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Re: Theory, not empirical and verifiable evidence (Genetic drift)

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  • stewart8724
    Charles P: This is probably the reason that James A Shapiro does not mention genetic drift in his book. Please notice that Joanna Masel uses the word
    Message 1 of 2 , Nov 19, 2012
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      Charles P: This is probably the reason that James A Shapiro does not
      mention "genetic drift" in his book. Please notice that Joanna Masel uses
      the word "theory" in the scientific writing about "genetic drift". Please
      notice the use of mathematics, observations in nature. Please notice that
      the word "gene" has a multitude of meanings based upon observations in
      nature.

      Stewart: Please notice the amount of utter drivel Charles will trot out in his desperate attempts to find even the most facile objections to science.

      Joanna Masel:
      http://www.sciencedirect.com/science/article/pii/S0960982211008827 Genetic
      Genetic drift: http://en.wikipedia.org/wiki/Genetic_drift Genetic dri...
      Although both processes affect evol....
      In natural populations, genetic drift and natural se....
      When the allele frequency is very small, dri...
      The mathematics of genetic drift d......
      Horizontal Gene Transfe.......
      Furthermore, HG.......
      James A Shapiro:
      http://www.huffingtonpost.com/james-a-shapiro/interkingdom-horizontal-d_b_2081420.html
      Inter-Kingdom Horizontal DNA Tran...
      James A Shapiro: References #22.....
      genome, including signals formattin.......
      James A Shapiro: See Natalie Angier's 2..

      Charles P: "The ice in the current ice sheet is as
      > old as 110,000 years". How do the scientists know this without making some
      > "assumptions"? What did they "assume"?

      Stewart: Why do you assume they made assumptions?

      I've condensed some portions of your post to make it less boring. I think it worked a treat, I mean it's still a meaningless and boring pile of Shiite, but it takes far less time to read.
      Incidentally are you entertaining the thought of defending any of your posts. The reason I ask is that every point you make is debunked almost before you've finished typing it. It seems to me that if you were treating this forum the tiniest bit seriously, you would try and give the impression that you believe at least some of what you write, if only for appearances sake.

      The Earth is only 6,000 - 10,000 years old – Debunked
      Instances of erosion in various parts of the world indicate the world wide flood mentioned in the Bible. - Debunked.
      Computer language is evidence of the intelligent design of life. – Debunked.
      Humans are not related to apes of any kind. - Debunked.
      There are no signs of intermediate species between extinct and existing forms. - Debunked.
      Scientists make assumptions for which they have no evidence. - Debunked.
      Laurie was once right about something. - Debunked.
      Evolution hasn't been falsified and is therefore unscientific – Debunked.
      Intelligent design is science. - Debunked.
      Scientists don't want people to know when they disagree with each other. - Debunked.
      Cells are capable of independent, intelligent thoughts and actions. - Debunked.
      There is no actual evidence for evolution. - Debunked.
      There is some evidence for intelligent creation. - Debunked.
      The word 'gene' has more than one meaning rendering it an unscientific phrase. - Debunked.
      Intelligent design in nature is self evident. - Debunked.
      Evolutionary theory has no accepted facts because there is no list beginning with the words 'It is written'. - Debunked.
      Evolution is a 20th century theory. - Debunked.
      Evolution is a 21st century theory. - Debunked.
      The similarities science identifies amongst species in the fossil evidence, is a case of apophenia. (I think Charles means pareidolia but never mind). - Debunked.
      More and more scientists are being converted to design theory on a daily basis. - Debunked.
      Intelligent design has nothing to do with religion. - Debunked.
      Intelligent design is not creationism. - Debunked.
      Genetic drift is just a theory and by definition not scientific. - Debunked.
      To disagree with Charles is evidence of an ad- hominem argument. - Debunked.
      Charles understands the theory of evolution better than Glaudys. - Debunked.
      To propose there are limits to carbon dating (as David did) is an example of circular reasoning. - Typically idiotic statement, and also – Debunked.
      Charles has an open mind. - Debunked.
      All theories should be accepted as axiomatic (taken for granted) prior to asking any questions. On them. - Debunked.
      Natural selection has no appreciable effect on the formation of species. - Debunked.
      There is empirical and undeniable evidence for Shapiro's 'natural genetic engineering'. - (This has not been debunked just yet, as no such evidence has been shown. Maybe it's secret evidence, for creationist eyes only).

