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Sunday, January 21, 2007

The PAH World

Discotic polynuclear aromatic compounds as a mesophase scaffolding at the origin of life

S. N. Platts

s.platts{*at*}gl.ciw.edu
"... le hasard ne favorise que les esprits préparés " (chance only favors prepared minds) Louis Pasteur (1822-1895)

The 'PAH World' is a novel chemical structural model for the plausible formation of oligomeric proto-informational templating materials on the early Earth; presumably progenitors of the widely expected RNA World in chemical evolution theory. The model is based on the self-assembling discotic mesogenic behaviors of polynuclear aromatic compounds, their photochemical edge-derivatizations, and the selectivity of such stacked supramolecular 'aromatic core' scaffolds for the edge-on binding and ~ 0.34 nm plane-parallel spacing of essentially random collections of small prebiotic heterocycles, taken up and concentrated directly from the presumed and surrounding 'dilute primordial soup.' The constrained inter-base separation distance would select for oligomerizing 'linkers' of fairly specific size, such as small methanal oligomers, which would also be taken up from the prebiotic chemical environment, condensing with the small heterocycles and also with each other to form the flexible structural backbone of a first generation of proto-informational oligomeric material, stabilized against both hydrolytic and photolytic degradations by its association with the parent discotic mesophase. A transient local pH decrease (e.g.,volcanic SO2(aq.)) would disrupt the hydrogen bond interactions anchoring the oligomer to the discotic scaffold, thereby releasing segments or portions of oligomeric material to explore intramolecular degrees of motional freedom out in solution, perhaps folding back on themselves to match up fortuitous base residue pairings via familiar Watson-Crick-like complementarities. Segments rich in such chance complementarities would likely persist by virtue of the combined cooperative strength deriving from (i.) the multiple intramolecular hydrogen bond interactions between paired bases, and (ii.) the attractive pi-pi stacking van der Waals interactions occurring between neighboring and stacked basepairs. This combination of interactions establishing the domains of essentially hydrophobic quasi-discotic mesophases in the secondary and tertiary structures of these oligomeric proto-informational materials; base mismatchings within such domains naturally leading to point replacements selecting to minimize conformational potential energies. The new 'PAH World' model is pleasing to chemical intuition, and provides the first satisfying structural answer to the problem of a likely origin for the phenomenon of life.
The figures below provide the details for this model.

Figure 1
Diagram illustrating a stacked and self-assembled mesophase-type arrangement of discotic polynuclear aromatic molecules, in which the aromatic cores of these molecules have become associated and the system has self-organized by virtue of the weak inter-molecular van der Waals forces of attraction operating between the ! molecular orbitals of nearest-neighbor PAHs; these weak nett attractive forces often simply being termed !-! stacking interactions . The stacked PAHs are disposed plane-parallel and are necessarily separated by ca. 0.34 nm (cf. the 0.34 nm interplanar spacing seen in the ideal crystal structure for mineral graphite, and the 0.34 nm inter-basepair helical rise in the classic 1953 Watson-Crick structural model for the B crystallographic form of DNA); this inter-PAH distance essentially reflecting the characteristic size of the 2pz atomic orbitals of the Period 2 atoms (i.e., mostly carbon, and occasionally nitrogen) comprising the aromatic core skeleta of these exogenous polynuclear aromatic compounds. Illustrated at right are three stacked molecules of an exemplar discotic polynuclear aromatic compound: hexa-peri-benzocoronene (C42H18 , hexabenzo[bc,ef,hi,kl,no,qr]coronene, HBC ). This particular PAH core has been of some considerable interest in the recent optoelectronics materials literature, where the field of discotics is advancing rapidly at the present time.

