Below is an excerpt (Chapter Ten) from the ebook entitled: ‘The Darwin Delusion: But Old Mr. Darwin wasn’t to Blame’. This sample chapter should also give you a flavour of the next project, which is well under way: the new paperback book by the title ‘Evolution: A Third Way?’ (part one is being professionally edited as we speak)..This is for anyone, like myself, who prefers a physical book and likes clear answers to complex questions.

Evolution: A third way?
Evolution: A third way?
*unfortunately the references in the sample chapter below are not clickable (I’m still finding my way with all this technology), but there are fully clickable links to all the references in the ebook – but just remember the book is much less than a Cappucino Grande and certainly less frothy – But Old Mr. Darwin wasn’t to Blame

Chapter Ten


The Epigenetic Caterpillar and the Story of the Blind Cave Fish (some case studies)

If you haven’t run away screaming yet, you are doing very well and, should congratulate yourself on at least having an open enough mind to hear me out thus far. The reason why I had to tell you about all the serious problems with the whole Darwinian Theory of evolution to begin with is to clear away the dead-wood, so to speak, so that we can perhaps begin to get at least a glimmer of how evolution may have actually unfolded, rather than, being continually thwarted in our efforts by the old engrained Darwinian explanation. I mean it is all so immensely awe-inspiring when you really look at it. But, when every aspect of it is continually interpreted in a very particular way (which just might happen to be entirely wrong), and this becomes all invasive in our minds, then we cease to question, stop wondering and actually miss the deeper mysteries embedded in the wondrous complexities of our natural world. I believe it is time to take off our blinkered Victorian monocles and put on a very broad set of spectacles instead; not rose tinted ones, but rather: infra-red types, so that we can begin to penetrate through to the dimly visible spectrum of the life (…But, not quite as we know, yet).

So, now having cleared away (hopefully) a good deal of the dead-wood, I thought that a good way to demonstrate all these Hox mechanisms, jumping genetics, extended epi-genesis/epigenetics and leaping evolutionary mechanisms as alternatives models of evolutionary change, would be to apply some of this new understanding in biology to a very traditional story of the Peppered Moths: the so-called ‘evolution in action’ by natural selection, which the Darwinists hold up as their poster-child and proclaim to be proof-positive of evolution by Darwinian means.

For example, the Guardian, (11 May 2002) an article entitled: Darwinism in a flutter: Did a moth show evolution in action? by Peter D. Smith’s reviewing a newly released book: Moths and Men: Intrigue, Tragedy & the Peppered Moth by Judith Hooper, is quite revealing. Below is part of the article:

The problem with Darwin’s theory of evolution by natural selection is that it describes events that occur over thousands of years, and is therefore difficult to prove empirically. But the industrial revolution seemed to offer scientists a perfect example of rapid environmental change, forcing organisms to adapt quickly.
…In 1848, a black or melanic form of the peppered moth appeared in Manchester. At the time, 50 tonnes of industrial fallout were deposited annually on each square mile of the city. These pollutants killed the lichens on tree bark, and in 1896 a naturalist linked this with the decline of the lighter form of the moth. In polluted areas the black moths were better camouflaged against the dark tree trunks, and so less likely to be eaten by birds. It was evolution in action, a perfect demonstration of the survival of the fittest. There was just one problem: no one had seen birds eating moths from tree trunks.

In 1953, Bernard Kettlewell, “a loud, eager man” who was invariably dressed in shorts and sandals, began an experiment that would transform the peppered moth into “evolution’s number one icon”.

His results were striking. The black moths were twice as likely to survive in the polluted woods as lighter moths. It was one of those rare “eureka” moments: Kettlewell’s experiment was what scientists had been waiting for, “living proof of Darwin’s theory of natural selection”… (83)

As you may have already guessed, I’m also showing you how controversial and outright ridiculous and obsessed Neo-Darwinists can get about supporting their theory. If they are so confident in it all, why don’t they just sit back and relax and let the science unfold as it should? So the saga continues….

…In the 1970s, the American lepidopterist Ted Sargent highlighted serious problems with Kettlewell’s experiment. But no one wanted to know: his research was ignored by the scientific community and his career stymied. The peppered moth experiment was “sacred”; critics were “demonised”, their views dismissed as “heresy”. But the evidence grew and in 1998 a prominent biologist, reviewing it in Nature , said his shock at the extent of the doubts was like discovering as a child “that it was my father and not Santa who brought the presents on Christmas eve”.

Like any good journalist, Hooper knows a scandal when she sees one. “The unspoken possibility of fraud hangs in the air,” she says, noting that Kettlewell’s field notes have conveniently disappeared… Hooper’s absorbing account of a flawed if not fraudulent experiment reveals an all-too-human side to scientists that will annoy professionals and enthral laypeople in equal measure. One thing is clear, though – science is much more than a collection of objective facts and figures. Ambition, jealousy, and megalomania are all part of this complex equation. (83)

Science writer Richard Milton in his fascinating and well-grounded book, if not rather controversial particularly regarding geological timescales (but facts are facts), entitled: The facts of life: shattering the myth of Darwinism (1992) as I alluded to in chapter one, has this to say about the peppered moth saga: “{…] although the story of the peppered moth sheds no light at all on natural selection or evolution, it sheds a great deal of light on how some Darwinists have constructed and promoted their theory” (84).

