Part Two: If it didn’t happen by Neo-Darwinian means, how did evolution occur?

WEEKLEY SERIES:  If it didn’t happen by Neo-Darwinian means, how did evolution occur?

the tree of life probably had many roots...
the tree of life probably had many roots…

Part Two

The Great World Wide Web (www.dot) of life

 Hybrid Speciation model of evolution & Genome remodeling via jumping genes

 (A review of the models presented in last week’s article in the light of the above)

I will start this discussion with one of several historically notable theories of evolutionary change and speciation (change in the species to bring about a new form), namely, the research of Hugo De Vries (a Dutch Botanist and early geneticist) whose Mutation model of evolution (not as the meaning of genetic mutation we use today) was based upon years of experimentation with hybrid plant species, and observations of:  “…, spontaneous alterations of genes that yield large modifications of the organism and give rise to new species. According to de Vries, a new species originates suddenly, produced by the existing one without any visible preparation and without transition”. (Ayala and Fitch 1997, 7692). http://www.pnas.org/content/94/15/7691.full.pdf

In a nut shell: De Vries’ theory and several other distinctly different theories, rejected gradualism and the idea of selection. For De Vries, gradualism was certainly not the way nature produced speces, as borne out by his years of studies and experiments. Furthermore, he argued that natural selection did not have the power to produce new and novel variations and in some cases was actually detrimental to evolving a new species. This is clearly documented in the review of De Vries’ Mutation Theory in the journal SCIENCE dating back to 1910:

It has long been recognized that natural selection really explains, not the origin of species, nor even the origin of adaptations, but the elimination of the unfit, and the persistence of adaptations; the fact that characters, both adaptive and non-adaptive, specific or not specific, must exist before they can be selected was previously well nigh lost sight of. The mutation-theory, then, seeks to account for “the origin of specific characters” (p. 211). In the second place, “Spontaneous variations are the facts on which this explanation is based” (p. 45), or, “We may express the essence of the mutation theory in the words: ‘Species have arisen after the manner of so-called spontaneous variations'” (p. 165). This marks the fundamental distinction between Darwinism and de Vriesism. … from the standpoint of the theory of mutation it is clear that the role played by natural selection in the origin of species is a destructive, and not a constructive one.” … Mutations are characterized first, by being entirely new features, “In contradistinction to fluctuating variations which are merely of a plus or minus character (p. 213); second, by the abruptness with which they appear, and third, by being transmitted by inheritance’ without selection. They arise suddenly and’ without any obvious cause; they increase and multiply because the new characters are inherited”

                                                    ——   ‘Science’, (May 13th 1910, p. 741)

http://www.jstor.org/stable/pdf/1634773.pdf?acceptTC=true

Our modern synthesis has consistently rejected leaps in complexity as a real fact of the fossil record. And Darwin’s species problem (how one species changes into another), remains unresolved as noted in ‘Resynthesizing Evolutionary and Developmental Biology’:

“The origin of species — Darwin’s problem — remains unsolved”

–  Gilbert, Opitz, and Raff (1996, 361)

 http://www.evolbiol.ru/large_files/gilbert.pdf

Even after the well-founded rejections of gradualism and selection by De Vries and other geneticists, botanists, embryologists and via experimental work in general around the turn of the 20th century, the modern synthesis eventually came to reject all things non-selection-based and certainly would not tolerate anything that suggested leaps of speciation, or anything that was environmentally determined (Lamarckian type acquired characteristics known as acquired characteristics and becoming widely accepted in modern science under the broad label of epigenetics – meaning to operate above the genes).  This latter rejection of Lamarckian evolutionary theory dating back to over two-hundred years and supported increasingly by Charles Darwin himself has been dealt with in some detail in a book relating to this alternative evolutionary series. It is entitled: ‘Lamarck and the Sad Tale of the Blind Cave-Fish’. https://www.smashwords.com/books/view/524805

(paperback version link) http://www.amazon.com/Lamarck-And-Tale-Blind-Cave-Fish/dp/178280465XI

I said in last week’s article that I would deal with epigenetic type evolution along with the topic now under discussion. However, I will discuss epigenetic evolution in more depth in next week’s article as this present discussion turned out to be a bit more extensive than originally anticipated.

Returning to De Vries, genetic mutations came to mean something entirely different to what De Vries had originally proposed. The modern synthesis now had a problem. If they had excluded any other means of changing a species, how was a species supposed to change? They did some experiments of genetic reshuffling of existing gene-pools of the same species and proposed that the only way to create genetic novelty (not employing De Vries’ ideas or any others who had demonstrate real, rapid and profound emergence of a new species) was to mathematically model the assumed rate of genetic mutations (mistakes in the copying process as genes are passed along the ancestral line) passed between populations, particularly those isolated and recombined gene-pools later down the line, and even though nobody ever seen a species change or become anything other than it was before (apart from some superficial type colour or variegated changes), they extrapolated this to all of evolution and based upon the assumption of direct ancestral relationships via linear descent from a common ancestor, attempted to demonstrate when one species gave rise to another (branching lineages and ancestral missing links were feverishly searched for) and calculated the timing of such assumed splits based upon the rate of genetic mutation (the molecular clock assumed to tick at the same rate for all species throughout evolution). Unfortunately, our ancestors may not be as common or related, at least not in the way we think and the genetic mutation (molecular) clock doesn’t appear to work that well:

DNA mutation clock proves tough to set

Geneticists meet to work out why the rate of change in the genome is so hard to pin down.

