Evolution: A Third Way? Preface & 1st chapter under construction

Evolution: A third way?
Evolution: A third way?

 

PREFACE
Truly, I never set out to dismantle the Neo-Darwinian synthesis, it simply fell apart, just by looking at it. Perhaps I should substantiate this rather provocative statement which, I feel is best summarized by Eugene Koonin (evolutionary & computational biologist):

. “The edifice of the Modern Synthesis has crumbled, apparently, beyond repair” (Koonin E.V. 2009) (1).

My main objective in writing this book, is to help to explain why the edifice is crumbling so drastically in the first place, and more importantly, to demonstrate that all is not lost – as out of its ashes, a new and exciting synthesis is emerging. As Professor Denis Noble (eminent physiologist) states:

[…] all the central assumptions of the Modern Synthesis (often also called Neo-Darwinism) have been disproven. Moreover, they have been disproven in ways that raise the tantalising prospect of a totally new synthesis […] (2)

And the conceptual changes and magnitude of this tantalizing new synthesis is perhaps best summarized by Prof. James A. Shapiro (an expert in bacterial genetics and professor of Biochemistry and Molecular Biology) in the following:

The conceptual changes in biology are comparable in magnitude to the transition from classical physics to relativistic and quantum physics. (3)

(Shapiro 1997) The Boston Review Feb/March 1997 ‘A Third Way’. *

The quantum-like new synthesis emerging as a result of our most recent molecular breakthroughs and a deeper understanding of biological complexity, will be the main focus of this book and is dealt with in more detail in Part Two, entitled, – A Third Way, as in the title of this book, but without the question mark. Part One, entitled: Why We Need a Third Way: presents the issues with our current model and the historical context for these new and not so new ideas.
However I promise, you don’t need to be a molecular biologist or a quantum physicist to follow this new paradigm in evolutionary thinking. I’m not any of these myself, and I certainly do not profess to have the credentials specific to biology or the caliber of scientific standing of the above Professors, but, being a freelance research archaeologist at least gave me some of the tools required to begin tackling such a complex topic, although, I believe the fact that I came to education so late in life helped the most in the end. Well, I was too old to worry about seeking academic tenure and, besides, they told me there was no future in it – archaeology that is.
A strange thing happened one day, when I was thinking, hypothetically (an idea I was working on for a fictional story while, taking a break from writing archaeological reports), about how a geneticist from the 22nd century would explain the details of how life evolved on planet earth to someone like me or you from the early 21st?
It’s an interesting thought experiment, as I found. Because, I discovered, as I dug deeper,(in an attempt to find a believable factional answer),that evolution looked nothing like how I had expected. I know, most of us truly believe that our current model of evolution via Darwinian means, is the only theory of evolution that we have or ever had, as I used to think myself not that long ago. However, a closer look at the science behind our current model of evolutionary thinking, soon reveals that it is gravely inadequate to explain the deeper complexities of how life evolved on our planet. The evidence for this is well supported and presented at the beginning of Part One of this book.
Furthermore, as noted above, our conceptual understanding of biological complexity is beginning to offer a radically different view of evolution, but as it turns out, not all these ideas are so new in principal after all; as I found after a great deal of deep search in the dusty old archives (Ok they’re now on the web so researchers don’t even need to get their hands dirty). As it happens, a close investigation into many of these older ideas, clearly show that they were remarkably sophisticated principals of evolutionary thought and indeed, dove-tail nicely with our most modern understanding and deeper discoveries within biology. In combination then, these form an over-arching (quantum-like) synthesis of biological evolution.
You are probably wondering then, why have we never heard much about these great theories of old? Well, you see they were heavily marginalized in the past, ridiculed and in some cases actually banned, but most were simply forgotten and became historically obscure. Therefore, I have documented this as part of the discussion of the major issues with our existing model in Part One of this book and Part Two: integrates and reintegrates in some cases, the various alternative views of evolution pre-dating and post-dating Darwin and right up to our present time. This provides the main tenets of the new evolutionary synthesis as a whole.
All of what you are about to read is of course entirely based on scientific principals, hard data and supported at every turn by peer-reviewed scientific literature presented in a straightforward way.
I hope you enjoy the journey, I know I did.

 

 

PART ONE
Why We Need A Third Way

…a great man of science … knows everything about everything, except why a hen’s egg don’t turn into a crocodile, and two or three other little things…
Charles Kingsley: The Water-babies (1886) – friend of Charles Darwin

Chapter One
________________________________________
Common Dissent

This chapter should clearly demonstrate that there is a growing number of scientists that find the Neo-Darwinian model of evolution no longer tenable. Indeed, there is nothing new in this sentiment, as there has always been common dissent amongst many scientists regarding the serious and fundamental issues inherent in our current model of evolution. This should become entirely clear as you read from the quotes from highly respected scientists throughout this chapter.

