Friday, June 29, 2012


"Without a wish, without a will,
I stood upon that silent hill
And stared into the sky until
My eyes were blind with stars and still
I stared into the sky." -Ralph Hodgson

~ Serbian proverb

Each of us experience a moment in our childhood where we learn a truth that haunts us for a long time. For me, that experience was when I found out that our sun is a star.  I had a hard time accepting that this wonderful, bright thing - my Sun - was like all other shining stars in the night sky. Worse yet, I was soon to learn that stars have finite lifetime.  Devastating.  I remember thinking: You mean, one day the sun will die? It will dim, and there will be darkness?  I suppose most children are frightened by the concept of an exploding sun.  But for me, whether the sun will extinguish by dimming or by dying in a fiery, catastrophic, deflagration was irrelevant. 
When I remember how scared I was, I think about how I should broach this subject to my child in a few years.  To say "nothing lasts forever, even the sun" will not do; and I would not want to watch her little heart break like mine did.  As I look back, my underlying fear was that the sun dimming meant the world ending: no human, no pets, no plants . . . no life.  Explaining that this won't happen for billions of years will be no help, for a child cannot imagine what billion years mean.

Instead, being truthful in an extraordinary way is the route I'll take.  Perhaps Joni Mitchell took poetic liberty when she sang "we are stardust."  But we are.  Think about how beautiful all the stars are and how each one of us has a little shining star inside.  Instead of how we came to be, I will focus on the magical stuff that makes us up.  And instead of the bigger picture, I’ll take the microscopic view.

I may be treading on a delicate issue here, but since this post is not meant to pit creationism vs. evolution, let me put my views on the table: I believe that the creation story should be taken as an allegory and that each day does not equal 24 hours of time.  For me there is no disagreement between the Genesis stories and what astrobiology explains about Earth’s formation.  To the contrary, the creation story in Breishit (Gen 2:7) about G-d forming man from dust is impressively close to the mark, considering that it was written a long time before we knew anything about the formation of planets. 
Whatever your theistic views are, science has shown that the same elements that make us up - atoms like carbon and oxygen - are also expelled by dying stars when their supplies of hydrogen fuel are consumed.  These elements are expelled when a star explodes and accumulate under the force of gravity into molecular clouds that ultimately form into planets.  The dying stars release carbon, which combines with hydrogen to form organic compounds in space.  Those organic compounds are the precursors of amino acids, which in turn make up the proteins of all living organisms including humans.    Other elements on earth are also created in the heart of the stars, from gold, lead and uranium, forged in a dying star's supernova explosion, to the iron in our blood, and the calcium in our bones.
In fact, on 28 September 1969, thirty-one years to the day before my daughter's birth, the Murchison meteorite fell as a bright fireball in Victoria, Australia.  This meteorite contained fatty acids, sugars, all five nucleobases, and over 70 different amino acids.  Only 21 amino acids are found in the human body.  As late as the eighteenth century, western civilization saw meteorites and comets as messengers; in a sense they are, delivering stardust materials to the Earth.  
We may be of stardust, but there is more.  We are golden.  We are more than the elements and atoms that make us.  Our skills, compassion, shrewdness, uniqueness, and tenacious spirit show us that.  “Luminous beings are we; not this crude matter," said Master Yoda.  Still, I am happy that we are made of star stuff.  The death of a star, a death that is in our own sun's future, brings a promise of other worlds and other races.  While this will not happen in my lifetime or my child's lifetime, there's a sense that when our sun stops shining, this wondrous gift of life may not cease to exist.  Instead, our sun's demise may be a catalyst for some unfathomable life to come.  And those luminous beings will be made of that same stardust that you and I are made of.  So when the time comes for that truth-about-the-sun discussion, I can tell my daughter to look to the stars to see magical stuff and the promise of more good things to come.  Or I can tell her to simply look inside.

Joni Mitchell, Woodstock

Note: This article is published in the July issue of the Chronicles, Etz Hayim's monthly newsletter. On July 4th, enjoy the fireworks, but when the smoke clears up, stay awhile, and gaze at the stars, or "up above" as Tamar likes to call them. I know I'll be doing just that while camping in Maine. Enjoy and stay safe everyone!

Tuesday, June 26, 2012

Science in Sesame Street

Sometimes you don't really need to look far out into space, or dive deep into textbooks to ask those thought-provoking questions. The truth is there are wonders all around and lots of questions waiting to be asked. Just read the lyrics of Tamar's favorite sesame street song, which has become mine as well.

