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EVOLUTION
A THIRD WAY?
Maria B. O’Hare
(PhD)
Eugene Koonin
(evolutionary & computational biologist):
. “The edifice of the Modern Synthesis has
crumbled, apparently, beyond repair”
(Koonin E.V. 2009)
WHY WE NEED A THIRD WAY
As Professor Denis Noble (eminent
physiologist) states:
[…] all the central
assumptions of the
Modern Synthesis (often
also called NeoDarwinism) have been
disproven. Moreover, they
have been disproven in
ways that raise the
tantalising prospect of a
totally new synthesis […]
AND THE TANTALISING NEW SYNTHESIS IS UPON US....
And the conceptual changes and magnitude of this tantalizing new synthesis is perhaps best
summarized by Prof. James A. Shapiro in the following statement:
“The conceptual changes in biology are comparable in magnitude to the
transition from classical physics to relativistic and quantum physics”. (3)
(Shapiro 1997) The Boston Review Feb/March 1997 'A Third Way’. *
Note that the title of this book is inspired by the title of Shapiro’s articles & sentiments therein.
AND IT’S QUANTUM...
QUANTUM BUTTERFLY EFFECT AS APPLIED TO
EVOLUTION
A science paper entitled: Complexity in biology. Exceeding the limits of
reductionism and determinism using complexity theory, by Fulvio Mazzocchi
(2008), states the following:
[Complex systems] might show regular and predictable
behaviour, but they can undergo sudden massive …
changes in response to what seem like minor
modifications. The metaphor of the ‘butterfly effect'—
whereby a single butterfly beating its wings can cause a
storm—describes, for example, the dependence of a
complex system on its initial conditions.
QUANTUM BUTTERFLY EFFECT IN EVOLUTION
CREATES SHAPES WE SEE ALL AROUND US
Sir D'Arcy Wentworth
Thompson (1860 –1948)
Scottish. A pioneering
mathematical biologist
‘On Growth and Form’ (1917)
MORPHOGENESIS
How natural growth & form
patterns and forces of natural
self-organization of
molecules/chemical/electrical
can shape the species during
development & this is applied
to understanding
EVOLUTIONARY development –
how species evolved.
Dürer's study of human proportions
E.g.. A scull being
formed during
development within a
morphogenetic field
(invisible like magnetic
field exerting forces on
growth & form)
MORPHOGENESIS –
A small change during development
& therefore evolution, will result in
scaled up proportions of that form.
The end result can be very profound,
but underlain by simple principles of
growth & form.
QUANTUM EVOLUTION: complex
theory in physics = Butterfly effect
(sensitive initial condition =
COMPLEX outcomes because of the
interacting parts.
Perhaps better known
for his pioneering
code cracking
abilities during World
War II, in his
publication entitled:
‘The Chemical Basis
of Morphogenesis’
he explores the
natural equations of
biological complexity
giving simple answers
to seemingly
mindboggling
variation in nature.
A. M. TURING (1952)
Stuart Alan Kauffman (1939 -) is an American theoretical
biologist and complex systems researcher who studies the
origin of life on Earth.
SELF-ORGANIZATION OF COMPLEX SYSTEMS
The Origins of Order: Self-Organization and Selection in
Evolution
In 1971, Kauffman proposed the self-organized [...]
arguing that the complexity of biological systems and
organisms might result as much from self-organization
and far-from-equilibrium dynamics as from Darwinian
natural selection[...] His hypotheses stating that cell
types are attractors of such networks, and that genetic
regulatory networks are "critical", have found
experimental support
SELF-ORGANIZATION OF COMPLEX SYSTEMS
PHYSICS: SCALING LAWS & FRACTAL-LIKE NETWORKS ARE FUNDAMENTALLY THE
SAME AT EVERY SCALE OF LIFE – NETWORKS FOLLOW PREDICTABLE GROWTH
PATTERNS (CELLS TO THE INTERNET TO THE UNIVERSE)– SELF SIMILAR SCALES OF
COMPLEXITY
The Internet
By following these predictable growth patterns, we can get an
insight into how evolution unfolded & how species evolved & it’s
all about the efficiency of the network – that is why they are
predictable – because nature is highly efficient, but it also
learned how to evolve via self-organizing prinicples
Hebbian’s Law:
“Cells that fire
together wire
together”
– cells that fire out of sync, lose their link”
as a recent neural study demonstrates in
real time
CELLS COMMUNICATE...
ALL ANIMALS & PLANTS ARE A WELL COORDINATED COLONY OF
CELLS THAT HAVE LEARNED HOW TO EVOLVE BY
COMMUNICATING AT A CELLULAR LEVEL
Learning to evolve: everything scales
according to mass & metabolic rate,
revealing the level of its evolutionary
complexity
A elephant is just a shrunken MOUSE
Their metabolic systems are the
same on a different scale....