Furthermore, towards the end of this chapter, I will highlight some quotes from various scientists and disciplines that are offering alternatives solutions to what they see as an increasingly limiting and almost entirely inadequate model of evolution. These alternative and much more dynamic models of evolutionary processes would be on the verge of replacing our current model of evolution, if this information were more widely available across disciplines and to people working in fields of medicine as well as non-specialists. Unfortunately it is not. These evolutionary alternatives and explanation of processes embedded in biological systems in combination would indeed create a much more powerful synthesis if any of us were actually aware of them.

The greatest obstacle to a wider dialogue and ability to disseminate these new and not so new alternative ways of seeing evolution and the issues embedded in our current model, is highlighted best in Shapiro’s great work, where he offers a science-based solution – a third way between, what has become an untenable situation of extreme ideologies: Creationists vs. Neo-Darwinism. Shapiro is very much the inspiration for this book, both its title and much of its research/content. Shapiro’s third way is based upon his own particular fields of scientific expertise, although, he has gone further than any other of his caliber (in my estimation) to bring his research to a wider specialist and non-specialist audience and to place these along with other fields of research into a larger evolutionary picture.

I have attempted to extend this approach by presenting the most cutting-edge ideas from scientists like Shapiro and others, by integrated our most current science with relevant traditional non-selection evolutionary ideas that were for the most part, heavily marginalized/ridiculed or ignored, while other evolutionary ideas were modified significantly to suit the Neo-Darwinian model, and others simply fell into obscurity over time. In other words, I have attempted to find a broader synthesis that also accommodates the great evolutionary thinkers of old as well as of our more modern times (I suppose it is the archaeologist in me that guided this particular approach). But, to really understand this broader new synthesis, we need to demonstrate why the old Darwinian model needs replacing in the first place.
Now just before presenting some of the modern issues embedded in our current model and a brief overview towards the end of this chapter of the their alternatives, I should firstly review the important historical context of Darwin’s original theory before it was modernized. This will facilitate a better understanding of the historical issues embedded within the subsequent Modern Darwinian Synthesis, which are the main focus of this present chapter. Now, to put the modern synthesis into perspective, it is important to bear in mind that there were older non-selection schools which became quite popular in many parts of Europe and Russian, and helped fill the gap resulting from the fact that Darwin’s selection theory of gradualism, which was believed by many, to be simply not powerful enough to explain the diversity of life – how one species ultimately changed into another (in more modern speak: macro-evolution which, Darwin’s theory extrapolated from micro-evolution, such as changes seen within a domesticated species of pigeon or dog-breeds to evolutionary species change). This is well documented in a book by Peter J. Bowler, The Eclipse of Darwinism: Anti-Darwinian Evolution Theories in the Decades around 1900 (1992) (4).

Therefore, the serious and well-founded scientific criticism in Darwin’s own time regarding his theory of selection and gradualism in particular, as borne out by reading his very considered and open replies to many of his critics via correspondences (these are all available on-line at Darwinonline for anyone to access), are important to bear in mind, as essentially it demonstrates that the modern synthesis was not founded on solid ground in the first place.

I will now focus on the more recent scientific issues regarding the modernized version of Darwin’s theory, where the main scientific objections remain fundamentally similar, even with the genetic modification of the theory using genetic population models, genetic mutations, selection theory or its gradualism, as it still did not resolve how one species becomes another (Macro-evolution), the very thing that needs to be explained in order to understand evolution. Indeed, the quotes below will confirm this statement and at the same time, point out the fact that the Modern Synthesis has become woefully rigid and dogmatic and ultra gene-centric in its views.

For instance, in a scientific paper (2012): the Logic of Chance: the Nature and Origin of Biological Evolution by Eugene V. Koonin Eugene Koonin’s (as quoted in the introduction as pointing out the crumbling state of the modern synthesis) makes the following statement regarding the inadequacies of the Modern Synthesis model to explain evolutionary complexities:

For all its fundamental merits, Modern Synthesis is a rather dogmatic and woefully incomplete theory. […the] Modern Synthesis makes a huge leap of faith by extending the mechanisms and patterns established for microevolution to macroevolutionary processes; it has nothing to say about evolution of microbes, which are the most abundant and diverse life forms on Earth; and it does not even attempt to address the origin of life. (6)

Indeed, returning to Shapiro, who has always been justifiably critical of the fundamental flaws embedded with the Darwinian theory to explain the deeper complexities of biological systems, reminds us that there is nothing new in these scientific objections:

The argument that random variation and Darwinian gradualism may not be adequate to explain complex biological systems is hardly new […] in fact, there are no detailed Darwinian accounts for the evolution of any fundamental biochemical or cellular system, only a variety of wishful speculations. It is remarkable that Darwinism is accepted as a satisfactory explanation for such a vast subject — evolution — with so little rigorous examination of how well its basic theses work in illuminating specific instances of biological adaptation or diversity
(Shapiro 1996, 64). (7)

