October 2003

"The existence in every human being of a vast array of attributes which are potentially measurable (whether by present methods or not), and often uncorrelated mathematically, makes quite tenable the hypothesis that practically every human being is a deviate in some respects." --Roger J. Williams1 We're all subtly, and beautifully, different. A byproduct of this individuality, or deviation as Williams called it, is disease. Now for the first time, there exists a reasonable possibility to mea

Ned Shaw The recent incidence of plagiarism at The New York Times set off some empathetic alarm bells throughout the academic community. According to a 2002-03 survey of 3,500 graduate students in US and Canadian universities, 23%-25% of students acknowledged one or more instances of "cutting and pasting" from Internet sources and/or published documents.1 Electronic journals, E-books, Internet "paper mills," and other high-tech sources of information have put a whole new spin on academic integ

Fowl Dentata A few months ago I saw in The Scientist1 the single most frightening image I have ever seen. It was a chicken with teeth. Although worse pictures have been served up over the years--death, destruction, mutilation--this was the most indigestible. A modern-day metaphor for science hailed as a breakthrough, as perhaps it truly is. I trust good will come from this in terms of genetic control of odontoblasts and suppression of evolutionary DNA repression. But give me a break.

Graph Revisionism I applaud Sam Jaffe's efforts to improve scientific data presentation.1 However, his statement that "bar graphs are a universal no-no" is not warranted. Worse yet, his suggested remedy is flawed. He suggests using line graphs to illustrate categorical data instead of bar graphs. The problem is that line graphs are based on the assumption that the data are continuously variable, unless there are breaks in the X axis. Also, points on a line graph do not solve his basic o

Not Unknown After All These Years Joseph Leidy was certainly a Renaissance man,1 but I humbly submit that the question of whether or not he's known today depends greatly on your field of interest. For those of us whose research is dependent on fossil vertebrates, Joseph Leidy is as well known today as any of the early founders of the fields in which we work (paleontology, anatomy, zoology, etc.). It makes me happy that the contributions of scientists such as Leidy are appreciated outsi

Peace of Mind Gained I read with great interest Karen Schindler's article.1 As one of millions of people who experienced the biggest blackout in North American history, I too tried to use my creativity in order to make the best out of a dark situation. Many of us realized that our normal modes of communication with the outside world, such as digital phone systems, cell phones, beepers, and computers, were no longer functioning. The hums of air conditioners, refrigerators, and other equipment

Click for larger version of graph (21K) What an eclectic collection: The Pianist, Finding Nemo, Amelie, O Brother, Where Art Thou. These were just some of the titles that 316 readers listed when telling us about their movie-viewing habits. More than half, 59%, watch a movie once or more per week. More than 90% watch movies at home on TV, videotape, or DVD. Although TV is the most popular medium for home viewing, 66% also frequent cinemas. Among our respondents, comedy, drama, and science fic

Frontlines | Marking the First Americans' Arrival Thom Graves Media Y-chromosome genetic markers show that people first arrived on the North American continent about 14,000 years ago, according to two papers in the American Journal of Human Genetics.1,2 This is more recent than previously thought; mitochondrial DNA (mtDNA) studies had suggested an entry date of 30,000 years ago. Researchers led by Mark Seielstad, Harvard School of Public Health, identified a single nucleotide polymorp

Frontlines | Harvesting Car Bodies and Airplane Wings Courtesy of the James Ford Bell Library, University of Minnesota  Hemp (Cannabis sativa) These days, farmers grow mainly food. But if the University of Toronto's Mohini Sain is right, in two to five years they'll also be growing material for auto bodies, airplane wings, football helmets, and artificial heart valves. Crops such as hemp, flax, wheat, and corn stalks can produce materials that are said to be as strong or stronger than

Foundations | Pauling, Meselson, and Socrates The Ava Helen & Linus Pauling Papers, Courtesy of Oregon State University  Pauling sent this telegram to President Kennedy in 1962. Matthew Meselson anticipated a lecture that night in 1954 when he heard Linus Pauling's slippety-slap footfall outside the lab. Meselson, then a graduate student in Pauling's lab at Caltech, had neglected his lab duties to organize scientists against atmospheric nuclear testing. Instead of a dressing-down

First Person | Alice D. Sullivan Courtesy of Melissa Jacobs Alice D. Sullivan, a retired California Superior Court judge, plays in a sandbox all week long. Twice weekly, she's playing beach volleyball with her buddies in San Diego; Otherwise, she's mediating or arbitrating disputes between companies and scientists. A former prosecutor who served as a judge for eight years, Sullivan, 60, has added to her existing mediation business an international panel of arbitrators and mediators to hand

5-Prime | It's All in the Translation Those who voted in the Best Places survey (see How They Measure Up: Scientific Institutions) live in many different towns. And while they may wear, eat, or do similar things, one would never know it by listening to them ... Tightening Bunnyhugs, Snapping Suspenders The men at Purdue University wear undershirts, called vests by those at the University of Manchester. While suspenders on men might be fine at Purdue, men at Manchester would never attach the