 In the past six years, more-direct measurements using ‘next-generation’ DNA sequencing have come up with quite different estimates. A number of studies have compared entire genomes of parents and their children — and calculated a mutation rate that consistently comes to about half that of the last-common-ancestor method.

A slower molecular clock worked well to harmonize genetic and archaeological estimates for dates of key events in human evolution, such as migrations out of Africa and around the rest of the world1. But calculations using the slow clock gave nonsensical results when extended further back in time — positing, for example, that the most recent common ancestor of apes and monkeys could have encountered dinosaurs. Reluctant to abandon the older numbers completely, many researchers have started hedging their bets in papers, presenting multiple dates for evolutionary events depending on whether mutation is assumed to be fast, slow or somewhere in between. (Callaway in Nature 10th March 2015)

http://www.nature.com/news/dna-mutation-clock-proves-tough-to-set-1.17079

 Furthermore, mutations don’t appear to bring about a new species, just deformed or dead things and population modelling used by the Neo-Darwinists has been described as numerology as seen in the following quotes by  LYNN MARGULIS

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

— (Teresi 2011, 68) ‘Discover Magazine’ April edition 

http://discovermagazine.com/2011/apr/16-interview-lynn-margulis-not-controversial-right

Mutations, in summary, tend to induce sickness, death, or deficiencies. No evidence in the vast literature of heredity changes shows unambiguous evidence that random mutation itself, even with geographical isolation of populations, leads to speciation.

 Margulis & Sagan (2008, 29) Acquiring Genomes: A Theory of the Origins of the Species  

http://books.google.ie/books?id=DS-VehE00ncC&q=Mutations%2C+in+summary%2C+tend+to+induce+sickness%2C+death#v=snippet&q=Mutations%2C%20in%20summary%2C%20tend%20to%20induce%20sickness%2C%20death&f=false

When evolutionary biologists use computer modeling to find out how many mutations you need to get from one species to another, it’s not mathematics—it’s numerology.

Teresi (2011, 71) ‘Discover Magazine’ April edition 

http://discovermagazine.com/2011/apr/16-interview-lynn-margulis-not-controversial-right

 

And then there is the problem of getting a species to change into another one and the fundamental problem with the ‘origins’ model:

Evolution of Drug-Resistant Bacteria

Bacteria in nature do evolve resistance to antibiotics faster than mutation and selection allow…

Campbell and Schopf (1994, 95)

https://books.google.ie/books?id=ve38UmPnfO0C&pg=PA95&lpg=PA95&dq=It+turns+out+that+bacteria+adapt+to+antibiotics+more+quickly+than+can+be+accounted+for+by+mutations&source=bl&ots=sLXsSOIxaw&sig=vYcZ0uLReQ2H9iBWWhcOCzrAZek&hl=en&sa=X&ei=Y_cSVanMNdPy7AaV_IC

Scant search for the Maker … (Review by Emeritus Professor of bacteriology  of paleontologist, Niles Eldredge book)

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

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

Linton (2001, 29)

 http://www.timeshighereducation.co.uk/books/scant-search-for-the-maker/159282.article

‘A FUNDAMENTALLY NEW PERSPECTIVE ON THE ORIGIN AND EVOLUTION’

      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…

                                                      — Liu (2008) Abstract

http://arxiv.org/ftp/arxiv/papers/0811/0811.3653.pdf

‘PATTERN PLURALISM AND THE TREE OF LIFE HYPOTHESIS’ 

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… 

       — Doolittle and Bapteste (2007) Abstract

http://www.ncbi.nlm.nih.gov/pubmed/17261804

‘THE CONCEPT OF MONOPHYLY: A SPECULATIVE ESSAY’

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. 

                                              — Gordon (1999, 331) Abstract

http://link.springer.com/article/10.1023%2FA%3A1006535524246#page-1

– Carl Woese –

‘THE UNIVERSAL ANCESTOR’

The universal ancestor is not an entity, not a thing. 

It is a process characteristic of a particular evolutionary stage. 

                                          — Woese (1998) Conclusion

http://www.pnas.org/content/95/12/6854.full

In other words, the species problem, the seeming gaps in the fossil record and the sudden eruption of a new species with no apparent transitional forms, remains the same and never went away.  As noted above, De Vries and others always had problems with the Darwinian concept of gradualism and selection,  and indeed, even within the ranks of true Darwinians (adhering to Darwin’s original concepts that are perceived as less rigid than the gene-centred model upheld by AKA: Richard Dawkins), there has been some controversy regarding gradualism and even the strictest form of selection (see quote books for issues with the entire modern synthesis and natural selection and gradualism in particular). For instance, attempts to address the obvious gaps and lack of transitional forms and sudden eruption of new and novel forms of species within the fossil record, led to a theory based around stasis (meaning stability, presumably as an attempt to keep it broadly within the Darwinian tradition) with the occasionally leaps (punctuated parts) proposed in the 1970s Gould and Eldredge known as the punctuated equilibria model of evolution where environmental factors were considered important to these occasional punctuated parts. This was and still is, a seriously tame version of De Vriesian evolution, but just to give you an insight into the manner in which this was considered as part of the Neo-Darwinian synthesis, which it was, but it was referred to by Richard Dawkins as “a minor wrinkle on the surface of the neo-Darwinian theory” (Dawkins 1986, 254),

