A Why, Where, When

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http://www.allaboutscience.org/symbiosis.htm

An insight into how many genes were lost to the host nucleus may be derived from the fact that the cytosol synthesises for the mitochondria the following proteins: aminoacyl-tRNA synthases; DNA replication enzymes; RNA polymerase; soluble enzymes of the citric acid cycle etc. It is clear that, since proteins are made at two independent sites, nuclear-coded proteins must be imported into mitochondria and chloroplasts. The principle difficulty lies in the fact that imported proteins have to cross subcompartments to get into both organelles as the organelles possess double membranes. Here is where chaperones are required to bind the polypeptide chains just as they emerge through spacial pores into the mitochondrial matrix. A similar process operates in the importing of proteins into the chloroplast. Because platn cells possess both chloroplasts and mitochondria, two different kinds of signal peptides are also required to send proteins to the correct addresses.

The immensely sophisticated transport arrangements raises the question as to how they arose and what selective advantages there would have been in relation to the original endosymbionts to share genomes with the nucleus of the host cell. As if this is not difficult enough, a further logistical problem is created by the fact that all of the host cell’s fatty acids and a number of amino acids are made by enzymes in the chloroplast stroma. We have now a transfer in reverse. Of course endosymbiosis could only take place when cells with highly developed metabolic systems were in existence. – See more at: http://www.allaboutscience.org/symbiosis.htm#sthash.atJEyEbd.dpuf

LM  Lynn Margulis

FROM THE APRIL 2011 ISSUE

Discover Interview: Lynn Margulis Says She’s Not Controversial, She’s Right

It’s the neo-Darwinists, population geneticists, AIDS researchers, and English-speaking biologists as a whole who have it all wrong.

That distinction led to her career-making insight. In a 1967 paper published in the Journal of Theoretical Biology, Margulis suggested that mitochondria and plastids—vital structures within animal and plant cells—evolved from bacteria hundreds of million of years ago, after bacterial cells started to collect in interactive communities and live symbiotically with one another. The resulting mergers yielded the compound cells known as eukaryotes, which in turn gave rise to all the rest—the protoctists, fungi, plants, and animals, including humans.

Are you saying that a free-living bacterium became part of the cell of another organism? How could that have happened?


At some point an amoeba ate a bacterium but could not digest it. The bacterium produced oxygen or made vitamins, providing a survival advantage to both itself and the amoeba. Eventually the bacteria inside the amoeba became the mitochondria. The green dots you see in the cells of plants originated as cyanobacteria. This has been proved without a doubt.

In contrast, the symbiotic view of evolution has a long lineage in Russia, right?


From the very beginning the Russians said natural selection was a process of elimination and could not produce all the diversity we see. They understood that symbiogenesis was a major source of innovation, and they rejected Darwin. If the English-speaking world owns natural selection, the Russians own symbiogenesis. In 1924, this man Boris Mikhaylovich Kozo-Polyansky wrote a book called Symbiogenesis: A New Principle of Evolution, in which he reconciled Darwin’s natural selection as the eliminator and symbiogenesis as the innovator. Kozo-Polyansky looked at cilia—the wavy hairs that some microbes use to move—and said it is not beyond the realm of possibility that cilia, the tails of sperm cells, came from “flagellated cytodes,” by which he clearly meant swimming bacteria.

Are you saying that the only harmful bacteria are the ones that share an evolutionary history with us?


Right. Dangerous spirochetes, like the Treponema of syphilis or the Borrelia of Lyme disease, have long-standing symbiotic relationships with us. Probably they had relationships with the prehuman apes from which humans evolved. Treponema has lost four-fifths of its genes, because you’re doing four-fifths of the work for it. And yet people don’t want to understand that chronic spirochete infection is an example of symbiosis.

You have upset many medical researchers with the suggestion that corkscrew-shaped spirochetes turn into dormant “round bodies.” What’s that debate all about? 


