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“Mammal-like Reptile” is simply wrong…Extinctions may be more rare than you think and marine “reptiles” may not be reptiles either…

Part Seven

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


“Mammal-like Reptile” is simply wrong…Extinctions  may be more rare than you think and marine “reptiles” may not be reptiles either…

how reptilian are you 

Something universal is going on… revisited and applied to the fossil record

I will review the principles of this alternative evolutionary model as it applies all the way up the species scale, or at least the tetrapod scale as we have reviewed briefly the earlier scales of complexity, but the principle is essentially applicable to all levels of evolutionary complexity and are therefore seemingly, universal. By attempting to identify these fundamentals, we may be able to reconstruct how evolution actually did unfold or leap, if it wasn’t via Neo-Darwinian means…

Proposed driver of evolution (not limited to vertebrates): Growth and development according to naturally self-organising systems and networks (universal scaling laws) seen in how metabolic systems drive biological complexity and organisation of form as discussed in the article below as it refers to biological scaling laws. It is entitled: The origin of allometric scaling laws in biology from genomes to ecosystems: towards a quantitative unifying theory of biological structure and organization by Geoffrey B. West and James H. Brown


.., all organisms share a common structural and functional basis of metabolism at the molecular level. The basic enzymes and reactions are universal, at least across the aerobic eukaryotes. Additional general rules based on first principles determine how this molecular-level metabolism is supplied and regulated at higher levels of organization: from organelles, to cells, to organisms, to ecosystems. The most important of these rules are those relating to the size of the systems, including the body size of the individual organisms, and the temperature at which they operate. Our theory of quarter-power scaling offers a unified conceptual explanation, based on first principles of geometry, biology, physics and chemistry for the size-dependence of the metabolic process. The theory is based on generic properties of the metabolic distribution networks in simplified, idealized organisms.


Nature cuts her clothe to her measure (an old tailor’s axiom) Applying the universal scaling laws

As noted above, the same fundamental principles of growth/form and evolutionary developmental and drivers of evolutionary complexity at every scale and seem to apply across the board. And just as there is a speed limit, at least in our local universe, (the speed of light and how it applies to matter) there seems to be rules and limits of growth and form within biological systems – and it is also all relative. For instance, the biosphere of planet earth had to evolve and in so doing, a co-evolution of its life forms also evolved. Everything develops directly and in accordance with everything else. Things don’t generally out compete (over-grow) with other things such as a tree growing in the forest gets too big for its boots and says: “move over buddy! There’s not enough light”. A snowflake or snow flower doesn’t put on one ice-crystal or petal at a time or outcompete for top dog position within populations of other snowflakes or flowers.

One is a collection of bonded and particular orientation of molecules and is almost entirely made of water. It shows predictable geometric growth patterns and its full display can be seen when viewed under a micro-scope, while the other is a collection of highly organised cells, made up almost entirely of water also, and like the snowflake, has predictable patterns of geometric growth (see first article in this series) when viewed in terms of its network and its outer symmetry when it develops into a flower. Yet, one is described a living, while the other inanimate matter and therefore not alive. However, both use natural resources in the environment to grow in a predictable (fractal-growth) way according to their innate (inherent) level or scale of complexity.

This begs the question: are atoms alive? Does organised matter, matter? Does it have a consciousness beyond this five sense reality? Yes, these are philosophical questions and should remain within that domain. Because we are exploring the very patterns behind evolution, it does raise these sorts of questions, but this is not what this topic is about and besides, I’m still exploring and discovering and wondering and asking the questions, but they are more of a personal nature. So I will leave that discussion in realm where it belongs: with the philosophers. Let’s just do the exploration of the evidence – the science, as the great evolutionists of old, before, during and after Darwinism took hold used to do and see where it takes us.

By applying these universals to biological evolution, we can begin to see why there is just the right amount of fish and all their vast variety (perhaps their initial starting conditions in the primordial pond sealed their fate from the get-go?) in all the watery environments of our planet and finely tuned and adapted to their particular watery niche. And if Nature worked according to Darwinian means, this evidence would be very difficult indeed, to reconcile with the concept of randomness and would possibly result in (if life ever got to that point of complexity in the first place): too many fishy-pods escaping their watery confinement to become great land-walkers and leaving all the big fish that didn’t make it flopping about in rather small muddy ponds.

Mother Nature’s recipes are Just Right!

 Recalling all the while, that not all organisms mature or have the same gestation period and typically, the more complex metabolism a species has: the longer its evolutionary gestation period would appear to be. It would seem that by employing Von-Baer’s principles and following other lines of evidence supporting his concepts, that present-day species mirror on micro-scales their species evolutionary developmental path on a macro-scale. By inference, it could be said that the more complex (metabolically) vertebrates took much longer to mature; specialise and fundamentally adapt, than their earlier and simpler vertebrate pioneers such as fish. In principle, Mother Nature takes more time to cook up the really sophisticated recipes or express them according to available ingredients. The more exotic, the spices: the more exotic the species. But once it is made, there is no good changing it into something else – especially if it is just right as it is.

The Butterfly Effect in Evolutionary Development

This latter statement seems to reflect an important concept within evolutionary development biology (EVO-DEVO) and scientists during the earlier half and beginning of the 20th century such as: Waddington’s epigenetic landscape  (you can research the term to find out more) and of course, there were pioneers such as: Thompson D’Arcy and his concepts of growth and form during development (see first  article in this series).   Interestingly, it is also a fundamental tenet of Chaos theory (which studies complex/whole systems of natural phenomenon) which attempts to establish patterns of how systems start seemingly unordered, tend to order or, how seemingly ordered systems tend to disorder over time. Biological life is an open system working in a feedback loop (exchange) with its environment. That is what makes the difference between the living and non-living snow flake or snow flower (leaving consciousness aside), as the former hasn’t evolved a means to  beat the second law of thermal dynamics, where as the latter can. But one could argue that the snowflake is part of the life-cycle of the flower – just another form. But, we won’t go there. Below is quite a good explanation to this quandary.

Q: Why doesn’t life and evolution violate the second law of thermodynamics? Don’t living things reverse entropy?

Posted on March 24, 2013 by The Physicist

Physicist: In very short: nope.

The second law of thermodynamics is sometimes (too succinctly) stated as “disorder increases over time”.  That statements seems to hold true, what with all of the mountains wearing down, machines breaking, and the inevitable, crushing march of time.  But living things seem to be an exception.  Plants can turn dirt (disordered) into more plants (order), and on a larger scale life has evolved from individual cells (fairly ordered) to big complicated critters (very ordered).


Another important aspect of Chaos Theory is that it helps explain how any system at the beginning, (sensitive initial conditions), will be highly sensitive to slight change and variation which can culminate as a (nested) cascading effect further down the line, resulting in a very big change further down the line. You may have heart of it. It is called the ‘Butterfly Effect’. Again you can look this up for more information.  This applied in principle to evolutionary development would suggest that even when organisms at an early stage in their development are not that different from one another: can diverge radically (in the end) from that form as they mature and develop and once a species begins to follow this course – like water finding its own natural level and path of least resistance: everything builds in repeated patterns of increasing scale and complexity, along this course (Waddington’s landscapes). 

Becoming a species: weather permitting

Proposed mechanism for further species adaptation: Environmentally triggered and timed Epigenetic expression of genetic novelty operating/orchestrating the Hox gene complex, particularly during development (the master switches for main body-plans such as limbs and digits in non-fish vertebrates for example), leading to continued epigenetic flexibility and increasingly refined adaptive programs causing further diversification and divergence between the species of fundamental vertebrate forms; again, according to inherent ancestral molecular complexity and further evolutionary development potential.

Representation of evolutionary and geological events leading to changes of oxygen content in earth’s atmosphere since the formation of the planet.Oxygen_atmosphere

 Source:   https://commons.wikimedia.org/wiki/File:Oxygen_atmosphere.png

Can you see a pattern? As the oxygen levels climbed, so did species of increasing complexity emerge. Note also that after the oxygen photosynthesis was established – with the rise of aerobic metabolism, we see the seemingly, almost exponential eruption (the Cambrian explosion) of the first obvious bursts of speciation of the plant and animal fundamental forms.  An earlier article on this topic discussed the temperature/metabolic dependency of brain size, i.e., bigger brains = higher temperatures and therefore more sophisticated metabolic regulation systems. Remember also that I discussed this misnomer about having reptile brains (reptiles don’t even have them) and how brains: not only seem to have evolved according to metabolism relating to the temperature – say of your primordial pond – but, they also have been shown through studies on vertebrate brains to have evolved from a common ancestral condition (shared) and later followed by divergences of various kinds, along with its independent evolutionary trajectory amongst various vertebrates. I will discuss this evidence further on.

Finding the missing ancestors in the proverbial haystack – and the needle is golden and made of straw

Proposed means of genetic novelty to drive complexity: The primordial genetic exchange across all domains of life (HGT- horizontal gene transfer, GD – genome doubling, hybridisation, epigenetic modification and reprogramming of cells, and remodelling of genomes/ via ‘jumping genes’), leading to a sophisticated tool-kit (the conserved Hox gene complex), inherent in all primitive generic vertebrate species (flipped invertebrate body-plan).

The point being that, complexity and evolutionary development is seemingly driven by metabolism in relation to the environment and the level of evolutionary complexity is limited by the inherent metabolism within the species. In other words, if a developing organism has not reached maturity (expressed all its evolutionary potential) as a specialising species, then, although it may superficially resemble very primitive type organisms whilst in its early stages of evolutionary development: like a growing embryo, it is difficult to tell what it is going to be when it grows up. Unless of course we can identify its parents, but at this stage in the evolutionary game of life, it would seem that the parents themselves are only beginning to emerge and their ancestral lineage is more like a clump of web-like networks. And besides, it probably doesn’t have specific parents, just like it doesn’t appear to have specific ancestors, just, seemingly, a commonly shared ancestral condition. 

Which came first: the chicken or the Egg?

This also begins to resolve the chicken and egg conundrum – which came first? Well the egg-cells of course. Then the embryo, then the organism that begins to show the fundamental body-plan of a vertebrate (Hox genes epigenetically orchestrated) and then sometime later, eggs become a fast-track way of reproducing these stabilised four limbed designs and start to show divergences (with a lot more cross-breeding and interesting environmental imprinting on their epigenome) and might eventually start to look like a bird via adaptations (remodelling in the egg) and much, much later on refine its features to finally become a small bird that can be domesticated by humans and then we can call it a chicken.

Because many of these creatures (particularly the vertebrates) are not fully-formed species as yet, recall the model that I am employing goes from the ancestral conditions and from the generalist to the specialist. The more complexity potential a species has inherent within its metabolism: the more time it will take to become a fully specialised species. That’s where we left off last week, talking and discussing the reason why fish couldn’t walk (because they didn’t have any fishy fingers). They had begun to stabilise as a species early on and presumably this was because they were innately less complex – metabolically speaking, than their vertebrate counterpart.

The Hour-Glass Model of Evolutionary Development

Model for Vertebrate evolution: A convergence on a shared ancestral condition and later species specialist diversification from the generalist to the specialist species form – divergence from an ancestral embryo-like/larval form (chordate form) via Metamorphosis – rapid and profound speciation via Leap-frog-type evolutionary development for all basal chordate into full vertebrate fundamental forms. This emerging modernised synthesis, where fundamental forms converge (after much more diverse multi-cellular primitive life) on a similar form during mid development (and applied to mid evolutionary development) and begin to diverge and specialise thereafter, is directly modelled in what is commonly referred to as the hourglass hypothesis. The illustration below is the best way to visualise this model.


