How related to chimps are we really?

Evolution: but not how you might think!
Evolution: but not how you might think!

How closely related are we really to chimps?

The Common Code of Life

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

http://www.mirror.co.uk/news/weird-news/humans-share-50-dna-bananas-2482139

Below is a summary of the main similarities genetically speaking between humans and other life-forms taken from an article on the UK human genome site entitled: ‘THE HUMAN GENOME: POEMS ON THE BOOK OF LIFE’ by GILLIAN K FERGUSON
http://www.thehumangenome.co.uk/THE_HUMAN_GENOME/Primer.html
• Mouse and man share 99% genetic similarity – including the genes to make a tail.
• Humans and mice shared a common ancestor about 100 million years ago.
• A mouse has about the same number of genes as a man.
• Due to preserved genetic similarities, even after 530 million years of separation, introduced human genes can operate within the Fruit Fly genome.
• The nematode worm shares many genes with human beings, including the genes to make muscle.
• Puffer fish and Zebra fish are so genetically similar to human beings that their genomes are being deciphered as ‘model’ organisms for research.
• The California purple sea urchin (Strongylocentrotus purpuratus) genome has 23,300 genes, of which 7077 are shared with human beings.
• The dog genome also reveals many shared genes and diseases with humans; about 94% of the dog genome shows conserved synteny with mice, rats and humans.
• Birds and human beings have three very similar genes affecting blunt limb buds.
• Genetic similarity between humans and chimpanzees is between 96% and 99.4%
• ‘LUCA’, the ‘Last Universal Common Ancestor’ existed around four billion years ago. We are probably descended from a mud-burrowing worm.
• The common ancestor of all placental mammals was probably a small nocturnal shrew-like creature, snuffling about more than 80 million years ago.
• Dogs, goldfish, and ferns have more chromosomes than human beings.
• 75% of our genetic make-up is the same as a pumpkin – 57% the same as a cabbage.
(http://www.thehumangenome.co.uk/THE_HUMAN_GENOME/Primer.html)

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

As it turns out genes are just the stage-play script, it needs its actors and dynamic interaction on stage to come to life. It needs its proteins and these have to be created and this is open to interpretation and little artistic licence as all good plays are. They are not written in stone and can be fairly flexible in their translation and interpretation of requirements. Once genes have in a roundabout way given the instructions to make specific proteins, via their RNA transcribers (translators), the genes (even if they are very similar to other genes in a seemingly closely related species) can be expressed differently in the end without actually changing the original instructions locked in the genes. The gene is only the instruction manual (blue-print) that is open to interpretation and tweaking which can occur outside the genes and therefore doesn’t change the blue-print itself. It is how these proteins do their merry dance that can result in the same coding being translated in different ways. The genes are the blue-print, after that, it’s up to the proteins and these in turn, as you will see by reading anything about epigenetics, are instructed via the environment. Genetically, proteins are US. For instance, Scientists hail new ‘map of life’ is the article title on the BBC News website:

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

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

In its complexity and simplicity, life is a dance of proteins.
There is the genome – the master genetic blueprint – that resides in the cell nucleus. The DNA makes a simpler molecule called RNA which interacts with ribosomes which churn out proteins based on the code in the genome.

BBC, UK, 2003
http://news.bbc.co.uk/2/hi/science/nature/3223318.stm

The coding DNA (genes) is the master blue-print as the article above highlights. However, it also highlights the fact that these are just the starting point for building (proteins) and when these instructions are activated there is a great deal of interaction and processes (molecularly) – the dance of proteins, that happens once these instructions are passed on. The genome is vast and only contains a tiny portion of actual DNA which codes for proteins and within the genome, many complex genetic engineering events via natural means can and do and have occurred in the evolutionary past – sculpting genomes without changing the genes themselves.
Most of our genome which includes our genes and all the DNA or RNA (RNA is a much more dynamic molecule, simpler and seemingly more primitive version of DNA), our coding and non-coding regions, is made up of non-coding regions (c. 97/98% according to most consistent figures across reliable sources) and was for a long time, thought to be functionless – hence the junk DNA term for this seeming wasteland of repeated segments of non-coding DNA.However, this is the very region, according to more recent studies, that reveals a rather convoluted and somewhat unexpected evolutionary past.

This region reveals past  hybridization amongst broadly similar classes of more complex animals as well as HGT (horizontal gene transfer) amongst even distinct domains of life, whole genome doubling particularly in the microbial world, all causing evolutionary relatedness to look rather web-like and less like a neat branching tree of life. Then, to make matters worse, all this novel genetic mixing goes through processes of restructuring of the genomes (natural genetic engineering) via mobile genetic elements according to environmental triggers, gene expression according to how tightly or loosely our chromosomes are packaged in each cell.

So you can image why perhaps, the great evolutionary assumption of common descent via a shared ancestor and lineage splitting is coming  under increasing fire in more recent times, and particularly since we began digging deeper into the genome and seen how much more there was to our evolution beyond the GENES. And as it turns out: they’re not even selfish.

Therefore, presumed degrees of ancestral relatedness (genetically speaking) are not quite as simple as once thought and molecular timing of lineage splits on our ancestral tree is not as absolute as once believed. In other words, now that a greater understanding of the genome of chimps, humans and many other creatures and life-forms have been established, it looks like our evolutionary histories are much more colourful and convoluted and intertwined than anyone could ever have imagined, especially when you bring hybridization, HGT and whole genome combinations and gene doubling and many other ways to get novelty and exchange of genetics into the mix.
Therefore, even when shared segments of genes line-up and tend to match each other quite closely, as in us and chimps and as you take in the evidence of inter-breeding in our more primitive ancestral forms, there is quite a difference between the two species genetically speaking when one looks closer. Much of this amazing tale of life ended up sharing the universal code and how humans came to be human and chimps came to be chimps has been hiding in the non-coding regions of the DNA (Junk DNA as it used to be called) and it is here that our story begins in the modern era.

