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 hav...
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 aga...
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 reas...
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 microorganism ...
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 homo ...
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 requir...
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 usually be ...
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

Treat the Pathway, not the Gene (from Precision Medicine and the Reinvention of Human Disease)
Treat the key pathway, not the genetic mutation (fromPrecision Medicine and the Reinvention of Human Disease)Some of the earliest and most successful Precision Medication drugs have targeted specific mutations occurring in specific subsets of diseases. One such example is ivacaftor, which targets the G551D mutation present in about 4% of individuals with cystic fibrosis [135]. It is seldom wise to argue with success, but it must be mentioned that the cost of developing a new drug is about $5 billion [136]. To provide some perspective, $5 billion exceeds the total gross national product of many countries, including Sierra L...
Source: Specified Life - February 5, 2018 Category: Information Technology Tags: clinical trials convergent pathways cost of precision medicine precision treatment Source Type: blogs

National Patient Identifiers (from Precision Medicine and the Reinvention of Human Disease)
Readers from outside the United States are probably wondering why the United States agonizes over the problem of patient identification. In many other countries, individuals are given a unique national identifier, and all medical data associated with the individual is kept in a central data repository under the aegis of the government ’s health service. A single, permanent identifier is used by a patient throughout life, in every encounter with a hospital, clinic, or private physician. As a resource for researchers, the national patient identifier ensures the completeness of data sets and eliminates many of the probl...
Source: Specified Life - February 4, 2018 Category: Information Technology Tags: confidentiality identification medical identifier national patient identifier privacy Source Type: blogs

Paradoxes of Classification (and terrible Class definitions)
The formal systems that assign data objects to classes, and that relate classes to other classes, are known as ontologies. When the data within a Big Data resource is classified within an ontology, data analysts can determine whether observations on a single object will apply to other objects in the same class. Similarly, data analysts can begin to ask whether observations that hold true for a class of objects will relate to other classes of objects. Basically, ontologies help scientists fulfill one of their most important tasks; determining how things relate to other things.A classification is a very simple form of ontolo...
Source: Specified Life - February 3, 2018 Category: Information Technology Tags: big data classification ontologies paradoxes precision medicine taxonomy Source Type: blogs

Precision Medicine and the Reinvention of Human Disease (not just about genes)
If everything you know about Precision Medicine comes from the lay press, you may have an unrealistic notion of what's happening in this field. The news seems to stress the one gene-> one disease paradigm that is easy to understand, but largely irrelevant to all the common diseases that occur in humans.The one gene-> one disease paradigm is this: the clinical expression of each disease is caused by a genetic mutation in a particular gene responsible for that particular disease, or a particular subtype of a disease, in a particular individual. By finding and targeting the gene responsible for an individual's disease, ...
Source: Specified Life - February 1, 2018 Category: Information Technology Tags: common diseases complex diseases disease biology monogenic pathogenetic precision medicine rare diseases Source Type: blogs

Precision Medicine and the Reinvention of Human Disease (a better definition)
We can define Precision Medicine as an approach to the prevention, diagnosis, and treatment of disease that is based on a deep understanding of the sequence of biological events that lead to disease. With this approach we are learning:(1) that we can develop new drugs that target specific steps in the development of disease;(2) that drugs developed to interfere with a cellular event or pathway may serve as effective treatments for those individuals whose disease is driven by the pathway; and(3) that a treatment effective for a subtype of one disease may also be effective against other diseases that happen to be driven by t...
Source: Specified Life - January 28, 2018 Category: Information Technology Tags: definition pathogenesis precision medicine Source Type: blogs

Precision Medicine and the Reinvention of Human Disease (not just the genome)
If you believe the lay press, Precision Medicine involves sequencing a patient's genome and determining the proper treatment based on the individual's unique genetic attributes. The NIH (National Institutes of Health) seems to be encouraging this interpretation of the field. From the US National Institutes of Health comes the following description: " Precision Medicine is an emerging approach for disease prevention and treatment that takes into account people's individual variations in genes, environment, and lifestyle. The Precision Medicine Initiative will generate the scientific evidence needed to move the concept ...
Source: Specified Life - January 27, 2018 Category: Information Technology Tags: definition genomics individualized treatments precision medicine Source Type: blogs