Spirochetes turn into round bodies in any unfavorable condition where they survive but cannot grow. The round body is a dormant stage that has all the genes and can start growing again, like a fungal spore. Lyme disease spirochetes become round bodies if you suspend them in distilled water. Then they come out and start to grow as soon as you put them in the proper food medium with serum in it. The common myth is that penicillin kills spirochetes and therefore syphilis is not a problem. But syphilis is a major problem because the spirochetes stay hidden as round bodies and become part of the person’s very chemistry, which they commandeer to reproduce themselves. Indeed, the set of symptoms, or syndrome, presented by syphilitics overlaps completely with another syndrome: AIDS.

Do you ever get tired of being called controversial?

I don’t consider my ideas controversial. I consider them right.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3131726/

HUMAN ENDOGENOUS RETROVIRUSES

We are familiar with viruses as the causative agents of infectious diseases, but we also need to recognise that, from the evolutionary perspective, they are also capable of bringing about genetic change in the germ lines of their hosts. This is known as viral symbiogenesis and it has major evolutionary potential [9]. Conceptually and mechanistically, this differs from the more familiar concept of genetic change through mutation, although it is complementary rather than contradictory to the classical concepts of evolution through mutation and selection.

The basic retroviral genome comprises three genetic domains, conventionally referred to as the genes, env, gag and pol, which code for a variety of proteins.

In Sardinian patients – Sardinia appears to suffer a relatively high incidence of MS – the Italian researchers, Dolei et al., confirmed the detection of MSRV in the plasma of 12.8% of healthy blood donors, meanwhile they found the virus in the plasma of all 39 MS patients tested, which included 24 suffering a relapsing remitting course, 4 secondary-progressive and the remainder newly diagnosed [27, 28].

Although the therapeutic options in MS have improved in recent years, currently there is no simple haematological diagnostic or prognostic assay that might assist clinicians in managing MS.

It seems that there are many diseases that according to Darwinian theory should have been eliminated from human lines but still manage to thrive.  MS, Fibromyalgia I & II,

Where did this mutualism come from?

Could it have stemmed from a solar flare?  One that suffused the planets?

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC135049/

HGT horizontal gene transfer

http://www.the-scientist.com/?articles.view/articleNo/42420/title/Horizontal-Gene-Transfer-a-Hallmark-of-Animal-Genomes-/

Many animal genomes include bacterial and fungal genes acquired by horizontal gene transfer (HGT) during evolution, according to a study published today (March 12) in Genome Biology. Scanning the genomes of fruit flies, nematodes, primates, and humans, among other animals, researchers found evidence to suggest that some of these horizontally acquired genes may even be functional.

Crisp’s team found that several of the foreign genes in metazoan genomes encoded enzymes and likely had active biochemical functions. In three nematode and all the primate genomes analyzed, the researchers found that 95 percent of foreign genes contained introns, suggesting that these genes have been “domesticated” over time.

“Since HGT events are not incredibly common, it seems likely that the mechanisms [operating] are very similar to the ones that would insert introns into any genes,” said Crisp. “Looking at recent HGT events can tell us how introns were inserted into other eukaryotic genes, or how transcriptional regulation of new genes evolves.”

The process of lateral gene transfer appears to be both ancient and active today. In human and other primate genomes, foreign genes appear to have entered the genome only in their last common ancestors. But in some Drosophila species and nematodes, the process appears to have occurred much more recently.

The results suggest that “if we use the same yardstick to measure a variety of model organisms, it’s possible to say that mammalian genomes have also been subjected to low levels of HGT, although it happened only on very rare occasions at the early stages of evolution,” said molecular geneticist Irina Arkhipova of the Marine Biological Laboratory in Woods Hole, Massachusetts who was not involved with the study. “Some species are more susceptible than others. But it definitely can happen and has happened during evolution, and has played a role in shaping functional diversity of the gene repertoire in metazoans.”

http://serialendosymbiosis.blogspot.com/2007/12/horizontal-gene-transfer.html

        Horizontal Gene Transfer    

Horizontal gene transfer – gene swapping – has blurred the evolutionary relationships (phylogeny) of prokaryotes (image), and continues to provide a mechanism for the sharing of antibiotic resistance between bacteria.