The theory of punctuated equilibrium will come to be seen in proportion, as an interesting but minor wrinkle on the surface of neo-Darwinian theory. It certainly provides no basis for any ‘lapse in neo-Darwinian morale’, and no basis whatever for Gould to claim that the synthetic theory (another name for neo-Darwinism) ‘is effectively dead’. It is as if the discovery that the Earth is not a perfect sphere but a slightly flattened spheroid were given banner treatment
under the headline: COPERNICUS WRONG. FLAT EARTH THEORY VINDICATED.

–   (Dawkins 1986, 254-255) ‘The Blind Watchmaker: Why the Evidence of Evolution Reveals a Universe without Design’

http://bikerman.co.uk/images/audio/science/Blindwatchmaker/files/basic-html/page255.html

In essence of De Vries’ experimental research and observations for its time, this concept gains support from not only hybrids studies which I will outline below, but also is supported in principle by more recent evidence as seen in more modern re-evaluations of the evidence for quantum leaps of complete and complex forms due to a much greater degree of genetic novelty being exchanged across all domain of life as proposed by Koonin (2007, Abstract) http://www.ncbi.nlm.nih.gov/pubmed/17708768, where, these large evolutionary leaps of whole fundamental forms are considerably more punctuated and more rapid and less rare than the now commonly accepted punctuated equilibria model.

This concept of leaping evolutionary complexity is much better supported than the selection or gradualistic model and goes well beyond even hybridisation as a means of speciation, even if De Vries did not fully understand that it was hybridisation that caused such large and rapid changes in the descendants of his experimental plants, his concept of large, rapid and radical changes (mutations) was what he observed and therefore what formed his theory. This is the basis of all good science. The article below outlines how De Vries came to inadvertently discover hybridisation as a means of speciation:

In the history of evolutionary biology, Hugo de Vries is known as a proponent of the mutation theory of evolution, in which new species are believed to arise by single mutational events … This theory is based on the breeding experiment he conducted for 13 years with the evening primrose Oenothera lamarckiana and its mutant descendants. In this experiment, he discovered a number of phenotypic variants, which bred true or segregated variant types in addition to the parental type.

http://gbe.oxfordjournals.org/content/3/812.full

Although De Vries did not fully understand why these mutations were occurring, the important thing is that he observed them. We know now that it was due to chromosomes “… he unknowingly found the importance of polyploidy and chromosomal rearrangements in plant speciation”. http://gbe.oxfordjournals.org/content/3/812.full.

The concept of hybridisation is not seriously considered within the Neo-Darwinian synthesis as one means of speciation and not thought to be of any great significant in the context of natural selection by Darwin as discussed in a recent science paper highlighting the influence of one of the leading lights of our modern synthesis: Ernst Mayr. As the paper outlines:

Mayr … rejected any idea that hybridization might contribute to adaptive evolution, especially hybrid speciation. Furthermore, because in 1942 he was concerned only with animal speciation, and animal chromosomes were still poorly known, he was able to argue that speciation by any sort of polyploidy was in essence absent (Mallet .p. 13. Mallet on Mayr and Darwin

http://www.ucl.ac.uk/taxome/jim/pap/Mallet_on_Mayr%26Darwin08.pdf

But these days we know better as seen below:

Today, armed with new and abundant molecular marker data, biologists increasingly find new examples where hybridization seems to facilitate speciation and adaptive radiation in animals, as well as plants….

http://www.ucl.ac.uk/taxome/jim/pap/mallet07_hybspn_Nature.pdf

Furthermore, as the evidence emerges for vast exchanges of genetics across entire domains of life (not just hybridisation as a means of speciation) which leads to many novel forms of highly organised complexity, it seems that the genetic exchange alone cannot account for the quantum-like nature of these forms, nor for their perfect adaptation according to their environmental niche. Answers to the organised nature of genetic modelling and moulding of the species and the genetic expression of this finely-tuned forms can be best explained via epigenetic process– the expression or not of these novel genetic exchanges according to environmental conditions. Further down in this article, I have touched upon jumping genes and their ability to reprogram cells and remodel genomes which is linked to epigenetic factors. This should give you an insight into the environmentally coordinated aspect of how nature moulds and shapes and ultimately adapts organisms using the genetic novelty exchanged between all domains of life. Also see last week’s blog for the introduction to epigenetics and the organised systems of evolutionary complexity according to growth/development laws in Part One of this series (Biology’s Big Bang: Something universal is going on…. Descent from a Common Ancestral Condition?) https://diggingupthefuture.com/2015/08/03/evolution-scaling-laws-something-universal-is-going-on/

