Well if it didn’t happen by Neo-Darwinian means, how did evolution occur? Part Three: Descent via Epigenetic Modification

Alternative evolutionary series

If it didn’t happen by Neo-Darwinian means, how did evolution occur?

Part Three

Descent by Epigenetic Modification

 epigenetic caterpillar screen shot close up http://multivu.prnewswire.com/mnr/mds-foundation/37124/docs/37124-epigenetics_unbranded.pdf

Sorry post is a day late – I messed up the Monday scheldule, but here it is now: The third part of alternative evolution:

Introduction: (re) discovering the importance of epigenetic evolution & rethinking the linear common descent model

Just to give you a little background on this present focus of epigenetic evolution, (recall last week’s article on jumping genes controlled and orchestrated ultimately via epigenetic processes in response to environmental cues – allowing jumping genes to remodel genomes to make a radical adjustment/adaptation to changing circumstances?) https://diggingupthefuture.com/2015/08/10/part-two-if-it-didnt-happen-by-neo-darwinian-means-how-did-evolution-occur/

not to mention the epigenetic control of how existing genes are expressed, or not, turned on or off, or amplified or toned down. Epigenetics, put in simplified terms can best be explained as operating above and beyond (outside the norm of the genes). Furthermore, as noted in the preface of the book: ‘Building the most Complex Structure on Earth: An Epigenetic Narrative of Development and Evolution of Animals’ by Nelson R. Cabej, states the following:

I include in epigenetics the vast areas of the nongenetic mechanisms of reproduction, growth, cell differentiation, development, and evolution. It is in this broader context that epigenetics promises to be the genetics of the twenty-first century….

– Cabej (2013, preface).

It is how these genes are controlled, epigenetically, that makes the difference to whether an insect looks and acts like a sluggy creature (a caterpillar) or looks and acts like a flying insect, yet it has the exact same genes, for example. (For more info and supporting references for discussion below, see: ‘The Epigenetic Caterpillar: An Alternative of the Neo-Darwinian Peppered Moth Phenomenon’). http://www.amazon.com/The-Epigenetic-Caterpillar-Alternative-Phenomenon-ebook/dp/B00OE16P46 or the currently free copy at https://www.smashwords.com/books/view/485914

Amazon don’t let you sell your books for free, but it is only just over a dollar there (all donations via buying my books will be gratefully received). The excerpt below from the Telegraph UK will give you an insight into the epigenetic mechanism and its historical context:

Epigenetics: How to alter your genes

We’ve long been told our genes are our destiny. But it’s now thought they can be changed by habit, lifestyle, even finances. What does this mean for our children?

Ever since the existence of genes was first suggested by Gregor Mendel in the 1860s, and James Watson and Francis Crick came up with the double-helix model in 1953, science has held one idea untouchable: that DNA is nature’s blueprint. That chromosomes passed from parent to child form a detailed genetic design for development. So when, 10 years ago, researchers finished mapping the human genome, it promised to revolutionise the field of molecular medicine.

… But only in the last few years has research revealed more detail of the vast array of molecular mechanisms that affect the activity of the genes. And that your DNA itself might not be a static, predetermined programme, but instead can be modified by these biological markers. Chief among them are what are called methyl groups – tiny carbon-hydrogen instruction packs that bind to a gene and say “ignore this bit” or “exaggerate this part”.

…In biological terms, the idea is heretical. After all, Darwin’s central premise is that evolutionary change takes place over millions of years of natural selection, whereas this new model suggests characteristics are epigenetically “memorised” and transmitted between individual generations. And yet, slowly but surely, the evidence is mounting….

– Bell (‘Telegraph’ 16th  Oct 2013)

http://www.telegraph.co.uk/news/science/10369861/Epigenetics-How-to-alter-your-genes.html

Now, it is important, I believe, to stress that epigenetic evolution is not a new concept.

We didn’t just not know any better and had to wait until they cracked open the human genome and the genomes of most other organisms since the 2000s, only to discover that genes didn’t carry the instructions to make 3D print outs of us and everything else on the planet. We have known for a long time that rapid and major changes in a developing organism happened, and operated beyond the genetic code. We knew that an organism (particularly a developing one) was shaped and formed by its environment (internal or external) as seen in the process of epigenesis/epigenetics, morphogenesis/chemical/physiological factors during development. Furthermore, we understood that ‘jumping genes’ could make radical and rapid alterations to existing species in real-time  – and that these facts had major implications for how fast and radically a developing species could be remodeled in evolutionary timescales in response to its environment (see part two of the alternative evolutionary series from last week).

