The latest update to the Developmental Lineage Classification and Taxonomy of Neoplasms is now available at:
http://www.julesberman.info/devclass.htm
The Neoplasms Classification contains about 135,000 neoplasm names collected under about 6,000 concepts. It is the largest neoplasm nomenclature in existence and is available as an open source document in several different file formats.
-Jules Berman
key words: nomenclature, ontology, cancer, tumors, terminology
Sunday, August 31, 2008
Friday, August 29, 2008
Books versus Google: Comment on Nicholas Carr's article
Nicholas Carr wrote a thoughtful but highly provocative article for the Atlantic, entitled Is Google Making us Stupid? As you might guess, his thesis is that surfing, and twittering, and Googling distract us from the serious business of book-reading and reduce our ability to think deeply.
There have been many subsequent blogs on the subject. Most of them criticize Carr as a sort of information Luddite who can't appreciate that the role of Google is to replace the near-defunct book.
Personally, I love Google and other web innovations. I assume that most of the readers of this blog feel the same way.
I also love books. I would say that my love of books has had two peaks. The first occurred when I was in high school and college. I devoured books back then, reading mostly science fiction books (Asimov, Clarke, Heinlein, Simak, Lem) plus lots of popular science books (Gamow, Eddington, Asimov (again), Clarke (again), Ley).
Then I went through a long period of life where I continued to read books, but never with the enthusiasm that I had when I was younger.
Today, in my late 50s, I've resumed my book reading with a passion. I read mystery novels, science books in many different fields, short stories, horror novels, biographies.... lots of different genres.
I've found that I can often (maybe always) identify another book lover within a few minutes of meeting them. Book lovers tend to think more deeply about subjects than other people. They can articulate opposing ways of thinking about a controversial issue. They attribute other sources of opinion (less absorbed with their own ideas, more willing to give credit to others). They are interested in many different things, and they don't mind exploring a subject with another person, for an extended time. They listen to other people.
I really like people who love books.
What is so special about books? A good book always tells a story and connects the reader to the narrative voice of the author. A well written book is about as close to a Vulcan mind meld as anything we have. If you really get into the book, it re-organizes our neural connections (as per Wolf in the Carr article) and builds relationships among different disciplines, helping us develop new hypotheses and helping us solve previously intractable problems (often by shifting the problem domain).
When people prophesy the demise of books, they are often thinking about written compilations of things (such as large textbooks); not narrative literature. Many textbooks are simply assemblages of topics written by committees of authors. In medicine, a fast-moving field, textbooks contain out-dated information the moment they're published. Textbooks can be replaced by e-books that can be easily updated. In many cases, a textbook can be replaced by a well-designed table of contents, with links to resources for each topic and sub-topic.
But narrative books are different from textbooks. A great book, even a science book, provides an intimate connection between the reader and the author. Most of the greatest informatics innovations involve human connections (cell phones, texting, twitter, facebook, blogs, role-playing games, and so on). Books are best appreciated when you think of them as a device that connects a reader to the narrative voice of the author through the medium of a story.
Readers, please send your thoughts on this subject.
- © 2008 Jules Berman
key words: book publishing, ebook, electronic publishing, textbook, multi-author volume, writing, reading, scientific discipline
Science is not a collection of facts. Science is what facts teach us; what we can learn about our universe, and ourselves, by deductive thinking. From observations of the night sky, made without the aid of telescopes, we can deduce that the universe is expanding, that the universe is not infinitely old, and why black holes exist. Without resorting to experimentation or mathematical analysis, we can deduce that gravity is a curvature in space-time, that the particles that compose light have no mass, that there is a theoretical limit to the number of different elements in the universe, and that the earth is billions of years old. Likewise, simple observations on animals tell us much about the migration of continents, the evolutionary relationships among classes of animals, why the nuclei of cells contain our genetic material, why certain animals are long-lived, why the gestation period of humans is 9 months, and why some diseases are rare and other diseases are common. In “Armchair Science”, the reader is confronted with 129 scientific mysteries, in cosmology, particle physics, chemistry, biology, and medicine. Beginning with simple observations, step-by-step analyses guide the reader toward solutions that are sometimes startling, and always entertaining. “Armchair Science” is written for general readers who are curious about science, and who want to sharpen their deductive skills.
There have been many subsequent blogs on the subject. Most of them criticize Carr as a sort of information Luddite who can't appreciate that the role of Google is to replace the near-defunct book.
Personally, I love Google and other web innovations. I assume that most of the readers of this blog feel the same way.
I also love books. I would say that my love of books has had two peaks. The first occurred when I was in high school and college. I devoured books back then, reading mostly science fiction books (Asimov, Clarke, Heinlein, Simak, Lem) plus lots of popular science books (Gamow, Eddington, Asimov (again), Clarke (again), Ley).
Then I went through a long period of life where I continued to read books, but never with the enthusiasm that I had when I was younger.
Today, in my late 50s, I've resumed my book reading with a passion. I read mystery novels, science books in many different fields, short stories, horror novels, biographies.... lots of different genres.