But to be fair, apparently they have carried out similar experiments since – properly this time, and got some confirmatory results – apparently (85). It is all on the: Why Evolution is True site by Jerry Coyne web-site. Now Jerry is a pretty heftily-credentialed defender of evolutionary Darwinism. For instance, the bio on his website states that he is a Ph.D, and a Professor in the Department of Ecology and Evolution at the University of Chicago, plus a member of both the Committee on Genetics and the Committee on Evolutionary Biology, and so on and so forth. Oh, and he also wrote a book by the same title of his website: Why Evolution is True. Now having read this defense of the Peppered Moth experiments in more recent times, I still cannot see how, by showing that birds tend to eat more light colored moths against dark trees is proof of evolution in action – via Darwinian natural selection? Maybe I’m missing something here? Now just as an aside, when I was perusing Coyne’s website, I noticed an interesting quote by Richard Dawkins that seemingly Jerry has in his author section as he greatly admires Dawkins’ position on Darwinian evolution, which is not dissimilar to his own:

Natural selection is the only workable explanation for the beautiful and compelling illusion of ‘design’ that pervades every living body and every organ. Knowledge of evolution may not be strictly useful in everyday commerce. You can live some sort of life and die without ever hearing the name of Darwin. But if, before you die, you want to understand why you lived in the first place, Darwinism is the one subject that you must study. — Richard Dawkins (85)

I really worry about these Darwinists sometimes. Do you not think that Dawkins is just a tad over the top in his devotion to his god? Now returning to the Peppered Moth Saga, does this actually prove evolution in action via Darwinian means I asked myself, now armed with some alternative mechanisms? Interestingly, I dug into the deeper mysteries of mimicry and insects taking on the characteristics of their environment, you know, like a stick insect looking exactly like, well – a stick, and such things of that nature? I was basically asking the question: could I find studies and empirical evidence, which would demonstrate rapid evolutionary change at a macro level that could be explained via natural developmental processes and epigenetic mechanisms, which would therefore, not require all those randomly mutating genetics (distributed amongst isolated gene pools of over-classified species floating about on lumps of land), which might happen to come in handy one day and be selected to give an organism a chance at survival?

Eventually, I found several studies and related articles talking about insects of all types, including moths and caterpillars and flies with wings and without wings depending upon the season and the timing of their birth morphing according to epigenetic triggers, and I also came across a really interesting story of serious evolution in action (macro and rapid) relating to much more complex creatures such as fish. However, this is a sorry tale once the Darwinists got their hands on it. I will tell you a bit of it further on. However, in the meantime, first I must explain that this mission of applying the alternative mechanisms to evolution in real time was not that straightforward at the beginning, as you might imagine. I had to get by those mainstream gatekeepers of the orthodoxy who filter out all this new evidence if it is looking anything like it might contradict the Darwinian position on evolution.

So, I went searching for evidence to explain phenomenon of mimicry/camouflage etc in the wild for example, as I wondered: how did the Darwinian Theory explain all of this weird and wonderful stuff? Unfortunately, at first, I made the mistake of looking for alternative mechanisms for the peppered moth phenomenon directly, and of course, I immediately got directed to all the claims of how the melanism in pepper moths was proof positive of Darwinian evolution in action. Or worse still, sites claiming that somehow the rapid and drastic changes seen in species organs and coloration were somehow explicable via a clever mathematical population, gene-jiggling mutation models that proved, using statistics, that these were lying in wait (selectionist style) to give the creature exactly what it required to survive its new surroundings.

Anyway, Google resisted my efforts to penetrate this Darwinian smokescreen by not allowing me to question this peppered moth enigma in this scientific manner that contravened the Darwinian stance, such as putting in the term epigenetics with Peppered Moths. Yes, I know, it was a really silly thing to do. Ok, maybe I’m being a little paranoid. Let’s just say, it redirected my questions straight to links: yes, you guessed it, I was flung straight into the quagmire of the religion vs. Dawkins type debates. Now before outlining some of what I found in the end, I just thought I would share the following saga regarding the only mainstream link to peppered moths and epigenetics. It is quite telling.

For instance, according to Wikipedia on its dedicated page for Peppered Moth Evolution, they note a number of opposing views of the interpretation of the moth’s bird predation (the selector) way back at the end of the 19th century. One alternative view was proposed by a fellow of the name of John William Heslop-Harrison, which was too Lamarckian for most. John Williams objected to J.W. Tutt’s proposition that moths changed their color due to bird predadation in the following:

John William Heslop-Harrison (1920) rejected Tutt’s differential bird predation hypothesis, on the basis that he did not believe that birds ate moths. Instead he advocated the idea that pollutants could cause changes to the soma and germ plasm of the organism. The origin of this hypothesis probably has its roots in the 1890s, when it was proposed as a form of Lamarckism. It is important to note its historical context. (86)

Yes, perhaps peppered moths don’t sit exposing themselves on the barks of trees waiting for their predators to come along and gobble them up and John Williams could be right about birds not liking moths. I think they like juicy caterpillars instead. As it turns out, we are not allowed to take John William Heslop-Harrison’s epigenetic-like (Lamarckian) explanation of changing color of moths seriously, because he was accused of fraudulently faking some rare species of flowers. How convenient. Wikipedia continue on the same page to list experiments carried out to disprove this Lamarckian type explanation which were as you might imagine pretty unsuccessful. I think epigenetics is a little subtler than some of the descriptions given by Wiki. For example, a man called Hoasebroek carried out experiments and I don’t think the insects reacted well to his poisons and gases, thus, Hoasebroek only produced deformed mutants.