The next quote is quite critical, again of the inadequacies of the Darwinian model to explain the deeper processes of evolution and the fact that this narrow view has had a significant negative impact upon other fields of biological research. This is written by Nigel Goldenfeld and Carl Woese (Department of Physics, Center for the Physics of Living Cells, and Institute for Genomic Biology, University of Illinois – 2010):

Evolution is the fundamental physical process that gives rise to biological phenomena. Yet it is widely treated as a subset of population genetics, and thus its scope is artificially limited. […] The lack of widespread appreciation for, and understanding of, the evolutionary process has arguably retarded the development of biology as a science, with disastrous consequences for its applications to medicine, ecology and the global environment. (8)

There are also many specific issues with the main tenets of the modern Darwinian synthesis as for example indicated in the above paper regarding the limiting application of population genetics. In another paper entitled: Re-synthesizing Evolutionary and Developmental Biology by (1996) by Scott F. Gilbert, John M. Opitz, and Rudolf A. Raff, outline an new synthesis based upon the most-to-date understanding of evolutionary developmental biology (otherwise known as EVO-DEVO for short) have this to say about population genetics:

Population genetics of the modern synthesis may become as irrelevant to evolution as Newtonian mechanics is to contemporary physics (9)

Population genetics proposes how genetic novelty arises within gene-pools to bring about change in the species (genetic mutations and natural selection working in tandem). And on the topic of both genetic via population modeling and natural selection, evolutionary biologist, Michael Lynch in his paper entitled: The Frailty of Adaptive Hypotheses for the Origins of Organismal Complexity, (PNAS 2007), gives his views in the following:

This narrow view of evolution has become untenable in light of recent observations from genomic sequencing and population genetic theory […] What is in question is whether natural selection is a necessary or sufficient force to explain the emergence of the genomic and cellular features central to the building of complex organisms. (10)

And the idea that genetic mutations upon which natural selection acts is also be strongly criticized by a highly regarded scientist (micro-biologists, who contributed a highly significant theory about early microbial evolution to evolutionary biology), Professor Lynn Margulis, as seen in the following statement:

Neo-Darwinists say that new species emerge when mutations occur and modify an organism. I was taught over and over again that the accumulation of random mutations led to evolutionary change [which] led to new species. I believed it until I looked for evidence.
(Teresi 2011, 68) (11)

Even a quick foray into clinical studies on bacteria (a really simple organism that should show mutations operating with selection to produce a change an adaptation) clearly, demonstrates that: “bacterial adapt to antibiotics more quickly than can be accounted for by mutations” (12). And, this particular study wasn’t even questioning the unquestionable assumptions embedded in the Neo-Darwinian synthesis – it just was an empirical observation made in a science lab regarding why bacteria adapt so quickly to antibiotics.

Taking a closer look at natural selection, the adaptation mechanism that is supposed to act upon those mutations generated from the population genetic models, that ultimately lead to a change in a species, leading to new ones, in a review written by Shapiro: Evolution: A View from the 21st Century, and review given by Adam S. Wilkins, Institute of Theoretical Biology, (2012), draws attention to the growing dissatisfaction with natural selection prominence as a driver of evolution (along with those mutations perhaps?) in the following:

[…] the book’s contention that natural selection’s importance for evolution has been hugely overstated represents a point of view that has a growing set of adherents. (13)

Indeed, even Darwin himself wasn’t that certain in the end about it all. And that was in the days before population genetic modeling, genetic mutations and a much more dogmatic application of the meaning of selection. For instance, several years after his first addition of ‘Origins,’ he begins to consider his own essential theory of natural selection.

In a correspondence, this to G. Bentham dated May 22nd 1863, as a Post script (P.S.), he reveals his inherent humility and willingness to be proven wrong, and his tireless patience as seen in most of his correspondences (which I have read with great admiration) as he responds to the valid and scientific issues inherent in natural selection and gradualism as a means of changing one species into another (speciation). This also reflects the main issue that many had with his theory as was quite continuous after his publication of ‘On the origin of species by means of natural selection, or the preservation of favoured races in the struggle for life’. (Darwin, C. R. 1859),
(14) C. Darwin to G. Bentham.
Down, May 22 [1863].

