Subject: Essay on Darwinism

From: [email-masked]
Date: Tue, 23 Jan 2007 22:10:43 EST

Dear Darwin Day Celebration Organizers:
 
I shared the following essay on Darwinism with the members of the Zoology  
Department at SIUC to see if it can be worked in with the Darwin Day celebration 
 there. So far, the only professor to respond said that this was way out  of 
his area (ichthyology, systematics) and that he had no real  expertise in 
something dealing with genome research.  But he did say  to send the essay to the 
SIUC Darwin Day organizer, which I had already  done.  I also shared it with 
the SIUC featured Darwin Day speaker, Massimo  Pigliucci, who said he is always 
skeptical of new evolution theories and that he  did not have time to read 
it, but wished me luck.  His response confused  me, because the majority of the 
essay is not about any new theory of  evolution, but rather is about the 
current theory as defined in  publications written by the working groups dealing 
with evolution from the  National Academy of Sciences. 
 
Before that, I had emailed it to Donald M. O'Malley, Ph.D. Harvard  
University, Associate Professor, Dept. Biology, Northeastern University,  who responded 
that he was not well versed in genomic  organization and early evolutionary 
theory, so he could not  offer  substantive comments but wished me good luck 
with my  endeavors.  Based on his response,  I sent it on to Michael  Shermer, 
who said that my discussion of Darwin looked good to him , although he  only 
had time to read it through quickly,  as he was under a  publisher's deadline to 
finish an article he was working on, and, likewise,  wished me good luck.
 
Here it is.  I know it is too long for your specifications, but since  people 
whose judgement on this topic is generally respected have given me  
encouragement,  I decided to send it to you anyway. My background  is  in phonetic 
reconstruction techniques to show how sets of currently  observed languages are 
historically related. 
 
Sincerely,
 
Lydia

 
 The Time-Segmented Structure of the  Evolution Derived Genome
By Lydia Hazel
Copyright 2007
 
Abstract
 
The current model of evolution is a modified and expanded version of  Darwin’
s original hypothesis,  where evolution occurs by means of natural  selection 
of traits expressed by mutated genes in populations.   This  model does 
explain observed instances of how particular populations have become  better suited 
to features of their environment.  But when one attempts to  extend the model 
to explain the origin of all species from one common microbial  ancestor in 
accordance with the fossil record,  he or she implicitly  depends on a structure 
for genomes that is surprisingly different from what  developmental 
geneticists have observed.  More specifically, as shown below  using facts from the 
chromosome theory of heredity, species that evolved in  accordance with the 
currently proposed model would necessarily have genomes  consisting of unique sets 
of pairs of identical genes for the transmission of  each hypothesized 
distinctly arising trait.  Instead,  developmental  biologists have found that these 
hypothesized distinctly arising traits are all  transmitted by essentially the 
same set of genes used in different ways.   As a result of this new 
information, they are positing  a different model  of evolution which, nonetheless, 
carries with it this same time-segmented genome  structure. The goal of this 
paper is to make this implicit structure explicit  and to explain why it has never 
been recognized by the scientific  community.  

The current model of evolution
 
The current model of evolution expands on the central concepts of Darwin’s  
original hypothesis to include facts from the science of genetics. 1, 2,  3    
Both the original hypothesis and the currently expanded  version rely on a 
particular relative chronology for the onset of specific  traits in accordance 
with the fossil record. 4, 5, 6     And  both explain this chronology as a 
result of contrasting traits within  prehistoric populations , 7, 8, 9, 10, 11 on 
which natural selection  acted.12,13,14,15  The expanded version restricts 
evolution to include only  those traits transmitted by mutated genes, 16  which 
provide the model’s  essential raw material. 17
 
