posted 25. March 2004 12:31                   

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DNA and RNA are the Biological Software, you can see that there was a designer of them.

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posted 26. March 2004 12:21                   

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the amazing miracle of life is that the Software and its products regulate the Hardware, and vice-versa.

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Yes. It's not a matter of "Which came first? The chicken or the egg?"

With life the hardware and the software are both required at the same time. It's obvious that abiogenesis never happened, yet evolutionists continue teaching it as fact.



I do have a question though: What is the best way to describe a gene regulatory network? Hardware? Software? Or both?

http://doegenomestolife.org/science/generegulatorynetwork.shtml

A regulatory network can be viewed as a cellular input-output device. At minimum, a gene regulatory network typically contains the following components: (1) an input signal reception and transduction system that mediates intra and extracellular cues (left box; often, more than one signal impinges on a given target gene); (2) a "core component" complex composed of transacting regulatory proteins and cognate cis-acting DNA sequences (circle; functionally similar components may be associated with multiple target genes, resulting in similar gene-expression patterns); and (3) primary molecular outputs from target genes, which are RNA and protein (box to right of circle). The net effects are changes in cell phenotype and function (right box). Direct and indirect feedbacks typically are important. More realistic networks often feature multiple tiers of regulation, with first-tier gene products regulating expression of another group of genes, and so on. Beyond GRN boundaries are signaling responses and feedbacks, such as those that drive bacterial chemotaxis, which do not involve regulation of gene expression but instead act directly on proteins and protein machine assemblies (dashed arrows). Some regulatory networks have no embedded GRN component.

posted 26. March 2004 12:31                   

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How might this "lipid life" have triggered the nucleic acid based biota we see today?

This is the topic of our next papers. We foresee a slow, graded takeover, in whi ch, driven by the rudimentary capacity of lipid GARD assemblies to replicate and evolve, ch emical selection will favor a small subset of monomers, PRIOR to any polymerization. N ext, very short polymers would gradually form, inside the GARD assemblies, and driven by t he vey high local concentration of monomers (dilution is one of polymerization's problems). All this will happen within an already existing mutually catalytic network, which as can be shown mathematically, will favor some reactions and abolish others. This gradual passa ge from a very primitive network with monomers only to ones with longer and longer polymer s may in fact be the solution to the Chicken & Egg problem. But the major answer to this question - we still have to work hard to find out how this happened. But, there is consolat ion in claiming that RNA and DNA are the RESULTS of an evolutionary process rather than is prerequisites.

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Mutually catalytic sets of simple organic molecules have been suggested to be capable of self-replication and rudimentary chemical evolution. Previous models for the behavior of such sets have analyzed the global properties of short biopolymer ensembles by using graph theory and a mean field approach. In parallel, experimental studies with the autocatalytic formation of amphiphilic assemblies (e.g., lipid vesicles or micelles) demonstrated self-replication properties resembling those of living cells. Combining these approaches, we analyze here the kinetic behavior of small heterogeneous assemblies of spontaneously aggregating molecules, of the type that could form readily under prebiotic conditions. A statistical formalism for mutual rate enhancement is used to numerically simulate the detailed chemical kinetics within such assemblies. We demonstrate that a straightforward set of assumptions about kinetically enhanced recruitment of simple amphiphilic molecules, as well as about the spontaneous growth and splitting of assemblies, results in a complex population behavior. The assemblies manifest a significant degree of homeostasis, resembling the previously predicted quasi-stationary states of biopolymer ensembles (Dyson, F. J. (1982) J. Mol. Evol. 18, 344-350). Such emergent catalysis-driven, compositionally biased entities may be viewed as having rudimentary "compositional genomes." Our analysis addresses the question of how mutually catalytic metabolic networks, devoid of sequence-based biopolymers, could exhibit transfer of chemical information and might undergo selection and evolution. This computed behavior may constitute a demonstration of natural selection in populations of molecules without genetic apparatus, suggesting a pathway from random molecular assemblies to a minimal protocell.

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Evolution produces complex and structured networks of interacting components in chemical, biological, and social systems. We describe a simple mathematical model for the evolution of an idealized chemical system to study how a network of cooperative molecular species arises and evolves to become more complex and structured. The network is modeled by a directed weighted graph whose positive and negative links represent "catalytic" and "inhibitory" interactions among the molecular species, and which evolves as the least populated species (typically those that go extinct) are replaced by new ones. A small autocatalytic set, appearing by chance, provides the seed for the spontaneous growth of connectivity and cooperation in the graph. A highly structured chemical organization arises inevitably as the autocatalytic set enlarges and percolates through the network in a short analytically determined timescale. This self organization does not require the presence of self-replicating species. The network also exhibits catastrophes over long timescales triggered by the chance elimination of "keystone" species, followed by recoveries

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posted 27. March 2004 12:32                   

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The abuse of “evolution” has been so shameless that a dominant figure in the U.S. science got publicly very upset because some stickers were declaring that the theory of evolution was just that, a theory, but not reality.

