Winace's excellent shared ERVs primer part 1

The last time I mentioned ervs, I should have posted the late, great Winace's excellent primer on ERVs. Let's make things right. I'm copy/pasting from the one that he originally posted on the old Christian Forums. It's an oldie, but a goodie.

ERVs, a startling line of evidence from genetics (not fossils) provides additional, overwhelming support for human/chimp common ancestry, one that establishes it beyond a shadow of a doubt.

Much like stellar parallax could be considered 'proof' of heliocentricism, so too do unique fingerprints of ancient retroviral infection demonstrate relatedness if found in the genome of two different organisms.

1. Background

Viral infections. We all know and hate them. From the common cold to the common cold sore, they're annoying little buggers. The virus particle invades a cell, injects its proprietary genome, hijacks the cellular machinery and turns it into a virus-making factory. Upon successful completion of this process, the cell begins releasing fresh copies of the virus, often by bursting and dying.

Occasionally, however, something goes wrong in the integration process. When this occurs, the cell can survive, but selected portions of the viral DNA remain in its genome. These vary from infection to infection, not just from virus to virus.

In effect, the cell becomes permanently scarred and carries the unique, identifiable fingerprint of its assailant. (Source)

Since the markers are now in the genome, they become hereditary--hence, any descendant of the afflicted cell will contain the same exact viral fingerprint(s) at the same exact spot in its DNA.

Viral infections are, of course, not limited to the mucous membranes, blood stream and lungs. Under certain conditions, they can also infect a germ line (egg or sperm) cell. The odds of this cell now surviving to adulthood are astronomically low; not only does it have to survive a viral infection, but be one of the extremely lucky few that ever make it to merge with their counterpart and form a viable zygote.

However, this does occur. When it does, the resulting offspring has the unique viral fingerprint embedded in every cell in its body, what is known as an "endogenous retroviral insertion", henceforth referred to as an ERV. (Source)

ERVs can be easily identified by their extreme similarity to known retroviruses. They even contain vestiges of gag, env and pol genes that code for viral surface proteins (explanation of GEP protein coats, information on their presence in ERVs).

We've directly observed creation of new, identifiable ERVs by viral integration into cells in vitro, as well, so this process is as well-documented (if not more) as fossil formation. When it occurs in ordinary cells, it can cripple vital genes, subsequently causing cancer. High-risk papillomaviruses have been indicted as one of the leading causes of cervical tumors, for example. (Source)

Like any genes, the viral elements can then piggyback on the success of an individual and become established in the entire species. In small populations, this can easily occur via genetic drift (random establishment of selectively neutral or deleterious alleles). In larger ones, natural selection can work to establish the few ERVs that yield a benefit to their host.

Each step in the process is not very common, and has unique aspects that are extremely unlikely to be reproduced in two independent cases of ERV creation. Hence, when they all occur, the organisms possessing the ERV are marked with a molecular fossil that will prove indispensible in tracing their origin.

2. Evolutionary Implications of ERVs

In a nutshell, this can serve as a "paternity test" of sorts: if you find the same endogenous retroviral insertion in two different organisms, the only viable explanation is that they inherited same from a common ancestor that, itself, possessed it. Offshoot species will have the same unlikely and easily identifiable ERVs, enabling us to construct accurate phylogenies from an independent line of evidence.


Human endogenous retroviral insertions in identical chromosomal locations in various primates. Notice just how well the standard evolutionary phylogeny, derived from fossil and anatomical evidence (humans and chimps closest, then orangutans and gorillas, then gibbons, then old world monkeys, then new world monkeys) is corroborated by this uniquely independent line of evidence.(Source)

As a side note, ERVs have also been used to reconstruct the relationships between dogs, jackals, wolves and foxes, among other species of domestic animal.

Needless to say, this offers a quick and easy way to experimentally test if any two similar organisms are unrelated. If they are, they won't share any ERVs. If you find the same one at the same place in their genomes, however, the hypothesis they originated independently is effectively falsified.

Due to the nature of the branching tree of life, ERVs shared between distantly-related organisms will have made their initial appearance in their common ancestor. Hence, they would have also been present as further, closer organisms split off from the lineage; if you find an ERV common to humans and monkeys, the ancestor of chimps must have had the insertion as well. Similarly, ERVs found in New World Monkeys and chimps will usually be present in humans. ERVs found in humans and gorillas should be found in chimps. And so on. This provides an additional way to test evolutionary predictions.

