THE DARWINIAN TREE BEGINS TO TOPPLE – sample chapter from the Darwin Delusion (entire book is FREE on Amazon today)

http://www.amazon.com/The-Darwin-Delusion-Maria-OHare-ebook/dp/B00KBH6SBM/ref=sr_1_1?ie=UTF8&qid=1401626405&sr=8-1&keywords=The+Darwin+Delusion Oh, No, not Dawkins againCHAPTER TWO THE DARWINIAN TREE BEGINS TO TOPPLE     The Darwinian Tree begins to Topple     […]   For instance, Lynn Margulis has a lot to say about Darwin’s Tree in: The Phylogenetic Tree Topples (2006) (57) and after pointing out the obvious fact of the evolution of all species over the past few billion years, Margulis (the president of American Scientist magazine) declares a rather loud “NO” to all the other assumptions embedded in the so-called facts of Darwinian Evolution and she proclaims the following:   […] Then how did one species evolve into another? This profound research question is assiduously undermined by the hegemony who flaunt their correct solution. Especially dogmatic are those molecular modelers of the tree of life who, ignorant of alternative topologies (such as webs), don’t study ancestors. […], they correlate computer code with names given by authorities to organisms they never see! Our zealous research, ever faithful to the god who dwells in the details, openly challenges such dogmatic certainty.”(57)   Yes, don’t you start to get the feeling that Margulis really had issues with those Neo-Darwinist, Ultra types, and in particular, with those random mutations that are supposed to create all the diversity we see in our world today? Furthermore, she really takes umbrage with those genetic population meddlers as you can probably tell from her above declaration of independence from the extreme Darwinist camp. As Margulis herself points out, the answer to how evolution actually may have unfolding lies in research like her own which begins to show the world wide web of live and not so much an evolutionary tree with a single stem from which all else follows as her title suggests. This is born out in an abstract of a more recent science paper (2008) entitled: A Fundamentally New Perspective on the Origin and Evolution of Life by Shi V. Liu (Eagle Institute of Molecular Medicine) in which the most fundamental flaw within the Darwinian model of evolution by common descent, is highlighted in the following:   “Darwin’s hypothesis that all extant life forms are descendants of a last common ancestor cell and diversification of life forms results from gradual mutation plus natural selection represents a mainstream view that has influenced biology and even society for over a century. However, this Darwinian view on life is contradicted by many observations and lacks a plausible physico-chemical explanation. Strong evidence suggests that the common ancestor cell hypothesis is the most fundamental flaw of Darwinism. By contrast, a totally different perspective on origin and evolution of life claims that cellular life forms were descendants of already diversified acellular life forms. Independently originated life forms evolve largely in some parallel ways even though they also interact with each other. Some evolutionary “gaps” naturally exist among evolutionary lines. Similarity may not be the only result of phylogenetic inheritance but may be a result of a convergent mechanism of origin and evolution. Evolution is not a random process but follows some basic physico-chemical principles as a result of the interplay of both energy and entropy on matter”. (58)   Indeed, the origin of species doesn’t even appear to have a single common origin. Moreover, the evolution of species in a neat tree-like branching pattern of splitting into another, as the updated Darwinian genetic (molecular) tree proposes, is more like a web. These observations are indicated by: W. Ford Doolittle and Eric Bapteste in their abstract of a paper entitled: Pattern pluralism and the Tree of Life hypothesis (PNAS 2007)where theydraw attention to the hierarchical assumption embedded in the traditional Darwinian assumption regarding the TOL (stands for the tree of life). (Note: Prokaryotes are less complex cellular life forms preceding the Eukaryotic organisms which include animals and plants):     Darwin claimed that a unique inclusively hierarchical pattern of relationships between all organisms based on their similarities and differences [the Tree of Life (TOL)] was a fact of nature, for which evolution, and in particular a branching process of descent with modification, was the explanation. However, there is no independent evidence that the natural order is an inclusive hierarchy, and incorporation of prokaryotes into the TOL is especially problematic. […] This is not to say that similarities and differences between organisms are not to be accounted for by evolutionary mechanisms, but descent with modification is only one of these mechanisms, and a single tree-like pattern is not the necessary (or expected) result of their collective operation. (59)   Similarly, in a paper entitled: The Concept of Monophyly: A Speculative Essay, by biologist Malcolm S. Gordon (1999) highlights the following:   Recent research results make it seem improbable that there could have been single basal forms for many of the highest categories of evolutionary differentiation (kingdoms, phyla, classes). The universal tree of life probably had many roots”. (60)   Related to this is what Carl Woese, a prominent and well respected microbiologists, who did some ground breaking work back in the 60s and 70s that started to upturn the old TOL or the Darwinian tree, (or at least the common assumption that many before and after Darwin believed to represent, albeit symbolically, how evolution preceded). For instance, Encyclopedia Britannica state the following regarding Woese’s theory: “[he] proposed a new model to replace the standard Darwinian theory of common descent—that all life on Earth evolved from a single cell or pre-cell. Woese proposed instead that various forms of life evolved independently from as many as several dozen ancestral pre-cells”.(61)  Furthermore, Woese (1998) states the following in another science paper entitled: The universal ancestor: The universal ancestor is not an entity, not a thing. It is a process characteristic of a particular evolutionary stage (62)   Returning to Encyclopedia Britannica, they also note that in Woese’s 2004 paper, he suggested that natural selection did not “become a factor in evolution until more complex life-forms evolved”.(61) I would tend to agree that natural selection does not operate during these earlier stages of evolution, but maybe as Woese is a microbiologist and doesn’t have to deal with natural selection dogs eating dogs and the like, he maybe is just assuming that natural selection might apply to other domains of life that he is not an expert in?   