If Human’s didn’t evolve by Neo-Darwinian means, how did we evolve? Pt.8 (final) of series on alternative evolution

Part Eight


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

If Human’s didn’t evolve by Neo-Darwinian means, how did we evolve?

Have you ever wondered?

Have you ever wondered how/why we humans are the only primates that habitually walk/run on two legs; have brains three times bigger in relation to our bodies than any other primate; have a unique voice box that allows most of us to use verbal language, and we also have exceptional dexterity with our hands and thus, we make rather sophisticated tools and other nifty technology? And of course, we are the only naked ape!

 Darwin the thinking monkey

…And how come we are the only primate that went from crossing the vast prairies of America in a canvas-topped wagon to flying aircraft, and finishing off by being launched into space in a rocket and landing on the moon in just three short generations as Edgar Mitchell (the sixth man on the moon) once pointed out in a documentary interview regarding his own family history back to the time of his Grandfather?

The purpose of this final article in this series of “If Evolution didn’t happen by Neo-Darwinian means, how did it occur?” is to present the evidence as to how our conventional linear descent from an actual ancestor that gave rise to chimps and humans where, the split is assumed to have occurred c. 5/6 million years ago, doesn’t actually stand up to scrutiny. The conventional evolutionary explanations are becoming increasingly untenable in the light of our deeper understanding of our less than straightforward, and rather convoluted evolutionary history.

This article, at the same time, aims to present the alternatives to our current standard theories based upon the most up to date scientific evidence and a reassessment of the fossil record in the light of this emerging wealth of evidence. It will explore the strong evidence for the emergence of a generic ape-like form (a shared ancestral CONDITION amongst all the higher primate types prior to their specific species specialisations) with the architecture for upright walking no less than 21 million years ago and focus on environmentally stimulated genome remodelling that may account for such dramatic adaptations and an assessment of how we got to be so uniquely human. Thereby, revealing the most likely means to our very probable means of speciation. In other words, this article: How Did Humans Evolve if it wasn’t by Neo-Darwinian means? Will explore and discuss the possibilities that point to a very different means of evolution which may not have happened just in the way that you might perhaps think it occurred. However, I would like you to go on the journey and see where it leads. The only thing that is required, is an open and enquiring critical mind and a review of the articles relating to this alternative proposal would be very useful also, if you haven’t already been following this series.

All in all, as explored throughout this entire series, the principle of species becoming speciated by going from the generalist tetrapod (proto-mammalian for example) and diversifying according to inherent complexity towards specialisms thereafter. As stressed previously, this process is seemingly applicable across all levels of evolutionary development which is proposed as being ultimately driven via environmental adaptations at a metabolic level. Therefore, this principle of species development  have been applied to ourselves as a generic tetrapod to mammalian condition with further innate complexity being expressed much later in the generic higher primate form and final specialisation of becoming fully human. I will summerise this principle as it applies to all evolutionary development at the end of this final article. It is called the Nested Russian doll scaled complexity model.

Review summary of last week’s article

Recall that generalist tetrapods were identified in the fossil record going, according to their seemingly innate metabolic complexity, towards more specialist species forms of amphibian, reptilian, or fundamentally mammalian. This is proposed as an alternative means to understand actual species diversification as illustrated in the fossil record if it is reviewed in this light and to address the issue of misclassification which was really a matter of terminology (misplaced) on the insistence of referring to mammals in their proto-primitive or stem stage, as “mammal-like reptiles” when they had nothing whatsoever to do with reptiles. Furthermore, other classified species of marine animals with all the traits of mammalian (giving birth to live young, being warm-blooded and air-breathing marine creatures and having an uncanny resemblance to modern dolphins) may have also been misclassified as reptilian where no evidence exists to justify this term other than an assumption that everything primitive was of the order of reptilia, which itself developed as a means of matching a theory (Darwinian) that came to assume common descent via a simplistic common ancestor. This alternative view proposes instead: Descent by epigenetic modification from an ancestral condition.

For instance, returning to holes (temporal fossae), these are directly related to the evolution and change morphology of the jaws and palate. The more generalist tetrapod forms show that these adaptations evolved to complexity according to the species level that that animal could ultimately reach. I.e. simpler vertebrates such as fish and amphibians did not develop further in terms of jaw, skull or palate morphology and sophistication remodelling of forms during species development, whereas, some reptilia and mammalian tetrapods did advance much further. Mammals appeared to make a fundamental leap in their complexity by going beyond the amniotic (egg-laying) stage of development and this is definitely what sets them apart from non-mammalian tetrapods (presumably due to being more metabolically complex than simpler cold blooded or even warm-blooded egg-layers that eventually became avian types). This brings us to how some mammalians beyond the monotreme (egg-laying and primitive   mammalian types) and the marsupial type of development evolved the sophisticated means of retaining the specialist amniotic egg.

This would have presumably had a profound impact leading to evolutionary changes (prior to becoming a more fixed and specialised mammalian species form) relating to sophisticated social behaviours, further brain wiring development due to longer gestation times (in the protected, and nutrient rich womb); contributing and further creating opportunities for further developmental complexity on their evolutionary journey. These expanding horizons available to some less defined mammalians, would have certainly led to richer and more diverse interactive opportunities as mobility (metabolically-driven) allowed them to colonise and expand into many new niches, plus, the new interbreeding opportunities that this would have provided along with a more exotic diet, could have all contributed to the ultimately sophistication and diversity seen within many mammalian groups today; which lead ultimately, to some mammalian forms becoming great apes of the higher primate order and finally, ourselves. 

As discussed throughout this series, the evidence strongly suggests that these adaptations in the species is directed/orchestrated environmentally via the epigenetic modification of genetic expression according to the adaptive needs of the particular amniotic animal in question. None of these modifications are unrelated to the whole system within the organism. Metabolism would appear to be the most fundamental aspect of whether a walking vertebrate evolves ultimately to all variations and diversifications of the anapsids, diapsid, or synapsid ancestral condition or form and some puzzling in-betweens in other groups, or even the euryapsids of the ichthyosaurs and the plesiosaurs forms.

In summary then, as discussed last week and within earlier parts of this series, environmentally triggered factors can seemingly radically alter a species, especially when it is a developing one. The resultant adaptation (remodelled form) can therefore look very different to its predecessors (modified descendents of their earlier forms as Lamarck suggested more than two hundred years ago). This is the pattern of evolution followed here which is beginning to seem plausible as an explanation in the light of more recent studies and begins to resolve the rapid and profound speciation events as seen in the fossil record. It begins to close gaps and resolves seemingly missing links and transitional fossils, as this model, taken to its natural conclusion would infer. It also strongly implies a reassessment of our concept of mass extinction followed by rapid novel radiations as noted previously by Shapiro.

How Related to Chimps and everything else – are we?

The following is loosely based on an earlier article on this site entitled: How closely related are we really to chimps?

Copy of monkey_man_Chandre_Oraon

 The Molecular Tree and the Fossil record don’t tally

Here is an example of the general assumption of how genetics link to the fossil record and give us timescales based on geological time-lines are used to re-produce our theoretical family tree. I use Wikipedia here as this thoroughly presents the mainstream (Neo-Darwinian) view of how evolution has supposed to have occurred:

“If the hypothesis of common descent is true, then species that share a common ancestor inherited that ancestor’s DNA sequence, as well as mutations unique to that ancestor. More closely related species have a greater fraction of identical sequence and shared substitutions compared to more distantly related species”.
Wikipedia ‘The Evidence of Common Descent


The timescales for these lineage splits such as when chimps and ourselves last shared a common ancestor 5/6 million years ago, (although this date goes back a little depending upon the most recent genetic models being employed) has a few embedded assumptions within the model in the first place that might be making the interpretation of results rather precarious. Not only that, but we have never found this illusive ancestor that gave rise to all the other homidea (great apes) including ourselves. There are no proto-chimps or gorillas and the only evidence for these creatures in the fossil record are when they are fully recognisable as chimps and found alongside homo species (humans).

The article below by Sally McBrearty and Nina G. Jablonski, “First Fossil Chimpanzee,” Nature 437 (2005): 105-08, explains:

First Chimp Fossils Found; Humans Were Neighbors

Researchers have found the first reported chimpanzee fossils in Kenya’s Rift Valley, providing the first physical evidence that chimpanzees coexisted with early human ancestors, known as hominins.


Furthermore, the evidence for ancestral common ancestor to the chimps and human line remains elusive as seen in this next article (note: a matrilineal ancestor simply means the female mother’s line of descent) and mt-TMRCA is the shortened version of mitochondrial DNA and this last common ancestor).