Dr. Geoffrey West is a physicist working with
a team of biologists at Los Alamos National
Laboratory
IT’S JUST ALL A MATTER OF SCALE.... A MOUSE IS NOT THAT DIFFERENT TO AN
ELEPHANT
IT’S JUST ALL A MATTER OF SCALE.... A MOUSE IS NOT THAT DIFFERENT TO AN
ELEPHANT
I believe that West sums the situation up best in his
statement below.as noted in an article in the New York
Times entitled: Of Mice and Elephants: a Matter of Scale
By GEORGE JOHNSON
Published: January 12, 1999
Dr. West liked to joke that if Galileo had
been a biologist, he would have written
volumes cataloging how objects of different
shapes fall from the Leaning Tower of Pisa
at slightly different velocities. He would not
have seen through the distracting details to
the underlying truth: if you ignore air
resistance, all objects fall at the same rate
regardless of their weight.
SELF-ORGANIZING COMPLEX SYSTEMS (AMOEBAS TO
ANTELOPES) SCALE TO PREDICTABLE EQUATIONS IN TERMS OF
THEIR METABOLIC RATE TO MASS & IT’S ALL ABOUT EFFICIENCY
As efficiency will occur
more rapidly and earlier
in more simple
organisms, it makes
sense that the more
complex biological
systems will specialize
much later.
AMOEBAS ARE EMBRYONIC-LIKE AS YET UNFORMED SPECIES
Elephants are larger
scale mice, but much
more complex biological
mammalian systems than
amoebas or fish
= Discrete & fundamental
forms of life scaled
according to the
efficiency of their
biological systems –
simple life becomes
efficient earlier than
complex forms of life
Britannica:
[...] Baer saw nature as a
whole, ...He viewed the
development of organisms
and of the cosmos in the
same light, and his allencompassing view of the
universe brought together
what might otherwise
have seemed diverging
threads in his thought.
Jane M. Oppenheimer
http://www.britannica.com/EBchecked/topic/48635/Kar
l-Ernst-Ritter-von-Baer
Karl Ernst von Baer
1792 –1876 Prussian
Founding father of embryology
‘Laws of Embryology’ (1828)
Von Baer seen: Natural Laws from the
development of an organism to evolution
of the species, the environments and the
cosmos, are following universal (whole)
principles applicable across all scales of
complexity are being confirmed empirically
by the most recent data:
EMBRYOLOGY DEVELOPMENT REFLECTS SPECIES
DEVELOPMENT – GOING FROM THE FUNDAMENTAL
(ARCHETYPE) FORM TO THE SPECIFIC SPECIES FORM
Von Baer […] maintained that the embryo of an animal
exemplified from the beginning of its gestation only the
archetype or Urform of that particular organism. “The
embryo of the vertebrate,” he asserted, “is already at the
beginning a vertebrate” (1828-1837, 1: 220). So a human
fetus, he held, would move through stages in which it
would take on the form of a generalized vertebrate, a
generalized mammal, a generalized primate, and finally a
particular human being. The form of the growing fetus
moved from the general to the specific. The human
embryo, in its early stages, therefore, never assumed the
mature form of an invertebrate or of a fish.
http://publishing.cdlib.org/ucpressebooks/view?docId=ft5290063h&chunk.
id=d0e2212&toc.id=d0e2205&brand=ucpress
Not to be confused with Recapitulation theory.
Recapitulation theory ='ontogeny repeats phylogeny' i.e. development of the animal
repeats the evolutionary history of the animal.
Darwin did not agree with this recapitulalion idea of a literal way of seeing
descent & it has since been disproven. But, Von Baer’s less literal common
descent idea was somehow misunderstood and formed the basis of
Darwinian biometrics (trying to establish via measurements of metabolic rate
etc the commonalities between animals). As this became a linear approach of
reductionist thinking and not whole system thinking, they seemed to have lost
the fundamentals of early researcher’s much overarching approach.
OLD LINEAR IDEA OF HOMOLOGY – FIN TO FOOT = DIRECT
COMMON DESCENT - DIRECT ANCESTRAL FEATURES:
People had missed the profoundly different principles proposed by Karl Ernst von
Baer
‘Laws of Embryology’ (1828) way before ‘Origin of Species’
Darwin agreed with Von Baer’s principles. However, the fundamentals
are distinctly different from our current thinking:
Darwin went with a popular idea of his own time: HOMOLOGY = change in
a body form could only come about as one species gave rise directly to
another and split in a branching manner into distinct lineages of species.
Von Baer’s laws = Seen descent (life had many origins) and a change in
the body form came about via environmental factors & natural laws
helping to shape and form an organism – Going from an archetypal form
(shared form driven by function) towards species specialism & diversity ,
from generalist to specialist as mirrored in their developmental process –
The more general characters of a large group appear earlier in the
embryo than the more special characters.
