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A more modern forgotten father of epigenetics

The Forgotten Father of Epigenetics

click on image for full article
click on image for full article

A theory put forward in the 1930s by E. E. Just, embryologist and African American, shares surprising connections with our emerging understanding of development.

W. Malcolm Byrnes

Despite the strides that have been made in recent decades to increase minorities‘ involvement in science, African Americans are still significantly underrepresented in scientific disciplines. A 2010 survey, for instance, showed that blacks make up only 5 percent of the science and engineering workforce, even though they make up 13 percent of the US population. Yet diversity is important not only for fairness in representation; it is also critical for enhancing creativity in scientific discovery.

In his 1989 book Discovering, physiologist and author Robert Root-Bernstein identifies four “inputs” into the discovery process: cultural context, the established body of science, “science in the making,” and the scientist himself or herself. The individual scientist, he notes, “will represent a unique mix of hereditary proclivities and environmental experiences.” …

The rest of the article is continued via link on image

Enoy!

Press Release: Author re-writes history of ‘Natural Selection’ theory…

3D Lamarck and fish book
paper back available soon on Amazon and then all other major outlets. e-book available NOW and free e-book the Epigenetic caterpillar by clicking image for link to SMASHWORDS

PRESS RELEASE

FOR IMMEDIATE RELEASE
1 April 2015 | Galway Ireland
Please e-mail http://diggingupthefuture@gmail.com for review copies of book, bio, photos etc.

AUTHOR RE-WRITES HISTORY OF ‘NATURAL SELECTION’ THEORY –
challenging previous assumptions about how species change

Maria B. O’Hare, Author of the newly released book Lamarck and the Sad Tale of the Blind Cave-Fish re-assesses the unjust suppression & more recent scientific vindication of the ‘Original Founder of Evolution’ Jean Baptiste Lamarck who presented his theory to the world the same year that Charles Darwin was born.

O’Hare, a PhD in archaeology (freelance researcher and writer) focuses on the evidence to show that Darwin was actually a Lamarckian when it came to explaining species change such as blindness in animals finding themselves in darkened environments (blind cave-fish for example) and how these concepts are being supported by our most recent molecular understanding in biology.

The Author highlights key points in history, taken from original sources, as to how, why and when Lamarckian principles of evolution were actively suppressed and how this was driven more by opposing philosophies than a desire to understand the deeper complexities of biological evolution. O’Hare also outlines how the unnatural promotion of Neo-Darwinian selection theory, which she refers to as the genetically modified version, was far removed from the form of selection that Darwin himself had actually proposed.

“evolutionary principles became part of a dynamic view of evolutionary thought being explored within the emerging fields of molecular biology, genetics and developmental studies at the turn of the 20th century (just as the Neo-Darwinian selection theory was seriously falling out of favour). Now, in the early 21st Century, these concepts are returning from their long imposed exile and beginning to form a major tenet of a dynamic and emerging evolutionary synthesis. Lamarckian principles could be described as a form of a ‘natural correction’– synonymous with epigenetics today (meaning to go beyond the fixed coding of the genes) and at the same time, epigenetics is seriously calling into question our current model of genetically-driven evolutionary change via natural selection”.

Maria O’Hare lives in the Gaeltacht, Spiddal, Galway with her son and partner and plays Irish traditional music regularly in an around local pubs and at festivals. She has a passion for research into anything relating to science and particularly, the history and philosophy of science and has written on her blog http://diggingupthefuture.com on such subjects as well as in other books.

-ENDS-

Please share press release if you think anyone would be interested in this topic

Cheers

MariaBrigit

How the snake lost its legs – Hox genes & Epigenetics switches?

Reptile Image Gallery
Spot the difference? Is it a snake or a legless lizard?
This article will work best if you also read the “Quotes” in ‘Evolution: Will the Real Ancestor Please Stand UP’ The Free E-book version can be downloaded elsewhere – much nicer than pdf. I’ll have details soon, but contact me in the meantime if you can’t wait at: digging up the future @ gmail dot com – thanks

Before getting into how snakes may have lost their legs seemingly via Hox genes and epigenetic processes and not by Neo-Darwinian means, I’ll begin with an interesting article about legless lizards and snakes and what the difference apparently is.

The article starts with the above image and describes it as follows:: “This legless lizard (an Ophisaurus apodus) is a different beast from its slithery look-alike, the snake” The image is from Joel Sartore/National Geographic/Getty Images

Link to view the whole article here: http://animals.howstuffworks.com/snakes/legless-lizard-vs-snake.htm or below is an excerpt:

What’s the difference between a snake and a legless lizard?

by

“In early 2008, in just one month of scouring the savanna of central Brazil, scientists discovered 14 new species. One of those new species was a type of legless lizard no one knew existed. A legless lizard? Wouldn’t that be called a snake?

Nope — they’re two entirely different animals from separate evolutionary lines. Legless lizards evolved from the legged lizards with which most of us are familiar; legless snakes evolved from four-legged snakes that most of us have never seen.

But the two do look an awful lot alike. Both have long, slender, cylindrical bodies; forked tongues; scaly exteriors and can often be found slithering through sand. And then, of course, there’s the leglessness. It’s tough for the casual observer to tell them apart. It’s not impossible, though.

[…] you’re out hiking and you come across a snake-looking creature, anywhere from 10 inches (25 cm) to 4 feet (122 cm) long. It has the typical reptile coloring, tan or brown, green, bronze or yellowish, and maybe it sports a dark stripe along its back. Is it a snake or a legless lizard?”