I've found that I can often (maybe always) identify another book lover within a few minutes of meeting them. Book lovers tend to think more deeply about subjects than other people. They can articulate opposing ways of thinking about a controversial issue. They attribute other sources of opinion (less absorbed with their own ideas, more willing to give credit to others). They are interested in many different things, and they don't mind exploring a subject with another person, for an extended time. They listen to other people.
I really like people who love books.
What is so special about books? A good book always tells a story and connects the reader to the narrative voice of the author. A well written book is about as close to a Vulcan mind meld as anything we have. If you really get into the book, it re-organizes our neural connections (as per Wolf in the Carr article) and builds relationships among different disciplines, helping us develop new hypotheses and helping us solve previously intractable problems (often by shifting the problem domain).
When people prophesy the demise of books, they are often thinking about written compilations of things (such as large textbooks); not narrative literature. Many textbooks are simply assemblages of topics written by committees of authors. In medicine, a fast-moving field, textbooks contain out-dated information the moment they're published. Textbooks can be replaced by e-books that can be easily updated. In many cases, a textbook can be replaced by a well-designed table of contents, with links to resources for each topic and sub-topic.
But narrative books are different from textbooks. A great book, even a science book, provides an intimate connection between the reader and the author. Most of the greatest informatics innovations involve human connections (cell phones, texting, twitter, facebook, blogs, role-playing games, and so on). Books are best appreciated when you think of them as a device that connects a reader to the narrative voice of the author through the medium of a story.
Readers, please send your thoughts on this subject.
- © 2008 Jules Berman
key words: book publishing, ebook, electronic publishing, textbook, multi-author volume, writing, reading, scientific discipline
Science is not a collection of facts. Science is what facts teach us; what we can learn about our universe, and ourselves, by deductive thinking. From observations of the night sky, made without the aid of telescopes, we can deduce that the universe is expanding, that the universe is not infinitely old, and why black holes exist. Without resorting to experimentation or mathematical analysis, we can deduce that gravity is a curvature in space-time, that the particles that compose light have no mass, that there is a theoretical limit to the number of different elements in the universe, and that the earth is billions of years old. Likewise, simple observations on animals tell us much about the migration of continents, the evolutionary relationships among classes of animals, why the nuclei of cells contain our genetic material, why certain animals are long-lived, why the gestation period of humans is 9 months, and why some diseases are rare and other diseases are common. In “Armchair Science”, the reader is confronted with 129 scientific mysteries, in cosmology, particle physics, chemistry, biology, and medicine. Beginning with simple observations, step-by-step analyses guide the reader toward solutions that are sometimes startling, and always entertaining. “Armchair Science” is written for general readers who are curious about science, and who want to sharpen their deductive skills.
Thursday, August 28, 2008
Using the Neoplasm synonymy and related term finder
Alternate and related terms for neoplasm names are available through my search engine at:
http://www.julesberman.info/neoget.htm
You can get a taste of what the search engine provides by clicking on any of the sample submit buttons below:
If you have doubts concerning the scientific uses of a nomenclature, you might want to read my article on the neoplasm classification, available at:
http://www.biomedcentral.com/1471-2407/4/10
-Jules Berman
key words: nomenclature, dictionary, thesaurus, ontology, tumor, tumour, neoplasia, neoplasm, cancer, pathology
Science is not a collection of facts. Science is what facts teach us; what we can learn about our universe, and ourselves, by deductive thinking. From observations of the night sky, made without the aid of telescopes, we can deduce that the universe is expanding, that the universe is not infinitely old, and why black holes exist. Without resorting to experimentation or mathematical analysis, we can deduce that gravity is a curvature in space-time, that the particles that compose light have no mass, that there is a theoretical limit to the number of different elements in the universe, and that the earth is billions of years old. Likewise, simple observations on animals tell us much about the migration of continents, the evolutionary relationships among classes of animals, why the nuclei of cells contain our genetic material, why certain animals are long-lived, why the gestation period of humans is 9 months, and why some diseases are rare and other diseases are common. In “Armchair Science”, the reader is confronted with 129 scientific mysteries, in cosmology, particle physics, chemistry, biology, and medicine. Beginning with simple observations, step-by-step analyses guide the reader toward solutions that are sometimes startling, and always entertaining. “Armchair Science” is written for general readers who are curious about science, and who want to sharpen their deductive skills.
http://www.julesberman.info/neoget.htm
You can get a taste of what the search engine provides by clicking on any of the sample submit buttons below:
If you have doubts concerning the scientific uses of a nomenclature, you might want to read my article on the neoplasm classification, available at:
http://www.biomedcentral.com/1471-2407/4/10
-Jules Berman
key words: nomenclature, dictionary, thesaurus, ontology, tumor, tumour, neoplasia, neoplasm, cancer, pathology
Science is not a collection of facts. Science is what facts teach us; what we can learn about our universe, and ourselves, by deductive thinking. From observations of the night sky, made without the aid of telescopes, we can deduce that the universe is expanding, that the universe is not infinitely old, and why black holes exist. Without resorting to experimentation or mathematical analysis, we can deduce that gravity is a curvature in space-time, that the particles that compose light have no mass, that there is a theoretical limit to the number of different elements in the universe, and that the earth is billions of years old. Likewise, simple observations on animals tell us much about the migration of continents, the evolutionary relationships among classes of animals, why the nuclei of cells contain our genetic material, why certain animals are long-lived, why the gestation period of humans is 9 months, and why some diseases are rare and other diseases are common. In “Armchair Science”, the reader is confronted with 129 scientific mysteries, in cosmology, particle physics, chemistry, biology, and medicine. Beginning with simple observations, step-by-step analyses guide the reader toward solutions that are sometimes startling, and always entertaining. “Armchair Science” is written for general readers who are curious about science, and who want to sharpen their deductive skills.