From the most general forms the less general are developed, and so on,
until finally the most special arises.
VON BAER’S CORRECTION OF DARWIN’S
ASSUMPTIONS...

Apparently, Darwin wrote several times that Von
Baer believed in a common ancestor hypothesis,
however, apparently, Von Baer had to correct him
on this issue. & point to the fact that his
embryological laws show at least four distinct
origins of life. Furthermore, he reminded him that
ancestral feature s could be shaped via geography
(environment) making them distinct species and
that all embryos went through a generalist stage to
the specialist - not literal descent as Darwin &
others had come to see evolution. Most recent
evidence confirms Von Baer’s laws.
DIVERGENCES FROM A COMMON ANCESTRAL
CONDITION – NOT SEQUENTIAL EVOLUTION –
2009 STUDY CONFIRMS VON BAER’S IDEA OF
EVOLUTION
“Rather than thinking of the common ancestor of all amniotes
as a stem reptile, which implies reptilian structures in the
brain as well as elsewhere, it is correct to think of the
common ancestor as a stem amniote. Some of the most
salient features of the brains of sauropsids (reptiles and
birds) and those of mammals represent divergences from
the common ancestral condition rather than sequential
evolution of either the extant mammalian or sauropsidian
condition to the other”.


Evolution of Vertebrate Brains
A B Butler, George Mason University, Fairfax, VA, USA 2009
OUR STANDARD MODEL IS NOT BEING SUPPORTED BY RECENT MOLECULAR
DATA


(2008) entitled: A Fundamentally New Perspective on the Origin and Evolution of Life by Shi V. Liu (Eagle
Institute of Molecular Medicine) in which the most fundamental flaw within the Darwinian model of
evolution by common descent, is highlighted in the following:
"Darwin’s hypothesis that all extant life forms are descendants of
a last common ancestor cell and diversification of life forms
results from gradual mutation plus natural selection represents a
mainstream view that has influenced biology and even society for
over a century. However, this Darwinian view on life is contradicted
by many observations and lacks a plausible physico-chemical
explanation. Strong evidence suggests that the common ancestor
cell hypothesis is the most fundamental flaw of Darwinism…”

MANY ORIGINS – LIFE IS A WEB
THE GREAT WEB OF LIFE


“At the macro-scale life appears to have had
many origins. The base of the universal tree of
life appears not to have been a single root, but
was instead a network of inextricably
intertwined multiple branches deriving from
many, perhaps 100 or more, genetic sources”
(M. Gordon et al. 1999 The Concept of Monophyly: A Speculative Essay, Biology and
Philosophy, p. 335).
Woese (1998) states the following in another science paper
entitled: The universal ancestor:
“The universal ancestor is not an entity, not
a thing. It is a process characteristic of a
particular evolutionary stage”
VON BAER & OTHERS THOUGHT THAT THE ORIGINS OF LIFE MAY HAVE HAD
MORE THAN ONE ORIGIN... IT SEEMS HE WAS CORRECT.
NOW MOLECULAR EVIDENCE & MICROBIAL BIOLOGY CONFIRMS DIRECT GENETIC
TRANSFER VIA HGT (HORIZONTAL GENE TRANSFER)
THE MICROBIAL WORLD IS FULL OF GENETIC EXCHANGE AND WHOLE GENOME
MIXING (SYMBIOSIS). (SEE PROF. LYNN MARGULIS’ RESEARCH). THIS IS RIFE
THROUGHOUT THE EARLIER AND SIMPLE WORLD OF MICROBES AND WAS THE
CAUSE OF GREAT DIVERSITY & COMPLEXITY THAT WAS TO COME AFTER MAKING
OUR EVOLUTIONARY TREE A GREAT WEB OF LIFE. THE GENETIC CAUSE IS HGT
(HORIZONTAL GENE TRANSFER) AS IT IS NOT LIKE NORMAL TRANSFER OF GENES
THROUGH BREEDING, BUT RATHER DIRECT BETWEEN ENTIRELY DISTINCT DOMAINS
OF LIFE AND EVEN BETWEEN COMPLETELY DISTINCT SPECIES. THIS HAS
IMPLICATIONS FOR THE GREAT WEB OF LIFE AMONGST MORE COMPLEX LEVELS OF
LIFE BEYOND THE MICROBIAL WORLD. IT OF COURSE HAS IMPLICATIONS FOR OUR
EVOLUTION AS WELL.
E.G. COWS HAVE SNAKE DNA SEQUENCES – DOESN'T SEEM LIKELY HERE – SO WHAT
COULD EXPLAIN THIS?