So in the light of all of the above, let us now look at the alternative Hybrid Speciation Theory (and other forms of novel genetic exchange across domains of life) – the great web of life. Hybridisation can be used as a fairly broad term as you will come to see as you read the quotes below. At any level of genetic exchange, the result is essentially similar: large leaps of organised complexity.  Hybridisation can account for rapid leaps of complexity and when this is understood along with many other means of creating genetic novelty leading to new and novel forms of traits, characters and whole new species, such as: whole genome mergers; fission/fusion and horizontal gene transfer (HGT) as highlighted by Koonin (2007) for example, as just some of the factors contributing to evolutionary complexity, but on a much more rapid and direct level, an evolutionary alternative for genetic novelty begins to emerge. Although, primitive organisms like bacteria do not actually hybridise in the technical sense of the word, as they have no sexual organs, but the result of their exchange of new and distinct genes having a rather instantaneous effects, is no less a form of hybridisation. There are many means to exchange genetics and this must have, as Koonin has proposed, contributed significantly to evolutionary big bang. Hybridisation along with all the other means of creating hybrids via genetic exchange has therefore, serious implications for how we view the evolutionary past and of course our family tree:

Even as far back as over 200 years ago and indeed before this time, hybridisation and its role in creating new species was discussed and observed in nature and had begun to be explored as a means of evolutionary change. For instance below is a quote relating to the importance of hybridisation as a means of evolutionary change by Jean Baptiste Lamarck, who I mentioned earlier regarding our modern concept of epigenetic evolution and whose theory clearly proposed a naturalistic mechanism and an obvious relationship between higher primates and humans:

1809

– Jean-Baptiste Lamarck –

‘Zoological Philosophy…’

Translation by Hugh Elliot 1914

(first trans., from French into English)

The idea of bringing together under the name of species a collection of like individuals, which perpetuate themselves unchanged by reproduction and are as old as nature, involved the assumption that the individuals of one species could not unite in reproductive acts with individuals of another species. Unfortunately, observation has proved and continues every day to prove that this assumption is unwarranted; for the hybrids so common among plants, and the copulations so often noticed between animals of very different species, disclose the fact that the boundaries between these alleged constant species are not so impassable as had been imagined.

— Lamarck (1809, 39)

https://archive.org/stream/ZoologicalPhilosophy/ZoologicalPhilosophyAnimals_Lak_506pgs51391278#page/n129/mode/2up

– New York Times –

‘HYBRIDS MAY THRIVE WHERE PARENTS FEAR TO TREAD’

DNA analysis is now allowing biologists to better decipher the histories of species and to detect past hybridisation events that have contributed new genes and capabilities to various kinds of organisms including, it now appears, ourselves…The discovery of hybrid species and the detection of past hybridizations are forcing biologists to reshape their picture of species as independent units. The barriers between species are not necessarily vast, unbridgeable chasms; sometimes they get crossed with marvelous results.

— Carroll (2010) ‘New York Times’ 13th September Issue

http://www.nytimes.com/2010/09/14/science/14creatures.html?_r=0

Human and Chimp Ancestors Might Have Interbred

Scientists can’t say how long the hybridization carried on, but the final speciation occurred around 5.3 million years ago, possibly because the two species’ genetic code[d] were too different to mix or the animals were simply physically unappealing to each other.

— Carey (2006) ‘Live Science’ Published May 17th

http://www.livescience.com/783-human-chimp-ancestors-interbred.html

‘ANCIENT HUMANS WERE MIXING IT UP…’

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 neighbours…

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.

— University of Arizona (2011) ‘Science Daily’ September 6th Issue

http://www.sciencedaily.com/releases/2011/09/110905160918.htm

‘ORIGIN & EVOLUTION of ANIMAL HYBRID SPECIES’

The increasing number of hybrid species, discovered in both vertebrates and invertebrates …, calls for a reevaluation of hybrid speciation and reticulate evolution in animals… Unexpected similarities are now apparent in hybrid evolution of animals as varied as insects, snails, fish, frogs and lizards.

— Bullini (1994) Abstract

http://www.sciencedirect.com/science/article/pii/0169534794901244

Caterpillars evolved from onychophorans by hybridogenesis

I reject the Darwinian assumption that larvae and their adults evolved from a single common ancestor. Rather I posit that, in animals that metamorphose, the basic types of larvae originated as adults of different lineages, i.e., larvae were transferred when, through hybridization, their genomes were acquired by distantly related animals.    

– (Williamson 1990)

http://www.pnas.org/content/106/47/19901.full.pdf

 Yes, well you can imagine what sort of trouble this scientist got into for that proposition. Not all scientists rejected it – it is pretty interesting though. Margulis noted above was instrumental in even letting him offer it as a hypothesis based upon a life-time of research. Now, a very primitive and extreme form of hybridisation and somewhat related to the above hypothesis that mergers of different larvae (hybridisation) creating a new adult form, has evidence in principle to support its premise. This brings us to whole genome mergers as a means of speciation. For instance, instance, in ‘The Origin of Eukaryotic Cells. Via mergers symbiosis’:

Symbiotic microbes = eukaryote cells?
In the late 1960s Margulis … studied the structure of cells. Mitochondria, for example, are wriggly bodies that generate the energy required for metabolism…It has become clear that symbiotic events have had a profound impact on the organization and complexity of many forms of life. Algae have swallowed up bacterial partners, and have themselves been included within other single cells. Nucleated cells are more like tightly knit communities than single individuals. Evolution is more flexible than was once believed.

http://evolution.berkeley.edu/evolibrary/article/history_24

Margulis’ symbiogenesis (origin via mergers of previously independent life) theory of early evolutionary life is now well accepted within evolutionary biology.

