Volume 1, Number 9    November, 2001                     

Design - Everywhere
The news the evolutionists don't want you to read!

Archea Save Earth from Overheating

At least part of the design for the removal of greenhouse gases from the early Earth may have been answered by a recent study. It seems that life itself (and rather remarkable life, at that) may have been responsible for keeping the earth from turning into a scorched planet like Venus. Scientists have discovered a methane metabolizing Archea in the extreme pressures of deep sea sediments. It is estimated that these bacteria-like organisms consume 300 million tons of methane each year, which prevent the Earth from turning into a furnace. According to Kai-Uwe Hinrichs, a biogeochemist at the Woods Hole Oceanographic Institution in Massachusetts and one of the authors of the study, "If they hadn't been established at some point in Earth's history, we probably wouldn't be here."

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"...on early Earth, these microbes might have been even more significant. Atmospheric scientists have suggested that methane levels in the atmosphere may have been 1000 times higher than they are today, created initially by volcanoes and later by methane-producing microbes (Science, 25 June 1999, p. 2111). At first, this methane may have been beneficial, creating a greenhouse effect that kept the planet from freezing. But if the rise in methane had gone unchecked, Earth might have become too hot for life, as Venus is today."

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(Zimmer, C. 2001. 'Inconceivable' Bugs Eat Methane on the Ocean Floor. Science 293: 418-419.)

Non-coding ("junk") DNA is Functional!

A recent study has shown that eukaryotic non-coding DNA (also called "secondary DNA) is functional as a structural element in the nucleus. Previously, there were two evolutionary theories that attempted to describe the reason for the existence of non-coding DNA One theory stated that non-coding DNA was "junk" that consisted of randomly-produced sequences that had lost their coding ability or partially duplicated genes that were non-functional. The second theory stated that non-coding DNA was "selfish", in that it consisted of DNA that preferentially replicated more efficiently that coding DNA, even though it provided no selective advantage (in fact was somewhat detrimental in that it was parasitic).
The new study examined the genomes of the single-celled photosynthetic organisms know as Crytomonads. These organisms exist as vastly different cell sizes, with the nucleus being proportional in size to that of the cell. Researchers discovered that the amount of non-coding DNA was proportional to the size of the nucleus, suggesting that more non-coding DNA was required in larger nuclei. As an added proof, the nucleomorph, a small piece of DNA contained within the plastid that codes for itself and photosynthetic function, was not changed in size, despite changes in cell size and nuclear content.
The new study is a stunning rebuttal to the evolutionary theories that attempt to discredit design and promote concepts such as "junk" DNA and "selfish" DNA. According to the authors:

"Furthermore, the present lack of significant amounts of nucleomorph secondary DNA confirms that selection can readily eliminate functionless nuclear DNA, refuting 'selfish' and 'junk' theories of secondary DNA"

Beaton, M.J. and T. Cavalier-Smith. 1999. Eukaryotic non-coding DNA is functional: evidence from the differential scaling of cryptomonal genomes. Proc. R. Soc. Lond. B. 266:2053-2059.

Related Story - "When 'Junk' DNA Isn't Junk"

Design of Proteins

Scientists have been attempting to be able to determine a protein's native conformation (or folding) by examining the amino acid sequence. Despite years of study, the ability to do this using even the fastest computers is beyond our reach. For example, for a typical 100 amino acid protein (moderate to small in size) could exist in any of 3²⁰⁰ possible backbone configurations. Using a super fast computer (10¹² computations/sec) it would take 10⁸⁰ seconds, which exceed the age of the universe by a factor of 60 orders of magnitude! This fact alone may give you a better perspective on the mind of God.
IBM is now making a new supercomputer to attempt to address the protein folding problem. A $100 million research initiative will build a supercomputer 500 times more powerful than the current record holder and be able to process 10¹⁵ computations/sec. Dubbed "Blue Gene," the computer will include over 1 million processors, each capable of 1 billion operations per second. Using special estimation techniques, the computer may be able to solve the protein folding of a small protein in about a year. However, at the end of that time, researchers may discover that it didn't work. If the estimations are not close enough to actual conformations, the folding may be incorrect. Calculating the exact folding of all positions would require 10⁷⁷ seconds, only 57 orders of magnitude longer than the age of the universe. This is what we in research call a long-term project!

Service, R.F. 1999. Big Blue Aims to Crack Protein Riddle. Science 286: 2250
Berendsen, H.J.C. 1998. Perspectives: Protein Folding. A Glimpse of the Holy Grail? Science 282: 642-643.

