• Origin of HIV

    Ed Rybicki's avatarViroBlogy

    I have previously posted a number of articles on “molecular archaeology” of viruses, and how one can use extant sequences, archived tissue samples, or even blood of pandemic survivors to speculate on the origins of specific viruses, of viruses generally, or on the nature of old pandemic strains.Now HIV falls under the spotlight – again – as the 2nd October issue of Nature publishes three articles (one letter, a commentary on it and an independent commentary) on the origins of HIV-1 pandemic strains.I picked up on the first news – evidence for an older-than-previously-thought origin for HIV-1 – via our local paper this morning. Now this is VERY impressive; they usually keep science news for a slow day, and here they were telling us about a Nature paper on the day it was published! Accessing Nature brought up the Nature News commentary by Heidi Ledford, titled “Tissue…

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  • very concise and apt article for students interested in virology

    Ed Rybicki's avatarViroBlogy

    This was originally written as an Answer to a Question posted to Scientific American Online; however, as what they published was considerably shorter and simpler than what I wrote, I shall post the [now updated] original here.

    The answer to this question is not simple, because, while viruses all share the characteristics of being obligate intracellular parasites which use host cell machinery to make their components which then self-assemble to make particles which contain their genomes, they most definitely do not have a single origin, and indeed their origins may be spread out over a considerable period of geological and evolutionary time.

    Viruses infect all types of cellular organisms, from Bacteria through Archaea to Eukarya; from E. coli to mushrooms; from amoebae to human beings – and virus particles may even be the single most abundant and varied organisms on the planet, given their abundance in all the waters of…

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  • A thin crust of unrequited love

    Frances Leech's avatartangerine drawings

    homemade garden pizza

    Once upon a time, four Parisians and a cat escaped to the south of France for a rural holiday, in a little yellow house with a large garden. They talked and read and lazed in deck-chairs. When they played pétanque, the cat raced up to each ball, like a referee judging distance. There was a jazz festival and a meteor shower. When it rained they sat around a fire with books, stirring only for tea and bread and jam. If they were too lazy to go the market, they only had to walk through the long grass to the vegetable patch. There were spaghetti squash (steamed, tossed with basil pesto, also from the garden) and beefheart tomatoes (sliced with salt and oil)  and long stalks of chard that were starting to go brown. (The chard went into everything – baked eggs, courgette soup, sauteed with chili and orange as a side dish.)

    The…

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  • 12 years have passed since she visited her school. She has herself become a teacher now. Yes, a teacher; but not quite the way she had expected. Her “gurudakshina” have turned into a sin. The principles she stood for all her life, she has defied one of them. Albeit this isn’t a first. The second broken principle and the second sin. 2 sins, 2 years apart. Each time she had broken one, she had lost a part of her “Guru”. The necessity for a greater “Gurudakshina” has increased. She have started taking tuitions. The very idea she disbelieved. She thought teaching as a duty. An inevitable obligation she must fulfil. A form of gratitude and the only mark of respect towards her teachers. A way of “Gurudakshina”, towards her motherland and teachers. Sadly, it had turned to be a last resort for survival. The “Guru” she sought in her motherland and her teacher, have been defiled.

    She finished the last line and went for a midnight stroll. While walking she came across a collapsing old house. She smiled, her first smile of the day. The house has been there since the past 6 years. As a child she used to wander in its alleys. It was a bridge to her way of thinking, a guide to this strange world. Much like her favourite teacher. One of her closest ideal of  “Guru”

    She remembered a saying by a renowned philosopher and teacher.

    “IDEAL TEACHERS ARE BRIDGES WHICH GUIDE STUDENTS TO THE OTHER SIDE. THEN LET THE BRIDGE COLLAPSE AND ENCOURAGE TO BUILD NEW ONES.”

    The old bridge has collapsed. It is time for a new bridge.

    She has to be THE BRIDGE.

  • Its been almost a year since she had put pen to paper. After a dull breakfast of cereals, she sat wondering.

    Suddenly, last evening’s conversation dawned on her. Her father was speaking of her cousin who is preparing for an US study endeavour. Unmindful, she heard the whole information series. Scarcely did she listen. The word “NEGRO” caught her ear. Yes, her father seemed it to be a suitable word to describe an African girl. Reminiscence of an old incident flashed back. Few months ago, her mother exclaimed of a girl with an uncalled for behaviour. The girl was apparently enjoying a cigarette on a sultry evening.

    The old yellow, green, red labels from her school days were back. This time, they were a more hard-hitting reality.

    She knew what to write about.

  • The rain that clears vision.

    The rain that makes love every time it falls.

    In foggy morning light,

    amidst misty twilight.

    The rain that makes you fall in love.

    The unknown passer-by’s song,

    the quarrelsome midnight feud.

    The rain that makes the poet write in monosyllables.

    Of words of frosty winter night,

    of someone’s frail eye-sight.

    The rain that makes you sad when you drench alone.

    Of long travelled past,

    twirling alleys of famished dust.

    The rain that sleeps as a little bemoaning kid.

    Tired of each day’s foul play,

    of building sand castles every way.

    The rain that rests in the crematorium by the night.

    Only to wake up at the voices of fright.

    The rain that will be again.

  • Of your sixty-nine,
    we are little over the line.
    In your nascent days,
    we were there to stay.
    since you’ve learned to walk,
    we’ve learned to talk.
    seldom we fray,
    into the narrow alley  where you stay.
    In your sixty-nine,
    we proclaim to be thine.
    Throughout the year,
    we seldom remember the line.

    Of your sixty-nine,
    I have hardly called you mine.
    Of your sixty-nine,
    I have barely known you nine.
    Of my twenty-four,
    I have known you all the more.
    So, on your sixty-nine;
    I would proudly call you mine.