After this little foray into the sordid history of natural history, and there are many more involving midwife toads and other such creatures, but time is of the essence and we must move on, so eventually I found the missing link between epigenetics, environmentally induced melanism, epigenetic causes of mimicry and camouflage and much more macro-changes (such as some insects were born with wings while others of the identical species only had buds during development, but never developed wings); this is referred to as polyphenism.

Basically, polyphenism does not fit in with our current paradigm of evolution by Darwinian means, and it is often referred to as a ‘special case’ in the natural world. This is because the same species of insect with essentially the same genetic make-up will sometimes look and act very different, yet they are essentially the same species. Polyphenism is becoming clearly recognized as an epigenetic phenomenon which I will review below, but there are a couple of terms that you will come across in these articles which I should explain briefly. Genotype, which is the genetic makeup of an organism and the Phenotype, which is essentially how an organism looks, e.g. does it have wings are important terms. And as I said earlier, sometimes the genotype can be very similar within quite different looking species, but if you bear in mind that it is the way that the genes which code for proteins are expressed that make the difference in the outcome of the phenotype. The following article explains polyphenic phenomenon in insects in, Oxford Journals, Bio Science, entitled: Control Mechanisms of Polyphenic Development in Insects (1999) by H. Frederik Nijhout:

Polyphenism is a special case of phenotypic plasticity; it refers to the ability of animals with the same genotype to develop two or more distinctly different alternative phenotypes without intermediates. The phenotype that is expressed depends on the environmental conditions that the organism encounters during its development.

Polyphenisms have many manifestations. Many insect species have distinctive seasonal adult phenotypes; these may be winged or wingless, may differ in the proportions of various body parts, and may have different food preferences, reproductive characteristics, and color patterns […]. Many of the phenotypic differences between seasonal forms are believed to be adaptations to the limitations and opportunities presented by a seasonally changing environment. The seasonal phenotypes of insects can be so different from each other that many were initially described as different species. (87)

Epigenetically speaking, a good comparison would be that identical twins are genetically identical, but not epigenetically identical. As the twins go through life, and have different experiences and, different exposures to foods, toxins, stress etc, they can grow epigenetically apart in quite profound ways. Environment is everything in epigenetics and this is particularly profound during the early stages of development when genomes are less fixed. Now polyphenism in insects is similar, in that certain genes will be expressed, while others will not, depending upon environmental changes and needs. So wings may be expressed in a batch of larvae and not within others. Remember the Hox gene clusters acting like master switches during development building a basic body plan? Well the wings are potentially in protein form to continue developing wings in those body plans, but epigenetic (an organism responding to its environment) factors are what triggers the gene expression or gene suppression, depending upon the requirements of the organism, the group, and the eco-system that they are operating in. Epigenetics in a sense fine-tunes by silencing or activating an organism after the main parts are in place.

In Genetics Research International (2012), entitled: Aphids: A Model for Polyphenism and Epigenetics by Dayalan G. Srinivasan and Jennifer A. Brisson, they stress the fact that these epigenetic systems are fully applicable to polyphenism and indeed, this model can be applied to all types of animal forms, not just the aphid fly. Don’t worry about some of the terms used below. They are not essential for you to get the main idea in the following abstract:

Environmental conditions can alter the form, function, and behavior of organisms over short and long timescales, and even over generations. Aphid females respond to specific environmental cues by transmitting signals that have the effect of altering the development of their offspring. These epigenetic phenomena have positioned aphids as a model for the study of phenotypic plasticity. The molecular basis for this epigenetic inheritance in aphids and how this type of inheritance system could have evolved are still unanswered questions.

With the availability of the pea aphid genome sequence, new genomics technologies, and ongoing genomics projects in aphids, these questions can now be addressed. Here, we review epigenetic phenomena in aphids and recent progress toward elucidating the molecular basis of epigenetics in aphids. The discovery of a functional DNA methylation system, functional small RNA system, and expanded set of chromatin modifying genes provides a platform for analyzing these pathways in the context of aphid plasticity. With these tools and further research, aphids are an emerging model system for studying the molecular epigenetics of polyphenisms. (88)

Obviously, the study above is clearly showing the link between polyphenism and epigenetic processes and how this model can be applied to other insects, which is interesting, as we are now getting closer to talking about moth-type creatures, or at least butterflies, which are not that different to moths as seen in this next piece of research, which, not only explains the polyphonic phenomenon in epigenetic terms, but also clearly outlines how the Darwinian version of evolution comes nowhere near to explaining something like (di-) or poly-phenism seen within identical species. In a book entitled: Epigenetic Principles of Evolution, Nelson Çabej states the following:

Any gradualist mechanism of the accumulation of favorable hereditary changes under the action of natural selection or genetic drift would immediately be rejected as an explanation of the seasonal diphenism. Indeed, no attempt has been made to explain the phenomenon from a neo-Darwinian view.