Wednesday, August 27, 2008
Inherited disorders associated with neoplasms: web page
Earlier this week I prepared a new web page featuring a long list of inherited conditions of man that are associated, in one way or another, with neoplasia. It is available at:
http://www.julesberman.info/omimneo.htm
In some cases, an inherited mutation is causally related to a narrow range of neoplasms (such as neurofibromatosis).
In some cases, an inherited mutation is causally related to a wide range of neoplasms (such as Li-Fraumeni syndrome).
In many cases, people who have the inherited condition have a medical condition or syndrome that comes with a higher than expected incidence of one or more specific types of neoplasms.
In some cases, the neoplastic tie-in to a listed inherited condition is rather tenuous.
I've provided links for each entry that will take you to the OMIM (Online Mendelian Inheritance in Man) record for the disease. You can read the full OMIM record and determine for yourself whether the information is relevant to your specific interests.
- © 2008 Jules Berman
key words: neoplasms, syndromes, cancer syndrome, familial cancer, inherited neoplasms, neoplasia, tumor, tumour
http://www.julesberman.info/omimneo.htm
In some cases, an inherited mutation is causally related to a narrow range of neoplasms (such as neurofibromatosis).
In some cases, an inherited mutation is causally related to a wide range of neoplasms (such as Li-Fraumeni syndrome).
In many cases, people who have the inherited condition have a medical condition or syndrome that comes with a higher than expected incidence of one or more specific types of neoplasms.
In some cases, the neoplastic tie-in to a listed inherited condition is rather tenuous.
I've provided links for each entry that will take you to the OMIM (Online Mendelian Inheritance in Man) record for the disease. You can read the full OMIM record and determine for yourself whether the information is relevant to your specific interests.
- © 2008 Jules Berman
key words: neoplasms, syndromes, cancer syndrome, familial cancer, inherited neoplasms, neoplasia, tumor, tumour
Tuesday, August 26, 2008
Neoplasm synonym look-up
I just created a web site that permits anyone to enter the name of a neoplasm and retrieve all of the synonyms and all of the related terms for the entry term.
The search engine is available at:
http://www.julesberman.info/neoget.htm
It uses the Developmental Lineage Classification and Taxonomy of Neoplasms, which consists of over 135,000 neoplasm terms. This open source dataset is available as compressed RDF, text or XML files:
The gzipped version of the RDF file (under 1 Megabyte)
http://www.julesberman.info/neorxml.gz
The flat file version, listing each term followed by its lineage (gzipped file).
http://www.julesberman.info/neoself.gz
The plain old XML version, with no RDF semantics (compressed gzip file).
http://www.julesberman.info/neoclxml.gz
The plain old XML version, with no RDF semantics (compressed zip file).
http://www.julesberman.info/neoclxml.zip
More information on uses for the Developmental Lineage Classification is available from my home page.
- Jules J. Berman
key words: ontology, tumors, cancers, neoplasia, medical terminology, nomenclature, dictionary, concept unique identifier, medical terminology, concept identifier, neoplasm classification, taxonomy
The search engine is available at:
http://www.julesberman.info/neoget.htm
It uses the Developmental Lineage Classification and Taxonomy of Neoplasms, which consists of over 135,000 neoplasm terms. This open source dataset is available as compressed RDF, text or XML files:
The gzipped version of the RDF file (under 1 Megabyte)
http://www.julesberman.info/neorxml.gz
The flat file version, listing each term followed by its lineage (gzipped file).
http://www.julesberman.info/neoself.gz
The plain old XML version, with no RDF semantics (compressed gzip file).
http://www.julesberman.info/neoclxml.gz
The plain old XML version, with no RDF semantics (compressed zip file).
http://www.julesberman.info/neoclxml.zip
More information on uses for the Developmental Lineage Classification is available from my home page.
- Jules J. Berman
key words: ontology, tumors, cancers, neoplasia, medical terminology, nomenclature, dictionary, concept unique identifier, medical terminology, concept identifier, neoplasm classification, taxonomy
Monday, August 25, 2008
Update of Medical Abbreviation Web Page
Today, I updated my medical abbreviation web page.
A journal article describes the web page and provides a discourse on medical abbreviations:
Berman JJ. Pathology Abbreviated: A Long Review of Short Terms. Archives of Pathology and Laboratory Medicine, 128:347-352, 2004.
The medical abbreviation page contains about 12,000 medical abbreviations. It is open source and is distributed under a GNU license.
A sampling of the page:
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.
I urge you to read more about my book. There's a generous preview of the book at the Google Books site. If you like the book, please request your librarian to purchase a copy of this book for your library or reading room.