Apparently there is a difference…
Anyway that becomes a case of semantics I believe:: “Legless lizards evolved from the legged lizards […]; legless snakes evolved from four-legged snakes”  as most of us have never seen a legless snake, and this distinction also becomes rather interesting when we actually look at the fossil record and draw on more recent molecular data to attempt to understand these creatures that once walked, whether in their serpentine or more lizard-like form. So let’s start at the beginning, a way back in the deep mists of time, when according to the Bible: “The Lord God said unto the Serpent, or maybe we won’t…
So, why did some naughty lizards lose their legs while, others did not?  I found the following article interesting in the light of what I am about to discuss in terms of snakes losing their legs via non-genetic means:
(based on Nicholas Bakalar, Snakes Evolved on Land, New Fossil Find Suggests, National Geographic, April 19, 2006)
In 2003, biologists from Argentina found a 90 million year old snake fossil in a terrestrial deposit in the Río Negro province of northern Patagonia. The snake fossil had a well-defined sacrum supporting a pelvis and functional hind legs outside of its ribcage. This snake was “made for walking.” The discovery of Najash rionegrina is consistent with the concept that snakes evolved on land and that they evolved from long-bodied lizards.
Anyway, moving on to the most recent findings and how this is beginning to be understood in rather non-Neo-Darwinian terms, I will attempt to explain how some reptiles actually may have come to lose their legs and why it certainly doesn’t appear to be via natural selection and far from gradual or genetically driven as promoted in typical mainstream articles as that outlined above. And of course, how this has major implications for our current model that proclaims that it can explain past evolutionary development and how species became species in the first place. For instance, we also have evidence of “Reversion of Limbs in Snakes” as the title of this next quote reveals, which is  both very non-biblical and un-Neo-Darwinian.:
“An interesting instance of reversion of limbs in snakes is inferred from the study of a 95-million-year-old fossil snake from the Middle East. It represents the most extreme hindlimb development seen so far in snakes. The limb consists of tibia, fibula, tarsals, metatarsals, and phalanges. The snake is nested with basal snakes, macrostomatans, which retained rudimentary hind limbs and represents a reversion to the ancestral limbed state (Tchernov et al., 2000)”
.- In Epigenetics comes of Age website dedicated to epigenetic research and developmental evolutionary biology – compiled and edited by highly credentialed biologist Nelson R. Cabej and published in the book Epigenetic Principles of Evolution (2012) link to
There are several answers to serpents losing their legs and becoming legless lizards/snake and regaining them again and becoming a non-snake or legless lizard, but I will keep it as simple as possible. 1. Environmentally-driven  habitat dependent and general influences of the environment during (evolutionary) development of the reptile-type creature. 2, Epigenetic (meaning that it is beyond/above the genes) and this causes real change and adaptation via molecular processes that don’t change the genes, only how they are expressed and 3, Saltation (jumps) evolution which is rather rapid and involves whole and large changes in an organism. (all supported by evidence presented in books relating to Lamarckian-type evolution which Charles Darwin came to support along with natural selection and even believed that in some cases Lamarckian evolution was a better explanation. Plus, the updated form of Lamarckian evolutionary principles in its updated developmental evolutionary biological and genetic form around the turn of the 20th century  see publications by O’Hare 2014 The Epigenetic caterpillar: An Alternative to the neo-Darwinian view of the Peppered Moth Phenomenon and/or Lamarck: and the Sad Tale of the Blind Cave-Fish – Spring 2015 and the quote book: But Old Mr. Darwin wasn’t to Blame: The Little Book of Evolutionary Quotes.
Yes, it doesn’t sound very Neo-Darwinian like, because it isn’t genetically driven, or gradual and slow, it is an EVO-DEVO   (short for evolutionary developmental biology with its underlying saltationist – leaps of evolutionary change) and an epigenesis/epigenetic explanation, which were fully naturalistic and testable evolutionary ideas which were heavily marginalised and suppressed by the formation of an ideologically driven form of gene-centric, selection theory – a far cry from what Darwin had ever envisaged, but is now finding full scientific validation by our most up-to-date scientific techniques and investigations as documented in the above publications by this present writer.
The updated genetic and non-genetic epigenetic explanation is given in a recent article entitled: Learn Genetics on the topic of Genetic science which should give you an idea of what I mean by genetics and then I will apply this to the studies and specific epigenetic studies relating directly to loss of limbs in serpents.
… The epigenome, on the other hand, can change rapidly in response to signals from the environment. And epigenetic changes can happen in many individuals at once. Through epigenetic inheritance, some of the experiences of the parents may pass to future generations. At the same time, the epigenome remains flexible as environmental conditions continue to change. Epigenetic inheritance may allow an organism to continually adjust its gene expression to fit its environment – without changing its DNA code. http://learn.genetics.utah.edu/content/epigenetics/inheritance/
This encapsulates what Lamarck proposed over 200 years ago in a pre-genetic age and what they were beginning to discover in developmental studies over 100 years ago and now being solidly confirmed by our most recent molecular data. In other words, the same genome/genes within the organism do not account for the rather dramatic difference in how the species looks or acts. It is epigenetics and what is going on in the epigenome that makes the difference in the end. Think of a caterpillar. Now think about its adult form – a butterfly or moth. Can you tell me what makes the difference in its dramatically distinctive form (phenotype)? Why does the adult have wings, and antenna and even spindly legs etc? If you think the difference is genetic (its genotype), then you are incorrect. The Neo-Darwinian explanation of different phenotypes: same genotype does not have an explanation for this as our current model believes that the genotype (genes) and their mutations according to selection is the cause of variation seen in the species. The answer is its epigenome that is environmentally sensitive particularly during development and depending upon the season, that causes the exact same genome of the juvenile to be expressed, epigenetically, after metamorphosis in a profoundly different way. (See The Epigenetic Caterpillar: An Alternative to the Neo-Darwinian view of the Peppered Moth Phenomenon).
The lizard  losing its limbs is no different in principle. The Neo-Darwinian explanation would say it is a genetic phenomenon, but this is fully inadequate to explain the evidence as you will see further on. On the other hand, the evidence is strongly pointing to an epigenetic explanation where, environmental-drivers during development ( and this can be easily extrapolated to evolutionary development when the species were less defined as proposed by Lamarck himself), determine the expression or degree of activation (buds of the limbs and degree of developmental expression of existing genes). In other words, the snake became an elongated  (serpentine) creature whose body got too long to be supported by legs and the hind legs remaining on some of these basal snakes (primitive forms) is probably due to a change of habit back in the mists of time (when not fully developed as a fixed and specialised species) when they began burrowing for a living and the hind legs were useful in this pursuit in giving the pushing power to burrow further as the evidence clearly indicates.

