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Re: What kind of evidence is acceptable?

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  • David
    ... Endosymbiosis : http://www.youtube.com/watch?v=-FQmAnmLZtE http://en.wikipedia.org/wiki/Endosymbiotic_theory Endosymbiotic theory From above: The
    Message 1 of 119 , Dec 30, 2012
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      --- In OriginsTalk@yahoogroups.com, "JamesG" <JamesGoff_960@...> wrote:
      > gluadys: "The theory of evolution does not require that bacteria turn into non-bacteria."
      > Me: "Actually, it does, otherwise the first life form (whatever it was) would still be the only living thing on earth, although in greater variety."
      > gluadys: "Not so. First, again, you are ignoring that bacteria and archaea and eukarya are different clades, and can only produce descendents in their own clade, not in a different clade."
      > As you may know, the earliest fossilized organisms were bacteria (referred to as "cyanobacteria"), which appeared in strata dating back some 3.5 billion years. For the sake of argument, then, let's assume that the first cellular life form (from which, as Darwinian theory would have it, all other cellular life presumably evolved) was a kind of bacteria. Would you still argue that "the theory of evolution does not require that bacteria turn into non-bacteria," or would you instead classify human beings as a kind of bacteria?
      > Jim in Missouri

      Endosymbiosis :


      Endosymbiotic theory

      From above:

      The Endosymbiotic Theory argues that mitochondria, plastids (e.g. chloroplasts), and possibly other organelles of eukaryotic cells, originate through symbiosis between multiple microorganisms. According to this theory, certain organelles originated as free-living bacteria that were taken inside another cell as endosymbionts. Mitochondria developed from proteobacteria (in particular, Rickettsiales, the SAR11 clade,[1][2] or close relatives) and chloroplasts from cyanobacteria.



      From above:

      Konstantin Mereschkowsky in his 1926 book Symbiogenesis and the Origin of Species, which proposed that chloroplasts originate from cyanobacteria captured by a protozoan.[1] Ivan Wallin also supported this concept in his book "Symbionticism and the Origins of Species". He suggested that bacteria might be the cause of the origin of species, and that species creation may occur through endosymbiosis. Today both chloroplasts and mitochondria are believed, by those who ascribe to the endosymbiotic theory, to have such an origin.

      In Acquiring Genomes: A Theory of the Origins of Species, biologist Lynn Margulis argued later that symbiogenesis is a primary force in evolution. According to her theory, acquisition and accumulation of random mutations are not sufficient to explain how inherited variations occur; rather, new organelles, bodies, organs, and species arise from symbiogenesis.


      Viral eukaryogenesis

      From above:

      Viral eukaryogenesis is the hypothesis that the cell nucleus of eukaryotic life forms evolved from a large DNA virus in a form of endosymbiosis within a methanogenic mycoplasma. The virus later evolved into the eukaryotic nucleus by acquiring genes from the host genome and eventually usurping its role. The hypothesis was proposed by Philip Bell in 2001, and gained support as large complex DNA viruses capable of protein biosynthesis (such as Mimivirus) have been discovered.

      Like viruses, a eukaryotic nucleus contains linear chromosomes with specialized end sequences (bacterial genomes have a circular topology), uses mRNA capping and separates transcription from translation. Eukaryotic nuclei are also capable of cytoplasmic replication. Some large viruses have their own DNA-directed RNA polymerase.[1] A transfer of an 'infectious' nucleus is documented in many parasitic red algae[2] Existing complex eukaryotic DNA viruses could also have originated through nuclear viriogenesis.[1]

      Recently, it was suggested that the transition from RNA to DNA genomes first occurred in the viral world.[3] A DNA-based virus may have provided a DNA-based storage for the ancient host that was previously using RNA to store its all genetic information.[1] Viruses could initially adopt DNA as a way to resist RNA degrading enzymes in the host cells. Hence the "contribution" from such a new component may have been as significant as the one of chloroplast or mitochondria. Following this hypothesis, Archaea, Bacteria, and Eukarya each obtained its DNA informational system from a different virus.[3] The RNA cell at the origin of Eukarya was probably more complex, featuring RNA processing.

      A number of precepts in the theory are possible. For instance, a helical virus with a bilipid envelope bears a distinct resemblance to a highly simplified cellular nucleus (i.e.: a DNA chromosome encapsulated within a lipid membrane). To consider the concept logically, a large DNA virus would take control of a bacterial or archaeal cell. Instead of replicating and destroying the host cell, it would remain within the cell. With the virus in control of the host cell's molecular machinery it would effectively become a "nucleus" of sorts. Through the processes of mitosis and cytokinesis, the virus would thus hijack the entire cell—an extremely favourable way to ensure its survival.



      From above:

      Protobionts are systems that are considered to have possibly been the precursors to prokaryotic cells. If RNA is trapped inside, the system can use the RNA or select for it.

      A protobiont is an aggregate of abiotically produced organic molecules surrounded by a membrane or a membrane-like structure. Protobionts exhibit some of the properties associated with life, including simple reproduction, metabolism and excitability, as well as the maintenance of an internal chemical environment different from that of their surroundings. It has been suggested that they are a key step in the origin of life on earth. Experiments by Sidney W. Fox and Aleksandr Oparin have demonstrated that they may be formed spontaneously, in conditions similar to the environment thought to exist on an early Earth. These experiments formed liposomes and microspheres, which have membrane structure similar to the phospholipid bilayer found in cells.