So They Say "I'll bet I'm the only high school student with one of these." --Craig Wallace, 18, of Salt Lake City, UT, on the nuclear fusion reactor he built from junkyard scraps based on plans from the Internet. From Deseret News. "All the normal excitatory signals that stimulate ejaculation, like touch, sight, sound and smell, can be replaced with the current from the probe. It's fascinating. Of course, this is a woman talking." --Professor of animal science Trish Berger, University of

Science Seen | Arabidopsis in Blue Courtesy of James Hayden  Researchers at the Wistar Institute in Philadelphia gave this photo some aesthetic forethought: It shows the dramatic difference in growth when a gene that detects blue light is removed from the Arabidopsis thaliana genome. function sendData() { document.frm.pathName.value = location.pathname; result = false if (document.frm.score[0].checked) result = true; if (document.frm.score[1].checked) result = true; if (document

November Calendar Click to view enlarged November calendar (198K) --Compiled by Christine Bahls(cbahls@the-scientist.com) function sendData() { document.frm.pathName.value = location.pathname; result = false if (document.frm.score[0].checked) result = true; if (document.frm.score[1].checked) result = true; if (document.frm.score[2].checked) result = true; if (document.frm.score[3].checked) result = true; if (document.frm.score[4].checked) result = true; if (!result) alert("Please

Genetic Testing Timeline The histories of the most well-known single-gene disorders started long before anyone ever thought about sequencing the human genome (see A Genetic Checkup: Lessons from Huntington Disease and Cystic Fibrosis). Click to view enlarged PDF (108K) --Compiled by Ricki Lewis function sendData() { document.frm.pathName.value = location.pathname; result = false if (document.frm.score[0].checked) result = true; if (document.frm.score[1].checked) result = true; if (

Thom Graves Media While genome sequencing may be the new kid on the block--perhaps now with a cracking voice and fuzzy facial hair--predicting phenotypes is the stuff of classical genetics, honed on the rare single-gene disorders, such as Huntington disease (HD) and cystic fibrosis (CF), which dominated the field in the last century (see Genetic Testing Timeline). "Geneticists today are portrayed as soothsayers of the future. But predictive medicine and testing has a significant history," says

Courtesy of Hannah Carey  OUT COLD: The Spermophilus tridecemlineatus or thirteen-lined ground squirrel, assumes a spherical posture when in torpor to reduce its surface to volume ratio and therefore rate of heat loss. Its heart rate will go as low as 3-5 beats per minute and its body temperature to just a degree or so above ambient temperature. In this cold room, that's 3° to 4° C. As days shorten and the cold encroaches, roughly two dozen mammalian species fatten up and settl

Courtesy of Gabriel Nuñez  AND NOW PRESENTING: In this model, microorganisms phagocytosed by the antigen presenting cell (left) release ligands recognized by NOD/CARD proteins and peptides that associate with MHC class II molecules. Recognition of intracellular ligands by NOD/CARD proteins and extracellular ligands by Toll-Like Receptors (TLRs) mediates NF-kB activity. These intracellular events induce cytokine secretion and antigen presentation, as well as the expression of co-stim

Research Briefs New Genes: The Ears Have 'Em; The Worker, The Soldier, The Candlestick Maker; For Genomes Without Borders, Biobanks Unite New genes: The ears have 'em While scouring a new cDNA library, researchers in the Netherlands discovered 80 novel expressed-sequence tags, including 25 preferentially expressed in human fetal cochlea.1 The researchers from the University Medical Center in Nijmegen (UMCN) found that 155 ESTs map to loci for nonsyndromic deafness, which is not associated

Front Page A Better Bottle; Turning to Yeast for Human Antibodies; An Open-Source Alternative to SMD GADGET WATCH | A Better Bottle? Courtesy of USA Scientific Glass reagent bottles may be standard fixtures in the lab, but they are not without problems. Their height can make them awkward to use, especially in a hood, and their narrow openings do not easily accommodate micropipettes. USA Scientific's new reagent bottles address these concerns. The Ocala, Fla.-based company's durable polypr

Click for larger version of in vitro transcription/translation diagrams (57K) Cells are, at a fundamental level, protein-production facilities. So naturally, when researchers need to make some particular protein, they should let the cells do the work for them. But living cells are not terribly good at making exogenous proteins; some proteins are toxic, while others are degraded or simply clumped into insoluble aggregates called inclusion bodies. These days, scientists sometimes take a minima

For most researchers, just keeping up with the scientific literature proves taxing. Actually organizing it in a useful way--to create a bibliography, for example--is even harder. That job can virtually handle itself, however, if a scientist uses bibliographic software. Casual discussions about bibliographic software spawn a range of replies from scientists. Molecular biologist Ted Able of the University of Pennsylvania says, "Yes, I do use bibliographic software. It is absolutely a necessity