NATIONAL GEOGRAPHIC (2013)
How a quarter of the cow genome came from snakes
And cows & snakes didn’t even have to hybridize – it’s all to
do with jumping genes (Horizontal gene transfer) & it’s more
direct
NATIONAL GEOGRAPHIC (2013)
How a quarter of the cow genome came from snakes



Genomes are often described as recipe books for living things. If that’s the
case, many of them badly need an editor. For example, around half of the
human genome is made up of bits of DNA that have copied themselves and
jumped around, creating vast tracts of repetitive sequences. The same is true
for the cow genome, where one particular piece of DNA, known as BovB, has
run amok. It’s there in its thousands. Around a quarter of a cow’s DNA is made
of BovB sequences or their descendants.
... If you draw BovB’s family tree, it looks like you’ve entered a bizarre parallel
universe where cows are more closely related to snakes than to elephants,
and where one gecko is more closely related to horses than to other lizards.
This is because BovB isn’t neatly passed down from parent to offspring, as
most pieces of animal DNA are. This jumping gene not only hops around
genomes, but between them.
by Keith Oliver & Wayne Greene in Australasian Science (2009) entitled: Jumping genes drive evolution:
Orthodox evolutionary theory does not tally with the fossil
record, but a new school of thought points towards ’jumping
genes‘ as essential agents of periodic changes in the rate of
evolution […]
These rapid bursts of evolution can happen when a new type
of jumping gene is suddenly transferred into a lineage from
some other lineage, or when a new type of jumping gene
naturally emerges from within a genome. Jumping gene
activity
JUMPING GENES (MOBILE GENETIC ELEMENTS OR TRANSPOSABLE ELEMENTS-TE),
GO BETWEEN SPECIES – THEY CREATE THE DIVERSITY OF LIFE – THE DRIVERS OF
EVOLUTION - MACRO EVOLUTION IN ACTION. THEY ALSO REMODEL YOUR GENOME
WHEN THEY ARE INSIDE
Way back in the 1940s Mc Clintock discovered jumping
genes, & demonstrated their importance for evolution –
confirmed independently in 1970s, but it wasn’t until the
1980s that she was awarded her Noble Prize in Genetics
HUMANS HAVE LOTS OF JUMPING
GENE JUNK – TELLS YOU
SOMETHING ABOUT OUR RATHER
CONVOLUTED EVOLUTION
(2002) entitled: Transposable Elements and Eukaryotic Complexity by Nathan J. Bowen and I. King Jordan (complex cellular
life making up plants and animals are Eukaryotes)
Eukaryotic transposable elements are ubiquitous and
widespread mobile genetic entities. These elements
often make up a substantial fraction of the host
genomes in which they reside. For example,
approximately 1/2 of the human genome was
recently shown to consist of transposable element
sequences. There is a growing body of evidence that
demonstrates that transposable elements have been
major players in genome evolution.
Jumping Genes versus Epigenetics: The Real Drivers of Evolution (2012 –
Jon Lieff, M.D.)
Epigenetic mechanisms are not only critical for the
entire transcription process and structure, but they
stimulate more jumping genes. These epigenetic
processes slow the effects of these multiple jumping
genes to a gradual effect. Epigenetic processes can
allow for dramatic restructuring and self-engineering of
eukaryote cells.
[...]
Interrelated Epigenetic mechanisms and Jumping Genes
Increasingly, these two processes, that is, TE’s and the
elaborate epigenetic mechanisms, have evolved
together in animal and plant lines. There is a question
now as to whether epigenetics is primarily concerned
with controlling the vast amount of jumping genes, more
than half of the DNA in humans.
EPIGENETICS (MEANING ABOVE THE GENES) IS
ANOTHER DIMENSION IN OUR
ENVIRONMENTALLY DRIVEN EVOLUTION.
ENVIRONMENT CAN TRIGGER THESE JUMPING
GENES (TRANSPOSABLE ELEMENTS) INTO
ACTION, BUT THE GOOD NEWS IS THAT
EPIGENETICS CONTROL THESE JUMPING GENES
FROM GETTING OUT OF HAND. ALL THE BIG
EVOLUTIONARY EPIGENETIC REMODELING OF
GENOMES ARE OVER THESE DAYS –
EPIGENETICS/JUMPING GENES JUST OPERATE
TO KEEP EVERYTHING FINE-TUNED &
CONTINUALLY ADAPTED AT A MICRO-SCALE
So if you wondered where this genetic novelity and
mechanism came from to create such diversity,
you may be beginning to understand. But the plot
thickens and our family tree looks even more weblike when you bring HYBRIDIZATION into the
question. Yes, our hidden (so-called junk DNA and
non-coding regions of the genome) also confirm
hybridization as a means of large and rapid
speciation in the evolutionary past.