As I said in the previous chapter, once they discovered that genes only accounted for a tiny proportion of our entire genome and the so-called non-coding DNA – junk stuff was prolific, accounting for c. 98%, that’s when we started to really see this great web of life emerging for all levels of life, not just the microbial life forms as identified previously by people like Woese and Margulis. You know how we are told, over and over, again, by the mainstream glossy magazines that we share 98% of our genes with a chimp and split from them around 6 to 7 million years ago and all that? However, do bear in mind that this timing is based upon an assumption that molecular clocks run at the same speed and as it turns out: molecular clocks are not as reliable as we once thought they were. I’m not kidding. These issues are highlighted in an article in Nature (1987): The molecular clock runs more slowly in man than in apes and monkeys by Wen-Hsiung Li and Masako Tanimura for example (63), and as far as the similarity between chimps and humans, we are only talking about the sharing 97 or so, per cent of the mere 2% which code for proteins (genes) within our entire genome: not the rest of the 98% of the non-coding regions.   Now if we take the reasoning of shared genetic similarities relates to our shared ancestry and our genes run the evolutionary show, and we leave epigenetic regulation/expression of those genes out, then as we share c. 50% of our genes (coding for proteins) with a banana, then we must be related to bananas; or, does that make us half banana? Hopefully, you get my logic. We look nothing like bananas, but some of us do act like them.   Yes, it is the junk regions, as I said previously. This is the region which separates us not just from bananas and little worms that can share up to 75% of  genetic material with ourselves,  but which makes the difference between even superficially similar species, such as chimps and humans. Did you know that we have more junk than any of the other creatures and life-forms on the planet?  For instance, according to Wikipedia:   […], over 98% of the human genome is noncoding DNA, [ref] while only about 2% of a typical bacterial genome is noncoding DNA. (64)   Does that not tell you something about our less than straightforward commonly assumed common ancestry from a lowly little worm? I’ll go into all this in more depth in book three: So Long & thanks for all the Walking Fish, but in the meantime, we’ll have a look at what is similar in terms of genetics and what is hidden inside all this junk DNA that begins to reveal how evolution (in molecular terms) may have operated. In other words, if we didn’t descend directly from chimps by splitting into the human lineage 6/7 million years ago, how else could it have happened?   As it turns out biologists once thought that they would find that it was the genetic differences that would reveal the differences between different organisms. But instead, they found that very dissimilar animals for example, had surprisingly similar genes. Essentially, it is within the so-called junk regions that a very different evolutionary story can be read, either hidden in the genome or the epigenome. As I also alluded to in Chapter One, evolution has been rather rapid and profound at times and looks nothing like what we thought is should be when we began to look deeper into the molecular side of life. The web-like pattern is revealing our evolutionary history as the pattern of early life noted above by Woese and others is  just as applicable to Eukaryotic (multi-cellular plants and animals) level of life as it is the uni-cellular (single celled) life-forms. But before outlining the distinct kingdoms of life and the genetic interactions and exchanges that provide a vast amount of genetic novelty to create macro-evolutionary change, we will look briefly at an important mechanism that may provide an alternative to the simplistic common descent model of life.   You may recall my discussion of Hox genes in the previous chapter in relation to EVO-DEVO ideas about rather rapid and profound evolution (macro-evolution)? Hox genes work rather like master switches for entire groups of genes. They have the ability to turn genes on and off (activating gene expression and silencing genes at different combinations and timed sequences). This brings us back to some of those more contemporary EVO-DEVO alternatives to Darwinian Theory (natural selection and evolution via slow and gradual means), which in their saltationist aspects (leaps in evolutionary development) reflect back to the old Mutationist school of thought. I should point out, however, that these alternative ideas of evolution still assumed common ancestry to be basis of evolution, where their main issue was how common descent could achieve speciation to explain the diversity we see all around us in the natural world.  More recently, however, some EVO-DEVO thinking is beginning to change in this matter as evidence to support their ideas has been hiding in the genome all this time.   On a popular science website: Science Daily, with the heading:  Millions of DNA switches that power human genome’s operating system are discovered (2012) sourced from the University of Washington the summary explains the role and discovery of these Hox Gene complexes and how they were, until recently, hidden within the genome (within the so-called junk regions) in the following:   Genes make up only 2 percent of the human genome and are easy to spot, but the on/off switches controlling those genes were encrypted within the remaining 98 percent of the genome. Without these switches, called regulatory DNA, genes are inert […] (65)   In relation to these Hox gene switches, a paper by Gilbert S. F. in Developmental Biology (2000) entitled:Hox Genes: Descent with Modification (66), as the title implies, Gilbert views evolution, not so much as a result of organisms being literally and linearly descendant each from the last group, but rather that there is a shared common process/mechanism, a tool-kit, if you like, by which basic body-plans of organisms such as animals can be laid out (built) according to a specific set of instructions as Gilbert states: “This means that the enormous variation of morphological form in the animal kingdom is underlain by a common set of instructions”(66), These are literately what Hox Genes (master switches for other genes) do. They build body-parts according to instructions during the very early stages of development by activating entire sequences of gene switches to be turned on, or not, which give instructions to build specific proteins according to a particular template; in a specific sequence and spatial arrangement.   