Richard Dawkins (about Lynn Margulis and her evolutionary theory)

“I greatly admire Lynn Margulis’s sheer courage and stamina … This is one of the great achievements of twentieth-century evolutionary biology…”

 – Brockman (1995, chapter Seven)

http://www.edge.org/documents/ThirdCulture/n-Ch.7.html

As drastic as this merger of simple organisms into much more complex ones like the eukaryotes – ourselves, all other animals and plants, genetic exchange across species and distinct domains of life is much more prevalent than any of us could perhaps have imagined. This is seen within yeast, bacteria as fission/fusion, not unlike how sperm with tails enter eggs for example and Margulis suggests that this was the origin of the fertilisation of the egg by symbiotic sperms as also noted in the above article, but seemingly in the early days of evolutionary development (and used as a mode of reproduction today by many simpler organisms),  yeast and bacteria acting out a primitive sex act under the right environmental conditions (perhaps an ambient mood and lighting) by giving off signals to attract mates do not fully merge, but transfer their genetics via a little tail.  Yes, rather dramatic don’t you think? But what about mating yeast?

Mate and fuse: how yeast cells do it.

Many cells are able to orient themselves in a non-uniform environment by responding to localized cues. This leads to a polarized cellular response, where the cell can either grow or move towards the cue source. Fungal haploid cells secrete pheromones to signal mating, and respond by growing a mating projection towards a potential mate. Upon contact of the two partner cells, these fuse to form a diploid zygote.

-(Merlini et al Abstract)

http://www.ncbi.nlm.nih.gov/pubmed/23466674

 And what about simple animals such as sponges?

SYNERGY AND THE EVOLUTION OF COMPLEX SYSTEMS

An illustration of the role of synergy in the evolution of complex systems can be found in sponges, one of the simplest multi – cellular organisms in the natural world… Although sponges come in many different sizes and shapes, the “model” sponge looks more like an urn or a vase than your typical kitchen sponge. Sponges are also the most rudimentary of all animals in terms of complexity. Indeed, they are often confused with plants because they are immobile and have no internal organs, no mouth, no gut, no sensory apparatus nor even a nervous system. They are more like a colony of cooperating independent cells. Sponges even have their own separate classification (Porifera, or “pore – bearers”), and they may have evolved separately from other animals.

– (Corning 2013,  15).

http://journals.isss.org/index.php/proceedings56th/article/viewFile/1932/658

Take slime-mould for example. A recent study shows that it completes a maze in record time – it has no brain, no mouth, or even a body.

Slime Mold Smarts

The slime mold Physarum polycephalum is a single cell without a brain, yet it can make surprisingly complicated decisions. .. slime mold navigates through a maze and solves a civil engineering problem.

– (Rothschild & Jabr 2012, Nova Science).

Meet the Microbes

 “During good times, they live as independent, amoeba-like cells, dining on fungi and bacteria. But if conditions become uncomfortable — not enough food available, the temperature isn’t right, etc. — individual cells begin gathering together to form a single structure. This happens when the cells give off a chemical signal that tells all of them to gather together. The new communal structure produces a slimy covering and is called a slug because it so closely resembles the animal you sometimes see gliding across sidewalks. The slug oozes toward light.

When the communal cells sense that they’ve come across more food or better conditions, the slug stops. It then slowly does a kind of headstand. Cells in the slug now begin to do different things. Some of the cells form an anchor for the upended slug.

Others in the middle of the slug begin making a stalk and some at the tip turn into what’s called a spore cap and others become spores in that cap. When a drop of rain or strong wind knocks the spore cap hard enough, the spores go flying out. These spores are like plant seeds. Each of them becomes a new amoeba-like cell when they land and each goes off on its merry way”

 (American Society for Microbiology 2006).

http://archives.microbeworld.org/microbes/protista/slimemolds.aspx

Can Answers to Evolution Be Found in Slime?

Some experiments show complex choreography of signals in some species that allow 20,000 individuals to form a single slug-like body. Some species gather by the thousands to form multicellular bodies that can crawl. Others develop into gigantic, pulsating networks of protoplasm.

(Zimmer 2011 New York Times October 3rd)

http://fission.sas.upenn.edu/caterpillar/index.php?action=retrieve&article=Slime%20Molds%20-%20Ancient%2C%20Alien%20and%20Sophisticated%20-%20NYTimes.com.pdf

 This reminds me of Hebb’s law: in Science Daily an article entitled: ‘Scientists control rapid re-wiring of brain circuits using patterned visual stimulation’ outline the following:

“Hebbian Theory,” named after the McGill University psychologist Donald Olding Hebb who first proposed it in 1949 has been confirmed in real-time experiments as reported in a science paper on neurology (2014) and confirmed the axiom: “Cells that fire together, wire together. Cells that fire out of sync, lose their link.”