In other words, there is a bit more to this epigenetic history than described in the article in the ‘Telegraph’ above. Again you’ll find out a lot more by reading the ‘Epigenetic Caterpillar e-book and it’s also available in paperback on Amazon and soon at many other retailers worldwide. Anyway, hopefully you get a sense of how epigenetic processes express, turn on, or turn off, amplify etc the tiny percentage of your existing genes, 2% (that code for proteins) found within your entire genome. This has profound implications for evolution as you will see as this article unfolds and as indicated in Cabej’s epigenetic model of evolution as a means of Building the most Complex Structure…’ The following excerpt will give you an idea about how important the so-called Junk DNA is – the other 98% of our genome, which because it didn’t code for proteins, was once thought to be useless – this is actually where the real evolutionary action is and it has a lot to do with epigenetics:

‘Junk’ DNA gets credit for making us who we are

The blueprint for life is not all about genes. Now we are finally pinning down how much differences in non-coding DNA – stretches of the molecule that don’t produce proteins and used to be considered “junk” – shape who we are.

In recent years, researchers have recognised that non-coding DNA, which makes up about 98 per cent of the human genome, plays a critical role in determining whether genes are active or not and how much of a particular protein gets churned out.

– (New Scientist 19th March 2010)

https://www.newscientist.com/article/dn18680-junk-dna-gets-credit-for-making-us-who-we-are/#.VZw_9VKo7LU

The next article excerpt should help with the concept of the  non-programmed genes and the flexibility of both the genome and the epigenome’s responsiveness to environmental change. The authors propose a co-evolution between organism and its environment, which of course runs counter to our traditional view of evolutionary thinking, although the article only suggests seriously revising the modern synthesis concept of evolution, not necessarily getting rid of it entirely. This is common within articles of the nature.

Does evolutionary theory need a rethink?

We hold that organisms are constructed in development, not simply ‘programmed’ to develop by genes. Living things do not evolve to fit into pre-existing environments, but co-construct and coevolve with their environments, in the process changing the structure of ecosystems. The number of biologists calling for change in how evolution is conceptualized is growing rapidly. Strong support comes from allied disciplines, particularly developmental biology, but also genomics, epigenetics, ecology and social science…

– (Laland et al. in ‘Nature’ 8th October 2014)

http://www.nature.com/news/does-evolutionary-theory-need-a-rethink-1.16080

Now just consider the amount of genetic exchange across entire species boundaries and whole domains of life (as outlined previously) and why nature doesn’t just printout 3D monsters of random mutations (even with selection if such a mechanism existed) from all the wonderous cross-breeding  and genetic exchange as highlighted in last week’s topic. Genes are not pre-programmed in the first place, they are the raw data for other processes such as epigenetics to act upon and reprogram this information. However, don’t forget that one species doesn’t morph into another these days due to the stabilising (metabolic growth restriction as discussed in the first article in this alternative evolutionary series – genome silencing mechanisms are in place, but there is still much room for adaptive change, even if the fundamental form of the species is relatively fixed in our present era). For example, (via HGT) snakes and cows came to share some of their genetics, not because of a common ancestor as we know the tree is a web and the molecular clock has broken down – but, probably due to common insect bites, where bacterial genomes became implanted and later used by viral-like processes – jumping genes to slice, dice, cut and paste and generally remodel genomes according to radically changing environments, like an SOS mechanism that Nature has evolved to make rapid adaptation to changing circumstances, where organisms didn’t need to be the lucky survivors in the Russian Roulette of Life, but rather, were already – all, survivors as they were endowed with the ability to adapt rapidly and align with whatever the environment threw at them. They have the ability to not just survive, but thrive. This is ultimately orchestrated via epigenetic processes.  See article below:

 

Tuning gene expression to changing environments: from rapid responses to evolutionary adaptation

Organisms are constantly exposed to a wide range of environmental changes, including both short-term changes during their lifetime and longer-term changes across generations. Stress-related gene expression programmes, characterized by distinct transcriptional mechanisms and high levels of noise in their expression patterns, need to be balanced with growth-related gene expression programmes. A range of recent studies give fascinating insight into cellular strategies for keeping gene expression in tune with physiological needs dictated by the environment, promoting adaptation to both short- and long-term environmental changes. Not only do organisms show great resilience to external challenges, but emerging data suggest that they also exploit these challenges to fuel phenotypic variation and evolutionary innovation

(Abstract López-Maury et al in ‘Nature’)

http://www.nature.com/scitable/content/tuning-gene-expression-to-changing-environments-from-35223

As I indicated above, epigenetic principles of evolution is not a new concept. The history of the concept of epigenetics really begins, I believe, in a pre-genetic age and was formulated into a comprehensive evolutionary theory by Jean-Baptiste Lamarck, perhaps best known for his concept of acquired characteristics, but there is more to his theory and even this concept has been frequently misunderstood. Lamarck’s theory goes back to over 200 years and even Charles Darwin began to take seriously, eventually. Lamarck’s evolutionary principles have virtually become synonymous with epigenetic inheritance (acquired characteristics) with the growing realisation amongst many scientists that epigenetic processes triggered by environmental factors can, do and have in the past as we can see much deeper into the genome these days, had a profound impact upon the formation of the species itself – basically, what Lamarck had proposed over two centuries earlier. This combined with older concepts of large and rapid evolutionary change and processes during morphogenesis and natural growth laws (as discussed in previous articles in this alternative evolutionary series) and combined with genomic remodelling and hybridisation/or any genetic exchange across the species, as a means of evolutionary novelty and rapid speciation (as discussed last week) are all old ideas and in the light of our most cutting edge understanding of molecular processes, is beginning to offer a rather dynamic alternative to our current standard model or, Neo-Darwinian version of evolutionary change.

