DAY 96 Genome

August 2nd, 2014 § 0 comments

I was appalled, as I expect you were, that this profligate government, while refusing to spend a penny on the real needs of asylum seekers or the NHS, is planning to blow our taxpayers’ money on extracting, and storing, the genetic data of every man, woman and child in the realm. I don’t know what is going to happen to Scottish genomes

franklinRosalind Franklin

if they opt for independence, and I don’t expect the Government has thought about it, either; but assuming:

(i) that we’re dealing with a population of 63.23 million;

(ii) that each of them has 32 chromosomes, each with 3 billion base pairs;

(iii) that each base pair has four possible values (A, C, T, G I think, but someone might correct me);

Skipping the back of an envelope calculation as usual, I turned to https://www.biostars.org/p/5514/ or, ‘How Many Bytes is A Complete Human Genome?’ genomes1_1As you might expect, I was completely confused by the variety of answers. Apparently, when the four bases are packed into one byte (why not?) the zipped genome is 770 Mb, giving us 4.86871 E 10 Mb, or (help!) around 48.6 petabytes for the whole population. Where are all these petabytes going to be stored? No prizes if you guessed GCHQ.

[It is this blog's earnest hope that errors of fact, particularly of calculation, should be checked by readers and pointed out. How else does progress occur?] Anyway, let’s now get down to the cost calculation. Here we also have sources, if a bit inaccurate; but let’s suppose I turn up at the lab – or at G4S or GCHQ more likely – with my sample of blood or sperm, and don’t charge for my labour in extracting it. Now, the people at Bloomberg (who should know) say that the cost of sequencing one genome is set to ‘drop to $1,000′ – it’s currently $10,000. To get 96 billion base pairs for that price seems ludicrously cheap; (exercise: how many base pairs can you get for a dime?)

So go figure. The government is aiming to hit the hard-pressed taxpayers for a minimum of sixty-three billion dollars, or thirty-seven billion pounds. This is far more than a rather low estimate (£20 billion) of the Trident replacement. How can a poor country like us afford it? I know you’ll say we can economize by not counting identical twins; twins

but they’re only 4 in 1000 births, which won’t save much.

No, it’s obvious that once the dark forces have gathered our genomes onto their database, they will try to recoup the huge cost by selling it off to one and all. The banks would want to know who had the overdraft gene; Ryanair might pay for finding out who had an inherited intolerance of cramped airliners, so they could adjust their rates. As you might imagine, whatever the government may say, the security of your data is the last thing they’ll think about.

[Added in proof. If the above reflections weren't enough, I invite you to consider - as the government blatantly has not - the fact that a so-called 'individual' or 'subject' in our population in in fact a complex ecosystem, a space in which (in whom?) multiple organisms coexist. [Another blow to Descartes?] See, for example, recent studies of the variety of bacteria – or even archaea – to be found in the navels even of those who had been washing themselves scrupulously. Some of whom (I mean the bacteria, not the so-called subjects) our researchers termed ‘oligarchs’, perhaps because of their frequency, although the implications of navel-inhabiting bacteria taking over Premier League football clubs are hard for this writer to take on board.everyone-blog-Bacillus-300x300

Belly-button bacteria

In any case, any serious study of the nation’s genomes must necessarily consider the genomes of the bacteria which inhabit its guts, its navel, et al. Which will inevitably cost more than the trivial $1000 per head, even if the average bacterial genome has only about a million base pairs (my information here is wildly erratic, and I’d welcome some help). But… at this point I run into problems of estimating the number of species, and so on. How much will it cost to launch the truly important Human Ecosystem Genome Project, sequencing every genome for every being inhabiting every inhabitant of our islands – even if we restrict to UK citizens? Of course, we can’t forget fleas.]

Well, that’s enough on my usual obsessions. On to the Muses! I thought that Psalm 23 would be fairly uncontroversial, since the followers of most religions think it’s one of the better psalms – not self-pitying, aggressive, and so on.

א  מִזְמוֹר לְדָוִד:    יְהוָה רֹעִי, לֹא אֶחְסָר. 1 A Psalm of David. The LORD is my shepherd; I shall not want.
ב  בִּנְאוֹת דֶּשֶׁא, יַרְבִּיצֵנִי;    עַל-מֵי מְנֻחוֹת יְנַהֲלֵנִי. 2 He maketh me to lie down in green pastures; He leadeth me beside the still waters.
ג  נַפְשִׁי יְשׁוֹבֵב;    יַנְחֵנִי בְמַעְגְּלֵי-צֶדֶק, לְמַעַן שְׁמוֹ. 3 He restoreth my soul; He guideth me in straight paths for His name’s sake.
ד  גַּם כִּי-אֵלֵךְ בְּגֵיא צַלְמָוֶת, לֹא-אִירָא רָע–    כִּי-אַתָּה עִמָּדִי;
שִׁבְטְךָ וּמִשְׁעַנְתֶּךָ,    הֵמָּה יְנַחֲמֻנִי.
4 Yea, though I walk through the valley of the shadow of death, I will fear no evil, for Thou art with me; {N}
Thy rod and Thy staff, they comfort me.
ה  תַּעֲרֹךְ לְפָנַי, שֻׁלְחָן–    נֶגֶד צֹרְרָי;
דִּשַּׁנְתָּ בַשֶּׁמֶן רֹאשִׁי,    כּוֹסִי רְוָיָה.
5 Thou preparest a table before me in the presence of mine enemies; {N}
Thou hast anointed my head with oil; my cup runneth over.
ו  אַךְ, טוֹב וָחֶסֶד יִרְדְּפוּנִי–    כָּל-יְמֵי חַיָּי;
וְשַׁבְתִּי בְּבֵית-יְהוָה,    לְאֹרֶךְ יָמִים.
6 Surely goodness and mercy shall follow me all the days of my life; {N}
and I shall dwell in the house of the LORD for ever. {P}

Music

While many of us believe the ‘Super Mario Theme’ to be the most popular song ever written, figures are hard to come by. Even harder for today’s choice, ‘The East is Red‘, since it might be thought that the entire population of China owned a copy, at least in the sixties. Anyway, it’s an interesting subject on which to open an unfruitful discussion. Bye for now.

 

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