– (Science Daily May 28, 2014)

http://www.sciencedaily.com/releases/2014/05/140528104953.htm

This brings us to the HGT (a less dramatic means of genetic exchange between species, than symbiotic mergers noted above) and as it turns out, horizontal gene transfer is not confined to the microbial world of yeast and bacteria, 

‘HORIZONTAL GENE ACQUISITIONS BY EUKARYOTES AS DRIVERS OF ADAPTIVE EVOLUTION’

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.

— Schönknecht et al (2013) Abstract

http://onlinelibrary.wiley.com/doi/10.1002/bies.201300095/abstract;jsessionid=2B28066CC31570B158F2D72C1550CE91.f01t03

 ‘COWS ARE 25 PERCENT SNAKE’

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. A study by Australia’s Adelaide and Flinders Universities and the South Australian Museum has 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 …

— Eichelberger (2013) ‘Mother Jones.com’, 3rd January Edition

http://www.motherjones.com/blue-marble/2013/01/dna-cows-snakes-adelaide-flinders-study

Space Invader DNA jumped across mammalian genomes

Genomes are often described as recipe books for living things. If that’s the case, many of them badly need an editor. For example, around half of the human genome is made up of bits of DNA that have copied themselves and jumped around, creating vast tracts of repetitive sequences. The same is true for the cow genome, where one particular piece of DNA, known as BovB, has run amok. It’s there in its thousands. Around a quarter of a cow’s DNA is made of BovB sequences or their descendants.

BovB isn’t restricted to cows. If you look for it in other animals, as Ali Morton Walsh from the University of Adelaide did, you’ll find it in elephants, horses, and platypuses. It lurks among the DNA of skinks and geckos, pythons and seasnakes. It’s there in purple sea urchin, the silkworm and the zebrafish.

The obvious interpretation is that BovB was present in the ancestor of all of these animals, and stayed in their genomes as they diversified. If that’s the case, then closely related species should have more similar versions of BovB. The cow version should be very similar to that in sheep, slightly less similar to those in elephants and platypuses, and much less similar to those in snakes and lizards.

But not so. If you draw BovB’s family tree, it looks like you’ve entered a bizarre parallel universe where cows are more closely related to snakes than to elephants, and where one gecko is more closely related to horses than to other lizards.

This is because BovB isn’t neatly passed down from parent to offspring, as most pieces of animal DNA are. This jumping gene not only hops around genomes, but between them.

This type of “horizontal gene transfer” (HGT) is an everyday event for bacteria, which can quickly pick up important abilities from each other by swapping DNA. Such trades are supposedly much rarer among more complex living things, but every passing year brings new examples of HGT among animals. For example, in 2008, Cedric Feschotte (now at the University of Utah) discovered a group of sequences that have jumped between several mammals, an anole lizard, and a frog. He called them Space Invaders.

(Yong – In Phenomena: ‘National Geographic’ November 3, 2008)

http://phenomena.nationalgeographic.com/2008/11/03/space-invader-dna-jumped-across-mammalian-genomes/

-Oliver & Green –

‘JUMPING GENES DRIVE EVOLUTION’

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.

— Oliver & Greene (2009) ‘Australasian Science’ September Edition

http://researchrepository.murdoch.edu.au/6496/1/jumping_genes.pdf

-Oliver & Green –

‘How Jumping Genes Drove Primate Evolution’

Jumping genes have been important in the evolution of higher primates, leading to faster brain function, improved foetal nourishment, useful red-green colour discrimination and greater resistance to disease-causing microbes – and even the loss of fat storage genes in gibbons.

http://www.australasianscience.com.au/article/issue-january-and-february-2012/how-jumping-genes-drove-primate-evolution.html

— Oliver & Greene (2012) ‘Australasian Science’

Jan / Feb Edition

http://www.australasianscience.com.au/article/issue-january-and-february-2012/how-jumping-genes-drove-primate-evolution.html

– SCIENTIFIC AMERICA –

‘The Human Genome Race

A tale of the Tortoise and the Hare… and the fly and the worm and the mouse’

Soon after the Human Genome Project published its preliminary results in 2001, a group of scientists announced that a handful of human genes—the consensus today is around 40—appear to be bacterial in origin. The question that remains, however, is how exactly they got there. Some scientists argue that the genes must have been transferred to humans from bacteria fairly recently in evolutionary history, because the genes aren’t found in our closest animal ancestors.

— Karow (2000) ‘Scientific America’ April 24th Edition

http://www.scientificamerican.com/article/the-human-genome-race/

So you try deciphering where we come in the family tree and how related to snakes are we really?

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 (complex cellular life making up plants and animals are 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.

http://www.horizonpress.com/cimb/v/v4/07.pdf

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.

http://www.eurekalert.org/pub_releases/1998-02/UoG-TEMH-090298.php

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 remodeling 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.

http://www.sciencedirect.com/science/article/pii/S0378111910000296

Barbara McClintock and the discovery of jumping genes

Sandeep Ravindran, Science Writer

Muted Reaction

For much of the 20th century, genes were considered to be stable entities arranged in an orderly linear pattern on chromosomes, like beads on a string (1). In the late 1940s, Barbara McClintock challenged existing concepts of what genes were capable of when she discovered that some genes could be mobile…

By the 1970s the great strides made in molecular biology led to the discovery of transposons in other organisms, starting with viruses and bacteria. We now know that transposons constitute more than 65% of our genomes and approximately 85% of the maize genome….