      This is only a taster, there's a good deal more. In fact there are so many I can't remember them all off the top of my head.



      ...

      --- In OriginsTalk@yahoogroups.com, Charles Palm <palmcharlesUU@...> wrote:
      >
      > Charles P: This is probably the reason that James A Shapiro does not
      > mention "genetic drift" in his book. Please notice that Joanna Masel uses
      > the word "theory" in the scientific writing about "genetic drift". Please
      > notice the use of mathematics, observations in nature. Please notice that
      > the word "gene" has a multitude of meanings based upon observations in
      > nature.
      >
      > Victor M: http://dir.groups.yahoo.com/group/OriginsTalk/message/29999 You
      > can define science in two ways. (1) Simple knowledge, such as observations
      > of bees and flowers. (2) A structured way of arranging knowledge based on a
      > first principle. Modern science is of the latter kind. It was contrived on
      > a single assumption, a first law, that the Bible predicted for the mockers
      > of the last days.
      >
      > Victor M: Scientists, whether creationists or evolutionists, try to
      > explain reality with symbolical, mathematical things no one has ever
      > detected.
      >
      > James A Shapiro: References #228, #229: Why and How to Avoid Using the
      > Term “Gene”. Throughout the book, the term “gene” appears in quotation
      > marks to indicate its hypothetical nature. This term has no rigorous and
      > consistent definition. It has been used to designate countless different
      > features of genome organization. In other words, the use of “gene” gives
      > the false impression of specifying a definite entity when, in fact, it can
      > mean any number of different genomic components.
      >
      > ********************************************************************************
      >
      > Joanna Masel:
      > http://www.sciencedirect.com/science/article/pii/S0960982211008827 Genetic
      > Drift.
      >
      > 1 In theory, in a small enough population genetic drift could also be
      > important even for common alleles. The effect of genetic drift over a given
      > time declines exponentially with increasing population size (Figure 1).
      >
      > 2 According to the theory of genetic drift, the variance in allele
      > frequency across the populations should increase by a factor of p(1 âˆ'p)/2N
      > each generation, where p is the current frequency and N is the population
      > size. Buri plotted the change in allele frequency as a function of p, and
      > got a curve with the right shape, but for Ne = 11.5 rather than N = 16. Ne
      > is called the ‘effective population size’. The fact that it is low means
      > that allele frequencies changed faster than expected.
      >
      > 3 There may be many more consequences that we don't know about yet: the
      > theory of selection at linked sites is still being worked out.
      >
      > 4 Hahn, 2008 M.W. Hahn Toward a selection theory of molecular evolution.
      > Evolution, 62 (2008), pp. 255â€"265.
      >
      > 5 John H Gillespie:
      > http://www.sciencedirect.com/science/article/pii/S0378111900004856 The
      > neutral theory in an infinite population.
      >
      > 6 Max Shpak:
      > http://www.sciencedirect.com/science/article/pii/S143176130500025X
      > Evolution of variance in offspring number: The effects of population
      > size
      > and migration.
      >
      > ********************************************************************************
      >
      > Charles P: Please notice the scientific writing based upon definitions and
      > theory, not empirical and verifiable evidence from observations in nature.
      >
      > Genetic drift: http://en.wikipedia.org/wiki/Genetic_drift Genetic drift
      > versus natural selection. The law of large numbers predicts little change
      > over time due to genetic drift when the population is large. When the
      > reproductive population is small, however, the effects of sampling error
      > can alter the allele frequencies significantly. Genetic drift is therefore
      > considered to be a consequential mechanism of evolutionary change primarily
      > within small, isolated populations.
      >
      > Although both processes affect evolution, genetic drift operates randomly
      > while natural selection functions non-randomly. While natural selection has
      > a direction, guiding evolution towards heritableadaptations to the current
      > environment, genetic drift has no direction and is guided only by the
      > mathematics of chance. As a result, drift acts upon the genotypic
      > frequencies within a population without regard to their phenotypic effects.
      > In contrast, selection favors the spread of alleles whose phenotypic
      > effects increase survival and/or reproduction of their carriers. Selection
      > lowers the frequencies of alleles that cause unfavorable traits, and
      > ignores those that are neutral.
      >
      > In natural populations, genetic drift and natural selection do not act in
      > isolation; both forces are always at play. However, the degree to which
      > alleles are affected by drift or selection varies according to population
      > size. The magnitude of drift on allele frequencies per generation is larger