Smallest Rotary Engine

Scientists have recently defined the molecular components of ATP synthase, the enzyme that synthesizes adenosine triphosphate (ATP) in virtually all life forms, which is the world's smallest rotary motor. This enzyme provides the cell with its energy storage molecule (ATP) by catalyzing the addition of inorganic phosphate to adenosine diphosphate (ADP). The ATP synthesized by this engine is used to drive nearly all chemical reactions that require energy input. The outer domain consists of a ring of 12 subunits that bind to the outer side of the membrane. The inner domain consists of 3 subunits that bind to the inner side of the membrane. A single subunit alternatively binds and releases to three paired sets of the other two subunits as it rotates around the molecule. The ADP and phosphate bind at one of the two paired subunits and are released as ATP when the single subunit rotates to the next pair. Yes, this rotary motor was formed by random chemical processes. Right!!!

Fillingame, R.H. 1999. PROTEIN STRUCTURE: Molecular Rotary Motors. Science 286: 1687-1688.

DNA/Protein Design in the Chromosomes

Everyone knows that DNA consists of a double helix - a twisting staircase of nucleotide base pairs. However, the actual 3 dimensional structure of the DNA is extremely complex, since the DNA double helix is tightly associated with a large number of histone and other proteins that control the DNA's expression. Scientists have found that when a small chemical entity called an acetyl group is glued to specific places on the histone proteins, the chromatin fiber opens up, allowing the cell's gene-reading apparatus to gain access to the genetic material. New work is now revealing that histone phosphorylation (adding a phosphate group) and methylation (adding a methyl group) opens up the structure of the DNA so that it can be acted upon. The new studies - which have only begun - are revealing the depths of design of the cell's genetic aparatus.

Hagmann, M. 1999. How Chromatin Changes Its Shape. Science 285: 1200-1203.

Proving the Perfection of the Honeycomb

Scientists had assumed that the hexagonal lattice of the honeycomb allows bees to store the most honey in a single layer of equal-sized cells, while using the least beeswax to separate them. Until this summer, however, no one could prove that a honeycomb was the most efficient solution. Now, a mathematician, Thomas Hales of the University of Michigan, confirmed this fact. The result also confirms the intuition of human engineers, who have relied on honeycomb composite materials made of paper, graphite, or aluminum to reduce the weight of components for cars, planes, and spacecraft with little sacrifice in strength.

Isn't it amazing how smart bees are to have figured this out before humans?

Mackenzie, D. 1999. Proving the Perfection of the Honeycomb. Science 285: 1338-1339.

Ribosomes - the molecular machines that manufacture proteins

Scientists recognize the machine-like nature of the ribosome, as indicated in a recent article describing attempts to determine is mechanism of action, "The ribosome is really a machine that moves along the messenger RNA, all the while transferring amino acids from incoming tRNA and forging peptide bonds in the growing protein." After four decades of intensive study, scientists are beginning to understand the incredible design of the ribosome, a molecular machine composed of two subunits of 54 proteins and 3 RNA strands (composed of 4500 nucleotides). It has taken decades to attempt to determine the structure of the ribosome through x-ray crystallography, because of its large size and difficulty to crystallize. A further trick has been to try to catch the ribosome in the act of producing proteins, with the tRNA and mRNA bound to it. The structure is dynamic, so that multiple snapshots of its action will be necessary to piece together the actual function. Much work remains to be done, but the first images are beginning to come in.
Pennisi, E. 1999. The Race to the Ribosome Structure. Science 285: 2048-2051
Liljas, A. 1999. Function Is Structure. Science 285: 2077-2078.

'Clothes dryer' for proteins removes wrinkles

Proteins that become damaged by misfolding can be fixed by a unique set of proteins called chaperonins. These chaperonins capture damaged proteins by means of a ring of hydro-phobic amino acids that line the entrance to the central cavity of its heptameric ring. The binding of ATP (a high energy molecule) results in a massive structural change that doubles the cavity volume and hides its hydrophobic binding surface. The damaged protein is then temporarily engulfed in the central cavity, where it is unfolded. Refolding of the protein results in restoration of its proper structure and function.

Mark Shtilerman, George H. Lorimer,  S. Walter Englander. 1999. Chaperonin Function: Folding by Forced Unfolding. Science 284: 822-825.

Design of the nucleic acid code

Molecular biology has progressed enough so that scientists can begin to ask some "why" questions for the basic design of life's genetic code. Their intent is not to look for intelligent design, but to ask why life evolved to use RNA and DNA instead of some other molecule. Scientists first asked why the base pairs were linked together the way there were. Base pairs are linked between the 3' and 5' carbons of the ring. When this was changed to the 2' and 5' carbons, base pairing strength decrease markedly and the strand itself was susceptible to hydrolytic cleavage. Scientists then constructed an alternative form of DNA, using a six-membered sugar ring instead of the usual five-membered ribose. They discovered that some of the new "DNA's" exhibited purine-purine pairing (pairing must be complimentary for it to work as a genetic system). Other constructed "DNA's" exhibited reduced guanine-cytosine pairing that was strongly dependent on the sequence of base pairs. All these problems made the alternate "DNA" unacceptable as a genetic system. Next, scientists constructed DNA's using alternate five-ring sugars. These alternate "DNA's" had a much more rigid backbone structure and enhanced base-pair bonding. However, these characteristics prevent these molecules from being a viable alternative to standard DNA.