No observed example of the current model of evolution relies on a  particular 
relative chronology in accordance with the fossil record, for the  events 
interpreted from that record are all in the remote past. 18   Instead,  the 
observed examples pertain exclusively to the second essential  component,  which is 
reliance on contrasting traits that arise in response  to new mutations 
within populations.  For instance, the Working Group on  Teaching Evolution from 
the National Academy of Sciences tells teachers that  evolution explains: the 
resistance that strains of bacteria have developed by  gene mutation against  
once-effective antibiotics; the resistance that rats  have developed by gene 
mutation to the poison warfarin; the resistance that  insect species and other 
agricultural pests have developed by gene mutation to  pesticides; and the 
resistance that certain plants have developed by gene  mutation to toxic metals. 19 
 Observed examples given to secondary students  by lecturers Carroll and 
Kingsley, whose HHMI 2005 Holiday Lectures on Science  the National Academy of 
Sciences lists among its evolution resources,   include such phenomena as:  a 
black coat being introduced by gene mutation  into a population of  rock pocket 
mice and then replacing the once  universal  sandy coat in those areas of the 
American northwest where there  have been lava flows; 20  and armor plates 
being reduced by gene mutation  in a population of sticklebacks and then replacing 
the once universal full armor  plates in fresh water environments to provide 
easier escape from certain  freshwater dwelling predators. 21 

Reconstructing genomes built up in accordance with the current model of  
evolution
 
Extending the current model of evolution to account for the origin of all  
species from one common single celled ancestor requires more than providing  
observed examples of evolution in response to mutation;  one must also  apply 
facts about contrasting conditions in populations to reconstruct genomes  built 
up in accordance with the relative chronology for the onset of traits  deduced 
from the fossil record. 22, 23, 24 
 
First, the model  requires that there currently exist descendant  copies of 
prehistorically mutated genes responsible for each separately evolved  
presently observed trait.  After all, evolved traits are precisely those  that result 
when a “gene variant improves adaptation to the environment.”  25    These 
prehistorically mutated genes, or “gene  variants”  provided the raw material 
on which natural selection originally  acted. 26 There is no provision in the 
model for this raw material essential to  the origin of a trait to disappear.  
If the raw material were to disappear,  so would the trait itself.   
 
Next, one can predict how these genes must presently be paired at any given  
loci along two homologous chromosomes.  27    For example,  one can predict 
that no two distinctly evolved traits that a species presently  possesses are 
the result of two distinct genes at the same locus (dominance  versus 
recessiveness); 28   or of two of a set of three or more  distinct genes at the same 
locus (multiple alleles whose combinations exhibit  various patterns of 
dominance, codominance, and recessivenes); 29   or  of multiple distinct genes at 
multiple loci, each gene being one of a set of  two, or one or two of a set of 
three or more, distinct genes occurring in a  population at the same locus 
(complementary genes, supplementary genes, and  polygenic inheritance). 30    For the 
history of life deduced  from the fossil record 31, 32, 33 disallows a 
supposedly later evolved trait  from having been introduced at the same locus, or 
loci, as a supposedly earlier  evolved trait.   Otherwise, natural selection 
would have been free to  select the later evolved trait over the earlier,   
thereby producing  species exhibiting a supposedly later evolved trait, for 
example,   lungs,  introduced at the onset of amphibians,   in the absence  of  a 
supposedly historically required earlier evolved trait , such as  vertebrae,  
introduced at the onset of simple fishes; 34 or natural  selection would have 
been free to select the earlier evolved trait over the  later, thereby failing to 
produce species in “increasingly complex forms.” 35  Finally,  if natural 
selection did not operate to eliminate one of the two  contrasting traits 
resulting from different mutant genes at the same  locus,  those traits would still 
contrast in populations, 36 which never  occurs, either in species represented 
in the fossil record, in hypothesized  ancestral forms, or in present day 
populations. For example, the traits any  prehistoric or observed mammal 
inherited from its first mammalian ancestors  never contrast with the traits it 
inherited from its first reptilian ancestors,  or from its first amphibian 
ancestors, or from its first simple fish type  ancestors, or from its first shell 
bearing ancestors, or from its first  multicellular ancestor, or from its first 
eucaryotic ancestor, or from its first  prokaryotic ancestor. 37   Instead, all 
supposedly later evolved  traits imply the universal expression of all 
supposedly earlier evolved  traits.  This is essential to the requirement of all 
theories of evolution  derived from the fossil record, which shows a specific “
order in which  increasingly complex forms of life appeared.” 38 
 
Not only do supposedly distinctly evolved species’ traits never   contrast 
with each other; they never contrast with any other trait, whether it  can be 
relatively dated using the fossil record or not.   That is,  unlike color in the 
pea populations Mendel studied, 39   which  alternates between  yellow or 
green, 40  no supposedly prehistorically  evolved trait in any presently existing 
population alternates with other traits;  as explained above,  the expression 
of each of these traits is obligatory  for all members.  Therefore, no member 
of a population is heterozygous 41  for any of its supposedly evolved traits. 
 That is, the locus or loci for  each distinctly evolved trait a species 
presently possesses must pair two genes  that are the same.   