Source: cartoon illustration of the hourglass developmental model from Richardson et al. 1998

The following abstract from an EVO-DEVO (short for evolutionary development) science paper discusses the hourglass model and how more recent support for it corresponds well with aspects of Von-Baer’s which I have been employing throughout this series.

The “developmental hourglass” describes a pattern of increasing morphological divergence towards earlier and later embryonic development, separated by a period of significant conservation across distant species (the “phylotypic stage”)


The evolutionary mechanism of conservation during embryogenesis, and its connection to the gene regulatory networks that control development, are fundamental questions in systems biology… Several models have been presented in the context of morphological, molecular, and genetic developmental patterns. The most widely discussed model is the “developmental hourglass”, which places the strongest conservation across species in the “phylotypic stage”. The first observations supporting the hourglass model go back to von Baer when he noticed that there exists a mid-developmental stage in which embryos of different animals look similar. On the other hand, the “developmental funnel” model of conservation predicts increasing diversification as development progresses…


In summary then, and just to bring this back to the application of Von-Baer’s evolutionary developmental principle, basically, by looking at the hourglass model, you should be able to see how it reflects the main evolutionary stages of the species and at the same time and on different time scales, you should begin to see how it applies to all of evolution on the grand more universal scale and at the other end of the spectrum, current modes or non-activated ancestral modes of development, that can be reactivated in some simpler vertebrate modern species as alluded to in last week’s article. Historically, I believe it is important to reiterate Von-Baer’s laws again, particularly as it relates to vertebrate evolutionary development: The article is from the embryo project website and based upon a study by M. Elizabeth Barnes on Karl Ernst von Baer’s  Laws of Embryology.

…In 1828, while working at the University of Königsberg in Königsberg, Germany, Karl Ernst von Baer proposed four laws of animal development, which came to be called von Baer’s laws of embryology.

Von Baer’s second law states that embryos develop from a uniform and noncomplex structure into an increasingly complicated and diverse organism. For example, a defining and general characteristic of vertebrates is the vertebral column. This feature appears early in the embryonic development of vertebrates. However, other features that are more specific to groups within vertebrates, such as fur on mammals or scales on reptiles, form in a later developmental stage. Von Baer argued that this evidence supporting epigenetic development rather than development from preformed structures. He concluded from the first two laws that development occurs through epigenesis, when the complex form of an animal arises gradually from unformed material during development.

Von Baer used the third and fourth laws to counter the recapitulation theories … which became increasingly popular in Europe throughout the eighteenth and nineteenth centuries.., these theories posit that as the ontogeny of an animal embryo progresses, the embryo’s different stages of development represent lower animals’ adult forms. For example, according to the recapitulation theory, the early human embryos have structures similar to gill slits, and thus that early stage represents the form of adult fish, which also have gill slits.

Von Baer’s third law states that animals from different species start out similar and become more dissimilar from one another as ontogeny proceeds. As an example, von Baer discusses the embryos of humans, fish, and chicks, all of which look similar to each other in the early stages of their development. As they grow, however, they look increasingly different from one another. The embryo of one species never resembles the adult of another species. Instead of recapitulating other animals’ adult forms, von Baer’s third law theorized that animal embryos diverge from one or a few shared embryonic forms. The fourth law states that the stages of development in more complex animals never represent the adult stages of less complex animals; they resemble only the embryos of less complex animals.


In other words, as illustrated above (the hourglass model) when viewed along with the proposed tadpole-like condition of all vertebrates (including fish), directly reflects the convergence seen in the funnel-neck of the hourglass model of evolutionary development represented by common tool-kit- the Hox gene complex which all vertebrates use like master gene switches during initial body-plan development. It presumably is Nature’s very efficient way of producing more predictable productions that are adapted at a macro-level to their fundamental niche, e.g., fish to water, tetrapods to land.  The mechanism for the subsequent divergence of the various fundamental kinds of species operates presumably, as the evidence strongly suggests, via epigenetic orchestration of the master switches according to changing environmental circumstances and conditions of existence. It is this mechanism that causes the differential genetic expression according to adaptive programming (timing is everything) of existing genes. When, where, how and to what degree genes are expressed depending upon developmental stage of an organism or species ‘in the making’, can have a profound outcome to what a more mature organism/species becomes in the end.

Epigenetically controlled Metamorphosis would begin to explain the rapid and profound speciation that we find in the fossil record and all diversifications according to adaptive needs of the species thereafter. Recall the research of De Vries (leaping evolutionary mutation theory that is not to be confused with our modern concept of genetic mutations) and others and the type of leaping Lamarckian evolutionary understanding that was emerging around the turn of the 20th century in particular (pre-lock down by the new modern synthesis movement). For instance, fish start out very primitive while and some go on to diversify as many variations on the theme of fish. The tetrapods that first come to land (presumably via leap-frog-type evolutionary mode of development – just as fish seem to become fish via the same mechanism – only somewhat earlier), also start out as rather experimental and primitive types – like the fish during the early stages. This is well illustrated in the fossil record as you will see further on. Then generalist tetrapods begin to diversify and specialise according to their inherent metabolism. This is clearly seen in the fossil record if you view the evidence while applying the models and studies that show clearly that evolution in vertebrates goes from the generalist to the specialist as seen in brain studies which I will review shortly and have highlighted previously.

The diversification from a common body-plan of tetrapod towards specialisms of amphibian, reptile (lizards, snakes etc – recall the article on ‘how the snakes or lizards, lost its legs for example as written about previously on this site?), perhaps the most surprising diversification of them all is that of mammals as they come much, much earlier as a fundamental form in the record and according to molecular studies, than you might have previously imagined. I’ll present the evidence further on. As you can imagine, mammals are very complex metabolically and therefore, as noted above, metabolism being a driver of evolutionary complexity and its universal growth limits must be considered in this reassessment of the fossil record and vertebrate evolution in general. Think how much more diverse a developing species could become if it wasn’t confined to ambient temperatures and were able to regulate their own metabolism/body heat exchange with the environment.

And I should also mention the new mode of development (presumably post amphibian speciation level), changes epigenetically to a radically more sophisticated egg. The eggs evolve in design as much as the little critters developing inside them. These are super eggs, built for the long haul and they don’t dry out. Remember that eggs can be reprogrammed according to temperature and weather permitting just as much as metamorphosis can be triggered via environmental/cellular signals during development. And if you think I’m cracked in suggesting that primitive mammals laid eggs, then think about our little primitive monotremes (such as modern day platypus) and the fact they lay eggs, yet they are mammals, albeit very primitive ones. Or the marsupials who haven’t quite decided whether to lay their eggs or keep them fully inside as placentals do – that’s us and all other kinds of mammals beyond these two groups. Obviously, if we look at the fossil record and apply what we know of modern species present day development modes, like Von-Baer did and maybe we can begin to see how actual tetrapod speciation unfolding too. This is the principle which I have applied to the whole reassessment of tetrapod evolution as you will see shortly.

Vertebrate Evolutionary model

What falls out of this investigation might surprise you, particularly the presumptions underpinning and informing our interpretation and reconstruction of the fossil record which I believe has led us on a ‘wild-goose chase’; finding many ‘red-herrings’ along the way; has ‘left us in the doldrums’; ‘up S*** creek without a paddle’ and down several blind ally – ways’ and all the other proverbial statements of losing our way and getting stuck that I can think of. I know that I was surprised at what I discovered once I managed to fight my way through the quagmire of assumptions built upon assumptions which were themselves based upon an idea that may or may not have been correct. And which is turning out by the day to be sinking into the quick sand – the foundations upon which it was built. It was only then, that I found a clear path and was finally, able to re-evaluate the fossil record and all the relevant evidence and apply the principles, the universals and the scaled level of complexity model. Below is some of what I found.

Review of last week’s article: Fish are possibly NOT US, or something along those lines…

Last week’s article on the topic of non-walking fish and the walking tetrapod via a type of leap-frog metamorphosis hypothesis outlined an alternative to the walking-fish hypothesis. This alternative scenario would appear to correlate much closer with what we actually see in the fossil record and is also well-supported by other lines of evidence.   Moreover, the leap-frog type hypothesis offers a much simpler way for vertebrates of the four-limbed variety to get easily unto land to become land-dwelling, air-breathing, specialist egg-laying, walking animals. It begins to give us an insight into how tetrapod (generalist – not yet defined and specialised as you will see further on) diversified into increasingly specialised and less primitive forms, ultimately reaching speciation in their more recognisable modern-day form. Again this is very much the pattern we see in the fossil record and finds further support from a range of studies that have looked deeper into these issues.

Evolution of Stem-Tetrapods

No Fish allowed – you have already begun to specialise and although they had the tool-kit, they did not have the inherent complexity (metabolism) to make the giant leap unto land, seemingly? timeline2


The graphic covers the last 600 million years

The conventional and popular promotion of this particular timeline is typical of the chart presented above (note the evolution of mammals is indicated for the famous period of the Jurassic, known best as this is the end of this epoch that all the non-avian -non-bird- dinosaurs were supposed to be wiped out).  This timeline will look significantly different to our conventional wisdom in the light of evidence presented below. You will also see that it is a matter of assuming a direct ancestor for each of these species and using particular conventions and terminology of classification based upon old assumptions, that had somehow lost sight of research such as Von-Baer’s laws (which Darwin supported for the most part) and certainly all things leaping and Lamarckian (epigenetic) were so marginalised that no other explanation seemed possible. But there is another alternative explanation of the fossil record in the light of these non-Neo-Darwinian principles. We will start with the reconstruction of the fossil record as these first tetrapods emerged and then assess this evidence against skull morphology (shape and characteristics) one of the main historically entrenched concepts which defines the main species of reptiles, mammals, amphibians etc that are typically interpreted on the basis of assumed direct common ancestry from one species type to another.

Experimental newcomers to land

For example, as the article below explains, better than I could as I am not a palaeontologist or dinosaur expert as the writer of this article is: I forgot to mention, that of course they are talking about lopped fish learning to breath and walk – this is normal for these types of articles, however, it is what the science writer on an educational site says regarding the characteristics of this rather experimental bunch of first tetrapods that is of interest here:

As is often the case in evolutionary history, it’s impossible to pinpoint the exact moment when the first tetrapods (the four-legged fish that crawled out of the shallow seas 400 million years ago and swallowed gulps of air with primitive lungs) turned into the first true amphibians. In fact, until recently, it was fashionable to describe these tetrapods as amphibians, until it occurred to experts that most tetrapods didn’t share the full spectrum of amphibian characteristics. For example, three important genera of the early Carboniferous period–Eucritta, Crassigyrinus and Greererpeton–can be variously (and fairly) described as either tetrapods or amphibians, depending on which features are being considered.


It’s only in the late Carboniferous period, from about 310 to 300 million years ago, that we can comfortably refer to the first true amphibians. By this time, some genera had attained relatively monstrous sizes–a good example being Eogyrinus (“dawn tadpole”), a slender, crocodile-like creature that measured 15 feet from head to tail. (Interestingly, the skin of Eogyrinus was scaly rather than moist, evidence that the earliest amphibians needed to protect themselves from dehydration.)

Bob Straus http://dinosaurs.about.com/od/otherprehistoriclife/a/tetrapods.htm

  By looking at the prehistoric timescale above we can see that many phases of life (periods) continued to evolve such as plant life, and then the really primitive swamp-like conditions of the Devonian setting the scene of the rich forests and vegetation and giant flying insects of the Carboniferous period. The era of the “dawn tadpole” and it’s loosely (or web-like) related kin or shared ancestral condition (showing mixed features of non-amphibian and amphibian primitive features) while being a generalist tetrapod perhaps, emerges unto scene somewhere between the period when swamps are giving way to great forests (which themselves evolved) and only begin to be confidently identified as particular amphibian types during the Carboniferous and as the article continues to point out below: these amphibious monsters are nothing like their supposed amphibian successors.