Figure 2 Various exemplar edge structures for partially derivatized PAH-type and/or graphene-type polynuclear aromatic molecules. The edges are shown vertically down the righthand side of each of the six PAH/graphene fragments illustrated, and hydroxy functionalities have been added into the edge structures at random, simply to be illustrative of photochemical and/or geohydrothermal derivatizations at the edges of polynuclear aromatic species. Other types of organic functionalization/derivatization (e.g., -COOH, =O) are certainly possible, especially given the known productive richness of organic photochemistry. The PAH/graphene edges shown are partially hydroxylated and are thus also partially oxidized relative to the parent aromatic hydrocarbons. There are clearly many more possible polynuclear edge structures than those being shown here, and the variety of conceivable edge structures is further increased by the various chemical functionalities that are possible. All common edge functions (e.g., hydroxyl, keto, carboxylic acid, etc.) can engage in hydrogen bonding, and the planar dispositions of such functions around the edges of individual PAHs arranged in stacked discotic arrays offers immediate potential for the edge-on binding and ca. 0.34 nm plane-parallel spacing of small sp2- hybridized heterocyclic molecules, moving firmly towards the first physicochemically plausible mechanism for the selection and concentration of prebiotic nucleobases and other similar small molecules out of the long presumed dilute prebiotic soup . The new PAH World structural model directly addresses the long recognized dilution and selection problems inherent in all dilute prebiotic soup models of the past, these problems having hitherto constituted two of the major chemical stumbling-blocks in the origins-of-life field during the now fifty-two years since Stanley L. Miller s breakthrough discoveries in prebiotic chemistry.

Figure 3 This figure is purely diagrammatic and is simply meant to help convey the essential features of the new PAH World model system. Three prebiotic nucleobases are shown hydrogen bonded to hydroxy functions in the edge structures of some derivatized and neighboring PAHtype molecules, which are themselves disposed in a stacked and discotic array. The exemplar polynuclear aromatic compound being envisaged here is 1,3-dihydroxy hexa-peri-benzocoronene (C42H18O2 , 1,3-dihydroxy hexabenzo[bc,ef,hi,kl,no,qr]coronene, HBC-1,3-diol ). The hydroxy functionalities, and their 1,3 dispositions, are merely meant to be illustrative of the general chemical principle of photochemical and/or hydrothermal derivatization at the edges of PAH-type and graphene-type molecules. The three nucleobases are being shown in their keto tautomeric forms, so as to be consistent with the seemingly reasonable assumption that prebiotic Hadean (i.e., > ca. 3.85 Ga) surface and rain waters were probably acidulous. The keto tautomers bear the pro-glycosidic purine and pyrimidine secondary amine nitrogens (i.e., the NH functions at N(9) and N(1), respectively) disposed outwards, and thus chemically accessible to the surrounding solution. Two unspecified prebiotic oligomers of formaldehyde, (HCHO)n , are shown between neighboring heterocyclics, and it seems likely that the fairly constrained interbase spacing would lead to the system selecting for oligomerizing linkers which are themselves of similar size. The derivatized PAH/graphene edge structures can now effectively be seen to represent something of an electronic phase boundary between the discotically arrayed aromatic cores of the PAHs and the presumed surrounding aqueous media of Darwin s warm little pond . The phenomenon of life might now be seen as deriving from what is effectively a phase separation between the discotic aromatic cores of the PAHs versus the surrounding aqueousbased phase. It seems probable that the essentially regular (2pz) inter-basepair plane-parallel spacing distance of ca. 0.34 nm was inherited by molecular biology as a chemical memory of this unique mode of origin, and that this structural molecular fossil has been conserved to us in the essentially quasi-discotic mesophase regions of heterocyclic nucleobase pairings in the secondary and higher order structures of extant nucleic acids.

Figure 4 The pyrimidyl and imidazole NH functions of the three nucleobases are now shown condensed via N-glycosidic-type covalent linkages to the presumed (HCHO)n oligomers, and the formaldehyde oligomers are themselves now shown having condensed together to produce an extended oligomeric backbone for the primitive proto-informational molecular material; albeit that this earliest backbone material is probably likely to have been branched in structure, rather than straightforwardly linear as depicted in the figure. At this stage, the nucleobase residues remain hydrogen bonded to the stacked and scaffolding array of functionalized PAH-type molecules, and the co-operative effects of these multiple hydrogen bonds together with the multiple !-! stacking interactions serves to stabilize and maintain the proto-informational oligomeric material against both hydrolytic and photolytic degradations during further growth. The N-glycosidic-type covalent bonds are not drawn to scale in the figure, and the methanalderived oligomeric backbone is simply indicated here by a zigzag line.