It’s not all Junk!

Our genome is massive, but only a very small part of it is made up of genes (DNA sequences that code for proteins the building blocks and maintainers of life). The non-coding (for proteins) regions of the so-called junk DNA which is by far the dominant portion of our genome compared to the tiny amount of coding (our genes), is where the real distinction between all life-forms can be seen, again even between genetically similar species. This, unlike the coding genetics, has been rather dynamically active and anything but conservative and slow to change in the evolutionary past and reveals a much greater complexity of genetic interrelationships than even the most creative mind could have conjured up.
Below is a summary about our human genome with a reference to this so-called junk DNA along with lots of interesting facts taken, again from the article on the UK human genome site entitled: ‘THE HUMAN GENOME: POEMS ON THE BOOK OF LIFE’ by GILLIAN K FERGUSON
http://www.thehumangenome.co.uk/THE_HUMAN_GENOME/Primer.html

The Human Genome

There are three billion letters in the Human Genome.
Written out, the Human Genome would stretch 5,592 miles, (9,000 km).
It would take a typist working eight hours a day half a century to type.
It would fill one million pages; 5,000 books stacked 200 feet high; or two hundred telephone directories.
Read out for 24 hours a day, it would take a century to finish.
The human body has 100 trillion (100 000 000 000 000) cells – each contains a copy of the entire Genome.
At latest belief, the Human Genome contains around 20-25,000 genes.
It has taken scientists 13 years to decipher.
[…]
The Human Genome is 97% ‘junk DNA’, the purpose of which is mostly unknown; the Human Genome Project also sequenced this DNA in the hope of future elucidation – it is already becoming clear it has functionality and is wrongly named.
Every person on Earth shares 99.9% of the same genetic code; only 0.1% of our genetic makeup differs.

This next article segment shows that 80% of the human genome has a purpose after all. And the fact that seemingly fixed coded genes (the 2 or 3% of the entire genome) can be influenced by activity in the so-called non-functional regions is pertinent to this discussion. Genes are only the initial code (and relatively conserved across all species), it is how these are activated/deleted/suppressed/expressed/turned on, or off, moved around and degree of expression of these genes and even the re-activation of old non-coding DNA segments that is written in the vast regions of the greater part of the genome, that shows the real evolutionary action.

ENCODE Project Writes Eulogy for Junk DNA

This week, 30 research papers, including six in Nature and additional papers published online by Science, sound the death knell for the idea that our DNA is mostly littered with useless bases. A decade-long project, the Encyclopedia of DNA Elements (ENCODE), has found that 80% of the human genome serves some purpose, biochemically speaking. Beyond defining proteins, the DNA bases highlighted by ENCODE specify landing spots for proteins that influence gene activity, strands of RNA with myriad roles, or simply places where chemical modifications serve to silence stretches of our chromosomes.
http://www.sciencemag.org/content/337/6099/1159

Before we started to decipher the entire human genome with all its so-called junk regions, we used to believe that genes ran the entire evolutionary show and when we cracked open the human genome, it would contain a gene for just about everything that made us uniquely human and what made us similar to other creatures. In other words, this assumption underpinned the entire modern Darwinian synthesis and it turned out to be wrong and I don’t say this lightly – this is all referenced in my first publication currently in E-Book form on Amazon entitled: ‘The Darwin Delusion’ in which the scientific support for this claim is fully referenced. It was assumed that the human genome would show us via genes, our evolutionary history and who exactly and how we were related to other creatures.
However, this was just a side-show compared to the more potentially lucrative objective which was to identify all those specific genes for deviant behaviour or advantageous traits, which would give us a better chance of survival and the specific genes for health conditions and disease. It was simple: if you can patent the gene that causes, say cancer: you can manufacture a cure to correct the gene and make a whopping amount of money on the patent and save lives at the same time – who would object to that? Alas, things did not turn out quite as hoped and as Scientific America highlighted in an article dated October 2010, the revolution in genetic medicine had to be postponed as seen in their title: ‘Revolution Postponed: Why the Human Genome Project Has Been Disappointing’, as these wonder genes for every ailment and disease as well as allowing us to tweak and redesign life itself, never materialized. http://www.scientificamerican.com/article/revolution-postponed/
I know, most of you probably think that what’s wrong with finding a cure for all ills. That is a very noble thing – the holy grail of life and longevity. But firstly, you should ask yourself who was going to benefit from these cures and promises of eternal youth and designer babies, the poor and perceived dissenters of the Brave New World – or Joe Blogs on the street who doesn’t comply with the medical insurance policy because he makes life choices that are not exactly seen as healthy? Furthermore, what they did discover within the human genome means that we will have to rethink our approach to medicine and health in a fundamental way that gives us much more control over our own lives and health, wellbeing in general.
These insights into how our genome actually operates are now leading towards alternative and much more empowering solutions, less invasive and more holistic approaches to even the most progressive and devastating diseases and disorders – essentially optimizing your body to do what it does best: cure itself. That is a topic for more qualified people than myself, but suffice to say: we are not victims of our selfish/robotically driven genes as Richard Dawkins would have you believe and your genetics and genes do not even run the evolutionary show, they are only the blue-print for maintaining it as it turns out, the basic code from which many variations are actualized.
Yes, one of the other main disappointments after the human genome project was completed around the turn of the millennia was that genes (sequences of DNA that code for proteins) only actually accounted for a tiny proportion of the entire genome, as noted above. Therefore, the first thing that we need to understand within this discussion is that when we are told that we share our genetics with other creatures and the more similar the genetics, the closer the ancestral relationship, just remember it is only around two to three per cent of the whole genome we are talking about. So even though most of us are genetically related to Richard Dawkins by 99.9%, don’t panic – this is only the mere 2 to 3% of coding DNA (genetic code) and perhaps the remaining 97% (so-called junk DNA) might tell a different story.
Another aspect of all this modernized assumptions about our gene-driven evolution was that as one creature was genetically much more similar (matched regions of genes sequences), then logically following the simplistic common descent model, the closer the relationship on the family tree was assumed to be. However, the junk regions and areas around the relatively conservative genes – the universal code of life, and the difference in their expression between even proposed closely related creatures are telling a very different story about our evolution. So let us see where this idea of degrees of relatedness originated from and how it got to be applied to our genes.