[…]There can be no doubt that the seasonal polyphenic adaptation did not arise instantly at the moment this butterfly diverged as a separate species from its ancestral stock. First, the butterfly might have evolved a phenotypic plasticity for wing patterning, where individuals of the same population, or even of the same brood (implying the same genotype), might express one of alternative phenotypes, as often occurs in cases of developmental polymorphisms.., (89)

Here is yet another piece of research about a similar topic and the relationship between epigenetic control of polyphenic changes in insects and again an insight into the difficulties with the Neo-Darwinian stance and its interpretation of this phenomenon. Mayr is noted in the abstract and just to remind you who he is, he was one of the leading Neo-Darwinists involved in the New Synthesis way back in the 1940s. So bear this in mind as you read the opening of this science paper entitled: Polyphenism in Insects by Stephen J, Simpson et al in Current Biology (2012), where the paper places Polyphenism in its historical context and in the abstract and part of the main text of the same paper, the epigenetic aspect of the phenomenon of polyphenism is explained. They also mention Lamarck:

Until publication of Mayr’s 1963 book, however, environmentally induced phenotypic plasticity suffered the taint of Lamarckism and was largely ignored in favour of the more respectable, or to use Mayr’s words, “more useful and precise” study of genetic polymorphisms, in which phenotypic variants are produced by different rather than the same genotypes {…]

[…] Polyphenism is the phenomenon where two or more distinct phenotypes are produced by the same genotype. Examples of polyphenism provide some of the most compelling systems for the study of epigenetics. Polyphenisms are a major reason for the success of the insects, allowing them to partition life history stages (with larvae dedicated to feeding and growth, and adults dedicated to reproduction and dispersal), to adopt different phenotypes that best suit predictable environmental changes (seasonal morphs), to cope with temporally heterogeneous environments (dispersal morphs), and to partition labour within social groups (the castes of eusocial insects) […]

We survey the status of research on some of the best known examples of insect polyphenism, in each case considering the environmental cues that trigger shifts in phenotype, the neurochemical and hormonal pathways that mediate the transformation, the molecular genetic and epigenetic mechanisms involved in initiating and maintaining the polyphenism, and the adaptive and life-history significance of the phenomenon. We conclude by highlighting some of the common features of these examples and consider future avenues for research on polyphenism […]

In addition to being environmentally determined, aphid wing polyphenism has also been shown to be under epigenetic control. During parthenogenetic reproduction, females can be induced to produce winged progeny by appropriate environmental stimuli; however, this winged next generation will themselves produce largely wingless progeny, even in the presence of wing-inducing stimuli. (90)

If that is not macro-evolution (rapid) in action, well, then I’m not sure what is. Whether an insect has wings or not really is quite a big deal. After all, we base our entire classification and our inferences of evolution upon presence or absence of things like wings. Can it fly: can it not? No, wonder Neo-Darwinian theory in its most updated form cannot begin to explain polyphenism and why Mayr as usual, just changed the definition to make it seem like less of a ‘special case’. Yes, and all that Lamarcky stuff was banned and therefore they could not possibly interpret polyphenism as an epigenetic phenomena.

Hopefully, you can see that epigenetic processes are empirically linked to insect polyphenism and this in turn has implications for how we have, up until more recent times, been viewing a vital clue in evolution – polyphenism. The above article also notes parthenogenetic reproduction, which is worth noting in this context as it literally means virgin birth. I wonder what the population modelers would make of that.

Yes, all this major (macro-evolutionary) change according to environmental information read at a cellular level by the organism (during development in particular) is epigenetic in nature and a much more dynamic explanation of evolutionary change than Darwinian theory has to offer. I.e., environmental stimuli can mean the difference between young sprouting wings or not.

I hope you are getting my point here. I really did have to come at this whole thing sideways, as there is so much out there that is simply saturated by the whole Neo-Darwinist version of evolution. My point being that: if seasonal polyphenic adaptation can make a whole creature’s wings come and go in a season depending upon what way the wind is blowing, what’s the big deal that a peppered moth would change from light colored to dark via epigenetic means? So now that we have established the clear link between epigenetics and polyphenism (rather than the totally inadequate attempts to describe the phenomenon of polyphenism – the special case), we will have a brief look at another study investigating the environmental sensitivity and (response) change in caterpillars, of the moth variety. I told you I would get to moths eventually even if they are the juicy caterpillars that the birds really like.

Here is an excerpt from a science paper that I found interesting and revealing, where an experiment with caterpillars of the moths and yes, they are the peppered moth variety and the research deals with color change also. It is taken from a paper in a scientific journal (2008) entitled: A Reversible Color Polyphenism in American Peppered Moth (Biston betularia cognataria) Caterpillar. Note the word Polyphenism which you should be well acquainted with by now in relation to epigenetic mechanisms. Here is a short overview of the experiment and some of the results:

B. betularia caterpillars are generalist feeders and develop body colors that closely match the brown or green twigs of their host plant. […] Under controlled rearing conditions, we manipulated diets and background reflectance, using both natural and artificial twigs, and show that visual experience has a much stronger effect than does diet in promoting precise color matching. Their induced body color was not a simple response to reflectance or light intensity but instead specifically matched the wavelength of light to which they were exposed. […] The camouflage protects the caterpillars from predation by birds. (91)

Simply put, these experiments with environment and diet were found to directly change the phenotype (i.e. how it looked in this case its color) and how this color developed in these young caterpillar under controlled conditions of different types of environments and showed color and light frequency changes that exactly corresponded to these environments; thus, demonstrating mechanisms for camouflage so often seen within insect species. There are several more studies like the one above, but I just highlighted this one as it gives you an idea of how it relates specifically to peppered moths and their coloration.

