Designer Genes, Designer Drugs: A Funny Thing Happened on the Way to the Forum Fred Stoss Science and Engineering Information Center SUNY University at Buffalo Upstate New York Science Librarians Annual Meeting Cornell University October 23, 2013

A FUNNY THING HAPPENED ON THE WAY TO THE FORUM Bull. Med. Libr. Assoc. 59 (4) Oct – June 2, 1971 – New York City – Annual Meeting Program Committee experimented – 9 different forums presented simultaneously – Repeated in afternoon – “A funny thing happened on the way to the Forum.... We communicated.”

“Traditional Biology”

Physiology: Membrane Transport “New”

Biochemistry

Forensics

High School Interests to College Enrolment in Forensics CSI: Crime Scene Investigation – Pace University Added undergraduate and grad-school degree programs – Purdue University Introduction to Forensic Science Elective – Virginia Commonwealth University Forensics majors from 114 to 220 – American Academy of Forensic Sciences fields about 25 inquiries per week from people contemplating forensic careers – five times more than in 2002/2003

Evolution of the “New Biology” “Old School” Biology & Life Sciences Physics Chemistry Biochemistry & Medicine Polymer Physics Medicinal Chemistry & Pharmacy Science Genetics DNA/RNA Structure & Folding Combinatorial Chemistry Cell Biology & Physiology Instrumentation New New: “Molecular & Structural Biology/Genetics, Genomics, Engineering Pharmacogenomics, Toxicogenomics, Proteomics Biotechnology Robotics Laboratory Automation NEWEST NEWEST: Informational Molecular Biology, Computational Biology, Systems Biology Chemical Biology, Translational Medicine, Mathematics & Statistics Metablonics, Metabolonics, Microbiome, Computer Science Translational Medicine, Clinical Genomics, Topology & Knot Theory Exposome, Hardware & Software Algorithmic Theory Information Science Gene Mapping, Micro-Array Analysis Simulations and Modeling Visualization Data Management Bioinformatics

Evolution of the “New Biology” “Old School” Biology & Life Sciences Physics Chemistry Biochemistry & Medicine Polymer Physics Medicinal Chemistry & Pharmacy Science Genetics DNA/RNA Structure & Folding Combinatorial Chemistry Cell Biology & Physiology Instrumentation New New: “Molecular & Structural Biology/Genetics, Genomics, Engineering Pharmacogenomics, Toxicogenomics, Proteomics Biotechnology Robotics Laboratory Automation NEWEST NEWEST: Informational Molecular Biology, Computational Biology, Systems Biology Chemical Biology, Translational Medicine, Mathematics & Statistics Metablonics, Metabolonics, Microbiome, Computer Science Translational Medicine, Clinical Genomics, Topology & Knot Theory Exposome, Hardware & Software Algorithmic Theory Information Science Gene Mapping, Micro-Array Analysis Simulations and Modeling Visualization Data Management Bioinformatics

Evolution of the “New Biology” “Old School” Biology & Life Sciences Physics Chemistry Biochemistry & Medicine Polymer Physics Medicinal Chemistry & Pharmacy Science Genetics DNA/RNA Structure & Folding Combinatorial Chemistry Cell Biology & Physiology Instrumentation New New: “Molecular & Structural Biology/Genetics, Genomics, Engineering Pharmacogenomics, Toxicogenomics, Proteomics Biotechnology Robotics Laboratory Automation NEWEST NEWEST: Informational Molecular Biology, Computational Biology, Systems Biology Chemical Biology, Translational Medicine, Mathematics & Statistics Metablonics, Metabolonics, Microbiome, Computer Science Translational Medicine, Clinical Genomics, Topology & Knot Theory Exposome, Hardware & Software Algorithmic Theory Information Science Gene Mapping, Micro-Array Analysis Simulations and Modeling Visualization Data Management Bioinformatics

Evolution of the “New Biology” “Old School” Biology & Life Sciences Physics Chemistry Biochemistry & Medicine Polymer Physics Medicinal Chemistry & Pharmacy Science Genetics DNA/RNA Structure & Folding Combinatorial Chemistry Cell Biology & Physiology Instrumentation New New: “Molecular & Structural Biology/Genetics, Genomics, Engineering Pharmacogenomics, Toxicogenomics, Proteomics Biotechnology Robotics Laboratory Automation NEWEST NEWEST: Informational Molecular Biology, Computational Biology, Systems Biology Chemical Biology, Translational Medicine, Mathematics & Statistics Metablonics, Metabolonics, Microbiome, Computer Science Translational Medicine, Clinical Genomics, Topology & Knot Theory Exposome, Hardware & Software Algorithmic Theory Information Science Gene Mapping, Micro-Array Analysis Simulations and Modeling Visualization Data Management Bioinformatics