HYBRIDIZATION AS A MEANS OF MACROSPECIATION
Maybe not as radical as this, but
back in the old days when
evolution was a whole lot more
experimental – as the fossil
record shows, things trans –
MUTATED more dramatically than
today’s cross-breeds
zonkies and grolar bears
 So, now you've heard of a zonkey... but
what about a wholpin?
 These pictures show some of the
world's strangest animal crosses.
 It emerged today that an extremely rare
zonkey - a cross between a zebra and a
donkey - was born at a Mexican zoo.
 But its not the only hybrid animal. These
pictures show a wholpin, which is a
cross between a whale and a dolphin.
 And what about a liger? These cute
creatures are hybrids of lions and tigers.
 Perhaps one of the funniest named
crosses is a grolar bear, a cross
between a grizzly bear and a polar bear.
EVOLUTIONARY IDEAS GO QUANTUM
Again, earlier alternative evolutionary thought were proposed as part of
developmental studies which suggested from their empirical studies &
observations, that large (macro-changes) in species could explain the
fossil record & evolutionary/developmental processes. One man in
particular, stands out: Hugo De Vries who was the founder of what became
known as: Mutation Theory , which didn’t mean genetic mistakes as it does
today. Mutation theory was taken to mean large global changes in the
species. Combined with the environmental drivers of evolution,
morphogenesis these older schools of thought were becoming very
dynamic and seen evolution as anything but slow and gradual. Indeed,
genetics was also coming into play and HYBRIDIZATION studies were taken
seriously as a means of large and rapid change.
HYBRIDIZATION/EMBRYOLOGY & ENVIRONMENTAL DRIVERS OF
EVOLUTION, WERE ALL IMPORTANT ASPECT S OF DE VRIES’ MUTATION
THEORY & OTHERS OF THE LATE 19TH & EARLY 20TH CENTURY
SALTATION EVOLUTION (LEAPS OF COMPLEXITY)
Hugo De Vries
1848-1935
Dutch biologist
Known best for being one of the 1st
geneticists. Developed mutation theory &
rediscovered laws of inheritance in 1890s
HYBRIDIZATION
AS A MEANS OF
MACROEVOLUTION,
SPECIATION
New York Times by Sean B. Carroll (2010) entitled: Hybrids May Thrive
Where Parents Fear to Tread), it seems that we are included in this evolutionary
speciation of hybridization:
DNA analysis is now allowing biologists to
better decipher the histories of species and to
detect past hybridisation events that have
contributed new genes and capabilities to
various kinds of organisms including, it now
appears, ourselves [...]
The discovery of hybrid species and the
detection of past hybridizations are forcing
biologists to reshape their picture of species as
independent units. The barriers between species
are not necessarily vast, unbridgeable chasms;
sometimes they get crossed with marvelous
results.
DESCENT VIA HYBRIDIZATION & HGT
(HORIZONTAL GENE TRANSFER)? & OTHER WAYS
OF EXCHANGING GENES?
In a paper published in the Proceedings of the National Academy of Sciences (PNAS), a team
led by Michael Hammer, an associate professor and research scientist with the University of
Arizona's Arizona Research Labs, provides evidence that:
“’Anatomically modern humans were not so unique that they
remained separate. We found evidence for hybridisation between
modern humans and archaic forms in Africa. It looks like our lineage
has always exchanged genes with their more morphologically diverged
neighbors […] We think there were probably thousands of interbreeding
events’, Hammer said. ‘It happened relatively extensively and regularly
[…] anatomically modern humans were not so unique that they
remained separate’, he added. ‘They have always exchanged genes with
their more morphologically diverged neighbors. This is quite common in
nature, and it turns out we're not so unusual after all’.”
HUMAN HYBRIDS EVERYWHERE - AT LEAST
MORE SO IN THE PAST
Anatomically modern humans
interbred with more archaic
hominin forms while in Africa
(2011) ….
Modern reconstruction of Neanderthal
– Look familiar?
Jean-Baptiste Lamarck who, in 1809, the
same year as Darwin’s birth, “published
Philosophie zoologique, the first
comprehensive and systematic theory of
biological evolution.” (Snait et al 2011)).
ANOTHER WHO SEEN HYBRIDIZATION AS A MEANS OF SPECIATION
HE ALSO BELIEVED IN A LESS SIMPLISTIC & LINEAR FORM OF DESCENT AND THAT
EVOLUTION WENT FROM THE GENERAL FUNDAMENTAL FORMS, LIKE VON BAER,
TOWARDS A MORE SPECIALISED SPECIES FORM DUE TO ENVIRONMENTAL
SCULPTING OF THE ORGANISMS PARTICULARLY WHEN THEIR FLUIDS WERE LESS
FIXED – THIS IS NOW KNOWN IN MOLECULAR TERMS AS EPIGENETIC EVOLUTION
For example, below are Darwin’s own views of Lamarck’s most
comprehensive theory within a later addition of ‘Origins’ dated to 1861:
Lamarck was the first man whose conclusions on
this subject excited much attention. This justly-celebrated naturalist first published
his views in 1801, and he much enlarged them in 1809 in his 'Philosophie
Zoologique,' and subsequently, in 1815, in his Introduction to his 'Hist, Nat. des
Animaux sans Vertèbres.' In these works he upholds the doctrine that all species,
including man, are descended from other species. He first did the eminent service
of arousing attention to the probability of all change in the organic as well as in the
inorganic world being the result of law, and not of miraculous interposition….