-© 2009 Jules J. Berman, Ph.D., M.D.
tags: common disease, orphan disease, orphan drugs, rare disease, subsets of disease, disease genetics, genetics of complex disease, genetics of common diseases, medical informatics, medical nomenclature,medical terminology, medical abbreviations - Jules J. Berman
A journal article describes the web page and provides a discourse on medical abbreviations:
Berman JJ. Pathology Abbreviated: A Long Review of Short Terms. Archives of Pathology and Laboratory Medicine, 128:347-352, 2004.
The medical abbreviation page contains about 12,000 medical abbreviations. It is open source and is distributed under a GNU license.
A sampling of the page:
aa = adriamycin
aa = african american
aa = alcohol abuse
aa = alcoholics anonymous
aa = alopecia areata
aa = amino acid
aa = amyloid protein A
aa = aortic aneurysm
aa = aortic arch
aa = aplastic anemia
aa = ara c
aa = arachidonic acid
aa = ascending aorta
aaa = abdominal aortic aneurysm
aaa = acquired aplastic anemia
aaa = acute apical abscess
aaa = aromatic amino acid
aaf = acetylaminofluorene
aag = alpha 1 acid glycoprotein
aah = atypical adenomatous hyperplasia
aai = acute alcohol intoxication
aall = anterior axillary line
aami = age associated memory impairment
aamtase = aklanonic acid methyltransferase
aaox3 = awake alert and oriented to date place & person
aark = automated anesthesia record keeper
aas = aarskog scott syndrome
aas = aortic arch syndrome
aas = atlantoaxial subluxation
aat = aachen aphasia test
aat = alpha 1 antitrypsin
aat = alpha antitrypsin
aau = acute anterior uveitis
aav = aids associated virus
ab = abdominal
ab = abortion
ab = antibody
ab = asthmatic bronchitis
aba = abscissic acid
abatc = azidobenzamidotaurocholate
abc = aneurysmal bone cyst
abc = apnea bradycardia cyanosis
abc = aspiration biopsy cytology
abd = abdomen
abd = abductor
abdom = abdomen
abdv = bleomycin doxorubicin dtic vinblastine
abe = acute bacterial endocarditis
abf = aortobifemoral graft
abg = aortic bifurcation graft
abg = aortobifemoral graft
abg = arterial blood gas
abi = arterial pressure index
abk = aphakic bullous keratopathy
abl = abetalipoproteinaemia
abl = abetalipoproteinemia
abl = african burkitt's lymphoma
abl = angioblastic lymphadenopathy
ablc = amphotericin b lipid complex
abm = alveolar basement membrane antibody
abmt = autologous bone marrow transplant
abn = abnormal
abnl = abnormal
abo = a system of classifying blood groups by a or b antibody
abo = abortion
abo = antibody
abo = bleo mtx vcr
abo hdn = abo hemolytic disease of the newborn
abp = arterial blood pressure
abpa = asthmatic bronchopulmonary aspergillosis
abpb = abductor pollicis brevis
abpl = abductor pollicis longus
abr = auditory brainstem response
abs = abdominal muscles
abs = abdominals
abs = absent
abs = acute brain syndrome
abs = affect balance scale
abs = anorexic behavior scales
abt = autologous blood transfusion
abu = asymptomatic bacteriuria
abv = actinomycin d, bleomycin, vincristine
abv = adriamycin, bleomycin, vinblastine
abv = bleo dox vbl
abvd = bleomycin dacarbazine doxorubicin vincristine
abx = antibiotics
ac = acute
ac = air conditioning
ac = air conduction
ac = alternating current
ac = amniocentesis
ac = ante cibum
ac = anterior chamber
ac = ascending colon
ac = assist control
ac/a = accommodation convergence/accommodation
aca = adenocarcinoma
aca = anterior cerebral artery
aca = anti cardiolipin antibody
acad = academy
acbe = air contrast barium enema
acc = acceleration
acc = accelerator
acc = accident
acc = accommodation
acc = adrenocortical carcinoma
acc = agenesis of corpus callosum
acc = alveolar cell carcinoma
acc = aplasia cutis congenita
acca = adenylate cyclase constitutive activator
acca = adrenal cortical carcinoma
acca = adrenocortical carcinoma
accom = accommodation
accpn = agenesis of the corpus callosum with peripheral neuropathy
acd = acid citrate dextrose
acd = actinomycin d
acd = adult celiac disease
acd = allergic contact dermatitis
acd = anemia of chronic disease
acd = arteriosclerotic coronary disease
acd = automatic cardiac defibrillator procedure
acd = corneal dystrophy
ace = acetylcholinesterase
ace = angiotensin converting enzyme
ace = cyclophosphamide doxorubicin
ace = dipeptidyl peptidase a
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.
I urge you to read more about my book. There's a generous preview of the book at the Google Books site. If you like the book, please request your librarian to purchase a copy of this book for your library or reading room.
-© 2009 Jules J. Berman, Ph.D., M.D.
tags: common disease, orphan disease, orphan drugs, rare disease, subsets of disease, disease genetics, genetics of complex disease, genetics of common diseases, medical informatics, medical nomenclature,medical terminology, medical abbreviations - Jules J. Berman
Thursday, August 14, 2008
Appeals Court Ruling on Open Source License
I thought I'd take a break from my series of blogs on Neoplasms to discuss this week's (August 13) important court ruling that upholds open source licenses. I'm referring to the following:
United States Court of Appeals for the Federal Circuit
2008-1001
ROBERT JACOBSEN,
Plaintiff-Appellant,
v.