As a result, epigenetics along with other related alternative views of evolutionary processes are seriously beginning to undermine the very foundations of our modern synthesis (Neo-Darwinism). Perhaps, therefore, it is poetic justice of sorts that these older alternatives are being reinstated in their modernised form, as it was the rather genetically modified version of Darwinism and the modern synthesis movement that grew out of its ideology (and I don’t say that lightly – see link below) that was instrumental in banning anything non-Darwinian and particularly anything Lamarckian in the first place. But we are not here to highlight these issues, just to find solutions and if you are interested in reading more about the historical aspects of Lamarck and the modern synthesis and why our modern synthesis is “crumbling, apparently beyond repair” as noted by Eugene Koonin not that long ago, follow the link to author’s books http://www.amazon.com/author/mariaohare or specifically to ‘Lamarck and the Sad Tale of the Blind Cave-Fish’ http://www.amazon.com/Lamarck-And-Tale-Blind-Cave-Fish/dp/178280465X

A Pre-Darwinian Theory of Evolutionary Development via epigenetics

As alluded to in part one of this alternative evolutionary series https://diggingupthefuture.com/2015/08/03/evolution-scaling-laws-something-universal-is-going-on/

one pre-Darwinian theory that was taken seriously before and after Darwin’s own time and indeed, was considered pertinent by Darwin himself, was the embryological laws as applied to species evolution, presented by Von Baer. Somehow, his theory became misunderstood and historically obscured and seems to have become overshadowed by Haeckel’s embryonic similarity charts across many different species – this ended up being abandoned as they were just a bit exaggerated and the result is that Von Baer’s more subtle and less direct common descent model from several different origins was lost. Most of us have heard of Ernst Haeckel and his famous – now infamous, drawings of different animal embryo drawings, still used in some biology text books today? Well, only seven years after Darwin wrote ‘Origin of Species’, Von Baer’s laws ran into Haeckel’s recapitulation theory  known as biogenetic law, as documented the Embryo Project website:

Ernst Haeckel’s Biogenetic Law (1866)

The biogenetic law is a theory of development and evolution proposed by Ernst Haeckel in Germany in the 1860s. It is one of several recapitulation theories, which posit that the stages of development for an animal embryo are the same as other animals’ adult stages or forms. Commonly stated as ontogeny recapitulates phylogeny, the biogenetic law theorizes that the stages an animal embryo undergoes during development are a chronological replay of that species’ past evolutionary forms.

https://embryo.asu.edu/search?text=biogenetic%20law#sthash.MGv8FPpQ.dpuf

— “the Biogenetic Law” “Ontogeny recapitulates phylogeny.”

…von Baer did not accept that all species shared a common ancestor. Despite von Baer’s objections to Haeckel’s biogenetic law and recapitulation in general, the biogenetic law persisted in biology until the turn of the twentieth century when new experimental and comparative evidence rendered it untenable.

https://embryo.asu.edu/pages/karl-ernst-von-baers-laws-embryology#sthash.9o6GySax.dpuf

But unfortunately by then, the Neo-Darwinists had begun their campaign to promote selection and genetic pre-formation theory and had banned everything to do with leaping Lamarckism. Furthermore, the direct common linear descent model had taken hold – fish to frog – to lizard etc, which became a little more sophisticated and fish-like (fishy-pod) ancestors were looked for in the fossil record and still the missing links continue. Population models were built upon abstract concepts and mathematised to give enough genetic novelty under geographically isolated and recombination conditions within imaginary species whose gene pools were acted upon via natural selection to account for speciation. Later we started to build molecular trees, assumed that the more common genes between the species: the more closely related that species was. The timescales were even given, based upon assumptions of relatedness and splits according to mutating genes (copy mistakes in the reshuffle) but if you read last week’s article, you will see why none of these assumptions hold true.