Another way of seeing this is to think about an embryonic chimp, which wouldn’t look that different to an embryonic human. Indeed, even at the early stages, after the cells differentiated, all vertebrate animals (including fish) have a similar layout of body plan; it is just that they develop in the end, to look extremely different to each other due to variations of genetic expression, which is environmentally driven – epigenesis. All vertebrate animals have a spine, a rib cage, internal organs laid out in a certain arrangement with a head, a brain, eyes, a mouth etc. The only difference is that a fish will form fins in the same region of the body to other vertebrates: non-fish vertebrates like you and me where the non-fish vertebrate go on to produce, after the budding stage (when limbs/wings and fins are being formed or differentiated), something approximating limbs and even digits, whereas, fish don’t. This is environmentally driven as fish do not presumably require digits like toes, claws and hands which would be quite useless in water.   The key point is that via epigenesis and epigenetic processes, all the fine-tuning of these template (Hox-built) body plans happen during the developmental stages when everything is still flexible and malleable, and it is the combination of genes that are activated, or not, which makes the incredible variations within the major class of animals known as vertebrate for example. Now, earlier evolutionary development may have followed a similar course to embryonic development and this is a key principal of EVO-DEVO thinking where, the study of development itself can give us insights into the evolutionary past. Interestingly, this idea of evolutionary stages being reflected in a developing organism was taken somewhat literally in the past. For example, the gills on an embryo (even humans) are not actually functional fish gills, but they look superficially like gills, so people thought we descended directly from walking fish etc. I know it may seem a ridiculous idea to us now, but people really used to believe in walking fish and even whales that once walking on land. OK, I’m being sarcastic as I know we still believe such things today.   Before the understanding the Hox complexes and their ability to activate or silence certain existing genes after laying out these similar body arrangements, the idea of common ancestry was reinforced by seeing the similarity in say: a fin or a foot or a wing (five rays) which, came to be known as homology (I deal with the origin of this idea in the last chapter of this book). It was believed that a change in bone-structure from a fin for example, gradually over time in the Darwinian model or, more rapidly in the Evolutionary Developmental biology model, became a foot, but it now seems that this is not the case. This idea of common ancestry and homology led to all of our endless searching for common links and transitional fossils. And it is this desperate and fruitless pursuit that has driven many a paleontologists’ crazy for all these decades. Saying that, perhaps it wasn’t exactly a thankless task, look at the fine fossil-record of fully formed creatures that lived and are still living (with a little variation) that we have today! Just to give you an insight into an alternative way of seeing evolution, in the same paper noted above: Hox Genes: Descent with Modification, Gilbert relates this interesting example of the evolutionary history of how the snake lost its legs, as identified from the Hox complexes:   One of the most radical alterations of the vertebrate body plan is seen in the snakes. Snakes evolved from lizards, and they appear to have lost their legs in a two-step process. Both paleontological and embryological evidence supports the view that snakes first lost their forelimbs and later lost their hindlimbs [refs] Fossil snakes with hindlimbs, but no forelimbs, have been found. Moreover, while the most derived snakes (such as vipers) are completely limbless, more primitive snakes (such as boas and pythons) have pelvic girdles and rudimentary femurs.The missing forelimbs can be explained by the Hox expression pattern in the anterior portion of the snake. In most vertebrates, the forelimb forms just anterior to the most anterior expression domain of Hoxc-6 [refs]. (66)   Gilbert continues after explaining how a snake lost its legs (and obviously it was via common descent from a lizard that had peculiarly short legs) that it may simply be that the set of genes for expressing legs (limbs) were switched off, and therefore, the reptile/lizard did not produce limbs/legs and he outlines the evolution of the Hox complex within various animals and their relative level of complexity in the following, which certainly points to the evolution of the Hox complex, as a mechanism for modification and this idea tallies much better with what we see in the fossil record as well.  Gilbert explains how the Hox complex have actually evolved, which of course has implications for how we may now reinvestigate the evolutionary record:   The number of Hox genes may play a role in permitting the evolution of complex structures. All invertebrates have a single Hox complex per haploid genome. In the most simple invertebrates—such as sponges—there appear to be only one or two Hox genes in this complex [ref] In the more complex invertebrates, such as insects, there are numerous Hox genes in this complex. [figs & refs].   By the time the earliest vertebrates (agnathan fishes) evolved, there were at least four Hox complexes. The transition from amphioxus to early fish is believed to be one of the major leaps in complexity during evolution [refs]. This transition involved the evolution of the head, the neural crest, new cell types (such as osteoblasts and odontoblasts), the brain, and the spinal cord. […] (66)   These genetic switches and their activation/non-activation are a highly orchestrated (non-random) process and timed in cascades of development once triggered according to the environmental cues (epigenesis). Now, the Hox genes don’t just randomly build anything according to ambient temperature (but perhaps they were more experimental earlier on in evolutionary history), no, Hox genes are highly conservative as are coding genes and these seem to be less adventurous these days keeping everything nice and stable.   In other words, Hox genes know what to build, have been doing it for a very long time and if it is not broken: don’t fix it comes to mind.  Furthermore, as I said above, all this major rewiring and re-engineering of body forms seems to have been most profound and rapid way back in our evolutionary past as the record shows. So no wonder nobody could get anything to change into anything else; not even bacteria, no matter how many generations they had been multiplying. This seems to be a safety mechanism (an insurance policy for nature) or, the fixity of the species, (silencing of genomes) where, the basic form is produced with not too many variations and then the adaptive variations of color, size, long-ears, short-ears, big snout, holes for nostrils, are just variations on these basic themes within a multitude of permutations according to environmental niche. This is epigenetic in nature and certainly does apply (micro-evolution) after the macro-evolutionary or developmental template is laid down genetically which is guided by other related environmentally induced processes of morphogenesis and epigenesis.   