Universal language of genes

The Genetic Code is the language with which DNA talks to the rest of your body chemistry.  The function of a gene is to give the body instructions for making a particular protein.  One gene, one protein.  And the letters in the DNA molecule (A, C, T, G) combine in 3-letter words, in which each 3-letter word stands for an amino acid.  Cells are equipped with machinery that speaks this language, and reading 3-letter codons from the DNA template, ribosomes add one amino acid at a time until a protein is built to spec.

Biochemists since Francis Crick in the 1950s have taken the Genetic Code to be an arbitrary language.  Now it turns out not to be so arbitrary.  There is a natural chemical affinity between each 3-letter codon and the corresponding amino acid.  This is a big hint about how the Genetic Code came to be.  It is possible that the Code was created first, and ribosomes came later, as a refinement.

New Scientist article

1 May 2010


Every practitioner of mindfulness learns that the longer we sit still, the deeper and more uncomfortable are the truths we are invited to confront.

Acknowledging the truth about who we are is a process that demands ruthlessness and tenderness in equal measure. 

— Josh Mitteldorf

2 May 2010

Invocation to Kali

It is time for the invocation, to atone
For what we fear most and have not dared to face:
Kali, the destroyer, cannot be overthrown;
We must stay, open-eyed, in the terrible place.

Every creation is born out of the dark.
Every birth is bloody. Something gets torn.
Kali is there to do her sovereign work
Or else the living child will be stillborn.

It is time for the invocation:

Kali, be with us.
Violence, destruction, receive our homage.
Help us to bring darkness into the light,
To lift out the pain, the anger,
Where it can be seen for what it is—
The balance-wheel for our vulnerable, aching love.
Put the wild hunger where it belongs,
Within the act of creation,
Crude power that forges a balance
Between hate and love.

Help us to be the always hopeful
Gardeners of the spirit
Who know that without darkness
Nothing comes to birth
As without light
Nothing flowers.

Bear the roots in mind,
You, the dark one, Kali,
Awesome power.

— May Sarton, born this day in 1912
Read fuller excerpt from poem.

3 May 2010

Paradigm and Paradox

Reason and imagination. Theme and improvisation. Structure and chaos.

Sometimes we stay within the lines, at other times, though not often enough, we bravely step outside the box to fly high or free fall or float along unencumbered.

We encounter paradigm daily in the norms and expectations, roles and regulations of religion and society.  Paradigm is clear and convincing and difficult to remove. Paradox, on the other hand, is contradictory and unbelievable, absurd and often compelling, impossible but true. It projects the tension of opposites that are held simultaneously, and is therefore given short shrift by the logical Western mind. We come up against it everywhere, and more often than not we dismiss it by saying, that’s just the way it is, or, it’s a mystery.

Miriam Therese Winter, from Paradoxology.

It is time we refuse to accept disempowering models that mimic community,
 time to reject outrageous behavior from those in leadership roles.

4 May 2010

Do not say ‘it is morning’ and dismiss it with the name of yesterday. See it for the first time as a newborn child that has no name.

Rabindranath Tagore

5 May 2010

New Scientist on quantum weirdness

It is tempting, faced with the full-frontal assault of quantum weirdness, to trot out the notorious quote from Nobel prize-winning physicist Richard Feynman: “Nobody understands quantum mechanics.”

It does have a ring of truth to it, though. The explanations attempted here use the most widely accepted framework for thinking about quantum weirdness, called the Copenhagen interpretation after the city in which Niels Bohr and Werner Heisenberg thrashed out its ground rules in the early 20th century.

With its uncertainty principles and measurement paradoxes, the Copenhagen interpretation amounts to an admission that, as classical beasts, we are ill-equipped to see underlying quantum reality. Any attempt we make to engage with it reduces it to a shallow classical projection of its full quantum richness.

Lev Vaidman of Tel Aviv University, Israel, like many other physicists, touts an alternative explanation. “I don’t feel that I don’t understand quantum mechanics,” he says. But there is a high price to be paid for that understanding - admitting the existence of parallel universes.

In this picture, wave functions do not “collapse” to classical certainty every time you measure them; reality merely splits into as many parallel worlds as there are measurement possibilities. One of these carries you and the reality you live in away with it. “if you don’t admit many-worlds, there is no way to have a coherent picture, says Vaidman.

Or, in the words of Feynman again, whether it is the Copenhagen interpretation or many-worlds you accept, “the ‘paradox’ is only a conflict between reality and your feeling of what reality ought to be”.