 

Origins & Evolution of ‘Descent of Man’

In order to understand the origins of the idea of common descent with modification, the assumption upon which our common ancestry from an ape-like creature that gave rise to the chimps and humans, we have to go back in time to see where even Darwin himself got the idea of common descent with modification upon which he based his theory of natural selection. (The following section of information is fully referenced in my first publication on this topic – see O’Hare 2014 1st edition of ‘Darwin Delusion’ on E-Book at Amazon).

You see, Darwin’s grandfather, Erasmus Darwin discussed evolution from a first filament through to more complex forms long before Darwin was born. However, the elder Darwin must not have heard about the great philosophers of old from Aristotle to the Muslim naturalists and from Descartes’ to Kant who had pondered our evolution through increasingly complex life-forms, from the primal slime and ultimately to the great ape and finally, MAN, as he seemed to write in hushed whispers as if this was something of a rather new and almost outrageous idea.

In other words, common descent from an ancestral form was a common assumption back in the day and no, those religious types who objected to a change in the species through time were not as crazy as they are made out to be in popular scientific press, after reading their work in some depth, I am now of the opinion that they had valid objections and sound alternative views. But, this is not the topic under discussion here, suffice to say: many people assumed, just like Darwin, that simpler life-forms gave rise to more complex forms via hereditary. Darwin was not the first to propose a naturalistic explanation, nor the first one to formalise this idea. There was another great thinker who had written a most comprehensive theory and published it the same year that Charles Darwin was born. This was Jean Baptiste Lamarck.

Interestingly, at a molecular level in principal, Lamarckian inheritance of acquired characteristics (modern term would be epigenetics) is being supported in labs all around the world, whereas Darwinian evolution in its updated genetic form (genetically modified in my opinion) is not. Furthermore, Lamarck’s ideas on common descent were less literal and simplistic than Darwin’s view of evolution. Lamarck allowed for several distinct origins of fundamentally distinct life-forms, driven to their ultimate evolutionary apex via natural means. Lamarck and many others still believed that monkeys and men were somehow related and as it turns out: we are, but not quite in the way that we have been told via the Neo-Darwinian model. Again, Lamarck is being supported in more recent years as it now seems that life and its origins is more web-like than a tree and indeed, there are several distinct origins of life, even in the pre-cellular world and indeed, many ways in which these distinct life-forms could exchange and did frequently, genetic information, including entire genomes.

So returning to the assumption that simple forms gave rise to more complex forms (common descent with modification) and our particular lineage split from a common ancestor of chimps and humans in more modern thinking, this updated genetic version of this common descent is ultimately based upon the very specific idea of Homology (the idea of the similarity of forms such as the fish’s fin, a bird’s wing or a five-digit foot/hand revealed a common ancestry) became the most fashionable way of viewing evolution in Darwin’s day.

The whole idea of common descent and ancestral homology of fin to foot, the younger Darwin had not only been persuaded that common descent from an ancestral form must be the way to go as many before and after him did, but he also came to accept the increasingly popular idea of literal descent from an ancestral form and fully embraced Homology as the basis of his natural selection theory. Thus, the real monkey business began with a literal interpretation of homology and as they say, the rest is history and can be defined with Thomas Henry Huxley in his 1863 publication of ‘Evidence as to Man’s Place in Nature’ https://archive.org/details/evidenceastomans63thom

With all those illustrations of ape-men and lumbering skeletons of apes looking a bit more upright towards the end, well, what could Charles Darwin do? He had a bit of catching up to do and although, he did not actually address the whole issue of monkeys and men until after Huxley’s publication, he did eventually get around to dealing with this whole topic some years later after his friend Huxley paved the way and Darwin published ‘Descent of Man’ which became a best-seller by all accounts, particularly within polite Victorian society and it did have ‘sex’ in the title, so perhaps that it is not all that surprising. Anyway, I digress. Yes, the modern means of interpreting common descent from the geological and fossil record, where homology is identified, not only in the changing bone (fossils) structures, but now within the genes and their mutations and their shared sequences, it is assumed that the closer the genetic makeup within species corresponds to other species: the closer the ancestral relationship is believed to be.

These divergences (when lineages may have split), giving rise to new, but still ancestral lineages are then plotted in space and time according to degree of relatedness and when lineages split from an ancestral form upon what has come to be known as a molecular tree of life. It is fundamentally similar to Darwin’s original concept of the great branching tree of life – increasing complexity (branching) from a simple stem, except that it is molecular and genetically based in accordance with the fossil record. Oh, and I should mention the fact that when they updated Darwin, which I have come to understand from research was by less than natural means, they had to throw population models into the equation to spice up the gene-pools so that there would be enough genetic novelty to work on for a change to take place and create a new species. So we will now look at this molecular evolutionary tree in action and see how it pans out in reality.

