John - No worries, I am not a Lamarckian true believer LOL - though I do
find the evidence for epigenetic hereditable traits to be incredibly
fascinating and thought provoking, and furthermore the fact that it does
seem to in fact occur suggests to me that it may play some, as yet, poorly
understood role in heredity. Even if it is just a supporting actor and DNA
has the leading role. just the fact that epigenetic wiring (if I can use
that metaphor) can make it across the profound generational barrier and make
the leap from one organism to its progeny is profound and amazing - IMO.

>> you need a way to separate the good acquired characteristics from the bad
(asthma is bad), and only Darwinian natural selection can do that. 
I take your point and agree. Darwinian natural selection - across many
generations -- is required in order to promote beneficial traits and
conversely to weed out those that are harmful or in some way mal-adaptive.
>From this more encompassing definition just the presence of inherited traits
is not sufficient. What is required for evolution to take place is also the
selective pressures imposed on each generation -- generation after
generation - over time promoting the viability and hence relative abundance
of individual organisms with desirable traits (according to environmental
pressures); while diminishing the proportion of individuals lacking those
traits or having other harmful mal-adaptions or mutations.

However epigenetics seems to play a vital and non-discountable role in
enabling complex living organisms to evolve and maintain their living
processes throughout the complex trajectory of life from the moment of
inception through embryogenesis and onto to maturity and then eventually to
whatever leads to death. Epigenetic mechanisms - Methylation and also
histone modification - themselves almost certainly co-evolved in life, and
the fact that it is so markedly present across so many species points to the
importance it must have for living systems. Darwinian evolution itself seems
to have selected for epigenetics.

This secondary and less irreversible - but not therefore unimportant -
coding system operates on top of the primary underlying and exquisitely
tightly packed DNA code. Most geneticists would agree, I believe, that for
most species epigenetics plays a vital role, and that absent this - still
poorly understood -- process complex life would not exist. 

By having this additional secondary encoding schema that operates on top of
the underlying DNA schema living things are able to alter that which gets
transcribed and expressed and to do so in a more stable manner than
transcription factors can alone - transcription factors choose genes for
transcriptional activation or repression by recognizing the sequence of DNA
bases in their promoter regions. This, secondary level of encoding schema
that controls the alternate expression of DNA sequences seems to be quite
prevalent. In fact, in the mammalian genome around 95% of multi-exon genes
generate alternatively spliced transcripts (Hnilicova and Stanek, 2011; Ip
et al., 2011);  this is a pretty astounding percentage of re-wiring of the
underlying DNA encoding during the process in which it is transcribed and
expressed in the resulting mRNA that then controls protein expression. 

We can all agree - I hope - that at the cellular level living things are
characterized by the proteins they produce and are made of. These proteins
themselves result from specific patterns of gene expression - encoded in the
mRNA that control the ribosome organelles protein production. Gene
expression itself is a complex and multi-phased process that ultimately
leads to the resulting mRNA. Some examples of this fast and furious
molecular activity during the transcription process are: pre-mRNA splicing,
in which introns are removed and exons joined;  chromatin remodeling, which
is the process by which tightly packed DNA is exposed for (or conversely
hidden from) the cellular transcription machinery, which is seeking to bind
to promoter sequence on coding regions of DNA.

Right from the very beginning of an organisms living trajectory, epigenetic
processes are vital, switching the underlying genetic expression on and off
in what seems to be a highly sequenced and well-orchestrated process. Life,
as we know it would not be possible without this epigenetic code dancing on
top of the code; in fact it appears that proper DNA methylation is essential
for cell differentiation and embryonic development. For example researchers
(Suzuki & Bird, 2008) have found that mice that lack a particular DNMT have
reduced methylation levels and die early in development; evidence that
epigenetics plays a vital role in the regulation of gene expression.
Researchers have also been able to determine that the DNA methylation
process tends to happen at certain specific locations within the genomes of
different species and has been shown to play a vital role in numerous
cellular processes. Furthermore it has also been shown that abnormal
patterns of methylation are statistically linked to several human diseases,
such as cancer for example.

>> It's not news that some chemicals increase the rate of mutation.

Epigenetic changes that effect what is transcribed is not mutation - at
least in the classic sense of changing - i.e. mutating - the underlying DNA.
The DNA is not mutated; the underlying sequence of bases remains unaltered.
Besides epigenetic control of genetic expression has been shown to play a
central and vital role in both embryogenesis (and when it becomes abnormal
in diseases such as cancer) 

Though I have been trying to wrap my head around this for years now; it
still boggles my mind (almost as much as Quantum Mechanic weirdness does)
and the more I research this area the more I realize how much I have yet to
learn. I believe that making the attempt to understand how life (and also
the brain and what we perceive as our own self-awareness) works - right down
to the molecular level - is one of the most promising approaches to working
backwards to underlying first principles. By, eventually/hopefully gaining a
clear understanding of how life actually works - both dynamically and in
terms of maintaining sufficiently stable (but not rigidly unchanging and
inertly dead) states and hereditary information repositories - we may gain
deep insight into what life/self-awareness etc. are and what leads to them. 

So far - it seems to me - that life dances on the knife edge between order
and chaos. Stray too far towards either chaos or order and life very quickly
stops living.




[] On Behalf Of John Clark
Sent: Saturday, August 10, 2013 7:56 AM
Subject: Re: Serious proof of why the theory of evolution is wrong


On Fri, Aug 9, 2013 at 9:43 PM, Chris de Morsella <>


> some feel Epigenetics should only refer to the actual molecular mechanisms
(such as DNA methylation and histone modification) that alter the underlying
gene expression; I find this restrictive and use epigenetics to also
describe inheritance of changes in the expression of genes. There appears to
be increasing evidence that points to epigenetic inheritance 

Yes, but that also means that epigenetic inheritance is fundamentally less
important than the traditional sort. If you don't have the gene then you
just don't have it and that's all there is to it, but if you have the gene
but it's not expressed because of one simple methyl group then one of your
sperm could lack those 4 atoms (CH3) and your offspring, or his offspring,
could inherit the fully functional complex gene even if there was no sign of
its expression in you. 

 > maternal nicotine exposure during pregnancy is linked to asthma in the
third generation in disease models. [...] 
Isn't this essentially describing a Lamarckian process?

I don't dispute the existence of epigenetic changes even if it's far less
important than Mendelian inheritance, but where is the acquired
characteristic? If exposure to nicotine led to nicotine tolerance in the
parent and the offspring then it would give some support to the inheritance
of acquired characteristics, but instead you've just got asthma. It's not
news that some chemicals increase the rate of mutation. And besides, you
need a lot more than the inheritance of acquired characteristics for
Lamarckian evolution to work, you need a way to separate the good acquired
characteristics from the bad (asthma is bad), and only Darwinian natural
selection can do that. 

  John K Clark

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