It should be noted that there are rare but observable genetic phenomena that can remove ERVs from the genome. However, we can almost always tell when this has occured, such as identifying the characteristic fingerprint of a deletion mutation right before the ERV 'should have' been found.

Nevertheless, the more basic question of 'are there shared ERVs between these species at all?' is a much more stringent, rock-solid test of evolution than the specific phylogenetic relationships individual insertions indicate, which can be erroneous on occasion.

When analyzed as a statistical whole, ERV insertion patterns will also recapitulate phylogenies drawn from independent data like the fossil record and comparative anatomy. This is a remarkable confirmation, and totally at odds with the predictions made by the hypothesis of independent origin of species.

As you can see by now, this is the strongest support for evolution I've ever come across; a truly powerful and damning smoking gun

Ida? I hardly knew her!

The interwebz are abuzz with news of the discovery of what has been termed "a missing link" in the ancestry of human evolution. Called Ida, it's big news and many news agencies, forums, etc, have caught the reporting bug, and therein lies the problem. The thing is, there isn't anything inherently wrong with spreading the news of the discovery; no, the problem is when articles and reporters - particularly major ones - make a hash of the entire dissemination of the science and fossil discovery.

Take the Sky News article, for instance. Within the first few paragraphs in the article, you find this gem:

Researchers say proof of this transitional species finally confirms Charles Darwin's theory of evolution, and the then radical, outlandish ideas he came up with during his time aboard the Beagle.

Wtf? Seriously? Finally confirms? No, this find doesn't finally confirm the theory of evolution: the many different lines of evidence for the occurrence of evolution ensured any confirmation years ago. What this find does is join a hot of other affirmations of the theory of evolution, and Darwin's "radical, outlandish ideas". Wait, actually, wouldn't it be a misnomer to call them simply ideas, considering the amount of work that went into building the theory?

Perhaps I'm being too pedantic. Then again, it might reduce the chance of several of the idiots - like the ones that responded to the sky article - getting muddled up about what the discovery entails.


That does bring me to an important point, though. For many, it would seem that the theory of evolution has no evidence. For some, that it's called a theory ("it's a theory, don't you know, a theory! Not fact") is enough dismiss the whole thing. While I find it a bizarre argument, I have heard it several times.

First, for anyone interested, a theory, a science theory, is the highest level of acceptance in science. To paraphrase that famous quip, theories aren't things that people think up on a drunken night out; they are findings that backed by some kind of evidence - see facts - and open to falsifiability. Thus, it should be understood that, contrary to what some misguided say, theories don't get "upgraded to laws". That doesn't happen. On the other hand, laws can be superseded - in a manner of speaking - by theories. For example, and probably the most famous case, Einstein's theory of relativity complementing and explaining some things that the Newton's law of gravity couldn't.


Second, there are several lines of evidence that affirm the theory of evolution. My personal favourite is the existence of shared endogenous retrovirus insertions between several species. That's all I'll write on the subject for now.

Third, fossilised remains of transitional organisms.

Anyway, this became longer than I intended. Welcome to the wide, wild world of celebridom, Ida.

The sky article gave the link and it's a good one: for any interested in Ida, the discovery of the fossilised remains, and the characteristics of the purported transitional.

http://www.revealingthelink.com/who-is-ida/

Ida is the most complete early primate fossil ever found, and scientists believe that she could be one of our earliest
ancestors. She is a remarkable link between the first primates and modern humans and despite having
lived 47 million years ago, her features show striking similarities to our own.

http://www.revealingthelink.com/the-implications/

Ida's discovery gives us unique insights into primate development at the root of anthropoid evolution – when primates were first developing features that would evolve in our own.

Key facts about the most complete primate fossil ever discovered
http://www.guardian.co.uk/science/2009/may/19/fossil-ida-at-a-glance


Righto!

State your controversial opinions

Background: This was sort of a response to someone arguing for legalised pedophilia - you know, the one where the adult insists that the child consented, so it's all good - on that website. What I've written should be read as is and understood with humour. No, really.

