Atoms, Bytes, Genes

In Books, The rest by tony1 Comment

Featured image: Detail from Genetic Drift 1, Tony Stewart, July 2004

ORT_Logo   Breadtag Sagas ©: Author Tony,  2 February 2017


Atoms, Bytes & Genes: Science in the 21st century

Preamble

I made a political statement about science in a recent article 1984 The Way We Were.

We also needed someone in the 1990s and in the twenty-first century to remind us that science and technology drove the development of affluence in the twentieth century. The current ‘age of ignorance’ and of antagonism towards science, will eventually stultify innovation.

However, despite the depressing times, I’ve become more optimistic. Science and technology power on regardless.


The three dangerous ideas of twentieth century science

On the first day of 2017 I read a quote in Siddhartha Mukherjee The Gene: An Intimate History Bodley Head 2016, which I received for Christmas from Denise’s sister Julie who thoughtfully reads reviews.

In his Prologue, Mukherjee mentions the three streams of science and technology that dominated the twentieth century and whose convergence will dominate the twenty-first. He says:

Three profoundly [dangerous] destabilizing ideas richochet through the twentieth century, trisecting it into three unequal parts: the atom, the byte, the gene. Each is foreshadowed by an earlier century, but dazzles into full prominence in the twentieth. Each begins life as a rather abstract scientific concept, but grows to invade multiple human discourses — thereby transforming culture, society, politics, and language. But the most crucial parallel between the three ideas, by far, is conceptual: each represents the irreducible unit — the building block, the basic organizational unit — of a larger whole: the atom, of matter; the byte (or “bit”), of digitized information; the gene, of heredity and biological information.

Anyone who is interested in science knows this, though at times we forget. But rarely is the idea put so forcibly. Almost everything new, all knowledge and innovation in science and technology can be put into one of these three streams (or into closely parallel topics) and perhaps the most exciting thing in the twenty-first century is that they are all converging and becoming intertwined.

I had a profound insight some years ago after reading about Maxwell’s Demon and then shortly after a popular account of modern physics, particularly Einstein’s relativity, and a brief account of new ideas in quantum mechanics. Followed shortly after by a book on critical mass and another on small world networks; and a mishmash of stuff on evolution, modern biology and genetics.

The insight was that the beginnings of the universe and physics on a large scale, quantum mechanics (physics on a small scale) and understanding life on earth — linked by entropy — would be all integrated by information theory, and the understanding that everything could be defined by information and its transmission.

Unfortunately, like a fool I didn’t write down the ideas and how they fitted, the logical steps or the books I was reading. (I may be able to resurrect some of the books and the concepts sometime.) However, I am loath to do so,  not because of the fear that I won’t be able to recapture it, but because of the greater fear that it will no longer be crystal clear.

Nevertheless, I am sure that cleverer people than I will do so and because of the speed with which things are going, it won’t be that far off!

Mukerjee elaborates further about these three things:

Why does this property — being the least divisible unit of a larger form — imbue these particular ideas with such potency and force? The simple answer is that matter, information, and biology are inherently hierarchically organized: understanding that smallest part is crucial to understanding the whole. When the poet Wallace Stevens writes, “in the sum of the parts, there are only parts,” he is referring to the deep structural mystery that runs through language: you can only decipher the meaning of a sentence by deciphering every individual word — yet a sentence carries more meaning than any of the individual words. And so it is with genes. An organism is more than its genes, of course, but to understand an organism, you must first understand its genes.

… but I don’t think the second statement or his further commentary in the Prologue are necessary.

Let’s look at the three streams in turn and I’ll try to explain why I was particularly struck by Mukerjee’s statement, when I read it on the first day of 2017.


Atoms and Modern Physics

Fortunately, I don’t have to go into too much depth here or I’d display my ignorance.

Several people at the start of the twentieth century were studying atoms. Ernest Rutherford was one of them, but there were many others. They discovered protons, neutrons and electrons and that seemed to be the end of it. It wasn’t!

At several stages during the twentieth century particle physics looked to be reaching an end, but then things got weirder and weirder. The study of particle physics is a good example of JBS Haldane’s statement that the world is queerer than anyone can imagine.

The converse is my vision of a group of old men making up some new religious revision to control believers. The salient factor is the serious lack of imagination. That is the power of science that the unthinkable is possible and perhaps likely, despite the scientists themselves.

Two other major contributions of twentieth century physics were:

1 Einstein’s general theory of relativity, which helped to understand things at a very large scale, the universe and the beginnings of the universe, and

2 Quantum mechanics.

Supposedly, in science a new theory replaces an older theory but that doesn’t necessarily happen. Einstein’s theory replaced Newtonian physics, but didn’t really. For most things Newtonian physics still works fine. It is only at extremes such as close to the speed of light or in the realm of atoms that it doesn’t.

