Index: Evolution's Clinical Guidebook
In the past few blogs, I ' ve been discussing the recent publication of my book,Evolution ’s Clinical Guidebook: Translating Ancient Genes Into Precision Medicine. The premise of this book is that modern medicine is based on an understanding of evolutionary processes. Evolution shows us the relationships between the subdisciplines of medicine that benefit directly from Precision Medicine (i.e., pathology, microbiology, clinical genetics, pharmacology, and bioinformatics). In Evolution ' s Clinical Guidebook, all of these diverse fields are brought together, under the subject of evolution. To illustrate, I have listed bel...
Source: Specified Life - May 11, 2019 Category: Information Technology Tags: bioinformatics clinical genetics evo-devo evolution precision medicine rare disease Source Type: blogs

Contents: Evolution ’s Clinical Guidebook: Translating Ancient Genes Into Precision Medicine
In yesterday ' s blog, I announced the publication of my book,Evolution ’s Clinical Guidebook: Translating Ancient Genes Into Precision Medicine. The premise of this book is that modern medicine is based on an understanding of evolutionary processes. Basically, without evolution, the fledgling field of precision medicine would wither and die, and we would lose our opportunity to prevent, diagnose, and treat the diseases that account for the bulk of morbidity and mortality in humans and in animals.This book is available fromAmazon or from thepublisher ' s website. If you are fortunate enough to have full institutional acc...
Source: Specified Life - May 10, 2019 Category: Information Technology Tags: bioinformatics clinical genetics evo-devo evolution precision medicine rare disease Source Type: blogs

Just Published: Evolution ’s Clinical Guidebook: Translating Ancient Genes Into Precision Medicine
This month, Academic Press has published my book,Evolution ’s Clinical Guidebook: Translating Ancient Genes Into Precision Medicine. The premise of this book is that modern medicine is based, in one way or another, on an understanding of evolutionary processes. If evolution were a fabrication, then we would not be able to make any sense of the genomic data that is pouring out of research laboratories. We would not be able to design rational, cost effective, screening protocols to test the effectiveness of new drugs. We would not be able to identify the human sub-populations that will benefit from gene-targeted therapies....
Source: Specified Life - May 9, 2019 Category: Information Technology Tags: bioinformatics clinical genetics evo-devo evolution precision medicine rare disease Source Type: blogs

Second Edition of Principles and Practice of Big Data now on Science Direct
The Second edition of my bookPrinciples and Practice of Big Data has just been released and is available for purchase at many sites, includingAmazon.For those of you fortunate enough to have access to Science Direct, you can download chapters of my book at:https://www.sciencedirect.com/science/book/9780128156094TABLE OF CONTENTS Author ' s Preface to Second Edition Author ' s Preface to First Edition Chapter 1. Introduction Section 1. Definition of Big Data Section 2. Big Data Versus small data Section 3. Whence Comest Big Data? Section 4. The Most Common Purpose of Big Data is to Produce small data Section 5. Big Dat...
Source: Specified Life - August 4, 2018 Category: Information Technology Tags: big data data analysis data sharing science direct Source Type: blogs

Read Precision Medicine and the Reinvention of Human Disease on ScienceDirect
It is regrettable that many of my textbooks are unaffordable to the majority of the potential market. For Example,Precision Medicine and the Reinvention of Human Disease sells on Amazon for $125. This book contains nearly a quarter-million words, and it must have cost the publisher a lot of money to print and distribute, but I certainly wish it could have been sold at a lower price.As a remedy, for some of you, this book is being marketed by Elsevier (the owner of the Academic Press imprint under which is was published) through ScienceDirect, a subscription online book catalog bought by university libraries. This means tha...
Source: Specified Life - May 9, 2018 Category: Information Technology Tags: book subscriptions library acquisitions precision medicine ScienceDirect Source Type: blogs

Inscrutable Genes
" In most cases, the molecular consequences of disease, or trait-associated variants for human physiology, are not understood. " from: Manolio TA, Collins FS, Cox NJ, Goldstein DB, Hindorff LA, Hunter DJ, et al. Finding the missing heritability of complex diseases. Nature 2009;461:747 –53. The 1960s was a wonderful decade for the field of molecular genetics. Hundreds of inherited metabolic diseases were being studied. Most of these diseases could be characterized by a simple inherited mutation in a disease-causing gene. Back then, we thought we understood genetic diseases. Here ’s how it all might have worked, if life ...
Source: Specified Life - February 15, 2018 Category: Information Technology Tags: genetic heterogeneity genetics multi-step pathogenesis precision medicine Source Type: blogs

Infections Develop Via a Sequence of Biological Steps
A prior post listed 7 assertions regarding the role of infectious organisms on the human genome. In the next few blogs we ' ll look at each assertion, in excerpts fromPrecision Medicine and the Reinvention of Human Disease. Here ' s the seventh:By dissecting the biological steps involved in the pathogenesis of infectious disease, it is possible to develop new treatments, other than antibiotics, that will be effective against a range of related organisms. Nature, by interfering with the different steps in the development of infectious diseases, has a variety of protective mechanisms against organisms. For example, to defend...
Source: Specified Life - February 14, 2018 Category: Information Technology Tags: biological steps infections disease pathogenesis precision medicine Source Type: blogs