(see The net of life: Reconstructing the microbial phylogenetic networkV. Kunin, L. Goldovsky, N. Darzentas, and C. A. OuzounisGenome Res. 1 July 2005. pdf)

Three mechanisms of horizontal (lateral) gene transfer are recognized: direct bacterial conjugation, bacteriophage mediated transduction between bacteria, and bacterial transformation by uptake of DNA fragments.

A major form of vertical gene transfer followed serial endosymbiotic events, in which ingested purple bacteria and Cyanobacteria became eukaryotic mitochondria and chloroplasts respectively. The ingested prokaryotes are believed to have relinquished certain genes to the nuclei of their host cells, a process known as endosymbiotic gene transfer.

Horizontal genomics is a new field in prokaryotic biology that examines DNA sequences in prokaryotic chromosomes that appear to have originated from other prokaryotes or eukaryotes. The prokaryotic mobile gene pool is referred to as the ‘mobilome‘. Various agents agents occur in all prokaryotes and effect DNA movement: plasmids, bacteriophages and transposons.

http://aeon.co/magazine/science/how-horizontal-gene-transfer-changes-evolutionary-theory/

What has become increasingly clear in the past 10 years is that this liberal genetic exchange is definitely not limited to the DNA of the microscopic world. It likewise happens to genes that belong to animals, fungi and plants, collectively known as eukaryotes because they boast nuclei in their cells. The ancient communion between ferns and hornworts is the latest in a series of newly discovered examples of horizontal gene transfer: when DNA passes from one organism to another generally unrelated one, rather than moving ‘vertically’ from parent to child. In fact, horizontal gene transfer has happened between all kinds of living things throughout the history of life on the planet – not just between species, but also between different kingdoms of life. Bacterial genes end up in plants; fungal genes wind up in animals; snake and frog genes find their way into cows and bats. It seems that the genome of just about every modern species is something of a mosaic constructed with genes borrowed from many different forms of life.

A different kind of transposon – one of the copy-and-paste variety – has spread through an equally diverse group of animals. In 2012, David Adelson, Ali Walsh at the University of Adelaide, and their colleagues, discovered that the transposon BovB – first found in cows (hence the bovine epithet) – is also present in anoles, opossums, platypuses, wallabies, horses, sea urchins, silkworms and zebrafish, to name a few. Once again, vertical inheritance via traditional evolutionary relationships could not explain the transposon’s haphazard materialisation here and there. On its epic journey through the tree of life, BovB has jumped between species at least nine times, and seems to have generally moved from reptiles to mammals.

How does one little piece of DNA get into all those distantly related creatures living in such different places – animals that likely never even encountered one another, let alone mated? It probably enlists the help of organisms that have mastered the art of hitchhiking: ticks. Adelson, Walsh and colleagues found BovB in several tick species known to vampirise reptiles. Likewise, a couple of years after first discovering SPINs, Feschotte and colleagues found them yet again in two creatures that – just like the mite with an appetite for fruit fly eggs – have the potential to transmit transposons from one animal to another: a blood-sucking insect known as the kissing bug (Rhodnius prolixus), which feeds on birds, mammals and reptiles alike; and the pond snail (Lymnaea stagnalis), which is host to many parasitic flatworms that infect various vertebrates. Alone, the kissing bug and pond snail cannot explain all of SPINs’ conquests; their habitats overlap with many but not all of the vertebrates that contain the transposons. But the available evidence suggests that this six-legged parasite and shelled parasite hotel are two key accomplices that allowed SPINs to infiltrate so many different animal lineages within the past 50 million years.