I wonder - sung by Ernie

Sometimes at night,
When I look up high,
I see a falling star in the sky.
And I wonder how, and I wonder why.
What makes a falling star go by?

Why does it fall?
And where does it go?
And how does it make that glittery glow?
I'm gonna find out 'cause I want to know.
And I wonder. I wonder.

  • For starters, falling stars are not stars, but are meteors traveling through space. As a meteor enter earth's atmosphere, the friction between its surface and of the air incinerates the meteor, leaving a blazing trail of light.
Sometimes I watch
A bumblebee fly
From rose to rose on a day in July.
And I wonder how and I wonder why.
What makes a bumblebee go by?

How does he fly
All covered in fuzz?
And why does he make that buzz that he does?
I'm sure it's more than just because
And I wonder. I wonder.
  • Well, the bumblebee's hair is thick to insulate it during cold weather, and serves a big role in pollinating flowers.  Think about your hair when you rub it with a balloon.  You create a static charge that makes it stand up.  When the bees fly, they build up the same charge that attracts pollens to their body hair, which they carry from flower to flower. As for the buzz, when the bees fly really fast to carry their weight, their wings create the sound.
How does a bunny hop, hop, hop?
And what makes popcorn pop, pop, pop?
Why does the rain fall drop by drop
And the lightning always come before the thunder?
I wonder.
  • The bunnies go hopping since their back legs are built strongly which make them good at escaping their predators.  They can also use their legs for kicking in self-defense when threatened. And the secret to a popcorn's pop is the small amount of water stored in a circle of soft starch inside the hard outer casing of the kernel. When the kernel is heated, the moisture inside creates a pressure build-up causing the casing to give way. Pop goes the popcorn!

  •   There are a couple of reasons why the raindrops don't combine to make a single stream. The main one being that raindrops start falling just as soon as they are too heavy to stay in the air. Second, because of the phenomena called "surface tension" and "air resistance" that prevents the drops from coming together as a stream as they fall downward. In fact, these two phenomena cause the droplets' shape.
  • And we all know about light traveling faster than sound, hence, lightning before thunder.
Do you ever wonder as you walk along
What makes a tiny little ant so strong?
Does every bird have a different song?
Do you wonder why?
Well, so do I. So do I. Hmm, I wonder why?
  •  Ants can lift objects 20 times their own body weight because of their small size. Its strength is related to volume and surface area, cubed and squared respectively. In other words, larger animals have to move the  greater mass of its own body than the tiny ant because of the ration of their surface area to volume. See? The ant is a beast!
  • Individual birds vocalize in complex many ways, using different words and phrases even if they're of the same species. They sing, squawk, chirp, caw, quack, hoot, cackle, screech and whistle. And some of them even bark! I only wish I knew what they're yapping about.

So the next time you find yourself watching Sesame Street where the puppets are singing about the wonders of this world, it's okay to enjoy it with your child, and hum along, and then find the answers. - maybe even together.

Friday, June 8, 2012

Phosphorus is still king (The arsenic bacteria saga)

The results are in. No arsenate backbone in bacterial DNA.  The much awaited paper comes from Rosie Redfield's group who has devoted their time and resources to refute the original Science paper by Felisa Wolfe-Simon's group on arsenic bacteria "A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus." Why expend so much energy to refute someone else's work?  Well, the original paper's claim essentially suggests that our society needs to expand our notions of what forms life can take since there may be more than sugar-phosphate backbone DNA out there. That's a big enough impetus if you ask me. I'm not saying that it couldn't be true, but precaution should be taken when you make world-changing claims. You better be sure - it's a part of doing responsible and respectable science - and you should be able to stand by your work after the media frenzy dies down and the critics emerge.

Just to give you a brief background, the headlines blew up over this "arsenic bacteria" paper speculating that this is the building blocks of extraterrestrial life.  As an example, Alien: "Did NASA Discover Life on One of Saturn's Moons?" The answer, of course, is NO, since the original authors got their samples from the arsenic-laced waters of Mono Lake in California, not from outer space.

The rebuttal paper will also be published in Science - surprise! surprise! - and is already available at ArxivBut I doubt that it will grab the front pages as the original paper did. How will the Wolfe-Simon's group respond? Dun-dun-dun. This story, from claim of new discovery to the rebuttal, is what makes Science so interesting! Democracy here is exemplified at its best, so the original authors are free to respond and deliver new proof. I'll keep my eyes peeled for the next Science manuscript and headlines, and maybe also on Retraction watch, but my gut feeling is that all this whole hullabaloo will die with a whimper.