Because chimps and humans share a matrilineal ancestor, establishing the geological age of that last ancestor allows the estimation of the mutation rate. However, fossils of the exact last common ancestor would be an extremely rare find. The CHLCA is frequently cited as an anchor for mt-TMRCA determination because chimpanzees are the species most genetically similar to humans. However, there are no known fossils that represent that CHLCA. It is believed that there are no proto-chimpanzee fossils or proto-gorilla fossils that have been clearly identified.
Wikipedia ‘Chimpanzee-human last common ancestor’


This is somewhat embarrassing as according to our most definitive evidence that we have and where the idea that chimps and ourselves shared a common ancestor 5/6 million years ago, although this date goes back a little, or a great deal, or forward depending upon the most recent genetic models being employed, and yet we have never found this illusive ancestor to the chimp and human lineage and chimps only emerge as fully formed chimps in the fossil record alongside homo species (humans). According to many published papers, there are a lot of issues with the assumption of a constant molecular rate that molecular clocks tick at and indeed the underlying assumption of which lineage split from which and the common ancestor of chimps and humans referred to as CHLCA (Chimp Human Last Common Ancestor) for example, again using Wikipedia as they are a one-stop source of reference for a good deal of the scientific literature regarding the problems surrounding the molecular last common ancestor hypothesis. http://en.wikipedia.org/wiki/Chimpanzee%E2%80%93human_last_common_ancestor#cite_note-7

Time estimates
The age of the CHLCA is an estimate. The fossil find of Ardipithecus kadabba, Sahelanthropus tchadensis, and Orrorin tugenensis are closest in age and expected morphology to the CHLCA and suggest the LCA (last common ancestor) is older than 7 million years. The earliest studies of apes suggested the CHLCA may have been as old as 25 million years; however, protein studies in the 1970s suggested the CHLCA was less than 8 million years in age. Genetic methods based on Orangutan/Human and Gibbon/Human LCA times were then used to estimate a Chimpanzee/Human LCA of 6 million years, and LCA times between 5 and 7 million years ago are currently used in the literature.

Wikipedia continues with an interesting quote:

“ One no longer has the option of considering a fossil older than about eight million years as a hominid no matter what it looks like. ”

—V. Sarich, Background for man

This is rather erratic in terms of time estimates and rather limiting in terms of which latest molecular estimate they have appeared to settle on don’t you think? Even if the fossil record is clearly showing human traits, even if they are rather primitive features combined, as is often the case with these early hominid fossils, you cannot call it a hominid prior to the dates laid down by a molecular clock that is based upon things like those proteins as you will see further on, are anything but fixed and stable once they are translated by a much more flexible molecule compared to DNA, RNA? Furthermore, the molecular rate is believed to be a constant and this is where the timing of those conflicting fossils comes from and those postulated lineage splits. So what if molecular clocks are wrong? Where does that leave our lineage-splitting estimates?

The molecular clock runs more slowly in man than in apes and monkeys

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.


Below is an extract from an article in a science journal is very important in demonstrating some of the misplaced assumptions embedded within the estimation of time based upon molecular studies which has established our so-called ancestral split (chimp and human line). Before reading the article extract, the following explanation of terms might help you decipher what is being said further on:

Molecular systematic – Molecular biology has revolutionized the field of systematics. DNA evolves by mutations being incorporated in the DNA and fixed in populations. This will lead to divergence of DNA sequences in different species. Although diverged, we can refer to two DNA sequences as homologous (just as we would for any morphological trait such as forelimbs). Nicely demonstrates descent with modification as a definition of evolution.


I have outlined a few terms below which should help to decipher the next article:

Cladism – The theory that cladistic methods based on shared characteristics of organisms yield their true evolutionary relationships and provide the basis for a natural biological classification http://www.merriam-webster.com/dictionary/cladism

Phylogenetic systematics – is the formal name for the field within biology that reconstructs evolutionary history and studies the patterns of relationships among organisms. http://evolution.berkeley.edu/evolibrary/article/phylogenetics_01

Here is the all important article excerpt:

Do Molecular Clocks Run at All? A Critique of
Molecular Systematics

Although molecular systematists may use the terminology of cladism, claiming that the reconstruction of phylogenetic relationships is based on shared derived states (synapomorphies), the latter is not the case. 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.

Review of the history of molecular systematics and its claims in the context of molecular biology reveals that there is no basis for the “molecular assumption.”….. Although many molecular analyses attempt to generate theories of relationship from distance measures—even with small and taxically underrepresented sample sizes—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.

An example is Yunis and Prakash’s (1982) paper on chromosomes, in which they claimed to have demonstrated a close relationship between humans and chimpanzees… Yet, the authors admit in their text that they first accepted the orangutan as the primitive outgroup of a human–chimpanzee–gorilla clade, which by necessity predisposed the analysis to finding similarities between the latter three hominoids to the exclusion of the former.


You might want to read the above statement again – I know I had to, several times. But, I believe it is really important that you understand that 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.
So, perhaps these serious doubts and underlying assumptions should be taken into account as you hear or read about the way chimps and humans are supposed to be related and when it all happened.

The more recent assumption that we and chimps split from a common ancestor 5/6 million years ago is one built on belief that may not be correct in the first place, and two: based upon a molecular clock that runs at different rates between the two species and therefore is not a constant. And, thirdly, it is built upon the assumption that similar features/characters/bone-structure and form as well as genetic similarity (homology in its updated version) are the result of direct common descent and all variation can only come about by genetic inheritance and by no other mechanism for change, it rules out the possibility that these similarities are the result of complex mechanisms and interactions between all life-forms from the earliest times and are environmentally driven (molecule machinery shapes the expression of genes that build proteins that build body-forms) and this is highly flexible particularly at a developmental/embryonic stage (which is all Lamarckian type evolution in its updated epigenetic form). Thus, similar function and environmental experience can result in similar forms and even genetics.

For instance, a deeper understanding of the genome is allowing us to see into our evolutionary past in a way that was not possible before and what they are finding is that hybridisation, even amongst ourselves has not been that uncommon after all. An article in the New York Times states the following:

Hybrids May Thrive Where Parents Fear to Tread

While one might think that these oddities are examples of some kind of moral breakdown in the animal kingdom, it turns out that hybridization among distinct species is not so rare. Some biologists estimate that as many as 10 percent of animal species and up to 25 percent of plant species may occasionally breed with another species. The more important issue is not whether such liaisons occasionally produce offspring, but the vitality of the hybrid and whether two species might combine to give rise to a third, distinct species.

Several such examples are now known from nature. Furthermore, DNA analysis is now allowing biologists to better decipher the histories of species and to detect past hybridization events that have contributed new genes and capabilities to various kinds of organisms including, it now appears, ourselves.

Another article explains our specific relatedness to the chimp-human lineage in the following:

Human, Chimp Ancestors May Have Mated, DNA Suggests

“The young age of chromosome X is an evolutionary smoking gun.”
Different regions of the human and chimp genomes were found to have diverged at widely different times, and the two species’ X chromosomes show a surprisingly recent divergence time.


Relating to this is another article which goes into a little more detail:

Genetic evidence for complex speciation of humans and chimpanzees.

The genetic divergence time between two species varies substantially across the genome, conveying important information about the timing and process of speciation. Here we develop a framework for studying this variation and apply it to about 20 million base pairs of aligned sequence from humans, chimpanzees, gorillas and more distantly related primates. … Our analysis also shows that human-chimpanzee speciation occurred less than 6.3 million years ago and probably more recently, conflicting with some interpretations of ancient fossils. Most strikingly, chromosome X shows an extremely young genetic divergence time, close to the genome minimum along nearly its entire length. These unexpected features would be explained if the human and chimpanzee lineages initially diverged, then later exchanged genes before separating permanently.


Leaving aside, the conflicting estimates of our so-called lineage split, this article really highlights the hybridisation between the common ancestor of chimps and humans. Now hybridisation as it turns out, as noted above, is not so uncommon after all as genomes were not seemingly as closed off and quiet (genetically speaking) back in the day of primitive apes (which I have come to refer to as generic forms as they do not appear to be specifically any species only fossils showing perplexing characters and traits of modern and primitive forms as palaeontologists invariably describe particularly when trying to figure out the human lineage) that seemingly weren’t too fussy about who they mated with.

The Monkey Wrench in the primate family Tree

You can imagine how hybridisation between a generic great ape with a novel set of genes and unique traits might fairly rapidly take a different evolutionary path almost overnight in geological timescales. You know that hybrids between distinct species of flowers and plants can create an entirely distinct species, almost instantaneously within a new population that has never been seen before? Well, it’s not that different a process between higher organisms – the results can be pretty dramatic. It is just that plants tend to have looser genomes in terms of less genetic barriers between distinct species than most distinct modern species of animals have today.

This different way of interpreting the evidence would therefore suggest that there was never a single common ancestor from which the chimp and the human line diverged, but instead, there was a generic great ape form with many variations on the basic template and depending upon their rather novel and mixed gene-pools, stimulating the development of increasingly unique traits such as increased ability to walk upright with more efficiency for example, would have been enough to take the human lineage (or the primates on their way to becoming fully human) on an entirely different trajectory. Do bear in mind that other generic apes that ended up on a different evolutionary path may have simply become adapted to their particular niche much quicker than the homi-form (and their genomes became quieter and genetic exchange between now quite divergent species may have been more restricted).