MATTHEW KATZER and
KAMIND ASSOCIATES, INC. (doing business as KAM Industries),
Defendants-Appellees.
DECIDED: August 13, 2008
The entire ruling is available at:
http://www.cafc.uscourts.gov/opinions/08-1001.pdf
Today's blog post is a layman's interpretation of the issues involved and the significance of the court's ruling.
Basically, software code taken from an open source application was used in a patented product, without citing the open source software as prior art. The copyright holder sued. The patent holder did not dispute taking some of the open source code, but insisted that the open source license was unenforceable and that he was within his rights to use the code for whatever he pleased. The lower court agreed, essentially invalidating the open source license.
The appeals court overturned the lower court ruling and upheld the legal standing of the conditions specified in the open source license. This ruling permits additional legal recourse to be taken by the open source copyright holder against the patent holder, but for the open source community, the importance of the ruling is that it upholds the legal validity of the conditions specified in the open source document (mostly, these are the requirements that pertain to maintaining the open source license for uses and redistributions of the original software, so that the software remains open source and available, and credited to the original copyright holder).
Why do some people think that the open source license has no legal validity? Basically, there is a long tradition that licenses and contracts and virtually all types of signed agreements, exist for some mercantile purpose. Agreements specify who owes what to whom. Some say that a license that gives something away for free is just a joke. There is no need for the courts to get involved in silly requirements imposed on people who are exchanging items that have no monetary value.
The requirements in an open source software license are called "viral inclusions," if they impose conditions that are transmissible from one user to the next user. If I allow Fred to use my software under a set of conditions that requires him to convey the same conditions on Sally, the next person who uses the software, then in effect, I have created a license between myself and Sally (without ever exchanging money and without having a meeting of the minds, with Sally). Some have claimed that the so-called "viral" propagation of license conditions is a legal absurdity and cannot be enforced.
Well, the open source advocates have had their day in court, and they have won their argument. It basically goes like this. People who use the open source license are using a new kind of legal device that serves their own valid interests and the interests of society. In addition, the open source license was created by very thoughtful and talented legal minds and is supported by legitimate public and private concerns (as evidenced by Amicus briefs entered for the proceedings) who would suffer losses if open source licenses were invalidated (i.e., the open source license supports mercantile efforts and is not just a give-away for software that has no value).
If there is no money exchanged, who benefits from an open source license? When a copyright holder distributes software under an open source license, she receives credit for the accomplishment from the user community, thus enhancing her standing, and her marketability, and contributing to a community effort that encourages others to do the same (so she can likewise benefit from software produced by her colleagues). The license specifies a set of conditions that makes the communal use of software possible while preserving copyright with the original creator of the software. The open source license is written to enforce certain rights and intentions of the copyright holder that benefit the copyright holder. Furthermore, those who do not like the conditions imposed in the open source license, are asked to contact the copyright holder to negotiate an alternate software conveyance (i.e., the open source license suggests a way to seek an alternate legal device to obtain use of the same software). If the courts were to invalidate the conditions imposed within the open source license, then the copyright holder would be hurt, and the communal effort to create open source software would quickly collapse, much to the detriment of society.
The Appeals court, in its published statement, recognizes the purpose and the validity of the so-called viral conditions imposed by the open source license.
This is my [layman's] interpretation of the ruling. I urge everyone to go to the original document and draw their own conclusions.
-Copyright (C) 2008 Jules J. Berman
Science is not a collection of facts. Science is what facts teach us; what we can learn about our universe, and ourselves, by deductive thinking. From observations of the night sky, made without the aid of telescopes, we can deduce that the universe is expanding, that the universe is not infinitely old, and why black holes exist. Without resorting to experimentation or mathematical analysis, we can deduce that gravity is a curvature in space-time, that the particles that compose light have no mass, that there is a theoretical limit to the number of different elements in the universe, and that the earth is billions of years old. Likewise, simple observations on animals tell us much about the migration of continents, the evolutionary relationships among classes of animals, why the nuclei of cells contain our genetic material, why certain animals are long-lived, why the gestation period of humans is 9 months, and why some diseases are rare and other diseases are common. In “Armchair Science”, the reader is confronted with 129 scientific mysteries, in cosmology, particle physics, chemistry, biology, and medicine. Beginning with simple observations, step-by-step analyses guide the reader toward solutions that are sometimes startling, and always entertaining. “Armchair Science” is written for general readers who are curious about science, and who want to sharpen their deductive skills.
United States Court of Appeals for the Federal Circuit
2008-1001
ROBERT JACOBSEN,
Plaintiff-Appellant,
v.
MATTHEW KATZER and
KAMIND ASSOCIATES, INC. (doing business as KAM Industries),
Defendants-Appellees.
DECIDED: August 13, 2008
The entire ruling is available at:
http://www.cafc.uscourts.gov/opinions/08-1001.pdf
Today's blog post is a layman's interpretation of the issues involved and the significance of the court's ruling.