Figure 5 Diagram showing the expected effect of a sudden decrease in ambient pH causing disruption of the inter-molecular hydrogen bonding interactions hitherto existing between sections of proto-informational oligomeric material and the stack of discotic and derivatized PAHs. A sudden decrease in local pH, such as would be caused by a volcanic release of acidic gases (e.g., SO2(g) and CO2(g)), would lead to significant degrees of protonation of the hydroxy, keto, and amino functions both in the PAH/graphene edge structures and in the heterocyclic bases, thus setting up strong Coulombic forces of inter-molecular repulsion between the positive electric charges which would be almost instantaneously resident on the oxygen and nitrogen functionalities in the PAH/graphene edges and also in the proto-informational oligomer s heterocyclic base residues. Sections of primitive proto-informational oligomeric template material would thus be released to explore conformational degrees of freedom out in solution. The sections of oligomer might be either totally freed of the PAH/graphene stack altogether, or might perhaps remain tethered to the discotic stack at one or both ends via some sort of structural branching/cross-linking. Once the pH catastrophe had passed, the levels of protonation of the heterocyclic base functions would decrease as the ambient pH returned to normal, and the sections of newly released oligomer would then be free to fold back on themselves to bring electrically neutral heterocyclic base residues into hydrogen bonding proximities, perhaps to match up adventitious Watson-Crick-like complementarities.

Figure 6 Two representations of a single section of newly released proto-informational oligomeric material which, having become dissociated from a stacked and scaffolding array of derivatized polynuclear aromatic species, has been free to explore conformational degrees of freedom out in solution. The ca. 0.34 nm inter-heterocyclic base-residue plane-parallel separation constraint, structurally inherited from the discotic derivatized PAH/graphene scaffold, would be expected to readily favor the intra-molecular matching up (i.e., hydrogen bonded basepairing) of complementary small heterocyclic base residues, as segments of protoinformational material came upon one another in the essentially blind process of exploring their individual available conformational parameter spaces. In the idealized and simplified example being shown here, involving a single molecule of an oligomer having an entirely linear (i.e, unbranched backbone) primary structure, a single strand of nascent proto-informational oligomer is shown having folded back upon itself, when it at once becomes intuitively conceivable that fortuitous Watson-Crick-like basepaired complementarities would be matched up. Further, that in the case of a single oligomeric molecule folding back on itself to form a stem-loop type secondary structural motif like that shown here, the backbone chains of the presumed intramolecular proto-duplex-like structure would thus be set to run anti-parallel, this being immediately reminiscent of a crucial and recurring secondary structural feature of extant nucleic acids, originating with the famous anti-parallel chain backbones described by Watson & Crick in their classic 1953 double helical structural solution for the B-form of DNA, and being very evident in the higher-order structures of ribosomal RNA and transfer RNA molecules. Having formed fortuitous Watson-Crick-like basepairs, it is entirely physicochemically conceivable that the co-operative reinforcing strengths of the multiple intra-molecular inter-heterocyclic hydrogen bonds and inter-basepair !-! stacking interactions would lead to the persistence of complementarity-rich segments of proto-informational material. Such complementarity-rich regions might themselves now usefully be considered as constituting quasi-discotics and to be exhibiting a mesophase-like behavior, with the nascent mesophase being stabilized against dissociation by virtue of the presence of the localizing and reinforcing oligomeric backbone. Given the seeming prebiotic implausibility of an oligomerized sugar-phosphate backbone at such an early stage in chemical evolution, it would seem that practically any prebiotically plausible and flexible backbone material could have initially sufficed towards fulfilling the primary requirement of stabilizing these complementarity-rich regions of proto-informational quasidiscotic mesophase material against dissociation and/or hydrolytic/photolytic environmental degradation. The maintenance of the characteristic ca. 0.34 nm inter-basepair spacing distance through geologic and evolutionary time to the present day, together with the structural and mechanistic chemistries of known ribozymic activity supporting an RNA World scenario, would suggest that the sugar-phosphate backbones of extant nucleic acids were selected for early in the history of life on Earth, both towards stabilizing and securing these quasi-discotic mesophase regions, and for the presumed chemical evolutionary advantages accruing at the essentially blindly-stumbled-upon origin of ribozyme-like chemical activities, extant examples of which crucially involve both the ribose-residue and the phosphate-residue moieties of the oligomeric backbone material itself in their ribozymic activities. In further regard to the etiology (borrowing Albert Eschenmoser s use of this term) of the oligomeric backbone, it would seem reasonable that the configurational locking-in of stereochemical chiral informational specificities at asymmetric carbon centers in the earliest backbone materials could certainly have moved these early systems towards minimizing the conformational potential energies of these first segments of proto-informational oligomeric material; this chiral lock in configurational parameter space presumably representing the long-expected and contingent frozen accident of causation of biological homochirality, and thus an early chance chemical evolutionary step in the downstream direction of something more nearly resembling a recognizable progenitor of the widely expected RNA World milestone in origins-of-life science. The conformational-potentialenergy- lowering selection for the conservation of complementarity-rich regions of protoinformational oligomeric materials may well be the single most important physicochemical and etiological factor towards a narrowing down of the informational possibilities in terms of the subset of small prebiotic nitrogenous heterocycles from which was eventually to be derived the biological genetic code of nucleobase residues for all life on Earth.