Precision Medicine and the Reinvention of Human Disease (from Preface)
Something has happened in the past two decades that has changed the way that modern biomedical scientist thinks about diseases. Because the changes in our perceptions have happened slowly, few of us have really taken notice of what it all means. The purpose of my latest book,Precision Medicine and the Reinvention of Human Disease, published January, 2018, is to show how advances in the field of Precision Medicine will forever change the way we understand and treat disease. Specifically, these advances are:Diseases develop in steps. Modern methodology has enabled us to dissect the biological events and metabolic pathways th...
Source: Specified Life - January 26, 2018 Category: Information Technology Tags: pathogenesis precision medicine rare diseases subtypes Source Type: blogs

Precision Medicine and the Reinvention of Human Disease (The Myth)
If you believe the hype, we are entering a new era of medicine in which each individual will receive unique treatment, determined by the sequence of his or her genome. This widely promulgated notion is simply ridiculous. There is no practical way to develop a unique treatment, test the treatment for safety and effectiveness, and titrate the correct dose, all for one person.The terms " Precision Medicine " and " Personalized Medicine " have given us the false impression that medical science is moving away from off-the-rack remedies and is seeking treatments tailored to the individual. In actuality, scien...
Source: Specified Life - January 25, 2018 Category: Information Technology Tags: complex diseases jules berman Ph.D. jules j berman M.D. precision medicine precision treatment subsets of common diseases Source Type: blogs

Precision Medicine and the Reinvention of Human Disease (Book Index)
In January, 2018, Academic Press published my bookPrecision Medicine and the Reinvention of Human Disease. This book has an excellent " look inside " at itsGoogle book site, which includes the Table of Contents. In addition, I thought it might be helpful to see the topics listed in the Book's index. Note that page numbers followed by f indicate figures, t indicate tables, and ge indicate glossary terms.AAbandonware, 270, 310geAb initio, 34, 48ge, 108geABL (abelson leukemia) gene, 28, 58ge, 95 –97Absidia corymbifera, 218Acanthameoba, 213Acanthosis nigricans, 144geAchondroplasia, 74, 143ge, 354geAcne, 54ge, 1...
Source: Specified Life - January 23, 2018 Category: Information Technology Tags: index jules berman jules j berman precision medicine Source Type: blogs

Announcement: Precision Medicine and the Reinvention of Human Disease
In January, 2018, Academic Press is publishing my latest book,Precision Medicine and the Reinvention of Human DiseaseHere is the book description, from the back cover:Despite what you may have read in the popular press and in social media, Precision Medicine is not devoted to finding unique treatments for individuals, based on analyzing their DNA. To the contrary, the goal of Precision Medicine is to find general treatments that are highly effective for large numbers of individuals who fall into precisely diagnosed groups.We now know that every disease develops over time, through a sequence of defined biological steps, and...
Source: Specified Life - January 22, 2018 Category: Information Technology Tags: book announcement carcinogenesis causality classification of disease genomics jules j berman pathogenesis precision medicine Source Type: blogs

CLASS BLENDING: Simpson's Paradox
For the past two days, we've been posting on Class Blending . Simpson's paradox is a special case that demonstrates what may happen when classes of information are blended. Simpson's paradox is a well-known problem for statisticians. The paradox is based on the observation that findings that apply to each of two data sets may be reversed when the two data sets are combined. One of the most famous examples of Simpson's paradox was demonstrated in the 1973 Berkeley gender bias study RbicaR. A preliminary review of admissions data indicated that women had a lower admissions rate than men: Men Number of applicants.. 8,44...
Source: Specified Life - March 29, 2016 Category: Information Technology Tags: classification classifications complexity data science data simplification irreproducible results ontologies ontology Simpson ' s paradox Source Type: blogs