However, you still may not be convinced that a similar switching on or off of certain other genes could occur during development to give a pepper moth (adult) a lighter or darker wing color to not protect it from bird predation, but as a means of blending in with its environment epigenetically. Well, it was very smoggy and quite toxic back in England in those days of the Darwinian pepper moths. So, perhaps as epigenetic (jumping genes) are triggered by stress and can recode an entire genome via cutting, pasting, duplication and general natural genetic engineering and all this can be inherited, does it not seem reasonable to suggest that these peppered moths thought it better to darken down (mimicry) to simply be more in tune with their darker environment. The frequency of the pigmentation (melanism) may have changed, as we know from the above studies how fine-tuned these critters are to even a slight change of background variation. Perhaps, the peppered moths never went extinct: they just changed their wing color and passed on these fixed traits to their offspring?

This is obviously a very un-Darwinian interpretation of the peppered moth story of evolution. But if you really sit down and think about it, this phenomenon really does go directly against the modernized Darwinian genetic version of mutating genes giving enough variation to be naturally selected in a population that just happens to outcompete with another population that were more visible to bird predation. The very un-Darwinian idea of epigenetic polyphenism in butterflies, moths, caterpillars, flies etc and insects across the board, show, that these creatures are highly tuned and responsive to their environments, particularly in their developmental stage. Whether an insect sprouts wings, or don’t sprout wings, or a stick insect resonates with a particular branch and forms a symbiotic relationship, which probably occurred way back in the mists of time rather rapidly and now looks terribly like a stick, or whether a juicy caterpillar is an exact match, not only of the color of leaves and twigs they are exposed to, but they also match the frequency of their surroundings which, protects them from bird predation (the very so-called selecting agent in the case of the peppered moths in Darwinian speak), really cannot be explained in any way, shape or form, by the Darwinian version of evolution.

Yes, all this subtle rewiring and changes in adaptive programs as I said above, occurs during development. I’m not talking about color changes in mid air, or the sudden loss of a wing or both, no, I mean that all these epigenetic studies show that if an adaptive change is important in a stressful situation, then the offspring will rapidly via epigenetic triggers which, if strong enough can mark the genome and these traits/changes can be inherited and expressed in later generations. In other words, epigenetic processes is a much more dynamic alternative to light-colored moths getting eaten by predator birds because all the lichen on the trees has fallen off, turned the trees dark and blew their cover (camouflage) making them stand out like sore thumbs. Now in the Darwinian scheme of things, the birds will have won and so would the dark moths who happened to out compete with their light-colored kin and just happened to have the right genetic makeup (genetic mutations for darkness) and quickly bred only that trait (naturally selected) and the poor light-colored moths were now extinct, well at least in that part of England at that time.

Now, that’s enough said about the peppered moths. So, let us look at other creatures, other than insects and moths and see how similar processes (environmentally educed triggers of re-wiring and different gene expression/non-expression) can also cause macro-evolution in higher organisms such as: fish. Although, as we move from insects to more complex creatures such as vertebrates polyphenism is not so obvious, but, in terms of the epigenetic/developmental evolutionary biological (EVO-DEVO) explanation of macro-evolutionary change, the same principals apply. For instance, in this next abstract, the link between epigenetic systems common to, not only insects, but vertebrates and all domains of life as outlined in: Functional Conservation of DNA methylation in the pea aphid and the honeybee (2010) by Brendan G. Hunt et al,

DNA methylation is an important epigenetic modification that plays a role in gene regulation in many organisms [refs]. Although DNA methylation occurs in all three domains of life, its genomic patterns how considerable variation among taxa [refs]. For example, vertebrate genomes exhibit global patterns of methylation, but invertebrate genomes tend to display reduced or minimal levels of methylation [refs…] (92)

So what I’m essentially saying is that, epigenetics and their markers (methylation) can actually tell us a good deal about how evolution unfolded and it also provides us with mechanism which does not actually change the genes themselves, but changes their expression, so no wonder we all look so different (all the different domains of life) yet, our genetics remain fairly similar. (remember the banana and how we share half our genes with them?).

Furthermore, epigenetic processes across all species provides a mechanism, a way of adapting and changing according to environmental changes which means, in a nut-shell, that they don’t need to hang around waiting for a random mutation that will give them some advantage to be passed along the genetic line. This alternative way of seeing evolution, as discussed in the previous chapters, is to see that these epigenetic mechanisms that operate on existing genes (causing macro and micro-changes) is actually a profoundly different to our traditional model of evolution when you think about all of its implications. This mechanism also begins to touch on explanations of metamorphic evolution also, but time is of the essence and this will be addressed in a later book within this series.

This is macro-evolution in action and thus has massive implications for evolution itself. There is no need for all that slow old gradual development of one wing at a time kind of evolution. Related to these epigenetic triggers and common gene sets that are orchestrated by the epigenesis/epigenetics causing profound changes to how a species looks, functions and behaves (remember the well-licked rats?) and of course as major changes can be brought about within an existing species and is often stress induced and regulated by an epigenetic mechanisms, then just as I discussed earlier regarding the power of jumping genes when triggered by stress to rapidly change entire segments of genomes, this also has profound implications for past evolutionary events and our understanding of them.

For instance, as one popular science site, sourced from peer-reviewed journals, Science Daily (source: Riken) puts it in an article heading entitled: Mechanism for stress-induced epigenetic inheritance uncovered in new study (2011):

Researchers have uncovered a mechanism by which the effects of stress in the fly species Drosophila are inherited epigenetically over many generations through changes to the structure of chromatin, the material that makes up the cell nucleus. […] marking a major advance in our understanding of non-Mendelian inheritance.