      > in small populations. The magnitude of drift is large enough to overwhelm
      > selection when theselection coefficient is less than 1 divided by the
      > effective population size. As a result, drift affects the frequency of more
      > alleles in small populations than in large ones.
      >
      > When the allele frequency is very small, drift can also overpower
      > selectionâ€"even in large populations. For example, while disadvantageous
      > mutations are usually eliminated quickly in large populations, new
      > advantageous mutations are almost as vulnerable to loss through genetic
      > drift as are neutral mutations. Not until the allele frequency for the
      > advantageous mutation reaches a certain threshold will genetic drift have
      > no effect.
      >
      > The mathematics of genetic drift depend on the effective population size,
      > but it is not clear how this is related to the actual number of individuals
      > in a population. Genetic linkage to other genes that are under selection
      > can reduce the effective population size experienced by a neutral allele.
      > With a higher recombination rate, linkage decreases and with it this local
      > effect on effective population size. This effect is visible in molecular
      > data as a correlation between local recombination rate and genetic
      > diversity, and negative correlation between gene density and diversity at
      > noncoding sites. Stochasticity associated with linkage to other genes
      > that are under selection is not the same as sampling error, and is
      > sometimes known as genetic draft in order to distinguish it from genetic
      > drift.
      >
      > *******************************************************************************
      >
      > Charles P: Please notice that HGT scrambles the information on which
      > biologists rely to reconstruct the phylogeny of organisms.
      >
      > Horizontal Gene Transfer:
      > http://en.wikipedia.org/wiki/Horizontal_gene_transfer_in_evolution The
      > fact that genes can move between distant branches of the tree of life even
      > at low probabilities raises challenges to scientists trying to reconstruct
      > evolution by studying genes and gene sequences in different organisms.
      > Horizontal gene transfer (HGT) effectively scrambles the information on
      > which biologists rely to reconstruct the phylogeny of organisms.
      >
      > Furthermore, HGT poses challenges for the ambitious reconstruction of the
      > earliest events in evolution. Because the early branches of the tree of
      > life spanned long time intervals and involved large numbers of organisms,
      > many low-probability HGT events are certain to have occurred.
      >
      > ********************************************************************************
      > James A Shapiro:
      > http://www.huffingtonpost.com/james-a-shapiro/interkingdom-horizontal-d_b_2081420.html
      > Inter-Kingdom Horizontal DNA Transfer in All Directions: Infectious
      > Bacteria Evolve by Acquiring Protein Domains From Eukaryotic Hosts.
      >
      > ********************************************************************************
      > James A Shapiro: References #228, #229: Why and How to Avoid Using the
      > Term “Gene”. Throughout the book, the term “gene” appears in quotation
      > marks to indicate its hypothetical nature. This term has no rigorous
      > and consistent definition. It has been used to designate countless
      > different features of genome organization. In other words, the use
      > of “gene” gives the false impression of specifying a definite entity when,
      > in fact, it can mean any number of different genomic components. In some
      > cases, such as when “gene” is used to indicate a continuous human DNA
      > sequence encoding a specific protein, it actually means something that
      > generally has no real existence in nature. This is because the genomic DNA
      > coding regions usually comprise several separated exons and are only joined
      > at the level of the RNA transcript. In place of “gene,” therefore, the term
      > coding sequence
      > indicates DNA regions that determine protein primary structure, in keeping
      > with the contemporary use of CDS to indicate proteinencoding regions in
      > genome sequence annotations. Moreover, the term genetic locus is
      > preferable, because it indicates a discrete identifiable region of the
      > genome, including signals formatting transcription and post-transcriptional
      > processing, that encodes one or more messenger RNA molecules, which in turn
      > encode one or more specific protein products. The reason for this
      > preference is that a genetic locus can be defined operationally by either
      > genetic or molecular analysis, and the two-word phrase does not carry the
      > same theoretical and confusing implications as the multifarious term “gene”.
      >
      > James A Shapiro: See Natalie Angier’s 2008 New York Times article
      > “Scientists and Philosophers Find That ‘Gene’ Has a Multitude of Meanings”
      > at
      > http://www.nytimes.com/2008/11/11/science/11angi.html?_r=3&sq=RNA%20genes&st=cse&scp=2&pagewanted=print
      > .
      >
      >
      > [Non-text portions of this message have been removed]
      >
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