Basically, software code taken from an open source application was used in a patented product, without citing the open source software as prior art. The copyright holder sued. The patent holder did not dispute taking some of the open source code, but insisted that the open source license was unenforceable and that he was within his rights to use the code for whatever he pleased. The lower court agreed, essentially invalidating the open source license.
The appeals court overturned the lower court ruling and upheld the legal standing of the conditions specified in the open source license. This ruling permits additional legal recourse to be taken by the open source copyright holder against the patent holder, but for the open source community, the importance of the ruling is that it upholds the legal validity of the conditions specified in the open source document (mostly, these are the requirements that pertain to maintaining the open source license for uses and redistributions of the original software, so that the software remains open source and available, and credited to the original copyright holder).
Why do some people think that the open source license has no legal validity? Basically, there is a long tradition that licenses and contracts and virtually all types of signed agreements, exist for some mercantile purpose. Agreements specify who owes what to whom. Some say that a license that gives something away for free is just a joke. There is no need for the courts to get involved in silly requirements imposed on people who are exchanging items that have no monetary value.
The requirements in an open source software license are called "viral inclusions," if they impose conditions that are transmissible from one user to the next user. If I allow Fred to use my software under a set of conditions that requires him to convey the same conditions on Sally, the next person who uses the software, then in effect, I have created a license between myself and Sally (without ever exchanging money and without having a meeting of the minds, with Sally). Some have claimed that the so-called "viral" propagation of license conditions is a legal absurdity and cannot be enforced.
Well, the open source advocates have had their day in court, and they have won their argument. It basically goes like this. People who use the open source license are using a new kind of legal device that serves their own valid interests and the interests of society. In addition, the open source license was created by very thoughtful and talented legal minds and is supported by legitimate public and private concerns (as evidenced by Amicus briefs entered for the proceedings) who would suffer losses if open source licenses were invalidated (i.e., the open source license supports mercantile efforts and is not just a give-away for software that has no value).
If there is no money exchanged, who benefits from an open source license? When a copyright holder distributes software under an open source license, she receives credit for the accomplishment from the user community, thus enhancing her standing, and her marketability, and contributing to a community effort that encourages others to do the same (so she can likewise benefit from software produced by her colleagues). The license specifies a set of conditions that makes the communal use of software possible while preserving copyright with the original creator of the software. The open source license is written to enforce certain rights and intentions of the copyright holder that benefit the copyright holder. Furthermore, those who do not like the conditions imposed in the open source license, are asked to contact the copyright holder to negotiate an alternate software conveyance (i.e., the open source license suggests a way to seek an alternate legal device to obtain use of the same software). If the courts were to invalidate the conditions imposed within the open source license, then the copyright holder would be hurt, and the communal effort to create open source software would quickly collapse, much to the detriment of society.
The Appeals court, in its published statement, recognizes the purpose and the validity of the so-called viral conditions imposed by the open source license.
This is my [layman's] interpretation of the ruling. I urge everyone to go to the original document and draw their own conclusions.
-Copyright (C) 2008 Jules J. Berman
Science is not a collection of facts. Science is what facts teach us; what we can learn about our universe, and ourselves, by deductive thinking. From observations of the night sky, made without the aid of telescopes, we can deduce that the universe is expanding, that the universe is not infinitely old, and why black holes exist. Without resorting to experimentation or mathematical analysis, we can deduce that gravity is a curvature in space-time, that the particles that compose light have no mass, that there is a theoretical limit to the number of different elements in the universe, and that the earth is billions of years old. Likewise, simple observations on animals tell us much about the migration of continents, the evolutionary relationships among classes of animals, why the nuclei of cells contain our genetic material, why certain animals are long-lived, why the gestation period of humans is 9 months, and why some diseases are rare and other diseases are common. In “Armchair Science”, the reader is confronted with 129 scientific mysteries, in cosmology, particle physics, chemistry, biology, and medicine. Beginning with simple observations, step-by-step analyses guide the reader toward solutions that are sometimes startling, and always entertaining. “Armchair Science” is written for general readers who are curious about science, and who want to sharpen their deductive skills.
Monday, August 4, 2008
Neoplasms: 22
This is the 22nd blog in a series of blogs on neoplasia.
Today, I thought I'd summarize the points that I've been trying to make in the preceding 21 blogs.
The common cancers of man have many causes and are genetically complex. The cancers seen in adults, which account for the bulk of cancer deaths, are constantly progressing toward even greater complexity and tumor heterogeneity.
The bulk of cancer research is directed towards finding a cure for the common cancers that occur in adults, but the common cancers have been the hardest cancers to cure. Advances in treatment for the common cancers have come through small extensions in the lifespan of cancer patients achieved through improved protocols developed in clinic trials. Clinical trials are long and expensive, and often produce negative results (i.e. demonstrating the inefficacy of a candidate treatment).
The cancers that we have learned to cure are rare tumors, characterized by simple genetic abnormalities. Cures for the rare cancers cannot yield large decreases in the number of people dying from cancer. Lessons learned from the rare cancers may one day lead to cures for the advanced* common cancers. At the present moment, there is no reason to think that a breakthrough in treating advanced, common cancers will happen any time soon.