 

The Molecular Tree and the Fossil record don’t tally

Here is an example of the general assumption of how genetics link to the fossil record and give us timescales based on geological time-lines are used to re-produce our theoretical family tree:

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

 

The timescales for these lineage splits such as when chimps and ourselves last shared a common ancestor 5/6 million years ago, (although this date goes back a little depending upon the most recent genetic models being employed) has a few embedded assumptions within the model in the first place that might be making the interpretation of results rather precarious. Not only that, but we have never found this illusive ancestor that gave rise to all the other homidea (great apes) including ourselves. There are no proto-chimps or gorillas and the only evidence for these creatures in the fossil record are when they are fully recognisable as chimps and found alongside homo species (humans). Sally McBrearty and Nina G. Jablonski, “First Fossil Chimpanzee,” Nature 437 (2005): 105-08

First Chimp Fossils Found; Humans Were Neighbors

Researchers have found the first reported chimpanzee fossils in Kenya’s Rift Valley, providing the first physical evidence that chimpanzees coexisted with early human ancestors, known as hominins.
http://news.nationalgeographic.com/news/2005/08/0831_050831_chimp_teeth.html

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

Because chimps and humans share a matrilineal ancestor, establishing the geological age of that last ancestor allows the estimation of the mutation rate. However, fossils of the exact last common ancestor would be an extremely rare find. The CHLCA is frequently cited as an anchor for mt-TMRCA determination because chimpanzees are the species most genetically similar to humans. However, there are no known fossils that represent that CHLCA. It is believed that there are no proto-chimpanzee fossils or proto-gorilla fossils that have been clearly identified.
Wikipedia ‘Chimpanzee-human last common ancestor’ http://en.wikipedia.org/wiki/Chimpanzee%E2%80%93human_last_common_ancestor

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

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

Wikipedia continues with an interesting quote:
“ One no longer has the option of considering a fossil older than about eight million years as a hominid no matter what it looks like. ”
—V. Sarich, Background for man

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

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

The molecular clock hypothesis postulates that the rate of molecular evolution is approximately constant over time. Although this hypothesis has been highly controversial in the past, it is now widely accepted. The assumption of rate constancy has often been taken as a basis for reconstructing the phylogenetic relationships among organisms or genes and for dating evolutionary events. Further, it has been taken as strong support for the neutral mutation hypothesis, which postulates that the majority of molecular changes in evolution are due to neutral or nearly neutral mutations. For these reasons, the validity of the rate constancy assumption is a vital issue in molecular evolution. Recent studies using DNA sequence data have raised serious doubts about the hypothesis.
http://www.ncbi.nlm.nih.gov/pubmed/3102974

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

Molecular systematic – Molecular biology has revolutionized the field of systematics. DNA evolves by mutations being incorporated in the DNA and fixed in populations. This will lead to divergence of DNA sequences in different species. Although diverged, we can refer to two DNA sequences as homologous (just as we would for any morphological trait such as forelimbs). Nicely demonstrates descent with modification as a definition of evolution.
http://biomed.brown.edu/Courses/BIO48/26.Systematics.HTML

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

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

Here is the all important article extract:

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

Although molecular systematists may use the terminology of cladism, claiming that the reconstruction of phylogenetic relationships is based on shared derived states (synapomorphies), the latter is not the case. Rather, molecular systematics is (largely) based on the assumption, […] that degree of overall similarity reflects degree of relatedness. This assumption derives from interpreting molecular similarity (or dissimilarity) between taxa in the context of a Darwinian model of continual and gradual change.

Review of the history of molecular systematics and its claims in the context of molecular biology reveals that there is no basis for the “molecular assumption.”….. Although many molecular analyses attempt to generate theories of relationship from distance measures—even with small and taxically underrepresented sample sizes—it is not uncommon to find studies claiming to have determined a close relationship between two taxa when, in reality, they only applied their data to an already assumed arrangement of phylogenetic relationship.

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

You might want to read the above statement again – I know I had to, several times. But, I believe it is really important that you understand that most studies attempting to establish relationships (molecularly speaking) and their timing are based upon an assumption of earlier relatedness and timing of lineage splitting as the starting point for their study. The initial assumption has never been empirically tested, but assumed. This may invalidate the results.
So, perhaps these serious doubts and underlying assumptions should be taken into account as you hear or read about the way chimps and humans are supposed to be related and when it all happened. The more recent assumption that we and chimps split from a common ancestor 5/6 million years ago is one built on belief that may not be correct in the first place, and two: based upon a molecular clock that runs at different rates between the two species and therefore is not a constant. And, thirdly, it is built upon the assumption that similar features/characters/bone-structure and form as well as genetic similarity (homology in its updated version) are the result of direct common descent and all variation can only come about by genetic inheritance and by no other mechanism for change, it rules out the possibility that these similarities are the result of complex mechanisms and interactions between all life-forms from the earliest times and are environmentally driven (molecule machinery shapes the expression of genes that build proteins that build body-forms) and this is highly flexible particularly at a developmental/embryonic stage (which is all Lamarckian type evolution in its updated epigenetic form). Thus, similar function and environmental experience can result in similar forms and even genetics. Remember the old alternative school of thought before homology became popular? Yes, a blue-print from which nature acted upon and sculpted the various creatures accordingly – Common FUNCTION, rather than literal Common Descent in all cases.

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

More recent molecular and fossil evidence is pointing to a different view of evolution which would both tally well with the fossil record and provide a mechanism for evolutionary that is rather more complex and convoluted than literal common descent from a single ancestral lineage idea embedded in the Darwinian model. Furthermore, it would also resolve the whole molecular clock business, which really isn’t helping much as a far as I can see from my research. In fact, it is actually, I believe clouding the issue and perhaps we should just put our old assumptions to the side and start actually following the real empirical evidence and try and understand what the actual fossil record is trying to tell us. Below is a very revealing study of brains of vertebrates (back-boned animals like fish, amphibians, mammals, reptiles and humans as well as chimps). As the following statement is rather radical I feel it is important to point out the author/researcher’s credentials. Dr. Butler is a Professor Emerita (retired) in the Molecular Neuroscience Department in the Krasnow Institute for Advanced Study
http://neuroscience.gmu.edu/people/abbutler.