DARWIN DID NOT DISAGREE WITH LAMARCKIAN PRINCPLES OF EVOLUTION WHERE ENVIRONMENT WAS
THE MAIN DRIVER OF EVOLUTIONARY CHANGE – DARWIN, IN LATER CORRESPONDENCE WISHES HE HAD
SEEN THE IMPORTANCE OF ENVIRONMENT A LOT SOONER & NOT MADE NATURAL SELECTION THE MOST
IMPORTANT DRIVER OF CHANGE.
Professor Denis Noble’s endorsement of a scientific collection of papers on Lamarck and the
field of epigenetics entitled: ‘Transformations of Lamarckism From Subtle Fluids to Molecular
Biology’: Noble states the following:
DNA methalation acting on the genes
“This book is long overdue. Lamarck and Lamarckian
ideas were not only ignored but actively ridiculed
during the second half of the 20th century. As the
subtitle of this book indicates, some of the most
cogent reasons for reassessing those ideas come
from within the citadel of molecular biology itself“
(Noble 2011)
Lamarck seen that a species could become specialized/perfectly adapted to
its environment according to its own level of complexity and what it was
exposed to environmentally. The greater the upheaval in the environment or
lack of resources and other pressures: the more an organism was forced to
adapt.
Indeed, how epigenetics processes are molecular processes working above
the GENES and operates by expressing those genes (turning them on or off)
and during development & the evolutionary past, when species were less
fixed and still developing, this mechanism appears to have had a profound
effect on the course evolution took. The DNA itself isn’t changed, just how it is
expressed and these changes can be inherited as markers or tags. This has
massive implications for how we evolved in response to our environments.
SALTATIONIST (LEAPS) EVOLUTION TAKES A QUANTUM LEAP & IS
EPIGENETICALLY CONTROLLED BY THE CELLS & THEIR
ENVIRONMENT
Jumping Genes are environmentally triggered and
cause rapid and profound changes (genome
remodeling). EPIGENETICS = LAMARKIAN
EVOLUTIONARY THEORY, working above the genes &
epigenetics ultimately controls JUMPING GENES
(transposable elements that move between species &
within the genome).

: ‘Transgenerational Epigenetic Inheritance: Prevalence, Mechanisms, and Implications
for the Study of Heredity and Evolution’ by Eva Jablonka and Gal Raz in the Quarterly
Review of Biology (2009),
…denied by the “Modern Synthesis” version of evolutionary theory, which
states that variations are blind, are genetic (nucleic acid‐based), and that
saltational events do not significantly contribute to evolutionary change [ref].
The epigenetic perspective challenges all these assumptions, and it seems that
a new extended theory, informed by developmental studies and epigenetic
inheritance, and incorporating Darwinian, Lamarckian, and saltational
frameworks, is going to replace the Modern Synthesis version of evolution
[ref]. We believe, therefore, that the impact of epigenetics and epigenetic
inheritance on evolutionary theory and the philosophy of biology will be
profound.
* I think they mean Darwin’s old idea that did not rule out Lamarckian principles
along with the more traditional idea of selection (but that’s a story for another time).
Lamarckian principles of
inheritance of acquired
characteristics and
environment as drivers of
change in the species &
therefore evolution, is
causing an EPIGENTIC
EVOLUTIONARY
REVOLUTION –
EPIGENETICS ACT AS SWITCHES FOR GENE EXPRESSION (TURNING GENES ON OR
OFF) ACCORDING TO ENVIRONMENTAL CUES & EXPERIENCE WITHOUT CHANGING
THE DNA SEQUENCE
E.G. WE SHARE 99% OF OUR GENETICS
WITH THE HUMBLE HOUSE MOUSE
SPOT THE DIFFERENCE ....
– YES IT’S ALL TO DO WITH THOSE JUMPING GENES, IN
YOUR GENOME & BETWEEN ALL LIFE & EPIGENETIC: IT
DEPENDS UPON WHICH GENES WERE SWITCHED ON OR
OFF, WHEN & IN WHAT ORDER & WHAT YOUR
ENVIRONMENT WAS DURING YOUR EVOLUTION PAST.
THAT MAKES A RATHER BIG DIFFERENCE IN THE END.