P.S.—In fact the belief in Natural Selection must at present be grounded entirely on general considerations. (1) On its being a vera causa, from the struggle for existence; and the certain geological fact that species do somehow change. (2) From the analogy of change under domestication by man’s selection. (3) And chiefly from this view connecting under an intelligible point of view a host of facts. When we descend to details, we can prove that no one species has changed [i.e. we cannot prove that a single species has changed]; nor can we prove that the supposed changes are beneficial, which is the groundwork of the theory. Nor can we explain why some species have changed and others have not. The latter case seems to me hardly more difficult to understand precisely and in detail than the former case of supposed change […] (15)

Darwin may have been correct, and willing to be proven wrong, unlike his followers, as it turns out that there is absolutely no evidence whatsoever of one species – even of bacteria, yeast or fruit-flies that should have shown some change given their rapid reproduction of continuous generations throughout the 150 years of experimentation as noted by Alan H. Linton, an emeritus professor of bacteriology at University of Bristol, entitled: Scant search for the Maker (2001).

I won’t go into the context and debate surrounding this article, (It’s a Creationist/Darwinian debate), but, the point is that Linton is referring to the fact that a well-known Darwinian paleontologist, Eldredge, claims a victory for the Darwin theory against the Creationists based upon the fact that Darwin’s theory of evolution has never been disproved. Linton writes the following in his comments regarding Eldredge’s new book:

[Referring to Eldredge’s claims…] after 150 years, science has failed to disprove the theory of evolution and, therefore, “evolution has triumphed”. In other words, the theory of evolution rests on the failure of science to show that it is false. Nevertheless, he believes the theory can be scientifically tested.

But where is the experimental evidence? None exists in the literature claiming that one species has been shown to evolve into another. Bacteria, the simplest form of independent life, are ideal for this kind of study, with generation times of 20 to 30 minutes, and populations achieved after 18 hours. But throughout 150 years of the science of bacteriology, there is no evidence that one species of bacteria has changed into another, […]

Since there is no evidence for species changes between the simplest forms of unicellular life, it is not surprising that there is no evidence for evolution from prokaryotic to eukaryotic cells, let alone throughout the whole array of higher multicellular organisms. (Linton 2001)(16)

This leads naturally to the fossil record and how it isn’t exactly conforming to the Darwinian theory. Even Darwin recognized the gaps and lack of transitional fossils back in his own day that didn’t exactly fit his gradualism and idea of natural selection and assumption of common descent, although even staunch defenders of Darwin and natural selection in more modern times clearly show that the layers that Darwin had wished for to prove his theory are still an issue today as it was back then.

Another well-known Darwinian paleontologist Stephen Jay Gould attempts to fill in the gaps in fossil, but before he does, he highlights the obvious issues with the record itself:
All paleontologists know that the fossil record contains precious little in the way of intermediate forms; transitions between major groups are characteristically abrupt. Gradualists usually extract themselves from this dilemma by invoking the extreme imperfection of the fossil record—if only one step in a thousand survives as a fossil, geology will not record continuous change. (17)

Gould then goes on to defend the fact that jumps do occur rarely as borne out by the fossil record, which he argues could be explained under certain extreme environmental conditions, in terms of the theory of punctuated equilibria, (Niles Eldredge as discussed above by Linton was Gould’s co-founder of this theory) (18). As it turns out, the newer and older alternative views are supporting their essential premise, although, the processes are nothing like how either could have imagined as they were both avid supporters of Darwin and of natural selection in particular, even if it was a softer form and both were quite outspoken within their own discipline about the hardened gene-centric, selectionist, Neo-Darwinian version (19).

Remaining with the fossil record, and its relationship to natural selection, in the field museum of natural history bulletin under the title: Conflicts between Darwin and Paleontology by David M. Raup (paleontologist) summarizes the issue as follows:

Darwin’s theory of natural selection has always been closely linked to evidence from fossils and probably most people assume that fossils provide a very important part of the general argument that is made in favor of Darwinian interpretations of the history of life. Unfortunately, this is not strictly true. We must distinguish between the fact of evolution — defined as change in organisms over time — and the explanation of this change. Darwin’s contribution, through his theory of natural selection, was to suggest how the evolutionary change took place. The evidence we find in the geologic record is not nearly as compatible with Darwinian natural selection as we would like it to be. Darwin was completely aware of this”. (20)

More recently, Craig Venter (the man who created the first synthetic genome using Mother Nature’s building blocks, the code of life) states the following in a rather muttered fashion in a debate entitled: What is Life? where Richard Dawkins was on the panel. Venter directs the following comment to (Prof.) Richard Dawkins as they are discussing how life evolved:

We have studied […] 60 million unique gene sets of deep sea organisms; we found about 12 that might show a slight branching (21)

Do you know I found it difficult to pick up all that Venter said from the discussion panel as a very loud bang erupted in the studio and everyone lost their train of thought – how convenient I thought. Anyway, through the kerfuffle, I could have sworn that he added: I think the tree of life is a fiction (21). Now don’t quote me on that, but I’m near certain.