Anyway, returning to Von Baer’s laws and principles, these were based upon the fundamental premise of non-preformation of the organism; that organisms/species were not pre-programmed from the beginning in a preformed way and then simply grew into whatever they are to become. In modern terms, the Neo-Darwinian model adheres to pre-formation in terms of believing that all an organism requires throughout its life and during development, is coded within the genes. Epigenetics/morphogenesis is the exact opposite to this concept. Many scientists, like Von Baer, even the later ones who also had an understanding of genetics, (mostly due to their own experimental observations) believed that an organism develops according to environmentally driven epigenetic/epigenesis processes during development. Employing De Baer’s principles and laws, therefore, De Baer specifically proposed that these epigenetic processes would also apply to evolutionary development of a species, where organisms were shaped as they developed according to their environmental experience. De Baer stressed the importance of the environment as a driver of evolutionary change and also rejected the strict sense of common ancestry as seen in the article below. Again, this information is taken from the Embryo Project Website:

From the general to the specialized: Von Baer’s first law states that the general characters of an animal group appear earlier in the embryo than the specialized characters do, which contradicted preformationist theories. Von Baer’s second law states that embryos develop from a uniform and noncomplex structure into an increasingly complicated and diverse organism. … Von Baer argued that this evidence support[ed] epigenetic development rather than development from preformed structures. He concluded from the first two laws that development occurs through epigenesis, when the complex form of an animal arises gradually from unformed material during development.

Von Baer used the third and fourth laws to counter the recapitulation theories of [others] which became increasingly popular in Europe throughout the eighteenth and nineteenth centuries.

Von Baer’s second law states that embryos develop from a uniform and noncomplex structure into an increasingly complicated and diverse organism.

https://embryo.asu.edu/pages/karl-ernst-von-baers-laws-embryology#sthash.9o6GySax.dpuf

As employed in the first part of this series, I have used Von Baer’s laws to present part of an alternative model of evolution. His laws give us a clue to our actual ancestry in more dynamic terms than the literal model of common descent allows. It seems that evolution has gone from the primitive (less-defined and almost experimental, to the more complex and diverse via natural environmental and molecular processes of increased specialist adaptation to environment, each stage builds upon the earlier systems of life and later refines them. The only way this can happen is via epigenetic and environmentally driven evolution. As the record clearly shows, as you will see as you read on, epigenetic systems do indeed have the power to change organisms in response to their environment, rather dramatically and rapidly. Furthermore, brain studies, as discussed in the first part of this series, supports Von Baer’s premise that organisms go from generalists (a common ancestral condition) to more specialist forms. Interestingly, Lamarck proposed something similar within his evolutionary theory of going from the least perfected to the perfected forms via what would be described today as epigenetic evolution. 

Just to conclude this section on the history and relevance of older evolutionary theories in the light of our current understand and particularly epigenetic evolution according to Von Baer’s laws as an alternative to literal common descent along a neat linear progression of branching genetic lineages, below is a brief overview of how De Baer’s laws are becoming more relevant in the light of our more modern understanding. You will hopefully see throughout this series that his laws are highly pertinent to evolutionary development.

With advances in multiple fields, including paleontology, cladistics, phylogenetics, genomics, and cell and developmental biology, it is now possible to examine carefully the significance of von Baer’s law and its predictions. In this review, I argue that, 185 years after von Baer’s law was first formulated, its main concepts after proper refurbishing remain surprisingly relevant in revealing the fundamentals of the evolution–development connection, and suggest that their explanation should become the focus of renewed research.

http://www.sciencedirect.com/science/article/pii/S0168952513001649

Epigenetics and Speciation – Descent by epigenetic modification according to environmental factors

Previously (last week’s article) we touched upon many of the different ways in which genetic novelty can be passed between many different spheres of life. From, symbiotic mergers, to yeast signalling and transfer of genetic material, from hybridisation across many species types and remodelling of genomes according to environmental stresses and changes in conditions. We discussed rapid adaptation of whole levels of complexity in the first part of this series and the scaling and growth laws relating to metabolic evolutionary complexity and genome silencing. Now, in many ways, epigenetic processes are the missing link in the mechanism to explain how nature manages to adapt so perfectly, all her organisms to their environments and specific species needs as epigenetics turn off or on (via genetic switches) vast arrays of genes. It can amplify some genetic expression, while toning down others. Chemical marker carrying the epigenetic memory of these flexible programs that are being continually re-written (but perhaps not as dramatically now as in the past as everything has stabilised – see first article in this series), orchestrate the great symphony of genetic and epigenetic diversity and variation.  Also bear in mind the key concept of stabilisation of the species once it has become a fundamental kind, insect, plant, fungi, microbe, yeast, bacteria, invertebrate animal such as a sponge, or vertebrate fish, amphibian, reptile, mammal, bird or higher primate; scales of metabolic complexity. Another key concept is that a less-developed organism (developmentally or evolutionary developing species) is more open to change than a mature adult species. Remember the Sigmoidal growth curves in part one of this series; a bit like the saying: you can’t teach old dog new tricks? You can of course, but it takes a lot longer as a more mature dog is more set in its ways, just like species have, kind of got used to being that species and it is much easier for it to function that way than to learn too many new tricks that belong to other species. A mature species or adult organism is going to become more fixed than its more primitive form as a developing organism and by extrapolation, a developing species (not yet specialised) is going to be more flexible and adaptable to its environment than one that already knows what it is. Evolution went in quantum leaps at the beginning because it was young, dynamic once the foundations were laid (the lag phase). Open system which is the principle of biological life within its environment can make quantum leaps in furthering its complexity if new and novel opportunities and/or dramatic changes in the environment occur and this requires adaptation. The less developed species can avail most of these, but not so much the established fundamental species. I call this differentiation of the species as early development pluripotent/stem cells (cells that fire together: wire together concept – Hebb’s law – see last week’s article). Below is an excerpt which will give you an idea of just how sensitive stem cells are to their environments and how they know what to become from simply having contact with a certain medium in a Petrie-dish. This is entirely epigenetic as each cell has the same genes. From the University of Wisconsin-Madison News website and article entitled: ‘In directing stem cells, study shows context matters’ is summarised below:

Figuring out how blank slate stem cells decide which kind of cell they want to be when they grow up — a muscle cell, a bone cell, a neuron — has been no small task for science.

Human pluripotent stem cells, the undifferentiated cells that have the potential to become any of the 220 types of cells in the body, are influenced in the lab dish by the cocktail of chemical factors and proteins upon which they are grown and nurtured. Depending on the combination of factors used in a culture, the cells can be coaxed to become specific types of cells…. To fully explore the idea that surface matters to a stem cell, Kiessling’s group created gels of different hardness to mimic muscle, liver and brain tissues. The study sought to test whether the surface alone, absent any added soluble factors to influence cell fate decisions, can have an effect on differentiation.

Results, according to Kiessling, showed that a soft, brain tissue-like surface, independent of any soluble factors, was catalyst enough to direct cells to become neurons, the large elaborate cells that make up the central nervous system. Stiffer surfaces favored the stem cell state.

“We didn’t change anything but switch from a hard surface to a soft surface,” Kiessling says. “They all started looking like neurons. It was stunning to me that the surface had such a profound effect.”

– Devitt (Sept. 8, 2014)

http://www.news.wisc.edu/23113

The cells in their pluripotent stem cell state may be akin to earlier generic forms of plant and animal life, not sure what they were going to be until they evolved. It all may have depended upon what primordial pond they developed in – context of early evolution and early development is everything. Recall that the epigenetic principle of evolution which I am applying is, based on De Baer’s laws of evolutionary development. It is also worth noting that Lamarck had actually touched on this concept as part of his evolutionary theory. Below a few of his most pertinent views on the matter: They are all taken from his 1809   ‘Zoological Philosophy…’ (Translation by Hugh Elliot 1914)

… I shall show that nature, by giving existence in the course of long periods of time to all the animals and plants, has really formed a true scale in each of these kingdoms as regards the increasing complexity of organisation; but that the gradations in this scale, which we are bound to recognise when we deal with objects according to their natural affinities, are only perceptible in the main groups of the general series, and not in the species or even in the genera.

— Lamarck (1809, 58)

https://archive.org/stream/ZoologicalPhilosophy/ZoologicalPhilosophyAnimals_Lak_506pgs51391278#page/n129/mode/2up

   … among the fossil remains found of animals which existed in the past, there are a very large number belonging to animals of which no living and exactly similar analogue is known; and among these the majority belong to molluscs with shells, since it is only the shells of these animals which remain to us.

     Now, if a quantity of these fossil shells exhibit differences which prevent us, in accordance with prevailing opinion, from regarding them as the representatives of similar species that we know, does it not necessarily follow that these shells belong to species actually lost? 

       Why, moreover, should they be lost, since man cannot have encompassed their destruction?  May it not be possible on the other hand, that the fossils in question belonged to species still existing, but which have changed since that time and become converted into the similar species that we now actually find.

 — Lamarck (1809, 45-46) 

https://archive.org/stream/ZoologicalPhilosophy/ZoologicalPhilosophyAnimals_Lak_506pgs51391278#page/n129/mode/2up

In the same climate, significantly different situations and exposures at first simply induce changes in the individuals who find themselves confronted with them. But as time passes, the continual difference in the situation of the individuals I’m talking about, who live and reproduce successively in the same circumstances, leads to changes in them which become, in some way, essential to their being, so that after many generations, following one after the other, these individuals, belonging originally to another species, find themselves at last transformed into a new species, distinct from the other.

For example, if the seeds of a grass or of any other plant common to a humid prairie are transported, by some circumstance or other, at first to the slope of a neighbouring hill, where the soil, although at a higher altitude, is still sufficiently damp to allow the plant to continue living, if then, after living there and reproducing many times in that spot, the plant little by little reaches the almost arid soil of the mountain slope and succeeds in subsisting there and perpetuates itself through a sequence of generations, it will then be so changed that botanists who come across it there will create a special species for it.