Albert Eschenmoser, A. 1999. Chemical Etiology of Nucleic Acid Structure. Science 284:2118.

RNA Signaling in Plants!

If you are like me, this story is going to blow you away. Viruses that infect animal cells often mimic host cell proteins in order to fool the cell to spread their infection. Researchers looking at a plant virus, which spreads its infection by producing a protein that opens channels in sieve elements, hypothesized that the protein was mimicking the function of some plant protein. By generating antibodies to the viral protein, they were able to isolate a plant protein with a similar structure. This plant protein was bound to RNA, and was acting to ferry this RNA into the phloem sap where it could be transported to other parts of the plants. The researchers hypothesized (but did not prove) that this system may function as a long-distance signaling system carried via RNA molecules. Such a system might explain how leaves transmit signals to buds as a means of conveying the need to flower in response the length of the day. (Strauss, E. 1999. RNA Molecules may carry long-distance signals in plants. Science 283: 12-13)

New Function for Motor Cortex

A recent study at the University of Minnesota has redefined the function and design of the motor cortex of the brain. It was previously thought that the motor cortex "just" controlled movement by signaling muscles to contract. The new study indicates that the motor cortex also performs cognitive tasks related to spatial organization. Specifically, the cells of the motor cortex seem to be involved in an analysis of the sequential presentation of visual events. Researchers examined the responses of hundreds of individual neurons and found that the firing of specific neurons was 100% predictive of the serial order of visual stimuli. So, not only does the motor cortex produce the complex set of neuron firings required to move the muscles, but it is involved in the analysis of visual events that may impact our need to move in response to visual clues. According to Dr. Apostolos Georgopoulos, one of the authors of the study, these results show that "we hardly know anything about the brain." (Wickelgren, I. 1999. Memory for order found in the motor cortex. Science 283: 1617-1618.)

Design and Packing of human DNA

Human cells contain 46 chromosomes consisting of very long strands of DNA (each one about 7 feet long!) All this DNA (more than the length of a football field) is packed into the nucleus of every cell (the width of the nucleus is only 0.0004 inches). Not only does this DNA need to be packed into the cell, but it must be available (it must be unpacked to be available) to the cell's machinery for both RNA transcription (which is required for protein synthesis and occurs continuously) and DNA replication (which occurs only during certain periods of the cell cycle. The new study shows that huge "factories" of DNA appear and disappear as the DNA is unwound for replication and transcription. The process and machinery that controls this winding and unwinding is still unknown, but must involve a complex design of protein and DNA interaction. (Cook, P. Duplicating a Tangled Genome. Science 281: 1466-1467.)

Design and dinosaur bone growth

A recent study by Kristina Curry, a graduate student at the State University of New York, Stony Brook, examined the bones of Apatosaurus (a huge sauropod) by sampling cores from the bones. She found concentric rings (presumably annual) that indicate that these huge dinosaurs grew to full size (up to 30 tons) within a period of only 10 years. This growth rate is faster than the fastest living species (ducks) and indicates an incredibly efficient design for such a large animal (Stokstad, E. 1998. Young Dinos Grew Up Fast. Science 282: 603-604).

Bat Sonar Exceeds Human Designs by Threefold

Researchers using mealworms as bait, have determined the limits of bat sonar. The brown insectivore Epesicus fuscus, is able to process overlapping echoes arriving just 2 millionths of a second apart with a resolution of 0.3 millimeters (1/80^th of an inch). Since the bat's sonar is three times better than any human design, the researchers have been given a grant by the Defense Department to apply the principles of bat sonar to human designed sonar.

Holden, C. 1998. Bats push limits of sonar. Science 282: 619.

Self Splicing Protein

Scientists have discovered a protein that exhibits a unique function that is difficult to explain by evolutionary mechanisms. The protein, termed an intein (a combination of the words intron and protein), is actually part of a polypeptide chain that is produced through the usual methods of DNA transcription (to make RNA) and RNA translation (to assemble the protein). The unique aspect of the intein is that it actually catalyzes the splicing of two proteins (translated from two separate genes) together to form one functional protein. The problem for the evolutionist is that this piece of protein has both binding capabilities and enzymatic activities that 1) form a peptide bond between the two protein chains and 2) cuts itself out of the newly-formed protein. Not only does the protein have at least three separate functions, but it requires the simultaneous mutation of both original proteins, which come from two distinct sequences on the chromosome. Design at its finest!

Vogel, G. 1998. PROTEIN CHEMISTRY: A two piece protein assembles itself. Science 281: 763-674.