Epigenetic cues allow the cellular structures to read its immediate environment, particularly during the development stages of an organism (macro-evolution) and this can be extrapolated back in time to evolution itself, at least back to the time when life on planet earth was very malleable and much less defined, just like a developing embryo/fetus passes through large developmental stages of growth and complexity, so has evolution gone in such profound leaps of complexity in the past, thus, supporting one of the main tenants within EVO-DEVO evolutionary ideas.     Returning to the similarity of genes and genetics versus, what makes their expression different, is a very good documentary from NOVA which explains how genes make us very similar, but master switches for the expression of these genes is what makes the difference along with the fine-tuning or epigenetic regulation and change in the expression of genes once an organism has been essentially formed, is worth a view. It is embedded in one of my blogs entitled: Identical twins are genetically identical, but not epigenetically identical. From the Nova website under the article of the same name as the documentary: Ghost in Your Genes, Nipam Patel outlines the following regarding the role of Hox gene switches and the different stages of development under genetic mechanisms during the earliest part of development. I will discuss the epigenetic mechanism and its relationship to development in the following chapter in a little more detail, but in the meantime, here is a little more about how Hox genes actually operate:   GENE SWITCHES  […] All animals, including you and me, begin as a single egg. Once fertilized, that egg becomes many different kinds of cells. […]  Altogether, multicellular organisms like humans have thousands of differentiated cells. Each is optimized for use in the brain, the liver, the skin, and so on. Remarkably, the DNA inside all these cells is exactly the same. What makes the cells differ from one another is that different genes in that DNA are either turned on or off in each type of cell.   Take a typical cell, such as a red blood cell. Each gene within that cell has a coding region. This region encodes the information used to make a particular protein, such as the hemoglobin in the red blood cells seen here. (Hemoglobin shuttles oxygen to the tissues and carbon dioxide back out to the lungs—or gills, if you’re a fish.) But another region of the gene, called “regulatory DNA,” determines whether and when the gene will be expressed, or turned on, in a particular kind of cell. If you’re a brain cell, for instance, you wouldn’t want the genes encoding hemoglobin proteins to be transcribed. This precise transcribing of genes is handled by proteins known as transcription factors, which bind to the regulatory DNA, thereby generating instructions for the coding region.   One important class of transcription factors is encoded by the so-called homeotic, or Hox, genes. Found in all animals, Hox genes act to “regionalize” the body along the embryo’s anterior-to-posterior (head-to-tail) axis. In a fruit fly, for example, Hox genes lay out the various main body segments—the head, thorax, and abdomen. […] Amazingly, all animals, from fruit flies to mice to people, rely on the same basic Hox-gene complex. […] Hox genes must be expressed in a precise way and at precise times.(67)   The main take home point is that common descent from a fishy-like creature may not be required here as there is a whole adaptive set of genetic equipment that orchestrates gene expression in such a way as to make the creature fully adapted to its environment. So it doesn’t have to flap around wishfully hoping to eventually grow a foot from that fin or all the other complex equipment like breathing apparatus to make it onto land. No, Mother Nature is much more efficient and if a new environment opens up, well, there is no point in adapting the existing fish as they are happy where they are, but that doesn’t stop her upgrading their eggs providing they have enough rich coding and raw materials to build the necessary proteins to in turn build a different creature based upon the previous body template of an earlier version.   So we may share the genes with everything else on the planet, but how these genes are expressed, activated, not activated, their timing and degree of expression, are what sets us apart from bananas and chimps. Yes past hybridization events of complex animals certainly can be seen in the genome, and we know that hybrids can in one leap make an entirely new species with all that novel genetic material, so I challenge anyone to find that illusive Auntie Ide, or was it that long lost cousin Lucy, and place them on the right branch of Gibbons, twenty times removed. You see old Hugo De Vries (Mutationist school of evolution) was not that far off after all. Now, chimps definitely may be related in a much more convoluted way to us, via early hybridization episodes and I mean way back in the mists of time when mammals were still primitive, but as we didn’t hybridize with bananas, then you have to ask: how did everything on the planet end up sharing their genetic code?   Now the plot thickens as we return to where all this novel genetic material came from in the first place to make such great diversity of the kingdoms of life so that this genetic material could be expressed in a multitude of different ways depending upon environmental conditions. Again, we have to return to the so-called junk regions of the genome: the non-coding parts and follow the web-like structure of our evolutionary past, even if our genes are very similar to other organisms, we are beginning to see that it is how these are expressed that made the big difference.  Indeed, it is within the non-coding regions (junk areas) of the genome that much of our confirmation of past hybridization events has come from also and this is not unrelated to another factor in our evolution that has definitely played havoc with our neat ancestral tree. This is a very powerful mechanism for dramatic and fairly instantaneous change in the species, and is akin to hybridization, in that genetic exchange/sharing of genomic/genetic information can occur between species, except that these organisms don’t even need to look remotely like each other.   