Evolution of the “New Biology” “Old School” Biology & Life Sciences Physics Chemistry Biochemistry & Medicine Polymer Physics Medicinal Chemistry & Pharmacy Science Genetics DNA/RNA Structure & Folding Combinatorial Chemistry Cell Biology & Physiology Instrumentation New New: “Molecular & Structural Biology/Genetics, Genomics, Engineering Pharmacogenomics, Toxicogenomics, Proteomics Biotechnology Robotics Laboratory Automation NEWEST NEWEST: Informational Molecular Biology, Computational Biology, Systems Biology Chemical Biology, Translational Medicine, Mathematics & Statistics Metablonics, Metabolonics, Microbiome, Computer Science Translational Medicine, Clinical Genomics, Topology & Knot Theory Exposome, Hardware & Software Algorithmic Theory Information Science Gene Mapping, Micro-Array Analysis Simulations and Modeling Visualization Data Management Bioinformatics

Biology Abstracting & Indexing Services – Pharmaceutisches Central-Blatt 1830 – Engineering Index1884 – Index Medicus1879 MEDLINE (1965) & PubMed (1996) – Science Abstracts1898 – Chemical Abstracts (SciFinder Scholar)1907 – Biological and Agricultural Index 1916/18 – Biological Abstracts1926 Abstracts of Bacteriology Botanical Abstracts – Applied Science & Technology Abstracts1932 – Excerpta Medica1947

Biology A&I Services, cont. Note niche titles appearing in late ‘60s – Science Citation Index (multidisciplinary)1961 – Genetics Abstracts * 1968 – Nucleic Acid Abstracts * 1970 – Amino Acid, Peptide, & Protein Abstracts1972 – BIOETHICSLINE1973 – Biology Digest * 1974 – Biotechnology Research Abstracts * 1982 – Derwent Biotechnology Abstracts1982 – Current Biotechnology1983 – Current Advances in Biochemistry1984 – Current Advances in Genetics and 1984 Molecular Biology

– Oncogenes and Growth Factors Abstracts * 1989 – Plant Genetic Resources Abstracts1992 – Current Advances in Protein Biochemistry1992 – Applied Science and Technology Abstracts1993 – Bioengineering Abstracts1993 – Medical and Pharmaceutical Biotechnology 1993 Abstracts – Scopus(multidiscplinary)2004 Trend for increased specialization of topical coverage of bibliographic databases * CSA Cambridge Scientific Abstracts

It Starts with DNA — The Molecule of Life

James Watson & Francis Crick 1962 DNA not a protein Erwin Chargaff – Equal number of A—T bases – Equal number of C—G bases Linus Pauling – Helical shape of protein X-Ray crystallography – Franklin’s Photo 51 Form of A, C, G, T bases Avery, MacLeod, & McCarty – DNA linked to heredity DNA “transforming factor” – Not cited “oversight” Watson Nobel with Maurice Wilkins – Rosalind Franklin died several years earlier

Physics Today, Vol. 56, no. 3, March 2003

Rosalind Franklin “The Dark Lady of DNA” – Determined chemical structure of DNA by molecular structure and X-ray crystallography Photo of the DNA molecule taken by Rosalin Franklin Photo shown to Watson by Maurice Wilkins, co-worker of Franklin and who shared Nobel Award with Watson & Crick Photo 51 – She didn’t know her photo was shown to them See: b50c-e9f6e395619b%40sessionmgr4004&vid=2&hid=4111&bquery=(rosalind+franklin)+ AND+(SO+(physics+today))&bdata=JmRiPWE5aCZ0eXBlPTEmc2l0ZT1laG9zdC 1saXZlJnNjb3BlPXNpdGU%3d

Its Multidisciplinary and New Search Language Emerges: Sequences

A Brief DNA History: Friedrich Mieschler “Friedrich Miesclher: The Man Who Discovered DNA” – by George Wolf in Chemical Heritage 21(2):10-11,37-41, 2003 – 1869 (not published until 1871) – Nuclein Proteins 1838 – Gerardus Johannes Mulder – Jöns Jakob Berzelius – Leukocyte nuclei from (pus) Looking for chemical composition Almost entirely “nuclein” – Phosphate, nitrogen, no sulfur – Sperm of Salmo salar (Atlantic Salmon)

Albrecht Kossel Nobel Prize ~ 1910 Physiology & Medicine Physiological chemist and medical doctor Studied proteins and nucleins Discovered a protein-like composition of nucleins Also a non-protein component: nucleic acids – Adenine – Cytosine – Guanine – Thymine – Uracil 1 st Nobel Prize (nucleic acids)