— Lamarck (1809, 39)

https://archive.org/stream/ZoologicalPhilosophy/ZoologicalPhilosophyAnimals_Lak_506pgs51391278#page/n129/mode/2up

This re-applied model of epigenetic evolutionary change according to environmental conditions has implications, such as: gaps in the fossil record begin to disappear when you realise that environmentally-driven factors can trigger epigenetic processes of patterning, creative remodelling and constraints in conjunction with the dynamic rapid response mechanism (SOS system) that nature employs via jumping genes which can remodel entire genomes and therefore the resulting change in what an organism may look like after it has developed at an evolutionary level – into a specialised species, may be rather dramatically different to what it looked like in its more primitive (generalist) state.

Returning to our epigenetic caterpillar analogy (i.e. a caterpillar and its adult form – a moth or butterfly), now, if we didn’t know any better and we found these two organisms in the fossil record (slug-like creatures near the bottom) and nothing environmentally changes and then, suddenly everything changes and we see just above this level a fully-formed flying insect (albeit a little spindly and primitive looking – we actually see this in the fossil record if you look closely and apply Von Baer’s laws), might you not perceive these creatures as entirely distinct from one another? Anyway, that is just a thought experiment for now and I will present the supporting evidence to go along with it. But, it is interesting don’t you think?

For example, returning to Cabej’s epigenetic theory of evolution: ‘Building the Most Complex Structure on Earth: An Epigenetic Narrative of Development and Evolution of Animals’ he states the following regarding epigenetic metamorphosis (note: Bauplan = body plan):

Metamorphosis is an amazing example of the dexterity of animals to switch to different development programs. This certainly contradicts the prevailing opinion that an egg or a zygote provided with a program that determines development up to the adult stage. This gains more significance when one remembers the ease with which some metamorphosizing amphibians can switch to a direct mode of development, or even skip metamorphosis altogether. It is possible that the same egg/zygote contains the programs for two different Bauplans, and sometimes even a program for skipping its species-specific Bauplan? Metamorphosizing species, besides their own developmental program, have incorporated and executed ancestral developmental programs. Amazingly, like biological Houdinis, they shift the gears of development both forward (insects and amphibians) and backward (ascidians).

Cabej (2013, 179)

We also know that epigenetics can switch genes back on that were previously switched off, so not all present-day organisms still use their evolutionary ancestral and more primitive modes of development. However, epigenetics can also explain the loss of limbs as in lizards becoming snakes, eggs coding for male or female depending upon the temperature, it can also explain new extended features such as digits in tetrapods (land walking animals with two sets of limbs) as well as shrinking and make giants of organisms depending upon available resources. Take for example, the recent article reported in Science Daily:

Honey, I shrunk the ants: How environment controls size

By increasing the degree of DNA methylation (a biochemical process that controls the expression of certain genes — a bit like a dimmer can turn a light up or down) of a gene involved in controlling growth called Egfr, they were able to create a spectrum of worker ant sizes despite the lack of genetic difference between one ant and the next. Essentially, the researchers found that the more methylated the gene, the larger the size of the ants.

“Basically, what we found was a kind of cascading effect. By modifying the methylation of one particular gene, that affects others, in this case the Egfr gene, we could affect all the other genes involved in cellular growth,” says Sebastian Alvarado, the McGill PhD who is the co-first author on the study that was published today in Nature Communications. “We were working with ants, but it was a bit like discovering that we could create shorter or taller human beings.”

(source: Mc Gill University, March 11, 2015)

http://www.sciencedaily.com/releases/2015/03/150311081258.htm

Or, the following article also reported in Science Daily, which could be re-titled: How do you like your eggs? Male or Female?

Molecular mechanism links temperature with sex determination in some fish species

A study led by the CSIC’s Institute of Marine Sciences, in collaboration with researchers from the Centre for Genomic Regulation (CRG), has found the epigenetic mechanism that links temperature and gonadal sex in fish. High temperature increases DNA methylation of the gonadal aromatase promoter in female.

The environmental temperature has effects on sex determination. There are species, such as the Atlantic silverside fish, whose sex determination depends mainly on temperature. And there are other species whose sex determination is written within its DNA but still temperature can override this genetic ‘instruction’.

(source: Centre for Genomic Regulation, January 2, 2012)

http://www.sciencedaily.com/releases/2011/12/111229203027.htm

Well if epigenetic methalation has the ability to override chromosomes or their equivalent that make you male or female and temperature is the driving force, what else did  epigenetic and environmentally-driven factors do to change the traits and characters of an evolving species? The mind boggles at the possibilities. Hopefully you are beginning to see Nature’s powerful ability to adapt her species to whatever the weather; and cut her clothe to her measure. Adaptation depending upon which way the wind is blowing, especially when the species is developing in evolutionary time-scales.

Now can you see how a big fish in a small pond may not do very well, but if its eggs spawn a new generation of fish, nature just might shrink them so that they not only survive, but thrive in that same pond as it can do it really quickly as seen in the article below:

Epigenetic mechanism for fast-tracking evolution

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.