Figure 7 Two-dimensional representation of some possible secondary structures for portions of nascent proto-informational oligomeric material newly released from attachment to discotic polynuclear aromatic functionalized PAH/graphene scaffolding, perhaps owing to a transient decrease in the local pH resulting from a sudden volcanic release of an acidic oxide (e.g., SO2(aq.)). The zigzag lines represent oligomeric backbone material (e.g., (HCHO)n ); the short straight lines represent individual prebiotic heterocyclic residues oriented with their z-axes in the plane of the paper (i.e., individual base residues are oriented edge-on to the viewer); and the longer straight lines represent hydrogen bonded pairs of complementary base residues. Note that the edge-on perspective has been maintained throughout for simplicity and ease of illustration. Whereas the previous figure (Fig. 6) showed the idealized case of a single molecule of a linear proto-informational oligomer, here are shown probably more likely examples of branched backbone primary oligomeric structures, showing regions of both intra- and inter-molecular interbase hydrogen bonding and !-! base stacking associations, in which fortuitous Watson-Crick-like basepairs have matched-up owing to chance complementarities of sequence. The essential planarity of the various base pairings, combined with degrees of rotational freedom in the backbone material itself, has led to the basepairs being able to behave as quasi-discotic mesogens, with the consequent formation of mesophase-like regions in which stabilizing !-! stacking van der Waals interactions are able to operate at the ca. 3.4 Ångström plane-parallel separation distances between neighboring and stacked basepairs. At the present stage of the model s development, formaldehyde (i.e., methanal, HCHO) oligomers appear to offer the simplest prebiotically acceptable solution to the problem of the likely original backbone materials, and the small variabilities in the inter-residue spacings shown in the figure reflects variability in the admissible sizes of the small linker molecules originally selected from the prebiotic chemical environment during the formation of the proto-informational oligomeric materials at the discotic scaffolds (i.e., reflecting degrees of inter-discotic lateral and rotational freedom in the supramolecular scaffolding structures). Branching and cross-linking in the backbones seems likely in terms of the primary structures of the oligomeric products being envisaged here, versus the linear primary structures of ribozymic oligonucleotides called for in the context of the widely regarded RNA World hypothesis. Further development of the new PAH World model in the downstream direction of something more strongly resembling the widely expected RNA World seems to await a full etiological explanation of the structural, chemical, and stereochemical reasons behind the chemical evolutionary selection for the sugar-phosphate oligomeric backbones observed in extant nucleic acids. The formation of quasi-discotic mesophase regions in such secondary structures as are being shown in the figure would be essentially independent of the precise chemical identities of the basepaired small heterocycles, and this feature of the model immediately suggests collections of essentially random sequence starting points at the origin of an incipient and blind informational potential and capacity.
Webpage Design: Chris McCarthy exoplanet{+}gmail{o}com