Now having set the scene, the key aspect of the above excerpt is that these fossils are not – seemingly, speciated amphibians as yet. The dawn tadpole is of particularly interest in the light of the alternative evolutionary interpretation which would view these pre-amphibians a generalist tetrapods (walking animals that breathed air for the first time – but if they had a tadpole stage – they wouldn’t have gulped at all, just got out of there as fast as possible so that they didn’t drown). Furthermore, I looked at the reconstruction of the dawn tadpole and it looks just like a developed and more elongated tadpole with only two legs at the rear and the little fins like tadpoles have at the front, along with the big tail that they lose later. They don’t call it the dawn tadpole for nothing and also, as the article explains, the first tetrapods aren’t quite as amphibian as we think.

 dawn tadpole Eogyrinus_BWhttps://upload.wikimedia.org/wikipedia/commons/thumb/1/11/Eogyrinus_BW.jpg/250px-Eogyrinus_BW.jpg

The article continues:

Another late Carboniferous/early Permian genus, Eryops, was much shorter than Eogyrinus but more sturdily built, with massive, tooth-studded jaws and strong legs. At this point, it’s worth noting a rather frustrating fact about amphibian evolution: modern amphibians (which are technically known as “lissamphibians”) are only remotely related to these early monsters. Lissamphibians (which include frogs, toads, salamanders, newts and rare, earthworm-like amphibians called “caecilians”) are believed to have radiated from a common ancestor that lived in the middle Permian or early Triassic periods, and it’s unclear what relationship this common ancestor may have had to late Carboniferous amphibians like Eryops and Eogyrinus. (It’s possible that modern lissamphibians branched off from the late Carboniferous Amphibamus, but not everyone subscribes to this theory.)


In other words, they don’t know. So what do you think? Is the first tadpole with little developing limbs and digits representative of the common ancestral condition shared amongst all non-fish vertebrates who are not quite sure what sort of species they are going to specialise in as yet? Recall from the above article on the experimental, not fully defined tetrapods that “it is only in the late Carboniferous period, from about 310 to 300 million years ago, that we can comfortably refer to the first true amphibians”. Therefore, even the most primitive and simplest land-dwelling or semi-aquatic amphibians take some time to become a little more defined as a species and recognisable – sort of, as an actual amphibian. And don’t forget, even these specialising tetrapods are very different to our modern specie of amphibians. Now it’s time to meet their contemporaries in the late Carboniferous period: the so-called lizard-like reptiles. The following article explains: “Hylonomus: The Earliest Reptile”. [Online]. Natural History Notebooks. Canadian Museum of Nature.
Last updated 2015-04-28. (Web site consulted 2015-09-12).

The earliest known reptile is Hylonomus lyelli. It is also the first animal known to have fully adapted to life on land. Hylonomus lived about 315 million years ago, during the time we call the Late Carboniferous Period. .. Hylonomus were about 20 cm (8 in.) long, counting the tail. These lizard-like reptiles were primarily insectivores, probably feeding on millipedes, insects and land snails. (At this time, plant-eating, backboned animals had not yet appeared). Females probably deposited eggs on land in moist, sheltered areas…The genus name, Hylonomus, comes from a combination of the Greek word for “wood” and the Latin word for “forest mouse”.


So there you have it, it is not apparently an amphibian, but would seem to be contemporary with them. It is lizard-like and given the classification of reptilian for reasons we will come to later. But the interesting Greek and Latin combination of its name, “forest mouse” is worth reiterating. We are after all reconstructing fossil bones and early and primitive anything at this stage will not be that different to one another and it is only later when we can begin to indentify more specialist features such as scales, smooth or haired skin etc that we can see these generic tetrapods specialising in their forms. Note, as the article mentioned, the vegetarians haven’t arrived on land yet and this is presumably because there is nothing suitable for them to eat – only inedible big trees that don’t even produce tasty morsels of seeds and as there are obviously tetrapods to come that have specialised already in their watery environments and developed an ability to digest only algae type plankton up to this point and therefore there would be no reason to morph and join the carnivorous tetrapods until later.  The next article is also about the earliest reptiles:

Published online 24 October 2007 | Nature 449, 961 (2007) | doi:10.1038/449961c

Footprints reveal reptiles showing their age


A set of fossilized footprints found in the Grande Anse rock formation in New Brunswick, Canada, seems to nudge back the date of the earliest known reptiles. Previously, the oldest evidence of reptiles was fossil skeletons of Hylonomus lyelli found in Nova Scotia in 1859 and dated to about 315 million years ago. But a team led by Howard Falcon-Lang of the University of Bristol, UK, has found reptile footprints a kilometre lower in the rock strata, indicating that they are between 1 million and 3 million years older than the previous find (H. J. Falcon-Lang et al. J. Geol. Soc. 164, 1113–1118; 2007)


So, the amphibians and lizard-like reptiles may not have a common ancestor after all as the traditional common descent model would propose, as amphibians and reptiles are now co-existing with no fossils showing a transition between them (the proposed ancestral link). They may have had a shared ancestral condition of being the stem-tetrapods and later some began to specialise as stem-amniotes (the amniotes are tetrapods that produce via a special non-amphibian type egg built for the long haul and doesn’t dry out). The evidence for these generalist non-specialised tetrapods, (apart from perhaps the indication of the amphibian form becoming a little more differentiated) is quite strong when you look at the actual evidence of the fossils themselves.

I would suggest that these are stem-amniotes as the tetrapod generalist begins to develop a more sophisticated means of production. Possibly they are beginning to leave their old metamorphic leap-frog type evolution behind and their eggs are becoming more specialised as they do not dry out as much, and begin to be built for the long-haul. This would allow a greater gestation period and development tuned to its particular environmental conditions – remodelling and reprogramming of the developing organism. For instance, as we know eggs are very sensitive still in some lizard species, where even a change of temperature can direct the fate of the growing organisms becoming male or female.

When is a mammal not a mammal? When it is presumed to be a mammal-like reptile as well as everything non-mammalian of course!

Below is a typical outline of how, what and when things occurred in terms of the evolution of the less primitive tetrapods of non-amphibian variety. This article highlights the main issue as I see it for our difficulties surrounding the problematic and illusive mammalian origins in relation to reptilian evolution in below. Interestingly, the article also highlights the environmental context for these tetrapods and it would seem that this would be a good time for those vegetarian tetrapods to come unto land at about this time. Do bear in mind the intrinsic importance of environmental changes in the timing, shaping and forming the ultimate direction of these developing (species) forms. The article excerpt is taken from National Geographic:

The lush swamp forests of the Carboniferous were gradually replaced by conifers, seed ferns, and other drought-resistant plants. Early reptiles were well placed to capitalize on the new environment. Shielded by their thicker, moisture-retaining skins, they moved in where amphibians had previously held sway. Over time, they became ideally suited to the desert-type habitats in which they thrive today.

Being cold-blooded, reptiles had to find ways to deal with big daily variations in temperature, from below freezing at night to over 100 degrees Fahrenheit (38 degrees Celsius) during the day. Some of the primitive pelycosaurs, which measured up to ten feet (three meters) long, had sail-like structures on their backs that are thought to have acted as heat exchangers, catching the sun in the morning to help warm the sluggish creatures.

Later, other mammal-like reptiles known as therapsids found an internal solution to keeping warm—scientists suspect they eventually became warm-blooded, conserving heat generated through the breakdown of food. These more metabolically active reptiles, which could survive the harsh interior regions of Pangaea, became the dominant land animals of the late Permian. http://science.nationalgeographic.com/science/prehistoric-world/permian/

So what is the impression you get from reading that? I presume it is that mammals – even mammals in the making are nowhere to be seen, because they are cold-blooded reptiles and some known as primitive pelycosaurs evolved a handy system of cooling itself down with a sail and became able to regulate – eventually, its body temperature and much later this creature’s offspring led to mammals of the true variety later on. Basically the article above suggests that some reptile-type, cold-blooded ancestors, after they took over the habitat of amphibians, spawned the significantly later mammalians. That is the conventional thinking, but it is not without its assumptions which are actually quite unfounded and simply built upon an idea of how things might have happened and remains a highly problematic area of research for palaeontologists. The reptilia to mammalian transition (or assumed linear descent model as assumed within our modern version of Darwinian theory) is, has been, and seemingly will remain problematic, unless we start viewing the fossil evidence in a different light. For instance, from the book by Nowak, R. M. 1999. Walker’s mammals of the world. 6th ed. Baltimore: Johns Hopkins University Press, the author states:

 There has been intensive debate regarding the morphological and temporal boundary between reptiles and the first mammals. Recent fossil studies have revealed some specimens that do not clearly fall into either group and have challenged the significance of the direct articulation of the lower jaw and skull as the key indicator of mammalian origin.

Nowak (1999, 1).

link to book

The above quote suggests primitive tetrapods who have not yet specialised and it also highlights the issues surrounded the so-called reptile to mammalian transition. Perhaps there never was a transition. Perhaps the problems arise from the assumptions embedded in the interpretation of the fossils and trying to make them fit a Darwinian model of evolution. Like most assumptions, they tend to have a history attached as to how these concepts became embedded in the public consciousness in the first place. Because they are there, doesn’t mean they are right or have any solid scientific basis. For instance, the article outlining the prehistoric animals and their metabolism according to conventional wisdom also uses the famous term of ‘mammal-like reptile’. What does this mean exactly and where did the term and its implications originate? Well, in a paper going back to the mid 1970s, the very issue of ‘the origin of the concept of mammal-like reptile’ as the title suggests states in the introduction: “Following the publication of Darwin’s Origin of Species, in 1859, biologists were eager to apply the theory of evolution to the paleontological record.” Aulie (1975, 21).

The American Biology Teacher © 1975 National Association of Biology Teachers


Need I say more… and the rest is history and a very interesting one at that as they basically never resolved it and this has become a matter of strong debate not only back then, but increasingly so now in our modern era as indicated above. It really comes down to the term mammal-like reptile as used above and explained as originating as a means to fit the theory of evolution as proposed by Darwin. Think about it. If you can only proceed and advance gradually from your ancestral state via a direct line of descent from your ancestors and by no other means – genetically, (apart from natural selection weeding out the weakest varieties), how else were mammals supposed to arise? It had to be from something more primitive. And of course, metabolically simpler, cold-blooded animals, thought to be earlier descendents of the amphibian line and ultimately all went back to fishy-pod ancestors, were a good candidate. Hence, mammal-like reptile as we cannot have mammals– not even proto-mammals or stem mammals, at this early stage, as how else could they have evolved/emerged?

Indeed, when we look at the early tetrapods they do really seem to be primitive generalists; even the amphibian-like types, before becoming more definable species of rather monstrous, never seen before: amphibians. Perhaps we need to stop making the assumption that we descended directly from some common ancestor that was more primitive than its protégé and begin applying older principles and more recent understanding and start listening to what the fossil record is actually trying to tell us. Basically, all of these generalist tetrapods overlap chronologically and once we identify that they are becoming fundamental species ultimately leading to amphibian, mammalian and reptilia and their respective evolutionary trajectories being directly ultimately by their underlying (inherent) metabolic complexity, we begin to get a clearer picture of how these tetrapods began diversifying into many grades of complexity and variations along these species lines. I put mammal before reptile as the evidence actually shows this to be the case as you will discover further on.