Evolution of Vertebrate Brains

… reptiles did not give rise to mammals any more than mammals gave rise to reptiles. In regard to embryological development, it likewise generally proceeds from the general (common ancestral features) to the specific (specializations of the taxon) […]. What is clearly established is that all taxa have their own specializations. Each taxon has a mix of primitive features.

http://brain.phgy.queensu.ca/pare/assets/Evolution2.pdf

The conclusion in this brain vertebrate study clearly indicates that the simplistic common descent model may be flawed. Indeed, increasing evidence suggests that all complex animals have evolved from their essential primitive form towards increased specialisation within their ecological niche. For example, a fish doesn’t need feet because fins are more efficient for its watery niche. Back before Darwin’s evolutionary theory was published, for decades before this, many believed in homologous (analogous) forms were independently evolved via a shared common FUNCTION rather than direct common ANCESTRY (convergent evolution as it would be known today), a type of blue-print (template) upon which nature developed many variations upon the same basic theme.
We are coming to understand that master gene switches known as Hox genes can trigger basic body plans during development in a fixed sequence, but what happens after these genes are initially activated or suppressed relates entirely to environmental conditions, including resource availability such as having enough calcium and other essential raw materials for building more complex skeletal structures seen in non-fish vertebrates like reptiles, amphibians and mammals. So you can imagine that if a fish produces a bud for a limb that becomes a fin but stops short and only other vertebrates go on via metamorphosis such as amphibians (spawn to tadpole to frog) then their coding is probably richer, their metabolic rate slower and they also have the resources to build new proteins and therefore body-parts. Nature has a mechanism inbuilt that has, itself, evolved and this can adjust the genetic expression without changing the blue-print that is shared amongst all vertebrates. It is how genes are expressed that makes a world of difference between even seemingly closely genetically related species like chimps and humans.

Pioneering Study Compares 13 Vertebrate Genomes

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

The organisms included human, chimpanzee, baboon, cat, dog, cow, pig, rat, mouse, chicken, zebrafish and two species of pufferfish (Fugu, Tetraodon)… By systematically comparing the patterns of a certain type of genomic change, called transposon insertions, among the different species’ sequences, these investigators were able to address a heated controversy in the field of evolutionary genomics. Their analyses confirm recently proposed trees of mammalian evolution indicating that primates (human, chimpanzee, baboon) are more closely related to rodents (mouse, rat) than to carnivores (cat, dog) or artiodactyls (cow, pig). Indeed, the evidence revealed by the new sequence data refutes alternative evolutionary trees that place rodents much farther away from primates….
The final set of findings reported in the study revealed that, while the general types of genome changes were similar among all vertebrates studied, differences in the relative contributions of the various changes have uniquely sculpted each species’ genome. These findings point to the complex ways that evolution has used millions of years of alterations to render each species’ genome into its modern-day form.

http://www.genome.gov/11008356

 

Of Mice & Men

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

I am proposing evolution going from the less defined to the more specific in line with the findings from the vertebrate study above. Going from shared common templates and genetic blue-prints of life and evolving from primitive common features to increasing specialization and refined adaptation and ultimately a finer resolution of what we would define as a specific species today. I am not saying that there was no gene exchange between ourselves as would-be humans (generalist great apes) and the other great apes in their more primitive forms, as there is certainly evidence for this which I will outlined further on, I am making the point that nature appears to build functional templates of life, from non-vertebrate to vertebrate, from fish to fishermen, from the less defined to the more refined within all major classes (taxa) of forms.

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

If you look at the changes within the genome, not the genes themselves then, the distinction between even superficially alike species becomes much clearer. It is how nature has acted upon the expression of the shared genetics that changes the species and can in the end appear to rearrange our family tree in showing that primates (including ourselves chimps and gorillas etc) have more in common in terms of changes in their genomes with rodents (mice and rats etc) than with cats, cows and dogs as the above study indicates.

As the article above points out, it is the sculpting of these genomes (changing the actual genome) via what have been called transposon insertions, or what is often referred to as Jumping Genes that is the most important aspect highlighted in this study. Could these little clever genome rearrangements be an alternative explanation for evolutionary adaptation and ultimately change within the species? Could it begin to explain evolution without selection and offer a less literal interpretation of the fossil record and genes based upon a simplistic common descent with modification model and could it all be environmentally driven where the cells sense their environment and therefore the organisms being a collection of cleverly organized colony of cells be able to adapt and change accordingly?

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

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

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

“In other words, it can be argued that much of genome change in evolution results from a genetic engineering process utilizing the biochemical systems for mobilizing and reorganizing DNA structures present in living cells”.
http://shapiro.bsd.uchicago.edu/Shapiro.1992.Gentica.NatGenEngInEvo.pdf

Bearing this natural genetic engineering process in mind, the following study is of some interest and might give us an insight into this natural genetic engineering in action.