This important evolutionary mechanism is often referred to as HGT (horizontal gene transfer), and this is now a well established means of rapid and quite dramatic evolutionary change. HGT is distinct from VGT, (vertical gene transfer) which refers to the sexual route of genetic transfer, which I think most of us know about. HGT on the other hand is sort of like sex between microbes, but they don’t have the sophisticated equipment to do all this genetic transfer, so they take the direct route and via chemical signaling for example, one bacteria can attract another and boom, they physically join, in some instances, or just pass on their bits of genes and ride off into the sunset never to be seen again.     Can you imagine, hybridization and horizontal gene transfer has done to our family tree?  We are living proof of it. This HGT is present in our evolutionary history as well as everything on the planet. Remember that Eukaryote cellular life is all the animals and plants, where bacteria, fungi and slime-mold for example are within kingdoms of archaea etc, so take for example the following article on this subject entitled: Horizontal gene acquisitions by eukaryotes as drivers of adaptive evolution by Schönknecht, G., et al (2013)   In contrast to vertical gene transfer from parent to offspring, horizontal (or lateral) gene transfer moves genetic information between different species. Bacteria and archaea often adapt through horizontal gene transfer. Recent analyses indicate that eukaryotic genomes, too, have acquired numerous genes via horizontal transfer from prokaryotes and other lineages. Based on this we raise the hypothesis that horizontally acquired genes may have contributed more to adaptive evolution of eukaryotes than previously assumed. Current candidate sets of horizontally acquired eukaryotic genes may just be the tip of an iceberg (68)   Here is an amusing article relating to HGT between entirely different classes of the animal kingdom, which, although it may be doesn’t tell us why Hox genes switched off the limb making proteins in snakes and made the poor little thing crawl about on its belly, but it does give you an idea of why we can’t really now say that mammals descended or split from lizards/reptiles from a suspiciously mammalian-like primitive creature which, we just happened to call reptilian-like, because it suited our classification system.  This story is on the Mother Jones website and demonstrates HGT in real life, in an article entitled: Cows Are 25 Percent Snake by Erika Eichelberger (2013) which states the following: Oh, just to remind you, this article and all HGT events completely blow Weismann out of the water. You vaguely know how DNA works, right? You get it from your parents. Well, hold onto your britches, because scientists from down under are about to turn your world upside down. study by Australia’s Adelaide and Flinders Universities and the South Australian Museumhas found that in complex organisms, DNA is not only transferred from a parent to its offspring like your science book told you, but can also be “laterally” transferred between species. The research, published in the peer-reviewed Proceedings of the National Academy of Sciences in the US, involved comparing dozens of DNA sequences from different species. It found that cows inherited up to a quarter their genes from reptiles […]   […] “[I]n higher organisms, vertebrates, mammals and so on we tend to believe that later or horizontal transfer of genetic material just doesn’t really happen,” Prof. David Adelson, study lead and head of Molecular and Biomedical Science at the University of Adeliade told Australian ABC News. “But what we’ve shown is that there are DNA segments…called jumping genes…which are able to jump between species.” The similar DNA sequence that the two species share is able to “cut and paste itself within the genome,” and thus replicate itself and jump to another species, Adelson explains. (69)   Now returning to the implications of earlier evolutionary life and how the exchange of genetic information has been ongoing and therefore, nigh impossible to separate any organism’s evolutionary history based upon their shared coding genes, which are expressed differently anyway depending upon their evolutionary route. Furthermore, as it is the non-coding (so-called junk) regions of the genome that show the real complexity of evolutionary diversity and as humans have more than any other creature on the planet (remember free-living bacteria have hardly any junk DNA), does this not tell us something regarding our rather convoluted path to our present form?   So how related to bacteria and microbes are we? Who can tell? So-called simpler organisms like bacteria are mainly made up of coding genes and very little junk. Yet, earlier life may have been incredibly diverse and actually stimulated much more complex forms depending upon what shared its genome with what. For example, the manner in which microbial life pass on their genetic information is exemplified in the research and theory by Lynn Margulis, (as quoted a number of times thus far) who developed a theory of the origin of earlier life that demonstrate that symbiotic relationships and whole genome exchange (merging of distinct organisms into a single one) were key factors in further complexity of later evolutionary life.   In Margulis’ article, entitled: The Phylogenetic Tree Topples (2006) (57) and an another publication: Acquiring Genomes: A Theory of the Origins of the Species, as also alluded to earlier, microbial life is described as having evolved by fairly opportunistic and unusual methods, such as: genome stealing, symbiosis and entire microbial worlds merging to become whole new kingdoms/classes of life may begin to explain the distinct origins and slightly later web-like pattern of the earlier evolutionary record as  noted at the beginning of this chapter. This merging of whole genomes is essentially HGT (horizontal gene transfer) on steroids.   It just occurred to me that you might be wondering at this stage what does Mr. Dawkins think of all of this and Lynn Margulis’ research in particular. Surprisingly, Dawkins had great respect for her research as a biologist, although I don’t think he is fully aware of the implications of this and similar research for his over-zealous support of the Neo-Darwinian doctrine which is entirely founded upon the common descent with modification model of evolution, which research such as Margulis’ entirely undermines. I thought it interesting what he had to say about her particular theory of Origins of the Species via acquired genomes:   I greatly admire Lynn Margulis’s sheer courage and stamina … This is one of the great achievements of twentieth-century evolutionary biology, and I greatly admire her. (Excerpt from the Third Culture: Beyond the Scientific Revolution by John Brockman 1995) (70)   So, if you thought that all this body-building according to specific templates, genetic exchange via hybridization, horizontal gene transfer and symbiosis was weird, wait until you hear what happens, epigenetically speaking, when this novel genetic mixing between organisms and across species boundaries (critical for macro-evolutionary change) is modified in different ways to adapt and fine tune any species to its environment, but it is not, as you can probably imagine, by Darwinian means. The physical adaptation of a species to its environment can and does occur rather rapidly, profoundly and operate on an organism shortly after the Hox genes have essentially laid out the body plan of an animal for instance. Epigenetics, combined with the EVO-DEVO ideas of Saltationist type evolution in the past and reflected in the developing stages of an embryo, are becoming dynamic theories for explaining many aspects of evolutionary complexity as indicated in the previous chapter.   