Quantum mechanics deals in the realm of the very small below the atomic, where things behave very oddly and one talks in terms of nano particles and nano measures. Einstein was never happy with quantum physics.

The one problem with modern physics is that the physics of the very large (Einstein) and of the very small (quantum mechanics) are currently incompatible. Physicists have diligently been seeking a unifying principle or a theory of everything, but nothing is on the horizon.

Despite its strangeness, and the unexpectedness of discoveries, modern physics has proven remarkably useful in generating new science, innovation and new technologies.

The dilemma has generated marvellous quotations:

Albert Einstein: God does not play dice with the universe. This was not a religious utterance, but despair at quantum mechanics and the new directions taken, particularly by Niels Bohr and his colleagues.

Niels Bohr: Anyone not shocked by quantum mechanics has not yet understood it.

Richard Feynman: If you think you understand quantum mechanics, you don’t. And, various variations.

Some of the key players were Rutherford, Einstein, Bohr and Planck, but there were many many others.


Bytes

Apart from Charles Babbage and his Difference Engine of 1822, which inspired a strand of Science Fiction called Steam Punk, and George Boole 1854, most practical developments in the bytes arena came after World War II. Nevertheless, there were many conceptual developments that arose from modern physics, but the technology (vacuum tubes) was not really adequate, until the development of solid-state electronics or the silicon chip.

Because the development of computing was more technology driven than other areas of science, its conceptual roots were also diverse. A few key names were Norbert Weiner and cybernetics (1948 and earlier), Claude Shannon and Information Theory (1937), Alan Turing and the theoretical Universal Turing Machine (1936; conceptualised by Alonzo Church independently), and John Von Neuman and the Von Neuman Architecture (1950).

Because of the secrecy of the British at Bletchley Park, their American allies were unaware of Colossus and thought they invented the first modern computer with ENIAC (1946). IBM dominated the mainframe computer era from the 1950s to the 1970s. Then came microcomputers or PCs, the world-wide-web, the Internet, the smart phone, etcetera.

I’ve covered these later developments in 1984 The Way We Were and in The Art of Prophecy and elsewhere in my posts and won’t cover them again here.

The computer age post World War II and in particular the massive leaps in computing power, mass storage and the Internet from the 1980s have made possible the vast leaps in gene and molecular biology since.

The ‘big data’ era will really accelerate new knowledge in science, biology, and even physics and mathematics, and it has barely begun.


Genes

The science of heredity begins with Charles Darwin’s Theory of Evolution with the publication of On the Origin of Species in 1859. Though natural selection was the breakthrough of the century, Darwin could not explain adequately the variation through heredity (genetics).

Gregor Mendel published his genetic experiments with pea plants in 1865 but in such an obscure journal that it wasn’t rediscovered until 1900. The science of genetics grew rapidly from 1990 leading to the Modern Synthesis of the theory of evolution in the 1930s, with genetics incorporated. Key figures in this period were Hugo de Vries, William Bateson, Thomas Hunt Morgan (fruit flies), Sewell Wright, Ronald Fisher, JBS Haldane and many more.

The next period from the 1930s to the 1970s was also prolific with many milestones.

The focus moved from proving genetics to the molecular development of genes and proteins and the physiological and human pathological mechanisms involved. The initial era of biochemistry and gene identification included such figures as Oswald Avery, Watson and Crick with the double helix structure of DNA (based on the crystallography of Rosalind Franklin), Sydney Brenner, Francois Jacob, the Cambridge worm group to name but a few.

Then came gene sequencing, splicing, recombination, genetic engineering and the human genome project (and the sequencing of thousands of other genomes).

Mukherjee quotes the summary from the publication of the human genome in Nature in February 2000, which said that since the rediscovery of Mendel’s laws in 1900 the scientific progress on genes divides the twentieth century into four phases spanning roughly each quarter of the century.

These were:

1 …The cellular basis of heredity: the chromosomes.

2 …The molecular basis of heredity: the DNA double helix.

3 …The informational basis of heredity (i.e., the genetic code), with the discovery of the biological mechanism by which cells read the information contained in genes and with the invention of recombinant DNA technologies of cloning and sequencing by which scientists can do the same.

4 …The sequence of the human genome, the project asserted, marked the stating point of the “fourth phase” of genetics. This was the era of “genomics” — the assessment of entire genomes of organisms, including humans.