The whole basis of this assumed ancestral lineage splitting from common ancestors all the way back to the LUCA (last universal common ancestor), is built upon an assumption, an idea that was becoming popular during Darwin’s own time – Homology, (as in literal descent where an ancestral and simpler feature such as a fin, is assumed to have evolved into a more complex limb such as a foot/claw/legs etc via direct common ancestry from the creatures that possessed these traits) which, Darwin then incorporated into his theory of natural selection and which has been updated molecularly/genetically by the Neo-Darwinian synthesis.
Even though this model has been updated, it still retains the fundamental flaws that were inherent in it even back in Darwin’s own day and therefore, it is not perhaps surprising that as it remains problematic, as it is essentially the same model in a genetically modified form that Darwin assumed within his theory. As genetic inheritance is seen by the modernized version of Darwin as being the only way that change could come about in a species – by passing on your genes, this rather limits our understanding of evolutionary processes. However, there is a solution to this direct common descent quandary, which will become much clearer as this story unfolds.

Now, the most fundamental assumption embedded within the Darwinian model – simplistic common descent with modification, has been updated and supposedly supported, according to conventional wisdom, by: molecular clocks. You may not know exactly what they are, other than to say that when we are told exactly how many million years ago we last shared a common ancestor and, even when they can’t find the ancestor in the fossil record, which is often the case, or if they do, it is usually fiercely debated amongst warring paleontologists for decades afterwards, just remember that this is entirely based upon molecular clocks and the assumption of direct common ancestry (homology which has now been modernized to see genes as homologous as well).

In other words, most studies attempting to establish relationships (molecularly speaking) and their timing are based upon an assumption of earlier relatedness and timing of lineage splitting as the starting point for their study. The initial assumption has never been empirically tested, but assumed. This may invalidate the results. In any other scientific discipline, it would.

For example, in a science paper in Nature, entitled: The molecular clock runs more slowly in man than in apes and monkeys. (1987) by Li WH. Tanimura, M., part of the abstract is as follows:

The molecular clock hypothesis postulates that the rate of molecular evolution is approximately constant over time. Although this hypothesis has been highly controversial in the past, it is now widely accepted. The assumption of rate constancy has often been taken as a basis for reconstructing the phylogenetic relationships among organisms or genes and for dating evolutionary events. Further, it has been taken as strong support for the neutral mutation hypothesis, which postulates that the majority of molecular changes in evolution are due to neutral or nearly neutral mutations. For these reasons, the validity of the rate constancy assumption is a vital issue in molecular evolution. Recent studies using DNA sequence data have raised serious doubts about the hypothesis. (22)

Another article questions the reality of the molecular clock at all as the basis attempting to establish the degree of relatedness between all species using, as the molecular clocks are themselves built upon assumptions that are in themselves built upon assumptions, in a paper entitled: Do Molecular Clocks Run at All? A Critique of Molecular Systematics by Jeffrey H. Schwartz & Bruno Maresca states:

Rather, molecular systematics is (largely) based on the assumption, […] that degree of overall similarity reflects degree of relatedness. This assumption derives from interpreting molecular similarity (or dissimilarity) between taxa in the context of a Darwinian model of continual and gradual change. […] it is not uncommon to find studies claiming to have determined a close relationship between two taxa when, in reality, they only applied their data to an already assumed arrangement of phylogenetic relationship.
(23)

Returning to Lynn Margulis, who also has a lot to say about Darwin’s Tree as well as the fact that mutations don’t create a new species. She points out in: The Phylogenetic Tree Topples (2006) (24) and after drawing attention to the obvious fact of the evolution of all species over the past few billion years, Margulis (the president of American Scientist magazine) declares a rather loud “NO” to all the other assumptions embedded in the so-called facts of Darwinian Evolution and she proclaims the following:

[…] Then how did one species evolve into another? This profound research question is assiduously undermined by the hegemony who flaunt their correct solution. Especially dogmatic are those molecular modelers of the tree of life who, ignorant of alternative topologies (such as webs), don’t study ancestors. […], they correlate computer code with names given by authorities to organisms they never see! Our zealous research, ever faithful to the god who dwells in the details, openly challenges such dogmatic certainty.” (24)

Margulis herself via her well-respected theory of symbioses (a symbiotic merger) of early microbial life forming entirely new organisms by combining their genomes and body parts, begins to give an answer to this quandary of how life evolved. This also raises the possibility of the very tree of life, having to be deconstructed. Furthermore, the single origins hypothesis (Last Common Ancestor LCA) is becoming increasingly uncertain.