Essentially, Lamarck developed the concept of disuse or use of organs, characters and features according to environmental adaptation particularly when organisms were less defined as noted above as one of the main means of adaptive change in the species, or acquired characters as it was termed. For example, the loss of limbs in animals such as snakes and blindness in cave-fish. This is what Lamarck wrote well over 200 years ago:

“The permanent disuse of any organ imperceptibly weakens and deteriorates it, and progressively diminishes its functional capacity, until finally it disappears”.
This quote is given in Cabej’s detailed review of research on epigenetic principles of evolution as referred to above. He goes on to outline Darwin’s own views on such phenomenon as the loss of organs via disuse (note that vestigialization refers to organs/limbs becoming redundant and metazoans is a very broad term for all animal forms, even the simplest amoeba like   animals) and Cabej continues to present the evidence for loss of limbs in reptiles (snakes) as an epigenetic phenomenon and the evidence against a Neo-Darwinian genetically driven one.
“Commonly evolutionary loss of structures is not an “All-or- none” process but the end result of an orderly process of vestigialization of the part or organ. From a Darwinian view, useless organs would not be lost if they would not be disadvantageous to the species. Charles Darwin believed that natural selection was not involved in vestigialization of organs in metazoans since useless organs would not be selected for or against:Rudimentary organs, from being useless, are not regulated by natural selection, and hence are variable. (Darwin, 1872c) […]
There are about 3,000 known reptile squamates (snakes and lizards) on Earth, which have repeatedly and independently experienced limb-reduction in every major continental region […]. Limb-reduced reptile squamates have snake-like body form and may be grouped in two ecomorphs: long-tailed surface dwellers and short-tailed burrowers (Wiens et al., 2006).Loss of Tetrapod LimbsLoss of limbs has occurred in three of four tetrapod groups (amphibians, reptiles, and mammals). It represents one of the most extreme morphological changes in the history of tetrapods (Lande, 1978) and has been associated especially with elongation of the body and increase in the number of vertebrae. It is believed that the loss of limbs occurred in response to new ways of locomotion as a result of a change in the life style of tetrapods. This seems to have been the case with transition of reptiles to a burrowing life style and reptant locomotion, which made their limbs useless. The loss and reduction in size of limbs in tetrapods was thought to have been a gradual process of sequential loss of limb components in the reverse order (distal-to-proximal) of their formation during the individual development (proximal-to-distal).Latter studies, however, have shown that often evolutionary processes of body elongation, reduction of limb size, and reduction of digits, occurred almost simultaneously (Wiens and Slingluff 2001).[…]What scientifically matters in this case is the fact that certain proportions of individuals of the same genotype, under the same environmental conditions, display different phenotypes. This clearly contradicts the basic tenet of the neoDarwinian paradigm that evolution of limblessness, as any other evolutionary change, requires accumulation of favorable mutations in relevant genes. Logically, this suggests that a nongenetic mechanism is inducing the loss of limbs in this snake species.

In other words, it is non-genetic and epigenetic in nature”.

– Taken from Epigenetic Principles of Evolution (2012) link to http://www.epigeneticscomesofage.com/Chapter_16.html

To explain the mechanism for such a radical makeover from walking tetrapod to snake in one simultaneous fell-swoop, or a bit slower in some cases as the fossil snake with the hind legs shows as outlined earlier, I will review another study by Gilbert, entitled: Hox Genes: Descent with Modification, has as is title suggests, fairly profound implications for our view of how species change and indeed offers an explanation in terms an underlying set of instructions common to all organisms in various scales of complexity depending upon their fundamental form (invertebrate/vertebrate etc). Gilbert gives a very solid example of just what these Hox complexes (that act like master switches during development giving instructions to build the fundamental body plan of the animal form according to its complexity) can end up activating (genetically expressing) or not, certain genes in specific order. Gilbert gives a very interesting example of the evolutionary history of how the snake lost its legs and reiterates the fact that snakes lose their forelimbs first and also makes reference to the more derived features of some less primitive type of snakes compared to other more primitive forms in the following. Although,  I should add that Gilbert does not discuss specifically the epigenetic mechanism of Hox complexes, i.e the genes are still present, it is their expression that makes a huge difference in the end, but I’ll return to several studies below that have dealt specifically with Hox gene switches and their epigenetic control:

Both paleontological and embryological evidence supports the view that snakes first lost their forelimbs and later lost their hindlimbs [refs] Fossil snakes with hindlimbs, but no forelimbs, have been found. Moreover, while the most derived snakes (such as vipers) are completely limbless, more primitive snakes (such as boas and pythons) have pelvic girdles and rudimentary femurs. The missing forelimbs can be explained by the Hox expression pattern in the anterior portion of the snake. In most vertebrates, the forelimb forms just anterior to the most anterior expression domain of Hoxc-6 […].
– Gilbert SF. Developmental Biology. 6th edition. Sunderland (MA): Sinauer Associates; 2000. Hox Genes: Descent with Modification. Available from: http://www.ncbi.nlm.nih.gov/books/NBK9978/
More specifically, regarding the epigenetic aspect of Hox gene control during development, in an article relating to the NOVA channel: Ghosts in your genes for example:
“[…] Gene switches such as Ubx make the initial decisions of which genes to turn on or off in
different body regions and cell types. .. This highly evolved, highly orchestrated ability to make
genes active or inactive—both genetically and epigenetically—is the key to the success of
multicellular plants and animals, including the most complex and mysterious of all, us”.
An article entitled: Epigenetic temporal control of mouse Hox genes in vivo is self-explanatory in linking the Hox gene switches to epigenetic processes during development. Another science paper entitled: Epigenetic control of Hox genes during neurogenesis, development, and disease (2010) outlines some of these epigenetic mechanisms and their role in the activation of Hox genes. and the epigenetic control (environmental) of Hox switches is clearly explained in: Epigenetic regulation of vertebrate Hox genes: a dynamic equilibrium, by Soshnikova and Duboule in the abstract they state the following:
 Temporal and spatial control of Hox gene expression is essential for correct patterning of many
animals. In both Drosophila and vertebrates, Polycomb and Trithorax group complexes control
the maintenance of Hox gene expression in appropriate domains. In vertebrates, dynamic
changes in chromatin modifications are also observed during the sequential activation of Hox
genes in the embryo, suggesting that progressive epigenetic modifications could regulate collinear
gene activation.
–  Epigenetics. 2009 Nov 16;4(8):537-40. Epub 2009 Nov 21
http://www.ncbi.nlm.nih.gov/pubmed/19923920
 Another paper discusses the molecular pathways and epigenetic processes and control of Hox genes during mammalian development and states:
The outcome is profoundly influenced by the role of epigenetics through transcriptional
regulation of key developmental genes. Epigenetics refer to changes in gene expression that are
inherited through mechanisms other than the underlying DNA sequence, which control cellular
morphology and identity. It is currently well accepted that epigenetics play central roles in
regulating mammalian development and cellular differentiation by dictating cell fate decisions via
regulation of specific genes.
Among these genes are the Hox family members, which are master regulators of embryonic
development and stem cell differentiation and their mis-regulation leads to human disease and
cancer. The Hox gene discovery led to the establishment of a fundamental role for basic genetics
in development. Hox genes encode for highly conserved transcription factors from flies to
humans that organize the anterior-posterior body axis during embryogenesis. Hox gene
expression during development is tightly regulated in a spatiotemporal manner, partly by
chromatin structure and epigenetic modifications. Here, we review the impact of different
epigenetic mechanisms in development and stem cell differentiation with a clear focus on the
regulation of Hox genes.
in, Ann Anat. 2010 Sep 20;192(5):261-74. doi:
10.1016/j.aanat.2010.07.009. Epub 2010 Aug 6.
http://www.ncbi.nlm.nih.gov/pubmed/20739155

Now returning to how quickly these epigenetically controlled (expressed or not) genetic switches (Hox genes) can operate and how they relate specifically to how the snake became legless, we’ll review some of the most pertinent parts of Cabje’s epigenetic study:

[…]Pythons have no forelimbs but they develop reduced hind limbs. Anatomical transformations in python limbs have been sudden rather than gradual and are related to the progressive expansion of Hox gene expression patterns (Cohn and Tickle, 1999).

The loss of forelimbs in pythons is believed to be related to an anterior expansion of expression pattern of Hox genes. Hind limb buds are initiated in pythons but the ZPA (zone of polarizing activity) does not develop and the ectoderm does not form an AER (apical ectodermal ridge) in the region where the limb bud emerges in tetrapods, even though all the signaling genes responsible for their development are present. This is believed to be caused by changes in mesodermal Hox gene expression:

Progressive expansion of Hox gene expression domains along the body axis can account for the major morphological transitions in snake evolution. (Cohn and Tickle, 1999)

[… ] With changes in genes excluded as cause of vestigialization and loss of limbs in pythons, the remaining alternative explanation is an epigenetic regulatory mechanism. […]

Epigenetic Explanation
Genes for enzymes for RA synthesis in vertebrates have not changed. What has changed is the spatio-temporal pattern of expression of RA in limbed and in limbless tetrapods […] This change is clearly nongenetic (all the limb-inducing genes are present and functional in both limbed and limbless species).Where may be the source of the epigenetic information that is used for these adaptive changes in expression patterns of Hox and other genes involved in the development of limbs or leading to limblessness in tetrapods?[…]In the process of vertebrate limb loss and reduction are also involved mechanisms of programmed cell death, which are epigenetically regulated as well […]
The fact that no changes have occurred in genes for the programmed cell death in limb tissues of tetrapods with reduced limbs, or that have lost their limbs, unequivocally shows that the cause of the programmed cell death is not genetic. […] the programmed cell death during the individual development is epigenetically determined via signal cascades that ultimately originate in the nervous system. Hence, evolution of the programmed cell death in limbless tetrapods has to start with changes in the activity or properties of neural circuits that produce signals that activating signal cascades for the programmed cell death.
So to summarise all this rather technical jargon about loss of limbs or organs or underused parts or change in habitats particularly during the earlier stages of evolutionary development, it would seem that nature has an in-built mechanism (an underlying set of instructions) to build using the genetic instructions, but with a level of flexibility (epigenetic/molecular and ultimately environmentally driven) that many variations can be derived from depending upon the habits, needs of a developing organism. Epigenetic inheritance, or acquired characters derived from these experiences and encounters in different environments passes on via tags/markers (chemical signals more than just genetic information but) epigenetic information. The signals and cascades during development will alter the control of master switches of the larger body plan and adapt, shape and sculpt an organism to its needs. Some of this signalling is informational and will allow for cell-death to take place of budding limbs and inhibit the full formation to continue to build that limb. Indeed, it would seem that nature wastes nothing and the extension of the spine by building more vertebrate, is a redirection of resources that would have otherwise been used to build bone and digits for the limbs. Therefore, if the serpentine creature is getting on much better as a burrowing animal – then the legs (appendages) are going to get in the way a little (particularly the front ones) and the extension of the vertebrate would necessitate only hind-limbs as it is easier to learn to slither and burrow with those hind legs to help, whereas, a set of four limbs would be under a lot of strain from an elongated body.
This is an entirely different form of evolutionary thought to the one we are used to but I believe we should let science speak for itself. And perhaps Mr. Darwin’s support of Lamarck and belief that selection didn’t play a part in the disuse of organs/limbs etc means that he and Mr. Lamarck were not that far off when they believed the loss of limbs was to do with environmental adaptation. And specifically, from disuse or epigenetic processes as it is known today and indeed was understood in the framework of updated Lamarckian evolution in its saltationist less genetically driven form of the early 20th and late 19th century before its ridicule, marginalisation and downright suppression in some cases by the Neo-Darwinian movement.
Lamarckian evolutionary principles may perhaps be contrasted with the Neo-Darwinian version of selection in being randomly genetically driven evolution (natural selection in its genetically modified form) by referring to it as NATURAL CORRECTION, as epigenetic adaptation according to environmental needs and niche specialisation as the species developed (as proposed in principle by Lamarck) is actually a highly adaptive self-correcting molecular system. If a snake doesn’t need it’s legs, well nature shrinks them until they disappear or at lease become inhibited from being fully expressed. This different way of seeing evolution certainly begins to explain the fossil record more clearly and why there are truly no transitional fossils when you look closely at it. Maybe it’s time to begin re-assessing everything we thought we knew about evolution in the light of Lamarckian epigenetic principles. Just a thought. So there concludes my epic tale of how the snake lost its legs, or at least, that is what the science is strongly suggesting how it might have happened….