There is an old conundrum in philosophy that asks if an intelligent machine can ever decipher its own instruction manual. For humans, the manual was now complete. Deciphering it, reading it and understanding it would be another matter. (Mukherjee)

Mukherjee says:

In 1969, on the eve of the revelatory decade, Robert Sinsheimer [wrote]…The capacity to synthesize, sequence, and manipulate would unveil “a new horizon in the history of man.”

He goes on to say:

As the geneticist J.B.S. Haldane had described it in 1923, once the power to control genes had been harnessed, “no beliefs, no values, no institutions are safe.” (One must add: the amazing Haldane!)


Comment

There is so much noise in the politico-economic system at the moment: fake news, Donald Trump, Brexit that we tend to forget that this doesn’t drive the world. Science and technology powers quietly along and the future is in our hands. We just have to realise it!

Our political systems are not serving us well at the moment but our own apathy and individualism is preventing us working together to seek better solutions.

I think reading this book and writing this article have made me think about how I am going to deal with 2017 and have provided at least a ray of optimism.

As with 1984 The Way We Were, The Art of Prophecy and several other articles, I am very interested in the future direction of science and technology this century and the amazing benefits that these may entail for us. Perhaps, the current age of ignorance, the apparent increase in right wing views and regimes, and terrorism are merely a reaction against the massive changes foisted upon us.

posted in Loikaw, Burma


Key words: Atoms, Bytes, Genes, Siddhartha Mukherjee, science, 20th century, 21st century, Maxwell’s Demon, James D Watson, The Double Helix, General Relativity, Quantum mechanics, Ernest Rutherford, Albert Einstein, Niels Bohr, Max Planck, Bletchley Park, Charles Babbage, George Boole, Claude Shannon, Alan Turing, John Von Neuman, Charles Darwin, On the Origin of Species, Evolution, Natural Selection, Gregor Mendel, Genetics, Hugo de Vries, William Bateson, Thomas Hunt Morgan, Drosophila, Sewell Wright, Ronald Fisher, JBS Haldane, Oswald Avery, James Watson, DNA, Francis Crick, Rosalind Franklin), Sydney Brenner, Francois Jacob, The Worm, C. elegans, Human Genome Project, Francis Sellers Collins, Craig Venter, Andreas Wagner, Arrival of the Fittest


Further Information

Siddhartha Mukherjee

Siddhartha Mukherjee The Gene: an Intimate History Bodley Head 2016

Mukerjee’s book is something special. It is a history of Gene research from Darwin’s Theory of Evolution to the present day. He is somewhat of a special writer, easy to read and he covers complex subjects in a very understandable way. I looked up several professional reviews and scanned the the Goodreads reviews but no-one did a good job of it, which means I may have to in the future.

Mukherjee divides his book into six parts by time periods: 1865-1935, 1930-1970, 1970-2001, 1970-2005, 2001-2015 and beyond 2015.

The best review I found was Natasha Mitchell The Gene review: Siddhartha Mukherjee’s thought-provoking exploration of science The Sydney Morning Herald, 29 July 2016. But even Mitchell skims the book.

The problem is that The Gene: an Intimate History is 600 pages of dense history and includes human medical and ethical issues as well as the research. It gets especially dense from 1975 partly because the field expands so rapidly, but also because of the problem outlined in the last post What is History 5: EH Carr Historians and their Facts that close to the present it is hard to winnow down what is important and what not. Nevertheless it is the dense last chapters that are the key to our future.

Mukherjee is a genius synthesiser of science and ideas, and The Gene is another thought-provoking opus, beautifully written and brilliantly told. (Natasha Mitchell SMH)


Siddhartha Mukherjee Biography

Born in 1970 in New Delhi of Bengali parents. Siddartha Mukerjee is a cancer physician and researcher, a stem cell biologist and a cancer. He is the author of The Laws of Medicine and The Emperor of All Maladies: A Biography of Cancer, which won the 2011 Pulitzer Prize in general non-fiction and the Guardian First Book Award (book jacket).

Currently, he is an assistant professor of medicine at Columbia University and staff physician at Columbia University Medical Center in New York City. He has been the Plummer Visiting Professor at the Mayo Clinic in Rochester, Minnesota, the Joseph Garland lecturer at the Massachusetts Medical Society, and an honorary visiting professor at Johns Hopkins School of Medicine (Wikipedia).

Being both a biologist and a doctor Mukherjee is the right person to write such a history, but it requires a genius at writing to carry it off.


Other Genetics books

Everyone should read James D Watson The Double Helix : A Personal Account of the Discovery of the Structure of DNA 1968.