Recent years have seen growing interest in the phenomenon of epigenetic inheritance: the idea that our genome, through epigenetic tags and other structural modifications, transmits more information than the sequence of letters encoded in its DNA base pairs alone. Stresses of various kinds have been shown to induce such epigenetic change […] (93)

The article is particularly interesting as it not only highlights the fact that this epigenetic inheritance passed on via tags, is non-Mendelian inheritance (remember the monk’s pea experiments that were supposed to lead to Darwin’s theory being reinstated because it was somehow an explanation for natural selection?) but, it also highlights the fact that there was real structural (physical) change that can be triggered by stress and this operates above the main genes, instead regulating them in such a way as they are expressed differently according to the stress.

A good example of this epigenetic/environmentally triggered stress phenomenon can be found specifically in what has come to be known as HSP90, a heat protein which, is particularly sensitive to heat but, is really just a protein that will respond to any drastically different, stressful and/or rapidly changing environment. Remember the bacteria, for example, that epigenetically rapidly adapted to a new strain of antibiotic and it adapted so quickly that: this change could not be accounted for by mutations, even if they were beneficial ones, we know they are not and certainly don’t appear to play a role in change of the species/evolution?

A number of scientific papers in peer reviewed journals have highlighted this next link for example explains the mechanisms between epigenetics and the heat shock protein (source: Swiss Institute of technology Zurich 2012) entitled: How environmental effects regulate genes by Maja Schaffner:

ETH-Zurich researchers provide evidence that a protein in the cell nucleus responds to environmental stimuli like a kind of sensor, regulates genes accordingly and thus exchanges information with the cell memory[…] If we get too hot, our body responds: it increases the blood flow to the skin so that more heat can be transported outwards and released. It sweats to cool us down through evaporation […].

However, inside the body a kind of SOS programme is launched: in the cells, a large number of heat-shock proteins are formed very quickly […] The gap between environmental influences and cell memory is bridged by Hsp90. The protein also controls genes that respond to stress and are linked to the cells’ memory. Hsp90 thus communicates directly with the cell memory. As a result of stressful environmental influences such as heat shock, in certain circumstances genes can be marked with proteins containing epigenetic flags. These decide how well or less well these genes can be activated in future – in this case, in preparation for potential heat stress later on. (94)

Another related article highlights the significance of Hsp90 in global activation of paused genes triggered by environmental stimuli. Entitled: Hsp90 Globally Targets Paused RNA Polymerase to Regulate Gene Expression in Response to Environmental Stimuli (2012) by Ritwick Sawarkar, Cem Sievers and Renato Paro:

Inhibition of Hsp90 leads to upregulation of target genes, and Hsp90 is required for maximal activation of paused genes in Drosophila and mammalian cells in response to environmental stimuli. Our findings add a molecular dimension to the chaperone’s functionality with wide ramifications into its roles in health, disease, and evolution.(95)

This next title is self explanatory: Evidence for an epigenetic mechanism by which Hsp90 acts as a capacitor for morphological evolution (2003), where they conclude in the abstract: “These findings suggest that Hsp90 acts as a capacitor for morphological evolution through epigenetic and genetic mechanisms”. (96). Unfortunately, they do use the old selection and mutation words, but we’ll forgive them as they are fully indoctrinated and don’t know any better. And now moving on to a different title, but with just a bit more about those Hsp90 proteins; and I promise I’ll move on to my point of laboring this particular connection of epigenetic mechanisms and the heat shock protein.

In this article: in Genetics Society of America Perspectives Anecdotal, Historical and Critical Commentaries on Genetics, entitled: Molecular Clock: ‘An Anti-neo-Darwinian Legacy’ by Naoyuki Takahata (2007) after pointing out all the issues with the molecular clock, this paper concludes that it should be retained even if it is not that accurate or applicable in certain cases depending upon what one is looking at: genes versus morphology etc. Anyway, apart from the fact that I think this author needs to have another look at the fact that they, as do most evolutionary biologists assume, that their clocks are measuring something that is correct in the first place, i.e. direct common descent from a single origin. Anyway, the article does eventually get onto the importance of the Hsp90 proteins and states the following:

It is true that organisms must adequately buffer the influences of mutation and environmental challenge to create a trade-off between stability and the potential for changes. Hsp90 does this job. It can store hidden phenotypic variation and its change can produce a profusion of morphological changes, for instance, by affecting interaction with various proteins in signal-transduction pathways or by inducing epigenetic alterations in gene expression. (97)

I don’t believe it. They used that mutant word again. Anyway, the important bit is the empirical link between epigenetics and this heat-shock protein Hsp90. You will soon know why I’m harping on about this link further on. There are many more examples, but I think you might have heard enough. The Hsp90 is epigenetic in nature and the bridge between the environmental changes/stresses, and organism via its cells (epigenetically controlled processes). This Hsp90 is stress related, akin to an emergency backup system, in case things turn out to be environmentally radically different to the norm. it is as though organisms have the ability to activate whole body parts or deactivate them (remember the polyphenism in seasonal wings in insects?) according to requirements, only with this epigenetic shock triggered protein, this is the emergency response unit in overdrive to a particular and usually dramatically changing situation. Take for example, the case of the blind cave fish.