Lamarck! Who mentioned the ‘L’ word?

all along...
all along…

In a recent paper entitled: Transgenerational Epigenetics: Current Controversies and Debates by David Crews and Andrea C. Gore, they outline the following under the heading: History of Epigenetics (2014):

Investigators in the field of epigenetics come from one of two distinct lineages, one derived from classic genetics and the other from evolutionary biology.[…] Preformationists believed that adult features were present fully formed in the egg and simply unfolded during growth; August Weissman belonged to this group and asserted that the eggs contained all of the elements (later known as genes) to determine the phenotype that would develop. Those believing in epigenesis held that traits emerge as a consequence of the progressive interaction of the constituent parts of the zygote with the environment in which it develops. Although others such as Jean-Baptiste Lamarck and Charles Darwin were believers in epigenesis, the pivotal role of the environment in the developmental process was first demonstrated empirically by Oscar Hertwig (1894) and subsequently by Richard Woltereck (1909). p. 372

http://www.utexas.edu/research/crewslab/pdfs/Crews_Gore_Chapter_Final.pdf

And Professor Denis Noble’s statement regarding his endorsement of an important collection of papers in book form entitled: Transformations of Lamarckism From Subtle Fluids to Molecular Biology, relating to Lamarckian principles of evolution and the epigenetic inheritance of non-genetic modifications (environmentally-driven adaptations) phenomenon clearly highlights the link to Lamarck and our current understanding of molecular processes in the following:


“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. A great strength of the book is that it does not seek to reintroduce Lamarckian ideas as they were originally formulated; rather, the Lamarckian perspective is used to assess where the modern synthesis needs extending or even replacing […}”(Noble 2011)

http://mitpress.mit.edu/books/transformations-lamarckism


Below is an excerpt from an article on Science Daily entitled:

Non-genetic inheritance and changing environments

Date:
November 1, 2013
Source:
De Gruyter

“Until recently, biological information was thought to be transmitted across generations by DNA sequencing alone. Furthermore, adaptation to the environment was thought to only occur with Darwin’s mechanism of rare mutations of the DNA that are selected for the reproductive advantage that they provide. However, scientists are now paying increased attention to non-DNA factors that are inherited and can actually help offspring adapt to their environment. An article published last week in Non-Genetic Inheritance — an open access journal by Versita, brings attention to this new mode of inheritance. The authors refer to a process called Transgenerational plasticity (TGP). Plasticity is a term used to describe how an organism changes its phenotype (e.g. morphology, physiology or behaviour) to adapt to its environment. For example, some animals become more hairy when bred in cold conditions. Transgenerational plasticity refers to offspring developing the adaptations, when the parents experience the environment.”

See link for full article http://www.sciencedaily.com/releases/2013/11/131101091739.htm

Now you might notice from reading the above quote from the science article, that if you know anything about epigenetics and Lamarckian acquired characteristics – as documented many times on this blog and the fact that Lamarckian evolutionary principles in more modern parlance – EPIGENETICS is synonymous with a radical new synthesis emerging within evolutionary biology, not once do they mention the ‘L’ (Lamarckian word) or even the ‘E’ word (epigenetics) for that matter. Yet Transgenerational plasticity which is non-genetic inheritance (epigenetic markers that change the expression of the genes without changing the DNA sequence itself) which is a highly adaptive (flexible plasticity) that all organisms have in-built and acts in response to their environments, is exactly what the article is talking about. Indeed, the article on ScienceDaily website quoted above goes on to quote Eva Jablonka – a scientist who has written extensively on EPIGENETIC inheritance and species adaptability according to environment by non-genetic means. Here is what she says in the article, but note the ‘E’ word is never mentioned, probably because many scientists are now concurring that it is essentially Lamarckian evolution in action.

“Commenting on the surveys, Eva Jablonka from The Cohn Institute for the History and Philosophy of Science and Ideas, at Tel Aviv University, says: “This excellent review raises pertinent questions about the adaptability of organisms and opens up important research questions. It is a vital contribution to our understanding on how organisms adapt to changing conditions, and I agree with the authors that trans-generational plasticity has to be considered if we are to predict the response of organisms to such conditions, an issue that seems to be of particular significance today.”

Please watch the short video where Eva talks explicity about the profound implications of epigenetics

Please, please, mainstream science promoters of the Neo-Darwinian genetic mutation driven evolutionary so-called synthesis, please stop this nonsense now and get with the wonderful new and diametrically opposite epigenetic (Lamarckian) synthesis instead. Darwin himself was certainly not opposed to Lamarckian type evolution (as documented in my blogs and books – see epigenetic caterpillar free e-book on site for example), so why have the Neo-Darwinists been so unjust in their suppression and ridicule of Lamarck? Well, that is another story, and again in some of my books and forthcoming works. Suffice to say, it is well documented and there is absolutely no reason why Lamarckian principles should have ever been subjected to the ridicule they have historically been exposed to. Furthermore, Lamarckian principles were updated and brought in-line with the deeper understanding of genetics (inheritance) around the turn of the 20th century and were gaining much popularity as the Saltationist/Mutationist (meaning large global changes seen in the development of cells and embryos could be extrapolated to understanding rather radical and profound changes in an evolving species in conjunction with its environment). I have written extensively on these alternative scientific and empirically testable ideas and experiments before the evangelising Neo-Darwinian movement began to take hold in the first part of the 20th century.