 

Why Fish don’t have fishy fingers

For instance, a recent article on a popular science site explains how this genetic blueprint works and how it is expressed or not, according to the vertebrate animal it is activated in. Note that a tetrapod is a land-living limbed vertebrate:

How the genetic blueprints for limbs came from fish

[…] the transitional path between fin structural elements in fish and limbs in tetrapods remains elusive. Both fish and land animals possess clusters of Hoxa and Hoxd genes, which are necessary for both fin and limb formation during embryonic development. Scientists compared the structure and behavior of these gene clusters in embryos from mice and zebrafish. The researchers discovered similar 3-dimensional DNA organization of the fish and mouse clusters, which indicates that the main mechanism used to pattern tetrapod limbs was already present in fish. {…}
Does this imply that digits are homologous to distal fin structures in fish? To answer this question, the geneticists inserted into mice embryos the genomic regions that regulate Hox gene expression in fish fins. ‘As another surprise, regulatory regions from fish triggered
Hox gene expression predominantly in the arm and not in the digits. Altogether, this suggests that our digits evolved during the fin to limb transition by modernizing an already existing regulatory mechanism’, explains Denis Duboule.
‘A good metaphor for what has probably happened would be the process of ‘retrofitting’, as is done in engineering to equip outdated machine frames with new technology. Only, in this case, it was a primitive DNA architecture which evolved new ‘technology’ to make the fingers and toes’, says Joost Woltering.
Fin radials are not homologous to tetrapod digits.
The researchers conclude that, although fish possess the Hox regulatory toolkit to produce digits, this potential is not utilized as it is in tetrapods. Therefore, they propose that fin radials, the bony elements of fins, are not homologous to tetrapod digits, although they rely in part on a shared regulatory strategy.
http://www.sciencedaily.com/releases/2014/01/140121183412.htm

The key phrase in this article in my opinion is …fin radials, the bony elements of fins, are not homologous to tetrapod digits, although they rely in part on a shared regulatory strategy”. Firstly, we now know that the old idea of homology which assumes common ancestry from a direct common ancestor to make homology work and explain evolution in terms of the up-dated Darwinian model is incorrect.

And secondly, evolution has evolved a mechanism to adapt its different organisms according to their environment – the regulatory strategy. Supporting this idea is the fact that other research relating to Hox gene switches which, I go into in more detail in another publication (O’Hare 2014), would suggest that what is going on in the above study is that the mechanism (molecular) was in place for the genetic expression of limbs, however, it may be that limbs were not expressed in fish as they had already become specialized within their environmental niche (their genomes became genetically more stable and quieter) and perhaps did not have the rich coding (software) or the raw materials (hardware) such as enough calcium reserves to activate these gene (protein building) body template, could become tetrapods due to more novel genetic coding (software) and hardware resources?
An analogy might be that, nature builds according to its resources. Or, cutting your cloth to your measure as some would say. You can build a sauna from wooden logs if you have enough of them in your mansion (if you have enough resources and materials to build one in the first place), but you can’t build a mansion from wooden logs. However, you could scale-down your blueprint of a house and build a log cabin instead. The body template or the genetic blue-print can only utilize its available resources. Once these are used up in terms of building any major new architecture (extensions), it seems that genes work with what they have already. It would appear that genomes become stable and the house (log-cabin or mansion with the sauna) can be refurbished, updated and a re-decorated, but it doesn’t suddenly become a car.

Genetic silencing (at least at the macro-evolutionary scale) seems to kick in – seemingly, nature’s way of stabilizing creatures so they don’t start morphing into monsters, although in the early days, change within primitive forms may have been somewhat genetically loose and experimental. This genome quieting seems to allow a creature to become specialised in its niche and therefore I would propose that the fish out of water hypothesis doesn’t appear to hold water and the study by Butler outlining how evolution proceeds from the general (primitive) to the specialized, tallies very well with the idea of a general (genetic blue-print and molecular mechanism/regulatory system) that is shared amongst fundamentally similar (e.g. vertebrates) animals who start out with a similar body template by which nature continues to sculpt until the piece is finalized. It seems that Mother Nature continues to tweak these macro-designs via adjusting the EXPRESSION of the genetic code, without changing the code itself (micro-evolution) and it does this via a ready-made, in-built mechanism for adaptation to environment and circumstances shared by all creatures.

Will the real ancestor please STAND UP

In many ways, the Hox genes and this mechanism evolved and in turn creatures evolved according to their resources and environmental niche. It seems that once a species such as fish was established, that it was just a matter of every possible variation on the theme of fish thereafter. But there is more to this saga as genetic exchange – how did fish arrive at being fish in the first place, has to be taken into account. Essentially all domains of life have and do exchange genes and always have and it is not always via inheritance. This is called HGT (horizontal gene transfer) as opposed to the more commonly understood VHT (vertical gene transfer) via breeding (inheritance) and this HGT along with whole genome/organism merging as seen in the microbial world is one sure way of creating distinct life-forms. It is akin to hybridization without the sex. It is complex and just let us say that insects that bite and suck your blood do have a significant role to play in our evolution as by doing this annoying and sometimes life threatening act, they can spread and have inserted whole segments of DNA between distinct species. This newer understanding of evolution is also a much more dynamic explanation of speciation (change in one species to another) than the genetic population model and natural selection of preserved traits underpinning the Neo-Darwinian model of evolution.
Certainly, we are not that different really from each other and genetically, our coding matches many regions seen in the chimp genome and if there was lots of inter-breeding between pre-chimp/human apes (generic forms) then this similarity is not at all surprising. All these novel ways of exchanging genetics is the reason why life is more of a web than a neat branching tree of evolving complexity. Furthermore, much of the novel genetic coding seen in the more complex animals comes from hybridization (an aspect of evolution not considered to be significant either by Darwin or the later Neo-Darwinists) which we are now coming to understand played a significant role in evolutionary speciation in the past and is indeed fairly common still within some lower orders of animals and certainly amongst plants.