I say it's about time we in the West started conscripting children into the Army. In fact, I propose that we start wars intentionally so that the children get a taste of blood in their teeth. I have no doubt that children have thought of fighting and killing, so it's up to adults to show them the way and help them experience their latent violent desires. It's even better if they consent.And, hey, if children aren't mature enough to fight in wars, they shouldn't be allowed to imagine violence or have disagreements with each other. Why? Because both sets of activities have the same end in mind: expression of the death drive in a natural manner. Now, if someone was only willing to interview select child soldiers from those War-torn African countries, I'm sure we''ll find that those who survive have benefited greatly from their experiences. As for any that want to give a negative picture of child soldiering, we can just point out that "hey, dipshit, you're still alive. Walk it off, pussy."Which brings me to trauma. The only reason any child can possibly be traumatised by having to fight for his or her (yes, girls must be allowed to fight too - especially if they want to) motherland has to be that the child has internalised societal beliefs that war is wrong.While I'm on the subject of kids, I say it's time that society get its dirty, normative inducing, controlling paws off them. If a kid wants to lead a country, company or whatever, on a whim, I say let them. If they have the instinct for it, then they evidently ready for the real thing.

Ed: Holy shit, Batman, seriously?


And that reminds me, isn't it about time someone killed that Batman, prick? Kids? Kids? Anyone?

Oh, Emily, how I do love thee

I've heard it said that it is almost impossible and improbable to have to pick out a favourite when it comes to art. I agree. In poetry, though, when all else fails, one of my favourite poets has to be Emily Dickinson. That lonely, wren-like, but wonderful poet heeded the call and wrote beautiful verses. Since I'm particuarly inclined towards paying undue attention to death, perhaps because I'm one of those mostly solitary introverts, her "death poems" intrigue me.
Two favourites:

Here's one:

Because I could not stop for Death,
He kindly stopped for me;
The carriage held but just ourselves
And Immortality.

We slowly drove, he knew no haste,
And I had put away
My labor, and my leisure too,
For his civility.

We passed the school, where children strove
At recess, in the ring;
We passed the fields of gazing grain,
We passed the setting sun.

Or rather, he passed us;
The dews grew quivering and chill,
For only gossamer my gown,
My tippet only tulle.

We paused before a house that seemed
A swelling of the ground;
The roof was scarcely visible,
The cornice but a mound.

Since then 'tis centuries, and yet each
Feels shorter than the day
I first surmised the horses' heads
Were toward eternity.

Another:

I heard a fly buzz when I died;
The stillness round my form
Was like the stillness in the air
Between the heaves of storm.

The eyes beside had wrung them dry,
And breaths were gathering sure
For that last onset, when the king
Be witnessed in his power.

I willed my keepsakes, signed away
What portion of me I
Could make assignable,-and then
There interposed a fly,

With blue, uncertain, stumbling buzz,
Between the light and me;
And then the windows failed, and then
I could not see to see.


I shall refrain from commenting on them; choosing, instead, for their words, metre, etc. to convey subjective meaning to reader in different/several readings.

The death poems aren't the only ones I find fascinating, as Dickinson's other poems are just as rich.

Gedankenpolizei

2:17 am. I need to sleep. I can't sleep. A strange thing seems to have happened: I'm thinking episodically especially at this time

I cut myself. It hurts. Bleed. Bleed. Bleed. Here's a plaster. Easy. Take heed. Small cuts tend to affect all sense of self belief.

Seriously, though, I told her "I think about death often, these days...well, more often these days." I think of life after death more often these days.

If I can summon the will, I'll make a boat. I'll travel out to sea. No one would be able to take that away from me. I'll sail and die then watch my body, for a while, while I float.

Since I cannot see what is going to happen, I'll resign myself to life. Not fully a knight of faith since I find myself resisting, I'll serve as a knight of resignation. I take life.

Pity is the worst offering, then, that can be given at this time. The thought of pity saddens me more. I think I'll try for sleep again. It is now 2:30 am.