On the other hand, apes with the ultimate evolutionary destiny of human, may have simply had more hardware and software to play with and go on, depending upon diet and many other environmental factors, such as being able to now expand well beyond their traditional niche because of the ability to walk and climb great distances, and mix with more of their own kind and do some interesting mating with similar, but genetically exotic types like themselves. This would in turn create interesting and novel new molecular pathways of evolution towards a more specialist human form. Take for example, the hybridisation studies for the archaic humans and our more modern selves:In a paper published in the Proceedings of the National Academy of Sciences (PNAS), a team led by Michael Hammer, an associate professor and research scientist with the University of Arizona’s Arizona Research Labs, provides evidence that:

‘Anatomically modern humans were not so unique that they remained separate. We found evidence for hybridisation between modern humans and archaic forms in Africa. It looks like our lineage has always exchanged genes with their more morphologically diverged neighbors … We think there were probably thousands of interbreeding events’, Hammer said. ‘It happened relatively extensively and regularly … anatomically modern humans were not so unique that they remained separate’, he added. ‘They have always exchanged genes with their more morphologically diverged neighbors. This is quite common in nature, and it turns out we’re not so unusual after all’.


So maybe you might pause and think a while, the next time you hear how we are so closely related to chimps because of our shared coding and descent from a common ancestor that has never been found. Or, the lack of evidence for the proto-chimp or the proto-gorilla and also ponder the reliability of the molecular clocks that they use to determine our divergence even if the fossil record (geologically dated) says otherwise. Maybe you will recall nature’s mechanism of gene expression or suppression depending upon environmental/niche needs and how similar body-forms and generic species say of the great ape, may have changed not only by common interbreeding creating a great deal of novel new coding, and even a change to a completely distinct species, but how there is a mechanism in place that can turn on or off genes even if those genes are essentially similar between broadly related species. How genes and to what degree and when genes are expressed – can make the difference between an upright walking smart ape who is good with their hands and have rather large and complexly wired brains like ourselves and chimps that may have adapted more rapidly to their niche, before we even became fully-modern humans – it seems we had a way to go yet. Perhaps we were more promiscuous and not so fussy about whom we bred with? Who knows?

Pioneering Study Compares 13 Vertebrate Genomes

Multi-Species Approach Provides Unprecedented Glimpse Into Function and Evolution of the Human Genome
BETHESDA, Md., Aug. 14, 2003 – In one of the most novel and extensive comparisons of vertebrate genomic sequences performed to date, a team led by the National Human Genome Research Institute (NHGRI) today reported results that demonstrate how such comparisons can reveal functionally important parts of the human genome beyond the genes themselves.
In a study published in the journal Nature, the researchers compared the sequence of the same large genomic region in 13 vertebrate species.

The organisms included human, chimpanzee, baboon, cat, dog, cow, pig, rat, mouse, chicken, zebrafish and two species of pufferfish (Fugu, Tetraodon)… By systematically comparing the patterns of a certain type of genomic change, called transposon insertions, among the different species’ sequences, these investigators were able to address a heated controversy in the field of evolutionary genomics. Their analyses confirm recently proposed trees of mammalian evolution indicating that primates (human, chimpanzee, baboon) are more closely related to rodents (mouse, rat) than to carnivores (cat, dog) or artiodactyls (cow, pig). Indeed, the evidence revealed by the new sequence data refutes alternative evolutionary trees that place rodents much farther away from primates….

The final set of findings reported in the study revealed that, while the general types of genome changes were similar among all vertebrates studied, differences in the relative contributions of the various changes have uniquely sculpted each species’ genome. These findings point to the complex ways that evolution has used millions of years of alterations to render each species’ genome into its modern-day form.


Well apart from the fact that this study is again assuming common descent from direct ancestors and lineage splitting and the old similarity of genetics corresponds to degree of relatedness on the family tree, oh, and the fact that little mice and rats have just scurried up the evolutionary tree to join us on a lower branch, leaving those poor old pigs, cows, cats and dogs behind, it is also revealing a fundamentally new way of seeing evolution in terms of a dynamic mechanism for genome sculpting. What the study if really picking up on, or not depending upon how you read it and how much you understand about the alternative ways that evolution could have itself evolved, is the fact that genes are the universal code for all life-forms as discussed earlier and the more similar the body-plan, physiology and behavioural forms, the more similarly arranged the genes (coding DNA segments) will be. However, this study and many others, interpret the degree of shared genetics and the more one creature looks and behaves like another, the more related they are assumed to be.

I am proposing evolution going from the less defined to the more specific in line with the findings from the vertebrate study above. Going from shared common templates and genetic blue-prints of life and evolving from primitive common features to increasing specialisation and refined adaptation and ultimately a finer resolution of what we would define as a specific species today. I am not saying that there was no gene exchange between ourselves as would-be humans (generalist great apes) and the other great apes in their more primitive forms, as there is certainly evidence for this which I will outlined further on, I am making the point that nature appears to build functional templates of life, from non-vertebrate to vertebrate, from fish to fishermen, from the less defined to the more refined within all major classes (taxa) of forms. The programs change according to environmental adaptations (epigenetic expression of existing genes) and this is ultimately only limited by the stage of development that a species is in (the less developed and more primitive an organism: the more flexible and open to dramatic changes an undifferentiated species will be) and the inherent metabolic complexity retained according to developmental /evolutionary experiences within a given organism.

In other words, depending upon metabolism and epigenetic expression of existing genetics etc, not all vertebrates had the ability to leave the water, not all vertebrates remained amphibious and not all vertebrates were restricted by their inability to go off and explore strange new worlds because of their body temperature regulation limits. Nor did all mammals go on to become higher primates and great apes, and finally, not all great apes created the ability to fly to the moon. My point being: the change within the genome does not actually change the genes or their initial instructions, but can interpret the instructions in a much more flexible way and therefore sculpt these shared body-plans in such a way that the variation of gene-expression can make a big difference in the end to whether a higher primate ends up as a chimp or a human.

We have to look beyond the genes themselves to find answers and relatedness is a futile exercise as finding the common genetic ancestor, rather than looking for an ancestral condition and process for evolutionary complexity and principles of growth, form and development, is as the studies above indicate, a messy business. It is a web of life. It is how nature has acted upon the whole genome in its expression of the shared genetics that changes the species and can in the end appear to rearrange our family tree in showing that primates (including ourselves chimps and gorillas etc) have more in common in terms of changes in their genomes with rodents (mice and rats etc) than with cats, cows and dogs as the above study indicates.

The Common Source Code of Life from which Nature writes many new programs

We have all heard over and over again how closely related we are to chimps. But did you know that we also share genetic similarity of up to 99% with a lowly house mouse  and almost half with bananas, as one article puts it: “Humans share 50% DNA with bananas: The fascinating facts about the scientific world around us”


we're all descended from bananas

Based upon an average overview of genetic similarity we could say: we are also fairly close to fruit-flies at 60% genetically speaking and we share a similar amount of genetics with a particular worm – an elegant one, the nematode. Perhaps it this is surprising, it was to me, the fact that we are more genetically similar to cats at 90% than cows (80%). So here is a little thought experiment. If we share almost 50% of our genetics with bananas, does that make us half banana? Or if we share 75% of our genetics with a pumpkin, does that make us more related to pumpkins than bananas? Obviously, not! Nature has many ways of sharing the universal code of life amongst all its life-forms and they did not all have to breed to share this code. Saying that, there was a great deal more direct sharing of genetics than previously anticipated and hybridisation was not that uncommon after all. Yes, even between the great ape, mammals and broad classes of animals in general. I will outline this evidence further on, although you can begin to imagine how this has messed up our family tree.

As it turns out genes are just the stage-play script, it needs its actors and dynamic interaction on stage to come to life. It needs its proteins and these have to be created and this is open to interpretation and little artistic licence as all good plays are. They are not written in stone and can be fairly flexible in their translation and interpretation of requirements. Once genes have in a roundabout way given the instructions to make specific proteins, via their RNA transcribers (translators), the genes (even if they are very similar to other genes in a seemingly closely related species) can be expressed differently in the end without actually changing the original instructions locked in the genes.

Genetically, proteins are US as their networks as the genes are the instructions for the proteins and therefore the resulting hardware is built, but these instructions are highly flexible and adaptable. For instance, Scientists hail new ‘map of life’ is the article title on the BBC News website:

Biologists have produced a detailed map of protein interactions in a complex organism – the fruit fly. Proteins, which are made by genes, are the building blocks of tissues as well as the basis for molecular interactions that enable an organism to live.

Dance of proteins

An organism’s genome is a two-dimensional and static description of a living creature. To come to life it must be translated into action, rather like a screenplay must be turned into acting. Genes in the nucleus of a cell act as the starting templates in a process that eventually leads to the production of proteins. These sophisticated molecules perform specific tasks, or get together with each other to make structures. Many proteins interact, for example, to liberate the energy a cell requires to function.

In its complexity and simplicity, life is a dance of proteins.

There is the genome – the master genetic blueprint – that resides in the cell nucleus. The DNA makes a simpler molecule called RNA which interacts with ribosomes which churn out proteins based on the code in the genome.