CLASS BLENDING: Simpson's Paradox
For the past two days, we've been posting on Class Blending. Simpson's paradox is a special case that demonstrates what may happen when classes of information are blended. Simpson's paradox is a well-known problem for statisticians. The paradox is based on the observation that findings that apply to each of two data sets may be reversed when the two data sets are combined. One of the most famous examples of Simpson's paradox was demonstrated in the 1973 Berkeley gender bias study RbicaR. A preliminary review of admissions data indicated that women had a lower admissions rate than men: Men Number of applicants.. 8,442 Per...
Source: Specified Life - March 29, 2016 Category: Information Technology Tags: classification classifications complexity data science data simplification irreproducible results ontologies ontology Simpson ' s paradox Source Type: blogs

Open for Comment
For the past several years, I've kept this blog closed to comments. Prior to that, most of the comments were thinly disguised advertisements for pharmaceuticals, and I got tired of rejecting them. For the past month or so, I've re-opened the blog for readers' comments, without announcing the change; just to check whether I'd be inundated with computer-generated promotions. It seems that neither software agents or readers have noticed the change. So, please, if you are a human and would like to send a comment, feel free to use the comments link at the bottom of every post. Your comments will be moderated, but I intend to a...
Source: Specified Life - March 28, 2016 Category: Information Technology Tags: announcement blog comments postings Source Type: blogs

Expunging a Blended Class: The Fall of Kingdom Protozoa
In yesterday's blog, we introduced and defined the term "Class blending". Today's blog extends this discussion by describing the most significant and most enduring class blending error to impact the natural sciences: the artifactual blending of all single cell organisms into the blended class, Protozoa.For well over a century, biologists had a very simple way of organizing the eukaryotes (i.e., the organisms that were not bacteria, whose cells contained a nucleus) (1). Basically, the one-celled organisms were all lumped into one biological class, the protozoans (also called protists). With the exception of animal...
Source: Specified Life - March 27, 2016 Category: Information Technology Tags: Apicomplexa classification complexity data science irreproducible results ontologies ontology protists protoctista protozoa Source Type: blogs

Intro to Class Blending
I thought I'd devote the next few blogs to a concept that has gotten much less attention than it deserves: blended classes. Class blending lurks behind much of the irreproducibility in "Big Science" research, including clinical trials. It also is responsible for impeding progress in various disciplines of science, particularly the natural sciences, where classification is of utmost importance. We'll see that the scientific literature is rife with research of dubious quality, based on poorly designed classifications and blended classes. For today, let's start with a definition and one example. We'll discuss many m...
Source: Specified Life - March 26, 2016 Category: Information Technology Tags: classification complexity data science irreproducible results ontologies ontology Source Type: blogs

Progress against cancer? Let's think about it.
It is difficult to pick up a newspaper these days without reading an article proclaiming progress in the field of cancer research. Here is an example, taken from an article posted on the MedicineNet site (1). The lead-off text is: " Statistics (released in 1997) show that cancer patients are living longer and even " beating " the disease. Information released at an AMA sponsored conference for science writers, showed that the death rate from the dreaded disease has decreased by three percent in the last few years. In the 1940s only one patient in four survived on the average. By the 1960s, that figure was up...
Source: Specified Life - March 25, 2016 Category: Information Technology Tags: cancer cancer cure cancer statistics cancer treatments orphan diseases progress in cancer research rare diseases Source Type: blogs

Progress against cancer? Let's think about it.
It is difficult to pick up a newspaper these days without reading an article proclaiming progress in the field of cancer research. Here is an example, taken from an article posted on the MedicineNet site (1). The lead-off text is: "Statistics (released in 1997) show that cancer patients are living longer and even "beating" the disease. Information released at an AMA sponsored conference for science writers, showed that the death rate from the dreaded disease has decreased by three percent in the last few years. In the 1940s only one patient in four survived on the average. By the 1960s, that figure was up to...
Source: Specified Life - March 25, 2016 Category: Information Technology Tags: cancer cancer cure cancer statistics cancer treatments orphan diseases progress in cancer research rare diseases Source Type: blogs