Read more: Seven wonders of the quantum world

You’ll forgive me if I don’t make a quantum leap to Vaidman’s Many Worlds perspective.  Which world do I live in?  Does it matter if I am the one making the measurement, or if it is someone else?  Is a measurement made whenever a macroscopic particle is affected, or only a conscious mind perceives something?  I remain mystified.

6 May 2010

Beyond all Shores and Seas

LIES yet a well of wonder
All shores and seas beyond,
Where shines that dimness under,
More deep than in a dream,
Full many a diamond
With elfin gleam,

Glows up the glimmering water
Full many a ruby’s fire:
If ever an earth-born daughter
Their wizard light behold,
She may no more desire
Our gems and gold.

Nay, some in sooth, who only
A dream thereon did gaze,
Thenceforth fare wandering lonely,
And seek with sorrow vain
The glory of such rays
To find again.

Oft, oft, high-heavenward turning
The quivering stars have conned,
Or watched the wide west burning
Nor shall their hearts appease,
Whose hope lies hid beyond
All shores and seas.

Jane Barlow

7 May 2010

Five Hindrances + One

In the Theravada Buddhist tradition, there are five obstacles to the ongoing practice of mindfulness:

  1. Clinging (I want)
  2. Aversion (Get that away from me)
  3. Agitation (’nuf of this sittin’ around)
  4. Torpor (yawn)
  5. Cynicism (yeah, yeah)
    ... to which Bob Chapra adds
  6. Doctrine (especially the making of numbered lists)

Just eliminate these tendencies from our minds, and we’ll be fine.  I guarantee it.

8 May 2010

How to teach

The lowest form of teaching is to repeat what has been taught to you.

Better is to share your experience with your students.

Best is to create a space in which students may have experiences of their own, process and share their responses with you and with each other.

-Josh Mitteldorf

9 May 2010

Birthday indulgence

I have come to realize that the way my emotional life has something in common with the way Charles Ponzi managed money. That is, I am constantly engaged in planning for the future, promising myself a success or a joy, and (what is ironic) delighting for real in the anticipation of a reward which is a mirage.

On days that I work hard, exercise for health, create something, learn something, reach for a political goal, I am genuinely happy.  On days that I seek to reap my reward (Happy Birthday!) I feel shortchanged, and consumed by emptiness. ‘Is this all there is?’

When I see through this it can be a Cosmic Tragedy, but equally well it may seem a Cosmic Joke.

— Josh Mitteldorf, born this day in 1949

The most successful Ponzi schemes make some investors quite rich before they collapse.

10 May 2010

Genetic basis for morality

‘With the help of well designed experiments, you can see glimmers of moral thought, moral judgment and moral feeling even in the first year of life. Some sense of good and evil seems to be bred in the bones.’ 

Paul Bloom (Yale Dept of Psychology)

Bloom and his coworkers conducted experiments in which they showed puppet shows to 6-month-old babies, and subsequently tested for
David Derbyshire article in Mail Online UK

Once we realize that aspects of morality are in our genes, hard-wired into our brains, does that give us more faith or less faith in morality?  On the one hand, it suggests that morality is more than a cultural construct, with validity limited to a given cultural context.  On the other hand, it puts morality in the same class with fear, aggression, hunger, greed and a host of other emotional responses that have been programmed by evolution into our brains.

Essay in Nature by Paul Bloom

11 May 2010

At peace with death

Gabriel Fauré, born this day in 1845, wrote a Requiem free of angst and suffering, absent the traditional Dies Irae* movement about the wrath of Judgment Day.

Listen to the Pie Jesu, with boy sopranos from Kings College Choir, 1987

* For contrast, listen to the Verdi Reqiuem, full of fire and brimstone.

12 May 2010

Moments of insight are all we get

WE sow the glebe, we reap the corn,
  We build the house where we may rest,
And then, at moments, suddenly,
We look up to the great wide sky,
Inquiring wherefore we were born…
  For earnest or for jest?

— Elizabeth Barrett Browning
          more here

13 May 2010

My brother

“You can rob a man of all he holds dear and get him to thank you for it.  But try to take away his suffering, and he’ll fight like hell.”

— Bruce Mitteldorf, born this day in 1952

Eat til you’re tired, sleep til you’re hungry.