& ONLY ONE OF THEM INVENTED THE MOUSE
THE Epigenetic CATERPILLAR AND THE
BUTTERFLY:
ONE Genome - TWO
Structures
When the caterpillar changes
into a butterfly, its genome –
its basic genetic sequence –
does not change. The
differences between its two
forms result from turning on
and off different genes.
These changes in GENE
EXPRESSION (turning a gene
on) and GENE SILENCING
(turning a gene off), which do
not change the underlying
DNA sequence, are
collectively referred to as
EPIGENETICS.
Same genes: same species. The
Difference is in how these genes are
expressed (turned on or off) It’s hidden in
the epigenome
THE EPIGENETIC CATERPILLAR BECOMES A QUANTUM BUTTERFLY VIA
JUMPING GENES & AN ADAPTIVE EVOLUTIONARY MECHANISM WHICH IS
SENSITIVE TO INITIAL CONDITIONS – THE EARLIER AND MORE PRIMITIVE
FORMS OF LIFE, ARE THE MOST ADAPTABLE (SMALL CHANGE AT THE
BEGINNING OF EVOLUTION HAS A LARGE OUTCOME IN THE END). ONCE
SPECIES FORMED AS GENERALISTS (SLUG-LIKE EMBRYOS), IT WAS JUST A
MATTER OF TIME – WHEN CONDITIONS WERE RIGHT, TO EXPRESS ALL
THEY HAD ACCUMULATED AND LEARNED ALONG THE WAY AND LEARN TO
BECOME A SPECIALIST (A DEFINABLE SPECIES) SELF-ORGANIZING
SYSTEMS THAT BECOME EFFICIENT AND STABILIZE – THE MORE
PRIMITIVE (SIMPLER SYSTEMS) STABILIZE THE SOONEST. NOW ALL
SPECIES ARE SPECIALIZED & REFLECT THEIR MODE OF EVOLUTION IN
THE PAST IN THEIR CURRENT MODE TODAY.
CONTROLLED EXPRESSION OF MILLIONS OF
GENE SWITCHES HIDDEN IN THE GENOME

. Another aspect of epigenetic processes during
development/evolution that is environmentally
driven, is the Hox genes, which act like master
switches for existing genes. So do bear in mind
that hybridization/HGT & other means of causing
large genetic novelty and change is controlled
ultimately by their environments via EPIGENETIC
processes. Remember: the DNA sequence doesn’t
change, but genetic expression does according to
environmental cues. This can be at a cellular level
as well during development MORPHOGENESIS
SO THIS BEGINS TO GIVE US CLUES TO HOW SPECIES
MAY HAVE ACTUALLY EVOLVED & GONE FROM THE
GENERALIST ARCHETYPES TO SPECIALIZED & HIGHLY
ADAPTED SPECIES

Is there an alternative to the walking fish
hypothesis?
A fish has fins, it doesn’t need
feet as fins are a perfect
adaptation to water not land.
TETRAPODS (WALKING VERTEBRATES) DIDN‘T
EVOLVE DIRECTLY FROM ANCESTRAL FISHYPOD
Science article (2014 )How the genetic blueprints for
limbs came from fish
[...] the transitional path between fin structural elements
in fish and limbs in tetrapods remains elusive. Both fish and
land animals possess clusters of Hoxa and Hoxd genes,
which are necessary for both fin and limb formation during
embryonic development. Scientists compared the structure
and behavior of these gene clusters in embryos from mice
and zebrafish. The researchers discovered similar 3dimensional DNA organization of the fish and mouse
clusters, which indicates that the main mechanism used to
pattern tetrapod limbs was already present in fish.
http://www.sciencedaily.com/releases/2014/01/140121183412.htm
Fin radials are not homologous to
tetrapod digits
The researchers conclude that,
although fish possess the Hox
regulatory toolkit to produce digits,
this potential is not utilized as it is in
tetrapods. Therefore, they propose that
fin radials, the bony elements of fins,
are not homologous to tetrapod digits,
although they rely in part on a shared
regulatory strategy.