Scientific Misconduct at Prestigious Research Centers
On January 23, 2009, the Office of Research Integrity made public their findings of scientific misconduct concerning a doctor who fabricated data for several grants projects funded by the NIH (1). The doctor was a former graduate student in the Department of Pathology, Harvard Medical School, a former research fellow and Instructor of Pathology, at Brigham and Women's Hospital in Boston, a former postdoctoral fellow in the Department of Biology, at the California Institute of Technology, and a former Associate Professor in the Department of Biology and the Center for Cancer Research at the Massachusetts Institute of Techno...
Source: Specified Life - March 24, 2016 Category: Information Technology Tags: ethics fraud Karolinska Institute ORI scientific misconduct Source Type: blogs

The Importance of Biological Taxonomy
Biological taxonomy is the scientific field dealing with the classification of living organisms. Non-biologists who give any thought to taxonomy, may think that the field is the dullest of the sciences. To the uninitiated, there is little difference between the life of a taxonomist and the life of a stamp collector. Nothing could be further from the truth. Taxonomy has become the grand unifying theory of the biological sciences. Efforts to sequence the genomes of prokaryotic, eukaryotic and viral species, thereby comparing the genomes of different classes of organisms, have revitalized the field of evolutionary taxonomy (p...
Source: Specified Life - March 22, 2016 Category: Information Technology Tags: classification data organization evolution taxonomy Source Type: blogs

DATA SIMPLIFICATION: Published At Last!
Blog readers can use the discount code: COMP315 for a 30% discount, at checkout.On March 17, my book Data Simplification: Taming Information with Open Source Tools was published by Morgan Kaufmann, an imprint of Elsevier. [the Elsevier site indicates that the book is still on preorder, buy you can ignore that]. This past month, I've posted on topics relevant to data simplification. Beginning tomorrow, I'll be moving onto new subjects for this blog site, but I wanted to make one additional comment for anyone who might be on the fence about buying this book. Most large data projects are total failures (1-21). Furthermore, i...
Source: Specified Life - March 21, 2016 Category: Information Technology Tags: computer science data analysis data repurposing data science data simplification information science simplifying data taming data Source Type: blogs

DATA SIMPLIFICATION: Persistent Data
This is the last of my blogs related to topics selected from Data Simplification: Taming Information With Open Source Tools (released March, 2016). I hope that as you page back through my posts on Data Simplification topics, appearing throughout this month's blog, you'll find that this is a book worth reading. Blog readers can use the discount code: COMP315 for a 30% discount, at checkout. A file that big? It might be very useful. But now it is gone.-Haiku by David J. Liszewski Your scripts create data objects, and the data objects hold data. Sometimes, these data objects are transient, existing only during a block or subr...
Source: Specified Life - March 19, 2016 Category: Information Technology Tags: computer science data analysis data science data simplification databases persistence simplifying data Source Type: blogs

DATA SIMPLIFICATION: The Many Uses of Random Number Generators
Over the next few weeks, I will be writing on topics related to my latest book, Data Simplification: Taming Information With Open Source Tools (release date March 17, 2016). I hope I can convince you that this is a book worth reading. Blog readers can use the discount code: COMP315 for a 30% discount, at checkout.If you are among the many students and professionals who are intimidated by statistics, then fear no more! With a little imagination, random number generators (to be accurate, pseudorandom number generators) can substitute for a wide range of statistical methods. As it happens, modern computers can perform two sim...
Source: Specified Life - March 15, 2016 Category: Information Technology Tags: computer science data analysis data repurposing data simplification Monte Carlo probability pseudorandom resampling simplifying data simulations Source Type: blogs

DATA SIMPLIFICATION: Abbreviations and Acronyms
Over the next few weeks, I will be writing on topics related to my latest book, Data Simplification: Taming Information With Open Source Tools (release date March 17, 2016). I hope I can convince you that this is a book worth reading. Blog readers can use the discount code: COMP315 for a 30% discount, at checkout."A synonym is a word you use when you can't spell the other one." -Baltasar GracianPeople confuse shortening with simplifying; a terrible mistake. In point of fact, next to reifying pronouns, abbreviations are the most vexing cause of complex and meaningless language. Before we tackle the complexities of...
Source: Specified Life - March 14, 2016 Category: Information Technology Tags: abbreviations acronyms complexity computer science data analysis data repurposing data simplification simplifying data Source Type: blogs