Confirmation that transposons were widespread among eukaryotes eventually led to the wider appreciation of her original discovery. McClintock received a number of prestigious awards, including the 1970 National Medal of Science and culminating in an unshared Nobel Prize in Physiology or Medicine in 1983…

McClintock described the initial reaction to her discovery as “puzzlement, even hostility” (8). Speaking of the scientific community at large she said “I was startled when I found they didn’t understand it; didn’t take it seriously” (4). The concept of transposition did not fit easily within the framework of genetics at the time… These pioneering studies foreshadowed later work showing the importance of epigenetics, heritable changes not caused by changes to the DNA sequence, in development.

http://www.pnas.org/content/109/50/20198.full

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.

– (Mc Clintock 1983).

http://www.nobelprize.org/nobel_prizes/medicine/laureates/1983/mcclintock-lecture.pdf

– James A. Shapiro –

‘Does Natural Selection Really Explain What Makes Evolution Succeed?’

….cytogenetics (the study of chromosome behavior in heredity using both genetic and microscopic methods)

…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).

— Shapiro (2012) ‘Huffington Post’ Blog, updated 10th December

http://www.huffingtonpost.com/james-a-shapiro/does-natural-selection-evolution_b_1769524.html

The next time you hear that we our closest relatives are chimps etc, try to put this into perspective and what they are actually saying is: out of the 2% of genes in your genome that code for proteins, 99% of this 2% are shared sequences. Now, if proteins and their networks build body parts and maintain and keep all those cells ticking and doing the right job, it seems that those proteins would be very similar in fairly similar functioning/looking animals. Mice can share up to 99% of their genetic makeup – does that make us both mouse and man? Man vs. mouse

“– Mice and humans both have about 30,000 genes – and share 99% of them”

 http://www.sfgate.com/news/article/OF-MICE-AND-MEN-Striking-similarities-at-the-2748350.php

 In other words, genes don’t run the evolutionary show, although they provide the raw genetic material for other processes to operate upon. It how these genes are expressed epigenetically that makes sense of all this genetic novelty. It is how nature uses the genetic code and produces ‘intelligent designs’ that would seem, according to the evidence that produces specialist species that are perfectly adapted to their environmental niches. In other words: “epigenetic mechanisms … the competent users of the genetic toolkit”.

Now are you beginning to see why we cannot use the molecular clock (assumed to tick at the same rate over evolutionary time and calculated on the assumption of direct common ancestry according to the rate of genetic mutations? The part presented in the next article is of some interest in the light of last week’s topic on how scaling (universal) laws seem to direct the fundamental level a species can reach based upon its metabolic acquired system (Biology’s Big Bang: Something universal is going on…. Descent from a Common Ancestral Condition?) https://diggingupthefuture.com/2015/08/03/evolution-scaling-laws-something-universal-is-going-on/

For instance, as discussed previously, elephants and mice are really not that different metabolically speaking as they are both mammals and an elephant being bigger is scales higher on the metabolic rate to mass scale, but a mouse-sized reptile will have a simpler metabolic rate than its mammal counterpart and therefore its mass to metabolic rate scaled much lower than any of the mammals, irrespective of size. Similarly, a reptile is more complex metabolically speaking than an amoeba, and will scale higher up the metabolic rate to mass scale. I also drew attention to the discrete scales of complexity indicated on these charts where although they complied broadly with the three-quarter scaling power law, there were discrete leaps of metabolic complexity between the most fundamental forms of life: mammalian, reptile, fish, birds etc.

The rate of DNA evolution: Effects of body size and

temperature on the molecular clock

Observations that rates of molecular evolution vary widely within and among lineages have cast doubts on the existence of a single ‘‘molecular clock.’’ Differences in the timing of evolutionary events estimated from genetic and fossil evidence have raised further questions about the accuracy of molecular clocks…

– (Gillooly, Allen, West and Brown 2004, Abstract)

The central role of metabolic rate in controlling biological rate processes implies that metabolic processes also govern evolutionary rates at higher levels of biological organization where the neutral molecular theory does not apply.

(Gillooly et al 2004, p. 144)

ftp://vm-lux.embl.de/users/lercher/Ka/Gillooly_Brown2005PNAS_bodysize.pdf

Can you see that the presumed ancestral splits from a fixed fundamental species – from a fish-like ancestor, to a reptilian type – to mammal to monkey and ape, at so many million years may not actually work? Perhaps, as noted in last week’s article, viewing evolution as going from the less defined – generalist forms of organisms to the more efficient (metabolically) stabilised specialist – species level, is a better way of viewing evolution, as our current model simply is not producing any meaningful answers. To put this re-evaluation in real terms (I’ll return to the specific evidence for this further on in this series), think of evolution going from an ancestral CONDITION or state of evolutionary development, such as: a basal chordate (the ancestral condition of all vertebrates including primitive vertebrate types such as fish), to more complex vertebrates such as: tetrapod: (four limbed land walkers), exhibiting evolving distinctly different and more complex modes of development, e.g. from cloning/budding to metamorphosis, to produce a more complex mode of development such as the tetrapods, some non-amphibian types becoming amniotic (egg-layers as still used today by many lizards, snakes and birds), to monetreme (mammal egg layers) to mammals that give birth to live young, to primates with longer gestation times and by extrapolation, longer evolutionary development times according to the complexity potential of the evolving species.

