December 2003

Did He Just Get the Year Wrong? By Richard Gallagher I was dreamin' when I wrote this, forgive me if it goes astray But when I woke up this mornin', could've sworn it was Judgment Day The sky was all purple, there were people runnin' everywhere Tryin' 2 run from the destruction, U know I didn't even care Cuz they say 2000 zero zero party over, oops, out of time! So 2night I'm gonna party like it's 1999! --"1999" Prince Looking back over 2003, we could easily find ourselves slidin

Integrity in Scientific Research Ned Shaw Last year, the Institute of Medicine published a major report1 that does not seem to have inspired much response. A fairly thorough search showed that only one journal, JAMA, mentions the IOM's Integrity in Scientific Research: Creating an Environment that Promotes Responsible Conduct (in a book review).2 Furthermore, the IOM's Web page, in announcing that a town meeting would be held to discuss the report, promises, but does not deliver, the w

Ned Shaw Here at Snapshot Central, global headquarters of the Snapshot section of The Scientist, it's been a hectic year. After months of effort from the Statistics Department, the Survey Division, and the Graphics Group, we have analyzed a year's worth of results in our attempt to dissect, diagnose, and define the average scientist. And what have our efforts revealed? By combining responses of more than 10,000 scientists to 23 surveys conducted this year, we can safely conclude that the aver

Foundations | BLAST From the Past Courtesy of Warren Gish In late 1994, BLAST was fast, but it wasn't as sensitive as programs that produced gapped alignments, such as Bill Pearson's FASTA. To keep the statistics in sync with the new search algorithm, I conjectured that the statistics of Samuel Karlin and Stephen Altschul might be empirically applied to the interpretation of gapped alignment scores. By early 1995, Altschul at the NCBI [National Center for Biotechnology Information] h

Frontlines | A Rediscovery, a New Species Courtesy of Luiz Claudio Marigo Much of the Brazilian Amazon remains accessible only by small boats, including the Rio Negro basin. Here, researchers conducting a long-term mammalian parasite study have rediscovered a forgotten bearded saki primate: Chiropotes israelita.1 Small, dark, and shy, Chiropotes lives high in trees. Its elusive nature and remote habitat contributed to the poor understanding of its taxonomy, says Shawn Lehman, anthropology

Today, Kafatos, 63, has not lost his drive.

Science Seen | A Comic Genius Courtesy of The American Philosophical Society  Lab picnics can be notoriously unfun affairs--the same faces, the same conversations, the same everything, save for the venue and missing white lab coats. That expectation, perhaps, makes photos like this all the more special: geneticist Barbara McClintock, in this photo from the 1980s, doing her best Groucho impression. function sendData() { document.frm.pathName.value = location.pathname; result =

So They Say "It's great. You can actually get him to agree with you." --Geneticist Bill Orr of Southern Methodist University in Dallas on why he likes the James Watson bobblehead doll. From The Scientist. "As a scientist, you cannot simply turn off the key and put the car in the garage." --Leeuwenhoek Medal-winner Karl Stetter on why he is starting up a biotech company in San Diego, instead of taking a pension since reaching Germany's mandatory retirement age. From Science. "It is

5-Prime | The Headline Grabbers This year's science newsmakers, besides comparative genomics and systems biology, include ... McSequence Remarkably, scientists completed the genomic sequence of the coronavirus responsible for the SARS pandemic less than two months after it was first identified. "We never had a disease [that] was so much into the public news," says Bhagirath Singh, scientific director of the Canadian Institute for Health Research's Institute of Infection and Immunity. He

January Calendar Click to view enlarged January calendar (245K) --Compiled by Christine Bahls (cbahls@the-scientist.com) and Maria W. Anderson (manderson@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.scor

Plants for Pain Click to view enlarged diagram (PDF, 255K) Painkillers have a small family tree. Most of the used, and sometimes abused, pain medications available have roots in either the willow tree or the poppy. Aspirin, originally derived from willow bark or other plant extracts, works on the same molecular pathways as medications with more recent origins, including the crop of highly targeted COX-2 inhibitors. And researchers time and again returned to the opium poppy to derive e

©2003 Elsevier NEUROPATHIC PAIN MECHANISMS: Neuropathic pain can originate from peripheral or central nervous system damage. (A) Following injury, damaged nerves attempt to regenerate. This often leads to accumulated nerve sprouts, gliosis, and a buildup of white blood cells. (B) After nerve damage, prominent changes in the dorsal root ganglion and dorsal horn can be observed. Sympathetic innervation occurs as does increased crosstalk between nociceptive and nonnociceptive neurons. (C

In eukaryotic genetics, the one-gene/one-protein concept has, for the most part, breathed its last. Researchers have rallied behind mechanisms such as alternative splicing, which may allow a lowly 30,000-gene genome to produce the dizzying variety of proteins that some believe is necessary to produce beings as complex as humans. Alternative splicing--the post-transcriptional editing process that can result in various mRNAs--was previously seen as an interesting but relatively uncommon sidesh