Sometimes, parasites transfer far more than a single gene into the genomes of their hosts. Like many insects, the fruit fly species Drosophila ananassae is home to parasitic bacteria known as wolbachia, typically found in an insect’s sex organs. Through a series of gene‑sequencing studies, scientists have confirmed that the wolbachia species living inside D ananassae has shuttled not just one, but all of its 1,206 genes into the fruit fly’s DNA. Consider this: insects are collectively the most numerous animals on the planet; wolbachia infects between 25 and 70 per cent of all insect species, and it’s probable that wolbachia has successfully completed such genetic mergers in far more than fruit flies. Think of the quintillions of insects in the world – all those buzzing, bristling, bug-eyed creatures. At their very core, most of them might not be individual organisms but at least two beasts in one.

Recently, while studying a virus that preys on wolbachia, Jason Metcalf and Seth Bordenstein of Vanderbilt University in Tennessee discovered the Napoleon of horizontal gene transfers: a little gene that has conquered every kingdom of life. The virus in question attacks and kills wolbachia using a gene named GH25-muramidase, which encodes an enzyme that can perforate bacterial cell walls. When Metcalf and Bordenstein traced the evolutionary lineage of GH25, they discovered a pattern of inheritance that looked anything but typical. The GH25 gene was scattered throughout the tree of life: in bacteria, plants, fungi and insects. This particular gene seems to have moved fluidly through the microbial world and then hopped laterally to viruses, plants, fungi and insects living in close association with different kinds of bacteria. ‘Every organism needs to fight bacteria off,’ Metcalf says. ‘If they can get a new method of antibacterial defence, that’s a huge evolutionary advantage for them.’

in Japan, some people’s gut bacteria have stolen seaweed-digesting genes from ocean bacteria lingering on raw seaweed salads

One of the most clear-cut instances of horizontal gene transfer is the story of the fungus and the pea aphid. Some fungi, plants and bacteria have genes encoding carotenoids, a diverse class of colourful molecules involved in everything from photosynthesis and vision to camouflage and sexual attraction. No one had ever found such genes in animals, though. In all known cases, animals acquired carotenoids from their diet (for instance, flamingoes become red and pink from eating plankton). In late 2009, Nancy Moran, an evolutionary biologist then at the University of Arizona, stumbled onto the fact that pea aphids have a carotenoid gene.

‘More than 270 million years ago, a lone aphid likely attained a carotenoid gene from a fungus’. Photo courtesy Wikipedia

Scientists already knew that pea aphids appear green or red depending on the carotenoids in their bodies, and that aphid populations shift their colours in response to certain threats: green aphids are more susceptible to parasitic wasps; red aphids are more vulnerable to ladybirds. But the origin of the pigments had always been something of a mystery. Aphids primarily feast on sap, which does not contain many carotenoids. And pea aphids were often found with very different carotenoids than the ones inside the plants they were eating. When Moran compared the aphid’s pigment genes with those in many different creatures, the closest match was in a family of fungus. More than 270 million years ago, a lone aphid likely attained a carotenoid gene from a fungus – perhaps one that was infecting it, or one it was munching. Other scientists have since discovered that spider mites and gall midges have also acquired carotenoid genes from fungi and bacteria.

Shake any branch on the tree of life and another astonishing case of interspecies gene transfer will fall at your feet. Bdelloid rotifers – tiny translucent animals that look something like sea slugs – have constructed a whopping eight per cent of their genome using genes from bacteria, fungi and plants. Fish living in icy seawater have traded genes coding for antifreeze proteins. Gargantuan-blossomed rafflesia have exchanged genes with the plants they parasitise. And in Japan, some people’s gut bacteria have stolen seaweed-digesting genes from ocean bacteria lingering on raw seaweed salads.

At this point, the tally is too high to ignore. Scientists can no longer write off gene-swapping among eukaryotes – and between prokaryotes and eukaryotes – as inconsequential. Clearly genes have all kinds of ways of journeying between the kingdoms of life: sometimes in large and sudden leaps; other times in incremental steps over millennia. Granted, many of these voyages are probably futile: a translocated gene finds itself to be utterly useless in its new home, or becomes such a nuisance to its genetic neighbours that it is evicted. Laterally transferred genes can be imps of chaos, gumming up or refashioning a genome in a way that is ultimately disastrous – perhaps even lethal to a species. In a surprising number of instances, however, wayfaring genes make a new life for themselves, becoming successful enough to change the way an organism behaves and steer its evolution.