      Nanobes or nanobacteria, being too small to be functional living organisms, may be an example of naturally occurring protobionts.



      From above:

      A biofilm is an aggregate of microorganisms in which cells adhere to each other on a surface. These adherent cells are frequently embedded within a self-produced matrix of extracellular polymeric substance (EPS). Biofilm EPS, which is also referred to as slime (although not everything described as slime is a biofilm), is a polymeric conglomeration generally composed of extracellular DNA, proteins, and polysaccharides. Biofilms may form on living or non-living surfaces and can be prevalent in natural, industrial and hospital settings.[1][2] The microbial cells growing in a biofilm are physiologically distinct from planktonic cells of the same organism, which, by contrast, are single-cells that may float or swim in a liquid medium.

      Extracellular matrix

      The biofilm is held together and protected by a matrix of secreted polymeric compounds called EPS. EPS is an abbreviation for either extracellular polymeric substance or exopolysaccharide. This matrix protects the cells within it and facilitates communication among them through biochemical signals. Some biofilms have been found to contain water channels that help distribute nutrients and signalling molecules[16] . This matrix is strong enough that under certain conditions, biofilms can become fossilized (Stromatolites).

      Bacteria living in a biofilm usually have significantly different properties from free-floating bacteria of the same species, as the dense and protected environment of the film allows them to cooperate and interact in various ways. One benefit of this environment is increased resistance to detergents and antibiotics, as the dense extracellular matrix and the outer layer of cells protect the interior of the community. In some cases antibiotic resistance can be increased a thousandfold.[17] Lateral gene transfer is greatly facilitated in biofilms and leads to a more stable biofilm structure.

      David Williams: My introduction to biofilms was an infection in my leg. The streptococcus banded together and cooperated. There was a central slime city that tunneled through my flesh in a radial pattern. At the end of each radius, was a new colony. The bacteria exhibited a rudimentary intelligence, communicating with each other through chemical signals. When they do this, they are harder to get rid of.
    • Charles Palm
      D R Lindberg (To Jim in Missouri): You agreed that intermediate fossils can be identified independently of of theory. That eliminates any circularity. Charles
      Message 119 of 119 , Jan 18, 2013
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        D R Lindberg (To Jim in Missouri): You agreed that intermediate fossils
        can be identified independently of of theory. That eliminates any

        Charles P: The old idea of *transitional fossils* from the old Theory of
        Evolution is not acceptable as empirical and verifiable evidence. Naming
        them *intermediate* or some other name is a distinction without a
        difference. Arguing *circularity* draws attention away from the central
        issue. Look at this unscientific collection of intermediate fossils that
        does not even meet the standards of Wikipedia. This page was last modified
        on 14 January 2013 at 03:13.

        List of transitional fossils:

        1 This article needs additional citations for verification.

        2 This documentation needs attention from an expert in Palaeontology.

        Introduction to cladistics:
        http://www.ucmp.berkeley.edu/clad/clad1.html There are three basic
        assumptions in cladistics: (1) Any group of
        organisms are related by descent from a common ancestor. Please read (2)
        and (3) for additional information.

        Charles P: Everyone understands human genealogy and the concept of *common
        ancestor* for humans. Everyone understands dog genealogy and the concept
        of *common ancestor* for dogs. Why should anyone consider the concept of a
        *common ancestor* between living things that are self-evident as being very

        Phylogenetic trees:
        http://encyclopedia.thefreedictionary.com/Phylogenetic+trees Limitations.

        1 Although phylogenetic trees produced on the basis of sequenced genes or
        genomic data in different species can provide evolutionary insight, they
        have important limitations.

        2 When extinct species are included in a tree, they are terminal nodes, as
        it is unlikely that they are direct ancestors of any extant species.

        3 Scepticism must apply when extinct species are included in trees that
        are wholly or partly based on DNA sequence data, due to the fact that
        little useful "ancient DNA" is preserved for longer than 100,000 years, and
        except in the most unusual circumstances no DNA sequences long enough for
        use in phylogenetic analyses have yet been recovered from material over 1
        million years old.

        Understanding homology and analogy:
        http://evolution.berkeley.edu/evolibrary/article/similarity_hs_01 Note:
        There is no empirical and verifiable method for determining *common
        ancestry* between non-related living things.

        Charles P: Common ancestry is assumed in the science of cladistics.
        Transitional fossils are assumed to be intermediate between other fossils.
        Transitional fossils are extinct species. Transitional fossils are
        terminal nodes. Transitional fossils are unlikely to be direct ancestors
        of any extant species.


        Charles P: The skeptic does not have to qualify as a *creationist*. The
        skeptic does not have to qualify as an *Intelligent Design Theorist*. The
        skeptic does not have to qualify as *anti-science*. All a skeptic needs is
        to do their homework to verify for themselves what is scientific and what
        is not scientific.

        [Non-text portions of this message have been removed]
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