It's a generation thing, buddy

The inspiration for this entry was a topic that was introduced and partially discussed in one of the seminars in my course. The wider context of the seminar was - or, I suspect, should have been - using Marxism to interpret literature. Instead, we mostly ended up discussing the implications and indictment of the modern English young working force suggested in the first part of Andrew O'Hagan's Orwell Memorial Lecture, The English. In the seminar, I managed to spout out some garbled nonsense about commodity fetish, upward mobility, and alienation - basically, things that could fit within the narrow context of Marxism in response to O'Hagan's polemic. However, I don't think those things begin to touch on the more important cause and effect of what seems to be disillusionment in the young English "proletariat".

This disenfranchised state in the mostly young (and I should mention that words like disillusionment, disenfranchisement, etc may well prove to be either misnomers or understatements) that suggests itself through an overwhelming amount of binge drinking and a high rate of depression is, I would suggest, the making of the effects of the post-modern condition. Post-modern condition: a vague term to be sure.

To be clear then, by post-modern condition, I mean the era marked by the appreciation of the implication of the "death of God". By that I mean a time in society when the people (begin to) realise that god has died and we humans are all alone in a vast universe.

The death of God, for anyone familiar with Nietzschean philosophy, was predicted to happen, and I don't know exactly when it happened. In any case, it happened; and while the mad man may have come too early for the occupants of The Gay Science, the news of god's death finally "reached the ears" of the English, and was transmuted to the young. That is the legacy with which we will have to live. However, with the death of god comes the inevitable loss of human transcendence. No longer made in the image of God. We poor creatures, evolved from what we would have previously derisively called "lowly beasts", have learnt to realise that we have no heavenly hand to tip a favour our way. The earth, it seems, is really just the palest of blue dots amongst innumerable other dots in the dark, stark ocean of space and time. In the true fashion of our oedipal instincts, we killed the father birthed to us by history - we destroyed his myths too. We had no choice.

Having destroyed the mythologies attached to God, it would have been necessary to create a new set of myths. Stories to encourage a meaning in life. Therein lied the problem. Killing god meant avoidance of metaphysics and overt pretensions towards attaching transcendental properties to humanity. We started constructing our modern mythos anyway. We had no choice.

These modern set of mythologies all bear the same instinct: perverse materialism. And in our extremely materialist mythologies, we gave into that base instinct that ensures we recreate in idealised images, and founded an unprecedented celebrity culture. With celebrity culture came high doses of commodity fetishism and the need to believe that life would be that much better if the average prole became a celebrity too. In fact, our myths evolved even more into something resembling: well, you might not become a celebrity, but life could still approach happiness and completion if you use the same commodities celebrities use. What a mythology. Further, with the availability of loans and credit, the finer parts of our myths were in some ways achievable - better yet, in a human lifetime.

The thing is, our myths were great until the reality of it all hit home. Perhaps that's the advantage the old myths had over ours: their aspirations were for a state after death; ours for status in life. Clearly our myths have shown themselves incapable. Worse, in the continued urbanisation of the better part of the world, they increase anomie and depression. Therefore, since nationalism is out, we need new religious myths. In America, the beginnings of a new religious myth can be seen: based on change through individuals feeling they are making a difference. Still retaining its humanist, secularist cloak, it, however, incorporates elements of transcendentalism of old mythos. Most importantly, though, the myth - built on a foundation of politics, nonetheless - has ensured that many of the people who at one time felt marginalised - alienated - now feel part of a community (even those opposed to the man central to the myth now have their own collective). Essentially, the individuals now feel they matter in an important way. Life has meaning then.

To sum up, I would say there's a problem in a community when a large number of its members seem to be channelling their death drive into binge drinking, etc. The solution may be not a socialist revolution, but invention of a mythos fit for our time.

New Year, No Resolutions

It feels like it's been a century since I last crapped in this here bog. A New Year has come - full circle in the human conception - and I feel I should continue posting my messages to my future self - writings exist in history; bringing us news from the past; reminding what we will be of what we once were; subtly erasing the death lines.

I loved 2008. In its own way it taught me many things I ought to know, and I truly hate to see it go. However, time marches on. The future beckons. I have no firm decisions that might be counted as resolutions, so I probably should refrain from solidifying any of my options through typing them. What comes to mind, though, is that I want to write, read, love and learn to a great degree this year. Yes, I think I'll do those. I'll start with those and see what happens next. It's 2009, and it, too, will die soon. The trick is to make sure it doesn't waste away.

Happy New Year, fellow traveller.