This is born out in an abstract of a more recent science paper (2008) entitled: A Fundamentally New Perspective on the Origin and Evolution of Life by Shi V. Liu (Eagle Institute of Molecular Medicine) in which the most fundamental flaw within the Darwinian model of evolution by common descent, is highlighted in the following:

Darwin’s hypothesis that all extant life forms are descendants of a last common ancestor cell and diversification of life forms results from gradual mutation plus natural selection represents a mainstream view that has influenced biology and even society for over a century. However, this Darwinian view on life is contradicted by many observations and lacks a plausible physico-chemical explanation. Strong evidence suggests that the common ancestor cell hypothesis is the most fundamental flaw of Darwinism… (25)

Similarly, in a paper entitled: The Concept of Monophyly: A Speculative Essay, by biologist Malcolm S. Gordon (1999) highlights the following:

Recent research results make it seem improbable that there could have been single basal forms for many of the highest categories of evolutionary differentiation (kingdoms, phyla, classes). The universal tree of life probably had many roots”. (26)

Related to this is what Carl Woese, a prominent and well respected microbiologists, who did some ground breaking work back in the 60s and 70s that started to upturn the old TOL or the Darwinian tree, (or at least the common assumption that many before and after Darwin believed to represent, albeit symbolically, how evolution preceded). For instance, Encyclopedia Britannica state the following regarding Woese’s theory: “[he] proposed a new model to replace the standard Darwinian theory of common descent—that all life on Earth evolved from a single cell or pre-cell. Woese proposed instead that various forms of life evolved independently from as many as several dozen ancestral pre-cells”. (27) Furthermore, Woese (1998) states the following in another science paper entitled: The universal ancestor:

The universal ancestor is not an entity, not a thing.
It is a process characteristic of a particular evolutionary stage (28)

Now, don’t worry, all is not lost as, out of the most cutting-edge and deeper understanding of biological processes, a new synthesis is emerging, as I pointed out in the Preface of this book as a conclusion of Professor Denis Noble’s great work as summarized in his quote (2). Furthermore, this new synthesis supports many of the evolutionary ideas that were previously marginalized by the hardening of the Neo-Darwinian synthesis. Thus, several alternative schools of thought are now beginning to return from the exile imposed upon them, as the statements from the following scientists clearly reveals.

For example, Professor Denis Noble’s endorsement of a scientific collection of papers on Lamarck and the field of epigenetics entitled: ‘Transformations of Lamarckism From Subtle Fluids to Molecular Biology’: Noble writes the following cautious, but important summary about the book:

This book is long overdue. Lamarck and Lamarckian ideas were not only ignored but actively ridiculed during the second half of the 20th century. As the subtitle of this book indicates, some of the most cogent reasons for reassessing those ideas come from within the citadel of molecular biology itself […}”(Noble 2011) (29)

These epigenetic (Lamarckian principals) form the focus of an important science paper entitled: ‘Transgenerational Epigenetic Inheritance: Prevalence, Mechanisms, and Implications for the Study of Heredity and Evolution’ by Eva Jablonka and Gal Raz in the Quarterly Review of Biology (2009):

…denied by the “Modern Synthesis” version of evolutionary theory, which states that variations are blind, are genetic (nucleic acid‐based), and that saltational events do not significantly contribute to evolutionary change [ref]. The epigenetic perspective challenges all these assumptions, and it seems that a new extended theory, informed by developmental studies and epigenetic inheritance, and incorporating Darwinian, Lamarckian, and saltational frameworks, is going to replace the Modern Synthesis version of evolution [ref]. We believe, therefore, that the impact of epigenetics and epigenetic inheritance on evolutionary theory and the philosophy of biology will be profound. (30)

There is no doubt that there is an epigenetic (Lamarckian) revolution going on in biology, and although, these authors, highlight this fact, they still maintain that at some level, Darwinian ideas can be accommodated within this emerging new synthesis, whereas, the evidence emerging would suggest otherwise, I feel. Returning to the importance of the Lamarckian (epigenetic) aspects of their study, as this is actually more radical for our evolutionary thinking than most people appreciate, and it goes much further than just epigenetic inheritance, which is profound enough, I will focus more on Lamarckian principals (epigenetics), rather than the other alternatives to the Darwinian model in this Part One of this book and particularly in the following chapters, and discuss the various theories, in combination with Lamarckian principals in Part Two, which in combination gives us the new emerging synthesis, alternative to the Darwinian model.

Lamarckian evolutionary principals, as you will see as this book proceeds, lay the foundation for the broader synthesis emerging as a complete alternative to the Darwinian model. In other words, Lamarckian principals form a fundamental component of the overall synthesis that I’m proposing based upon a wide range of other scientific and historical evidence. As this book unfolds, you may come to appreciate the deeper significance of what Lamarck himself actually proposed and perhaps even be amazed, as I was, at his depth of insight considering that he formulated the theory over 200 years ago.

Furthermore, Lamarckian evolution theory and its principals, when placed within the historical framework of the marginalization of alternative theories by the increasingly dogmatic version of the Neo-Darwinian synthesis, will help explain a great deal about how our current model of evolution turned out to be so flawed in the light of our more recent discoveries in biology in the first place. Essentially, it never had the firm scientific foundation that the otherwise marginalized alternatives had.

