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AVX-512, Reverse the Biosphere update, and Sid Mukherjee

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Sid Mukherjee, The Gene: An Intimate History, here. This guy has the juice, big time.

The Gene is the story of one of the most powerful and dangerous ideas in our history, from best-selling, prize-winning author Siddhartha Mukherjee.

Spanning the globe and several centuries, The Gene is the story of the quest to decipher the master code that makes and defines humans, that governs our form and function.

The story of the gene begins in an obscure Augustinian abbey in Moravia in 1856, where a monk stumbles on the idea of a ‘unit of heredity’. It intersects with Darwin’s theory of evolution and collides with the horrors of Nazi eugenics in the 1940s. The gene transforms postwar biology. It reorganises our understanding of sexuality, temperament, choice and freewill. This is a story driven by human ingenuity and obsessive minds – from Charles Darwin and Gregor Mendel to Francis Crick, James Watson and Rosalind Franklin and the thousands of scientists still working to understand the code of codes.

This is an epic, moving history of a scientific idea coming to life by the author of The Emperor of All Maladies. But woven through The Gene like a red line is also an intimate history – the story of Mukherjee’s own family and its recurring pattern of mental illness, reminding us that genetics is vitally relevant to everyday lives. These concerns reverberate even more urgently today as we learn to ‘read’ and ‘write’ the human genome – unleashing the potential to change the fates and identities of our children.

Majestic in its ambition and unflinching in its honesty, The Gene gives us a definitive account of the fundamental unit of heredity – and a vision of both humanity’s past and its future.

Green, Rubin, and Olson, nature, The future of DNA sequencing, here. They can sequence so, Church’s Thesis says there is code, CRISPR shows there is a stack in the DNA code and there is cut and paste, find the code for cell division and reverse the biosphere.

Forty years ago, two papers1, 2 described the first tractable methods for determining the order of the chemical bases in stretches of DNA. Before these 1977 publications, molecular biologists had been able to sequence only snippets.

The evolution of DNA sequencing from these nascent protocols to today’s high-throughput technologies has occurred at a breathtaking pace3. Nearly 30 years of exponential growth in data generation have given way, in the past decade, to super-exponential growth. And the resultant data have spawned transformative applications in basic biology and beyond — from archaeology and criminal investigation to prenatal diagnostics.

What will the next 40 years bring?

Joel Hruska, ExtremeTech, Intel May Deploy AVX-512 in Upcoming 10nm Cannon Lake Cpus, here. Yes, but will it make my Big Decimal code faster?

AVX-512-F: Foundational support. Required for all AVX-512 products. Anything advertised as AVX-512-capable must support AVX-512-F.
AVX-512-CD: Conflict Detection. Allows a wider range of loops to be vectorized. Supported on Skylake-X (Skylake-SP and Skylake-X use the same architecture).
AVX-512-ER: Exponential and Reciprocal instructions designed to help implement transcendental operations. Supported in Knights Landing.
AVX-512-PF: New prefetch capabilities. Supported by Knights Landing.

All of the below operations were introduced with Skylake-X earlier this year:

AVX-512-BW: Byte and Word operations to cover 8-bit and 16-bit operations.
AVX-512-DQ: Doubleword and Quadword instructions. New 32-bit and 64-bit AVX-512 operations.
AVX-512-VL: Vector Length extensions. Allows AVX-512 to operate on XMM (128-bit) and YMM (256-bit) registers.

The following instructions will be introduced with Cannon Lake, in addition to AVX-512-F, AVX-512-CD, and all three Skylake-X capabilities):

AVX-512-IFMA: Integer Fused Multiply-Add with 52-bits of precision.
AVX-512-VBMI: Vector Byte Manipulation Instructions. Adds additional capabilities not in AVX-512-BW.

 

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