The alternative scenario that I am presenting doesn’t fit into the Neo-Darwinian version of evolutionary events. Perhaps this is why there is still a strong resistance to alternative theories and even stronger insistence upon using the term mammalian-like reptile. Indeed, as the article excerpt from Berkeley Education (University Museum of Palaeontology) below points out: it is a misleading term and should not be used any longer.

… pre-mammalian groups of synapsids have at times been called “mammal-like reptiles”. This term is now discouraged because although many had characteristics in common with mammals, none of them were actually reptiles.


Ben Waggoner 1997

The excerpt from the same website is presented below and it discusses the mammalian lineage of synapsida which includes the earlier pelycosaurs. Recall the National Geographic article above that clearly lined the early pelycosaurs to the late Carboniferous and essentially referred to them as a form of reptilia (mammal-like reptiles)? The article below explains that these are actually a stem mammalian group with their distinct non-reptile features such as likely warm-blooded metabolism. This should make you rethink the above description of the assumed reptile pedigree of these species during and contemporary with distinct reptile species along with their side-lined amphibian types within the late Carboniferous period and as the article below also points out: “by the beginning of the Permian, pelycosaur genera account for 70 percent of all the known amniotes, outnumbering the reptiles”.

Below are a few useful terms to do with the all important metabolism, or what I would describe as the driver of evolutionary complexity:

  • Endothermic: Generating internal heat to moderate body temperature, e.g., modern birds and mammals.
  • Ectothermic: Relying on the environment and behavior to regulate body temperature, e.g., typical reptiles.
  • Homeothermic: Maintaining a constant internal body temperature, e.g., modern mammals, birds, and some others.
  • Poikilothermic: Having a fluctuating internal body temperature depending on the local environmental conditions, e.g., typical reptiles and actinopterygiian fish.


Introduction to the Pelycosaurs

Synapsids with attitude

…pelycosaurs are not reptiles, since reptiles have two such openings in their skulls. … It is believed that the pelycosaurs, like their living mammal relatives, were endothermic, which means that they maintained a constant internal body temperature. This is another characteristic that sets pelycosaurs apart from the reptiles. If this view is correct, then pelycosaurs are one of the earliest examples of endothermic animals.

…The “pelycosaurs” are members of the Synapsida, a major branch of the Amniota. Pelycosaurs are the earliest, most primitive synapsids, a group characterized by a single dermal opening in the skull permitting muscle attachment to the jaw. …In fact, the only currently living synapsids are the mammals. It is believed that the pelycosaurs, like their living mammal relatives, were endothermic, which means that they maintained a constant internal body temperature. This is another characteristic that sets pelycosaurs apart from the reptiles. If this view is correct, then pelycosaurs are one of the earliest examples of endothermic animals.

In many respects, the pelycosaurs are intermediate between the reptiles and mammals, and so they have commonly been referred to as “mammal-like reptiles”. The pelycosaurs indeed resemble large lizards in their overall appearance, but as we have seen, this is a misnomer since pelycosaurs are not reptiles

 … Pelycosaurs first appeared during the upper Carboniferous (Lower Pennsylvanian)

…However, it must be noted that not all pelycosaurs had sails. Still, most pelycosaurs were similar to Dimetrodon in that they also were carnivores with large, powerful jaws, and two types of teeth: sharp canines and shearing teeth…

This adaptation allowed pelycosaurs to flourish, and by the beginning of the Permian, pelycosaur genera account for 70 percent of all the known amniotes, outnumbering the reptiles.

… Pelycosaurs are an important lineage preserved in the fossil record. They are the earliest known synapsids, the first to evolve specializations that would play an important role in the rise to mammals. .. Firstly, no intermediate form represents a totally intermediate character. This is to say that no evolutionary condition has been found in any taxon where all characteristics are present of both taxa that the condition is intermediate to. Secondly, evolutionary transformation predominates in the extremities…

The pelycosaurs exhibit the first substantial progress of crawling to running. This evolution in the extremities required a modification of the metabolism in the muscular system to provide the energy required for more strenuous activity. The resulting change in the axial system brought about endothermy. Supporting this idea is the fact that as later pelycosaurs and later synapsids evolved, the surface area of sail to body mass ratio decreased. This shows the trend of reduced need for outside thermoregulation, which would require an increased use of endothermy, an important characteristic today separating the reptiles and mammals.


Brian R. Speer et al (2000)


Can you see the conventional model as presented in the timeline graph earlier of mammals arising at the dawn of the period that seen the demise of the great dinosaurs, who themselves are only thought to emerge very late in the fossil record and somehow evolve from the ancestral lineage of reptilia. What if, on the other hand, the earliest tetrapod were all generalists as the record clearly indicates, if we can leave the old misleading presumption of non-mammalian reptile and indeed, reptilian for nearly everything else aside. We can begin to read the fossil record with more clarity and watch out for the points of differential divergences as these fundamental forms of tetrapod begin to specialise as fundamental species and all variations upon these themes thereafter until they reach their final specialised form. And when we review the geological and climate record for these leaps of speciation and remodelling events, interesting correspondences emerge.

I will now review the evidence for the morphological characters (the shape and formation and main characteristics) that are used to define the various types of early forms of vertebrate animals. This has led as much to the confusion regarding the classification and underlying assumptions of referring to stem amniotes as mammalian-like reptiles, inferring direct reptile ancestry and at the same time, it is the basis for re-interpreting the fossil record in light of more recent supportive evidence for non-Darwinian concepts of evolutionary development.

MODIFICATIONS as seen in the fossil record and clues to evolutionary development

The earliest specialising species or most primitive (metabolically) simpler modern-day vertebrates such as fish, amphibians and turtles typically have one thing in common: their skulls have no fossa (hole). The holes in other species are called the Temporal Fossae. The holes relate to the evolution of the jaw as you will see below and other features such as palette (the mouth) and related features to the jaw as in the middle ear bone and it is these features that palaeontologists used to identify and classify species of non-fish vertebrates in the fossil record. We will start with the holes in the skull.

Fossae (cavities, pits, or holes), are modifications of the skull that allow for more powerful jaws. They provide more space in the skull for the jaw muscles to expand during contraction and they offer a more secure area for the muscles to attach.

Fish skulls have no fossa and are therefore called anapsid…. The turtle skull, like the fish skull, has no fossa and is anapsid… In reptiles (excluding turtles), there evolved a pair of openings on either side of the skull in the temporal region, called the temporal fossa. ..The presence of two temporal fossae is the diapsid condition and is found in some reptiles and birds….


The following study of brain (vertebrate animals including fish) is rather revealing in its findings. See further support in the article ‘How Reptilian are YOU?’

The ancestral condition shared by all tetrapods appears to be evident in their skulls as clearly illustrated in: ‘Comparative Vertebrate Neuroanatomy: Evolution and Adaptation’ by Ann B Butler William Hodos

Box 4-2. The Early Divergence of Synapsids

An idea that is common among newcomers to the field of vertebrate evolution is that the earliest mammals evolved from reptile ancestors. This idea can lead to summary statements of tetrapod phylogeny a being something along the line of amphibians-reptiles-birds and mammals. Unfortunately, this sequence is not consistent with current data about the times of divergence of various tetrapod lineages.

Reptiles, which are diapsides (having two teporal fenestrae, …), did not appear in the fossil record until 10 million years after the origin of the line leading to modern mammals. As shown in Figure 1, approximately 350 million years ago, the stem tetrapods split into two lines, one leading to modern amphibian and a second line that became the stem anapsids, which were the ancestors of the amniotes. 320 million years ago, the stem synapsids branched from the anapsid line.

 stem anapsids fig 1 Butler study 2005

 Main diagram taken from Fig. 1.

Figure 2 (top) shows the skull of an anapsid, with no temporal opening, and the skull of a synapsid (middle) with a single temporal opening, shown in dark gray. As indicated in Figure 1, the synapsids eventually led to the emergence of mammals. Ten million years after the appearance of the first synapsids, the anapsid lineage diverged again into two lines of diapsids, as shown in Figure 2 (bottom). Thus, the stem diapsids produced one branch that led to the modern lizards and snakes and a second branch the [n?] led to crocodiles and birds, turtles, and tuararas.

 Anapsid Synapsid Diapsid fig 2 Butler study

  Main diagram taken from Fig. 2

Butler and Hodos (2005, 81).


Everything, including birds and dinosaurs and indeed, pelycosaurs/synapsids (although they are not technically classed as reptilian as they have a synapsid scull with non-paired holes as discussed above, the very use of the term non-mammalian pelycosaurs or synapsids or mammal-like reptiles implies some reptile ancestral link or origins) in its primitive and post amphibian stage has been classified in some form or other as reptilian according to the Darwinian evolutionary theory being applied to the fossil record. But as highlighted above, this is a misleading and simply incorrect term particularly regarding early mammals and indeed, it may even be inappropriate for everything else that is non-mammalian.

Before going there, I will first outline a few more evolutionary important features that are worth addressing continuing on with the holes in skulls and the relationship to jaw development, and middle ear bones and developing palates etc and not forgetting evolving modes of development, this brings us back to perhaps the main driver of these levels of complexity – metabolism. Obviously, warm blooded is a fundamental feature of the mammalian condition, but it is not so straight forwards when it comes to reptilia.

Again, it may be a point of misclassification that is clouding our judgement regarding the fossil record and its interpretation. You see, all diapsids are more or less – beyond the primitive turtles and a few other primitive types, like the fish and amphibians, are anapsid (have no hole in the skull which would appear to be an ancestral feature) all reptilia are described as such based upon their diapsid type ancestral skull openings. However, as discussed above also, even the mammalian types were and still are, when described in their primitive form: as mammalian-like reptiles.  Therefore, this makes just about everything post amphibian, reptilian in some form or other at an ancestral level. There could be a problem with this line of reasoning.

Being classed as reptilia, based on the main feature of having certain hole numbers on a certain position on the skull has arisen from an old assumption of direct linear descent from a common ancestor as it fits with one particular theory of evolution known as Darwinian theory as highlighted above. Furthermore, what do fossil hunters or the paleontogists of Darwin’s era or our more modern era (employing Darwinism as the means of interpreting the fossil record) do when they reconstruct these early forms of walking, land-dwelling tetrapods? They reconstruct them in fantastic detail as reptiles or even show fossils classified as Dinosaurian with evidence of stubby-like primitive feathers (more like chick downing) as fully-fledged bird-like dinos. Imagine an EMU as a fossil? Even the mammalians in the making are portrayed as reptilian-like and given the name to reinforce the link between: everything primitive after the amphibians split away from the fishy-pods and others going on to bigger and better things was essentially some form of reptilia as these are obviously more simple animals than mammals. This has been reinforced in our modern era by the orthodox teaching on the subject. I have summarised an excerpt from the Berkeley Education (Museum of Palaeontology) web page for vertebrate diapsids below to illustrate this point:

Vertebrata – diapsids = The reptiles (except turtles)

All members of the group called the Reptilia … except for the anapsids (turtles and their ilk), and a few extinct groups, are diapsids.

The main diagnostic physical character for a diapsid is the presence of two openings on each side of the skull; the upper and lower temporal openings, i.e., the post-orbital fenestrae … Even the birds are considered diapsids (and hence reptiles), because they are descended from certain dinosaurs (which are also diapsids), and ancestrally have the paired skull openings along with other physical characteristics that unite them with diapsids. Thus, they are considered diapsids by their ancestry, which is illuminated by shared derived traits.

What does the word “reptile” really mean?