DATA SIMPLIFICATION: Doublet Lists
Over the next few weeks, I will be writing on topics related to my latest book, Data Simplification: Taming Information With Open Source Tools (release date March 17, 2016). I hope I can convince you that this is a book worth reading. Blog readers can use the discount code: COMP315 for a 30% discount, at checkout.Yesterday's blog covered lists of single words. Today we'll do doublets. Doublet lists (lists of two-word terms that occur in common usage or in a body of text) are a highly underutilized resource. The special value of doublets is that single word terms tend to have multiple meanings, while doublets tend to have s...
Source: Specified Life - March 13, 2016 Category: Information Technology Tags: complexity computer science data analysis data repurposing data simplification doublet lists n-grams open source tools word lists Source Type: blogs

DATA SIMPLIFICATION: Building Word Lists
Over the next few weeks, I will be writing on topics related to my latest book, Data Simplification: Taming Information With Open Source Tools (release date March 23, 2016). I hope I can convince you that this is a book worth reading. Blog readers can use the discount code: COMP315 for a 30% discount, at checkout.Word lists, for just about any written language for which there is an electronic literature, are easy to create. Here is a short Python script, words.py, that prompts the user to enter a line of text. The script drops the line to lowercase, removes the carriage return at the end of the line, parses the result into...
Source: Specified Life - March 12, 2016 Category: Information Technology Tags: complexity computer science data analysis data repurposing data simplification data wrangling information science simplifying data taming data word lists Source Type: blogs

DATA SIMPLIFICATION: ImageMagick
Over the next few weeks, I will be writing on topics related to my latest book, Data Simplification: Taming Information With Open Source Tools (release date March 23, 2016). I hope I can convince you that this is a book worth reading. Blog readers can use the discount code: COMP315 for a 30% discount, at checkout. In yesterday's blog, I discussed using system calls within your scripts. One of my examples called an ImageMagick. Today, I thought I'd describe ImageMagick, and some of its benefits. ImageMagick is an open source utility that supports a huge selection of robust and sophisticated image editing methods. Its source...
Source: Specified Life - March 11, 2016 Category: Information Technology Tags: complexity computer science image magick information science simplification simplifying data system calls taming data Source Type: blogs

DATA SIMPLIFICATION: System Calls
Over the next few weeks, I will be writing on topics related to my latest book, Data Simplification: Taming Information With Open Source Tools (release date March 23, 2016). I hope I can convince you that this is a book worth reading. Blog readers can use the discount code: COMP315 for a 30% discount, at checkout.A system call is a command line, inserted into a software program, that interrupts the script while the operating system executes the command line. Immediately afterwords, the script resumes, at the next line. Any utility that runs from the command line can be embedded in any scripting language that supports syste...
Source: Specified Life - March 10, 2016 Category: Information Technology Tags: complexity computer science data analysis data repurposing data simplification data wrangling information science perl python Ruby simplifying data system calls taming data Source Type: blogs

DATA SIMPLIFICATION: Specifications to the Rescue!
Over the next few weeks, I will be writing on topics related to my latest book, Data Simplification: Taming Information With Open Source Tools (release date March 23, 2016). I hope I can convince you that this is a book worth reading. Blog readers can use the discount code: COMP315 for a 30% discount, at checkout.Today's blog continues yesterday's discussion of Standards and Specifications Despite the problems inherent in standards, government committees cling to standards as the best way to share data. The perception is that in the absence of standards, the necessary activities of data sharing, data verification, data ana...
Source: Specified Life - March 9, 2016 Category: Information Technology Tags: complexity computer science data analysis data repurposing data simplification data wrangling information science simplifying data specifications standards taming data Source Type: blogs