The fact that horizontal gene transfer happens among eukaryotes does not require a complete overhaul of standard evolutionary theory, but it does compel us to make some important adjustments. According to textbook theories of evolution, the major route of genes moving between organisms is parent to child – whether through sex or asexual cloning – not this sneaky business of escorting genes between unrelated organisms. We must now acknowledge that, even among the most complex organisms, vertical is not the only direction in which genes travel.

Likewise, standard theory says that mutations are supposed to happen within a species’s own genome, not come from somewhere else entirely. We now know that the appearance of new genes does not necessarily result from tweaks to native DNA, but might instead represent the arrival of far-flung visitors. ‘We need to start thinking about genomes as ecological units rather than monolithic units,’ says Jack Werren of the University of Rochester in New York, one of the scientists who discovered the wolbachia/fruit fly Russian doll. ‘We’re dealing with a new category by which unique genes can evolve.’

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In some cases, this genetic hopscotching ‘could exert a very powerful evolutionary force’, says Li. ‘It can introduce novelties that cannot be achieved by gradual genetic mutations.’ Consider that a plant acquiring a gene from a bacterium, or an aphid from a fungus, is not receiving some half-constructed genetic prototype. Rather, it gets the benefit of all the aeons of natural selection that have whittled that gene in another creature, honing its power. An introduced gene might need some tweaks before it whirs in sync with its new neighbours, but it could be closer to such harmony than a de novo mutation that was caused by, say, a cell-division error or UV radiation. Horizontal gene transfer opens the possibility of a creature instantaneously acquiring a gene-trait combo that its own genome would have been unlikely to invent by itself.

Laterally transferred genes can sway evolution’s tiller in more subtle ways, too. Certain types of introduced genes duplicate themselves many times over, often leaving behind either little bits and pieces or entire replicas. In the process, they can rearrange large chunks of native DNA, change the way certain genes are expressed, or create whole new genes out of all this shuffling. By making a host genome larger and more diverse, these genetic immigrants increase the probability of copying and editing errors, some of which can be serendipitous and spur rapid evolution, as might have happened with the little brown bat.

We can unite these various corollaries to standard evolutionary dogma by re-imagining the tree of life. In the classic textbook depiction, the tree of life has a single trunk that splits into three big domains – bacteria, archaea (which resemble bacteria but are genetically and molecularly distinct) and eukaryota. These three domains of life branch into all known species. Every creature that ever existed presumably ‘descended from some one primordial form’, as Charles Darwin put it in 1859. And genes ostensibly flow in one direction: up from the trunk.

Scientists such as Ford Doolittle and Carl Woese at the University of Illinois have argued that this portrayal is an oversimplification. Rather than rising from a single trunk, they say, the tree of life stands on an interweaving root system. Rather than evolving from one ‘last universal ancestor’, all life arose from a communal pool of primitive cells with unbridled zeal for exchanging DNA. For relatively simple cells with only a handful of genes each, swapping DNA was an excellent strategy for acquiring and preserving the best adaptations around.

At some point, Woese proposed, cells reached a certain threshold of complexity at which it became detrimental to embrace a bombardment of foreign genes. A primordial cell harbouring a small group of genes can potentially gain a lot by adding new genes to its repertoire; but a more sophisticated cell with hundreds or thousands of genes risks imbalancing an intricate genome fine-tuned by a longer period of natural selection. So, complex eukaryotic cells evolved new ways to protect their DNA and expunge genetic invaders.