14 May 2010

Political activism - not optional

“The 10,000 year experiment of the settled life will stand or fall by what we do or don’t do now...Now is our last chance to get the future right.”
— Ronald Wright, A Short History of Progress


“Reformers who are always compromising, have no yet grasped the idea that truth is the only safe ground to stand upon.”
Elizabeth Cady Stanton (1815-1902)

15 May 2010

The only refuge

Our life’s work as humans: the transition from seeking comfort in predictability and stasis to taking comfort in mystery, unpredictability, and faith in a larger benevolence. For followers, this transition is usually made through a social group, and the faith is in religious doctrines received.  But for scientific types, there exists another path to this same place: it consists in pursuing science to its endpoint, and appreciating the oceans of mystery that border the scientific islands of understanding. 

— Josh Mitteldorf

“The most important question any human being can ask himself is, ‘Is this a friendly Universe?’”

16 May 2010

Breathing Exercise: A How-To Poem
For Gil Fronsdal, and in memory of Mark O'Brien (1949-1999)

The distance between the brightness
at the top of the spine
and the darkness below it

is not far
but when you shrink your mind
it is enormous

the whole length
of human history
can be fit inside it

One way to reduce it a little
is with practice and preparation

(the latter takes minutes each morning
the former has taken me years)

to gather the sensations in our belly
into our in-breath

(do this slowly and with enjoyment
the darkness deep inside us
should be like the jungle in Thailand

where we may acknowledge the presence
of unseen pythons and kraits

but our actual sensations
as we search the deep canopy
for crimson sunbirds

are of lazy butterflies
and flowering lianas)

and then by a skilled relaxing
of both muscle and nerve
guide our breathing

slowly up the back of our spine
so that it breaks over the top
like a wave breaking over a quiet beach

to drench the scattered thoughts
spread out to no purpose
and then draw them slowly back down

in the descent of the out-breath
to the dark easy rhythm

of the untiring diaphragm
where the in-breath began

Relax the spaces in between
each vertebra
let each space slightly expand

until in each out-breath
you can exhale metta (loving kindness)

commingling the cool light
and warm darkness

to those whom you usually consider
enemies and friends

Peter Dale Scott

17 May 2010

From an Inaugural NYTimes Philosophy Blog

Socrates tells the story of Thales, who was by some accounts the first philosopher. He was looking so intently at the stars that he fell into a well...What is a philosopher, then? a laughing stock, an absent-minded buffoon, the butt of countless jokes...

As Wittgenstein says, “This is how philosophers should salute each other: ‘Take your time.’”...

Socrates says that those in the constant press of business, like lawyers, policy-makers, mortgage brokers and hedge fund managers, become “bent and stunted” and they are compelled “to do crooked things.” The pettifogger is undoubtedly successful, wealthy and extraordinarily honey-tongued, but, Socrates adds, “small in his soul and shrewd and a shyster.” The philosopher, by contrast, is free by virtue of his or her otherworldliness, by their capacity to fall into wells and appear silly .... Because of their laughable otherworldliness and lack of respect for social convention, rank and privilege, philosophers refuse to honor the old gods and this makes them politically suspicious, even dangerous.

Simon Critchley

18 May 2010


Enceladus is a minor moon of Saturn, given up by astronomers as a boring hunk of rock until recent photos returned by the Cassini spacecraft told a curious story.

There are geysers spewing steam many miles and into space from Enceladus’s south pole.  The earth has vulcanism from a hot, iron core.  But Enceladus is much smaller than the earth, and its core should have cooled off long ago.  What’s going on? The best guess is a two-part explanation: 

  • First, ‘boiling hot’ doesn’t mean the same thing on such a small planet.  Because the atmosphere is so thin, water can boil at temperatures that you and I might not call hot.  In fact, the high temperature found by satellites was 116 degrees C below zero - still hot enough to boil water in the near-vacuum of space.
  • But even this is hotter than the planet ought to be, since it is so far from the sun and it is white, so it absorbs very little sunlight.  Our best theory about the the energy in the interior is that it comes from sloshing around of molten rock in the interior from powerful tidal forces.  (Tidal forces come from the fact that one side of the moon is closer to the sun, and is pulled harder by the sun’s gravity, while the other side is closer to Saturn, and so is pulled harder by Saturn.  A few days later, the moon moves so that the sun and Saturn are now on the same side of it, and so molten rock in the interior is drawn back and forth repeatedly.) 

Maybe there’s an ocean of liquid water under Enceladus’s surface.  Maybe there’s life in that ocean.