What They Started 2013

“Making Sense of Next Big Things in Science” Zabel, Diane, and Stankus, Tony Reference & User Services Quarterly – Winter 2002, Vol. 42 Issue 2, p110. 9p. Offers a model for collection development in emerging new areas of science and technology that offer huge economic market potential, a.k.a., the Next Big Thing (NTB): in this case, the area of proteomics, or protein science. Aims to assist librarians in developing a strategy for collection building without having the advantage of the explicit advice of exhaustive studies with heavy-duty bibliometrics that have yet to materialize. Focuses on how to make enough sense of what scientists involved in proteomics are saying to one another in journals so that a librarian can begin to assemble a working collection, to be later followed by confirmation, modification or extension in light of what truly expert librarians have to say in neighboring fields. Explains how to correctly get the first few things bought for proteomics until sufficient experience with the newly recruited faculty allows for locally guided collection growth.

“Proteomics” Marc Wilkins coined the term proteome in 1994 in a symposium in Siena in Italy. Marc Wilkins It appeared in print in 1995 with the publication in Wilkins's PhD thesis. Wilkins used the term to describe the entire complement of proteins expressed by a genome, cell, tissue, or organism. First conference paper 1994 First Use 1994 First Dissertation 1994 First article 1994 First Book 1995 First Review 1996 (153 Refs) First Journal Title 2001 (Proteomics)

What Bibliometrics Tells Us Web of Science Core SciFinder: CA

New Kid on the Block: The “Microbiome” Joshua Lederberg 2001 “Totality of microorgan- isms and their collective genetic material present in or on the human body or in a nother environment.” The wide diversity of species that make up the microbiome is hard to fathom.

“Microbiome” WoS Core

Human Genome Project ~

Managing the Data & Information Established in 1988 public databases, conducts research in computational biology develops software tools for analyzing genome data disseminates biomedical information National Center for Biotechnology Information (NCBI) Major Transition: Clinical & Therapeutic Outcomes, Translational & Systems Biology

Simple NCBI Directory GETTING STARTED NCBI Education NCBI Help Manual NCBI Handbook Training & Tutorials Submit Data RESOURCES Chemicals & Bioassays Data & Software DNA & RNA Domains & Structures Genes & Expression Genetics & Medicine Genomes & Maps Homology Literature Proteins Sequence Analysis Taxonomy Variation POPULAR PubMed Bookshelf PubMed Central PubMed Health BLAST Nucleotide Genome SNP Gene Protein PubChem FEATURED Genetic Testing Registry PubMed Health GenBank Reference Sequences Gene Expression Omnibus Map Viewer Human Genome Mouse Genome Influenza Virus Primer-BLAST Sequence Read Archive NCBI INFORMATION About NCBI Research at NCBI NCBI News NCBI FTP Site NCBI on Facebook NCBI on Twitter NCBI on YouTube NLM NIH DHHS USA.gov National Center for Biotechnology InformationInformation (NCBI) U.S. National Library of Medicine 8600 Rockville Pike Bethesda MD, USA

Historic Growth of Genomic Data

NCBI: RefSeq Growth,

Final Four

Animations of Biological Processes Howard Hughes Medical Institute – – Scroll ¾-down to Biological Clock Animations The Drosophila Molecular Clock Model The Human Suprachiasmatic Nucleus The Mammalian Molecular Clock Model Measuring Circadian Activity in Drosophila – View other animations for some interesting perspectives on chemistry driving molecular and structural biology

Chemical Controls of Biological Function Per1 & Per2: “Biological Clocks” Circadian Rhythm CRY Genes (Cryptochrome): light-independent inhibitors of circadian rhythm in mammals BMAL & CLOCK: Genes encoding proteins regulating circadian rhythms Dimer: Chemical structure of two similar monomers joined by weak or strong bonds Animation – Biochemical Analysis of the Canonical Model for the Mammalian Circadian Clock –

Staying Current The Scientist – Chemical & Engineering News – pubs.acs.org/cen/index.html Science (AAAS) – l291/issue5507/ index.shtml Nature – Bio-IT World – Nucleic Acid Research – 1 st January: Database Reviews Reviews and updates of database developments articles per issue (1996 to present) – 1 st July: Web/Internet Reviews Reviews Web servers and services articles per issue (2003 to present) – nar.oupjournals.org/contents-by-date.0.shtml

Structural & Molecular Biology & Genetics Dynamic and mechanical processes of DNA replication and transcription – motor proteins translocate along, and rotate around DNA carry out polymerization reactions, separate DNA strands, resolve topological issues, repair DNA damage, and modify DNA-binding proteins

DNA’s Structure Begins with Physics

Human Genome Project 1990

Human Genome Project 1990