BBC, UK, 2003


The gene is more like source code from which many programs of adaptation can be written and applied. It seems that it is the dynamic dance of proteins that makes this a creative and responsive process. It is a dynamic responsive system and is open to interpretation without changing the source code itself. It is how these proteins do their merry dance that can result in the same coding being translated in different ways. The adaptive programs are written in response to the needs of the organism and its environment. As noted many times throughout this series, the programs for adaptation appeared to be much more radical in the evolutionary past, and similarly, the environmental upheavals were rather dramatic in the evolutionary past compared to our present. In other words, we have stabilised as fundamental species and the adaptations have been on a finer scale of gradation and adjustment thereafter. Yes, we are still evolving and adapting to our environments, but thankfully, all the big morphing is over now and this means that monkeys will never become men and mice will not become pigmy elephants with long snouts.

The genome is vast and only contains a tiny portion of actual DNA which codes for proteins and within the genome, many complex genetic engineering events via natural means can and do and have occurred in the evolutionary past – sculpting genomes without changing the genes themselves. So the next time you hear about how you are related directly to chimps, based upon 98% shared genetics, remember that this is a mere 2% of the genes that code for proteins and the other 98% (that were until more recent times referred to as junk) of the genome is where the real action is, or at least was very active in the evolutionary past by all accounts. And even the proteins that are instructed by the genes are open to widely different interpretations.

ENCODE Project Writes Eulogy for Junk DNA

This week, 30 research papers, including six in Nature and additional papers published online by Science, sound the death knell for the idea that our DNA is mostly littered with useless bases. A decade-long project, the Encyclopedia of DNA Elements (ENCODE), has found that 80% of the human genome serves some purpose, biochemically speaking. Beyond defining proteins, the DNA bases highlighted by ENCODE specify landing spots for proteins that influence gene activity, strands of RNA with myriad roles, or simply places where chemical modifications serve to silence stretches of our chromosomes.


Evolution via natural genetic engineering & Genetic exchange between non-specialist Generic forms?

More recent molecular and fossil evidence is pointing to a different view of evolution which would both tally well with the fossil record and provide a mechanism for evolutionary that is rather more complex and convoluted than literal common descent from a single ancestral lineage idea embedded in the Darwinian model. Furthermore, it would also resolve the whole molecular clock business, which really isn’t helping much as a far as I can see from my research. In fact, it is actually, I believe clouding the issue and perhaps we should just put our old assumptions to the side and start actually following the real empirical evidence and try and understand what the actual fossil record is trying to tell us. Recall the earlier articles in this series that demonstrated via brain studies of vertebrates for example that vertebrate, tetrapod, amniotic and the earliest and near contemporary emergence (only slightly earlier) of fundamental mammalian (synapsid) forms compared to reptilia (diapsid) classes of animals that strongly support the concept of species having gone from generalists to specialists originating not so much from an actual common ancestor, but from a shared ancestral common CONDITION. See http://neuroscience.gmu.edu/people/abbutler.


The conclusion in this brain vertebrate study clearly indicates that the simplistic linear common descent model may be flawed. Indeed, increasing evidence suggests that all complex animals have evolved from their essential primitive form towards increased specialisation within their ecological niche. This follows the laws and principles of development as applied to evolutionary development proposed within an earlier pre-Darwinian theory by Von Baer which is also finding more recent support and has been employed as an alternative model of evolutionary development throughout this series. Recall for example, the studies that demonstrated why fish don’t in fact appear to grow fishy fingers and how this begins to reflect the model of once a species begins to specialise, it will fundamentally remain of that order of species. It begins to explain why a fish doesn’t need feet because fins are more efficient for its watery niche.

Related to this of course, is the concept and epigenetic mechanism that operates above the genetic master switches known as Hox genes which can trigger basic body plans during  development in a relatively fixed sequence these days as most creatures have fundamentally speciated, but seemingly back in more primordial and primitive times, before species were not quite sure what they were going to be when they grew up (became a stabilised species), things might have morphed and been rather less conservative about their body plans. This is actually a tool-kit shared amongst all animals with more sophisticated in some tool-kits than in others and of course, it is how these tools are used that makes a big difference in the end. Of course the more complex vertebrates have the most complex and sophisticated genetic tool-kit of them all. The difference between how these are used between different vertebrates is related seemingly, to the in-built metabolic complex of the particular form of animal. Yes, mammals are much more metabolically complex than fish or reptilia.

So you can imagine that if a fish produces a bud for a limb that becomes a fin but stops short and only other vertebrates go on via metamorphosis such as amphibians (spawn to tadpole to frog) then their coding is probably richer, their metabolic rate slower and they also have the resources to build new proteins and therefore body-parts. In other words, Nature has a mechanism in-built that has, itself, evolved and this can adjust the genetic expression without changing the source-code itself. This is the source code, just reprogrammed in many different ways that is shared amongst all vertebrates and indeed every living thing on the planet. It is how genes are expressed that makes a world of difference between even seemingly closely genetically related species like chimps and humans.

Nature appears to have evolved systems to evolve species complexity and diversification whilst retaining her more primitive and specialised earlier forms of life, where the entire system works as a whole, each interdependent upon the other. Yes, we even need our gut bacteria to stay healthy and thrive and they have formed a symbiotic relationship with us and therefore have hitched a ride to their own pinnacle of evolutionary development. However, they will always remain as bacteria as all the big macro-evolutionary stuff has settled down these days. Nature continues to fine-tune and refine these fundamental organisms from bacteria to bats and from monkeys to men. However, the past seems to have been quite a different story where genomes were remodelled and the result produced profound changes in the phenotype (what the species looked like). One important mechanism for this can be seen in what has been called transposon insertions, or Jumping Genes as discussed earlier as the seeming cause of all that strange relatedness of monkeys and mice etc.

Could these little clever genome rearrangements be one of the major driving forces of evolutionary species change and an alternative explanation for profound and rapid remodelling resulting from genomic adaptation and ultimately change within the species? Could it begin to explain evolution without selection, but instead a sort of Natural Correction and offer a less literal interpretation of the fossil record and genes based upon a simplistic common descent with modification model and could it all be environmentally driven where the cells sense their environment and therefore the organisms being a collection of cleverly organised colony of cells be able to adapt and change accordingly?

Via a deeper understanding of how genes can be expressed differently at every level of speciation within all organisms, across all boundaries and within the various animals and how genomes can be re-arranged/reprogrammed in response to its needs lead us to a less extreme version of homology (common features via common descent) of analogous organs, traits and limb design based more upon function/ driven and shaped (sculpted) via experience and efficiency of form? Are we seeing evolution converging on a broadly similar body form – A generic great ape perhaps, with further refinements and divergences of forms such as full bipedalism, increased brain size, opposable fingers and thumbs and many other divergences converging into a new species of HOMO? Does gene silencing (another aspect of transposons/jumping genes being controlled by epigenetic factors) in a sense fix a species of great ape within its own kind such as become a fully formed chimp, while other great apes still had relatively noisy genomes (more novelty within their genes that can be expressed differently resulting in actual physical – phenotype, and behavioural change) and had further to travel on their evolutionary journey?

Well some highly respected scientists have highlighted the importance of such mechanisms as fundamental to offering a much more dynamic and explanatory explanation of evolution as Professor James A Shapiro advocates. He refers to nature’s molecular mechanism for rearranging genomes as natural genetic engineering (NGE) as an alternative and much more dynamic and explanatory process for how species may have evolved and it is neither slow or gradual to the more traditional view of genetic based population models with their accidental mutations being naturally selected, environmentally, giving a creature adaptive traits and therefore a better chance of survival. NGE is a dynamic, rapid response system that reprograms genes via responsive cellular mechanisms according to environmental challenges. These mobile (genetic) elements that move around the genome, cut, paste, delete and re-arrange existing DNA are sometimes called Jumping genes and are also referred to as transposons creating insertions and deletions within the genome.

Genetica 86: 99-111, 1992.
Natural genetic engineering in evolution J.A. Shapiro

“In other words, it can be argued that much of genome change in evolution results from a genetic engineering process utilizing the biochemical systems for mobilizing and reorganizing DNA structures present in living cells”.


Bearing this natural genetic engineering process in mind, the following study is of some interest and might give us an insight into this natural genetic engineering in action. One fairly drastic way of re-modelling genomes (ala: Prof. James A. Shapiro’s natural genetic engineering as discussed above), is to relax the epigenetic control of gene expression and trigger mobile genetic elements (TEs) or jumping genes into action. The scientist, who initially brought this jumping genetics phenomenon to the attention of the world, once she finally got the recognition, was Barbara McClintock and her decades of research on transposable or mobile elements triggered by environmental challenges & controlled by the epigenome.


In her paper presented during her Nobel award in 1983, entitled: THE SIGNIFICANCE OF RESPONSES OFTHE GENOME TO CHALLENGE she writes:

It is the purpose of this discussion to consider some observations from my early studies that revealed programmed responses to threats that are initiated within the genome itself, as well as others  similarly initiated, that lead to new and irreversible genomic modifications. These latter responses, now known to occur in many organisms, are significant for appreciating how a genome may reorganize itself when faced with a difficulty for which it is unprepared. Conditions known to provoke such responses are many. A few of these will be considered, along with several examples from nature implying that rapid reorganizations of genomes may underlie some species formations.

In the future attention undoubtedly will be centered on the genome, and with greater appreciation of its significance as a highly sensitive organ of the cell, monitoring genomic activities and correcting common errors, sensing the unusual and unexpected events, and responding to them, often by restructuring the genome.