The RNA World

by Sidney Altman
1989 Nobel Laureate in Chemistry
April 2, 2001

 

The phrase "The RNA World" was coined by Walter Gilbert in 1986 in a commentary on the then recent observations of the catalytic properties of various RNAs. The RNA World referred to an hypothetical stage in the origin of life on Earth. During this stage, proteins were not yet engaged in biochemical reactions and RNA carried out both the information storage task of genetic information and the full range of catalytic roles necessary in a very primitive self-replicating system. Gilbert pointed out that neither DNA nor protein were required in such a primitive system if RNA could perform as a catalyst. At that time, it had only been demonstrated that RNA could cleave or ligate phosphodiester bonds. Nevertheless, as is a frequent occurrence in science, a general hypothesis was constructed from a few specific instances of a phenomenon. This hypothesis proved to be very effective in stimulating thought about the origin of life on Earth. Ensuing discoveries of other natural catalytic RNAs that could cleave and ligate phosphodiester bonds, and the very recent observation that the region surrounding the peptidyl transferase center of a bacterial 50S ribosomal subunit contains RNA and no protein, further buttress the hypothesis. Finally, the so-called "evolution in vitro" methodology, which is able to scan an enormous number of nucleic acid sequences in vitro for any given function, has revealed that RNA, indeed, can have many different catalytic functions as so can, presumably, DNA.

On further reflection, many doubts have been raised about whether or not the original genetic/catalytic material could have been RNA as we know it today because extreme conditions on the primitive Earth might have led to the rapid chemical degradation of RNA. Nevertheless, even if the precise chemical nature of the early genetic/catalytic material differed from present-day RNA, it seems reasonable to conclude that the RNA World did exist at some time. If very primitive life on Earth did not arise until about 3.5

billion years ago, there was, perhaps, a period of 0.5 billion years in which to sample many polymer sequences that originally arose through non-biochemical mechanisms and that ultimately evolved directed the first self-replicating systems.

My involvement in the discovery of the first catalytic RNA began in innocence during a study of tRNA biosynthesis in Escherichia coli. I was fortunate enough to isolate and characterize a precursor tRNA, one of the intermediates in the metabolic pathway leading to the synthesis of mature tRNA. As in all biochemical pathways, if one has an intermediate compound, there must be an intra-cellular enzyme that acts on this intermediate to take it to the next step in the pathway. This enzyme, ribonuclease P (RNase P), was readily identifiable. Its function was to cleave a phosphodiester bond at the start of the mature tRNA nucleotide sequence, thereby releasing the upstream extra or "precursor" nucleotides.

The total purification of RNase P proved to be a very difficult task. However, a perceptive and hard-working graduate student, Ben Stark, noticed that an RNA copurified with the protein in the enzyme preparation. He then devised a test to see if the RNA molecule was essential for the function of the enzyme. This test used the same strategy that Avery, MacLeod and McCarty had used to prove that DNA was the essential ingredient in bacterial transformation. In Stark's experiment, the test showed that the RNA was essential for RNase P function. This result explained why the purification, which had been designed to isolate a proteinaceous complex, was so difficult. It also led to much disbelief in the community of enzymologists.

We soon suggested that the RNA subunit of RNase P was part of the active center of the enzyme, by analogy to the then current picture of the ribosome. A few years later, however, Cecilia Guerrier-Takada, a postdoctoral fellow, demonstrated that this RNA, itself, was a true enzyme in vitro. At that time, Tom Cech had recently and independently observed phosphoester bond cleavage and ligation by a different RNA molecule. Cech's observation and ours, while still greeted skeptically by some members of the enzymological community, were soon universally accepted and within a few years other catalytic RNAs derived from plant pathogens and the human delta RNA were also found.