Courtesy of Amnis High-throughput cell screening has been, and still is, a cornerstone of fast-paced drug-discovery labs, but nowadays speed is not always enough. Content is key, and a Seattle-based startup company has entered the high-throughput cell imaging market with a novel system that could dramatically increase the amount of information available in a given assay. Amnis' ImageStream™ system combines the throughput of flow cytometry with the imaging power of microscopy to offer fa

Courtesy of Invitrogen Protein kinases play a pivotal role in the signal transduction pathways that regulate cellular metabolism, growth, proliferation, differentiation, and death. By catalyzing the transfer of phosphate groups from ATP to specific serine, threonine, or tyrosine residues on other proteins, protein kinases modulate those proteins' activity, ultimately inducing changes in gene expression. Deregulation of these events can lead to pathology (Alzheimer disease, diabetes, or cancer,

Chunkier Chips Courtesy of Affymetrix A new GeneChip® brand CustomExpress array launched by Santa Clara, Calif.-based Affymetrix raises the bar for gene expression arrays with its ability to measure up to 61,000 transcripts, a three-fold increase from the company's previous standard of 23,000 probe sets. The new array contains 1.3 million individual features, a density Affymetrix achieved by reducing the array's feature size from 18 microns to 11 microns. This new data capacity makes t

Protein Rainbow Previously available by license only, Palo Alto, Calif.-based BD Biosciences-Clontech is now offering academic and nonprofit researchers access to its collection of novel reef coral fluorescent proteins, which include AmCyan1, ZsGreen1, ZsYellow1, DsRed2, AsRed2, and HcRed1. These six spectrally distinct proteins, encoded on both bacterial and mammalian expression vectors, range from cyan, green, and yellow to three shades of red. Engineered to optimize brightness and increas

TIP TROVE | Ethics and the Scientist Courtesy of Michael Kalichman Because research is a social enterprise and is intended to provide a public benefit, the conduct of research is riddled with competing interests. Resolution of such interests requires that a researcher be aware of the ethical dimensions of research; seek out the necessary information and resources to address such concerns as they arise; apply his or her critical thinking skills to find courses of action that are ethically de

Brad Fitzpatrick As the first biotech drugs begin to lose patent protection in the next few years, the US biotechnology industry is beginning to fear it will soon face price-cutting generic competition. Unlike the system for approving traditional, chemically based drugs, no regulatory process exists for the approval of generic versions of the newer bioengineered medicines. Many biotech executives had come to believe their products would enjoy monopolistic pricing even after their patents expir

Courtesy of NASA When the space shuttle Columbia erupted into flames on re-entry, killing its crew of seven astronauts, criticism of the National Aeronautics and Space Administration grew to a fever pitch. Attackers came from all sides. Government experts wanted to know where the money was going, and science policy gurus questioned whether NASA could not better use its $15 billion (US) yearly allotment. The outcome of this debate and resultant soul-searching is especially relevant to the smal

©1999 J. E. Armstrong, Illinois State University The first legally binding international agreement governing the shipment of genetically modified organisms across borders has reinvigorated critics of the Convention on Biological Diversity (CBD). The new agreement, the Cartagena Protocol on Biosafety, requires that the governments of signatory nations be notified when living GMOs such as crop plants are to be brought into the country with the intention of introducing them into the environ

Ned Shaw Open your file drawer all the way, and force your fingers to pry through the folders wedged in the back. Or take down that black binder from a decade ago, labeled with the name of a student you can no longer picture. Perhaps you saved that dataset for the sparkling nugget of an unexpected finding, hoping to determine later whether it might be fool's gold or the real thing. But, in relinquishing it to the vault, it's become like mystery meat, wrapped tightly in aluminum foil inside a

File Photo Major peer-reviewed science journals are toughening rules that require authors to say when they have a financial stake in topics of their articles. The moves from Science and Nature come in response to letters exposing what critics say were a series of publications by people whose pocketbooks could have been hurt or helped by articles published in the journals. Nature's new policy takes effect in October, while Science has underlined its existing policy and asked its editorial boar

File photo This week I cleaned out a former colleague's lab bench to make room for someone new. Once I got started, the other people in the lab joined in. We cleared out solutions that were no longer sterile, called hazardous waste pickup to come get a bottle of diluted fixative, and recycled journal articles that can be stored as PDF files on a computer. Before I knew it we were engaged in a time-honored tradition: team cleaning. It's a thankless job but hey, sometimes it just has to get do

In America's National Football League, a player gets full credit only for a so-called sack when he alone brings down the quarterback. In the world of US patents, a patent holder rakes in all the royalties if he or she is the sole name on the invention. If there's more than one name, the money is equally shared. It's called Laplace's Principle of Insufficient Reason: Without grounds for specifying unequal portions, the rational approach is to apportion equally. And it is, I'm convinced, the m