This leaves only the following  prediction consistent with the hypothesis of 
evolution for the genetic  configuration of any two distinctly arising traits 
on any one genome:  they  must be the result of unique sets of one pair, or of 
multiple pairs, of  identical genes; that is, the locus, or loci,  of the 
distinct pair, or  pairs, of identical genes responsible for any hypothesized 
earlier originating  trait must be separate from the locus, or loci,  of the 
distinct pair, or  pairs,  of identical genes responsible for any hypothesized 
later  originating trait.  
 
In other words:  
 
1) the traits any prehistoric or observed mammal inherited from its  
mammalian ancestors must be the result of specific sets of one pair, or of  multiple 
pairs, of identical genes; 
 
2) those genes must be spatially separate in terms of their loci and  
qualitatively different from the unique sets of one pair, or of multiple  pairs,  of 
identical genes responsible for the traits it inherited from its  reptilian 
ancestors; 
 
3) which must be spatially separate in terms of their loci and  qualitatively 
different from the unique sets of one pair, or of multiple pairs,  of 
identical genes responsible for the traits it inherited from its amphibian  
ancestors; 
 
4) which must be spatially separate in terms of their loci and  qualitatively 
different from the unique sets of one pair, or of multiple pairs,  of 
identical genes responsible for the traits it inherited from its simple fish  type 
ancestors; 
 
5) which must be spatially separate in terms of their loci and  qualitatively 
different from the unique sets of one pair, or of multiple pairs,  of 
identical genes responsible for the traits it inherited from its shell  bearing 
ancestors; 
 
6) which must be  spatially separate in terms of their loci and  
qualitatively different from the unique sets of one pair, or of multiple  pairs,  of 
identical genes responsible for the traits it inherited from its  non-vertebrate 
and non-shell bearing multicellular ancestors;
 
7) which must be spatially separate in terms of their loci and  qualitatively 
different from the unique sets of one pair, or of multiple pairs,  of 
identical genes responsible for the traits it inherited from its single  celled 
eucaryotic ancestors;
 
8) which must be spatially separate in terms of their loci and  qualitatively 
different from the unique sets of one pair, or of multiple pairs,  of 
identical genes responsible for the traits it inherited from its prokaryotic  
ancestors. 42  

How actual genomes differ from those reconstructed using the current  model 
of evolution 
 
Data from developmental genetics indicate that all of the supposedly  
separately evolved traits built up in accordance with the fossil record are not  each 
the result of unique sets of identical gene pairs.  Instead  observations 
show that they are the result of the same recurring set of toolkit  genes across 
all of the metazoa. 43  
 
In other words:
 
1) the traits any prehistoric or observed mammal inherited from its  
mammalian ancestors are not the result of specific sets of one pair, or of  multiple 
pairs, of identical genes that are spatially separate in terms of their  loci 
or qualitatively different from the genes responsible for the traits it  
inherited from its first reptilian ancestors; 
 
2) nor are the genes responsible for the traits it inherited from its  
reptilian ancestors spatially separate in terms of their loci or qualitatively  
different from the genes responsible for the traits it inherited from its first  
amphibian ancestors; 
 
3) nor are the genes responsible for the traits it inherited from its  
amphibian ancestors separate in terms of their loci or qualitatively different  from 
the genes responsible for the traits it inherited from its  simple  fish type 
ancestors; 
 
4) nor are the genes responsible for the traits it inherited from its   
simple fish type ancestors spatially separate in terms of their loci or  
qualitatively different from the  genes responsible for the traits it  inherited from 
its shell bearing type ancestors; 
 
5) nor are the genes responsible for the traits it inherited from its shell  
bearing type ancestors spatially separate in terms of their loci or  
qualitatively different from the genes responsible for the traits it inherited  from 
its non-vertebrate and non-shell bearing multicellular ancestors;
 
6) nor are the genes responsible for the traits it inherited from its  
non-vertebrate and non-shell bearing multicellular  ancestors spatially  separate in 
terms of their loci or qualitatively different from  the genes  responsible 
for the traits it inherited from its single celled  eucaryotic  ancestors;
 
7) nor are the genes responsible for the traits it inherited from its first  
eucaryotic ancestor spatially separate in terms of their loci or qualitatively 
 different from the genes responsible for the traits it inherited from its 
first  prokaryotic ancestors.
 