Courtesy of Nadya Lumelsky and Ron McKay  PANCREATIC CELL PUZZLE: A cell sub-population in differentiated embryonic stem cell cultures produces pancreatic islet hormones, insulin (red) and glucagon (green). Although most cells produce only one type of hormone, the cells shown in yellow produce both. The co-production of the two hormones might signify developmental immaturity. The ethical dimension of embryonic stem cell research looms so large in the public consciousness that the underly

Stem cells weave a web of hope Courtesy of Duncan Stewart University of Toronto investigators showed that injecting endothelial progenitor cells (EPCs) into the pulmonary circulation of rats results in microvasculature regeneration, a process they say might translate into therapy for pulmonary arterial hypertension. Current treatment of PAH, a rare but deadly disease of largely unknown origin, is merely palliative. Team leader Duncan Stewart says that research to date has missed the point b

Newsday NODS OF APPROVAL A single breakout season can earn a major league baseball player the accolade of his own bobblehead doll. Scientists have a tougher time, though. Nobel laureate James Watson had to wait 50 years to earn head-nodding credibility; he joins a small pantheon of scientists so honored. Francis Crick, Watson's colleague in the discovery of DNA's structure, hasn't made the cut, but Albert Einstein has. And for the psychiatry world, Sigmund Freud nods approvingly. ($21.95; www

Courtesy of Getty Images That discovery is fraught with unpredictability poses an enormous problem when evaluating research priorities and allocating funding. It also sends many scientists scrambling for cover when they are asked to prognosticate the future. The Scientist asked anyway. Research scientists, venture capitalists, patent attorneys, even a biomedical professor-turned-mystery author offered their opinions on what will be the hottest new technologies five years hence. Their response

Courtesy of Cellomics  CRYSTAL CLARITY: Confocal microscopy provides unprecedented resolution of cellular structures Confocal microscopy, a decades-old technique,1 has experienced a relatively recent explosion in popularity. The technology's greatest impact has been felt in the life sciences, where its ability to generate crystal-clear images of biological structures and to monitor changes in living samples in real time enables functional analysis of biological processes. The key advant

Courtesy of Won-Ki Huh  LOCAL COLOR: Researchers used librar-ies of tagged proteins to determine where those proteins accumulate, and to what levels. Shown are representative localization (top) and co-localization (bottom) data. Researchers from the University of California, San Francisco, have probed the yeast proteome in the highest level of detail to date. Using sets of fusion-tagged proteins, the scientists, led by Howard Hughes Medical Institute investigators Erin O'Shea and Jonatha

Courtesy of Allometra Davis, Calif.-based Allometra has released software that will appeal to biologists and personal finance aficionados alike. Based on an algorithm that converts numerical data to color values, PyMood can display any kind of data, from yeast proteins to bank statements, in two- and three-dimensional space using up to one million colors, says Marta Matviemko, Allometra's founder and CEO. But its main function is to display the results of BLAST outputs. "The majority of our c

Courtesy of Mirjam Lohmann Microarray processing often takes place in core facilities and includes multiple instruments: a hybridization chamber, a fluidics station, a scanner, and a spotter for printing customized arrays. Now scientists can perform genotyping, gene expression profiling, and resequencing experiments at their own lab benches. The geniom® one from Mannheim, Germany-based febit, recently launched in Europe and slated for US release in 2004, is a fully automated benchtop micr

Data Points | Foreign Ownership in U.S. Biotechs Click for larger version of graph (25K) 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 select") return result; }

File photo Ah, the holidays. A time for gathering, feasting, celebrating, and some pretty complicated explaining. With all those family gatherings and holiday parties comes the dreaded question no postdoc really knows how to answer: "So, what do you do?" Usually something similar to the following dialogue ensues: "I'm a postdoctoral fellow in neuroscience at Emory University." "Emory? So you're some kind of doctor?" "Yes, I have a PhD." "So you're one of those fake doctors?" "Well, I don'

File photo This column is for anyone entering or already in the third age, my preferred term for that period of extended middle age and active elderhood that roughly spans ages 50 to 80. You may wish to ignore or repress thoughts about leaving or changing your career. It's easier to assume that you'll die in your lab or at your computer, or that something will magically present itself when it's time for you to retire. Even if you realize you are stagnating, it can be hard to proactively seek

The clock is ticking for the implementation of a common set of rules that will regulate the conduct of clinical trials in EU member states. The European Commission (EC) passed the EU directive on clinical trials in May 2001 in an attempt to simplify the clinical testing of medicines in Europe and to ensure that trials meet the highest standards of quality. Member states must comply with the new rules by May 1, 2004. But, some scientists worry that the proposed regulations will damage noncommer

"A [student] ther was of oxenford also ... Ful thredbare was his [overcoat] ... For hym was [rather] have at his beddes heed Twenty bookes, clad in blak or reed, Of Aristotle and his philosophie, Than robes riche, or [fiddle], or gay psaltry." --Geoffrey Chaucer, The Canterbury Tales, circa 1386 "I can understand why the faculty would want to wear sandals, but do they have to be flip-flops?" --Caltech postdoc, 2003 True, we now have teraflop computers instead of parchment, but in on