Cheers

Maria Brigit

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Lamarck & the Epigenetic revolution in evolution (Press Release) Available from Amazon in paperback & all major book outlets from 20th Dec 2014

press release in paint

PRESS RELEASE
“LAMARCK was RIGHT as seen in the SILENT EPIGENETIC REVOLUTION IN EVOLUTION”

Dig-Press (contact Maria B. O’Hare)
E-mail: diggingupthefuture@gmail.com
Website: http://diggingupthefuture.com

New Paperback Book entitled: THE EPIGENETIC CATERPILLAR: AN ALTERNATIVE TO THE DARWINIAN VIEW OF THE PEPPERED MOTH PHENONMENON by MARIA B. O’HARE (PHD). ISBN: 978-1-78280-388-1 (Launch date: 20th December 2014) will be available from Amazon & all other major book sellers in paperback & e-book versions.

This little book of less than 80 pages, including fully researched scientific and historical bibliography, opens with the following quote under the heading of ‘A new synthesis is Dawning’ by a pre-eminent physiologist Professor Denis Noble:

“… all the central assumptions of the Modern Synthesis (often also called Neo-Darwinism) have been disproven. Moreover, they have been disproven in ways that raise the tantalising prospect of a totally new synthesis.”

This clearly demonstrates the need for such a publication & at the same time, the author of ‘The Epigenetic Caterpillar’ uses the quote to highlight one important aspect of this new synthesis, namely epigenetics (meaning beyond the genes) which in principle, essentially confirms the main tenets of an evolutionary theory dating to over 200 years ago by a famous French natural historian – Jean Baptiste Lamarck. O’Hare reveals how Charles Darwin was Lamarckian in his own ideas, and how he became increasingly so, as revealed in his own writings. To give the reader an idea of how radical this silent epigenetic revolution in evolution actually is, the author presents this quantum-like concept through the analogy of what she calls an epigenetic caterpillar, and uses it to conceptualise an alternative version of evolution and to specifically address industrial melanism of peppered moths – a famous text-book case of what has often been described as: “Darwinian evolution via selection in action” to counter this claim. Her argument is that the caterpillar has exactly the same genes as its adult form – a butterfly/moth, and yet: “looks nothing like a flying insect”. O’Hare goes on to explain using empirical studies that the dramatically different characters and traits displayed within the same insect depending on which form it is in its development (via metamorphosis), is fully explicable by environmentally-driven/epigenetic means (differential expression of the same genes in response to environmental changes). The author does not profess to be an expert in biology, but as a researcher with credentials in archaeology, and a life-time of diverse experiences, she brings a unique and enlightening perspective to this somewhat controversial evolutionary topic. Maria O’Hare lives in Spiddal, Galway, Ireland, with her son and partner.
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See the table of contents & Prologue for the book below as sample:

Table of Contents
PROLOGUE VII
A NEW SYNTHESIS IS DAWNING – 1 –
THE EPIGENETIC CATERPILLAR – 5 –
LAMARCKIAN EVOLUTIONARY PRINCIPLES EQUAL EPIGENETIC EVOLUTION – 13 –
THE EPIGENETIC CATERPILLAR & THE PEPPERED MOTH SAGA – 21 –
AN ALTERNATIVE VIEW OF THE PEPPERED MOTH PHENOMENON – 29 –
THE EPIGENETIC CATERPILLAR GOES QUANTUM – 43 –
ABOUT THE AUTHOR – 53 –
RECOMMENDED VIDEOS & FURTHER READING RELATING TO RESEARCH – 55 –
OTHER PUBLICATIONS BY THE AUTHOR – 59 –
BIBLIOGRAPHY – 63 –
END NOTES – 69 –

Prologue
I am delighted that you discovered this little book, but to be perfectly honest, I must tell you from the outset that my ‘formal qualifications’ for writing about epigenetics amount to zilch, other than that I have immersed myself deeply in the topic ever since I began to fathom its significance for our current view of evolution. Even my qualifications for writing about caterpillars are pretty sparse and I can’t say that Peppered Moths are my specialty either. I’m a research archaeologist, but I should say that I was once warned that there was no future in archaeology, and that is perhaps why I found my skills being put to other uses and ended up researching this fascinating topic instead.
The Epigenetic Caterpillar, as suggested in the main title of this book, is used to help conceptualise an alternative version of evolution and to specifically address industrial melanism of peppered moths – a famous text-book case of what has often been described as: “Darwinian evolution via natural selection in action”. It would appear, now having thoroughly researched this topic in great depth using the most up-to-date scientific literature, that the Neo-Darwinian explanation of colour change in moths cannot have been caused by genetic variation (inherited beneficial or neutral mutations), but by how the genes are expressed, which does not change the DNA sequence (code) itself. In other words, species change and variation is via environmentally-driven EPIGENETIC processes.
Therefore, I have used the epigenetic caterpillar as an example because a caterpillar has exactly the same genes as its adult form – a butterfly/moth, and yet it looks nothing like a flying insect. The dramatically different characters and traits displayed within the same insect depending on which form it takes during development (stage of metamorphosis), is fully explicable by environmental/epigenetic means (differential expression of the same genes at different times/seasons and during the evolutionary past). The same genes in the same insect or similar genes in the same species, cannot account for this drastic variation of form. Genes are actually relatively conservative and fixed within a given species, whereas, how they are expressed is a highly flexible adaptive mechanism used by all species. As the wealth of studies, which are emerging increasingly, are unequivocally demonstrating, epigenetic processes can change gene expression, causing variation in species traits and characters and these variations and adaptations can be inherited. Thus, this has major implications for our current genetically-driven version of evolutionary change.
As I was saying, being an archaeologist, I do love to dig things up and discover and/or rediscover lost and obscured historical knowledge. This all led to this little booklet amongst other publications in various stages of production. You see, not that long ago, when I was digging through the old dusty archives, well they are not so dusty admittedly these days as they are mainly on the internet – thanks be to goodness for it, I stumbled upon the fact that our more recent understanding of molecular epigenetic type evolution was not so new in their underlying principles.
These concepts had been around before Darwin was even born and had evolved to become real scientific alternatives to what has now become our current doctrine of evolutionary thought. I further discovered that there were reasons why these somewhat revolutionary ideas, now being confirmed by our most recent molecular biological investigations, did not make it through the 20th and into the 21st century. It is a complex history, intertwined in ideological and philosophical intrigue, which makes it all the more strange when you come to realise, as I eventually did, that Darwin himself was not adverse to some of these rather radically different views of evolution which became so heavily marginalised by the very movement that holds him in such high esteem.
Consequently, you may not be fully aware of the significance of the epigenetic revolution going on in evolutionary biology and the full gravity of its implications for our current model of evolution. Therefore I would like to present the epigenetic principle in such a way that its full significance can be grasped. That is why I refer to it as the silent biological revolution, because most of us are unaware of it happening at all, or if we are aware, we don’t generally get its deeper implications. I only aim to share what I have discovered so that it might stimulate some constructive debate in the light of these facts. I do hope you enjoy the brief journey and this little book may stimulate your own participation in this philosophical discussion and positive change that evolutionary biology needs at this time.
Cheers, Maria Brigit

