Ricki Lewis’ Time Machine (2)

By: James V. Kohl | Published on: January 24, 2016

(click to enlarge)

Reported here as: Ricki Lewis’ Time Machine

Physics’s pangolin

Trying to resolve the stubborn paradoxes of their field, physicists craft ever more mind-boggling visions of reality

Excerpt 1) with my emphasis

Physicists are deeply aware of the schizophrenic nature of their science and long to find a synthesis, or unification. Such is the goal of a so-called ‘theory of everything’. However, to non-physicists, these competing lines of thought, and the paradoxes they entrain, can seem not just bewildering but absurd.

Excerpt 2)

Based in mathematics, the classifications of physicists are supposed to have a rigour that other sciences lack, and a good deal of the near-mystical discourse that surrounds the subject hinges on ideas about where the mathematics ‘comes from’.

My comment: Added absurdities show up in articles like this. Ask “Where the mathematics ‘come from’ as you try to read it: Human brain networks function in connectome-specific harmonic waves
Excerpt:

We demonstrate the self-organization of these connectome-specific harmonics patterns from the interplay of neural excitation and inhibition in coupled dynamical systems as described by neural field models. Interestingly, due to the emergence of these harmonic patterns in various natural phenomena, ranging from acoustic vibrations, electromagnetic interactions and electron wave functions to morphogenesis, it is tempting to suppose that human brain activity might also be governed by the same underlying principles as other natural phenomena.

My comment: Self-organization and emergence are included in mathematical models that fail to link atoms to ecosystems via energy-dependent hydrogen-atom transfer in DNA base pairs. Does the emergence of self-organized connectomes in the context of a mathematical model make sense to schizophrenic physicists with their “theories of everything” else?

See for comparison: Primate CpG Islands Are Maintained by Heterogeneous Evolutionary Regimes Involving Minimal Selection

Excerpt:

…allele frequencies at polymorphic CpG sites can distinguish between maintenance of CpG islands by selection and stabilization of CpG islands through mere hypodeamination. As demonstrated by evolutionary simulations (Figures 7A and 7B , Figure S6A and S6B ), both low level of deamination and selection for minimal CpG content will result in high steady state CpG content. However, in the selective regime, polymorphic CpGs are expected to have significantly lower allele frequencies (average heterozygosity), and thus a higher frequency of low heterozygosity alleles than that observed in G/C dinucleotides.

My comment: The allele frequencies are nutrient energy-dependent and the different alleles link hydrogen-atom transfer in DNA base pairs to RNA-mediated cell type differentiation via the physiology of reproduction and fixation of amino acid substitutions that stabilize the organized genomes of all living genera.

The 100 year stand-off between theoretical physicists, evolutionary theorists, and serious scientists ended. But, few serious scientists are trying to win any confrontations over ridiculous theories compared to facts. The theorists simply add another theory and tell the serious scientists to prove that their theory is not important to understanding how to link physics and chemistry to biologically-based cause and effect. Their ridiculous theories never link hydrogen-atom transfer in DNA base pairs to all biomass via the sun’s biological energy. Thus, no matter what a serious scientist like Ricki Lewis does to promote the serious science produced by others, the pseudoscientists run away and try to start a fight somewhere else.

See: A Challenge to the Supremacy of DNA as the Genetic Material

Excerpt:

The news last week seemed to validate Drs. Annila and Baverstock’s concern about genome sequencing entering the clinic when we don’t fully understand how genes interact at the level of their products, the proteins.

See the comments. PZ Myers attacks the expertise of Drs. Annila and Baverstock, whose works have since been linked from nutrient-dependent microRNAs and hydrogen-atom transfer in DNA base pairs to RNA-mediated cell type differentiation via adhesion proteins and supercoiled DNA, which protects organized genomes from virus-driven entropy.

Baverstock tells people how epigenetically-effected RNA-mediated events are linked from amino acid substitutions to cell type differentiation in all cell types of all individuals of all species, and Myers claims: “Your version of the central dogma is idiosyncratic and wrong.” Myers has also since done that to Perry Marshall, author of “Evolution 2.0.”