The chemical details of catalysis by RNase P remain to be fully worked out although a rough picture of this reaction is now available. A fascinating aspect of the RNase P "problem" is the vast difference in chemical make-up of subunits and catalytic mechanism of this enzyme as it is found in eukaryotes (e.g., the RNA subunit is not active in vitro) compared to these properties in prokaryotes. Evolution has presented us with contemporary versions of this enzyme that undoubtedly will someday tell us an interesting story of its progression from an RNA to various complexes of RNA and protein.


References:

Orgel, L. E., The origin of life on the Earth. Scientific American, October 1994, Volume 271, pages 76-83.

Orgel, L. E., The origin of life - a review of facts and speculations, Trends in Biochemical Sciences, December 1998, Volume 2-3, pages 491-495.

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Monday, January 15, 2007

the Basics
  1. What is evolution?  
  Biological evolution refers to the cumulative changes that occur in a population over time. These changes are produced at the genetic level as organisms' genes mutate and/or recombine in different ways during reproduction and are passed on to future generations. Sometimes, individuals inherit new characteristics that give them a survival and reproductive advantage in their local environments; these characteristics tend to increase in frequency in the population, while those that are disadvantageous decrease in frequency. This process of differential survival and reproduction is known as natural selection. Non-genetic changes that occur during an organism's life span, such as increases in muscle mass due to exercise and diet, cannot be passed on to the next generation and are not examples of evolution.
Learn More
Evolution of Diversity
 
  2. Isn't evolution just a theory that remains unproven?  
  In science, a theory is a rigorously tested statement of general principles that explains observable and recorded aspects of the world. A scientific theory therefore describes a higher level of understanding that ties "facts" together. A scientific theory stands until proven wrong -- it is never proven correct. The Darwinian theory of evolution has withstood the test of time and thousands of scientific experiments; nothing has disproved it since Darwin first proposed it more than 150 years ago. Indeed, many scientific advances, in a range of scientific disciplines including physics, geology, chemistry, and molecular biology, have supported, refined, and expanded evolutionary theory far beyond anything Darwin could have imagined.
Evolution Revolution   Learn More
Evolution Revolution
 
  3. Are all species related?  
  Yes. Just as the tree of life illustrates, all organisms, both living and extinct, are related. Every branch of the tree represents a species, and every fork separating one species from another represents the common ancestor shared by these species. While the tree's countless forks and far-reaching branches clearly show that relatedness among species varies greatly, it is also easy to see that every pair of species share a common ancestor from some point in evolutionary history. For example, scientists estimate that the common ancestor shared by humans and chimpanzees lived some 5 to 8 million years ago. Humans and bacteria obviously share a much more distant common ancestor, but our relationship to these single-celled organisms is no less real. Indeed, DNA analyses show that although humans share far more genetic material with our fellow primates than we do with single-celled organisms, we still have more than 200 genes in common with bacteria.

It is important to realize that describing organisms as relatives does not mean that one of those organisms is an ancestor of the other, or, for that matter, that any living species is the ancestor of any other living species. A person may be related to blood relatives, such as cousins, aunts, and uncles, because she shares with them one or more common ancestors, such as a grandparent, or great-grandparent. But those cousins, aunts, and uncles are not her ancestors. In the same way, humans and other living primates are related, but none of these living relatives is a human ancestor.
All in the Family   Learn More
All in the Family
  Learn More
Jane Goodall Video Clip
View in QuickTime or RealPlayer
 
  4. What is a species?  
  Members of one species do not normally interbreed with members of other species in nature. Sometimes, members of different species, such as lions and tigers, can interbreed if kept together in captivity. But in nature, geographic isolation and differences in behavior, such as choice of habitat, keep these sorts of closely related animal species apart. Similarly, closely related species of plants can sometimes be hybridized by horticulturists, but these hybrids are rarely found in nature. A species, then, is defined by science as a group of interbreeding or potentially interbreeding populations that is reproductively isolated from other such groups.
An Origin of Species   Learn More
An Origin of Species
 