Monday, June 4, 2012

Rosalind's DNA

April 25, 2012. I was reading scientific articles in my office – it’s part of my day job - when I came across a citation for the very first publication correctly identifying the structure of deoxyribonucleic acid, better known as DNA. As you may know, this discovery has helped scientists understand how genetic information is passed on from parents to their children. For all the biochemistry work that I have done, I must confess that I've never read this original masterpiece. Thanks to technology, a few seconds later and voila! "Molecular structure of nucleic acids" is on my screen, despite it being originally published on . . .  April 25, 1953! Eerie coincidence? If that coincidence were the most significant thing that happened to me this day, it would have been sufficient.

Copyright (c) Henry Grant Archive/Museum of London
But no, reading that paper on its 59th anniversary of its publication brought me back to my college years when I fought tooth and nail to get that A+ in Biochem. One bottom line lesson for my exam was this: James Watson and Francis Crick uncovered the elusive structure of DNA in the most crucial scientific race of the 20th century. By being the first to correctly identify DNA’s structure, beating out Linus Pauling, unarguably the most influential chemist at the time, Watson, Crick, and their lesser-known colleague, Maurice Wilkin were deservingly awarded the Nobel Prize in Physiology or Medicine in 1962. And yes, I remember learning that there was a female X-ray crystallographer who helped them out by taking a photograph of DNA's helical structure. At the time, I never really thought about Rosalind Franklin as anything other than the DNA ”photographer”. But what a triumph for man, and I ended up with that coveted A+ too. And if these memories were the end of my preoccupation for that day, it would have been sufficient.

As I moved forward in my career in science through the years, I realized that Rosalind Franklin’s work was the key to DNA’s discovery and that she was not properly credited for it. In fact, her colleagues had let it slip that her data was obtained without her knowledge. Worse yet, she was not even mentioned in Watson and Crick's Nobel Prize acceptance speeches. Because Rosalind died in 1958 at the young age of 37, she was not even considered for the Nobel, which is not awarded posthumously.  Since then, I started looking up to her as the unsung heroine in science, one of the few brilliant women among the sea of male scientists. In his best-selling biography, The Double Helix, James Watson painted Rosalind Franklin as an unattractive woman from a blue-collar upbringing, and a frustrating scientist who “had to go or be put in her place.” In spite of this unflattering image, her DNA photographs were described as being “among the most beautiful X-ray photographs of any substance ever taken.” But then again, history is written by the victors. Was it sexism in that era that made her colleagues dismiss her so easily? Some claims that her omission was also a result of anti-Semitism.  She was Jewish, born to upper-middle class British parents, and went to a university where largest department was theology. Her uncle, Herbert Samuel, was the first high commissioner of Palestine.  In the epilogue to Watson’s biography, written after Rosalind's death, he acknowledged that he was wrong in his impression of Rosalind, and how she faced great struggles as a woman in science in spite of her brilliance. We will never know Rosalind’s true story, I suppose. And if this story ended here, it would have been sufficient.

The day’s preoccupation reminded me this:  Science has flaws. We look to science to be rational, when too often it is not. Drama, anarchy, lies, fear, and sheer luck all rear their heads in science, just as in any other field of endeavor. Still, I do believe that Watson and Crick deserved the Nobel Prize. Their amazing discovery of how the DNA base pairs interact paved the way for our understanding that a single misspelling or a few letters’ deletion in our 3 billion letters of DNA code can account for rare diseases such as cystic fibrosis. But in many ways, Rosalind’s story is a tragedy. Scientists work for the betterment of the world, typically with minimal reward - prestige and legacy. That’s why successful businessmen have yachts, whereas even the best scientists that I know can boast only of paper boats in their tubs. Truly, Franklin’s DNA story is one for the books - literally. As we celebrate the 50th anniversary Watson and Crick's Nobel Prize this year, I hope that the newest editions of biochemistry text books include Rosalind Franklin’s role in DNA’s history, and give her the credit that she’s due.  The recognition would come far too late. But, since we cannot change the past, it would be sufficient.

Note: This is an article I wrote for the May issue of The Chronicles, Etz Hayim's monthly newsletter.