How right she was. For instance, did you know that we have a uniquely fused chromosome compared to all the other great apes? According to McClintock’s research as indicated above, chromosome fusions are quite common and this can come about due to stressful challenges in the environment. I have applied McClintock’s observations on this process to our own distinct fusion of chromosomes which makes us very distinct from other primates and great apes. For instance, hybridization is one shock to contend with that might jolt those silent jumping genes into action. Chromosomes and their ends (telomeres) get split and made into new ones, or repaired if mismatched or ruptured, by fusing two chromosomes into one. The following two papers in science journals outline this fusion as follows:

Similarities in Chromosome banding patterns and hybridization homologies between ape and human chromosomes suggest that human chromosome 2 arose out of the fusion of two ancestral ape chromosomes (1-3).

Genomic Structure and Evolution of the Ancestral Chromosome Fusion Site in 2q13–2q14.1 and Paralogous Regions on Other Human Chromosomes Humans have 46 chromosomes, whereas chimpanzee, gorilla, and orangutan have 48. This major karyotypic difference was caused by the fusion of two ancestral chromosomes to form human chromosome 2… Because the fused chromosome is unique to humans and is fixed, the fusion must have occurred after the human–chimpanzee split, but before modern humans spread around the world …Many other cross-hybridizing sites were observed in the genomes of nonhuman primates … reflecting the evolutionary mobility of sequences homologous to the region surrounding the fusion site.


Are they assuming that this fusion must have occurred after the chimp-human split because we are assuming that we split from an ancestral ape to chimps and humans in the first place? As discussed earlier, if we see all variations on the basic theme of Great Ape (a generic form) as having divergent evolutionary paths from this basic evolutionary template, then the evidence starts to make more sense. The fusion could have occurred at any time and across even highly diverse populations of great apes who had perhaps the greatest genetic novelty within their genomes. New genes can be made from old segments of DNA lying around the genome which, can be re-programmed and therefore remodel the genome itself and in turn, the organism. This can occur quite rapidly and radically as demonstrated via the work of McClintock and many others.

We have to ask ourselves, as these major remodelling events are triggered by major environmental stresses, what could have been the stress related event that fused the human chromosomes and made such a fundamental difference to our genome and therefore our ultimate destination of becoming human? Could it have been a shock to the genome due to hybridization itself between fairly novel genetic exchanges? We may never know, but this is an interesting line of enquiry as we come to understand that this explanation of genome remodelling via natural adaptive mechanisms along with genetic exchange (including hybridisation) are much more dynamic explanations of rapid, profound and far-reaching speciation impact than our traditional model of common descent from an ever elusive ancestral form that gave rise to ourselves and the chimps.

After all, how does the modern Darwinian model of evolution explain how this ancestor with the new chromosome arrangement (just 46 chromosomes versus 48 in all other great apes) and how this trait survived and was passed on so that every single human of modern and more archaic form had this uniquely human trait? Therefore, when discussing our ancestral link to chimps and all other life-forms on the planet, it is worth remembering that the degrees of genetic similarity is only a partial piece of the evolutionary puzzle and as this is a conserved universal source code, it actually demonstrates stability more than a means of dynamic change and therefore speciation. The rest of the genome and particularly the non-coding parts, show these past radical rearrangements. Another way of changing the expression of genes, without changing the genes themselves, which may account for part of the mechanism outlined above, can be seen in how genes can change expression via how tightly or loosely chromosomes are packed in each cell.

For instance, chromosomes and how these are packaged can make a massive difference between how a species will act, appear and function. It is how the universal source code is interpreted and that seems to control what, when and how genes are expressed. As a segment from a recent article in Nature outlines:

Cells package their DNA not only to protect it, but also to regulate which genes are accessed and when…cells control gene expression is by modifying their histones with small chemical groups, such as methyl and acetyl groups in the N-terminal tails that extend from the core particle. Different enzymes catalyze each kind of N-terminal modification. Scientists occasionally refer to the complex pattern of histone modification in cells as a “histone code.” Some of these modifications increase gene expression, whereas others decrease it…. Chromosomes are made up of a DNA-protein complex called chromatin that is organized into subunits called nucleosomes. The way in which eukaryotes compact and arrange their chromatin not only allows a large amount of DNA to fit in a small space, but it also helps regulate gene expression.


This, along with other factors we touched on above, such as jumping genes (transposable elements – TEs) which re-structure genomes, are important to understanding why there is such difference even between species (chimp and humans) that share so much of their DNA which codes for proteins. It is how much protein is built, say for a human brain as the article below indicates versus a lesser amount of protein to build the brain of a chimp is activated and this is regulated by the packaging of the chromosomes that express the same gene protein differently as discussed above.

Transcription factors guide differences in human and chimp brain function

Humans share at least 97 percent of their genes with chimpanzees, but, as a new study of transcription factors makes clear, what you have in your genome may be less important than how you use it.

The study, in Proceedings of the National Academy of Sciences, found that broad differences in the gene activity of humans and of chimpanzees, affecting nearly 1,000 genes, appear to be linked to the action of about 90 transcription factors. Transcription factors are proteins that bind to specific regions of the DNA to promote or repress the activity of many genes. A single transcription factor can spur the transcription of dozens of genes into messenger RNA (mRNA), which is then translated into proteins that do the work of the cell. This allows specific organs or tissues to quickly ramp up a response to an environmental change or internal need.

“The chimp network looks very much like the human one except there are a few transcription factors in different positions and with different connectivity,” Stubbs said. “Those are of interest from the point of view that they signal a major gene regulatory shift between species, and this shift may help us explain some of the biological differences.”

The new findings indicate that certain transcription factors are working together in a coordinated way to regulate the changes in seen in gene expression between humans and chimps, the researchers said.
“Once this network of transcription factors is established, changes in the network can be amplified because transcription factors control other genes,” Nowick said. “Even a small change in transcription factor expression can therefore produce a large effect on overall gene expression differences between chimpanzees and humans.”

The article above, shows that even when the genes are very similar, it is how they are used (transcribed/translated) in our own species and the chimps that can make quite a big difference. Basically, the genes themselves are controlled and regulated in unusual ways. The result of this regulation can make a big difference between chimps and humans. This is just one process linked to environmental factors that can make a big difference between us and chimps, even though, our genetics are very closely matched.

Remember that genes are akin to a basic universal source code of life that initiates conservative body-plans and templates of fundamentally similar life-forms. They don’t do a 3D print out of a banana instead of a chimp by mistake – genes abide by a safe and relatively constrained set of instruction that becomes flexible as it is handed over to the vastly complex and molecular processes involved in the translation of these instructions to build proteins. This molecular process (dance of proteins) is guided by the specific requirements of that organism within its environment both in the evolution past (at a macro-scale) and in more recent evolutionary timescales of fine-tuning the species (micro-scale). These processes adjust, adapt, reprogram (re-model the genome) and generally sculpt and fine-tune (tweak) this generic blue-print that open to interpretation. These transcription factors (mRNA) intermediary translation from DNA to RNA to make the protein (non-direct) within the genome of chimps and humans show distinctly different expression in the genes.


Applying the remodelling programmes to the ancestral condition of Generic Ape

The Descent of Darwinism

“The Upright Ape: A New Origin of the Species” by Aaron G. Filler (2007).

Foundation and Fate: Anomaly at Moroto

Introduction – A Revolution in Origins

In the opening scene of the Stanley Kubrick/Arthur C. Clarke masterpiece, 2001: A Space Odyssey, a totally incongruous black obelisk appears in the ground of an ancient African plain millions of years in the past. Its sudden arrival changes everything. Before it appears, the apes living nearby are mere animals. Afterward, however, although they have changed little in outward appearance, the apes that find the obelisk are transformed in a way that seems to make them human. In this artistic context, the obelisk symbolizes our desire for a discrete and definitive dividing line between what is human and what is animal.

The discovery of a single , ancient lumbar vertebra near the slopes of the Moroto volcano in East Africa bears many of the hallmarks of that obelisk. It is almost completely incongruous. Nearby, palaeontologists have found the remains of numerous species of the early apes that differed little in appearance from monkeys. That vertebra, however, bore an amazingly similar appearance to a lumbar vertebra of a human. That vertebra changes everything.

In fact, the Moroto vertebra is a surprise only because of our existing theories and models of human evolution. As we know, the vertebra itself cannot be out of place; therefore, it represents unalterable truth. What must be incorrect is our expectation of what the structure of the spine of an ancestral ape of the African Miocene era should be.

A New Body Plan for a New Type of Primate

It is now clear that 21 million years ago, in what is now equatorial Africa, a mutation occurred that created a new type of body plan: the hominoid body plan.

Filler (2007, 191).

 Filler goes on to discuss the Hox complex and as you should be familiar by now, the epigenetic aspect of the Hox gene (master switches) involved in body plans of all animals and the generic groups of vertebrates with varying detail according to innate complexity being able to express limbs, or repress limbs as in the case of some lizards that became snakes for example as discussed in an article of the same name on this blog. And also recall that the use of the word mutation historically has a very different meaning to how it is generally implied by our modern synthesis. Recall that mutation historically meant rapid and profound jumps of whole changes to the organism as in the traditional use of the word as applied during the late 19th and early 20th century by De Vries and others..