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

For instance, again as reported in Science Daily, with the heading:  ‘Millions of DNA switches that power human genome’s operating system are discovered’ (2012) sourced from the University of Washington, the summary explains the role and discovery of these Hox Gene complexes and how they were, until recently, hidden within the genome (within the so-called junk regions again) in the following:

Genes make up only 2 percent of the human genome and are easy to spot, but the on/off switches controlling those genes were encrypted within the remaining 98 percent of the genome. Without these switches, called regulatory DNA, genes are inert …

http://www.sciencedaily.com/releases/2012/09/120905135326.htm

So it isn’t just a case of your genes being unpacked and read and the proteins built according to a fixed set of instructions, but rather a fairly flexible set of instructions that are open to interpretation (epigenetic memory) according to environmental cues. However, this is a fairly fixed process and ultimately guided by epigenetic processes. Otherwise, the templates might perhaps start metamorphosing into all manner of strange creatures, which might actually be how it happened back in the evolutionary past, but it seems that fundamental animal forms have finished morphing and their genomes relatively stable with just enough flexibility to allow for continually fine-tuning and adaptive systems for the unexpected. This mechanism for stabilising genomes is indeed indicated in Bird’s study of the silencing effects identified after two major transitions of leaps of complexity as seen within the eukaryote and vertebrate evolutionary boundaries as highlighted in last week’s article in this present series.

These Hox master gene switches and epigenetic factors are specifically noted in the article relating to the NOVA channel: ‘Ghosts in your genes’ just below and I have referenced a few other articles that clearly show the importance of the role of epigenetics in how, what, when and to what degree these genetic master switches are deployed:

…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.

http://www.pbs.org/wgbh/nova/genes/fate-nf.html

Epigenetic regulation of vertebrate Hox genes: a dynamic equilibrium.

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 science paper entitled: Epigenetic control of Hox genes during neurogenesis, development, and disease (2010) http://www.ncbi.nlm.nih.gov/pubmed/20739155

 outlines some of these epigenetic mechanisms and their role in the activation of Hox genes. Another paper which outlines the following:

the process of mammalian development is established through multiple complex molecular pathways acting in harmony at the genomic, proteomic, and epigenomic levels. 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.

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

In the journal entitled: Epigenetics (2009) an article entitled: Epigenetic regulation of vertebrate Hox genes: a dynamic equilibrium, stresses the dynamic aspects of this type of phenomenonhttp://www.ncbi.nlm.nih.gov/pubmed/19923920, and in the journal of Science (2009) an article entitled: Epigenetic temporal control of mouse Hox genes in vivo http://www.ncbi.nlm.nih.gov/pubmed/19498168 to name but a few.

The epigenetic differential expression of genes and particularly early on as they are being activated or not activated/expressed or not-expressed, when and to what degree, can have a big impact on what an organism ends up looking like in the end and indeed can shape its  entire evolutionary trajectory.

For instance, in a paper by Gilbert S. F. in Developmental Biology (2000) entitled: Hox Genes: Descent with Modification

as the title implies, Gilbert views evolution as being driven in part by a commonly shared process/mechanism, a tool-kit, if you like, by which basic body-plans of organisms such as animals can be laid out (built) according to a specific set of instructions as Gilbert states: “This means that the enormous variation of morphological form in the animal kingdom is underlain by a common set of instructions”

http://www.ncbi.nlm.nih.gov/books/NBK9978/

Well, perhaps, but these instructions are open to epigenetic interpretation. These instructions are not fixed – it just saves Nature a great deal of time in doing the initial body printout, not having to reinvent the wheel every time. As the book description for Cabej’s epigenetic evolution model for the most complex structures, “epigenetic mechanism… are the competent users of the genetic toolkit”. Genetic switches are essential for the activation of the initial body patterns. These are ultimately controlled and guided via epigenetic processes operating above the genes themselves, and act as controllers of the master genetic switches. This is seemingly why all the genetic novelty exchanged amongst and between whole domains of life didn’t print out lucky monsters, but instead, highly symmetrical and coordinated organisms that were entirely adapted to their environment. Interestingly although Gilbert does not discuss the specific epigenetic aspect of the Hox genes, he does however, describe how Hox gene complexes actually evolved within each of the major types of animals.