This brings us to another aspect of the modern synthesis: its reliance on genes/genetics within a one-way system of inheritance, an ancestral route with no direct impact on a developing organism to change its genes via environmental interaction. In other words, if you could only get your genes via your parents and they could only get their genes from their parents and grandparents and ultimately their distant ancestors, and the only means of changing the genetics was via mistakes in the copying process (mutating genes) and re-shuffling of genetics resulting from these genes being passed on in various combinations depending upon the variability of genetic mixing of these gene-pools, then the literal common descent model was the only explanation of all evolutionary change and speciation. However, if you bring hybridization into the evolutionary scenario, then things look very different indeed and as it turns out genes is only part of the evolutionary picture. And the mixing of these genes may not as been as clear-cut as we once thought.

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

Hybrids May Thrive Where Parents Fear to Tread

While one might think that these oddities are examples of some kind of moral breakdown in the animal kingdom, it turns out that hybridization among distinct species is not so rare. Some biologists estimate that as many as 10 percent of animal species and up to 25 percent of plant species may occasionally breed with another species. The more important issue is not whether such liaisons occasionally produce offspring, but the vitality of the hybrid and whether two species might combine to give rise to a third, distinct species.
[…}
Several such examples are now known from nature. Furthermore, DNA analysis is now allowing biologists to better decipher the histories of species and to detect past hybridization events that have contributed new genes and capabilities to various kinds of organisms including, it now appears, ourselves.

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

Human, Chimp Ancestors May Have Mated, DNA Suggests

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

http://news.nationalgeographic.com/news/2006/05/humans-chimps_2.html

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

Genetic evidence for complex speciation of humans and chimpanzees.

Abstract
The genetic divergence time between two species varies substantially across the genome, conveying important information about the timing and process of speciation. Here we develop a framework for studying this variation and apply it to about 20 million base pairs of aligned sequence from humans, chimpanzees, gorillas and more distantly related primates. … Our analysis also shows that human-chimpanzee speciation occurred less than 6.3 million years ago and probably more recently, conflicting with some interpretations of ancient fossils. Most strikingly, chromosome X shows an extremely young genetic divergence time, close to the genome minimum along nearly its entire length. These unexpected features would be explained if the human and chimpanzee lineages initially diverged, then later exchanged genes before separating permanently.
http://www.ncbi.nlm.nih.gov/pubmed/16710306

Leaving aside, the conflicting estimates of our so-called lineage split, this article really highlights the hybridization between the common ancestor of chimps and humans. Now hybridization as it turns out, as noted above, is not so uncommon after all as genomes were not seemingly as closed off and quiet (genetically speaking) back in the day of primitive apes (which I have come to refer to as generic forms as they do not appear to be specifically any species only fossils showing perplexing characters and traits of modern and primitive forms as palaeontologists invariably describe particularly when trying to figure out the human lineage) that seemingly weren’t too fussy about who they mated with.
So what if, as strongly indicated in the fossil record, the chimp and gorillas and any number of other great ape primates, were never technically proto-chimps/gorillas etc? What if, as the fossil record does suggest, all great apes, including our primitive selves, were at one time simply less defined and generalist apes on the way to becoming more specialist and adapted to our particular niche? Why would it be so strange for a homindea form with a shared genetic blue-print – generic form of ape, and predisposed to bipedalism as suggested by some researchers (see the upright ape) to exist and between hybridization and environmental factors (epigenetic processes or Lamarckian type acquired characteristics) come to be increasingly more defined and specialized as seen with all other vertebrate evolution outlined in Butler’s study?
You can imagine how hybridization between a generic great ape with a novel set of genes and unique traits might fairly rapidly take a different evolutionary path almost overnight in geological timescales. You know that hybrids between distinct species of flowers and plants can create an entirely distinct species, almost instantaneously within a new population that has never been seen before? Well, it’s not that different a process between higher organisms – the results can be pretty dramatic. It is just that plants tend to have looser genomes in terms of less genetic barriers between distinct species than most distinct modern species of animals have today.
This different way of interpreting the evidence would therefore suggest that there was never a single common ancestor from which the chimp and the human line diverged, but instead, there was a generic great ape form with many variations on the basic template and depending upon their rather novel and mixed gene-pools, stimulating the development of increasingly unique traits such as increased ability to walk upright with more efficiency for example, would have been enough to take the human lineage (or the primates on their way to becoming fully human) on an entirely different trajectory. Do bear in mind that other generic apes that ended up on a different evolutionary path may have simply become adapted to their particular niche much quicker than the homi-form (and their genomes became quieter and genetic exchange between now quite divergent species may have been more restricted).
On the other hand, apes with the ultimate evolutionary destiny of human, may have simply had more hardware and software to play with and go on, depending upon diet and many other environmental factors, such as being able to now expand well beyond their traditional niche because of the ability to walk and climb great distances, and mix with more of their own kind and do some interesting mating with similar, but genetically exotic types like themselves. This would in turn create interesting and novel new molecular pathways of evolution towards a more specialist human form. Take for example, the hybridization studies for the archaic humans and our more modern selves:
In a paper published in the Proceedings of the National Academy of Sciences (PNAS), a team led by Michael Hammer, an associate professor and research scientist with the University of Arizona’s Arizona Research Labs, provides evidence that:

‘Anatomically modern humans were not so unique that they remained separate. We found evidence for hybridisation between modern humans and archaic forms in Africa. It looks like our lineage has always exchanged genes with their more morphologically diverged neighbors […] We think there were probably thousands of interbreeding events’, Hammer said. ‘It happened relatively extensively and regularly […] anatomically modern humans were not so unique that they remained separate’, he added. ‘They have always exchanged genes with their more morphologically diverged neighbors. This is quite common in nature, and it turns out we’re not so unusual after all’.
http://www.sciencedaily.com/releases/2011/09/110905160918.htm

