies. It is a violation of their own naturalistic principles to portray Nature as a miracle-working goddess. Give honor to whom honor is due.
For refutations of Behringer’s misguided claims about homology and embryonic similarities, see Jonathan Wells’ rebuttals of these icons of evolution. Behringer seems to hope children watching oversimplified PBS Evolution programs will be sufficiently Darwinized early, before reading the truth about molecular machines in the journal Cell as college biology majors. We think they would be better inspired and better educated by watching Unlocking the Mystery of Life.
First Life Had To Play It Cool 06/14/2002
Dr. Jeffrey Bada of the Scripps Institute of Oceanography, a prominent astrobiologist, with a Mexican colleague, claims “Some Like It Hot, But Not the First Biomolecules.” His article is in the June 13 issue of Science. While arguing against hydrothermal vents as likely places for life to self-organize, he scans the gamut of current thinking on the origin of life, and highlights the many problems that remain unsolved since Oparin first ventured a theory in the 1930s. Some of the problems Bada mentions are:
- The formation of polymers from monomers is a “thermodynamically unfavorable process.”
- Organic soup molecules needed to be concentrated and localized.
- DNA can only last 100,000 years.
- RNA is much more fragile than DNA, yet RNA-world scenarios are among today’s top contenders.
- Proponents of non-RNA/DNA autocatalytic prebiotic reactions usually prefer hydrothermal vents, but “Various metabolic reaction schemes have been proposed and investigated, but none have been demonstrated to be autocatalytic. Nor are there any empirical indications that this is even possible in a prebiotic context.”
- High-temperature scenarios for peptides are unlikely: ”… peptide bonds are also rapidly hydrolyzed at elevated temperatures. The steady-state concentration of peptides under hydrothermal conditions is therefore problematic.”
- But was it too cold? “Because of the reduced luminosity of the young Sun, Earth may indeed have been completely covered with ice during its early history.” Yet the needed reactions proceed much more slowly in the cold.
- No future without accurate replication: “But regardless of its initial complexity, autocatalytic chemical-based metabolic life could not have evolved in the absence of a genetic replication mechanism ensuring the maintenance, stability, and diversification of its components. In the absence of hereditary mechanisms, autotrophic reaction chains would have come and gone without leaving any direct descendants able to resurrect the process.”
- Information is required somehow: “Life as we know it consists of both chemistry and information. If metabolic life existed on the early Earth, converting it to life as we know it would have required the emergence of some type of genetic information system.”
- How did prebiotic life survive the battlefield: “If the transition from abiotic chemistry to the first biochemistry on the early Earth indeed took place at low temperatures, it could have occurred during cold, quiescent periods between large, sterilizing impact events. But regardless of how the first life arose, it may not have survived subsequent impacts.”
In conclusion, Bada rules out hot or warm environments such as hydrothermal vents. That leaves only cold or cool environments where reactions would have been much slower, especially if the earth were icy. But life needed to get a foothold, and somehow evolve an information system, between meteorite bombardments. Maybe it happened, though, and more than once: “Life may have originated several times before surface conditions became tranquil enough for periods sufficiently long to permit the survival and evolution of the first living entities…”
These admissions are telling, coming from a believer in chemical evolution. He does more to undermine the plausibility of chemical evolution than support it. Not a shred of evidence does he present; just hope against all hope in a minefield of devastating problems. Each one of these problems single-handedly falsifies chemical evolution, and he didn’t even mention one of the worst: the mystery of left-handed proteins. His faith is stitched together with the words may and could have, found 15 places in the brief article, but at least he is honest about the problems. It’s almost laughable at the end, though, when after walking past all these insurmountable hurdles, and not offering empirically plausible options, he speculates that the miracle of life originating by itself might have happened not just once, but multiple times! For the coup de grace, read the next headline, below.
Cell’s DNA Translation Machinery Revealed in Unprecedented Detail 06/13/2002
Japanese scientists publishing in the June 13 issue of Nature have revealed the molecular structure of the RNA polymerase holoenzyme, including its initiation factor, at 2.3 angstrom resolution (an angstrom is one ten billionth of a meter). This enzyme is one of the most important molecular machines in the cell; “The DNA-dependent RNA polymerase (RNAP) is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living organisms.” It builds all the RNA molecules: messenger RNA, transfer RNA, ribosomal RNA, and others. Moreover, the machine consists of five subunits that “are evolutionarily conserved in sequence, structure and function from bacteria to humans.”