Therefore, you might be able to figure out how this remodelling of the architecture may have erupted in a whole new species of higher primates, where some of those generic apes actually made real use of that new body design much more than others. Some that used this new remodelling went on to become ourselves. There are a few more articles relating to the amazing Moroto fossil which are outlined below:

“An extraordinary advance in human origins research reveals evidence of the emergence of the upright human body plan over 15 million years earlier than most experts have believed. More dramatically, the study confirms preliminary evidence that many early hominoid apes were most likely upright bipedal walkers sharing the basic body form of modern humans.”

Extract from Science Daily article: Early Apes Walked Upright 15 Million Years Earlier Than Previously Thought, Evolutionary Biologist Argues

October 10, 2007

…The critical event involves a dramatic embryological change unique to the human lineage that was not previously understood because the unusual human condition was viewed as “normal.”

“From an embryological point of view, what took place is literally breathtaking,” says Dr. Aaron Filler, a Harvard-trained evolutionary biologist and a medical director at Cedars Sinai Medical Center’s Institute for Spinal Disorders.

In most vertebrates (including most mammals), he explains, the dividing plane between the front (ventral) part of the body and the back (dorsal) part is a “horizontal septum” that runs in front of the spinal canal. This is a fundamental aspect of animal architecture. A bizarre birth defect in what may have been the first direct human ancestor led to the “transposition” of the septum to a position behind the spinal cord in the lumbar region. Oddly enough, this configuration is more typical of invertebrates.

The mechanical effect of the transposition was to make horizontal or quadrupedal stance inefficient. “Any mammal with this set of changes would only be comfortable standing upright. I would envision this malformed young hominiform — the first true ancestral human — as standing upright from a young age while its siblings walked around on all fours.”

The earliest example of the transformed hominiform type of lumbar spine is found in Morotopithecus bishopi an extinct hominoid species that lived in Uganda more than 21 million years ago. “From a number of points of view,” Filler says, “humanity can be redefined as having its origin with Morotopithecus. This greatly demotes the importance of the bipedalism of Australopithecus species such as Lucy (Australopithecus afarensis) since we now know of four upright bipedal species that precede her, found from various time periods on out to Morotopithecus in the Early Miocene.”

Citation: Filler AG (2007) Homeotic Evolution in the Mammalia: Diversification of Therian Axial Seriation and the Morphogenetic Basis of Human Origins. PLoS One 2(10): e1019. doi:10.1371/journal.pone.0001019,http://www.plosone.org/doi/pone.0001019


Extracts from an article in Live Science: Human Ancestors Walked Upright, Study Claims

Charles Q. Choi   |   October 09, 2007

“the other great apes we see now, such as chimps or gorillas or orangutans, might have descended from human-like ancestors,” researcher Aaron Filler, a Harvard-trained evolutionary biologist and medical director at Cedars-Sinai Institute for Spinal Disorders in Los Angeles, told LiveScience….

Filler analyzed how the spine was assembled in more than 250 living and extinct mammalian species, with some bones dating up to 220 million years old.”I am getting the feeling that a revolution in our thinking about the origins of bipedality is now under way,” said evolutionary anthropologist Robin Crompton at the University of Liverpool in England.

He discovered a series of changes that suggest walking upright-and not with our knuckles-might actually have been the norm for the ancestors of today’s great apes…

“Humanity can be redefined as having its origin with Morotopithecus,” Filler said. He detailed his findings online Oct. 10 in the journal PLoS ONE.

This research pushes back the date for the origins of bipedalism roughly 15 million years, to before the last common ancestor of humans, chimps, gorillas and orangutans, as well as lesser apes such as gibbons…


After the very early generic phase and the remodelling of the fundamental architecture that would allow upright walking – one of the definitive traits of becoming human, amongst many others, we are now looking for the development of this defining trait, along with enlarged and more sophisticatedly wired brains; the use of voice and language and cognitive development as well other unique features that sets humans, even archaic and primitive proto-humans apart from the other generic apes that presumably refined their own specialisms towards becoming fully speciated, in the end, as  Chimp, Bonobo, Gorilla, Orangutan, Siaman or other forms of non-human Great Apes. Perhaps we are literally what we eat, as if we had not have had a high protein diet with particular enzymes that build big brains with complex wiring, then maybe we would have specialised as any of the above higher primates instead.  This line of thinking brings us to another theory relating to human evolution. It offers evidence and processes that begin to explain how we may have come to be uniquely human. One of the main tenets of this hypothesis relates to environmental interactions being the stimulus for our unique development. And as discussed throughout this series, as they often say in the real-estate or estate agency business: location, location, location.., hopefully you are beginning to see that context (environment or location) and experience is really everything in the evolutionary business as well.

The only aspect of this theory that I would suggest requires a rethink, is its timescale – when things happened in terms of becoming human AKA: Lucy and the presumed 5/6 million year old split between us and everything else. This and the discussion of our missing ancestors could fill the pages of an entire book explaining the controversy surrounding fossils of so-called ancestors to modern humans and their interpretation and presumptions of splits or missing ancestor. You can imagine the type of stuff I’m talking about. But, to cut a very long story short, the alternative theory is in itself essentially sound and very plausible, but if it is extrapolated back to more realistic timescales employing the model of going from the generalist or generic form (recalling the undeveloped – species in the making stage of evolutionary development – our generic ape-like condition) via epigenetically orchestrated modification of the Hox gene complex, then this brings us naturally back to the time Moroto as discussed above.

The alternative theory is often referred to as: the Aquatic Ape theory or hypothesis, or AAT/ AAH for short. The aquatic part has a great deal to do with it – being water. Our unique human evolutionary development has also a great deal to do with the diet and environment that comes with a semi-aquatic existence. It begins to explain how we came to be full-time upright walker, learned to speak (via the diving reflex), why we still love water and particularly as babies and small children, how we have a more aquatic layer of insulation under our skins compared to other higher primates, how we grew particularly complex and large brains which related to a rich aquatic diet full of brain building proteins etc. It can even begin to explain how humans with such big heads survived at all, as water birthing would be a great deal safer and less traumatic for mother and child.

 And no, contrary to misinformed and unfortunately, popularised belief, the aquatic ape theory has not been dismissed as pseudo-science. The theory and this whole issue have been fully addressed in the article ‘A Tribute to Elaine Morgan: the Aquatic Ape Theory revisited’. Elaine essentially argued that the aquatic ape theory was much better for explaining our unique traits and particular evolutionary direction than the conventional hypothesis (the Neo-Darwinian standard model version) known as the ‘Savannah hypothesis’, where we were  all supposed to have been forced out of the forests and had to learn to stand on our own two feet to walk vast distances to find new shelter and food and of course fight off all the wild-life out in the prairies and thus, this made our hunting and fighting strategies develop and in turn we got big brains.

However, we know the ‘Savannah hypothesis’ has been seriously challenged in more recent times and Elaine Morgan is the woman that clearly pursued and fought for the alternative explanation to this old and seriously unscientific and out of date thinking.  Obviously, there is more to this human story, not to mention the evidence for fairly pandemic cross-breeding episodes across many broader species in the early days. Don’t forget about all the genome remodelling and the many other factors that contributed to the remodelling and further refinements of many generic forms, and the differential specialisms and diversifications that for some mammals, ultimately resulted in the mammalian higher primates and finally – ourselves.

A Tribute to Elaine Morgan
Who challenged the scientific establishment on, how we got to be so UNIQUELY HUMAN

Photo Credit: Ian Taylor, Jez Dixon, Water Babies.

You can take a scientist to knowledge, but you can’t make him THINK!
(I use the male pronoun for a scientist quite deliberately and you might see why in a moment…)

This article is a tribute and celebration of the work of Elaine Morgan, who is sadly no longer with us as of last year, but she remains as an inspiration to all of us who knew her work. And, I hope that this article will do some justice in introducing, or reintroducing, Elaine and her research to anyone who has ever been curious about our human origins and felt that the conventional explanation given for our uniquely human characteristics just don’t seem to add up.

See full article on Graham Hancock’s site:


Or read it on this site Tribute to Elaine Morgan by Maria B O Hare diggingupthefuture

Now to apply the remodelling concept to a very specific example in the fossil record, I ask the question: To Be Human or Not To Be Human…? Another case of classification perhaps, which is stopping us seeing the wood for the proverbial (Darwinian) trees. Rather than going through the whole controversy of ancestral fossils that gave rise, eventually to modern man, I decided to focus on one story in particular which will give you an insight into the types of approaches and mean of interpreting and dating fossils in the hominid lineage. Of course you can make up your own mind after you have assessed the evidence, but the most important point of presenting this particular article is that is raises the question of how we define our species – when is a human not a human? Or is it a new and distinct species? And the obstacles that are seemingly insurmountable when we keep insisting that the square peg must fit inside the round hole, because that is what our assumptions embedded in our current paradigm of Darwinian think tells us. What if our classification system, our terms and our assumptions were fundamentally flawed from the beginning? What if one of the most revealing human traits is actually to care for members of our family that would not have been able to contribute much to the tribe and actually not be able to be fully independent? The following is based on a previous blog on this site entitled: Because Homo Floresiensis had Down Syndrome, doesn’t mean that Hobbits didn’t exist -Humans in the Making?