80 page cover epigenetic caterpillar edit

EVOLUTION: Not by genetic mutations, but by Epigenetic Adaptation

microbes

This article focusses on bacterial evolutionary change, but the principle of what is discussed is fully applicable to all organisms including ourselves. For instance, a Neo-Darwinian explanation of bacterial evolution and other species across the whole spectrum of life would go something like this: Species evolve and eventually can become a different species via generations of changes in the DNA due to mutations (non-destructive and/or neutral mutations). The only problem is that species of bacteria never change into anything other than bacteria. And the idea that genetic mutations upon which natural selection acts is also be strongly criticised by a highly regarded scientist (micro-biologists, who contributed a highly significant theory about early microbial evolution to evolutionary biology), Professor Lynn Margulis, as seen in the following statement:

“Neo-Darwinists say that new species emerge when mutations occur and modify an organism. I was taught over and over again that the accumulation of random mutations led to evolutionary change [which] led to new species. I believed it until I looked for evidence” (Teresi 2011, 68)

http://discover.coverleaf.com/discovermagazine/201104?pg=68#pg683.

If it isn’t via genetic mutations, then what is driving adaptation within existing species and what is the driver of evolutionary (species) change? The answer in part, along with many other interactive processes, lays in the epigenetics. See Free e-book at ww.smashwords.com/books/view… For instance, one clincal study with bacteria (a really simple organism that should show mutations operating with selection to produce a change an adaptation) clearly, demonstrates that: “bacterial adapt to antibiotics more quickly than can be accounted for by mutations” (Janusz 2008) http://epigenome.eu/en/3,35,1110 The article is taken from the Epigenome NoE website which is a European funded project promoting excellence in science and research envolving the epigenome. The study on bacteria proposes the epigenetic explanation as it is environmentally-driven, adapting the organism’s response to stimuli (new antibiotics) by changing how the genes are expressed without changing the DNA sequence itself. We are only recently beginning to understand the epigenome as an article on Medical News Today outlines:

What is a gene? What are genes? Initially, after the Human Genome Project was completed, we thought that much of the instructions for making the proteins that make an organism was contained in a tiny part of the genome, while the rest was simply “junk” DNA, without any useful function. Later on, geneticists discovered another layer of heritable genetic data that are not held in the genome, but in the “epigenome”… In this area there are instructions on how to interpret the DNA code for the production of proteins. Some of the code for manufacturing the proteins of the epigenome was found to be hiding in junk DNA…That discovery helped us understand that the c.23,000 genes in the human genome that can be found in all the cells of the human body are expressed differently in different organs and tissues. How they are expressed depends on gene regulation instructions located in the epigenome. (Nordqvist 2013)
The complex factors working alongside epigenetic evolutionary processes involved in our emerging non-Darwinian and quantum-like evolutionary synthesis is, I believe is best summarised in the following quote by Professor James Shapiro in his blog post in the Huffington Post online: entitled: Does Natural Selection Really Explain What Makes Evolution Succeed? (2012):
In combination, cytogenetics and molecular genetics have taught us about many processes that lead to biological novelties “independently of natural selection” — hybridization, genome duplication, symbiogenesis, chromosome restructuring, horizontal DNA transfer, mobile genetic elements, epigenetic switches, and natural genetic engineering (the ability of all cells to cut, splice, copy, and modify their DNA in non-random ways). As previous blogs document and as future blogs will discuss, the genome sequence record tells us that these processes have accompanied rapid changes in all kinds of organisms. We know that many of them are activated by stress under extraordinary circumstances. (Shapiro 2012)
The last part pertaining to the activation of rather radical and rapid species adaptation by stress (environmental conditions) is fully applicable to bacteria and as a relatively simple and more primitive, but continually adapting organism, it begins to give us an insight into past evolutionary change when much more complex organisms, such as plants and animals, had not yet fulfilled their evolutionary potential and were less evolved, and not yet fully defined, they were generalists. This idea is not a new one, but one that has been around for a very long time and can be best conceptualised by applying the idea of cellular and embryonic development when the organism is highly sensitive to its internal and external environment and just like stem cells that have not yet been differentiated (can become anything in the early stages), similarly early and more primitive organisms were more susceptable to evolutionary change according to the environment they found themselves in and their genomes were also less fixed (genomically noisy). It is a complex process, but simply put: A developing embryo goes through the similar stages of development at a fundamental level to an evolving (developing) species. (E.G. see Von Baer on slide presentation/video on this site and O’Hare forthcoming – EVOLUTION: A THIRD WAY?).

The Epigenetic Revolution in Evolution is long overdue… but it’s happening

Junk & the Epigenetic caterpillar

how new and not so new discoveries in biology are overturning our conventional model of evolution & health

junk DNA

(credit: Wikispaces educational resources)

A new synthesis is dawning…

Professor Denis Noble (eminent physiologist) states:

[…] all the central assumptions of the Modern Synthesis (often also called Neo-Darwinism) have been disproven. Moreover, they have been disproven in ways that raise the tantalising prospect of a totally new synthesis.

