Monday, March 28, 2016

The Forest Unseen: A Year's Watch in Nature

Delightful read! Enjoyed every page.

Winner of 2013 Best Book Award from the National Academies.
Finalist for 2013 Pulitzer Prize in General Nonfiction.

Winner of the 2013 Reed Environmental Writing Award.
Winner of the 2012 National Outdoor Book Award for Natural History Literature.

Runner-up for 2013 PEN/E. O. Wilson Literary Science Writing Award.

"A biologist reveals the secret world hidden in a single square meter of forest
 
Written with remarkable grace and empathy, The Forest Unseen is a grand tour of nature in all its profundity. Biologist David George Haskell uses a one-square-meter patch of old-growth Tennessee forest as a window onto the entire natural world. Visiting it almost daily for one year to trace nature's path through the seasons, he brings the forest and its inhabitants to vivid life. Beginning with simple observations--a salamander scuttling across the leaf litter, the first blossom of spring wildflowers--Haskell spins a brilliant web of biology, ecology, and poetry, explaining the science binding together ecosystems that have cycled for thousands--sometimes millions--of years."


http://www.amazon.com/Forest-Unseen-Years-Watch-Nature/dp/0143122940/ref=sr_1_1?s=books&ie=UTF8&qid=1459205126&sr=1-1&keywords=the+forest+unseen

The Vital Question;Energy, Evolution, and the Origins of Complex Life

I recently finished a book that goes immediately to my shelf of favorites, "The Vital Question; Energy, Evolution, and the Origins of Complex Life" by Nick Lane. It took me about 6 weeks to read. The closely argued story of life ascending was only clear to me after rereading many passages several times, and only when I was alert and rested. In every session of reading I found multiple epiphanies and delightful passages. I have been reading about evolutionary biology, genetics, epigenetics and biochemistry for about a dozen years, with excursions into geohistory and biochemistry. This very clearly written book severely stressed my layman's knowledge.
Lane brings together the current knowledge of geohistory (what the earth and oceans were like 4 billion years ago), alkaline hydrothermal vent discoveries, and basic redox chemistry, to make plausible the bacterial beginnings of life. The process included discussion of bioenergetics and lipid chemistry, with genetics of bacteria and archaea. These two domains hung around very little changed for about 2 billion years, making a living by various biochemical tricks, and sharing their genes haphazardly. They could not take much advantage of natural selection because they had no organized nucleus. They produce clones. They proliferated widely over the earth, and are still everywhere, and continue to adapt to their environments. 
Then a very unlikely event happened. An archaea merged with a bacteria and the combination prospered. Their genomes interacted and one, the archaea, became host and the bacteria became the mitochondria via natural selection. All multi celled creatures and plants are descended from that event. This story, modulated by the energetics of all life, ATP production,and modern genomics and biochemistry, is what this book is about, why is complex life the way it is. 

There is a 4 page section plus a figure starting on page 238 that brought home to me why this book is so fascinating. The passage discusses the respiratory proteins in mitochondria, which transfer electrons from food to oxygen, along a series of protein complexes embedded in the mitochondrial membrane while pumping protons across the membrane. The complete story is more complicated than I can reproduce here, but the depth of scientific knowledge is breathtaking. Each complex is made up of dozens of proteins, consisting of hundreds of amino acids. The exact  positioning of the complexes and the amino acid placement is critical in the quantum tunneling of the electrons along the membrane from complex to complex to the ATP synthase all embedded in the membrane. Many genetic diseases arise from slight faults in the arrangement if the proteins. One angstrom makes a 10 fold difference in the transfer rate, in turn affecting the ATP production rate. The figure shows a model of the membrane with the embedded complexes. The figure has shading that shows which part of the overall structure is produced from the DNA blueprint in the cell nucleus and which part is from the blueprint in the 13 genes in the mitochondria!. There is a discussion of how the bioenergetics and natural selection brought this complexity about. He also shows 
why complex beings have sex, just  two sexes, and death as part of this discussion. Consilience!

The knowing detail in this passage blows my mind. How can human beings decipher this amazing factory that is in all animal cells? Lots of Nobel prizes came out of this area.  This type of passage fills the book. My enjoyment in this reading comes from putting the discovered facts into a logical structure, suddenly seeing "the big picture"

I also like to read history, economics, mysteries and modern novels, but this kind of book thrills me. 

http://www.amazon.com/The-Vital-Question-Evolution-Origins/dp/0393088812?ie=UTF8&keywords=Lane%20Nick&qid=1459201268&ref_=sr_1_1&sr=8-1

The Meaning of existence

The latest by my hero E O Wilson. He writes with great conviction and clarity.

http://www.amazon.com/Meaning-Human-Existence-Edward-Wilson/dp/1631491148/ref=sr_1_1?s=books&ie=UTF8&qid=1442085013&sr=1-1&keywords=the+meaning+of+human+existence