In previous blogs, I suggested that the best approach to eradicating cancers may be through the precancers. By treating precancers, we can stop cancers from developing.
-Copyright (C) 2008 Jules J. Berman
*An advanced common cancer is one that has spread extensively from its site of origin.
key words: cancer, tumor, tumour, carcinogen, neoplasia, neoplastic development, classification, biomedical informatics, tumor development, precancer, benign tumor, ontology, classification, developmental lineage classification and taxonomy of neoplasms
Today, I thought I'd summarize the points that I've been trying to make in the preceding 21 blogs.
The common cancers of man have many causes and are genetically complex. The cancers seen in adults, which account for the bulk of cancer deaths, are constantly progressing toward even greater complexity and tumor heterogeneity.
The bulk of cancer research is directed towards finding a cure for the common cancers that occur in adults, but the common cancers have been the hardest cancers to cure. Advances in treatment for the common cancers have come through small extensions in the lifespan of cancer patients achieved through improved protocols developed in clinic trials. Clinical trials are long and expensive, and often produce negative results (i.e. demonstrating the inefficacy of a candidate treatment).
The cancers that we have learned to cure are rare tumors, characterized by simple genetic abnormalities. Cures for the rare cancers cannot yield large decreases in the number of people dying from cancer. Lessons learned from the rare cancers may one day lead to cures for the advanced* common cancers. At the present moment, there is no reason to think that a breakthrough in treating advanced, common cancers will happen any time soon.
In previous blogs, I suggested that the best approach to eradicating cancers may be through the precancers. By treating precancers, we can stop cancers from developing.
-Copyright (C) 2008 Jules J. Berman
*An advanced common cancer is one that has spread extensively from its site of origin.
key words: cancer, tumor, tumour, carcinogen, neoplasia, neoplastic development, classification, biomedical informatics, tumor development, precancer, benign tumor, ontology, classification, developmental lineage classification and taxonomy of neoplasms
Saturday, August 2, 2008
Neoplasms: 21
This is the 21st blog in a series of blogs on neoplasia.
Time is not on our side in the war on cancer. Modern clinical trials are long and expensive. The process of testing a prospective new drug can take many years. In the realm of cancer trials, the Prostate, Lung, Colorectal and Ovarian Cancer Screening Trial (PLCO, NIH/NCI trial NO1 CN25512) serves as an example. The PLCO is a randomized controlled cancer trial. Between 1992, when the trial opened, and 2001, when enrollment ended, 155,000 women and men between the ages of 55 and 74 joined PLCO. Screening of participants and the collection of follow-up data will end around 2016. The purpose of the study is to determine if screening will reduce mortality from these cancers. We will need 24 years to answer this question.
Though prospective trials are often considered the only way of determining the efficacy and safety of new treatments, and diagnostic tests, the public may legitimately ask whether society has the time, money and patience for these studies. Those engaged in clinical trials may well ask themselves whether some clinical trials be replaced by new, innovative models producing clinically sound results in less time and for less money?
There are literally thousands of different neoplasms of man, all requiring stage-stratified clinical trials to find effective treatments. Can we go on the way we have in the past? Do we, as a society, have the time or money, to test all of the potential chemotherapeutic agents (most of which will be ineffective) on all of these cancers?
In the next blogs, we'll consider these questions and discuss possible alternative approaches.
-Copyright (C) 2008 Jules J. Berman
key words: cancer, tumor, tumour, carcinogen, neoplasia, neoplastic development, classification, biomedical informatics, tumor development, precancer, benign tumor, ontology, classification, developmental lineage classification and taxonomy of neoplasms
Time is not on our side in the war on cancer. Modern clinical trials are long and expensive. The process of testing a prospective new drug can take many years. In the realm of cancer trials, the Prostate, Lung, Colorectal and Ovarian Cancer Screening Trial (PLCO, NIH/NCI trial NO1 CN25512) serves as an example. The PLCO is a randomized controlled cancer trial. Between 1992, when the trial opened, and 2001, when enrollment ended, 155,000 women and men between the ages of 55 and 74 joined PLCO. Screening of participants and the collection of follow-up data will end around 2016. The purpose of the study is to determine if screening will reduce mortality from these cancers. We will need 24 years to answer this question.
Though prospective trials are often considered the only way of determining the efficacy and safety of new treatments, and diagnostic tests, the public may legitimately ask whether society has the time, money and patience for these studies. Those engaged in clinical trials may well ask themselves whether some clinical trials be replaced by new, innovative models producing clinically sound results in less time and for less money?
There are literally thousands of different neoplasms of man, all requiring stage-stratified clinical trials to find effective treatments. Can we go on the way we have in the past? Do we, as a society, have the time or money, to test all of the potential chemotherapeutic agents (most of which will be ineffective) on all of these cancers?
In the next blogs, we'll consider these questions and discuss possible alternative approaches.
-Copyright (C) 2008 Jules J. Berman
key words: cancer, tumor, tumour, carcinogen, neoplasia, neoplastic development, classification, biomedical informatics, tumor development, precancer, benign tumor, ontology, classification, developmental lineage classification and taxonomy of neoplasms
Friday, August 1, 2008
Neoplasms: 20
This is the twentieth blog in a series of blogs on neoplasia.