The science site – Science Daily is a case in point. The article (2013), sourced from Whitehead Institute for Biomedical Research, describes the loss of sight and eyes in fish in dark caves that, did not require them any longer. The heading reads: Rapid evolution of novel forms: Environmental change triggers inborn capacity for adaptation. And nothing in the title or the rest of the text actually uses the term epigenetic, yet the study reveals a mechanism of rapid change, adaptation and the integral role of the heat-shock gene (protein), specifically Hsp90 in this amazingly rapid, environmentally triggered loss of eyes within a relatively short period of time and generations when seen within geological timescales. Pertinent parts of the article are given below:

In the classical view of evolution, species experience spontaneous genetic mutations that produce various novel traits—some helpful, some detrimental. Nature then selects for those most beneficial, passing them along to subsequent generations. It’s an elegant model. It’s also an extremely time-consuming process likely to fail organisms needing to cope with sudden, potentially life-threatening changes in their environments. Scientists now report that, at least in the case of one variety of cavefish, one agent of evolutionary change is the heat shock protein known as HSP90. […]

Although seemingly counterintuitive, the loss of eyes is thought to be an “adaptive” or beneficial trait, as the maintenance of a complex but now useless organ would come at a high metabolic cost. Thus, the fish could reallocate their finite physiological resources to biological functions more helpful in the cave setting.
This is the first study showing that this HSP90-mediated mechanism can be applied to vertebrates for real morphological adaptive traits […] this latest work should help quiet those who are skeptical of the impact of this mechanism throughout the plant and animal kingdoms […] We now have enough evidence to say that large, rapid environmental change can reveal new variation and change the outcomes of real evolution in nature [..] (98)

Amazing, really and how clever: a silent mechanism waiting to spring into action if the going gets tough, or resources need redirecting – a perfect adaptation mechanism and all done by epigenetic processes. But this is a sad tale as I warned you at the beginning of this chapter. Not because of blind fish had lost their sight, but because of the hijacking of this mechanism by the population geneticists. It is a woeful tale indeed. The saga continues in the same article as above: (I nearly fell off my computer chair when I read this bit):

[…] Eye loss in these fish is considered to be a demonstration of an evolutionary concept known as “standing genetic variation,” which argues that pools of genetic mutations — some potentially helpful — exist in a given population but are normally kept silent. The manifestations of these mutations, that is, their impact on observable phenotypes, don’t emerge until the population encounters stressful conditions. But what exactly keeps those mutations at bay?

Enter Whitehead Member Susan Lindquist, whose research has shown that HSP90 silences such genetic variation in a variety of organisms, from fruit flies, to yeast, to plants. […] The loss of HSP90 activity allowed phenotypic changes to emerge quite rapidly. […] (98)

I thought that Hsp90 was a mechanism used by fruit flies, yeast, plants, bacteria, insects, and even mammals, well at least according to my research. And I quoted one article above that said categorically that if you want a rapid adaptation to a rapidly changing environment, then: “Hsp90 does this job. It can store hidden phenotypic variation and its change can produce a profusion of morphological changes, for instance, by affecting interaction with various proteins in signal-transduction pathways or by inducing epigenetic alterations in gene expression. (97)

Does this shock protein mechanism for rapid adaptive change to say: being trapped in a dark cave and not requiring sight any longer, not apply to fish then? Or is that getting too close to the bone because it might begin to show how there might be another mechanism for our supposed transition from water to land and it might not actually have anything to do with a fin becoming a foot as studies have shown that fins can produce floppy limb-like (HOX regulation genes) structures but not actually produce the essential and much needed digits to form an actual foot (more of that in book two).

Umm, this does get very frustrating after a while. No, apparently, according to the article about the blind cavefish, it was via random mutating genes muddled up in population genetics and gene flow (standing genetic variation) and these fish just so happened to accumulate enough lucky random mutations that just happened to be naturally selected as adaptive to the dark cave. I wonder did one of these lucky fish have an ancestor, who also happened to be a mutant with small eyes, or perhaps none at all? How all pervasive is this genetic variation stuff is. But where’s your evidence? I don’t want conjecture and fancy models done on a computer and really complex mathematical formula, I want real empirical evidence as is the case with epigenetic studies, not “wishful speculations” as Professor James Shapiro has been known to say regarding the Neo-Darwinian version of evolution (1). Sorry for my rant. But, it really drives me cracked this whole invasive theory of everything that floats, swims or crawls.

Ok, I’ve calmed down now. I went to the Harvard medical paper which stated that these blind cave fish had become blind due to the actions of this Hsp90 protein activator. They appeared to be genuinely excited at the discovery; after all, it was all so radical and rapid, which is certainly very un-Darwinian. It was all so new, guess what they called it? Well it is in the title of their article: Revealing the Mechanisms of ‘Cryptic’ Genetic Variation (99) I looked up the word cryptic on Google and its meaning: that is mysterious or obscure and various other meanings are given: Enigmatic, mysterious, confusing, mystifying, perplexing, puzzling, obscure etc (100). Then I realized there was a second meaning under Zoology: which read: (of coloration or markings) serving to camouflage an animal in its natural environment. Ha, haa, I thought, the first definition of cryptic was correct and would the camouflage have anything to do with peppered moths by any chance? The science review article from Harvard continues to reveal the mechanism for this cryptic standing genetic variation mechanism and I read with great interest the following:

It’s a very cool story in terms of the speed of evolution,” said Nicolas Rohner, a postdoctoral researcher in the lab of HMS Department of Genetics head Clifford Tabin and first author of the paper. “By studying these exceptional fish, we believe we’ve identified an additional mechanism explaining how evolution can work.[…] The work provides the first evidence that HSP90 can facilitate morphological evolution in a natural setting rather than only in a lab […] (99)

Of course they talk about that well known shock protein HSP90 which is controlled at an epigenetic level, but do not (under any circumstance mention that Lamarcky nonsense of epigenetic processes). I read on, curious to know what their explanation of this new cryptic mechanism was that involved the heat-shock protein mechanism and found to my disappointment that they genuinely seemed perplexed by the whole phenomena of rapid evolutionary change of adaptation to the environment as seen in these blind cave fish in their darkened cave, I think the blind cave fish could see better. They took a couple of guesses and tried to make sense of it all. After all how else could it have happened?

The Harvard study essentially, went with the old mutating genes theory. Which as I highlighted above, apparently, according to reputable scientists doesn’t even create any change in species, only deformities? And of course the exact same epigenetic shock protein Hsp90 would have absolutely nothing to cause a rapid adjustment in the fish as they found themselves over generations in darkened caves, no longer requiring their genes that activate eyes to kick in as they don’t need them anymore. Indeed they are a hindrance and take far too much effort and resources and energy to maintain. Lamarckian dis-use comes to mind here.

But if you want to still believe that the fish lost their sight and their eyes because of some random genetic variation that was hanging around waiting to do its thing, that’s fine by me. I really do wander do these scientists actually talk to each other? Have they not read all these peer-reviewed papers on epigenetics and the link between big rapid changes in the genome and the heat shock protein HSP90? Or perhaps they are simply so locked into the Neo-Darwinian mind-set that they can’t possibly entertain or even think of another type of mechanism. But this story gets worse. Just when I was feeling sorry for all those, very excellent scientists working away and really finding stuff out but then going and spoiling their results with silly Victorian inspired interpretations of the data instead of seeing the really weird and wonderful mechanism going on in the background. Then I came across this article, I really could not believe it when I read it in its entirety. The article is entitled: A Theory Evolves How evolution really works, and why it matters more than ever by Thomas Hayden in US Today (2002). Here is the first part.

Scientists have confirmed virtually all of Darwin’s postulates. For example, Ward Watt of Stanford University has demonstrated natural selection in action. In a hot environment, he found, butterflies with a heat-stable form of a metabolic gene outreproduced their cousins with a form that works well only at lower temperatures. “Darwin was more right than he knew,” says Watt. Darwin also held that new species evolve slowly, the result of countless small changes over many generations, and he attributed the lack of transitional forms–missing links–to the spotty nature of the fossil record… And last year, paleontologists announced that they had recovered fossils from the hills of Pakistan showing, step by step, how hairy, doglike creatures took to the sea and became the first whales. (101)

I promise I did not make up that last sentence. This is the sort of thing we are up against. I’m not trying to change your mind. If you still want to hang on to the old Darwinian paradigm, be my guest. I just think it is an awful shame that this exciting new discoveries of epigenetic caterpillars or possibly caterpillars that grew up to become peppered moths who live in England even to this day, only perhaps camouflaged a bit so you might not have noticed them, and these rapid response mechanisms to adapt (epigenetically) all manner of creatures (including fish I’m sure) to their environments, and the implications of this for real evolutionary events of the past, is simply not filtering through to many scientists working in the broader field of biology. It would really stop them scratching their heads, if only they knew and were encouraged to look at other peer-reviewed journals that were not precisely within their field of expertise. Ah well, just a thought.

And the crazy thing about all this is that our current doctrine of Darwinian evolution bears very little resemblance to the original ideas of Darwin himself. Furthermore, Darwin didn’t even come up with the idea of common descent from a simple worm-like creature to more complex smart monkeys like our-selves, apparently. He just based his theory of natural selection upon this fairly common belief that we descended directly from something simpler, like fish. Perhaps some became blind and never made it out of their caves and grew their eyes back later when they escaped and seen that all the other fish had gone on to bigger and better things; just cod-ding of course. I find it interesting that in On the Origin of Species: By Means of Natural Selection, 6th Edition, Charles Darwin, writes about the fact that the vestigial eyes of moles and of cave-dwelling animals are “probably due to gradual reduction from disuse, but aided perhaps by natural selection.” (102).

Talking about blind cave fish and moles, (I told you it was a sad tale) even poor Lamarck became blind, but it wasn’t from disuse of his eyes, but perhaps because he was in so much darkness due to his struggle with poverty. According to the Berkeley college website, Lamarck spent most of his life in a constant struggle against poverty; to make matters worse, he began to lose his sight around 1818, and spent his last years completely blind, cared for by his devoted daughters (he had been married four times). When he died, on December 28, 1829, he received a poor man’s funeral (although his colleague Geoffroy Saint-Hilaire gave one of the orations) and was buried in a rented grave; after five years his body was removed, and no one now knows where his remains are.


2 thoughts on “Peppered Moths revisited: The epigenetic caterpillar & the story of the Blind Cave Fish

  1. Fascinating to me that your piece here hasn’t gotten more comments. Have you managed to avoid allying your work with the more direct assaults on Darwin’s work by creationists?

    Well, anyway, the story of Kettlewell’s peppered moths, it turns out, is solid as ever.

    See here:

    And here:


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