This brings us to other marginalized scientific alternative views of evolution which are also indicated within the article on epigenetic inheritance, as forming part of the new synthesis. This paper points out the importance of more Saltionist (large evolutionary changes) thinking for example. This is confirmed in a number of science articles which I will briefly review below. These not only highlight the marginalization of their own field of research by the strict application of Neo-Darwinism, but the fact that a new synthesis is emerging from these fields (generally referred to as EVO-DEVO – evolutionary development biology for short).

For instance, Eugene K. Balon, writes from slightly more recent perspective of this same theme as he highlights the emerging and re-emerging alternative synthesis to Darwinism in his science paper entitled: Evolution by epigenesis: farewell to Darwinism, neo- and otherwise (2004):

In the last 25 years, criticism of most theories advanced by Darwin and the neo-Darwinians has increased considerably, and so did their defense. Darwinism has become an ideology, while the most significant theories of Darwin were proven unsupportable. The critics advanced other theories instead of ‘natural selection’ and the survival of the fittest’. (31)

In another science paper coming from a similar EVO-DEVO perspective: Resynthesizing Evolutionary and Developmental Biology by (1996) by Scott F. Gilbert, John M. Opitz, and Rudolf A. Raff, as quoted earlier, these authors highlight the emerging new synthesis, and again, this is formed from the alternative evolutionary ideas that were previously marginalized and now being supported by more current science:

A new and more robust evolutionary synthesis is emerging that attempts to explain macroevolution as well as microevolutionary events. This new synthesis emphasizes three morphological areas of biology that had been marginalized by the Modern Synthesis of genetics and evolution: embryology, macroevolution, and homology. The foundations for this new synthesis have been provided by new findings from developmental genetics and from the reinterpretation of the fossil record. […](9)

These papers are only the tip of the iceberg when it comes to the criticisms of our Neo-Darwinian synthesis and its increasingly untenable status as being able to explain the greater complexities of evolution and biology. However, these otherwise marginalized fields of research which are providing new and not so new ways of seeing the deeper complexities of nature, is only part of a much larger evolutionary story. However, EVO-DEVO, or a more saltationist evolution perspective, becomes particularly powerful when epigenetic evolutionary principals are applied to these dynamic alternatives. This is indeed happening in more recent times as a result of Lamarckian principals being verified by molecular processes. What is particularly interesting, is the fact that EVO-DEVO itself grew out of more Saltationist/Mutationist ideas of evolution which, had already integrated Lamarckian principals into their research as noted above; at least that was until Lamarck was exiled and these other schools of thought were either gradualized/modified in their principals to accommodate Neo-Darwinian genetic mutation theory or simply ignored by the strictest neo-Darwinians themselves.

But even this reconciliation is not the full evolutionary story, for as exciting as all this new and not so new macro-evolutionary/epigenetic synthesis is, no one discipline, or combination of disciplines, has all the answers. This is why I have had to take a much broader approach, to at least attempt to form a more over-arching synthesis. For instance, it gets even more complex as Shapiro sees the solutions to the restrictive model of the Neo-Darwinian synthesis in terms of the complex mechanisms and processes observed within microbial and molecular biology. For instance, he refers to the fact that the genome can be remodeled, rather radically and rapidly, making adaptive changes to an organism according to their response to environmental stresses (activated via jumping genes – I’ll go into these processes in more detail in Part Two) as natural genetic engineering (32). Now if that doesn’t change the evolutionary story of adaptation according to your environment (epigenetically driven evolution), I don’t know what does.

Moreover, Shapiro is one of very few, who actually draws attention to our current simplistic common descent model, along with Margulis (who I quoted above regarding mutations not creating a new species and her work on microbial domains providing an alternative view of our family tree). Both recognize the overall genetic exchange across whole domains of life that seriously need to be considered within this emergent new synthesis. And they also offer alternative explanations based upon their respective fields of expertise of other means of descent. Again, although all of the above views, observations and studies are critical to our understanding, there is still more pieces of the puzzle to be assembled. Basically, the new synthesis is beginning to look nothing like how Darwin or anyone else could have perceived it and it is starting to go quantum as Shapiro is quoted as saying. Here is the extended quote:

Prof. Shapiro (1997) describes a conceptual quantum leap and describes as follows:

The past […] decades of research in genetics and molecular biology have brought us revolutionary discoveries. Upsetting the oversimplified views of cellular organization and function held at mid-century, the molecular revolution has revealed an unanticipated realm of complexity and interaction more consistent with computer technology than with the mechanical viewpoint which dominated the field when the neo-Darwinian Modern Synthesis was formulated. (3)

His observation is confirmed in other aspects of biological research which are a little less direct, but still adding a whole new, and as it turns out, not so new, dimension to our over-arching new synthesis. As the study of using natural laws and processes driven by forces of nature and the cosmos, principals that are traditionally used in physics to describe natural phenomenon, is being applied to biological systems and evolution more commonly these days. However, the principals of natural growth and form laws (morphogenesis etc), as applied to biology, have in the past been applied in real terms experimentally, to molecule, cells, and embryology, (biological processes), but, once again, these principals of evolution that were essentially alternatives to Neo-Darwinian theory, have become increasingly obscure over the decades.