This reinterpretation of the fossil record takes its cue from Von Baer’s laws of development/evolution where, a developing organism never goes through the adult stage of another organism. In other words, once a species has matured such as a fish, a mammal is not going to go through a fish stage during its development. It only reflects the more primitive stages and the current mode of development of the main types of organisms (single-celled organisms, simple sponge animals, insects, amphibians, reptiles, birds and mammals) which in turn, broadly reflects the evolutionary mode of their speciation. E.g. sponges = budding and cloning, insects = metamorphosis via a caterpillar stage, amphibians go from tad-pole stage (invertebrates) to land-walking, and air breathing animals via a more complex form of metamorphosis, reptiles and birds are amniotic egg-layers and mammals of the primitive variety such as monotremes lay eggs, while other slightly more complex mammals are marsupials – (a cross between egg-laying and live birth) and of course, we have the typical mode of development in mammals of giving birth to live young.

So rather than seeing descent from actual ancestors of any of these groups, perhaps it is better to view these species as once primitive generic and fundamental forms of these broad groups and they hybridised a lot more than we have hitherto imagined, not to mention the mergers, symbiotic relationships, HGT and general networking going on at a cellular level before this. The mammals at least must have gone through ALL the evolutionary stages of development such as: from a symbiotic merger between egg and sperm (remember the yeast and mitochondria?), a cellular differentiation phase (recall the really primitive cellular colonies – cells that wire together fire together: cells that fire out of sync – lose their link); then there is the embryonic phase (not perhaps unlike the primitive chordate/tadpole-like stage) and finally became more defined as in a foetal phase (the primitive species is a generalist tetrapod after metamorphosis from a tad-pole stage). Then if you take the higher primates, during development, they lose their tails, but humans have much more complex brain wiring and a longer gestation period than other higher primates. We still grow our brains long after being born and indeed, have bigger brains in proportion to our bodies compared to any other primate and then, we actually spend quite some time crawling about on all fours and after many mishaps and toppling over, one day, we reach the toddler stage and manage to co-ordinate our bodies and walk-upright keeping our big heads balanced on top of our spindly necks. Some even go on to become Olympic sprinters.  Could we be rewinding via development our actual evolution?  Similarly, the mode of development may simply reflect their particular mode of evolutionary species development; going from the generalist to the specialist species.

So hopefully you are beginning to see why we don’t have an evolutionary branching tree of life, but a web and finding your great, great, great……….., Auntie Ida that gave rise the primate lineage may be an impossible task. She may never have existed, but perhaps a generic generalist form of a more complex mammal on its way to becoming something more defined such as a primate of every colour and hue and degree of complexity once it became proficient at whatever it had the potential to ultimately become. Indeed, there may have been whole tribes of wandering primitive mammalian tetrapods on their way to becoming something as yet undefined (as the fossil record shows as you will see as this series unfolds). These generalist tetrapods being more complex (metabolically speaking) than their reptile cousins (several times removed and twice thrown out) may not have been quite sure what they were going to be when they actually grew up to become a stabilised and relatively fixed species of monkey, baboon, chimp, ape, man. It may have been a matter of who mated with whom and what experience they had and even what they ate that directed their fate as a refined species in the end. Even their experience, nutrients and/or chemical composition and genetic exchange during their pre-metamorphic sojourn in the primordial pond would have sent them ultimately on a different evolutionary trajectory from the get-go. This is because epigenetics and environmental factors can have a profound impact upon a developing organism and by extrapolation these factors would impact upon the evolutionary development and course of a species.  In other words, if we apply the modern syntheses (Neo-Darwinian) model of evolution, it would be akin to trying to find the proverbial needle in a haystack with the added complication of discovering that the needle is golden in colour and, in part, also made of hay. If we knew that the needle could be detected by using a magnet, then we might have a chance of finding it. Similarly, if we know the mechanisms actually involved in evolutionary processes, we might have a chance of seeing the wood despite the great big evolutionary tree that has been blocking our view.

This reinterpretation is well supported by molecular evidence and the fossil record and I will get to the nitty-gritty of these in due course. I also presented in last week’s blog, the mechanisms such as genome silencing which appear to be linked to natural evolutionary growth laws that are universal for all natural organised systems, even cosmological ones.  The next article will deal more specifically with the epigenetic mechanisms that guide the evolutionary show so that all these crosses between distinct forms of life do not produce random lucky monsters. See article entitled:

Evolution: Revenge of the hopeful monster http://www.nature.com/news/2010/100217/full/463864a.html

Epigenetics are the competent user of the genetic variation exchanged across so many levels of life. It is how these novel genetics are expressed, when, where, how and to what degree, that make the big difference in the end.

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