Article and pictures at SolarViews
NASA’s Cassini results
Wikipedia article

19 May 2010

Don’t think too hard about whether it’s possible

Rabbi Tarfon used to say, ‘It is not incumbent upon you to finish the task, neither are you free to desist from it.’

פרקי אבות (Wisdom of our Fathers 2:21)

20 May 2010

Privilege for what?

Elizabeth Fry was an early British Quaker, moved to translate her faith in God into work for political change.  Her family founded the Barclay Bank of England, but she worked to house the homeless.  She used her freedom to work on behalf of prisoners, advocating successfully for reform.

I wish the state of enthusiasm I am now in may last, for today I FELT there is a God. I have been devotional and my mind has been led away from the follies that it is mostly wrapped up in.

Elizabeth Fry, born this day in 1780, is now depicted on the British 5 pound note.

Oh Lord, may I be directed what to do and what to leave undone

21 May 2010

The Silken Tent

She is as in a field a silken tent
At midday when a sunny summer breeze
Has dried the dew and all its ropes relent,
So that in guys it gently sways at ease,
And its supporting central cedar pole,
That is its pinnacle to heavenward
And signifies the sureness of the soul,
Seems to owe naught to any single cord,
But strictly held by none, is loosely bound,
By countless silken ties of love and thought
To everything on earth the compass round
And only by one’s going slightly taut
In the capriciousness of summer air
Is of the slightest bondage made aware.

— Robert Frost

22 May 2010

Like genius and madness,

Ecstasy and terror are next door neighbors.

— Josh Mitteldorf

Be sure to avoid the left turn into numbness.

23 May 2010

Principia Mathematica,

the masterpiece of Bertrand Russel’s youth, was published 100 years ago today.  In it, he and Alfred Whitehead sought to put mathematics on a firm logical footing, by proving that every well-formed statement that could be made from a minimal set of math symbols was either true or false.  Math may be subtle, but at least mathematicians can be sure that they’re not on a fool’s errand, trying to devise a proof when, in fact, none is possible.  Russell and Whitehead published their book, despite recognizing that there was a small loophole left to be plugged in

This was a bulwark of Logical Positivism, helping to distinguish a philosophy that eschews abstraction, and posits that the physical universe is all we have, and all that we have any business talking to each other about.

No one imagined that the thesis could be false, except Kurt Godel, a young German mathematician who worked hard not to prove but to disprove it. In 1926, he demonstrated that every mathematical system has an infinite number of statements that seem to make perfect sense, but they are are ‘in limbo’, forever neither true nor false.  There is no proof and no disproof that can resolve this.

Other problems with the Positivist program soon surfaced. The Quantum Theory at the basis of physical descriptions of reality describes a world quite alien the Logical Positivists.  For example, individual particles have no separate existence, but can only be described (as in a laser) as part of an indivisible multi-particle state.

Today, Logical Positivism is alive and well, in that most Westerners who think of themselves as enlightened and above superstition treat the world as if it were rational and objective.  The fact that the foundation of their faith has failed the test of empiricism doesn’t seem to bother them.

To me, the point is that there is a portal from science to mysticism.

24 May 2010

Those who dwell among the beauties and mysteries of the earth are never alone or weary of life.

— Rachel Carson, born this day in 1907

25 May 2010

All the world

The fiction of dignity helps to define humanity and the status of humanity helps to define human rights. There is thus a real sense in which an affront to our dignity strikes at our rights. Yet when, outraged at such affront, we stand on our rights and demand redress, we would do well to remember how insubstantial the dignity is on which those rights are based. Forgetting where our dignity comes from, we may fall into a posture as comical as that of the irate censor.

Life, says Erasmus’s Folly, is theater: we each have lines to say and a part to play. One kind of actor, recognizing that he is in a play, will go on playing nevertheless; another kind of actor, shocked to find he is participating in an illusion, will try to step off the stage and out of the play. The second actor is mistaken. For there is nothing outside the theater, no alternative life one can join instead. The show is, so to speak, the only show in town. All one can do is to go playing one’s part, though perhaps with a new awareness, a comic awareness.

We thus arrive at a pair of Erasmian paradoxes. A dignity worthy of respect is a dignity without dignity (which is quite different from unconscious or unaffected dignity); an innocence worthy of respect is an innocence without innocence. As for respect itself, it is tempting to suggest that it is a superfluous concept, though for the workings of the theater of life it may turn out to be indispensable. True respect is a variety of love and may be subsumed under love; to respect someone means, inter alia, to forgive that person an innocence that, outside the theater, would be false, a dignity that would be risible.