Explain this Darwin

Brings to mind that old Shakespearian quote: “Speak to me only with thine eyes…”

Homo floresiensis

According to the Australian Museum, Homo Floresiensis (the species of very small humans often referred to as hobbits)

“…archaeological evidence suggests H. floresiensis lived at Liang Bua from at least 95,000 to 13,000 years ago. These dates make it the latest-surviving human apart from our species H. sapiens”.

– See more at: http://australianmuseum.net.au/Homo-floresiensis#sthash.nCcL6FH5.dpuf

They go on to say that these remains of humans are:

“One of the most controversial and surprising hominin finds in a century…

Conflicting interpretations and debates surround the remains of these tiny humans from Indonesia. H. floresiensis are not our ancestors but their unusual features and recent survival suggests our human family tree is more complex than once thought” 


The key points in the above extract, apart from our evolution is certainly more complex than hitherto imagined (see other blogs on human evolution on this site) in my opinion, based upon more recent re-assignment of the entire species of Homo Floresiensis (hobbits) to a non-distinct human species (No Hobbits allowed) because a single representative of this population, turns out to possibly have had Down Syndrom according to a recent article published in a scientific journal a few days ago, essentially throwing out the entire species of Homo Floresiensis even though the rest of the population were  small, had distinctive primitive and more modern features and lived over the course of 80,000 years on this island. See article below entitled: Flores bones show features of Down syndrome, not a new ‘hobbit’ human.


The reason being, apparently, that LB1 (named after the site and the fact that it was the first and main find – a scull in particular, which a great deal of focus and fuss and controversy has surrounded concerning the distinct ‘new human’ label or NOT) is the one with DS (Down Syndrome).  However, a slightly earlier science paper dating to May 2014 has outlined another interpretation based upon the same evidence within the wider context of other remains and artefacts from the same site as LB1 and the rest of the region in their paper entitlted: Evolved developmental homeostasis disturbed in LB1 from Flores, Indonesia, denotes Down syndrome and not diagnostic traits o f the invalid species Homo floresiensis


This more integrated examination of the facts demonstrates that the main skull LB1 which is the one with the proposed DS (Down Syndrome) and often represented (reconstructed) in popular science outlets as the sole representative of this deminuitive species, essentially, are pointing out that we can’t throw out the baby with the bath water as the rest of this  distinctive human (small) species are well represented at the site and span a vast period of time and obviously don’t all have the DS condition.

In other words, LB1 may have had Down Syndrome (common enough amongst ourselves, chimps and apes etc), but it doesn’t make all the other hobbits (Homo-floresiensis) disappear because it may turn out that one of the population had this condition. If anything, in my opinion, it shows how having DS still meant that (LB1) she survived until about 30 years old and presumably she was well cared for by her family and community.

Otherwise, this distinct human species found at Flores had fully-modern type jaws, but were missing chins which all modern humans have. They had very strange primitive features in their wrists and their arms were rather long for their bodies. (primitive and modern mix of features), yet, judging by their hunting habits, they were in the main brainy. They hunted with rather sophisticated tools and points and cooked big beasties (remember these are quite small and seemingly not quite fully modern human yet). They of course walked fairly well by all accounts – on both feet, even if their feet were quite large (I wonder were they hairy?).

see http://australianmuseum.net.au/Homo-floresiensis

Yes, it is amazing what you find out if you look at all the evidence from one archaeological site and not just a clincal study of an isolated case of a syndrome and a brain scull. I do tend to have a bias here as I am an archaeologist and know how important context is. Anyway, essentially what I’m saying is that many of those rejecting the new species status focus only on the remains of LB1, and ignore the rest of this population and their remains/artefacts of stone and the geology of the site showing occupation by this same group for over 80,000 years, if not more, that show many of the same characteristic features as LB1 which are irrelevant to her possible DS condition.


All in all, far too much has been made of one scull from flores (LB1). Yes, it was exceptionally small, but tests and endocastes of the interior folds of the frontal lobes (impressions made when brain case was more maluable) and show obviously different folding (modern human type) rather than anything resembling a chimp’s soft-tissue arrangements. In other words, even with the DS condition, LB1 was more human-brained than chimp-brained.

See video below:


Below are more archaeological points on the Homo-floresiensis population as a whole from Flores.

Further fossil finds from Flores by Daniel E. Lieberman
New fossil discoveries on Flores, Indonesia, bolster the evidence that Homo floresiensis was a dwarfed human species that lived at the end of the last ice age. But the species’ evolutionary origins remain obscure

The new fossils consist of the right humerus, radius and ulna of the LB1 skeleton, the mandible of a second individual (LB6), and assorted other remains including two tibiae, a femur, two radii, an ulna, a scapula, a vertebra, and various toe and finger bones. The researchers think that the sample includes the remains of at least nine individuals. The analysis focuses on the new mandible (LB6), a new tibia (LB8) and the LB1 skeleton’s reunited arm bones. Of the many details, several merit special attention. First, the new mandible is extraordinarily similar to the first one. They almost certainly belong to the same species. Both mandibles share distinctive dental features, and they lack chins — a chin being a unique feature of all Homo sapiens regardless of their stature, including most microcephalics …

 In addition, the new tibia and arm-bone fossils not only confirm that the Liang Bua hominids were short, about a metre tall, but also indicate that they had relatively long arms… Although the original LB1 skeleton is estimated to be 18,000 years old, a child’s radius was found in deposits estimated to be 12,000 years old, and the new mandible is estimated to be 15,000 years old; other finds may be as old as 95,000 years 2,3. The fossils also all seem to be similarly small, refuting the contention that the LB1 skeleton was simply an aberrantly dwarfed, pathological specimen. If they were pathological, then the Liang Bua fossils would have had to have come from a population of short,  microcephalic humans that survived for a long time, or one that was susceptible to high frequencies of microcephaly and dwarfism. Such possibilities strain credulity; moreover, a three-dimensional analysis of the LB1 braincast found the brain to be unlike a micro-cephalic’s, and more like that of H. erectus than H. sapiens


And again from the Australian Museum website:

All remains come from the cave of Liang Bua on the island of Flores in Indonesia. Flores lies towards the eastern end of the Indonesian island chain. Flores has always been separated from mainland Asia – even at low sea levels the water-crossing was at least 24 kilometres. It is known that other animals reached Flores by swimming or floating on debris. How or when H. floresiensis reached the island is unknown.

Jaws and teeth

  • lacks the bony point on the chin found in modern humans
  • relatively large jaw and teeth that resemble H. erectus but with more primitive features
  • premolar roots different from H. sapiens
  • small post-canine and canine teeth
  • parabolic or V-shaped dental arcade typical of Homo
  • bony shelf at the front of the lower jaw which is a primitive feature not seen in H. erectus

Limbs and pelvis

  • bones and joints of the arm, shoulder and the lower limbs suggest that H. floresiensis was more similar to early humans than modern humans
  • characteristic bipedal foot that includes a big toe aligned with other toes and a locking mechanism on the middle of the foot to help stiffen the arch after heel lift occurs
  • several primitive features include a relatively long foot for its body size (70% as long as the thigh bone, compared with 55% for modern humans), a flat arch lacking the spring-like mechanism used to store and release energy during running, and a short big toe. These features are similar to ancient hominins such as H. habilis (OH8) and australopithecines and suggest the gait was different from and less efficient than modern humans.
  • unusual low twist in the upper arm bone
  • wide leg bones compared to the length
  • relatively short and curved clavicle
  • shape of the shoulder blade resulted in the shoulder being moved forwards slightly as if hunched
  • wrist bones differ significantly from the those of modern humans and are more similar to African apes or australopithecines. They lack features that evolved with the ancestors of modern humans at least about 800,000 years ago. In particular, the trapezoid bone is pyramidal in form, whereas modern humans have a boot-shaped trapezoid.
  • primitive flared ilium blades in the pelvis, similar to australopithecines, and females have wider pelvises than H. sapiens females
  • relatively long arms




Stone tools were found in a number of different layers dating from 90,000 to 13,000 years ago. Tools include simple flakes, points, perforators, blades and microblades which were possibly hafted as barbs. Some were found with the remains of LB1, but most came from the same location as the remains of the extinct pygmy elephant Stegodon. This suggests that H. floresiensis was hunting these small elephants. Stone tools produced by heavier percussion were also recovered from layers not associated with H. floresiensis occupation. These tools date to about 102,000 years ago. The makers are unidentified.

There has been some speculation that the stone tools associated with H. floresiensis were actually made by H. sapiens. The basis for this is purely the belief that humans with such small brains couldn’t make such sophisticated stone tools – there is no other evidence in support of this. However, those studying the tools claim they are not as sophisticated as they appear and regard them as ‘simple’.

Analysis of the residues and polish on some of the tools revealed they were used for working wood and fibrous materials, perhaps to make spear shafts or items such as traps. Cut marks on the Stegodon bones also suggest some of the tools were used to process meat.