One of the main mechanisms responsible for much of the evolutionary adaptations according to the environment of any given organism is via transposable elements (TEs), a process that is intimately linked to epigenetics. These TEs are sometimes referred to as jumping genes and they have the ability to cut and paste/rearrange and generally move a lot of genetic material around to different locations in the genome. They have the ability to replicate in every cell, a bit like a virus, but this is more a viral mechanism used as a delivery system for little adaptive programs rather than the type of viruses/malware you can end up with on your hard-drive. Now, there’s a novel thought. Imagine if they could input a new adaptive program/app to spread throughout your computer in a similar way to reprogram the virus to neutralize it or make it work for the benefit of your computer, continually upgrading as required. That is not entirely, it would appear, unlike how life has evolved on our planet. This is why perhaps, humans have so much functionless (junk) DNA, as we have the greatest wastelands of TEs strewn across vast reaches of our genome that are like a fossilized record of these rearrangements of odds and ends of DNA that are not as essential to our adaptability as they were in the past. Furthermore, when these rearrangements of genetic material did occur, apparently it was major and fast.   According to KeithOliver & Wayne Greene in an article in Australasian Science (2009) entitled: Jumping genes drive evolution, in which they essentially vindicate Stephen Jay Gould & Niles Eldredge’s Punctuated Equilibrium hypothesis of occasional leaps in the fossil record, they state the following:   Orthodox evolutionary theory does not tally with the fossil record, but a new school of thought points towards ’jumping genes‘ as essential agents of periodic changes in the rate of evolution […] Punctuated equilibrium is rapid evolution followed by slow evolution, or a stoppage in evolution, as is observed in the fossil record. This can be explained by the fact that jumping gene activity does not occur at a low and uniform rate over time. Instead, it sporadically occurs in sudden bursts resulting in rapid evolution, followed by decreasing activity and slowing evolution. These rapid bursts of evolution can happen when a new type of jumping gene is suddenly transferred into a lineage from some other lineage, or when a new type of jumping gene naturally emerges from within a genome. Jumping gene activity (71)   Essentially, these mobile genetic elements use the same system of delivery to viruses and they have gotten pretty clever over millennia at reprogramming your genome or should I say: epigenome, as much of this activity has been hidden deep within the genome all this time and lots of it was hiding in the junk regions. Now if that isn’t going to make a mess of our nice ordered model of evolution, I don’t know what is? Jumping genes can be triggered into action within the genome by a dramatic change in the environment for example. Now I can think of several really stressful environmental changes that occurred throughout evolutionary history that just might have stimulated serious rearrangement, cutting, splicing, dicing and calling into action vast amounts of novel DNA. Who needs population genetics when you have this type of process going on?   It was the geneticist and Nobel Laureate Barbara McClintock who introduced the idea of jumping genes from her experiments carried out back in 40s/50s, which were later confirmed by independent experimentations in the 60s and 70s. Jumping genes or mobile genetic elements that were triggered into action by environmental stress were shown to cause (dramatic) changes that were made to the organisms, (plants) and these changes were passed on to future generations without showing up on the genes themselves. It was the genes that were being triggered or suppressed, the expression of genes, the epigenome which was carrying these markers (changes) that we now understand is epigenetic in nature.   But as you can imagine, McClintock didn’t immediately get the recognition she deserved, and indeed, she was an old woman by the time she received her award. And as far as I know, she was not nominated for any Darwin awards either. Basically, jumping genes were ignored, as was McClintock herself. The genes were considered to be ‘parasitic’ or ’junk‘ DNA; so they say, but science is science, I don’t think they were ready for Lamarck to return just yet. Indeed, they are not ready now, but, they have no choice as the evidence from deeper understandings of the genome and molecular systems is producing such overwhelming support. The epigenetic aspect of these jumping genetics and their control of these mobile elements (jumping genes) cannot be ignored any longer. And in many ways they are being recognized as being of evolutionary importance, although, as even the scientists who are beginning to recognize this are still of the opinion that evolution occurred via direct common ancestry from a single or a few similar type amoeba type cellular life, I don’t think they really are seeing the bigger implications of all of this, just yet.   