The color models show a complex structure shaped somewhat like a lobster claw. It doesn’t work until the initiator named sigma (with four subunits itself), like a key, turns it on and attaches it to a promoter on the DNA molecule. Then it ‘melts’ the DNA at that point and unwinds the section of DNA to be transcribed, and releases the promoter. At that point, the machine undergoes a significant change in shape, and crawls along the strand, attaching RNA subunits into a chain. Apparently, two precisely-placed magnesium ions at the active site are essential for this catalytic activity. During the operation, the DNA appears to run through the cleft of the claw, the ‘active site’ somewhat like a zipper, with a series of alternating switch and trigger functions snapping together the ingredients and preparing the machine to move to the next step. To get a feel for how the machine works as it moves along, here is their description, jargon and all:
Taken together, these structural data allow us to propose a possible mechanism for RNAP translocation during RNA synthesis. At the step of ‘relaxation’ (after translocation, before the next reaction), the template base at position i+1 is paired with the substrate nucleoside triphosphate (NTP), the bridge helix is in an all -helical conformation, the Arg 1,096 bridges the i and i+2 DNA phosphates, and the flexible trigger loop is distal (rather than proximal) to the bridge -helix. After phosphodiester bond formation, a signal induces the movement of the trigger loop towards the bridge -helix, pushing out the ‘switch’ residues. In their flipped-out conformation, the switch residues may engage the DNA phosphate at position i+1 and bring the bridge -helix under the DNA backbone towards the i+2 nucleotide. During this step, Arg 1,096 may also switch its interacting partner from DNA phosphates to the side chain of an acidic (polar) switch residue, thus simultaneously stabilizing the flipped-out conformation of the switch residues and facilitating the translocation of the enzyme.
The above is a description of one step along the chain, which in real life operates faster than a human hand can zip up a dress.
Update The August 7 issue of the journal Structure has additional details about RNA polymerase, with detailed shaded models of how the DNA and RNA parts work their way through the clefts and clamps of this machine into the active site where the actual transcription occurs.
We are at an exciting time in scientific discovery when the actual molecular machinery of the cell is coming into focus with unprecedented detail. In some ways, this time is even more exciting than 1676, when Leeuwenhoek was astonished to find millions of microscopic animals living in a drop of water. Now we can zoom in 1000%, and what do we see? a factory of actual machines made out of molecules, performing operations with a speed and efficiency unmatched by human engineering. Remember that RNA polymerase does not act alone, but in concert with many other machines, such as gatekeepers, which expose the DNA strand from its carefully-guarded locked-up state, to proofreaders, which follow up the operation with quality control, and linemen, that provide disaster recovery – all under the control of regulatory factors. If Leeuwenhoek liked the sneak preview, he should have seen the main show!
The authors note that this machinery is highly conserved (i.e., identical, unevolved) between bacteria and humans (and by inference, sharks, dinosaurs, giant Sequoias, grass, butterflies and earthworms). It seems an insult to call anything a “lower form of life” any more. Yet evolutionists believe humans and all these creatures evolved from bacteria, which evolved from simple molecules. As we have seen so often, the authors of this paper merely assume evolution. Nowhere in this paper do they explain how such a complex system came about. The closest they come is to observe differences between a thermophile and a bacterium, and then to dismissively state, “This observation raises the possibility that these structural segments have evolved from a common ancestor. Their structural similarity and the presence of HtH motifs suggest that the nonconserved ND1 region of [sigma, the initiator] might have served as an alternative DNA-binding site at some stage of evolution” (emphasis added) That’s it. No credible sequence of lucky accidents, each of which would have had to merit survival value or be eliminated, to explain how just a portion of the initiator element of this system could have evolved; just an assumption that it did evolve somehow, somewhere, somewhen. Faith is too gentle a word for such credulity.
RNA polymerase is busily at work right now in your eyeball, liver, heart, brain, leg muscle, little finger, and every one of the trillions of cells in your body. The remarkable action of this molecular machine is beautifully illustrated in the new film Unlocking the Mystery of Life, which we highly recommend. Seeing RNA polymerase in action, in the context of a multitude of other complex machines coordinating their actions in a symphony of manufacture, will make you stand up and shout “Glory!”.