Precursors to this tool kit may come from earlier sites on Flores. Tools excavated from Mata Menge (about 50km from Liang Bua) in 2004-5 are at least 700,000 years old, and those from the Soa Basin date to about 880,000 years old. Tool kits from both sites show some similarities and technological continuity with those found in Liang Bua cave. The identity of the makers is unknown, but they could possibly be ancestral to H. floresiensis.


There is evidence of the use of fire in Liang Bua cave. The remains of numerous juvenile Stegodon have charred bones, possibly indicating that H. floresiensis was able to control fire for cooking.


There are no traces of pigments, ornaments or deliberate burials in the layers associated with H. floresiensis – all of which characterise the modern human levels from the upper parts of the cave.

Environment and diet

Flores is a heavily forested tropical island with mountain peaks reaching over 2000 metres. The environment during H. floresiensis time would have been similar. The nature of their environment and the limited food sources typical of such islands provides strong clues to the evolution of H. floresiensis. When a small population becomes separated, changes can occur very quickly. This particular environment favours reduced energy requirements with dwarfing a response to this. Several dwarf species, including Stegodon, have been recovered on Flores and other small islands.

This species shared the island with pygmy elephants Stegodon, giant rats and large lizards like Komodo dragons. Evidence of cut marks on the Stegodon bones from Liang Bua cave show that H. floresiensis was at least hunting and eating this animal.

– See more at: http://australianmuseum.net.au/Homo-floresiensis#sthash.nCcL6FH5.dpuf

Relationships with other species


When first discovered, it was suggested that H. floresiensis was possibly descended from Javanese H. erectus. However, more detailed analysis of skeletal remains has uncovered traits more archaic than Asian H. erectus and more similar to australopithecines, H. habilis or the hominins from Dmanisi in Georgia (classified as Homo ergaster or Homo georgicus). Most scientists that accept H. floresiensis as a legitimate species now think its ancestor may have come from an early African dispersal by a primitive Homo species similar in appearance to H. habilis or the Dmanisi hominins. This means that it shared a common ancestor with Asian H. erectus but was not descended from it….

Unfortunately, no transitional forms, or the actual remains of H. erectus itself, have been found in Flores. However, stone tools that may have been made by H. erectus (or a similar species) were discovered on Flores. These date to 840,000 years ago, so indicate that a hominin species was probably living on the island at that time.


…All remains come from the cave of Liang Bua on the island of Flores in Indonesia. Flores lies towards the eastern end of the Indonesian island chain.

Flores has always been separated from mainland Asia – even at low sea levels the water-crossing was at least 24 kilometres. It is known that other animals reached Flores by swimming or floating on debris. How or when H. floresiensis reached the island is unknown.


Could a more archaic less specialised population of Homo Flores arrived (swam over – see aquatic ape theory & past posts on the hobbit species on this site) to the island longer than our current model of evolution allows us to suggest?

A Generic Human on the way to being more specialised & you don’t even need transitional fossils to prove it? Furthermore, I believe that Hobbits became the living ancestors of many modern Indonesians and particularly those from Flores? Heresy, for some I know. But, truly this is the type of scenario unfolding as we apply the more recent data, particularly the molecular data, to what we find in the fossil record.

Take for example the fact that it doesn’t matter how big your brain is – it is how you use it. The article below deals with the non-gene difference between humans and chimps and it is to do with Transcription factors – how genes are expressed, which is ultimately controlled by epigenetic processes/natural genetic rearrangements of genome and these are orchestrated according environmental cues.

Transcription factors guide differences in human and chimp brain function


Humans share at least 97 percent of their genes with chimpanzees, but, as a new study of transcription factors makes clear, what you have in your genome may be less important than how you use it. Gene regulatory networks differ between human and chimp brains, the researchers found. Humans share at least 97 percent of their genes with chimpanzees, but, as a new study of transcription factors makes clear, what you have in your genome may be less important than how you use it.

The study, in Proceedings of the National Academy of Sciences, found that broad differences in the gene activity of humans and of chimpanzees, affecting nearly 1,000 genes, appear to be linked to the action of about 90 transcription factors. Transcription factors are proteins that bind to specific regions of the DNA to promote or repress the activity of many genes. …”Our very strong bias is to believe that these transcription factors are involved in speciation and traits that make species unique,” she said.

“The chimp network looks very much like the human one except there are a few transcription factors in different positions and with different connectivity,” Stubbs said. “Those are of interest from the point of view that they signal a major gene regulatory shift between species, and this shift may help us explain some of the biological differences.”
The new findings indicate that certain transcription factors are working together in a coordinated way to regulate the changes in seen in gene expression between humans and chimps, the researchers said.
“Once this network of transcription factors is established, changes in the network can be amplified because transcription factors control other genes,” Nowick said. “Even a small change in transcription factor expression can therefore produce a large effect on overall gene expression differences between chimpanzees and humans.”


So, although I’m not saying that the Hobbits of Flores were anything to do with chimps, I am saying that when chimps weren’t chimps and humans weren’t fully human, they may have been generic apes on their way to becoming rather rapidly by all accounts, distinct from each other and it may have been something as simple as their interbreeding habits and how genes and proteins are regulated (expressed) via transcription factors and natural genetic engineering processes that are ultimately driven by environmental factors that may have made the difference in the end.

Therefore, in the light of newer ways of seeing the fossil record and our own evolution and its application to the Hobbits of Flores, another way of interpreting all this evidence is to see this long-established variation of the generic ape/human template according to a very specific island niche, where hybridization, which was more common than previously understood between all sorts of archaic and more modern humans, when combined with isolation within this region and interbreeding within their own kind thereafter, probably did lead to the creation of the more modern populations around the island of Flores as the indigenous people themselves claim.

And so finally, all this brings us to our overarching model of evolutionary development – not by Neo-Darwinian means. The simplest way I can express this principle that applies seemingly at every level of growth, form and evolutionary complexity, is outlined below:

Nested Russian Dolls model of Evolutionary Nested Scales of Increasing Complexity

nested dolls

The ‘Matryoshka Principle’ of Evolutionary Development

Nested Scales of Complexity

Russian-Matroshka Russian-Matroshka2


A matryoshka doll …also known as a Babushka doll, Russian nesting doll, or Russian doll, refers to a set of wooden dolls of decreasing size placed one inside another. The name is believed to be a derivative of “Matriosha” or “Matriona,” which were female names that enjoyed immense popularity among Russian peasants. The name connotes the matriarch of a big Russian family.

This generalist to specialist principles seems to operate at all scales of speciation. Indeed, seemingly there are gradations of complexity within all the major groups, where some mammals become very complex higher primate forms, while at the other end of the spectrum, monotreme types still remain fundamentally of the more primitive mammalian form. Reptilia (or let’s call them at their development stage – Generalist Diapsids until they speciate into their various forms of everything that is not mammalian, fish or amphibian), seem to diversify and become specialists and become increasingly refined as particular forms of species that we begin to recognise today; except for the diminutive dinosaurs, or the remodelled bipedal dinos that took to flight because of their plight perhaps?  

If the common ancestral condition is Anapsid – primitive vertebrates (jawed fish); amphibians; and even some turtle-types, and it is also the primitive condition, until divergence of the stem amniotes to synapsid and shortly (10 million years) thereafter, diapsid primitive tetrapod conditions, and maybe even the euryapsids are all diversifications of fundamental themes arises after modifications throughout their evolutionary development, then this brings to mind, the concept of nested scales of complexity within a fundamental form. (proposed as being entirely extinct, like everything else that doesn’t now exist in its primitive form such as all the pelycosaurs). They include the ichthyosaurs and the plesiosaurs. (Note the end part of these terms have ‘saur’ in them which implies reptile origins). The ichthyosaurs and plesiosaurs for example, also used to have one fenestra behind the eye,

Basically, as is the case with all the fundamental forms of land-dwelling tetrapods, all varieties of different levels of complexity potential led to more specialised features on the fundamental theme of broader species form, resulting in vast and novel niche-filling diversifications via epigenetic modifications. As this process continued for all the main groups until their final speciated form, as I said before, the more complex a species is the longer its evolutionary (gestation) development. By applying this principle of scales of complexity and refinement (almost like nested Russian Dolls – as the nested size of the outer and most refined and detailed doll is part of a larger set and its own shape and form is ultimately directed by even the smallest baby-doll that initiates the whole set.

Each doll in the set is formed according the shape of the former doll and in turn, the larger and later dolls will be shaped and formed according to the previous forms. Fundamentally, they are a full nested set of self-similar creations on different scales of both size and complexity. The detail and colour of the painted doll is much more discernible on the later versions, built around the same template, yet they are only limited in their detail by the availability or paint and range of colours. Similarly, a much larger set with many dolls of ever decreasing size and detail can only be produced if there is enough wood from which to carve the larger set. However, if less wood is available and less paint of many hue and colours, the nested set can still be produced, but it would be simpler and not have as many dolls contained within.

This is a fractal model of evolution and as many studies are beginning to show: the whole of biological life, shape, form and function is underpinned by fractal patterning, networks and seemingly, it’s universal! (See first article in the series) https://diggingupthefuture.com/2015/08/03/evolution-scaling-laws-something-universal-is-going-on/


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