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

Re-modelling the genome without changing the universal code of life

Beyond this mixing and most likely means of macro-evolutionary, changing one species into a distinct one in record fast time, once these genes are in the mix, it seems that further adjustments are then made where sculpting of the genome creates further refinements to this common body-plan (micro-evolution). Essentially, there are many other mechanisms that can continue to work with these novel genetic combinations, without even changing the genes themselves, only how they are expressed. You see, there is a whole lot more going on besides the genetic blueprint which is open to interpretation by the RNA and results in proteins of all manner of variations on the theme of the initial instructions, our genetic code (DNA that codes for proteins) is not only a very small piece of the puzzle, but remarkably conservative across all species and slow to change once it has been established.
However, the instructions within these otherwise stable genes can be translated according to the needs of the organism and even the way these genes are expressed (turned on or off without changing the code) in different ways between even genetically very similar species, can make a big difference further along the evolutionary line. One fairly drastic way of re-modelling genomes (ala: Prof. James A. Shapiro’s natural genetic engineering as discussed above), is to relax the epigenetic control of gene expression and trigger mobile genetic elements (TEs) or jumping genes into action. The scientist, who initially brought this jumping genetics phenomenon to the attention of the world, once she finally got the recognition, was Barbara McClintock and her decades of research on transposable or mobile elements triggered by environmental challenges & controlled by the epigenome http://www.nobelprize.org/mediaplayer/index.php?id=1617
In her paper presented during her Nobel award in 1983, entitled: THE SIGNIFICANCE OF RESPONSES OFTHE GENOME TO CHALLENGE she writes:

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

In the future attention undoubtedly will be centered on the genome, and
with greater appreciation of its significance as a highly sensitive organ of the
cell, monitoring genomic activities and correcting common errors, sensing the
unusual and unexpected events, and responding to them, often by restructuring
the genome.
http://www.nobelprize.org/nobel_prizes/medicine/laureates/1983/mcclintock-lecture.pdf

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

Similarities in Chromosome banding patterns and hybridization homologies between ape and human chromosomes suggest that human chromosome 2 arose out of the fusion of two ancestral ape chromosomes (1-3).
http://www.pnas.org/content/88/20/9051.full.pdf

Genomic Structure and Evolution of the Ancestral Chromosome Fusion Site in 2q13–2q14.1 and Paralogous Regions on Other Human Chromosomes
Humans have 46 chromosomes, whereas chimpanzee, gorilla, and orangutan have 48. This major karyotypic difference was caused by the fusion of two ancestral chromosomes to form human chromosome 2… Because the fused chromosome is unique to humans and is fixed, the fusion must have occurred after the human–chimpanzee split, but before modern humans spread around the world

…Many other cross-hybridizing sites were observed in the genomes of nonhuman primates (Fig. 2), reflecting the evolutionary mobility of sequences homologous to the region surrounding the fusion site.

http://genome.cshlp.org/content/12/11/1651.full

Are they assuming that this fusion must have occurred after the chimp-human split because we are assuming that we split from an ancestral ape to chimps and humans in the first place? As discussed earlier, if we see all variations on the basic theme of Great Ape (a generic form) as having divergent evolutionary paths from this basic evolutionary template, then the evidence starts to make more sense. The fusion could have occurred at any time and across even highly diverse populations of great apes who had perhaps the greatest genetic novelty within their genomes. New genes can be made from old segments of DNA lying around the genome which, can be re-programmed and therefore remodel the genome itself and in turn, the organism. This can occur quite rapidly and radically as demonstrated via the work of McClintock and many others.
We have to ask ourselves, as these major remodelling events are triggered by major environmental stresses, what could have been the stress related event that fused the human chromosomes and made such a fundamental difference to our genome and therefore our ultimate destination of becoming human? Could it have been a shock to the genome due to hybridization itself between fairly novel genetic exchanges? We may never know, but this is an interesting line of enquiry as we come to understand that this explanation of genome remodelling via natural adaptive mechanisms along with genetic exchange (including hybridisation) are much more dynamic explanations of rapid, profound and far-reaching speciation impact than our traditional model of common descent from an ever elusive ancestral form that gave rise to ourselves and the chimps.

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

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

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

http://www.nature.com/scitable/topicpage/chromosomes-14121320

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

Transcription factors guide differences in human and chimp brain function

Summary:
Humans share at least 97 percent of their genes with chimpanzees, but, as a new study of transcription factors makes clear, what you have in your genome may be less important than how you use it.
The study, in Proceedings of the National Academy of Sciences, found that broad differences in the gene activity of humans and of chimpanzees, affecting nearly 1,000 genes, appear to be linked to the action of about 90 transcription factors. Transcription factors are proteins that bind to specific regions of the DNA to promote or repress the activity of many genes. A single transcription factor can spur the transcription of dozens of genes into messenger RNA (mRNA), which is then translated into proteins that do the work of the cell. This allows specific organs or tissues to quickly ramp up a response to an environmental change or internal need.
[…]
“The chimp network looks very much like the human one except there are a few transcription factors in different positions and with different connectivity,” Stubbs said. “Those are of interest from the point of view that they signal a major gene regulatory shift between species, and this shift may help us explain some of the biological differences.”
The new findings indicate that certain transcription factors are working together in a coordinated way to regulate the changes in seen in gene expression between humans and chimps, the researchers said.
“Once this network of transcription factors is established, changes in the network can be amplified because transcription factors control other genes,” Nowick said. “Even a small change in transcription factor expression can therefore produce a large effect on overall gene expression differences between chimpanzees and humans.”
http://www.sciencedaily.com/releases/2009/12/091207151220.htm

 

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

 

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

 

I hope you have enjoyed and gotten something from the above blog. I will outline a few articles in the next part of this series about how unrelated we are to chimps. In the meantime, keep in touch and share these articles with someone you think might be interested.

Thanks

Maria Brigit

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