DATA SIMPLIFICATION: Substandard Standards
Over the next few weeks, I will be writing on topics related to my latest book, Data Simplification: Taming Information With Open Source Tools (release date March 23, 2016). I hope I can convince you that this is a book worth reading. Blog readers can use the discount code: COMP315 for a 30% discount, at checkout."The nice thing about standards is that you have so many to choose from." -Andrew S. Tanenbaum Data standards are the false gods of informatics. They promise miracles, but they can't deliver. The biggest drawback of standards is that they change all the time. If you take the time to read some of the comp...
Source: Specified Life - March 8, 2016 Category: Information Technology Tags: complexity computer science data analysis data repurposing data simplification data wrangling information science simplifying data specifications standards taming data Source Type: blogs

DATA SIMPLIFICATION: Poor Identifiers, Horrific Consequences
Over the next few weeks, I will be writing on topics related to my latest book, Data Simplification: Taming Information With Open Source Tools (release date March 23, 2016). I hope I can convince you that this is a book worth reading. Blog readers can use the discount code: COMP315 for a 30% discount, at checkout.All information systems, all databases, and all good collections of data are best envisioned as identifier systems to which data (belonging to the identifier) can be added over time. If the system is corrupted (e.g., multiple identifiers for the same object, data belonging to one object incorrectly attached to ot...
Source: Specified Life - March 7, 2016 Category: Information Technology Tags: complexity computer science data analysis data repurposing data simplification data wrangling identifiers information science simplifying data taming data Source Type: blogs

Data Simplification: Identifiers
Over the next few weeks, I will be writing on topics related to my latest book, Data Simplification: Taming Information With Open Source Tools (release date March 23, 2016). I hope I can convince you that this is a book worth reading. Blog readers can use the discount code: COMP315 for a 30% discount, at checkout. "I always wanted to be somebody, but now I realize I should have been more specific." -Lily Tomlin An object identifier is anything associated with the object that persists throughout the life of the object and that is unique to the object (i.e., does not belong to any other object). Everyone is familia...
Source: Specified Life - March 6, 2016 Category: Information Technology Tags: complexity computer science data analysis data repurposing data simplification data wrangling identifiers information science simplifying data taming data Source Type: blogs

Data Simplification: Hitting the Complexity Barrier
Conclusions have no value until they are independently validated. Anyone who attempts to stay current in the sciences soon learns that much of the published literature is irreproducible (8); and that almost anything published today might be retracted tomorrow. This appalling truth applies to some of the most respected and trusted laboratories in the world (9), (10), (11), (12), (13), (14), (15), (16). Those of us who have been involved in assessing the rate of progress in disease research are painfully aware of the numerous reports indicating a general slowdown in medical progress (17), (18), (19), (20), (21), (22), (23),...
Source: Specified Life - March 5, 2016 Category: Information Technology Tags: complexity computer science data analysis data repurposing data simplification data wrangling information science simplifying data taming data Source Type: blogs

Data Simplification: Chapter Synapses
Over the next few weeks, I will be blogging on topics selected from Data Simplification: Taming Information With Open Source Tools. Those of you who are computer-oriented know that data analysis typically takes much less time and effort than data preparation. Moreover, if you make a mistake in your data analysis, you can often just repeat the process, using different tools, or a fresh approach to your original question. As long as the data is prepared properly, you and your colleagues can re-analyze your data to your heart's content. Contrariwise, if your data is not prepared in a manner that supports sensible analysis, th...
Source: Specified Life - March 4, 2016 Category: Information Technology Tags: computer science data analysis data repurposing data simplification data wrangling information science simplifying data taming data Source Type: blogs

Data Simplification: Contents
On March 23, my book, Data Simplification: Taming Information With Open Source Tools, will be published. Here is a preview of the contents: TABLE OF CONTENTSChapter 0. Preface References for Preface Glossary for PrefaceChapter 1. The Simple Life Section 1.1. Simplification drives scientific progress Section 1.2. The human mind is a simplifying machine Section 1.3. Simplification in Nature Section 1.4. The Complexity Barrier Section 1.5. Getting ready Open Source Tools for Chapter 1 Perl Python Ruby Text Editors OpenOffice Command line utilities Cygwin, Linux emulation for Windows DOS batch scripts ...
Source: Specified Life - March 3, 2016 Category: Information Technology Tags: computer science data analysis data repurposing data simplification data wrangling information science simplifying data taming data Source Type: blogs