Life Ascending - 10 greatest inventions of evolution

Outstanding tour of the most important and interesting developments of evolution. Clear explanations of important transitions in story of life on earth.

http://www.amazon.com/Life-Ascending-Great-Inventions-Evolution/dp/0393338665/ref=sr_1_2?s=books&ie=UTF8&qid=1442083054&sr=1-2&keywords=Ten+greatest+inventions

Lifelines -


 Some insights but very defensive and prone to setting up straw men to pompously put down. Seemed jealous of the funds spent on genomics and molecular biology. Very PC about feminism!

http://www.amazon.com/Lifelines-Life-beyond-Steven-Rose/dp/0195150392/ref=sr_1_39?s=books&ie=UTF8&qid=1442082699&sr=1-39&keywords=lifelines

Atkinson Trilogy of US in WWII

-All volumes excellent. Detailed history of US Army in WW@2 in No Africa, Italy and EU. Interesting portraits of leading figures.

http://www.amazon.com/Army-Dawn-1942-1943-Liberation-Trilogy/dp/0805087249/ref=sr_1_2?s=books&ie=UTF8&qid=1442082565&sr=1-2&keywords=atkinson+rick

How Chemistry Becomes Biology

Interesting book I read before The Vital Question. Less broad in scope, more about dynamic stability in chemical systems.

"Living things are hugely complex and have unique properties, such as self-maintenance and apparently purposeful behaviour which we do not see in inert matter. So how does chemistry give rise to biology? What could have led the first replicating molecules up such a path? Now, developments in the emerging field of 'systems chemistry' are unlocking the problem. Addy Pross shows how the different kind of stability that operates among replicating molecules results in a tendency for chemical systems to become more complex and acquire the properties of life. Strikingly, he demonstrates that Darwinian evolution is the biological expression of a deeper, well-defined chemical concept: the whole story from replicating molecules to complex life is one continuous process governed by an underlying physical principle. The gulf between biology and the physical sciences is finally becoming bridged."


http://www.amazon.com/What-Life-Chemistry-Becomes-Biology/dp/0199687773/ref=sr_1_1?s=books&ie=UTF8&qid=1459202190&sr=1-1&keywords=how+chemistry+becomes+biology

Sunday, July 6, 2014

Flash Boys by M Lewis

Another excellent reporting job by Lewis. The high frequency traders of Wall Street have been getting away with slices of investors orders since 2005. They spent millions on technology to get an unfair edge and have been making gobs of money by conning investors. Lewis also shows up the "dark pools" run by big banks. Congress is finally investigating, and Barclay's has been indicted.

Monday, May 26, 2014

When the Music Stopped

The author, Blinder, is an insider who has the background to describe the events accurately and assess the causes properly. I have read several books on the crisis and found this one to be the most complete and believable. It is 440 pages, but not a difficult read. Blinder makes the events understandable and places blame for the debacle, in my opinion, fairly. There is plenty of blame to be assigned, to the many regulating agencies, the many investment banks all around the world, AIG, the mortgage lenders of all stripes, the politicians, and the Federal Reserve, the Treasury, FNMA and Freddie Mac, and the rating agencies. The public grabbing loans they knew they could not afford were also a big contributor. Greed, fraud, and short term, wishful thinking led to gambling with other peoples money to make short term killings. The system was a mess. Top management had little appreciation for their risk management systems. They were making too much money to care.
The Dodd-Frank law, an attempt to prevent this happening again, was passed shortly after the crisis cooled down, but regulations actually implementing the law have not been completed, largely through fierce lobbying by the villains of this piece.
I am still amazed that more arrests were not made.

Monday, December 30, 2013

Bad Pharma, Very Important book

Dr Ben Oldacre is a young Brit doctor that is incensed by the state of the medical industry, particularly the big Pharma. He shows how they hide clinical trials that do not come out the way they want, and distort the results they do let get published. They pay medical journals to publish their papers, and support monetarily professional societies to favor them. Doctors are paid to give talks favoring drugs manufactured by the company, without admitting the connection. The detailers lie to doctors about the efficacy and side effects of drugs they are marketing. Drug companies spend twice as much on marketing as on research. Much of what they call marketing, in my opinion, could be called bribery.

Regulators cravenly ignore the problems, and hide data that should be public.

Read some of the reviews and comments from the link below, then read the book if you have the stomach for it.

http://www.amazon.com/Bad-Pharma-How-Medicine-Broken-ebook/dp/B008RLTUUA/ref=sr_1_1?s=books&ie=UTF8&qid=1388447537&sr=1-1&keywords=bad+pharma

Dr Oldacre makes many good suggestions to help fix these problems.

Also see his blog for an update on happenings since the publication of his book.
http://www.badscience.net/2013/12/free-here-is-the-new-what-happened-next-update-chapter-from-bad-pharma-2013/#more-3056