…”Reptile” refers to the Reptilia, which includes the ectothermic snakes, lizards, crocodiles, turtles, and the endothermic birds. Or, if you consider yourself in the cladistic school of thought like most paleontologists, then if you say Reptilia, you are referring to all anapsids and diapsids (the usual snakes, lizards, crocodiles, turtles, and their friends, including dinosaurs … and their descendants, the birds). …

The term “reptile” may carry a lot of psychological baggage with it, conjuring up outmoded images of slow, stupid, inferior creatures, but it is a valid term applied to the group comprising the first reptile and all of its descendants. By this convention, birds are considered Reptilia, just like bats are mammals and snails are mollusks. Birds are certainly quite different from other living Reptilia, but the traits that modern birds possess were acquired gradually over many millions of years of evolution. The first birds were quite different than modern birds, and looked much more like good traditional reptiles than hawks, doves, or turkeys do.



Maybe the early birds were just birds in the making and we just labelled them Reptilia based on our assumption of common ancestral origin along a linear line of descent, rather than considering epigenetic modifications and all that genetic exchange making the great diversity of genetics for environmental adaptations and genome remodelling during early development of the species which would have essentially sculpted these primitive forms into being specialised species of birds, reptiles (proper), lizards, snakes, crocodiles, turtles, molluscs, wolves, elephants, mice and men when they finally specialised as such.

The conventional assumption of everything being Reptilia, is perhaps slightly forgivable (but it doesn’t make it good science) as these early tetrapods would superficially seem like reptiles of our modern era – but perhaps a little more monstrous and experimental and far more exciting than trying to illustrate a primitive monotreme type with primal jaw and strange protruding teeth, sprawling, unrefined limbs and clumsy claws and an undefined body of baldy bits having a very rudimentary growth of hair made out of the same material as the claws/nails etc as these are the most primitive version of the land-dwelling vertebrate form. Even today, reptilia of the lizard form are fairly primitive looking, but imagine how this would not be reflected in the reconstruction of their fossil bones. Now they have their scales (made from available materials of slightly different chemical composition) and all manner of fancy camouflage – I’m sure in the early days when the lizards were becoming more like lizards, that they didn’t show all the refinement and adaptive features of their more modern counterparts, just as the really primitive mammals would not have refined and expressed all that it had the potential to be.

 It is things like metabolic complexity that matters in the end, and directs the ultimate evolutionary fate of any of these developing tetrapods. It is what is inside       which counts.

With this concept in mind, of even the simpler land-dwelling vertebrates going from the generalist to the specialist forms within their fundamental group of metabolically complex, or simpler (cold blooded or warm-blooded) ancestral condition, a very different pattern emerges. Think of several grades of metabolism and how the shared ancestral features and condition of these generalist (generic) amniotes could diversify over time going through many modification into their various forms and it is only in the final stages of these great periods leading up to the Cretaceous and ending with the Tertiary (c. 140 – 65 million years ago – culminating in the great so-called extinction of the really big reptilian – the Dinosaurs) (See timeline and discussion on dinosaurs further on) that we see the final culmination and refinement of all that has gone before.

Even beyond these proto-mammalian or generalists arising from an amniotic ancestral condition, like some of the other forms of life exhibiting diapsid type holes, these could have been generalist and not fully refined species (or adult species forms as yet). We cannot just make the assumption that because all these generalist tetrapods had so many holes in their scull relating to the practical function of the jaw and its ongoing modifications and secondary or primary type palate, meant that they were all from the same lineage and presumed to be all reptilia. Furthermore, just because we classify the diapsid as Retilia, doesn’t mean it ever had anything to do with a reptile. The specialised tetrapods may have become, in the end, what they became, because of their metabolic complexity. It is that we give them labels and classify them, this doesn’t actually inform us, or shouldn’t inform us of how they came to be in the first place.

I would like to suggest that mammals are the only living synapsids because they were the only ever living synapsids. Prior to this they shared a body-plan and other generalist features with stem-anapsids of the amniotic variety of tetrapods. Not to be confused with the primitive ancestral condition of all the other anapsids such as fish and amphibians. Probably fundamental metabolic complexity may have made the divergence even more pronounced as warm-blooded animals could do many things that more simplistic metabolic systems could not.

If we replace our presumed ancestral linear descent model of being descended directly from a reptile like ancestor and replace it with an ancestral condition common to both reptiles and mammals of tetrapod stem amniotes or based on their skulls, stem anapsids, then the fossil record and its interpretation makes much more sense. See article on ‘How Reptilian are You?’ for example. These were both mammals and reptiles in the making it would seem. And the fact that stem-amniotes began making it to primitive mammalian forms 10 million years BEFORE reptiles is of some interest don’t you think? Given this newer molecular information, if we applied the Darwinian concept of direct linear descent and didn’t take into account all the leaping evolutionary hybridisation of the past, never mind all the genetic transfer across all domains of life, it would look like the mammalian stem gave rise to the reptiles.

One group not noted in this review thus far, is the euryapsids (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, but its position differed from the synapsids in that was above the postorbital and not below. I will not spend much time in this present article discussing this fascinating group, but I will outline the following main points which should make you wonder, have we misclassified these vertebrates also and should in fact see them as generalist and primitive forms of marine mammals. For instance, they were warm-blooded, live-young bearing, air breathing, and yet they are classed as:  “marine reptiles”. Again, like our mammal-like reptiles, they bare no relation to actual reptiles in, or out of water; it is simply a convention of terminology and classification based upon old Darwinian linear descent assumptions.

Furthermore, our modern species of dolphins for example, bare an uncanny resemblance to these ‘now presumed to be dead and extinct species’. And they are often called ‘dolphin-like marine reptiles. Moreover, the modern ancestry of marine mammals of our modern era (dolphins, whales etc) is according to conventional Darwinian thinking, is supposed to have arisen via the land-dwelling mammals returning to the water fusing their toes and forming fins. Personally, I think reclassifying theme as marine mammals with nothing what so ever to do with reptiles – except a shared ancestral condition of amniotes, would be a much easier option. For supporting quotes and references please refer to the Free e-book or pdf links on this site entitled: Will the real ancestor please stand up.

Adaptive Modifications of the Species

Returning to the modification and features relating to inherent complexity, such as metabolism, we will now look at the reason for the holes in skulls; the jaw in relation to those holes which is more to do with modifications and adaptations than classification and species forms. Another important modified feature is the vertebrate palate as outlined below in an articles which points out some interesting and revealing elements of this vertebrate adaptation. For instance regarding modifications for breathing air, the Secondary Palate states:

Modifications for breathing air: evolution of the secondary palate. The secondary palate separates the oral passageway from the nasal passageway. There have been three stages in the evolution of the secondary palate:

The fishes and amphibia have a complete roof to the mouth which is the primary palate. ..This was inconvenient when breathing while eating. ..

Reptiles show a trend in the evolution of a secondary palate. The turtle on demonstration shows a development of the maxilla, premaxilla, which turn inward to form a shelf, and a new bone, the palatine, which provided a partial secondary palate.

… The alligator is a further stage and shows a complete bony secondary palate.

… In order to save weight, birds have a totally fleshy secondary palate…

Mammals (wolf, ox) have a functional complete secondary palate, though not the complete bony palate of alligator, the posterior portion being the fleshy soft palate, with the hard palate in the anterior.


The same educational website continues to outline the morphology of the jaw and its attachment to the skull:

Jaw Suspension:

…. In tetrapods, the upper jaw alone suspends the lower jaw. .. This frees the hyomandibular of the hyoid arch from jaw suspension and it is incorporated into the ear. The number of upper and lower jawbones becomes reduced. Mammals have only one paired bone, the dentary, in the lower jaw. The articular and quadrate bones are jaw joints in most vertebrates but are moved to the ear in mammals. The entire upper jaw is incorporated into the baincase and jaw suspension is craniostylic.


This outline would appear to support the idea that these features are adaptive and have themselves evolved in complexity within more complex and derived (diversified) animals.  These primitive features are typically referred to as reptile features, simply because they are more primitive. However, I believe that what they should be saying, rather than referring to these as reptile-like features, is that these are primitive features, which have not yet evolved into their secondary or more sophisticated form. Another feature that seems to have evolved at least to a more sophisticated level in mammals, is the mammalian mode of production. Again, this may be an adaptive and evolving trait which begins to show a further divergence away from the ancestral primitive form of stem-amniote with their specific synapsid type skull. If you read the following article, keeping the concept of evolving primitive forms to more advanced features in some animals in your mind, then, evolutionary development may begin to make more sense.


Why Odd Egg-Laying Mammals Still Exist

by Charles Q. Choi, Live Science Contributor   |   September 21, 2009 11:06am

 The platypus, found only in Australia is one of the five mammal species of that lay eggs instead of giving birth to live young. The other egg-laying mammals are four species of echidna…The reason that odd, egg-laying mammals still exist today may be because their ancestors took to the water, scientists now suggest. The egg-laying mammals — the monotremes, including the platypus and spiny anteaters — are eccentric relatives to the rest of mammals, which bear live young. In addition to laying eggs, other quirks make them seem more like reptiles than our kin. They have a reptilian gait with legs on the sides rather than underneath the body, for instance, and a single duct for urine, feces and sex instead of multiple openings.

These oddballs are often considered primitive “living fossils” that shed light on what our distant ancestors might have looked like.

Australian invasion

Long ago, monotremes and their close relatives were the dominant mammals in the whole of Australia. Now only two kinds of monotremes are left on the planet — the duck-billed platypuses and the four species of echidnas, or spiny anteaters. Like all mammals, they possess hair, milk, sweat glands, three middle ear bones and a brain region known as the neocortex.

The monotremes were almost totally swept aside when their pouch-bearing marsupial cousins — modern examples of which include the kangaroos — invaded Australia 71 million to 54 million years ago. Marsupials appear to have a number of advantages over monotremes — their bodies seem more efficient at locomotion, and the fact that they give birth to live offspring could provide better care of young.

“Platypus-like fossils are known from at least 61 million years ago. It was thought that the much shorter fossil record for echidnas, from about 13 million years ago, was just due to the patchy nature of the fossil record,” Phillips said. Their new findings suggest “the lack of early echidna fossils was in fact because they simply had not evolved yet.”

Since a trait often considered primitive — egg-laying — might actually have helped monotremes survive to the present day, future research could investigate whether the same holds for other characteristics of theirs. For instance, their reptile-like shoulders are poor for running fast, but they provide strong bracing. This allows for huge shoulder and arm musculature for use in rapid maneuvering in the water for the platypus or digging for echidnas, Phillips said.


My favourite line in this whole article is: “the lack of early echidna fossils was in fact because they simply had not evolved yet.” Perhaps now you can see why I used this particular example of really primitive egg-laying mammals in relation to their next evolutionary development – the marsupials, to illustrate the following point. If our modern species of monotremes specialised more rapidly, owing to their inherent complexity compared to their more complex counterparts, does this not indicate that the modes of development were actually evolving within the mammalian species as a whole? For instance, some mammals (primitive type – but not reptile in their features, just undeveloped) were able to become more advanced and experimented with pouch developmental modes and many more simply were able to eventually retain their special amniotic eggs internally in a womb?

Can you see that if we stop referring to anything primitive in mammals as reptile features and assuming an ancestral link to reptiles of some form or other, then a much clearer emerges? Monotremes and marsupial types are probably the ancestral representatives of monotreme or marsupial more primitive mode of development for warm-blooded mammalians. In many ways these ‘living fossils’ are captured in their primitive state like a snap shot in evolutionary history as once an  organism becomes stabilised, using up all of its inherent complexity accumulated thus far, it becomes a relatively fixed species thereafter. Meanwhile, other mammals continue to cross-breed presumably as discussed previously in these articles and begin to express different permutations of all this genetic novelty to eventually perfect their more advanced features.