I will deal with some of these principals towards the end of this book in Part Two and how they can be applied to biological complexity, the cells, the species and their environments, and therefore this approach begins to give us the final piece of the evolutionary puzzle as complex systems and scaling laws in biology actually begin to show us relatively simple principals of natural laws that biological life ultimately conforms to. Again, these principals are being supported in more recent times as quite a few scientists coming from physics disciplines are beginning to apply their skills and knowledge to biology.
A science paper entitled: Complexity in biology. Exceeding the limits of reductionism and determinism using complexity theory, by Fulvio Mazzocchi (2008), reiterates the work and sentiments of several other regarding the rather inadequate way of studying biological diversity as it outlines the various systems approach to understanding our natural world, whether it be the planets or biology itself and highlights the fact that our old way (reductionist thinking as in the main issue which I would propose: the Neo-Darwinian synthesis is a prime example) of explaining complexity, has failed and has essentially run its course and proposes instead, a new approach to help explain biological complexity and diversity in the following:

[….] biologists might be reaching the limits of this approach. Despite their best efforts, scientists are far from winning the war on cancer, owing largely to the complex nature of both the disease and the human organism. […] On a macro level, ecosystems and human societies present the same challenge. What is needed is a new approach to study these systems. Complexity theory can provide new conceptual tools that will inevitably question many of the assumptions of Newtonian science.

Complex systems exist at different levels of organization that range from the subatomic realm to individual organisms to whole populations and beyond. They include, for example, molecules, cells, organisms, ecosystems and human societies. Despite their differences, these all share common features, such as emergent properties. In addition, randomness and order are both relevant for the behaviour of the overall system.

[Complex systems] might show regular and predictable behaviour, but they can undergo sudden massive and stochastic changes in response to what seem like minor modifications. The metaphor of the ‘butterfly effect’—whereby a single butterfly beating its wings can cause a storm—describes, for example, the dependence of a complex system on its initial conditions.(33)

I believe that Dr. Geoffrey West sums the situation up best in his statement below. West is a physicist working with a team of biologists at Los Alamos National Laboratory, as noted in an article in the New York Times entitled: Of Mice and Elephants: a Matter of Scale
By GEORGE JOHNSON
Published: January 12, 1999

Dr. West liked to joke that if Galileo had been a biologist, he would have written volumes cataloging how objects of different shapes fall from the Leaning Tower of Pisa at slightly different velocities. He would not have seen through the distracting details to the underlying truth: if you ignore air resistance, all objects fall at the same rate regardless of their weight.(34)

Perhaps you are beginning to see the type of new synthesis that I am proposing, based on a broad range of disciplines of older and more modern form relating to biological complexity and therefore evolution. Furthermore, I hope you now understand that the declaration that the old edifice is crumbling, so irrevocably as stated by Koonin (2009) in the Preface of this book (1) is not an overstatement. You may even be wondering how the Neo-Darwinian synthesis got so woefully rigid in the first place and why we have not been allowed to question our current model of evolution considering the fundamental issues embedded within it. Even Darwin allowed for its revision and certainly was never as dogmatic about his theory as his followers were. Well, I will attempt to answer this question in the chapter three and leave you with Shapiro’s thoughts on why the Neo-Darwinian Synthesis should never have been permitted to grow in its scientific dogmatism in the first place:

From a scientific point of view, then, the Law of Gravity has quite properly been under continuous challenge. Dogmas and taboos may be suitable for religion, but they have no place in science. No theory or viewpoint should ever become sacrosanct because experience tells us that even the most elegant Laws of Nature ultimately succumb to the inexorable progress of scientific thinking and technological innovation. The present debate over Darwinism will be more productive if it takes place in recognition of the fact that scientific advances are made not by canonizing our predecessors but by creating intellectual and technical opportunities for our successors.
http://shapiro.bsd.uchicago.edu/Shapiro.1997.BostonReview1997.ThirdWay.pdf http://www.bostonreview.net/br22.1/shapiro.html pg 5 (3)

 

End of Reveiw of Preface & first chapter of new book: Evolution: A Third Way? Sorry about the lack of clickable number links – it is on its way to being a physical book and the first draft is just in for editing. I thought the quotes were quite informative though and this will give you an idea of my current writing project. I’ll post updates here.

Cheers Maria Brigit

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