Though there has been little success in curing the advanced* common cancers, there has been remarkable success in finding cures for some of the rare cancers, particularly several rare cancers of childhood. Why is it possible to cure rare cancers? Why would rarity have anything to do with curability? In this blog, and in the next few blogs, we'll be exploring the properties of common tumors and how they differ from the properties of rare tumors.
We can cure a few of the rare or uncommon tumors
List. Tumors that can be cured with chemotherapy [1]
- Choriocarcinoma
- Acute lymphocytic leukemia of childhood
- Burkitt lymphoma
- Hodgkin lymphoma
- Acute promyelocytic leukemia
- Large follicular center cell (diffuse histiocytic) lymphoma
- Embryonal carcinoma of testis
- Hairy cell leukemia (probable)
- Seminoma
The new anticancer drugs, targeted at specific pathways activated in tumors, are most effective against rare tumors, characterized by simple, well-characterized mutations and translocations.
A good example is GIST (gastrointestinal stromal tumor). Gist is a rare tumor that is highly responsive to a relatively non-toxic chemotherapeutic agent, imatinib. Many cases of this tumor have a mutation in the C-KIT gene, which codes for a tyrosine kinase receptor that is inhibited by imatinib. GIST is an example of a very simple tumor, that seems to be characterized by a single gene mutation (usually C-KIT), resulting in over-expression of a single protein (tryosine kinase receptor), which is apparently singlehandedly responsible for driving the growth of the tumor, and which can be treated by a non-toxic agent targeted against a specific molecule. Of course, nothing in the field of cancer is ever so simple, and recent studies have uncovered a variety of complicating factors. Still, GIST stands as one of the simplest cancers of humans. Similarly, several other rare tumors characterized by specific tyrosine kinase mutations, including chronic myelogenous leukemia, and systemic mastocytosis, are responsive to imatinib.
It is unlikely that we will develop a cure for the common cancers before we have developed a variety of approaches to curing genetically simple cancers. Sometimes, you need to crawl before you can walk.
1. [Holland Frei Cancer Medicine. Kufe D, Pollock R, Weichselbaum R, Bast R, Gansler T, Holland J, Frei E, eds. BC Decker, Ontario, Canada, 2003.]
-Copyright (C) 2008 Jules J. Berman
*An advanced cancer is one that has directly spread extensively from its primary site or that has metastasized to a distant site
key words: cancer, tumor, tumour, carcinogen, neoplasia, neoplastic development, classification, biomedical informatics, tumor development, precancer, benign tumor, ontology, classification, developmental lineage classification and taxonomy of neoplasms
Though there has been little success in curing the advanced* common cancers, there has been remarkable success in finding cures for some of the rare cancers, particularly several rare cancers of childhood. Why is it possible to cure rare cancers? Why would rarity have anything to do with curability? In this blog, and in the next few blogs, we'll be exploring the properties of common tumors and how they differ from the properties of rare tumors.
We can cure a few of the rare or uncommon tumors
List. Tumors that can be cured with chemotherapy [1]
- Choriocarcinoma
- Acute lymphocytic leukemia of childhood
- Burkitt lymphoma
- Hodgkin lymphoma
- Acute promyelocytic leukemia
- Large follicular center cell (diffuse histiocytic) lymphoma
- Embryonal carcinoma of testis
- Hairy cell leukemia (probable)
- Seminoma
The new anticancer drugs, targeted at specific pathways activated in tumors, are most effective against rare tumors, characterized by simple, well-characterized mutations and translocations.
A good example is GIST (gastrointestinal stromal tumor). Gist is a rare tumor that is highly responsive to a relatively non-toxic chemotherapeutic agent, imatinib. Many cases of this tumor have a mutation in the C-KIT gene, which codes for a tyrosine kinase receptor that is inhibited by imatinib. GIST is an example of a very simple tumor, that seems to be characterized by a single gene mutation (usually C-KIT), resulting in over-expression of a single protein (tryosine kinase receptor), which is apparently singlehandedly responsible for driving the growth of the tumor, and which can be treated by a non-toxic agent targeted against a specific molecule. Of course, nothing in the field of cancer is ever so simple, and recent studies have uncovered a variety of complicating factors. Still, GIST stands as one of the simplest cancers of humans. Similarly, several other rare tumors characterized by specific tyrosine kinase mutations, including chronic myelogenous leukemia, and systemic mastocytosis, are responsive to imatinib.
It is unlikely that we will develop a cure for the common cancers before we have developed a variety of approaches to curing genetically simple cancers. Sometimes, you need to crawl before you can walk.
1. [Holland Frei Cancer Medicine. Kufe D, Pollock R, Weichselbaum R, Bast R, Gansler T, Holland J, Frei E, eds. BC Decker, Ontario, Canada, 2003.]
-Copyright (C) 2008 Jules J. Berman
*An advanced cancer is one that has directly spread extensively from its primary site or that has metastasized to a distant site
key words: cancer, tumor, tumour, carcinogen, neoplasia, neoplastic development, classification, biomedical informatics, tumor development, precancer, benign tumor, ontology, classification, developmental lineage classification and taxonomy of neoplasms
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