– (Noble 2013)
http://onlinelibrary.wiley.com/doi/10.1113/expphysiol.2012.071134/full

And the nature of this tantalizing new synthesis is described by Prof. James A. Shapiro (an expert in bacterial genetics and professor of Biochemistry and Molecular Biology) in the following:

The past […] decades of research in genetics and molecular biology have brought us revolutionary discoveries. Upsetting the oversimplified views of cellular organization and function held at mid-century, the molecular revolution has revealed an unanticipated realm of complexity and interaction more consistent with computer technology than with the mechanical viewpoint which dominated the field when the neo-Darwinian Modern Synthesis was formulated. The conceptual changes in biology are comparable in magnitude to the transition from classical physics to relativistic and quantum physics.

– (Shapiro 1997)

The Boston Review Feb/March 1997 ‘A Third Way’.

http://new.bostonreview.net/BR22.1/shapiro.html

It’s all in the Junk

Most of the epigenetic factors involved in our health, inheritance and evolutionary development is found in the so-called junk region of the genome as outlined in the following science article in Medical News Today, under the heading: What is a gene? What are genes? by C. Nordqvist (2013):

Initially, after the Human Genome Project was completed, we thought that much of the instructions for making the proteins that make an organism was contained in a tiny part of the genome, while the rest was simply “junk” DNA, without any useful function.

Later on, geneticists discovered another layer of heritable genetic data that are not held in the genome, but in the “epigenome”. In this area there are instructions on how to interpret the DNA code for the production of proteins. Some of the code for manufacturing the proteins of the epigenome was found to be hiding in junk DNA.
That discovery helped us understand that the c.23,000 genes in the human genome that can be found in all the cells of the human body are expressed differently in different organs and tissues. How they are expressed depends on gene regulation instructions located in the epigenome.

http://www.medicalnewstoday.com/articles/120574.php

epigenetic caterpillar screen shot close up

(Source: Press Release from a clinical center for myelodysplastic syndromes relating to a rare blood disorder).

The Epigenetic Caterpillar

The nature of epigenetics means that we now need to re-evaluate our understanding of health as well as our current model of evolution. This is perhaps best illustrated in a clinical article below, as epigenetic processes effect, to what degree, genes are regulated/ expressed (switching on and off of genes and epigenetic inheritance) without actually changing the DNA sequence itself. This principle can be best seen within a well known species and process of development, metamorphosis of a caterpillar to a butterfly. This exemplifies the way in which epigenetic switches can alter the EXPRESSION of genes without changing the genotype (the gene/DNA sequence) which, in turn, can radically alter how an organism looks and its overall characters (phenotype). This therefore, has profound implications for our current gene-centered model of evolution.

Furthermore, this gene regulation/expression is equally applicable to our health and well-being as within even identical twins with identical genomes, their life-style, environmental exposure and stress-levels can have a rather different outcome in the end as epigenetic markers are formed on the epigenome and indeed these can be inherited (See recommended videos at the end of this article). The good news is that nothing is irreversible. In other words, Identical twins = identical genomes: but their epigenomes become increasingly distinct as they go through life.

 

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.
In some cases – the caterpillar and butterfly, for example – these changes are normal and expected and may be required for development.

http://multivu.prnewswire.com/mnr/mds-foundation/37124/docs/37124-epigenetics_unbranded.pdf

Epigenetics gives us a deep insight into health and disease and the healing mechanisms already present in the body and therefore, you are not a victim of your genes. .Judging by my research to date, the epigenetic caterpillar and all this entails for understanding how species change through time, will, I believe, profoundly change the way we think of evolution and indeed, our health.  When you really think about the way genes can be changed in their expression and how amazing it is that a caterpillar looks and acts so different to a flying insect (a butterfly or moth), yet it has the same genes, does this not tell you something about how species may have changed through time and how we have been looking in the wrong place all this time (the genes) to find the changes brought about in the species, when infact it was environmentally-driven epigenetics all along. Our current model of evolution only allows for a change in genes and their mutations to cause variation: we do not yet, fully grasp that genes can be altered dramatically without even changing the DNA sequence. However, it is unfortunate, (for various historical and ideological reasons which I have gone into elsewhere in my books), that epigenetic systems and their role in evolutionary change and the developmental biology have been fiercely resisted, ridiculed and generally ignored as a viable alternative to our current model of evolution. Otherwise, I feel we would be much, much further on in our biological thinking and how epigenetics and its understanding will, when it is fully recognised, cause nothing less than a paradigm shift (a quantum leap) in our understanding of ourselves, our lives, our planet and all life on it. Nature is so much more clever than any of us could begin to imagine.

Fortunately, things are beginning to change a little and in more recent assessments of Lamarckian principles which are essentially synonymous with Epigenetics are being recognised as valid within our current science as highlighted by Professor Denis Noble’s endorsement of a scientific collection of papers on Lamarck entitled: ‘Transformations of Lamarckism From Subtle Fluids to Molecular Biology’:

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)

http://mitpress.mit.edu/books/transformations-lamarckism

 

Bearing in mind that Darwin’s original concept of natural selection allowed for Lamarckian drivers of evolution as seen particularly in Darwin’s later additions of ‘Origins’ and the modern synthesis is quite different to its original form and the fact that earlier ideas of the importance of environmental drivers of evolution (Lamarckian) came to be integrated with saltation ideas of developmental biology or its more modern term: EVO-DEVO (meaning large and rapid changes during development and applied to evolution of the species) will make more sense of the following science paper entitled: ‘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 […]. 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 […]. We believe, therefore, that the impact of epigenetics and epigenetic inheritance on evolutionary theory and the philosophy of biology will be profound.

http://www.jstor.org/stable/10.1086/598822

More Info:

For more information and historical background on this epigenetic evolutionary principle and its impications for offering a very different interpretation of nature and biological evolution see other publications by this author. An Ebook is available to download on any device for free on usual platforms: Barnes & Noble, i-tunes (Apple) etc or find the direct link on this site.

Recommended videos:

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