Several science papers are beginning to see these fundamental implications of mechanisms such as TEs (transposable elements) or jumping genes and their ability to remodel genomes and therefore a serious driver of evolutionary change. For instance, regarding epigenetics and jumping genes as an evolutionary mechanism in the science journal Gene, by Rita Rebolloa et al (2010) state the following in their article entitled: Jumping genes and epigenetics: Towards new species Transposable elements (TEs) are responsible for rapid genome remodelling by the creation of new regulatory gene networks and chromosome restructuring. TEs are often regulated by the host through epigenetic systems, but environmental changes can lead to physiological and, therefore, epigenetic stress, which disrupt the tight control of TEs. The resulting TE mobilization drives genome restructuring that may sometimes provide the host with an innovative genetic escape route. We suggest that macroevolution and speciation might therefore originate when the host relaxes its epigenetic control of TEs. (72)   In another science journal (2002) entitled: Transposable Elements and Eukaryotic Complexity by Nathan J. Bowen and I. King Jordan outline the importance of TEs (Jumping genes) make up a very large part of our genome and appear to have played a major role in evolution (we are a collection of complex cells like plants and animals known as Eukaryotes) Eukaryotic transposable elements are ubiquitous and widespread mobile genetic entities. These elements often make up a substantial fraction of the host genomes in which they reside. For example, approximately 1/2 of the human genome was recently shown to consist of transposable element sequences. There is a growing body of evidence that demonstrates that transposable elements have been major players in genome evolution. A sample of this evidence is reviewed here with an emphasis on the role that transposable elements may have played in driving the evolution of eukaryotic complexity. A number of specific scenarios are presented that implicate transposable elements in the evolution of the complex molecular and cellular machinery that are characteristic of the eukaryotic domain of life.(73)   Here is an example of how important transposable elements are seen in terms of larger evolutionary adaptations and how jumping genes are not confined to the world of plants, as one science paper by John McDonald, professor in the department of genetics at the University of Georgia, in a science paper entitled: Transposable Elements May Have Had A Major Role In The Evolution Of Higher Organisms (1998) shows:     It now appears that at least some transposable elements may be essential to the organisms in which they reside. Even more interesting is the growing likelihood that transposable elements have played an essential role in the evolution of higher organisms, including humans. (74)   Well, there you go, jumping genes have been essential, seemingly, in our evolution as well. So those Darwinists can no longer say that all this gene swapping and symbiosis belongs to the world of micro-organisms and doesn’t apply to the rest of life. That’s what they used to believe you know. They thought, it was OK that Darwinian evolution didn’t apply to the earlier microbial life-forms, as they simply ignored the fact that it was equally applicable to humans and higher domains of life. So now you might understand why I don’t believe, as others have also pointed out, that natural selection can actually be applied to evolution at the macro-level as it doesn’t apply to the micro-level of life. Why would it simply change strategy and operate in another way entirely?     Thus, as this process is neither, random or gradual and we do not population models or mutant genes to be selected to create macro-evolution (I’m not certain with all this epigenetic stuff that naturally selected mutant genes can create even micro-evolution at this stage), nor is it gene driven, even the activation of Hox genes is ultimately orchestrated by environmental factors, and it seems that common ancestry isn’t even the model of evolution we should be following: one has to ask, is there actually any evidence that lends support to the Neo-Darwinian synthesis? I am trying hard to think of something, maybe you can think of something, and you would let me know, as long as you have evidence to back it up of course.     Epigenetics, morphogenesis, epigenesis (Hox gene evolution) and TEs/jumping genes, to name but a few mechanisms, are all interactive dynamics that when combined with the many ways of gaining genetic novelty such as: hybridization, symbioses and HGT, present serious drivers of evolution and offer a much more dynamic alternative to population genetics, natural selection and indeed, our commonly held assumption of simplistic common descent.     It seems to me that what is emerging from these more recent studies, which are invariably confirming older and much aligned research, that evolution is not a game of chance and survival of the fittest, but a driven system obeying natural universal laws which I deal with in the final book of this series. It appears that life is self-organized/self-evolved and it has gotten pretty efficient and smart over these past few billion years, once it figured out which way it was going. It is about symbiotic and inter-dependent ecological systems and organisms within these systems. Dare I say: a co-operative system of mutually supporting life-forms?  How un-Malthusian/Darwinian indeed!     I hope you can now see why the base of the ancestral tree of life, its presumed growth pattern and indeed the tree itself, are all being called into question. Yes, it is altogether much more complex than any of us could have imagined. All those jumping genes springing into action when a stressed is induced via a signal is received from the environment and our genome now shows that these events have occurred many times in our evolutionary past. Professor James Shapiro puts all these different, but interrelated ways, of gaining genetic novelty and the reprogramming mechanisms involved in creating large, rapid and non-random change in the species and how this demonstrates processes, independent of natural selection, in the following 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. (75)     So we have to ask ourselves, are all this molecular stuff new and how were the poor old Neo-Darwinists to know?  Well, as you might have gathered thus far, they could have gone with some of the existing theories that are actually being borne out in labs today, but they refused to take any of it on board and look where that got them? As you now know, this stuff isn’t that new. Yes, certainly our understanding of it has just got more sophisticated because of breakthroughs in molecular processes thanks to the work of Shapiro and many, many others in more recent times, but it is also important to keep in mind that many experiments were not even carried out because of the restricting nature of the Neo-Darwinian mindset that meant that resources were not available to many scientists to investigate alternative mechanisms and indeed, many scientists did not even think to ask pertinent questions in their research, because they were under the illusion that these questions were resolved.   