Data Simplification: Why Bother?
Conclusions that cannot be validated have no scientific value. 3) Data simplification is not simple. There is something self-defeating about the term, "data simplification". The term seems to imply a dumbing down process wherein naturally complex concepts are presented in a manner that is palatable to marginally competent scientists. Nothing can be further from the truth. Creating overly complex data has always been the default option for lazy-minded or cavalier scientists who lacked the will or the talent to produce a simple, well-organized, and well-annotated collection of data. The act of data simplification ...
Source: Specified Life - March 2, 2016 Category: Information Technology Tags: computer science data analysis data repurposing data simplification data wrangling information science simplifying data taming data Source Type: blogs

Data Simplification: Book Announcement
On March 23, my book, Data Simplification: Taming Information With Open Source Tools, will be published. Those of you who are computer-oriented know that data analysis typically takes much less time and effort than data preparation. Furthermore, if you make a mistake in your data analysis, you can often just repeat the process, using different tools, or a fresh approach to your original question. As long as the data is prepared properly, you and your colleagues can re-analyze your data to your heart's content. Contrariwise, if your data is not prepared in a manner that supports sensible analysis, there's little you can do ...
Source: Specified Life - March 1, 2016 Category: Information Technology Tags: announcement data analysis data repurposing data simplification Source Type: blogs

Rare Disease Day is Here!
It's finally come; the rare day that comes every four years, Rare Disease Day. For the past several weeks, leading up to February 29, I've been blogging about rare diseases. The basic theme of all my blogs is that the rarity of rare diseases is not a numeric accident. The rare diseases form a distinct class of diseases having a distinct set of unifying biological properties that distinguish them from common diseases. In the past 30 years, most of the great advances of medicine have been in the realm of the rare diseases; not the common diseases. In many cases, progress in the common diseases has come as a secondary gain f...
Source: Specified Life - February 29, 2016 Category: Information Technology Tags: common diseases complex diseases funding for rare disease research medical research orphan diseases orphan drugs rare disease day zebra diseases Source Type: blogs

Rare Diseases Hiding Among Common Diseases
In June, 2014, my book, entitled Rare Diseases and Orphan Drugs: Keys to Understanding and Treating the Common Diseases was published by Elsevier. The book builds the argument that our best chance of curing the common diseases will come from studying and curing the rare diseases. Here is an excerpt from Chapter 12:It is easy to find cases wherein a rare disease accounts for a somewhat uncommon clinical presentation of a common disease. 12.1.2 Rule—Uncommon presentations of common diseases are sometimes rare diseases, camouflaged by a common clinical phenotype. Brief Rationale—Common diseases tend to occur with ...
Source: Specified Life - July 18, 2014 Category: Pathologists Tags: common disease cryptic disease disease genetics genetics of common diseases genetics of complex disease orphan disease orphan drugs rare disease subsets of disease Source Type: blogs

Pareto's Principle and Long-Tailed Distribution Curves
In June, 2014, my book, entitled Rare Diseases and Orphan Drugs: Keys to Understanding and Treating the Common Diseases was published by Elsevier. The book builds the argument that our best chance of curing the common diseases will come from studying and curing the rare diseases. The book has an extensive glossary, that explains the meaning and relevance of medical terms appearing throughout the chapters. The glossary can be read as a stand-along document. Here is an example of one term, "Pareto's Principle", excerpted from the glossary.Pareto’s principle - Also known as the 80/20 rule, Pareto’s princ...
Source: Specified Life - July 17, 2014 Category: Pathologists Tags: 80/20 rule common disease data analysis glossary orphan disease orphan drugs rare disease statistics Source Type: blogs