This brings us to another distinct feature of mammals, noted in the article above, whether primitive or more developed and that is the distinctively mammalian middle ear. The article excerpt below describes this unique feature and most importantly, how the developmental studies of modern species shows how this feature develops in real time and may reflect how it developed in mammalians in the evolutionary past.

…the mammalian middle ear represents one of the most fundamental morphological features that define this class of vertebrates. Its skeletal pattern differs conspicuously from those of other amniotes and has attracted the attention of comparative zoologists for about 200 years. .. Mammalian middle ear evolution can now be interpreted as a series of changes in the developmental program of the pharyngeal arches… We propose that to understand mammalian middle ear evolution, it is essential to identify the critical developmental events underlying the particular mammalian anatomy and to describe the evolutionary sequence of changes in developmental and molecular terms. We also discuss the degree of consistency between the developmental explanation of the mammalian middle ear based on molecular biology and morphological changes in the fossil record.

J. Exp. Zool. (Mol. Dev. Evol.) 314B 2010


In other words, during development in a mammal, the ear bone goes through similar stages migrating to its definitively mammalian feature as development proceeds. This supports the evolutionary principles of development proposed in Von-Baer’s laws. Another science paper in SCIENCE www.sciencemag.org entitled: ‘Independent Origins of Middle Ear Bones in Monotremes and Therians’ by Thomas H. Rich et al, discusses in detail the evolution of the middle ear in as seen from the fossil record of mammalian species and  how this relates to more recent studies of development of modern species and its implications and controversies this has raised as well as the evidence for independent origins in the more primitive types discussed earlier.

… bones retained attachment to the lower jaw in a basal monotreme indicates that the definitive mammalian middle ear evolved independently in living monotremes and therians (marsupials and placentals). In the evolutionary transition from primitive synapsids (the so-called mammal-like reptiles) to extant mammals, the dentary bone of the lower jaw established a neomorphic articulation with the squamosal bone of the skull, and three of the accessory lower jaw bones… An additional synapsid element, the quadrate (which with the articular forms the primitive synapsid jaw joint), became the mammalian incus.

A controversy exists as to whether the transformation of jaw bones to middle ear bones occurred independently in the two clades of living mammals: the Monotremata (platypuses and echidnas) and Theria (marsupials and placentals). In other words, did the accessory jaw bones that gave rise to the ear ossicles and ectotympanic become detached from the lower jaw only once … in the common ancestry of monotremes and therians (a monophyletic origin), or did they become detached from the jaw independently in the two living groups subsequent to their evolutionary divergence from a common ancestor (a polyphyletic origin) …?

Assertions of fundamental differences in development and morphology between monotreme and therian ears are no longer supported .., so the primary argument for a polyphyletic origin lies in the existence of mammal-like dentaries from the Late Triassic to Early Cretaceous … that show evidence of a persisting contact of putative ear bone homologs with the lower jaw.

Unfortunately, the contentious nature of the phylogenetic relations of Mesozoic mammals has until now prevented the establishment of a reliable link between fossil mammals with accessory jaw bones and living and fossil mammals with true ear ossicles. Here we present evidence of such a link between a fossil monotreme with accessory jaw bones …and living monotremes in which certain of those bones are entirely within the middle ear….One of the most compelling pieces of fossil evidence for the transformation of jaw to ear bones is seen in Morganucodon .., a Late Triassic/Early Jurassic near-mammal(mammaliaform).

Essentially, the next science paper, once again supports Von-Baer’s principles of evolutionary development as reflected in embryological development, but do watch out for the trap of the article referring to the mandible as a reptilian one. The paper also discusses the Hox gene complex and its implications in other changes in mammal features such as the spine (lumber) – this is worth bearing in mind as this discussion unfolds. The article is entitled: ‘A new eutriconodont mammal and evolutionary development in early mammals’ by Zhe-Xi Luo et al in Nature  2007:


Detachment of the three tiny middle ear bones from the reptilian mandible is an important innovation of modern mammals. Here we describe a Mesozoic eutriconodont nested within crown mammals that clearly illustrates this transition: the middle ear bones are connected to the mandible via an ossified Meckel’s cartilage.

The connected ear and jaw structure is similar to the embryonic pattern in modern monotremes (egg-laying mammals) and placental mammals, but is a paedomorphic feature retained in the adult, unlike in monotreme and placental adults. This suggests that reversal to (or retention of) this premammalian ancestral condition is correlated with different developmental timing (heterochrony) in eutriconodonts. This new eutriconodont adds to the evidence of homoplasy of vertebral characters in the thoraco-lumbar transition and unfused lumbar ribs among early mammals. This is similar to the effect of homeobox gene patterning of vertebrae in modern mammals, making it plausible to extrapolate the effects of Hox gene patterning to account for homoplastic evolution of vertebral characters in early mammals.



I’m not going to go through all the diversity of all the early synapsids or the developing mammalian types and evolving modes of development – you can look them up and try applying the principle of developing modes of speciation driven by epigenetic remodelling and environmental conditions and continued cross-breeding of generic mammals will give you a clue. Each primitive stage in the mammal reflects its own evolutionary path.

Mother Nature’s Natural Correction system would give the developing species a means of rapid adaptation for radical remodelling if the need arose.


Modified descendents driven by environmental upheavals?

This brings us to perhaps the most controversial aspect of this evolutionary alternative, although, it is founded upon strong evidence pointing to this possibility. The mass extinction hypothesis is also interesting as often a bottle neck in the species is followed by massive radiation of new and novel forms. Where eggs reprogrammed for something more adapted to radically different environments? Remember that these are still for the most part – developing species. Most have seemingly become metabolically stabilised within their main trajectory of reptile, mammalian etc, but things are still developmentally plastic at a cellular level – just like a developing foetus. Just because we find their fossils and they look a bit different to modern species, doesn’t mean that later models didn’t remodel their form and refine their features epigenetically in response to environmental upheavals as they were still developing as a species. They are not for the most part fully developed species as yet. Except for the more simple and primitive types who have seemingly stabilised at a fundamental species level, but are still flexible enough to change variations of the same theme. See for example below:

Can Genomic Changes be linked to Ecological disruptions? again Professor James Shapiro summarises this situation as follows:

Among the most striking features of the fossil record are the periods of accelerated mass extinctions followed by periods of accelerated mass “originations” (appearances of morphologically novel organisms)… Although high-level changes in the biosphere have been considered [ref], little attention has been paid to the relationship between ecological disruption and genetic change. The influence that stimulus-sensitive regulatory processes and changes in population structure may have on the processes of genome restructuring requires greater scrutiny.

Shapiro (2011, 139-142)

link to book


– Jean-Baptiste Lamarck –

‘Zoological Philosophy…’

(Translation by Hugh Elliot 1914)

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

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

— Lamarck (1809, 39)

– Jean-Baptiste Lamarck –


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

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

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


— Lamarck (1809, 45-46)


But alas, our conventional model would say otherwise and even though Darwin himself supported, and came to increasingly support Lamarck’s concepts of natural corrective evolution, now understood as epigenetic and combined with older theories long after Lamarck’s time, are forming a dynamic epigenetic and environmentally-driven evolutionary explanation. These older principles and alternatives to Darwinism, particularly when Darwin’s own theory was suffering a major eclipse even in the light of clear understanding of genetic inheritance, are now, finally beginning to be reinstated to their rightful place in the scientific literature and well supported by more recent studies. These are the very concepts with good foundational principles that our modern synthesis either marginalised, misunderstood, or simply forgot, and in some cases actually banned, ridiculed, dismissed and generally attempted to discredit at all levels and particularly anything Lamarckian – and as history shows, these accusations were entirely unfounded (See Lamarck and the Sad Tale of the Blind Cave Fish).

So returning to the dinosaurs (species in the making perhaps?) and the dolphin-like marine reptiles that I definitely believe having looked at the evidence, should be reclassified as primitive marine mammals or proto marine anything other than reptiles, as they are nothing to do with reptiles. At least let us stop referring to everything that isn’t classified according to orthodoxy a mammal, a mammal-like reptile or non-mammalian Synapsid (if it isn’t an actual reptile, then what is it?). Furthermore, let us stop referring to everything else that isn’t a fish, or amphibian type, a REPTILE or of the order of REPTILIA – it just completely messes up and confuses the entire interpretation of the fossil record and this makes it impossible to see the wood from the great big Darwinian tree, hindering our understanding of what the fossil record is trying to reveal. At the very minimum, we need to seriously re-evaluate the whole thing.

The timeline is used as a guide to give you an idea of the timescales I am talking about as illustrated and conventionally described on the palaeo site at Bristol University, UK below:

  timeline for reptile and mammals


The Dinosaurs

Amniote evolution followed a very new course during the Triassic. The devastation of the end-Permian mass extinction wiped out most of the dominant therapsid synapsids, and left an empty, bare world. Some therapsids survived, and re-radiated (notably the plant-eating dicynodonts and the flesh-eating cynodonts). But two new diapsid groups expanded to fill many niches: the rhynchosaurs as herbivores and the archosaurs mainly as carnivores. The basal archosaurs diversified, and gave rise to one group that would dominate for the rest of the Mesozoic era.

Dinosaurs appeared in the Late Triassic, and they dominated through the Jurassic and Cretaceous. The first dinosaurs were small flesh-eating bipeds, such as Eoraptor and Herrerasaurus from Argentina, and Coelophysis from North America. The plant-eating prosauropods appeared early, including Saturnalia from Brazil and the 5-metre long Plateosaurus from Germany. The first ornithischian also appeared at this time, Pisanosaurus from Argentina, but this group remained rare until the Jurassic.

The Jurassic and Cretaceous periods were the time of greatest reptile diversity. Dinosaur fossils have been uncovered all over the world. Pterosaurs of all sizes flapped about in the sky, and plesiosaurs and ichthyosaurs swam in the seas. This all came to an end with the mass extinction at the end of the Cretaceous, the KT event.

Tertiary and Modern Reptiles

With the extinction of the dinosaurs, pterosaurs, and great marine reptiles, the Earth was again an empty place. Reptiles never again ruled, and their dominant places on land were taken by the mammals. Birds took over as the major group of flying animals, and sharks and whales took over some of the roles of the ichthyosaurs and plesiosaurs.

Modern reptile groups had appeared mainly in the Triassic and Jurassic. The first turtles, the first crocodilians, and the first sphenodontids are known from the Late Triassic, the first lizards from the Mid Jurassic, and the first snakes from the Early Cretaceous. These groups all diversified under the noses of the dinosaurs and pterosaurs, but they never became hugely important. During the Tertiary, lizards and snakes became much more diverse, but the turtles and crocodilians remained specialized and did not change their habits a great deal.


It makes you wander where all these fantastically different species appeared from? It sounds to me like there was some serious remodelling of the tetrapods that had further to go on their evolutionary journey, triggered by the massive environmental upheavals! What do you think?

Now I can fully understand if you don’t want to go as far as bringing all those dead species back from the brink of extinction as this not so new model proposes when applied to the fossil record and taken to its natural conclusion. However, I would like to suggest that this concept is actually well supported if one re-evaluates the older concepts of a different form of evolution and it could be argued from the position of some of the most cutting-edge scientific evidence that clearly demonstrates rapid, profound and dramatic modifications to even modern day species when applied during development and by extrapolation, it is not such a strange leap of the imagination to apply these principles to developing (not fully formed) evolving species.