The only conclusion consistent with these observations is that all  
supposedly separately evolved traits each species possesses could not have come  from 
natural selection of contrasting traits arising from mutated gene variants  in 
prehistoric populations, as the current model of evolution 44, 45  requires.  
Observations further show that the toolkit genes responsible for  formative 
anatomy are ultimately regulated by non-gene material, including what  are 
called gene switches, which are non-protein coding sections of DNA  
strands. 46, 47

The newly proposed model of evolution
 
In response to this new information about toolkit genes and their  
regulation, evolutionary biologists have posited a new model of evolution that  does not 
rely on contrasting genes at the same locus but rather on contrasting  gene 
switches as mentioned above.48,49   At present, there are no  known laws 
governing variations of traits transmitted by contrasting gene  switches in 
populations because there are no known observations of gene switch  trait variations 
in populations on which to base them.  In other words,  there is no way to 
compare differences in gene switch traits between parents and  offspring because 
there are no known observations of such  differences.   Instead, all recorded 
examples, such as variations in  the switch for hind fin formation in some 
sticklebacks 50  and in the  switch for pigment formation in fruit flies, 51   are 
across  species,  whose members are non-mating.  For this reason, 
evolutionary  biologists explicitly state that the only  known way of investigating  
switch variations is by looking across species, 52  rather than within  
populations.

Differences between the newly proposed model and the current one
 
This makes the current model  fundamentally different from the  contrasting 
switch model.   No breeder, like Darwin with his pigeons,  53  or cultivator, 
like Mendel with his peas, 54   has been known  to have produced strains of 
animals or plants by relying on principles  underlying gene switch variations.   
In the current model, nature as  selector is analogous to humans as selector; 
55  in this new model, the  analogy no longer exists, making the first eight 
chapters of Darwin’s book on  the origin of species, as well as all of Mendel’
s work on peas irrelevant.   It also makes irrelevant all of  the observed 
examples of  evolution  given by the National Academy of Sciences in their 
special booklets for  teachers. It further makes irrelevant all the examples of 
artificial selection  and all but one example of evolution given by the lecturers 
for the Howard  Hughes Medical Institute during their 2005 holiday series, 
which the National  Academy of Sciences lists on its web site as an evolution 
resource.  

Observational evidence for the newly proposed gene switch model
 
As mentioned above, there is at least one known set of observations  
indicating  that evolution by means of natural selection of traits  introduced by 
mutated gene switches rather than by mutated genes has  occurred.  More 
specifically, marine species of sticklebacks have full hind  fins while freshwater 
species often have theirs reduced, and crosses using  artificial fertilization 
techniques suggest that this contrast comes from a  mutation in a switch at the 
same locus. 56 But observations from artificially  mated individuals from 
different species do not give any information about the  principles governing 
contrasting gene switch variations within a population,  which is the sole unit on 
which natural selection is defined to act.  57   Furthermore, observed across 
species variations in traits like  hind fin expression and fly wing pigment  
are insufficient to prove  evolution by natural selection of switch mutations 
for the same reason that  presently observed within species variations are 
insufficient to prove evolution  by natural selection of gene mutations.  Evolution 
is not a hypothesis  about any presently observed variations across species:  
it is a hypothesis  that specific non-observable variations within 
prehistoric populations occurred,  by which microbes ultimately evolved by natural 
selection into humans. 58   The biologist must allow himself to consider the 
possibility that the causes of  the succession of traits in the fossil record are 
not the same as the causes of  the succession of traits between observed parents 
and offspring in populations;  that is, the biologist must allow himself to 
consider the possibility that the  fossil record is not a genealogy.  
Otherwise, he investigates with a  perpetual handicap to his pursuit of knowledge. 