See: PZ Myers – Perry Marshall Debate Evolution on Podcast

But first, look at these comments from Ricki Lewis’ site:

I’m not sure if I understand your point, as I’m still an undergrad student. I think the chaperones are a measure to widen a possible proteome (as alternative splicing), and since chaperones and alternative splicing factors are passed on through cytoplasmatic continuity, these should be also considered as an unit of heredity. I agree with this view, but I think it is already a predominant view with, lets say, developmental biologists – who seek out for function of certain genes during morphogenesis, for example. The same gene in different also locations can give rise to different structures – and this is certainly due to different proteomes in these locations.

1. Keith Baverstock
  
  March 21, 2014 at 8:18 pm
  
  In our view genes do not have a function. Function arises from a process entailing the interaction of active and information bearing proteins (mainly) and it is this process that we propose is the “unit of inheritance”. It can be regarded as a unit because it can be encapsulated by a quasi-stable state of the cell and as we said at the outset of the piece: it is the state of the cell that is inherited at cell division. as well as the DNA. I think you are pretty close to the idea. Good luck with your studies.
PZ Myers

March 22, 2014 at 1:48 am

Say what? Perhaps you need to go back and read what biologists were saying in the 1950s and 1960s. Your version of the central dogma is idiosyncratic and wrong.
Chaperones do not violate the central dogma.
Alternative splicing does not violate the central dogma.
There are bits of what you wrote that I think you’d find most biologists would agree with, because they’ve been saying them for years. But that nonsense about finding a violation of the central dogma, and then listing phenomena do not refer at all to the fact that information does not flow from protein sequence back into nucleotide sequence, tells me that you really do not have enough respect for the discipline of biology to bother examining what we actually say.
1. Keith Baverstock
  
  March 22, 2014 at 9:40 am
  
  We will agree to disagree then.
  1. James V. Kohl
    
    March 24, 2014 at 10:51 pm
    
    PZ Myers decided to tell his minions I am a ‘crank’ based on my detailed model of nutrient-dependent pheromone-controlled epigenetic effects on genome organization in species from microbes to man. Thus, it is appropriate for you to agree to disagree with him, unless you want to be subjected to unceasing attacks from those he has recruited to his blog.
    Thank you for bringing biophysical constraints back into what recently became mutation-driven evolution via “constraint-breaking” mutations. Perhaps theorists will now address how mutations lead to species diversity in cases where they do not lead to physical diseases and mental disorders.
    The duality of their proposed function(s) still goes far beyond my ability to grasp in the context of biologically-based receptor-mediated cause and effect. But I’m certain that PZ is not going to try to explain anything that, in his world, “just happens.”
    1. Keith Baverstock
      
      March 26, 2014 at 7:55 am
      
      Thanks James for the warning!
      See others and also:
      
      James V. Kohl
      
      March 24, 2014 at 11:18 pm
      
      A single–amino acid change enabled a unicellular pathogen to effect a specific host by disabling an enzyme in the host. The tragic result was the Irish Potato Famine. Although no epigenetic effect of a specific nutrient on a specific base pair that conclusively led to a specific amino acid substitution was demonstrated, nutrient-dependent amino acid differences link algae to cell type differentiation in plants (okay, viruses, too). Thus, the atoms to ecosystems approach continues to be based on some speculation, but it is also based on experimental evidence, which comes from others who also have speculated about the thermodynamics of intercellular signaling, which leads to organism level thermoregulation, in species from microbes to man via amino acid substitutions.
      Had I known about this excellent work by Annila and Baverstock, which fills in all, or nearly all the required details of biophysical constraints on ecological adaptations, I would probably violated copyright laws by including too much of what they have accurately represented in an already submitted invited review in an attempt to move evolutionary theorists forward into the 21st century.
      
      Pedro
      
      March 26, 2014 at 2:32 pm
      
      “Attributing cause and effect to microbes that have somehow mutated and become resistant to antibiotics is pseudoscientific nonsense.”
      Well, I think trying to explain all resistence and adaptation with no recourse to mutation is pseudoscientific nonsense too. Anyway, as long your work provides new insight, regardless of what survives later on, I’m all for it.
      
      See: Ricki Lewis’ Time Machine (3)