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posted 27. March 2004 12:49                   

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WGD followed by massive gene loss and gene specialization offers an important path for large-scale evolutionary innovation. Compared to multiple independent duplications and divergence of individual genes or segments, WGD may be more efficient and may offer great opportunities for coordinated evolution. Although organisms clearly can undergo WGD resulting in complete polyploids (as evidenced by existing tetraploid species of plants and animals 34–37), it has been unclear whether WGD can then be followed by massive genome reshaping to yield diploids with expanded gene content. Our analysis of K. waltii definitively proves that S. cerevisiae is the descendant of an ancient WGD, as originally proposed by Wolfe 3 on the basis of subtle genomic patterns. Comparison with K. waltii allows rigorous study of the many evolutionary innovations that arose in this dramatic event. We note that a similar analysis of the Ashbya gossypii genome has been carried out (P. Philippsen, personal communication). The results here suggest that it may also be fruitful to search for similar genomic signatures of ancient WGD in other organisms 38–40. It will be interesting to see just how far such distant echoes of genomic upheaval may be traced.

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Between 1866-1873 Mendel corresponded with Carl Nägeli (1817-91), Professor of Botany at the University of Munich and an authority in plant hybrids. Nägeli was convinced that hybrids were generally unstable and he could not agree with Mendel's theory that the characters passed onto hybrids from their parents were constant. The period of Mendel's correspondence with Nägeli [i] coincides with the experiments with the Hieracium which disappointingly seemed to prove Nägeli right. Mendel's observed what he called "a peculiar behaviour of the hybrids" which he was unable to explain - i.e. that the Hieracium exhibited both sexual and a-sexual reproduction (a phenomenon known as apomixis).

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All these results were never published by MENDEL. They are preserved in the correspondence with C. v. NÄGELI. C.CORRENS edited and published it in 1905. Supported by C. v. NÄGELI MENDEL did also work on Hieracium hybrids, especially such of the subgenera Pilosella and Archhieracium. The choice of these objects proved to be rather unhappy, since Hieracium is a genus that poses difficulties to botanists even today. Often stable transitional forms occur, whose existence MENDEL could not explain. Besides the technical problems (flowers of composites are never easy to work with) were his experiments disturbed by a phenomenon that was not understood until much later: The seeds of several species develop directly from the mother cells of the embryo sac or a cell of the surrounding tissue, meiosis does not take place. Such a way of seed development is called agamospermy. The mother plant develops seeds without being pollinated. These seeds behave like layers of the mother plant. Additionally species exist, where part of the seeds develop from agamospermy and part from pollinated egg cells. This leads to completely confusing ratios, because the preconditions upon which MENDEL's laws are founded are not fulfilled any more.

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Nägeli also offered Mendel "fatal" advice: to continue his investigations using the hawkweed (Hieracium), a plant belonging to the family of the asters. It was only later that botanists discovered these plants’ asexual reproduction, which meant that experiments in hybridisation with hawkweed were bound to be inconclusive, since the genetic information is transferred exclusively via the maternal

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posted 27. March 2004 20:22                   

A good webpage on Haeckel

FIGURE 1. Haeckel's 1874 version of vertebrate embryonic development. The top row shows an early stage common to all groups, the second row shows a middle stage of development, and the bottom row shows a late stage embryo. Groups from left to right are: fish, salamander, turtle, chicken, pig, cow, rabbit, and human. (Adapted from Gilbert, 1997.)


FIGURE 3. Photographs of a fish, amphibian, reptile, mammal, and bird embryo at the "phylotypic" stage. Photographs courtesy of M. Richardson.

Richardson has written quite extensively on this topic.

A particular paper of interest may be: Haeckel's ABC of evolution and development Biol. Rev. (2002), 77, pp. 495-528

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ABSTRACT
One of the central, unresolved controversies in biology concerns the distribution of primitive versus advanced characters at different stages of vertebrate development. This controversy has major implications for evolutionary developmental biology and phylogenetics. Ernst Haeckel addressed the issue with his Biogenetic Law, and his embryo drawings functioned as supporting data. We re-examine Haeckel's work and its significance for modern efforts to develop a rigorous comparative framework for developmental studies.
Haeckel's comparative embryology was evolutionary but non-quantitative. It was based on developmental sequences, and treated heterochrony as a sequence change. It is not always clear whether he believed in recapitulation of single characters or entire stages. The Biogenetic Law is supported by several recent studies if applied to single characters only. Haeckel's important but overlooked alphabetical analogy of evolution and development is an advance on von Baer. Haeckel recognized the evolutionary diversity in early embryonic stages, in line with modern thinking. He did not necessarily advocate the strict form of recapitulation and terminal addition commonly attributed to him. Haeckel's much-criticized embryo drawings are important as phylogenetic hypotheses, teaching aids, and evidence for evolution. While some criticisms of the drawings are legitimate, others are more tendentious. In opposition to Haeckel and his
embryo drawings, Wilhelm His made major advances towards developing a quantitative comparative
embryology based on morphometrics. Unfortunately His's work in this area is largely forgotten. Despite his obvious flaws, Haeckel can be seen as the father of a sequence-based phylogenetic embryology.

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posted 01. April 2004 01:18                   

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Fernando:
The genomic analysis of human populations that we have now presents a history that many reject, a short antiquity for mankind with a further bottleneck.

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