Predictions of the newly proposed model
 
One known fact about gene switches, namely, that they reside on chromosomes  
in a specific location, 59 leads to the same prediction as does the current  
model for the spatial configuration of the genetic matter causing supposedly  
distinctly arising traits:  any two supposedly distinctly arising traits a  
species possesses must be the result of unique sets of  switches; that is,  the 
locus, or loci,  of the unique switch, or switches, responsible for any  
hypothesized earlier originating trait must be separate from the locus, or  loci,  
of the switch, or switches, for any hypothesized later originating  trait.  For 
the raw material on which each of these traits depends, in this  case,  a 
descendant copy of a prehistorically mutated switch, or descendant  copies of 
prehistorically mutated switches,  rather than a descendant copy  of a 
prehistorically mutated gene, or descendant copies of prehistorically  mutated genes,  
must still exist, as there is no provision in the model for  this raw material 
to disappear.  
 
In other words, 
 
1) the traits any prehistoric or observed mammal inherited from its   
mammalian ancestors must be the result of specific gene switches; 
 
2) those switches must be qualitatively different from the unique switches  
responsible for the traits it inherited from its reptilian ancestors; 
 
3) which must be qualitatively different from the unique switches  
responsible for the traits it inherited from its amphibian ancestors; 
 
4) which must be qualitatively different from the unique switches  
responsible for the traits it inherited from its simple fish type ancestors; 
 
5) which must be qualitatively different from the unique switches  
responsible for the traits it inherited from its shell bearing ancestors; 
 
6) which  must be qualitatively different from the unique switches  
responsible for the traits it inherited from its non-vertebrate and non-shell  bearing 
multicellular ancestors;
 
7) which must be qualitatively different from the unique switches  
responsible for the traits it inherited from its single celled eucaryotic  ancestors;
 
8) which must be qualitatively different from the unique switches  
responsible for the traits it inherited from its prokaryotic ancestors.
 
Since there are no facts about contrasting conditions in populations with  
regard to switches, 60 there is no way to reconstruct how, or if, these switches 
 would have to be paired along homologous chromosomes.  

Why  evolutionists fail to recognize the time-segmented genome  structure of 
both the present and newly posited models of evolution  
 
The variations under domestication selected by breeders 61 that Darwin  
analogized to the variations in the wild selected by nature 62,63,64,65 all  result 
from the fact that potentially different genes in a population pair at  the 
same locus along homologous chromosomes. 66  But Darwin and his  supporters did 
not know this when they accepted his hypothesis. 67,68  By  the time these 
facts about genes and why their traits vary in populations became  expected 
knowledge for people studying heredity,   Darwin’s theory was  already taken for 
granted as the key to the great “mystery of mysteries”  underlying the origin 
of all species. 69 As a result,  the only way people  studying origins thought 
they could advance science was “to reconcile [these]  new findings about the 
mechanisms of inheritance with evolution through natural  selection.”  70 That 
is, they accepted as dogma that anything learned about  heredity had to “
buttress and extend evolution theory,” not undermine it.  71  They did not think 
to use these findings from Mendel to determine if  evolution in accordance with 
the fossil record had happened, for in their minds  this was an already 
answered question; the only point of inquiry left was  how.  So they focused all 
their efforts on mutation 72 rather than on what  the world’s hereditary matter 
would presently have to look like if it had been  the result of naturally 
selected genes acquired in a specific order dictated by  the fossil record. 
 
This attitude of always having “to reconcile new findings about the  
mechanisms of inheritance with evolution through natural selection” 73 still  
persists.  When confronted with the fact that naturally selected gene  variants in 
accordance with the succession of traits presumed from the fossil  record could 
not have caused the presently observed set of  the world’s  genomes, biologists 
still insist that evolution in accordance with the fossil  record happened. 
Yet in their effort to preserve this one fundamental component  on which Darwin 
relied, they have done away with the other, that is, observable  contrasting 
traits within populations.  By taking population genetics out  of  evolution 
and replacing it with comparisons of switches across species,  they are 
changing heredity from an empirical science based on observed  differences between 
parents and offspring 74 to a complete abstraction, where  observed differences 
between  parents and offspring are no longer the  issue. 75   Ironically, this 
gutting of the empirical nature of the  study of heredity may prove just as 
deficient in producing a genome segmented in  accordance with the succession of 
traits shown in the fossil record as has the  current focus on population 
genetics.  Biologists will have to recognize  that deficiency to answer the 
origin of species question.

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