Non-immunologic Causes of Increased Susceptibility to Disease
A prior post listed 7 assertions regarding the role of infectious organisms on the human genome. In the next few blogs we ' ll look at each assertion, in excerpts fromPrecision Medicine and the Reinvention of Human Disease. Here ' s the sixth:Cellular defects that have no direct connection to immunity may increase susceptibility to infectious organisms. If we want to understand why certain individuals are susceptible to infections and other individuals are not, we must understand that immune deficiencies cannot account for all infections. Infectious diseases, just like any other disease, develop in steps, and it stands to ...
Source: Specified Life - February 13, 2018 Category: Information Technology Tags: immune system non-immunologic precision medicine susceptibility to disease Source Type: blogs

Infection without Disease (from Precision Medicine and the Reinvention of Human Disease)
A prior post listed 7 assertions regarding the role of infectious organisms on the human genome. In the next few blogs we ' ll look at each assertion, in excerpts fromPrecision Medicine and the Reinvention of Human Disease. Here ' s the fifth:Normal defenses can block every infectious disease. Hence, every infectious disease results from a failure of our normal defenses, immunologic and otherwise. For any given infectious agent, no matter how virulent they may seem, there are always individuals who can resist infection. Moreover, as a generalization, the majority of individuals who are infected with a pathogenic microorgan...
Source: Specified Life - February 12, 2018 Category: Information Technology Tags: commensals host organisms latent infection precision medicine symbiotes symbiotic Source Type: blogs

Cellwise, We Are Mostly Inhuman
A prior post listed 7 assertions regarding the role of infectious organisms on the human genome. In the next few blogs we ' ll look at each assertion, in excerpts fromPrecision Medicine and the Reinvention of Human Disease. Here ' s the fourth:Most of the cells residing in human bodies are nonhuman There are about 10 times as many nonhuman cells living in our bodies as there are human cells [40]. The human intestines alone contain 40,000 different species of bacteria [9]. These 40,000 species contain about 9 million different genes. Compare that with the paltry 23,000 genes in the human genome, and we quickly see that we h...
Source: Specified Life - February 11, 2018 Category: Information Technology Tags: commensals host organisms precision medicine symbiotes symbiotic Source Type: blogs

Genome-Specific Responses to Infection
A prior post listed 5 assertions regarding the role of infectious organisms on the human genome. In the next few blogs we ' ll look at each assertion, in excerpts fromPrecision Medicine and the Reinvention of Human Disease. Here ' s the third:A good portion of the genes in humans (perhaps 10%) are involved in responses to infectious organisms. It has been estimated that over 1000 human genes are involved in inflammation pathways [37]. Several studies have shown that following an inflammatory challenge or challenged by the introduction of a pathogen, more than a hundred genes are activated [38 –40]. The activated genes in...
Source: Specified Life - February 10, 2018 Category: Information Technology Source Type: blogs

Vertebrate Evolution Driven by DNA from Infectious Organisms
A prior post listed 5 assertions regarding the role of infectious organisms on the human genome. In the next few blogs we ' ll look at each assertion, in excerpts fromPrecision Medicine and the Reinvention of Human Disease. Here ' s the second:Some of the key steps in the development of vertebrate animals, and mammals in particular, have come from DNA acquired from infectious organisms. Thehuman genome has preserved its viral ballast, at some cost. At every cell division, energy is expended to replicate the genome, and the larger the genome, the more energy must be expended. Why do we spend a large portion of the energy re...
Source: Specified Life - February 9, 2018 Category: Information Technology Tags: evolution precision medicine viral virus Source Type: blogs

Relic dna in the human genome
Yesterday ' s post listed 5 assertions regarding the role of infectious organisms on the human genome. In the next few blogs we ' ll look at each assertion, in excerpts fromPrecision Medicine and the Reinvention of Human Disease. Here ' s the first:The majority of the human genome consists of relic DNA derived from ancient invasive organisms.Nearly half of the human genome is filled with sequences such as LINE and Alu, and DNA transposons, all derived from ancient retroviruses [21]. About 8% of our genome is derived from longer sequences with similarity to known infectious retroviruses, and these longer sequences can usual...
Source: Specified Life - February 8, 2018 Category: Information Technology Tags: evolution human genome infectious diseases precision medicine Source Type: blogs

Infections have made their mark on the Human Genome
In the context of Precision Medicine, infections draw our attention because they have played an important role in the evolution of the eukaryotic genome. Over the next few blog posts, we will explore the following:The majority of the human genome consists of relic DNA derived from ancient invasive organisms.Some of the key steps in the development of vertebrate animals, and mammals in particular, have come from DNA acquired from infectious organisms.A good portion of the genes in humans (perhaps 10%) are involved in responses to infectious organisms.Most of the cells in the human (at least 90%) consist of infectious organi...
Source: Specified Life - February 7, 2018 Category: Information Technology Tags: evolution infections precision medicine resistance to infection Source Type: blogs

Precision Medicine and Public Health (from Precision Medicine and the Reinvention of Human Disease)
Excerpted fromPrecision Medicine and the Reinvention of Human DiseaseDespite having the most advanced healthcare technology on the planet, life expectancy in the United States is not particularly high. Citizens from most of the European countries and the highly industrialized Asian countries enjoy longer life expectancies than the United States. According to the World Health Organization, the United States ranks 31st among nations, trailing behind Greece, Chile, and Costa Rica, and barely edging out Cuba [42]. Similar rankings are reported by the US Central Intelligence Agency [43]. These findings lead us to infer that acc...
Source: Specified Life - February 6, 2018 Category: Information Technology Tags: cancer cancer vaccines precision medicine prevention public health Source Type: blogs