So I’ll go all out here and suggest that maybe the dinosaurs were not actually fully speciated animals as yet (they hadn’t reached their full evolutionary potential) and many of them were not giants, there were lots of bird-like forms. Just because they are big or large versions, doesn’t actually make them into a different species. Think of the giant dragonflies of the lush vegetation and forests of Carboniferous period when all the tetrapods were roaming around and still maturing at an evolutionary level and how the weather had a lot to do with their size as the plants were also giants and as noted above, Mother Nature cuts her cloth to her measure. Therefore these potential non-adult species may have laid dino eggs which were significantly smaller as resources were now significantly reduced  due to the bad weather and all. What I am suggesting is the big wasn’t best any more, but small was beautiful and then all the energy and resources that once went into making massive things, went into other refinements and tweaking of the system. Did dino-eggs shrink? This rapid adaptation in a developing organism (species) is as discussed many times before, a very important and real aspect of evolutionary adaptation. It is all according to environmental cues and the more dramatic the upheavals: the greater the modifications and radiations of distinct forms seen thereafter as noted above by Shaprio.

The timeline (conventional chart) certainly indicates these major upheavals, the only difference being: they interpret the evidence according to the Darwinian version of evolutionary events and see this as mass extinctions that give way to newer and better survivors. As discussed throughout this article series, nature doesn’t work that way. There is an in-built SOS emergency response system that is particularly useful for responding to any stressful situations and environmental stress when species were still developing would have been a classic example of this system in action. Evolution and speciation via Natural Correction.

Recall for example, the stress of fish finding themselves in a darkened environment and within a relatively rapid time scale, epigenetically modified themselves to adapt and became blind and used their resources, instead of building eyes and putting all their energy into seeing, they developed more heightened senses of movement etc. This is covered in the book: ‘Lamarck and the Sad Tale of the Blind Cave-Fish’. The only big difference in this analogy is that these are speciated adult forms and remain as fish, whereas, in this earlier scene of species actually becoming for the first time – species, the modification could be even more dramatic.

Also see the articles on this topic which discusses present-day experiments of dramatically changing the outcome of the size – in this case shrinking – of an animal by simply applying an increase of methylation during develop. This is an epigenetic modification effect which causes a different expression of the same genes (globally) and just maybe, it could be suggested by extrapolation that some of those avian type dinos with hollow boned legs and warm-blood type metabolism which weren’t quite sure what they were going to really be when they grew down, had some seriously rapid remodelling to do in order to not only survive, the massive upheavals, but to go on and strive as fully speciated forms thereafter.

Crazy I know, but humour me, anything is actually possible at this stage, if you apply the principle that none of these animals are fully established as adult and stabilised species, well at least not these more complex tetrapods – of species in the making, until after the big Dino proposed extinction event. Anyway, it is an interesting thought experiment and besides, it is good fun to play with the possibility.

Now with this in mind, the next time you read a popular science webpage on the topic, you might at least stop and think about all that I have just said. Try replacing the words and concepts of reptile, reptilia, mammal-like reptile, or non-mammalian form with diapsid generalists or synapsid generalist who diverged from a common ancestral condition of stem amniote. Think more of the concept of several developing generalist tetrapods that can be defined by their complexity (present day and evolutionary development) by their metabolism (self-regulating or not).

However, the most fundamental leap of complexity that seems to set mammals apart from even the most advanced warmblooded diapsids, the so-called reptilia – the birds, is their respective modes of development. Although, this may ultimately be directed and driven by metabolic variations within these groups that we are not able to discern as yet, as we have not posed this question. I think that it is however, worth pointing out that I have observed several charts plotting the different types of fundamental species, such as fish and birds and amphibians, and of course mammals, and there does seem to be discrete groupings within these kinds (see the first article in this series on scaling laws). 

Regarding the distinct divergence away from the common ancestral condition of egg development, even primitive mammal types (inaccurately described as mammal-like reptiles) started out as egg-layers as strongly indicated by following the developmental modes of the most primitive modern-day mammals, such as captured within the modern species of egg-laying monotremes and the more marsupial mode of development. This, along with the middle ear and specialised hearing of mammals and the advanced form of nurturing young and retaining amniotic eggs internally, not to mention the evolutionary knock on effect that would lead to very sophisticated mammals such as ourselves and dolphins, is what sets mammals apart from even the smart dino birds.

It is all about timeing, seemingly, as the pattern seems to be that if a species reaches a certain level of efficiency – metabolically speaking, then this species – I would suggest –  rapidly begins stabalising and specialising within the parameters of its own innate complexity (genome silencing).

Interestingly, much of the stabilisation of the more advanced warmblooded amniotes of the braoder synapsid (inclusive of the proposed marine proto-mammalians) and diapsid forms, only really appear to begin their final stage of more specialised and ultimate species (adult-type) form around the time of the so-called mass extinction of the dinosaurs leading up to the Tertiary period. Could it be that as the snakes, the lizards, the dino-birds and even eventually the dolphins and whales matured into their stabilised forms to form what we could call a near modern species, could it be that some more complexley endowed mammals had further to go on their evolution journey – a further bit of tweaking of the generic ape-like higher primate form perhaps? Until finally, via many more refinements and modification (not to mention all that cross-breeding and genetic remodelling) diversify into the various groups of modern day type primate forms?  Yes, and even some generic apes may have diversified from their generic ape condition and began specialising to ultimately become what we would call archaic human today.

This brings us then to the topic of next week’s article, which will finish this series. It will discuss the evolution of ourselves and how we may have walked upright much earlier than you could imagine as well as why we may be so uniquely human in the first place and I will finish off with a short summary model which should encaptualate the entire alternative model of evolution.

Until then,



EVOLUTION: Not by genetic mutations, but by Epigenetic Adaptation


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

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


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

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


DNA, Epigenome, genes
DNA, Epigenome, genes

Below is an article about mobile elements in the genome. It explains how mobile elements (jumping genes) can remodel the genome. These are triggered via environmental stressers etc. The article is  quite technical, but nevertheless worth looking at as I have come to understand that this is one fast and dramatic way of  changing a species or modifying an existing one. Not as drastic perhaps as it was back in the day when things were genetically more flexible. Evolution is akin to the developmental stages of cells (stem-cells as yet undifferentiated), to an embryo (with the main template laid out via an activation of master switches of genes -HOX GENES). And further refinements and specialization thereafter.


In other words: from the generalist to the specialist. All of these systems are ultimately epigenetic (and operate above the gene/genome without changing the DNA sequence itself – via expression of the genes. This makes a very big difference in the end to what a species looks like. So no wonder our genes are seemingly so similar to many other species, that look nothing like us. It is all to do with how they are activated, expressed, turned on or off and their timing via environmental triggers and stimuli. So one of the ways nature does this remodeling of species, is to remodel the genome itself – see article below with supplementary article.


Natural Genome Remodeling

Stephen L. Talbott

This article was written as a rather more technical (but still quite readable) “sidebar” to “Evolution and the Illusion of Randomness”, and can best be read in conjunction with that essay. Both pieces are part of a larger work in progress entitled: Toward a Biology Worthy of Life. Original publication: November 10, 2011. Date of last revision: July 9, 2012. Copyright 2011, 2012 The Nature Institute.

By clicking on the shaded rectangles at the end of many scientific terms, you can immediately read a definition of the terms in a separate glossary window (or tab, if your browser is set that way).

You can also read a summary of this article or browse all the documents associated with this project.

In her 1983 Nobel address, geneticist Barbara McClintock cited various ways an organism responds to stress by, among other things, altering its own genomelink. “Some sensing mechanism must be present in these instances to alert the cell to imminent danger”, she said, adding that “a goal for the future would be to determine the extent of knowledge the cell has of itself, and how it utilizes this knowledge in a ‘thoughtful’ manner when challenged” (McClintock 1983). Subsequent research has shown how far-seeing she was.

It is now indisputable that genomic change of all sorts is rooted in the remarkable expertise of the organism as a whole. By means of endlessly complex and interweaving processes, the organism sees to the replication of chromosomes in dividing cells, maintains surveillance for all sorts of damage, and repairs or alters damage when it occurs — all with an intricacy and subtlety of well-gauged action that far exceeds, at the molecular level, what the most skillful surgeon accomplishes at the tissue level. But it’s not just a matter of preserving a fixed DNAlink sequence. In certain human immune system cells, portions of DNA are repeatedly cut and then stitched together in new patterns, yielding the huge variety of proteins required for recognizing an equally huge variety of foreign substances that need to be rendered harmless. Clearly, our bodies have gained the skills for elaborate reworking of their DNA — and, we will see further, in many different ways.

Depending on stage of developmentlink, cell type, and state of health, among other things, our cells convert millions of their genomic “letters” (most often the letter ‘C’, standing for the cytosinelink base) to an altered letter in a process known as “DNA methylationlink”. The new letter, 5-methylcytosine, is often referred to as the “fifth base” of the genome, and it has profound implications for gene expression that are far too extensive to survey here. The organism also contrives to effect several other kinds of DNA letter changes. The DNA sequence, it turns out, is subject to intense revision through its participation in the life of the larger whole.

More emphatically, and with remarkable nuance, the organism contextualizes its genome, and it makes no sense to say that these powers of contextualization are under the control of the genome being contextualized. Thus, the human genome yields itself to a radical and stable “redefinition” of its meaning in the extremely varied environments of some 250 different cell types found in brain and muscle, liver and skin, blood and retina. It is well to remember that the genes in your stomach lining and the genes in the cornea of your eye are supposed to be the “same” genes, and yet the immediate context makes very different things out of them. An especially revealing case of contextualization occurs when a genome fit for the needs of all the varied cells of a worm-like larva is subsequently pressed into perfectly adequate service for the entirely different cell types — and different bodily organization and different overall functioning — of a graceful, airborne butterfly. The genome, it appears, is to one extent or another like clay that can be molded in many different ways by the organism as a whole, according to contextual need.

Jumping for Change. Quite aside from such contextualization, it has long been known that the organism generates altogether new genetic material by duplicating entire genes, modifying them, and supplying them with regulatorylink elements. This can occur through direct duplication of genes or even larger chromosomal segments, and also through reverse transcriptionlink, whereby messenger RNAlink molecules, produced from DNA, are transcribedlink back into new DNA, which can then be modified. But “the array of mechanisms underlying the origin of new genes is compelling, extending way beyond the traditionally well-studied source of gene duplication”, writes Henrik Kaessmann of the Center for Integrative Genomics in Switzerland.

In a broad overview of the relevant studies, Kaessmann documents a dizzying variety of techniques by which the organism diversifies and enlarges its genetic repertoire. For example, two duplicated genes can, via a number of different pathways, fuse into a single chimeric genelink. And not only protein-coding RNAslink, but also small, regulatory RNAs, can be reverse transcribed into DNA and their functions diversified. And again, various repetitivelink and mobile elements called “transposonslink” can move around in the genome, often being duplicated in the process and then co-opted either as new protein-coding geneslink or new regulatory genes (Kaessmann 2010).

Let’s pause for a moment to look a little more closely at these transposons. “It now is undeniable”, writes a team of researchers from the U.S., Canada, Spain and the U.K., “that transposable elements, historically dismissed as junk DNA, have had an instrumental role in sculpting the structure and function of our genomes” (Beck et al. 2011). Directly and indirectly, transposable elements are being found crucial to many aspects of genome organization and renovation. And the diverse means by which the cell employs and regulates them have only begun to be delineated.

These transposons, also known as “jumping geneslink” (whose discovery led to Barbara McClintock’s Nobel prize), may hold the key to a puzzle about inbred mice. Such mice, with their perfectly matched genes, are sometimes reared in the laboratory under the strictest and most identical conditions possible. The frustration for researchers, according to Fred Gage, a neuroscientist at the Salk Institute for Biological Studies in San Diego, is that “you control for everything you can, and in behavioral tests, the variance is enormous”. Even within a single litter, “one mouse will be unusually smart, another below average”. Gage and others are proposing that jumping genes help account for this otherwise mysterious diversity (Vogel 2011).