http://www.sciencedaily.com/releases/2014/01/140121183412.htm
A COMMONLY SHARED IN-BUILT ADAPTATION SYSTEM -HOX
GENES
Hox genes are a shared common toolkit that actually is a highly
efficient way of doing a 3D printout of a basic vertebrate and letting
variation be expressed via an epigenetic adaptive mechanism –
Therefore it is a highly efficient way of expressing vast sequences of
genes very rapidly. From the General to the Specialist where the
mechanism is in place to refine (sculpt) an organism ever adapting it to
its particular environmental niche. Hox genetic master switches
(activated during development) all animals have an inbuilt SOS system
(jumping genes) to accelerate adaptation if need be, as well as
explaining how something as dramatic as how a snake lost its legs, or
a caterpillar doesn’t express its flying insect form until the time is right
scales of complexity: the caterpillar is a primitive generalist organism
and can even become a specialized species given enough time – but
metamorphosis is a rather quick & efficient way of changing one
species into another

EVO-DEVO = EVOLUTIONARY DEVELOPMENTAL BIOLOGISTS ARE RE-DISCOVERING
THEIR FOUNDING PRINCIPLES OF MUTATION/SALTATIONIST THEORY &
MORPHOGENESIS, BUT NOT HAVE REALIZED THE PROFOUND IMPLICATIONS OF
REINTRODUCING LAMARCKIAN PRINCIPALS

Homology is an important aspect of EVO-DEVO principles, meaning the Hox
genes which all animals have as a means of modification: a common toolkit
as noted by Gilbert (2000). Most EVO-DEVO biologists will accept
Waddingtons theoretical Epigenetic landscapes (canalization), meaning
that during embryological development – a small change at the beginning
can have a rather complex outcome in a certain direction, given its sensitive
initial conditions (just like complex systems physics principles). He also
proposed (back in the 1940s) that epigenesis = epigenetics, where the
former stage of embryological development was effected by the immediate
cellular environment. Evo-DEVO biologists are returning to more overt
Lamarckian /epigenetic principles in more recent times as they begin to
recognize the importance of environment beyond the developmental stages
of organisms/species
SPOT THE WALKING FISH
THE PRE-CAMBRIAN PERIOD BEFORE BIOLOGY’S BIG BANG DATING TO MORE THAN
HALF A BILLION YEARS AGO IS FULL OF LARVAL/EMBRYO-LIKE ANIMALS
BUT AMOEBA-LIKE ORGANISMS WENT THROUGH A LARVAE STAGE TO
METAMORPHOSIS – EVEN FISH AS MOLECULAR STUDIES HAVE REACTIVATED THIS
MEANS OF RAPID AND PROFOUND DEVELOPMENT IN MODERN FISH
NO TRANSITIONAL FISH TO TETRAPOD FOSSILS TO BE FOUND OR
ANY OTHER TRANSITIONS – REALLY, WHEN YOU LOOK CLOSELY
AT FOSSIL RECORD

FISH NEVER had the skeletal frame and girdle to
support a body on limbs, never mind evolving
special air breathing lungs etc - but
metamorphosis (which has been reactivated in
fish IN RECENT STUDIES), would get a tadpole
(fishy creature) onto land if it hadn’t have become
a specialist fish – limited by its metabolic rate –
other tadpole-like chordates had a more
sophisticated metabolism & made it unto land -
ALL THREE HAVE THINGS IN
COMMON
1.
2.
3.
WARM BLOODED
GIVE BIRTH TO LIVE YOUNG
BREATH AIR
DIFFERENCE:
TWO ARE HUNDREDS OF MILLIONS OF
YEARS OLDER THAN OUR MODERN
DOLPHIN& OUR DOLPHIN IS CLASSED
AS A MAMMAL BECAUSE IT IS WARM
BLOODED, GIVES BIRTH TO LIVE
YOUNG & BREATHS AIR. THE OTHER
TWO, APART FROM HAVING POINTIER
NOSES & SLIGHTLY DIFFERENT
DORSAL FINS ETC, ARE CLASSED AS
MARINE REPTILES, FOR NO OTHER
REASON THAN THEY EMERGE IN THE
FOSSIL RECORD TOO EARLY TO CALL
THEM MAMMALS –
DID OUR DOLPHINS SPECIALIZE FROM
PRIMITIVE MARINE ‘REPTILES’ (THAT AREN’T
ACTUALLY REPTILES)?
THE FOSSIL RECORD CLEARLY SHOWS
PRIMITIVE FEATURES FOR ALL MARINE
MAMMALS – COULD THIS ANSWER THE STICKY
QUESTION OF WALKING WHOLPHINS?
All of these traditional evolutionary theories are in
principle being verified by our most cutting-edge
molecular data – A new ,or not so new, synthesis
is beginning to emerge – a third way perhaps?
helping us navigate through the quagmire of
ideologically-driven biological (evolutionary)
debate.
‘
A NOT SO NEW SYNTHESIS....IS DAWNING
De-Vries’ hybridization & original genetic mutation (saltation)
underpinned by Lamarckian evolution principals, D’Arcy’s concepts of
development morphogenetic growth and its application to evolution
using simple equations and laws and principals of physics supports
in turn, Von Baer’s overarching synthesis that physics & biological life
share the same principals and can be used to explain evolution.
Specifically, Von Baer’s concept of several distinct lineages is being
supported by a re-evaluation of the fossil record from the perspective
of his laws of embryology as applied to evolution which are less literal
& simplistic than our current idea of direct common descent via
branching lineages. – from the general common ancestral
CONDITION to the specialized species and/or decent with
modification via a common epigenetic/genetic tool-kit