Just before finishing this part of the discussion, I would just like to remind you of one person who actually proposed independent origins of life as a viable process of evolution. Lamarck proposed such an idea back in the mists of time. Although he did believe that humans descended ultimately from apes etc which, I will outline further on in more detail, he proposed an idea that certain domains of life had independent origins and had reached a level of complexity within their own kind. This reflects some of what we are coming to understand about the origins of distinct pre-cellular life and the fact that the ancestor may not actually be an entity but a process as suggested by Woese above. Lamarck was thoroughly acquainted with anatomy and he stressed the main divisions of complexity of formation and segmentation (fundamentally similar body plans) between vertebrates and non-vertebrate life. Now in the relation to the Hox gene switches actually having evolved in complexity within these major divisions of life as pointed out by Gilbert in his paper: Hox Genes: Descent with Modification. (2000), I feel that this aspect of Lamarck’s theory should be looked at again in this light. It seems that Lamarck was at least thinking along the right lines.     All in all, it seems that we may just need to reconsider our current model of common descent with modification. Indeed, I think we need to go back to the drawing board and think again. Furthermore, we should look again at the fossil record in the light of these new and not so new findings and ideas of how evolution may have actually unfolded and take it from there. Indeed, Shapiro in his book: Evolution: A View from the 21st Century, proposes based upon research by several scholars, a correlation between the past evolutionary upheavals ending in mass extinction episodes, which invariably show a diverse radiation of novel forms of species shortly thereafter, is explicable by these molecular processes kicking into action and adapting existing forms to new and novel environmental conditions (49). This certainly would make a great deal more sense of what we actually see in the fossil record and confirm a much more radical molecular interpretation of evolution.  Again Lamarck actually proposed something similar back in the day and the more I look at Lamarck’s evolutionary theory, the more it tells me that he was simply following the evidence and therefore was actually gaining good scientific insights into evolution that have unfortunately taken over 200 years to resurface.     Finally, the old Darwinian family tree is beginning to strain irrevocable under the weight of all of this new genetic, epigenetic and molecular evidence that is beginning to vindicate and reinstatie older principals that were always valid and, I believe, much more dynamic alternatives to the Darwinian doctrine. Indeed, I think the old tree is about to give entirely – Watch Out!   TIMBER!   Chapter two (57). Margulis, L (2006) “The Phylogenetic Tree Topples” in  American Scientist, (May-June 2006) Volume 94, Number 3, pg.1,   https://www.americanscientist.org/issues/pub/2006/3/the-phylogenetic-tree-topples   (58). Shi V. Liu   A Fundamentally New Perspective on the Origin and Evolution of Life  Eagle Institute of Molecular Medicine  Apex, NC 27502, USA http://arxiv.org/ftp/arxiv/papers/0811/0811.3653.pdf   (59). W. Ford Doolittle* and Eric Bapteste Pattern pluralism and the Tree of Life hypothesis,  Proc Natl Acad Sci U S A. Feb 13, 2007; 104(7): 2043–2049. Published online Jan 29, 2007. http://www.pnas.org/content/104/7/2043.abstract doi:  10.1073/pnas.0610699104 PMCID: PMC1892968   (60). M. Gordon et al., (1999) “The Concept of Monophyly: A Speculative Essay,” Biology and Philosophy, p. 331  http://link.springer.com/article/10.1023/A:1006535524246    (61). They also note that Woese in a more recent paper did not believe that natural selection became “a factor in evolution until more complex life-forms evolved”. http://www.britannica.com/EBchecked/topic/915011/Carl-R-WoeseI     (62).“The universal ancestor” by Carl R. Woese, which appeared in number 12, June 9, 1998, of Proc. Natl. Acad. Sci. USA (95, 6854–6859) http://www.ncbi.nlm.nih.gov/pmc/articles/PMC22660/   (63)  Nature 326, 93 – 96 (05 March 1987); doi:10.1038/326093a0 The molecular clock runs more slowly in man than in apes and monkeys WEN-HSIUNG LI & MASAKO TANIMURA http://www.nature.com/nature/journal/v326/n6108/abs/326093a0.html   (64) http://en.wikipedia.org/wiki/Noncoding_DNA   (65)http://www.sciencedaily.com/releases/2012/09/120905135326.htm Millions of DNA switches that power human genome’s operating system are discovered September 5, 2012 Source: University of Washington   (66)Gilbert SF. Developmental Biology. 6th edition. Sunderland (MA): Sinauer Associates; 2000. Hox Genes: Descent with Modification.  Available from: http://www.ncbi.nlm.nih.gov/books/NBK9978/   (67) Nipam Patel (1996-2007) professor in the Departments of Molecular and Cell Biology and Integrative Biology at UC. PBS Online by WGBH http://www.pbs.org/wgbh/nova/genes/fate-nf.html   (68)  Horizontal gene acquisitions by eukaryotes as drivers of adaptive evolution Gerald Schönknecht,A ndreas P. M. Weber, Martin J. Lercher Article first published online: 13 NOV 2013 DOI: 10.1002/bies.201300095 http://onlinelibrary.wiley.com/doi/10.1002/bies.201300095/abstract;jsessionid=2B28066CC31570B158F2D72C1550CE91.f01t03 http://onlinelibrary.wiley.com/doi/10.1002/bies.201300095/pdf    (69) http://www.motherjones.com/blue-marble/2013/01/dna-cows-snakes-adelaide-flinders-study Study: Cows Are 25 Percent Snake, by Erika Eichelberger Thu Jan. 3, 2013  ://www.motherjones.com/blue-marble/2013/01/dna-cows-snakes-adelaide-flinders-study   (70)  “Gaia Is a Tough Bitch” Excerpted from The Third Culture: Beyond the Scientific Revolution by John Brockman (Simon & Schuster, 1995) . Copyright © 1995 by John Brockman. http://www.edge.org/documents/ThirdCulture/n-Ch.7.html   (71) Keith Oliver & Wayne Greene in an article in Australasian Science (September issue 2009) entitled: Jumping genes drive evolution, http://researchrepository.murdoch.edu.au/6496/1/jumping_genes.pdf http://www.sciencedirect.com/science/article/pii/S0378111910000296 (72). Rita Rebollo, Béatrice Horard, Benjamin Hubert, Cristina Vieira, Jumping genes and epigenetics: Towards new species, Gene, Volume 454, Issues 1–2, 1 April 2010, Pages 1-7, ISSN 0378-1119, http://dx.doi.org/10.1016/j.gene.2010.01.003. (http://www.sciencedirect.com/science/article/pii/S0378111910000296)   (73)Curr. Issues Mol. Biol. (2002) 4: 65-76. Transposable Elements and Eukaryotic Complexity 65,  2002 Caister Academic Press, Transposable Elements, and the Evolution of Eukaryotic Complexity, Nathan J. Bowen and I. King Jordan http://www.horizonpress.com/cimb/v/v4/07.pdf   (74)http://www.eurekalert.org/pub_releases/1998-02/UoG-TEMH-090298.php Public release date: 9-Feb-1998,  John McDonald University of Georgia, Transposable Elements May Have Had A Major Role In The Evolution Of Higher Organisms   (75)Shapiro, J.A (2012) “Does Natural Selection Really Explain What Makes Evolution Succeed?” Posted: (08/12/2012)           http://www.huffingtonpost.com/james-a-shapiro/does-natural-selection-evolution_b_1769524.html

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