Whatever may be going on with the mice, it has now been shown that transposons move around in the developing mammalian brain, altering the genome from cell to cell. They provide enough diversity among neurons, according to Gage, so that “you can optimize your response to the variety of environments you might encounter throughout life”. And now it’s being found that transposons also “jump” in other cell types much more readily than was previously thought. This particularly includes various cells of the early embryo, in which case each genetically altered cell propagates its changes into a subset of the mature organism’s tissues, making them genetically distinct from other tissues. “Given how often this may happen in the early embryo, there may be much more genomic variation within individuals than most researchers had assumed,” writes one reporter in Science (Vogel 2011).

None of this looks particularly haphazard. In embryonic stem cells the regulatory DNA elements known as enhancerslink of gene expressionlink contain an elevated number of transposons. And germ cellslink (of which I will have more to say in a moment) are also especially susceptible to these mutable, or mobile, elements (Teng et al. 2011). The cell-type-specific and DNA-element-specific nature of transposon activity points to a meaningfully orchestrated process. In general, there is a bias for many transposable elements to insert themselves upstream of transcription start siteslink, which “prevents damage to functional coding elements and enhances the potential for a constructive regulatory change” (Shapiro 2006).

Are transposons mere parasites? An extraordinarily profound role for jumping genes has just recently come to light with the announcement by Yale University researchers that the evolution of placental development (and hence prolonged pregnancy) in mammals was intimately bound up with the regulatory role of transposonslink. The Yale team found that a network of 1532 genes recruited for expressionlink in the human uterus (but not in marsupials, a mammalian group whose members give birth to undeveloped young a mere two weeks after conception) is coordinated by transposons. “We used to believe that changes only took place through small mutationslink in our DNAlink that accumulated over time”, remarked the lead researcher in the project, Günter Wagner. “But in this case we found a huge cut-and-paste operation that altered wide areas of the genomelink to create large-scale morphological change” (Hathaway 2011).

The study authors say that their findings “strongly support the existence of transposon-mediated gene regulatory innovation at the network level, a mechanism of gene regulationlink first suggested more than forty years ago by McClintock . . . Transposable elements are potent agents of gene regulatory network evolution” (Lynch et al. 2011).

It is no wonder, then, that when genomic researcher David Haussler of the University of California, Santa Cruz, was asked by the journal Cell what has been most surprising about the human genome, one of the things he cited was “mounting evidence” that transposons “play a critical role” in the turnover and reinvention of regulatory elements in DNA (Page et al. 2011). And, responding in Science to a report about the work on jumping genes in mammalian brains, Southern Illinois University neuroscientist, David King, wrote that the “dismissive dictum, ‘Mutations are accidents’, has grown obsolete”, adding that protocols for “the spontaneous, non-accidental production of genetic variation are deeply embedded in genomic architecture” (King 2011).

One other remark about transposons. They exemplify a growing (and, for biologists, embarrassing) class of cellular constitutents that were initially dismissed as more or less functionless simply because they didn’t fit into a kind of neat (but now hopelessly outmoded) digital coding schema linking DNAlink as Master Cause, to RNAlink as precisely programmed mediary, to protein as definitive final result. Making up a sizable portion of the human genome, transposons are to this day often referred to as “junk” or “parasitic” elements. Because they play a particularly prominent (and still barely explored) role in the germlinelink, one often hears about the germ cell’slink “defensive mechanisms” to protect itself from these highly mobile, “selfish” elements, with their genome restructuring potentials. How this kind of thinking could go on for many years without most biologists suspecting a positive role for transposons as genome remodelers with potentially powerful implications for evolution is, for me, a great mystery. Certainly transposons, like everything else in the cell, are subject to intense oversight by their larger context — and viruses may indeed have played a role in their origin, as many suppose — but this hardly makes them mere parasites in the organisms that have so intently taken them up and put them to use.

Out of thin air? With transposons the organism reshapes its genomelink through elaborately organized and synchronized processes often affecting considerable stretches of DNA. But even more striking, Kaessmann notes, is the recent discovery of protein-coding geneslink being composed “from scratch” — that is, from non-protein-coding genomic sequenceslink altogether unrelated to pre-existing genes or transposable sequences. He cites a famous paper by the preeminent French biologist, François Jacob (1977), to the effect that the probability for creation of new protein-coding geneslink de novo (from scratch) by random processes “is practically zero”. Such creation was widely thought to be virtually impossible. And yet, Kaessmann goes on, “recent work has uncovered a number of new protein-coding genes that apparently arose from previously noncodinglink (and nonrepetitivelink) DNA sequences”.

If we take seriously Jacob’s “practically zero” probability for random, de novo assembly of functional, protein-coding genes from noncoding DNA sequences, then, given that such assembly does in fact somehow occur, the obvious thing to suspect is that the process is not random. Nor does the scale of the problem, as it is now emerging, look trivial. There is, we’re told by two biologists working in Germany — one at the Max Planck Institute for Evolutionary Biology and one at Christian Albrechts University — “accumulating evidence that de novo evolution of genes from noncoding sequences could have an important role” in a class of genes representing “up to one-third of the genes in all genomes” (Tautz and Domazet-Lošo 2011). The seemingly unbridgeable gap between “practically zero” and this recent, extraordinary claim invites evolutionary geneticists to do a lot of soul-searching.

Concerted change in the germline. There is nothing in the picture so far to suggest that, when turning our attention to genetic change in reproduction, we will find much evidence of randomness. Everything we’ve looked at so far occurs in germlinelink cells as well. But in these cells we witness additional powers of change that could hardly be exceeded. Nowhere, for example, do we see the genome more concertedly re-shaped than in the two meioticlink cell divisions leading to the formation of gameteslink in sexual reproduction — a choreography we hear described in the accompanying article as the “meiotic ballet”.

One of the central features of this ballet, referred to as “chromosomal crossoverlink” or “genetic recombination”, involves an insistent re-shuffling of stretches of DNAlink between chromosomeslink, resulting in genetic variation in the offspring. You could hardly imagine a more carefully and delicately staged dance than the one resulting in chromosomal crossover — and, with researchers speaking of “recombination hotspots” and all sorts of regulation, we can be sure it is not at all random. As usual in the cell, many different factors within the larger whole come to bear on any specific point:

As is the case for transcriptionlink, no single type of DNA site, transcription factorlink, or histone modificationlink can account for the regulated positioning of all recombination. Instead, these elements function combinatorially (with potential for synergism, antagonism and redundancy) to establish preferential sites of action by meiotic recombination protein complexes (Wahls and Davidson, 2010).

Context, as always, figures strongly (and nonrandomly) in shaping and directing local activities.

Kaessmann further points to studies in animals showing that the testes play a “potentially central role in the process of gene birth and evolution”. For example, there is an “overall propensity” of young retrogenes — genes copied back into DNA by reverse transcription from RNA — to be expressed in the testes. “The testis may represent a crucible for new gene evolution, allowing novel genes to form and evolve, and potentially adopt functions in other (somaticlink) tissues with time”.

Likewise, pluripotentlink cells such as stem cellslink, which bear certain similarities to germlinelink cells, possess genomes that are “amazingly plastic”: “The incredible plasticity of pluripotent genomes is a notable discovery, and reveals the view of an unexpectedly dynamic mammalian genome for many of us” (Blasco et al. 2011).

Powers of change converging from all sides. In sum, recent work in genomics has laid bare

an astounding diversity of mechanisms underlying the birth of more recent genes. Almost any imaginable pathway toward new gene birth seems to have been documented by now, even those previously deemed highly unlikely or impossible. Thus, new genes have arisen from copies of old ones, protein and RNA geneslink were composed from scratch, protein-coding geneslink metamorphosed into RNA genes, parasiticlink genome sequences were domesticated, and, finally, all of the resulting components also readily mixed to yield new chimeric geneslink with unprecedented functions. (Kaessmann 2010)

None of this is yet to mention the way the organism massively structures, restructures, and regulates its genome through the intricate remodeling of chromatinlink (the DNA/protein/RNA complex comprising our chromosomeslink), or the way it shapes the dynamic, three-dimensional organization of the cell nucleuslink, which in turn has a great deal to do with how genes get expressedlink. (See the earlier article in this series, “Getting Over the Code Delusion”.) Even regarding the bare DNA sequencelink in the narrowest sense, Italian geneticist Vittorio Sgaramella, after noting the various alterations of the sequence throughout the cells of our bodies, was led to ask, “Which is our real genomelink. . . ?” And he adds, “The human genome seems more complex but less autonomous than originally believed” (Sgaramella 2010). Less autonomous because so many concerted activities of the organism are brought to bear on it.

And there is still much more we could have spoken about. For example, there is a consensus today that entire organelles of the cell originated in evolutionary history through a kind of cooperative fusion of distinct microorganisms, a process requiring an almost unimaginable degree of intricate coordination among previously independent life processes. Likewise, hybridization involving distinct species — with a corresponding merger of genomes — is being found to play an unexpectedly significant role in evolution. There is also the well-demonstrated reality of lateral gene transfer, which looks like invalidating the image of an evolutionary “tree,” especially at the level of simpler organisms: repeated horizontal exchanges of genetic material between distinct species make large portions of the tree look more like a complex web. Then, again, there is good evidence that viruses have played a major role in contributing to the genomes of more complex organisms, including mammals and humans. In all this we find organisms bringing their separate, highly coordinated life processes to bear upon each other in a symbiotic or other interactive manner that can no more be described as “random” than can, say, the complex and elaborately orchestrated mating processes we see among sexually reproducing organisms. “Our standard model of evolution is under enormous pressure,” says John Dupré, philosopher of biology at the University of Exeter, UK. “We’re clearly going to see evolution as much more about mergers and collaboration than change within isolated lineages” (quoted in Lawton 2009).

We could also have looked at convergent evolutionlink and the way it commonly involves changes to corresponding genes in widely different organisms, which “implies a surprising predictability underlying the genetic basis of evolutionary changes” (Nadeau and Jiggins 2010). And there is the rapidly rising interest in a kind of neo-Lamarckianlink, epigeneticallylink mediated inheritance of acquired characteristics. But we have already seen enough to realize that, by one means or another, the organism pursues its own genomic alterations with remarkable insistence and subtlety.

Where is randomness? All these revelations about coherent genomic change have prompted University of Chicago geneticist James Shapiro to speak of “natural genetic engineering”. “We have progressed from the Constant Genome, subject only to random, localized changes at a more or less constant mutationlink rate, to the Fluid Genome, subject to episodic, massive and non-random reorganizations capable of producing new functional architectures” (Shapiro 1997). Crucially, “genetic change is almost always the result of cellular action on the genome” (Shapiro 2009).

Likewise, two geneticists from the University of Michigan Medical School, writing in Nature Reviews Genetics, remember how “it was previously thought that most genomic rearrangements formed randomly”. Now, however, “emerging data suggest that many are nonrandom, cell type‑, cell stage- and locus‑specific events. Recent studies have revealed novel cellular mechanisms and environmental cues that influence genomic rearrangements” (Mani and Chinnaiyan 2010).

Bear in mind that we’ve been looking at the one aspect of organismal functioning — the mutational aspect — where we are assured most confidently that “blind chance”, or randomness, becomes visible within the evolutionary process. Certainly from the organism’s side we see nothing to suggest any fundamental role for randomness. The accompanying article explores the question in a larger context, where our understanding of evolutionary fitness becomes crucial.


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Steve Talbott :: Natural Genome Remodeling