However, as has become clear in the past decade, horizontal gene transfer did not halt among eukaryotes and their microbial denizens. A mischievous breeze continued to blow DNA this way and that, from one branch on the tree of life to another. Wolbachia, pea aphids and hornworts all encourage us to accept a truth that seems unsettling at first, but ultimately invites us into greater communion with all life on the planet.

we can no longer pretend that gene-mixing between species is ‘unnatural’, that it is some misguided practice that would never exist if not for our meddling latex-gloved hands

There seems to be a notion in the public consciousness that the DNA of one species should not mix with the DNA of another. This belief becomes especially clear in the ongoing debate about genetically modified organisms (GMOs). Opponents frequently argue that the kind of gene transfers scientists make between different species would never happen outside the lab. Putting a wheat gene into a chestnut tree, or a bacterial gene into corn, or a fish gene into a tomato? Surely that’s unnatural. The ostensible perversion of mixing genes is struck like a gong, again and again. The supermarket chain Whole Foods, for example – which counsels its customers on how to avoid genetically modified foods – defines GMOs as ‘organisms whose genetic make-up (DNA) has been altered in a way that does not occur naturally.’

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But it does. Genetic promiscuity is far more prevalent in nature than we realised. This fact alone is not an argument in favour of GMOs; simply because something occurs in nature without assistance from humans does not mean it is inherently good or bad. Confronted with this fact, however, we can no longer pretend that gene-mixing between species is ‘unnatural’, that it is some misguided practice that would never exist if not for our meddling latex-gloved hands. We did not invent gene transfer; DNA did. Genes are concerned with one thing above all else: self-perpetuation. If such preservation requires a particular gene to adapt to a genome it has never encountered before – if riding a parasite from one species to another turns out to be an extremely successful way of guaranteeing perpetuity – so be it. Species barriers might protect the integrity of a genome as a whole, but when an individual gene has a chance to advance itself by breaching those boundaries, it will not hesitate.

That’s the thing about DNA: its true loyalty is to itself. We tend to think of any one species’s genome as belonging to that species. We have a strong sense of ownership over our genes in particular – an understanding that, even though our genome overlaps with that of other creatures, it is still singular, is still ‘the human genome’. So strong is our possessiveness that the mere idea of mixing our DNA with another creature’s – of any two species intermingling genes – immediately repulses us. As far as DNA is concerned, however, the supposed walls between species are not nearly so impermeable. Up in the branches of the great tree of life, we are no longer immersed in the ancient communal pool that watered its tangled roots. Yet we cannot escape the winds of promiscuity. Even today – as was true from the start – ‘our’ genes are not ours alone.

11 December 2014

Read more essays on ecology & environmental sciences, evolution and genetics

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http://www.redicecreations.com/specialreports/paranormaldna.html

http://www.dailymail.co.uk/sciencetech/article-2994187/Mystery-alien-genes-Scientists-discover-DNA-NOT-ancestors-say-change-think-evolution.html

wiki

crab claw sail

The crab-claw sail is something of an enigma. It has been demonstrated to produce very large amounts of lift when reaching, and overall seems superior to any other simple sail plan

One popular but disputed theory is that the crab-claw wing works like a delta wing, generating vortex lift. Since the crab claw does not lie symmetric to the airflow, like an aircraft delta wing, but rather lies with the lower spar nearly parallel to the water, the airflow is not symmetric.

The crab claw sail may be better suited to capturing fresh water than many other sail designs, and it is known that long distance sailors in the Pacific did catch rainwater in their sails.[5]

The  most amazing thing to me is that in history boat are the darling of the researchers yet ocean boats go nowhere without sails.  So is there research into the creation of sails?  No

Oh, and science has now corrected the misunderstanding of why airplane wings lift.

physdotorg airplane wing

“What actually causes lift is introducing a shape into the airflow, which curves the streamlines and introduces pressure changes – lower pressure on the upper surface and higher pressure on the lower surface,” clarified Babinsky, from the Department of Engineering. “This is why a flat surface like a sail is able to cause lift – here the distance on each side is the same but it is slightly curved when it is rigged and so it acts as an aerofoil. In other words, it’s the curvature that creates lift, not the distance.”

The crab claw?  Curved supports.

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