J.M. Coetzee

26 May 2010

Every happiness is the child of a separation it did not think it could survive.

        — Rainer Maria Rilke (tr Anita Barrows and Joanna Macy) full text here


27 May 2010

Being a scientist is a special privilege: for it brings the opportunity to be creative, the passionate quest for answers to nature's most precious secrets, and the warm friendships of many valued colleagues. Collaborations extend far beyond the scientific achievements, no matter how great the accomplishments might be, the rich friendships which have no national borders are treasured even more.

Stanley Prusiner, born this day in 1942, discovered that an infectious agent could exist without any DNA or RNA.  It is simply a misfolded version of one of the body’s essential proteins.  Is it just chance misfortune that copies of this protein twisted in a particular way have the ability to transform other, properly folded proteins into the wrong shape?  The Creutzfeldt-Jakob prion reproduces selfishly as though it were an evolved parasite.  But evolution works on DNA, not on proteins (which are always derived from DNA, and never vice versa.)  This mystery remains unresolved.

Because our results were so novel, my colleagues and I had great difficulty convincing other scientists of the veracity of our findings and communicating to lay people the importance of work that seemed so esoteric! As more and more compelling data accumulated, many scientists became convinced.

Prusiner is being modest.  He began his researches 20 years after the first prion hypothesis, and though his results seemed absolutely conclusive, it required another 15 years for the medical community to accept his results. 

28 May 2010

‘This is our purpose: to make as meaningful as possible this life that has been bestowed upon us; to live in such a way that we may be proud of ourselves; to act in such a way that some part of us lives on.’

Oswald Spengler, born this day in 1880, read broadly about distant cultures and ancient times, saw clearly the great heights and political dangers of his time and of ours.  I am particularly struck by his appreciation of the ease with which a free press can be made subservient to the larger-than-life lies of a political regime:

‘The press today is an army with carefully organized weapons, the journalists its officers, the readers its soldiers. But, as in every army, the soldier obeys blindly, and the war aims and operating plans change without his knowledge. The reader neither knows nor is supposed to know the purposes for which he is used and the role he is to play. There is no more appalling caricature of freedom of thought. Formerly no one was allowed to think freely; now it is permitted, but no one is capable of it any more. Now people want to think only what they are supposed to want to think, and this they consider freedom.’

29 May 2010

Faith in what?

It matters little in what object we invest our faith.  It is faith itself that releases us from fear, liberating our self-expression, our experience and our development.
— Josh Mitteldorf

That said, I would not advocate faith in violence, in social theories that privilege some groups to subjugate others, or in political or religious demagogues.  It is not the faith that is at fault here, but rather the consequences of blind obedience to leaders or ideologies that gain their power by promoting conflict.

We who come from a rational, enlightened tradition may find that the very arbitrariness of the object of faith becomes a hindrance to belief. Can we raise faith through an act of will? I submit that we can, and that it is stubbornness and hubris to deny ourselves the benefit of faith as we stand on ceremony as exclusively rational beings.

I resolve this conflict in my own life as I consciously evoke and reinforce my faith, beginning at the point where scientific understanding leaves off.

30 May 2010

Women lead toward peace

LYSISTRATA:  We need only sit indoors with painted cheeks, and meet our mates lightly clad in transparent gowns of Amorgos silk, and perfectly depilated; they will get their tools up and be wild to lie with us. That will be the time to refuse, and they will hasten to make peace, I am convinced of that!


CLEONICE: ...But if our husbands drag us by main force into the bedchamber?

LYSISTRATA:  Hold on to the door posts.

CLEONICE:  But if they beat us?

LYSISTRATA:  Then yield to their wishes, but with a bad grace; there is no pleasure in it for them, when they do it by force. Besides, there are a thousand ways of tormenting them. Never fear, they'll soon tire of the game; there's no satisfaction for a man, unless the woman shares it.

In 411 BC, Aristophanes wrote about bold women who put their bodies on the line to strike for an end to the Peloponnesian Wars.  In 1915, in response to the madness engulfing Europe, Jane Addams organized the Women’s International League for Peace and Freedom.  Today, some of the bravest and most creative actions to expose the lies that support war in the Middle East come from Code Pink.

31 May 2010

Queen of Hearts — Archive of past entries. Bullfrog Design