  5. What do genes have to do with evolution?  
  Genes are the portions of an organism's DNA that carry the code responsible for building that organism in a very specific way. Genes -- and, thus, the traits they code for -- are passed from parent to offspring. From generation to generation, well-understood molecular mechanisms reshuffle, duplicate, and alter genes in a way that produces genetic variation. This variation is the raw material for evolution.
Learn More
Evolution Since Darwin
 
  6. What role does sex play in evolution?  
  Sexual reproduction allows an organism to combine half of its genes with half of another individual's genes, which means new combinations of genes are produced every generation. In addition, when eggs and sperm are produced, genetic material is shuffled and recombined in ways that produce new combinations of genes. Sexual reproduction thus increases genetic variation, which increases the raw material on which natural selection operates. Genetic variation within a species -- also known as genetic diversity -- increases a species' opportunity for change over successive generations.
The Advantage of Sex   Learn More
The Advantage of Sex
 
  7. Is evolution a random process?  
  Evolution is not a random process. The genetic variation on which natural selection acts may occur randomly, but natural selection itself is not random at all. The survival and reproductive success of an individual is directly related to the ways its inherited traits function in the context of its local environment. Whether or not an individual survives and reproduces depends on whether it has genes that produce traits that are well adapted to its environment.
Life's Grand Design   Learn More
Life's Grand Design
 
  8. Are evolution and "survival of the fittest" the same thing?  
  Evolution and "survival of the fittest" are not the same thing. Evolution refers to the cumulative changes in a population or species through time. "Survival of the fittest" is a popular term that refers to the process of natural selection, a mechanism that drives evolutionary change. Natural selection works by giving individuals who are better adapted to a given set of environmental conditions an advantage over those that are not as well adapted. Survival of the fittest usually makes one think of the biggest, strongest, or smartest individuals being the winners, but in a biological sense, evolutionary fitness refers to the ability to survive and reproduce in a particular environment. Popular interpretations of "survival of the fittest" typically ignore the importance of both reproduction and cooperation. To survive but not pass on one's genes to the next generation is to be biologically unfit. And many organisms are the "fittest" because they cooperate with other organisms, rather than competing with them.
Learn More
Adaptation and Natural Selection
 
  9. How does natural selection work?  
  In the process of natural selection, individuals in a population who are well-adapted to a particular set of environmental conditions have an advantage over those who are not so well adapted. The advantage comes in the form of survival and reproductive success. For example, those individuals who are better able to find and use a food resource will, on average, live longer and produce more offspring than those who are less successful at finding food. Inherited traits that increase individuals' fitness are then passed to their offspring, thus giving the offspring the same advantages.
An Origin of Species    Learn More
An Origin of Species
 
  10. How do organisms evolve?  
  Individual organisms don't evolve. Populations evolve. Because individuals in a population vary, some in the population are better able to survive and reproduce given a particular set of environmental conditions. These individuals generally survive and produce more offspring, thus passing their advantageous traits on to the next generation. Over time, the population changes.
Sex and the Single Guppy   Learn More
Sex and the Single Guppy
 
  11. Does evolution prove there is no God?  
  No. Many people, from evolutionary biologists to important religious figures like Pope John Paul II, contend that the time-tested theory of evolution does not refute the presence of God. They acknowledge that evolution is the description of a process that governs the development of life on Earth. Like other scientific theories, including Copernican theory, atomic theory, and the germ theory of disease, evolution deals only with objects, events, and processes in the material world. Science has nothing to say one way or the other about the existence of God or about people's spiritual beliefs.
Science and Faith   Learn More
Science and Faith


I bought a really nice book all on the molecular biology of cells.

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Sunday, October 08, 2006

http://youtube.com/watch?v=CQ8_bIji7gQ
Part 1

http://youtube.com/watch?v=o4xIi-TwY-Y&mode=related&search=
Part 2

"In science class, why can't they simply teach science?"
---Richard Dawkins

"... it was noticable that God or Jesus came on every page."
---RD



Saturday, October 07, 2006






I'm currently reading the book "Animal Behavior".