Transcription Model Elucidated

Transcription is the means by which the cell transcribes (or makes) RNA from a DNA template. It is a necessary process to produce the RNA required to make proteins and the various parts of cellular machinery required during the process. The transcription process has been explained for the simpler organisms (prokaryotes such as E. coli). The mechanism used in higher organisms (eukaryotes such as us) is admittedly much more complex, but has an underlying similar mechanism (which is not surprising, since all life is based upon DNA, RNA, and proteins).

von Hippel, P.H. 1998. An integrated model of the transcription complex in elongation, termination, and editing. Science 281: 660-665.

Cell Cycle Proteins

A recent study examining the role of cell cycle regulatory proteins has shown that these proteins play a role not only in the cell cycle during cell division, but also play a role in the differentiation of certain cell types. The intricate functioning of these proteins in multiple cell regulatory pathways is yet another indication of irreducible complexity.

Tyler Jacks and Robert A. Weinberg. May 15, 1998. The Expanding Role of Cell Cycle Regulators. Science 280: 1035.
Ferdinando Di Cunto, Gabrielle Topley, Enzo Calautti, Jimmy Hsiao, Lydia Ong, Prem K. Seth, G. Paolo Dotto. May 15, 1998. Inhibitory Function of p21Cip1/WAF1 in Differentiation of Primary Mouse Keratinocytes Independent of Cell Cycle Control. Science 280: 1069.

Topoisomerase type I in the news

The complex structure of eukaryotic (non-microbial) DNA is such that it must be relaxed whenever it is needed for transcription (making of messenger RNA) or replication. Topoisomerase, a multi-subdomain enzyme, is able to accomplish this task on both positively and negatively supercoiled DNA. The 20 = (angstrom) pore provides a highly positively charged region that binds to DNA regardless of genetic sequence. The recent evidence shows that the Topoisomerase type I from eukaryotes shares no sequence or structural similarity with that from prokaryotes. Evolution would predict that eukaryotic topoisomerase type I would share some sequence homology with prokaryotic topoisomerase type I.

Rebinbo, M.R., et al. March 6, 1998. Crystal structure of human topoisomerase I in covalent and non-covalent complexes with DNA. Science 279: 477.)

See Ran Run

A recent study indicates that a small protein called Ran acts as the dispatcher, coordinating the direction of transport and linking the various nuclear transport pathways with vital cellular processes. Because critical processes such as cell division and protein synthesis depend on molecules that have to be carried into or out of the nucleus at exactly the right time, these new findings demonstrate the increased complexity and intelligent design within the cell.

Elizabeth Pennisi. February 20, 1998. Cell Biology: The Nucleus's Revolving Door Science 279: 1129

The Human Brain Drain

Modern humans have brain sizes larger than any other placental mammal relative to body size. The human brain uses a tremendous amount of energy - up to 60% of total energy consumed in newborns. A recent study suggests that the large increase in brain size was balanced by a similar reduction in the size of the gastrointestinal tract. However, other mammals, such as pigs, with small intestines don't have brains as large as ours. In addition, the theory doesn't hold for birds or bats. The presence of large brains in humans presents a problem to evolutionists, since it presents a large energy drain upon the species, especially before the advent of agriculture and reliable food supplies.

Ann Gibbons. May 29, 1998. Solving the brain's energy crisis.. Science 280: 1345

The Kinetochore - Premiere Molecular Motor

A recent discovery of the "kinetochore," which regulates cell division during chromosomal segregation provides more evidence of design in eukaryotic genomes. As Dr. Tim Yen (Fox Chase Cancer Center, Philadelphia) stated, "Not only is the kinetochore a structural part of the chromosome that contains molecular motors, but you have regulatory components [there], all in the same place." Therefore another part of the "junk DNA" is now shown to have a significant function.

(Elizabeth Pennisi. January 23, 1998. Cell Division Gatekeepers Identified Science 279: 477.)

Transcriptional Regulators Stand in the GABP

Many different kinds of proteins are involved in transcriptional regulation (regulation of RNA transcription from DNA). Many of these proteins bind to similar sequences of DNA. The specificity of this binding is critical to the proper functioning within the cell. Proteins GA-binding protein (GABP) is a transcriptional regulator composed of two structurally dissimilar subunits. A recent study shows that this protein's specificity of binding is determined through the interaction of multiple domains on each of the subunits of the protein. This protein and other transcriptional regulatory proteins bind to DNA that was once considered "junk," since it did not code for protein synthesis. In fact, special non-coding regions of the DNA are required for the regulation of nearby gene transcription.

Adrian H. Batchelor, Derek E. Piper, Fabienne Charles de la Brousse, Steven L. McKnight, Cynthia Wolberger. February 13, 1998. The Structure of GABP: An ETS Domain-Ankyrin Repeat Heterodimer Bound to DNA. Science 279: 1037.)