As Gilbert explains:

The number of Hox genes may play a role in permitting the evolution of complex structures. All invertebrates have a single Hox complex per haploid genome. In the most simple invertebrates—such as sponges—there appear to be only one or two Hox genes in this complex … In the more complex invertebrates, such as insects, there are numerous Hox genes in this complex. … By the time the earliest vertebrates (agnathan fishes) evolved, there were at least four Hox complexes. The transition from amphioxus to early fish is believed to be one of the major leaps in complexity during evolution… This transition involved the evolution of the head, the neural crest, new cell types (such as osteoblasts and odontoblasts), the brain, and the spinal cord…

http://www.ncbi.nlm.nih.gov/books/NBK9978/

Gilbert also gives a very solid example of just what these Hox complexes can end up expressing or not, in the following interesting example of the evolutionary history of how the snake lost its legs:

One of the most radical alterations of the vertebrate body plan is seen in the snakes. Snakes evolved from lizards, and they appear to have lost their legs in a two-step process. Both paleontological and embryological evidence supports the view that snakes first lost their forelimbs and later lost their hindlimbs … 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 …

http://www.ncbi.nlm.nih.gov/books/NBK9978/

Now are you beginning to see how switches according to environmental needs and adaptations while an organism was developing as a species, if we literally apply Von Baer’s laws, the earlier and more primitive forms have shorter evolutionary gestation periods and the later and more complex forms have longer evolutionary gestation periods – all start out as generalists and via epigenetic environmental changes, become more defined and more diverse from each other. And don’t forget of course, all the genetic novelty that some organisms had to play within their tool-kit for adaptations and how ultimate evolutionary trajectory of the species was directed by their inherent molecular complexity according to scaling laws of growth/development and efficiency to being all it could be from all that it had picked up and experienced in its environment on its evolutionary journey.

Therefore, we have began to touch on a few alternative models of how species come into being rather rapidly, fully-formed at least at their fundamental level of development and this is all orchestrated according to adaptive needs, the conditions an organism finds itself in and overseen, ultimately by metabolic exchange systems that have evolved themselves evolved. Nature has means of providing a genetic tool-kit to be reprogrammed according to the needs of an organism in the context of its environment. The species didn’t so much become complex, it was rather that some species had more tools in their kit than others to become more complex than other species. Nature has found a shortcut to fast-track evolution. Furthermore, she doesn’t put all her eggs in one genetic basket and in a sense, epigenetics is a form of natural correction, which begin to replace the wholly inadequate mechanism proposed via natural selection. Epigenetics is the flexible part of the genetic system. Jumping genes are the radical part of the morphing system but epigenetics has a way of releasing its hold on these when life demands it.  Genes are the highly conserved part of the evolutionary story and as we seen last week, genetic mutations don’t actually cause one species to change into another, but hybridisation, HGT, genome mergers, genome remodelling and the genetic controller (epigenetics) and epigenetic markers imprinted on the epigenome ultimately driven by environmental change, can.  Therein may lie the answer to biology’s big bang/s, This rather radically different model of evolution (ultimately based upon historically forgotten or marginalised and some cases, suppressed, alternatives to the Neo-Darwinian version) begins to close the seemingly widening gaps in the fossil record and taken to its logical conclusion, can argue that certain species did not actually go extinct, but remain as thriving modernised and specialised forms of their more primitive selves.

Palaeontologists could save a heck of a lot of money, time and resources if they could only look at the fossil record through the eyes of an epigenetic caterpillar don’t you think?

Epigenetic processes can also explain how embryonic-type pre-Cambrian animals morphed into the seeming explosion of life without any precursors. It can explain how a clone or polyp doesn’t even have to come from a fertilised egg and yet be different epigenetically, but genetically identical to its mother. It explains why pluripotent stem cells know what to be – bone, skin, neuron, or organ cells as each cell in your body contains the same genes and chromosomes given to you by your parents. Epigenetics can explain how these cells ‘know what to be’. It can even begin to let us see a different form of evolution, going from a generalist to a specialist species,  an amphibian generalist (that metamorphosed from a chordate – tadpole-type stage, into a walking tetrapod; how generalist tetrapods perhaps adapted to become more specialist proto-mammals (warm-blooded with more complex metabolism) and other tetrapods (due to their simpler metabolic rate) became stabilised earlier leaving them as fundamentally cold-blooded tetrapods who via hybridisation and any number of genetic exchange (in the primordial pond and after due to biting insects inserting their own genes between whole domains of life) could specialise within this form.   So next week’s topic will start with the Pre-Cambrian and we’ll begin applying all these different evolutionary models to the actual fossil record and perhaps see evolution in a different epigenetic light.

I’ll just leave you with this epigenetic quote about the Cambrian (biology’s big bang) first:

The concept ‘that epigenetic mechanisms are the generative agents of body plan and morphological character origination helps to explain findings that are difficult to reconcile with the standard neo-Darwinian model, e.g., the burst of body plans in the early Cambrian, the origins of morphological innovation, homology, and rapid change of form.

Abstract NEWMAN & MÜLLER

https://www.nymc.edu/sanewman/PDFs/Epigenetic%20mechanisms%20MDE.pdf

Advertisements

One thought on “Well if it didn’t happen by Neo-Darwinian means, how did evolution occur? Part Three: Descent via Epigenetic Modification

Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out / Change )

Twitter picture

You are commenting using your Twitter account. Log Out / Change )

Facebook photo

You are commenting using your Facebook account. Log Out / Change )

Google+ photo

You are commenting using your Google+ account. Log Out / Change )

Connecting to %s