Three other books I’ve read in the past ten years are

Martin Brookes Fly: An experimental life Wiedenfeld & Nicholson 2001

This is a very well-written history of the fruit fly Drosophila spp. in genetic research beginning of course with TH Morgan

Andrew Brown In the Beginning Was the Worm: Finding the Secrets of Life in a Tiny Hermaphrodite Simon & Schuster 2003

This is an excellent history of the Cambridge Group and its worm study. It captures the excitement and arrogance of the team at the forefront of genetic molecular biology, even though their life work would be swept away by the abilities of fast gene sequencing technologies not too many years later. By analogy it also reveals what earlier molecular biologists thought when they were sequencing proteins and the structure of DNA.

Andreas Wagner Arrival of the Fittest: solving evolution’s greatest puzzle, 2014.

I mentioned this in Further Information to  What is History 1: Introduction, Both Neil and I found this a difficult read.

Arrival of the Fittest covers the recent advances in molecular biology that overcome the problem of the chance evolution of complex molecules, beyond that discussed by Mukherjee. Wagner’s laboratory combining research and massive computational models is at the forefront of this research related to recent work on self-organising networks and the like. It is pivotal research concerning evolvability, innovability and robustness at the molecular level, not explained by Darwinian evolution or the modern synthesis of Darwin. However, Arrival of the Fittest does not explain the breakthroughs very clearly and one can find better descriptions elsewhere in Wagner’s work (see Review). I said: watch this space as I’m sure better books will be forthcoming in the near future.


Atoms and Physicists

Wikipedia on the history of Physics

Wikipedia on the history of Physics

Wikipedia on the history of Modern Physics

Wikipedia on the history of Modern Physics

Wikipedia on Maxwell’s Demon

Wikipedia on Maxwell’s Demon


Physicists

James Clerk Maxwell (1831 – 1879)

Wikipedia on James Clerk Maxwell

Ernest Rutherford (1871 – 1937)

Wikipedia on Ernest Rutherford

Albert Einstein (1879 — 1955)

Wikipedia on Albert Einstein

Max Planck (1858 – 1947)

Wikipedia on Max Planck

Niels Bohr (1885 – 1962)

Wikipedia on Niels Bohr


Bytes

Byte History

History of computer science

Wikipedia on History of computer science

Bletchley Park

Wikipedia on Bletchley Park

Bletchley Park Site


Individuals

Charles Babbage (1791 – 1871)

Wikipedia on Charles Babbage

George Boole (1815 – 1864)

Wikipedia on George Boole

Norbert Weiner (1894 – 1964)

Wikipedia on Norbert Weiner

Claude Shannon (1916 – 2001)

Wikipedia on Claude Shannon

Alan Turing (1912 – 1954)

Wikipedia on Alan Turing

John Von Neuman (1903 – 1957)

Wikipedia on John Von Neuman


Genes

The Worm C. elegans (& the Cambridge Group)

Wikipedia on The Worm

The Worm Classroom

The Worm Book

The Human Genome Project

Wikipedia on The Human Genome Project

Francis Sellers Collins (born 1950) and Craig Venter (born 1946)

Wikipedia on Francis Sellers Collins

Wikipedia on Craig Venter


Individuals

Charles Darwin (1809 — 1882)

Wikipedia on Charles Darwin

Charles Darwin On the Origin of Species, 1859

Gregor Mendel (1822 — 1884)

Wikipedia on Gregor Mendel

Biography.com on Gregor Mendel

Hugo de Vries (1848 – 1935)

Wikipedia on Hugo de Vries

William Bateson (1861 – 1926)

Wikipedia on William Bateson

Thomas Hunt Morgan (1866 – 1945)

Wikipedia on Thomas Hunt Morgan

The developers of the mathematical and statistical basis of genetics

Ronald A. Fisher (1890 — 1962)

Wikipedia on Ronald A. Fisher

Sewell Wright (1889 — 1988)

Wikipedia on Sewell Wright

 J.B.S. Haldane (1892 — 1964)

Wikipedia on J.B.S. Haldane

Oswald Avery (1877 – 1955)

Wikipedia on Oswald Avery

Francis Crick (1916 – 2004)

Wikipedia on Francis Crick

James D. Watson (born 1928)

Wikipedia on James D. Watson

James D. Watson The Double Helix 1968.

Rosalind Franklin (1920 – 1958)

Wikipedia on Rosalind Franklin

Sydney Brenner (born 1927)

Wikipedia on Sydney Brenner

Francois Jacob (1920 – 2013)

Wikipedia on Francois Jacob

 

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